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Cryptococcosis due to Cryptococcus gattii is endemic in various parts of the world , affecting mostly immunocompetent patients . A national surveillance study of cryptococcosis , including demographical , clinical and microbiological data , has been ongoing since 1997 in Colombia , to provide insights into the epidemio...	Cryptococcosis is caused by Cryptococcus neoformans and C . gattii , with the most serious manifestation of disease being infection of the central nervous system ( CNS ) . C . neoformans tends to cause disease in immunosuppressed patients , especially those infected with HIV , while C . gattii affects immunocompetent p...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mycology", "medicine", "and", "health", "sciences", "medical", "microbiology", "epidemiology", "biology", "and", "life", "sciences", "microbiology" ]	2014	Retrospective Study of the Epidemiology and Clinical Manifestations of Cryptococcus gattii Infections in Colombia from 1997–2011
Protrusion and retraction of lamellipodia are common features of eukaryotic cell motility . As a cell migrates through its extracellular matrix ( ECM ) , lamellipod growth increases cell-ECM contact area and enhances engagement of integrin receptors , locally amplifying ECM input to internal signaling cascades . In con...	Cells crawling through tissues migrate inside a complex fibrous environment called the extracellular matrix ( ECM ) , which provides signals regulating motility . Here we investigate one such well-known pathway , involving mutually antagonistic signalling molecules ( small GTPases Rac and Rho ) that control the protrus...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cell", "physiology", "cell", "motility", "engineering", "and", "technology", "enzymes", "signal", "processing", "biological", "cultures", "enzymology", "cell", "polarity", "developmental", "biology", "gtpase", "signaling", "cell", "cultures", "melanoma", "cells", "cell...	2017	A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns
Numerous experimental and epidemiological studies have demonstrated a link between Clonorchis sinensis ( C . sinensis ) infestation and cholangiocarcinoma ( CCA ) as well as hepatocellular carcinoma ( HCC ) . The underlying molecular mechanism involved in the malignancy of CCA and HCC has not yet been addressed . Cssev...	Multiple studies have contributed to the association between Clonorchis sinensis ( C . sinensis ) infestation and cholangiocarcinoma ( CCA ) as well as hepatocellular carcinoma ( HCC ) in past years . However , studies on the underlying pathogenic mechanisms of C . sinensis lag behind those of other parasitic diseases ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "death", "invertebrates", "medicine", "and", "health", "sciences", "helminths", "cell", "processes", "carcinomas", "cancers", "and", "neoplasms", "light", "microscopy", "permeability", "gastrointestinal", "tumors", "animals", "liver", "diseases", "trematodes", "...	2017	Csseverin inhibits apoptosis through mitochondria-mediated pathways triggered by Ca2 + dyshomeostasis in hepatocarcinoma PLC cells
The biology of the metastatic colonization process remains a poorly understood phenomenon . To improve our knowledge of its dynamics , we conducted a modelling study based on multi-modal data from an orthotopic murine experimental system of metastatic renal cell carcinoma . The standard theory of metastatic colonizatio...	We used mathematical modelling to formalize the standard theory of metastatic initiation , under which secondary tumours , after establishment in a distant organ , grow independently from each other and from the primary tumour . When calibrated on the experimental data of primary tumour and total metastatic burden in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Computational Modelling of Metastasis Development in Renal Cell Carcinoma
TORC1 is a master regulator of metabolism in eukaryotes that responds to multiple upstream signaling pathways . The GATOR complex is a newly defined upstream regulator of TORC1 that contains two sub-complexes , GATOR1 , which inhibits TORC1 activity in response to amino acid starvation and GATOR2 , which opposes the ac...	TORC1 is a conserved multi-protein complex that regulates metabolism and cell growth in response to many upstream inputs including nutrient availability . When amino acids are limiting , the GATOR1 complex inhibits TORC1 activation . The inhibition of TORC1 slows cellular metabolism and promotes cell survival during ti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "cell", "death", "lysosomes", "autophagic", "cell", "death", "reproductive", "system", "medicine", "and", "health", "sciences", "hela", "cells", "cell", "processes", "biological", "cultures", "cloning", "animals", "animal", "models", "developmental", ...	2016	The GATOR2 Component Wdr24 Regulates TORC1 Activity and Lysosome Function
Peribunyaviridae is a large family of RNA viruses with several members that cause mild to severe diseases in humans and livestock . Despite their importance in public heath very little is known about the host cell factors hijacked by these viruses to support assembly and cell egress . Here we show that assembly of Orop...	The Peribunyaviridae is a large order of RNA viruses that are globally distributed and may cause human diseases . In this study , we analyzed the assembly pathway of Oropouche virus ( OROV ) , a peribunyavirus of the orthobunyavirus genus that is the etiologic agent of a frequent arthropod-transmitted viral disease in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "vesicles", "hela", "cells", "biological", "cultures", "cell", "processes", "microbiology", "light", "microscopy", "membrane", "proteins", "microscopy", "cell", "cultures", "golgi", "apparatus", "confocal", "microscopy", "cellular", "structures", "and", "organelles", "e...	2018	ESCRT machinery components are required for Orthobunyavirus particle production in Golgi compartments
Anatomical substructures of the human brain have characteristic cell-types , connectivity and local circuitry , which are reflected in area-specific transcriptome signatures , but the principles governing area-specific transcription and their relation to brain development are still being studied . In adult rodents , ar...	Genome-wide measurements of gene expression across the human brain can reveal new principles of brain organization and function . To achieve this , we aim to discover which genes are differentially expressed and in what brain regions . We found that almost all genes in the adult human brain bear a developmental ‘footpr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "brain", "development", "neuronal", "differentiation", "neuroscience", "cell", "differentiation", "age", "groups", "developmental", "biology", "adults", "organism", "development", "genome", "analysis", "developmental", "neuroscience", "animal", "cells", "gene", "expression"...	2016	On Expression Patterns and Developmental Origin of Human Brain Regions
Chlamydia trachomatis is an obligate intracellular human pathogen that exhibits stage-specific gene transcription throughout a biphasic developmental cycle . The mechanisms that control modulation in transcription and associated phenotypic changes are poorly understood . This study provides evidence that a switch-prote...	Chlamydia trachomatis is the leading cause of both bacterial sexually transmitted infection and infection-derived blindness world-wide . No vaccine has proven protective to date in humans . C . trachomatis only replicates from inside a host cell , and has evolved to acquire a variety of nutrients directly from its host...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Rsb Phosphoregulatory Network Controls Availability of the Primary Sigma Factor in Chlamydia trachomatis and Influences the Kinetics of Growth and Development
Enteropathogenic Yersinia circulate in the pig reservoir and are the third bacterial cause of human gastrointestinal infections in Europe . In West Africa , reports of human yersiniosis are rare . This study was conducted to determine whether pathogenic Yersinia are circulating in pig farms and are responsible for huma...	Diarrhea is a major public health problem in developing countries , especially in Africa , but the causative agents are often unknown , impeding the implementation of appropriate therapeutic measures . Although pathogenic Yersinia enterocolitica are a frequent cause of gastroenteritis in developed countries , reports o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "bacteriophages", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "viruses", "diarrhea", "bacterial", "diseases", "farms", "signs", "and", "symptoms", "...	2017	Yersinia enterocolitica, a Neglected Cause of Human Enteric Infections in Côte d’Ivoire
Tunisia has one of the highest burdens of extrapulmonary tuberculosis ( EPTB ) among tuberculosis ( TB ) cases but the contribution of MTBC-mediated human EPTB is unknown . EPTB diagnosis is challenging due to the paucibacillary nature of clinical samples . Therefore , a need of a simplified molecular method for sensit...	Mycobacterial related EPTB diagnosis remains a challenge . In fact the paucibacillary nature of human specimens realized from inaccessible sites might be one of the causes giving a low sensitivity of routine used diagnostic tests . Therefore the use of Real time PCR ( qPCR ) contributes to a specific , sensitive and ra...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "bovine", "tuberculosis", "tropical", "diseases", "bacterial", "diseases", "histology", "molecular", "biology", "techniques", "bacteria", "research", "and", "analysis", "methods", "infectious", "diseases", "zoonoses", "artificial",...	2017	First-time detection and identification of the Mycobacterium tuberculosis Complex members in extrapulmonary tuberculosis clinical samples in south Tunisia by a single tube tetraplex real-time PCR assay
For many infectious disease processes such as emerging zoonoses and vaccine-preventable diseases , and infections occur as self-limited stuttering transmission chains . A mechanistic understanding of transmission is essential for characterizing the risk of emerging diseases and monitoring spatio-temporal dynamics . Thu...	This paper focuses on infectious diseases such as monkeypox , Nipah virus and avian influenza that transmit weakly from human to human . These pathogens cannot cause self-sustaining epidemics in the human population , but instead cause limited transmission chains that stutter to extinction . Such pathogens would go ext...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "zoonoses", "disease", "ecology", "mathematics", "epidemiological", "methods", "theoretical", "biology", "infectious", "disease", "epidemiology", "epidemiology", "statistics", "biostatistics", "biology", "infectious", "disease", "modeling...	2013	Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
The biological effects of interventions to control infectious diseases typically depend on the intensity of pathogen challenge . As much as the levels of natural pathogen circulation vary over time and geographical location , the development of invariant efficacy measures is of major importance , even if only indirectl...	While control options for plant , animal , and human pathogens are emerging rapidly , reliable assessment of the effect of interventions in biological systems presents many challenges . A major question is how to connect laboratory experiments and measurements with the relevant process in natural settings , where hosts...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics", "statistics", "(mathematics)", "population", "modeling", "biology", "and", "life", "sciences", "population", "biology", "biostatistics", "physical", "sciences", "computational", "biology" ]	2014	Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens
While we lack a complete understanding of the molecular mechanisms by which parasites establish and achieve protection from host immune responses , it is accepted that many of these processes are mediated by products , primarily proteins , released from the parasite . Parasitic nematodes occur in different life stages ...	To succeed in infection , parasites must have ways to reach the host , penetrate its tissues and escape its defense systems . As they are not necessarily fatal , most helminth parasites remain viable within their host for many years , exerting a strong influence over the host immune function . Many of these functions a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "chemical", "biology/protein", "chemistry", "and", "proteomics" ]	2008	Stage- and Gender-Specific Proteomic Analysis of Brugia malayi Excretory-Secretory Products
There is evidence to suggest that the yaws bacterium ( Treponema pallidum ssp . pertenue ) may exist in non-human primate populations residing in regions where yaws is endemic in humans . Especially in light of the fact that the World Health Organizaiton ( WHO ) recently launched its second yaws eradication campaign , ...	The success of any disease eradication campaign depends on considering possible non-human reservoirs of the disease . Although the first report of T . pallidum infection in baboons was published in the 1970’s and the zoonotic potential was demonstrated by inoculation of a West African simian strain into humans , nonhum...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Validation of Serological Tests for the Detection of Antibodies Against Treponema pallidum in Nonhuman Primates
Stimulus-specific adaptation ( SSA ) occurs when the spike rate of a neuron decreases with repetitions of the same stimulus , but recovers when a different stimulus is presented . It has been suggested that SSA in single auditory neurons may provide information to change detection mechanisms evident at other scales ( e...	For processing real-life auditory scenes , it is not enough that auditory neurons code only for basic stimulus properties , such as frequency and intensity; at some point , these isolated properties must be woven into a pattern . Stimulus-specific adaptation ( SSA ) , whereby neurons adapt to common stimuli but otherwi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "circuit", "models", "computer", "science", "computer", "modeling", "computational", "neuroscience", "biology", "neuroscience", "coding", "mechanisms" ]	2011	A Neurocomputational Model of Stimulus-Specific Adaptation to Oddball and Markov Sequences
Plant zygote divides asymmetrically into an apical cell that develops into the embryo proper and a basal cell that generates the suspensor , a vital organ functioning as a conduit of nutrients and growth factors to the embryo proper . After the suspensor has fulfilled its function , it is removed by programmed cell dea...	Similar to animals , plants eliminate tissues and organs that have transient function via programmed cell death ( PCD ) . This is especially apparent during plant embryogenesis , when a plant zygote divides into an apical cell , which develops into a mature embryo , and a basal cell , which generates a single organ cal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "cell", "biology", "plant", "science", "biology" ]	2013	A Bipartite Molecular Module Controls Cell Death Activation in the Basal Cell Lineage of Plant Embryos
Many protein engineering problems involve finding mutations that produce proteins with a particular function . Computational active learning is an attractive approach to discover desired biological activities . Traditional active learning techniques have been optimized to iteratively improve classifier accuracy , not t...	Engineering proteins to acquire or enhance a particular useful function is at the core of many biomedical problems . This paper presents Most Informative Positive ( MIP ) active learning , a novel integrated computational/biological approach designed to help guide biological discovery of novel and informative positive ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry/molecular", "evolution", "oncology", "computational", "biology/synthetic", "biology", "biotechnology/bioengineering", "computational", "biology", "biochemistry/structural", "genomics" ]	2009	Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
Given the extraordinary ability of humans and animals to recognize communication signals over a background of noise , describing noise invariant neural responses is critical not only to pinpoint the brain regions that are mediating our robust perceptions but also to understand the neural computations that are performin...	Birds and humans excel at the task of detecting important sounds , such as song and speech , in difficult listening environments such as in a large bird colony or in a crowded bar . How our brains achieve such a feat remains a mystery to both neuroscientists and audio engineers . In our research , we found a population...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "neuroscience", "biology", "sensory", "systems", "neuroethology", "neuroscience" ]	2013	Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise
Emerging insecticide resistance is a major issue for vector control . It decreases the effectiveness of insecticides , thereby requiring greater quantities for comparable control with a net increase in risk of disease resurgence , product cost , and damage risk to the ecosystem . Pyrethroid resistance has been document...	Aedes aegypti is a competent vector of mosquito-borne diseases and is the primary transmitter of yellow fever , zika , chikungunya , and dengue viruses . Through repeated insecticide treatments over the years , many populations of mosquitoes have developed resistance . Pyrethroid resistance is widespread in Aedes aegyp...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "microbiology", "animals", "alphaviruses", "toxicology", "viruses", "toxicity", "ddt", "chikungunya", "virus", "rna", "v...	2017	Pyrethroid resistance alters the blood-feeding behavior in Puerto Rican Aedes aegypti mosquitoes exposed to treated fabric
Successful tumor development and progression involves the complex interplay of both pro- and anti-oncogenic signaling pathways . Genetic components balancing these opposing activities are likely to require tight regulation , because even subtle alterations in their expression may disrupt this balance with major consequ...	Successful carcinogenesis involves the integration of both pro- and anti-oncogenic pathways . We postulated that genes critical for balancing these opposing pathways are likely to be precisely controlled in tumors , since even subtle alterations in their activity might cause substantial alterations in tumor growth and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/bioinformatics", "oncology", "computational", "biology/genomics", "genetics", "and", "genomics/gene", "expression" ]	2008	A Precisely Regulated Gene Expression Cassette Potently Modulates Metastasis and Survival in Multiple Solid Cancers
Astroviruses ( AstVs ) are positive sense , single-stranded RNA viruses transmitted to a wide range of hosts via the fecal-oral route . The number of AstV-infected animal hosts has rapidly expanded in recent years with many more likely to be discovered because of the advances in viral surveillance and next generation s...	With the advances in next generation sequencing and pathogen discovery , astrovirus ( AstV ) , leading cause of diarrhea in children , the elderly and immunocompromised people , detection in diverse animal hosts has increased . Yet , to date there has been no detection of AstVs associated with human infections in anima...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections
Absence epilepsy is believed to be associated with the abnormal interactions between the cerebral cortex and thalamus . Besides the direct coupling , anatomical evidence indicates that the cerebral cortex and thalamus also communicate indirectly through an important intermediate bridge–basal ganglia . It has been thus ...	Epilepsy is a general term for conditions with recurring seizures . Absence seizures are one of several kinds of seizures , which are characterized by typical 2–4 Hz spike-and-slow wave discharges ( SWDs ) . There is accumulating evidence that absence seizures are due to abnormal interactions between cerebral cortex an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "theoretical", "biology", "biology" ]	2014	Bidirectional Control of Absence Seizures by the Basal Ganglia: A Computational Evidence
Kawasaki disease ( KD ) is a pediatric vasculitis that damages the coronary arteries in 25% of untreated and approximately 5% of treated children . Epidemiologic data suggest that KD is triggered by unidentified infection ( s ) in genetically susceptible children . To investigate genetic determinants of KD susceptibili...	Kawasaki disease is an inflammatory pediatric condition that damages the coronary arteries in a quarter of untreated patients and is the commonest cause of childhood acquired heart disease in developed countries . While the infectious trigger ( s ) remain unknown , epidemiologic evidence suggests that human genetic var...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "infectious", "diseases" ]	2009	A Genome-Wide Association Study Identifies Novel and Functionally Related Susceptibility Loci for Kawasaki Disease
The Staphylococcus aureus HrtAB system is a hemin-regulated ABC transporter composed of an ATPase ( HrtA ) and a permease ( HrtB ) that protect S . aureus against hemin toxicity . S . aureus strains lacking hrtA exhibit liver-specific hyper-virulence and upon hemin exposure over-express and secrete immunomodulatory fac...	Staphylococcus aureus infects almost every tissue within the human body utilizing a range of virulence factors to combat host defenses . The expression of these virulence factors is a tightly regulated process; however , the signals sensed by S . aureus during infection remain elusive . It has been hypothesized that he...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "microbiology/immunity", "to", "infections", "immunology/immunomodulation", "microbiology/innate", "immunity", "microbiology/cellular", "microbiology", "and", "pathogenesis", "immunology", "microbiology", "immunology/immun...	2010	Membrane Damage Elicits an Immunomodulatory Program in Staphylococcus aureus
Enteropathogenic E . coli ( EPEC ) and related enterobacteria rely on a type III secretion system ( T3SS ) effector NleE to block host NF-κB signaling . NleE is a first in class , novel S-adenosyl-L-methionine ( SAM ) -dependent methyltransferase that methylates a zinc-coordinating cysteine in the Npl4-like Zinc Finger...	Pathogens often manipulate host functions by posttranslational modifications such as ubiquitination and methylation . The NF-κB pathway is most critical for immune defense against infection , thereby frequently targeted by bacterial virulence factors . NleE , a virulence effector from EPEC , is a SAM-dependent methyltr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "enzyme", "structure", "signal", "transduction", "cell", "biology", "post-translational", "modification", "proteins", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "enzymology", "microbiology" ]	2014	Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway
Ascaris lumbricoides and Ascaris suum are socioeconomically important and widespread parasites of humans and pigs , respectively . The excretory-secretory ( ES ) molecules produced and presented at the parasite-host interface during the different phases of tissue invasion and migration are likely to play critical roles...	The gastro-intestinal nematodes Ascaris lumbricoides and Ascaris suum are amongst the most prevalent parasites of humans and pigs , respectively . To date , little is known about A . suum excretory-secretory proteins , which are present at the parasite-host interface and likely to play a critical role in the induction ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Proteomic Analysis of the Excretory-Secretory Products from Larval Stages of Ascaris suum Reveals High Abundance of Glycosyl Hydrolases
Many genes are expressed in bursts , which can contribute to cell-to-cell heterogeneity . It is now possible to measure this heterogeneity with high throughput single cell gene expression assays ( single cell qPCR and RNA-seq ) . These experimental approaches generate gene expression distributions which can be used to ...	Many genes are expressed in bursts , which can contribute to cell-to-cell variability . We construct a pipeline for analyzing single cell gene expression data that uses the mathematics behind bursty expression . This pipeline includes one algorithm for clustering cells ( Simulated Annealing for Bursty Expression Cluste...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "applied", "mathematics", "messenger", "rna", "cell", "differentiation", "dna", "transcription", "simulation", "and", "modeling", "algorithms", "developmental", "biology", "mathematics", "stem", "cells", "re...	2016	Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
Changes in gene expression are commonly observed during evolution . However , the phenotypic consequences of expression divergence are frequently unknown and difficult to measure . Transcriptional regulators provide a mechanism by which phenotypic divergence can occur through multiple , coordinated changes in gene expr...	Changes in gene regulation are thought to play an important role in evolution . While variation in gene expression between species is common , it is hard to identify the phenotypic consequences of this variation since many changes in gene expression may have subtle or no phenotypic effects . In this study , we investig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "genetics", "and", "genomics" ]	2012	Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance
Fungal pathogens elicit cytokine responses downstream of immunoreceptor tyrosine-based activation motif ( ITAM ) -coupled or hemiITAM-containing receptors and TLRs . The Linker for Activation of B cells/Non-T cell Activating Linker ( LAB/NTAL ) encoded by Lat2 , is a known regulator of ITAM-coupled receptors and TLR-as...	Fungal infections are a major healthcare problem and the incidence of fungal infections has increased significantly in recent years . Mortality rates are high even with treatment , highlighting the need for a better understanding of anti-fungal immunity in order to develop improved therapies . Adaptive T-helper 1 and T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cytokines", "immunity", "immune", "defense", "immunology", "immunity", "to", "infections", "biology", "immune", "response", "immune", "system" ]	2013	LAB/NTAL Facilitates Fungal/PAMP-induced IL-12 and IFN-γ Production by Repressing β-Catenin Activation in Dendritic Cells
Prion diseases are fatal neurodegenerative disorders characterized by a long pre-symptomatic phase followed by rapid and progressive clinical phase . Although rare in humans , the unconventional infectious nature of the disease raises the potential for an epidemic . Unfortunately , no treatment is currently available ....	Prion diseases are a group of infectious neurodegenerative disorders producing a rapid and devastating clinical deterioration . The disease is 100% fatal and affected patients usually die within one year from the appearance of the first clinical alterations . Currently there is no treatment available for these diseases...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neurological", "disorders/prion", "diseases" ]	2010	Calcineurin Inhibition at the Clinical Phase of Prion Disease Reduces Neurodegeneration, Improves Behavioral Alterations and Increases Animal Survival
Reactivation of chronic Chagas disease , which occurs in approximately 20% of patients coinfected with HIV/Trypanosoma cruzi ( T . cruzi ) , is commonly characterized by severe meningoencephalitis and myocarditis . The use of quantitative molecular tests to monitor Chagas disease reactivation was analyzed . Polymerase ...	Chagas disease is endemic in Latin America and is caused by the flagellate protozoan T . cruzi . The acute phase is asymptomatic in the majority of the cases and rarely causes inflammation of the heart or the central nervous system . Most infected patients progress to a chronic phase , characterized by cardiac or diges...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2011	Real-Time PCR in HIV/Trypanosoma cruzi Coinfection with and without Chagas Disease Reactivation: Association with HIV Viral Load and CD4+ Level
Stereo “3D” depth perception requires the visual system to extract binocular disparities between the two eyes' images . Several current models of this process , based on the known physiology of primary visual cortex ( V1 ) , do this by computing a piecewise-frontoparallel local cross-correlation between the left and ri...	Stereo depth perception requires the brain to detect displacements of features between the two eyes' images . Several current models use local cross-correlation between the two eyes' images , looking for small patches that are the most similar between the two images . There is evidence that cells in primary visual cort...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "visual", "system", "computational", "neuroscience", "biology", "sensory", "systems", "neuroscience" ]	2011	Spatial Stereoresolution for Depth Corrugations May Be Set in Primary Visual Cortex
Contractile function of striated muscle cells depends crucially on the almost crystalline order of actin and myosin filaments in myofibrils , but the physical mechanisms that lead to myofibril assembly remains ill-defined . Passive diffusive sorting of actin filaments into sarcomeric order is kinetically impossible , s...	Muscle contraction driving voluntary movements and the beating of the heart relies on the contraction of highly regular bundles of actin and myosin filaments , which share a periodic , sarcomeric pattern . We know little about the mechanisms by which these ‘biological crystals’ are assembled and it is a general questio...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "physics", "biophysic", "al", "simulations", "biophysics", "theory", "biology", "cell", "mechanics", "biophysics", "simulations", "biophysics", "biomechanics", "computational", "biology" ]	2012	Sarcomeric Pattern Formation by Actin Cluster Coalescence
Antiviral resistance in influenza is rampant and has the possibility of causing major morbidity and mortality . Previous models have identified treatment regimes to minimize total infections and keep resistance low . However , the bulk of these studies have ignored stochasticity and heterogeneous contact structures . H...	Resistance of influenza to common antiviral agents carries the possibility of causing large morbidity and mortality through failure of treatment and should be taken into account when planning public health interventions focused on stopping transmission . Here we present a mathematical model of influenza transmission wh...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "organismal", "evolution", "social", "and", "behavioral", "sciences", "influenza", "applied", "mathematics", "sociology", "microbiology", "mathematics", "microbial", "evolution", "social", "networks", "population", "biology", "infectious", "diseases", "evolution...	2013	The Timing and Targeting of Treatment in Influenza Pandemics Influences the Emergence of Resistance in Structured Populations
Calcium ions ( Ca2+ ) are important mediators of a great variety of cellular activities e . g . in response to an agonist activation of a receptor . The magnitude of a cellular response is often encoded by frequency modulation of Ca2+ oscillations and correlated with the stimulation intensity . The stimulation intensit...	The calcium ion ( Ca2+ ) , a universal signaling molecule , is widely recognized to play a fundamental role in the regulation of various biological processes . Agonist–evoked Ca2+ signals often manifest as rhythmic changes in the cytosolic free Ca2+ concentration ( ccyt ) called Ca2+ oscillations . Stimuli intensity wa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "nervous", "system", "endoplasmic", "reticulum", "cell", "processes", "junctional", "complexes", "electrophysiology", "neuroscience", "gap", "junctions", "waves", "cellular", "structures", "and", "organelles",...	2016	The Effect of Gap Junctional Coupling on the Spatiotemporal Patterns of Ca2+ Signals and the Harmonization of Ca2+-Related Cellular Responses
Bacteria use a variety of stress-sensing systems to sense and respond to diverse stressors and to ensure their survival under adverse conditions . The gram-positive bacterium Bacillus subtilis responds to energy stress ( ATP depletion ) and to environmental stressors using two distinct stress-sensing pathways that conv...	All living things must sense and respond to stress in order to survive . Because bacteria are often subjected to rapidly changing conditions in nature , they have evolved stress-response mechanisms that are poised to respond to harsh environmental conditions . Many of the proteins that mediate bacterial stress response...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "cell", "cycle", "and", "cell", "division", "pathogens", "cell", "...	2017	Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis
Cyclin T1 is a regulatory subunit of a general RNA polymerase II elongation factor known as P-TEFb . Cyclin T1 is also required for Tat transactivation of HIV-1 LTR-directed gene expression . Translation of Cyclin T1 mRNA has been shown to be repressed in human monocytes , and this repression is relieved when cells dif...	Monocytes do not support HIV-1 replication , in part because they do not express adequate levels of essential cellular cofactors that mediate steps in the viral replication cycle . Monocytes become permissive for viral replication upon differentiation to macrophages , indicating that cellular cofactors are induced duri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "virology/immunodeficiency", "viruses", "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2009	miR-198 Inhibits HIV-1 Gene Expression and Replication in Monocytes and Its Mechanism of Action Appears To Involve Repression of Cyclin T1
Observability of a dynamical system requires an understanding of its state—the collective values of its variables . However , existing techniques are too limited to measure all but a small fraction of the physical variables and parameters of neuronal networks . We constructed models of the biophysical properties of neu...	To understand a complex system such as the weather or the brain , one needs an exhaustive detailing of the system variables and parameters . But such systems are vastly undersampled from existing technology . The alternative is to employ realistic computational models of the system dynamics to reconstruct the unobserve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience", "neurological", "disorders/epilepsy" ]	2010	Assimilating Seizure Dynamics
The hallmark of Philadelphia chromosome positive ( Ph+ ) leukemia is the BCR/ABL kinase , which is successfully targeted by selective ATP competitors . However , inhibition of BCR/ABL alone is unable to eradicate Ph+ leukemia . The t ( 9;22 ) is a reciprocal translocation which encodes not only for the der22 ( Philadel...	The t ( 9;22 ) is a reciprocal translocation , which causes chronic myeloid leukemia ( CML ) and a subset of high risk acute lymphatic leukemia ( ALL ) . The derivative chromosome 22 is the so called Philadelphia chromosome ( Ph ) which encodes the BCR/ABL kinase . Targeting BCR/ABL by selective ATP competitors , such ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Functional Interplay Between the t(9;22)-Associated Fusion Proteins BCR/ABL and ABL/BCR in Philadelphia Chromosome-Positive Acute Lymphatic Leukemia
Hepatitis B virus ( HBV ) core protein ( HBc ) contains an N-terminal domain ( NTD , assembly domain ) and a C-terminal domain ( CTD ) , which are linked by a flexible linker region . HBc plays multiple essential roles in viral replication , including capsid assembly , packaging of the viral pregenomic RNA ( pgRNA ) in...	The hepatitis B virus ( HBV ) is a major human pathogen that infects hundreds of millions of people worldwide and represents a major cause of viral hepatitis , liver cirrhosis , and liver cancer . The HBV capsid protein ( HBc ) plays multiple roles in the viral life cycle and has emerged recently as a major target for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "microbiology", "viral", "structure", "sequence", "assembly", "tools", "physiological", "processes", "genome", "analysis", "dna", "dna", "synthesis", "chemical", "synthesis", "re...	2018	Multiple roles of core protein linker in hepatitis B virus replication
Deletion of Severe Acute Respiratory Syndrome Coronavirus ( SARS-CoV ) envelope ( E ) gene attenuates the virus . E gene encodes a small multifunctional protein that possesses ion channel ( IC ) activity , an important function in virus-host interaction . To test the contribution of E protein IC activity in virus patho...	Several highly pathogenic viruses encode small transmembrane proteins with ion-conduction properties named viroporins . Viroporins are generally involved in virus production and maturation processes , which many times are achieved by altering the ion homeostasis of cell organelles . Cells have evolved mechanisms to sen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "synthetic", "biology", "immunology", "microbiology", "histology", "developmental", "biology", "molecular", "development", "prote...	2014	Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Ion Channel Activity Promotes Virus Fitness and Pathogenesis
Family studies suggest a genetic component to the etiology of chronic kidney disease ( CKD ) and end stage renal disease ( ESRD ) . Previously , we identified 16 loci for eGFR in genome-wide association studies , but the associations of these single nucleotide polymorphisms ( SNPs ) for incident CKD or ESRD are unknown...	Chronic kidney disease ( CKD ) affects about 6%–11% of the general population , and progression to end stage renal disease ( ESRD ) has a significant public health impact . Family studies suggest that the risk for CKD and ESRD is heritable . Unraveling the genetic underpinning of risk for these diseases may lead to the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "public", "health", "and", "epidemiology", "biomarker", "epidemiology", "chronic", "kidney", "disease", "dialysis", "clinical", "epidemiology", "genetic", "testing", "genetic", "epidemiology", "personalized", "medicine", ...	2011	Association of eGFR-Related Loci Identified by GWAS with Incident CKD and ESRD
HIV-1 cell entry commonly uses , in addition to CD4 , one of the chemokine receptors CCR5 or CXCR4 as coreceptor . Knowledge of coreceptor usage is critical for monitoring disease progression as well as for supporting therapy with the novel drug class of coreceptor antagonists . Predictive methods for inferring corecep...	HIV-1 cell entry requires a chemokine coreceptor in addition to the CD4 cell surface receptor . The two most common types of HIV coreceptors are called CCR5 and CXCR4 . Whereas CCR5-using viral variants dominate directly after infection and during early stages of the disease , in about 50% of the patients , CXCR4-using...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "molecular", "biology", "infectious", "diseases", "computational", "biology" ]	2007	Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
Neisseria meningitidis ( Nme ) asymptomatically colonizes the human nasopharynx , yet can initiate rapidly-progressing sepsis and meningitis in rare instances . Understanding the meningococcal lifestyle within the nasopharyngeal mucosa , a phase of infection that is prerequisite for disease , has been hampered by the l...	Neisseria meningitidis ( Nme ) , a common cause of bacterial meningitis , are carried asymptomatically in the nasopharynx by a substantial proportion of healthy individuals . Their strict adaptation to the human as host has so far impeded the development of animal models to study the meningococcal lifestyle in vivo . W...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meningococcal", "infections", "immunizations", "medicine", "bacterial", "diseases", "infectious", "diseases", "adaptive", "immunity", "immunity", "innate", "immunity", "host-pathogen", "interaction", "biology", "microbiology", "infectious", "disease", "modeling" ]	2013	In Vivo Adaptation and Persistence of Neisseria meningitidis within the Nasopharyngeal Mucosa
Trypanosoma cruzi , the causative agent of Chagas disease , presents wide genetic diversity . Currently , six discrete typing units ( DTUs ) , named TcI to TcVI , and a seventh one called TcBat are used for strain typing . Beyond the debate concerning this classification , this systematic review has attempted to provid...	Trypanosoma cruzi , the causative agent of Chagas disease , has been classified into six genetic groups ( discrete typing units , DTUs ) named TcI-TcVI and a seventh one called TcBat . Currently , several genetic molecular markers are used to classify the strains after their isolation in culture or directly from biolog...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "population", "dynamics", "population", "genetics", "geographical", "locations", "vertebrates", "animals", "mammals", "par...	2016	Over Six Thousand Trypanosoma cruzi Strains Classified into Discrete Typing Units (DTUs): Attempt at an Inventory
The Caenorhabditis elegans one-cell embryo polarizes in response to a cue from the paternally donated centrosome and asymmetrically segregates cell fate determinants that direct the developmental program of the worm . We have found that genes encoding putative deubiquitylating enzymes ( DUBs ) are required for polariza...	In eukaryotes , modification of proteins by the covalent ligation of a protein called ubiquitin is an important regulatory mechanism . In this study we found that deubiquitylation enzymes , which are known to cleave ubiquitin off of target proteins , are required for asymmetry in one-cell embryos of the nematode C . el...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "enzymes", "gene", "classes", "gene", "function", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "molecular", "genetics", "cytoskeleton", "embryology", "enzyme", "classes", "biology", "biochemis...	2012	Deubiquitylation Machinery Is Required for Embryonic Polarity in Caenorhabditis elegans
SslE , the Secreted and surface-associated lipoprotein from Escherichia coli , has recently been associated to the M60-like extracellular zinc-metalloprotease sub-family which is implicated in glycan recognition and processing . SslE can be divided into two main variants and we recently proposed it as a potential vacci...	Escherichia coli are the predominant facultative anaerobe of the human colonic flora . Although intestinal and extraintestinal pathogenic E . coli are phylogenetically and epidemiologically distinct , we recently proposed a number of protective antigens conserved in most E . coli pathotypes . In this study , we have el...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "urology", "microbial", "metabolism", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "microbiology", "escherichia", "coli", "animal", "models", "bacterial", "diseases", "model", "organisms", "emerging", "infectious",...	2014	SslE Elicits Functional Antibodies That Impair In Vitro Mucinase Activity and In Vivo Colonization by Both Intestinal and Extraintestinal Escherichia coli Strains
Rheumatic heart disease ( RHD ) prevalence and mortality rates remain especially high in many parts of Africa . While effective prevention and treatment exist , coverage rates of the various interventions are low . Little is known about the comparative cost-effectiveness of different RHD interventions in limited resour...	Rheumatic heart disease is a major cause of cardiovascular morbidity and mortality in Africa . Although there are effective medications and surgical procedures for rheumatic heart disease , they are under-used . What is more , these interventions can be expensive—even if they are feasible and effective . Unfortunately ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "cost-effectiveness", "analysis", "demography", "economic", "analysis", "geographical", "locations", "social", "sciences", "cardiovascular", "medicine", "surgical", "and", "invasive", "medical", "procedures", "hea...	2016	A Cost-Effectiveness Tool to Guide the Prioritization of Interventions for Rheumatic Fever and Rheumatic Heart Disease Control in African Nations
Single microRNAs are usually associated with hundreds of putative target genes that can influence multiple phenotypic traits in Drosophila , ranging from development to behaviour . We investigated the function of Drosophila miR-210 in circadian behaviour by misexpressing it within circadian clock cells . Manipulation o...	In recent years , the role of microRNAs in regulating the endogenous circadian clock and its rhythmic outputs for behaviour/physiology has been recognized . We have observed that depletion or over-expression of miR-210 in Drosophila melanogaster modulates the phase of locomotor activity , without affecting the molecula...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "gene", "regulation", "neuroscience", "animals", "circadian", "oscillators", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "micrornas", "experimental", "organism", "systems", "chronobiology"...	2018	Modulation of miR-210 alters phasing of circadian locomotor activity and impairs projections of PDF clock neurons in Drosophila melanogaster
RNA-binding proteins ( RBPs ) establish the cellular fate of a transcript , but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules . Using MS2 RNA tagging , we have purified proteins associated with individual mRNA species induced by osmo...	When confronted with external physical or chemical stress , cells respond by increasing the mRNA output of a small number of genes required for stress survival , while shutting down the majority of other genes . Moreover , each mRNA is regulated under stress to either enhance or diminish its translation into proteins ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biochemistry", "rna", "cellular", "stress", "responses", "cell", "biology", "nucleic", "acids", "proteins", "protein", "translation", "gene", "expression", "genetics", "ribonucleoproteins", "biology", "and", "life", "sciences", "messenger", "rna", "cell", "processes", ...	2018	The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock
Amino acids are among the earliest identified inducers of yeast-to-hyphal transitions in Candida albicans , an opportunistic fungal pathogen of humans . Here , we show that the morphogenic amino acids arginine , ornithine and proline are internalized and metabolized in mitochondria via a PUT1- and PUT2-dependent pathwa...	Candida albicans is an opportunistic fungal pathogen that exists as a benign member of the human microbiome . Immunosuppression , or microbial dysbiosis , can predispose an individual to infection , enabling this fungus to evade innate immune cells and initiate a spectrum of pathologies , including superficial mucocuta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "carbohydrates", "organic", "compounds", "glucose", "developmental", "biology", ...	2019	Mitochondrial proline catabolism activates Ras1/cAMP/PKA-induced filamentation in Candida albicans
Drug resistance represents one of the main problems for the use of chemotherapy to treat leishmaniasis . Additionally , it could provide some advantages to Leishmania parasites , such as a higher capacity to survive in stress conditions . In this work , in mixed populations of Leishmania donovani parasites , we have an...	Chemotherapy is currently the only treatment option for leishmaniasis , a neglected tropical disease produced by the protozoan parasite Leishmania . However , first-line drugs have different types of limitations including toxicity , price , efficacy and mainly emerging resistance . The WHO has recently recommended a co...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Fitness of Leishmania donovani Parasites Resistant to Drug Combinations
Genome instability is a hallmark of cancer cells . One class of genome aberrations prevalent in tumor cells is termed gross chromosomal rearrangements ( GCRs ) . GCRs comprise chromosome translocations , amplifications , inversions , deletion of whole chromosome arms , and interstitial deletions . Here , we report the ...	Cells must ensure the integrity of genetic information before cellular division . Loss of genome integrity is particularly germane to tumorigenesis , where it is thought to contribute to the rapid evolution of the malignant cell towards the fully cancerous phenotype . It is therefore imperative that we understand fully...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nutrition", "homo", "(human)", "genetics", "and", "genomics", "saccharomyces" ]	2007	A Screen for Suppressors of Gross Chromosomal Rearrangements Identifies a Conserved Role for PLP in Preventing DNA Lesions
The formation of single-stranded DNA ( ssDNA ) at double-strand break ( DSB ) ends is essential in repair by homologous recombination and is mediated by DNA helicases and nucleases . Here we estimated the length of ssDNA generated during DSB repair and analyzed the consequences of elimination of processive resection pa...	Chromosomal breaks occur spontaneously or are induced by ionizing radiation and many chemotherapeutic drugs . DNA double-strand breaks are processed by nucleases and helicases in yeast and human to generate single-stranded DNA that is then used for repair by recombination with homologous chromosome . Single-stranded DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "genetics", "and", "genomics/gene", "therapy", "molecular", "biology/dna", "repair" ]	2010	Defective Resection at DNA Double-Strand Breaks Leads to De Novo Telomere Formation and Enhances Gene Targeting
A fundamental goal in cellular signaling is to understand allosteric communication , the process by which signals originated at one site in a protein propagate dependably to affect remote functional sites . Here , we describe the allosteric regulation of the receptor tyrosine kinase KIT . Our analysis evidenced that co...	The majority of functionally important biological processes are regulated by allosteric communication within individual proteins and across protein complexes . Receptor tyrosine kinases ( RTKs ) control signal transduction pathways and consequently represent a typical paradigm . The mutation-induced deregulation of RTK...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "biology", "computational", "biology" ]	2012	Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase
Adult schistosomes live in the host's bloodstream where they import nutrients such as glucose across their body surface ( the tegument ) . The parasite tegument is an unusual structure since it is enclosed not by the typical one but by two closely apposed lipid bilayers . Within the tegument two glucose importing prote...	Schistosomes are parasitic worms that live in the blood streams of ∼200 million people globally . They import glucose from host blood directly across their skin ( the tegument ) . In the tegument the parasites possess glucose transporter proteins designated SGTP1 and SGTP4 . SGTP4 sits on the outermost tegumental membr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/chemical", "biology", "of", "the", "cell", "developmental", "biology/microbial", "growth", "and", "development", "cell", "biology/microbial", "growth", "and", "development", "infectious", "diseases/helminth", "infections", "microbiology/parasitology", "chemical", ...	2010	Suppressing Glucose Transporter Gene Expression in Schistosomes Impairs Parasite Feeding and Decreases Survival in the Mammalian Host
This study aimed to investigate the spatiotemporal clustering and socio-environmental factors associated with dengue fever ( DF ) incidence rates at street level in Guangzhou city , China . Spatiotemporal scan technique was applied to identify the high risk region of DF . Multiple regression model was used to identify ...	Dengue fever ( DF ) as a mosquito-borne viral disease remains a challenge for the prevention and control caused by the increased population , global development , human movement , and urbanization in the last five decades . The largest DF outbreak occurred with more than 40 , 000 cases in Guangdong in 2014 since DF re-...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "china", "applied", "mathematics", "geographical", "locations", "tropical", "diseases", "census", "animals", "simulation", "and", "modeling", "algorithms", "research", "design", "mathematics", "longitude", "cluster...	2018	Dynamic spatiotemporal analysis of indigenous dengue fever at street-level in Guangzhou city, China
Recent evidence suggests that the presence of more than one pathogenic mutation in a single patient is more common than previously anticipated . One of the challenges hereby is to dissect the contribution of each gene mutation , for which animal models such as Drosophila can provide a valuable aid . Here , we identifie...	Genetic diseases with complex syndromic constellations may be caused by mutations in more than one gene . Most examples studied so far describe genetic interactions of known disease genes , suggesting that a large number of multilocus diseases remain unexplored . Assessment of mutation pathogenicity can be achieved usi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "microcephaly", "cardiovascular", "anatomy", "animals", "fibroblasts", "animal", "models", "organisms", "developmental", "biology", "mutation", "drosophila", "melanogaster", "model", "organisms", "analysis", "of", ...	2018	A homozygous KAT2B variant modulates the clinical phenotype of ADD3 deficiency in humans and flies
Processes that repeat in time , such as the cell cycle , the circadian rhythm , and seasonal variations , are prevalent in biology . Mathematical models can represent our knowledge of the underlying mechanisms , and numerical methods can then facilitate analysis , which forms the foundation for a more integrated unders...	Network models of biological systems are appearing at an increasing rate . By encapsulating mechanistic detail of chemical and physical processes , mathematical models can successfully simulate and predict emergent network properties . However , methods are needed for analyzing the role played by individual biochemical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "mammals", "computational", "biology" ]	2007	The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism
The corpus callosum ( CC ) is the major commissure that bridges the cerebral hemispheres . Agenesis of the CC is associated with human ciliopathies , but the origin of this default is unclear . Regulatory Factor X3 ( RFX3 ) is a transcription factor involved in the control of ciliogenesis , and Rfx3–deficient mice show...	The Corpus Callosum is the major brain commissure that links the two cerebral hemispheres in mammals . Absence or reduction of the corpus callosum is the most frequent brain malformation observed at birth in humans and leads to cognitive and behavioural deficits . Agenesis of the Corpus Callosum is frequently observed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	The Ciliogenic Transcription Factor RFX3 Regulates Early Midline Distribution of Guidepost Neurons Required for Corpus Callosum Development
Many biological activities originate from interactions between small-molecule ligands and their protein targets . A detailed structural and physico-chemical characterization of these interactions could significantly deepen our understanding of protein function and facilitate drug design . Here , we present a large-scal...	The life of a living cell relies on many distinct proteins to carry out their functions . Most of these functions are rooted in interactions between the proteins and metabolites , small-molecules essential for life . By targeting specific proteins relevant to a disease , drug molecules may provide a cure . A deep under...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
Translesion synthesis ( TLS ) polymerases are specialized DNA polymerases capable of inserting nucleotides opposite DNA lesions that escape removal by dedicated DNA repair pathways . TLS polymerases allow cells to complete DNA replication in the presence of damage , thereby preventing checkpoint activation , genome ins...	Unrepaired DNA damage on the template strand poses a problem for the progression of the replication fork . Specialized translesion synthesis ( TLS ) polymerases are capable of bypassing DNA lesions without repairing them . Here , we use the nematode C . elegans , to show that there is modulation of the choice between r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "radiobiology", "model", "organisms", "genetic", "screens", "genetics", "genetics", "and", "genomics", "biology", "genetic", "toxicology", "toxicology", "gene", "function" ]	2012	A Broad Requirement for TLS Polymerases η and κ, and Interacting Sumoylation and Nuclear Pore Proteins, in Lesion Bypass during C. elegans Embryogenesis
Long INterspersed Element-1 ( LINE-1 or L1 ) is the only active autonomous retrotransposon in the human genome . To investigate the interplay between the L1 retrotransposition machinery and the host cell , we used co-immunoprecipitation in conjunction with liquid chromatography and tandem mass spectrometry to identify ...	Long INterspersed Element-1 ( LINE-1 or L1 ) is the only active autonomous retrotransposon in the human genome . L1s comprise ~17% of human DNA and it is estimated that an average human genome has ~80–100 active L1s . L1 moves throughout the genome via a “copy-and-paste” mechanism known as retrotransposition . L1 retro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition
The unintended consequences of gene targeting in mouse models have not been thoroughly studied and a more systematic analysis is needed to understand the frequency and characteristics of off-target effects . Using RNA-seq , we evaluated targeted and neighboring gene expression in tissues from 44 homozygous mutants comp...	Insertion of foreign DNA into mammalian genomes , and the deletion of DNA , may have unintended consequences extending beyond the site of the mutation . In the mouse , the insertion of foreign DNA , including foreign regulatory DNA , combined with the deletion of part of the targeted gene , had striking effects on the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "gene", "regulation", "dna", "manipulations", "genome", "analysis", "dna", "construction", "molecular", "biology", "techniques", "mammalian", "genomics", "rna", "sequencing", "research", "and", "analysis", "methods", "exon", "mapping", "genom...	2016	Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression
The evolution of altruism is a fundamental and enduring puzzle in biology . In a seminal paper Hamilton showed that altruism can be selected for when rb − c>0 , where c is the fitness cost to the altruist , b is the fitness benefit to the beneficiary , and r is their genetic relatedness . While many studies have provid...	One of the enduring puzzles in biology and the social sciences is the origin and persistence of altruism , whereby a behavior benefiting another individual incurs a direct cost for the individual performing the altruistic action . This apparent paradox was resolved by Hamilton's theory , known as kin selection , which ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology" ]	2011	A Quantitative Test of Hamilton's Rule for the Evolution of Altruism
Behavior and physiology are orchestrated by neuropeptides acting as central neuromodulators and circulating hormones . An outstanding question is how these neuropeptides function to coordinate complex and competing behaviors . In Drosophila , the neuropeptide leucokinin ( LK ) modulates diverse functions , but mechanis...	Animals ranging from jellyfish to humans use multiple neuropeptides to orchestrate various aspects of behavior and physiology . A major question in biology is how animals are able to coordinate complex and competing behaviors to ensure maintenance of a stable internal environment . To address this , we delineated the f...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "nervous", "system", "diet", "neuroscience", "animals", "biological", "locomotion", "endocrine", "physiology", "animal", "models", "starvation", "physiological", "processes", "drosophila", "melanogaster", "model", ...	2018	Modulation of Drosophila post-feeding physiology and behavior by the neuropeptide leucokinin
In eukaryotes , RNA species originating from pervasive transcription are regulators of various cellular processes , from the expression of individual genes to the control of cellular development and oncogenesis . In prokaryotes , the function of pervasive transcription and its output on cell physiology is still unknown...	Bacillus subtilis is a widely used model to study cell differentiation in the bacterial world . This soil-dwelling bacterium can engage in several alternative developmental programs , which generate distinct cell types adapted to different lifestyles , to cope with its complex and changing natural environment . The und...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "biofilms", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "bacillus", "microbiology", "operons", "bacterial", "sporulation", "dna", "transcription", "prokaryotic", "models", "exper...	2017	Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis
We report association mapping of a locus on bovine chromosome 3 that underlies a Mendelian form of stunted growth in Belgian Blue Cattle ( BBC ) . By resequencing positional candidates , we identify the causative c124-2A>G splice variant in intron 1 of the RNF11 gene , for which all affected animals are homozygous . We...	Recessive defects in livestock are common , and this is considered to result from the contraction of the effective population size that accompanies intense selection for desired traits , especially when relying heavily on artificial insemination ( as males may concomitantly have a very large number of offspring ) . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "genetics", "and", "genomics", "veterinary", "science" ]	2012	A Splice Site Variant in the Bovine RNF11 Gene Compromises Growth and Regulation of the Inflammatory Response
We study local calcium dynamics leading to a vesicle fusion in a stochastic , and spatially explicit , biophysical model of the CA3-CA1 presynaptic bouton . The kinetic model for vesicle release has two calcium sensors , a sensor for fast synchronous release that lasts a few tens of milliseconds and a separate sensor f...	Chemical synaptic transmission in neurons takes place when a neurotransmitter released from a nerve terminal of the presynaptic neuron signals to the postsynaptic neuron that an event has occurred . The goal of our research was to model the release at a type of synapse found in the hippocampus , a part of the brain tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "biophysics/biomacromolecule-ligand", "interactions", "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/neuronal", "and", "glial", ...	2010	Modelling Vesicular Release at Hippocampal Synapses
Highly pathogenic avian influenza A viruses ( HPAIV ) of the H5N1 subtype occasionally transmit from birds to humans and can cause severe systemic infections in both hosts . PB1-F2 is an alternative translation product of the viral PB1 segment that was initially characterized as a pro-apoptotic mitochondrial viral path...	Influenza A viruses can infect avian and mammalian hosts . Human infections with seasonal influenza virus strains are usually confined to the respiratory tract and are cleared within days by the immune system . In contrast , highly pathogenic avian influenza viruses can spread throughout the whole body , usually result...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virulence", "factors", "and", "mechanisms", "viral", "transmission", "and", "infection", "virology", "neurovirulence", "immunology", "biology", "microbiology", "immune", "response" ]	2011	Differential Contribution of PB1-F2 to the Virulence of Highly Pathogenic H5N1 Influenza A Virus in Mammalian and Avian Species
The bHLH transcription factor , PHYTOCHROME INTERACTING FACTOR 3 ( PIF3 ) , interacts specifically with the photoactivated , Pfr , form of Arabidopsis phytochrome B ( phyB ) . This interaction induces PIF3 phosphorylation and degradation in vivo and modulates phyB-mediated seedling deetiolation in response to red light...	Plants monitor their environment for informational light signals that are used to direct adaptive morphogenic responses . The phytochrome ( phy ) family of photoreceptors are central to this process . Upon photoperception , phy molecules rapidly translocate to the nucleus where they interact with basic helix-loop-helix...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "biochemistry/protein", "chemistry", "plant", "biology" ]	2009	Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3
Chronic Obstructive Pulmonary Disease ( COPD ) is a complex disease . Genetic , epigenetic , and environmental factors are known to contribute to COPD risk and disease progression . Therefore we developed a systematic approach to identify key regulators of COPD that integrates genome-wide DNA methylation , gene express...	Chronic Obstructive Pulmonary Disease ( COPD ) is a common lung disease . It is the fourth leading cause of death in the world and is expected to be the third by 2020 . COPD is a heterogeneous and complex disease consisting of obstruction in the small airways , emphysema , and chronic bronchitis . COPD is generally cau...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "genetics", "biology", "and", "life", "sciences", "computational", "biology" ]	2015	Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD
Rates of spontaneous mutation have been estimated under optimal growth conditions for a variety of DNA-based microbes , including viruses , bacteria , and eukaryotes . When expressed as genomic mutation rates , most of the values were in the vicinity of 0 . 003–0 . 004 with a range of less than two-fold . Because the g...	Spontaneous mutations are key drivers of evolution and disease . In microbes , most mutations are deleterious , some are neutral ( without significant impact ) , and a few are advantageous . Because deleterious mutations reduce fitness , there should be constant selection for antimutator mutations that reduce rates of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics" ]	2009	Avoiding Dangerous Missense: Thermophiles Display Especially Low Mutation Rates
It is often assumed that parasites are not virulent to their vectors . Nevertheless , parasites commonly exploit their vectors ( nutritionally for example ) so these can be considered a form of host . Trypanosoma cruzi , a protozoan found in mammals and triatomine bugs in the Americas , is the etiological agent of Chag...	Parasites are often assumed to cause little harm to their arthropod vectors , even though they commonly reproduce inside the arthropods and exploit their nutrients , even causing lesions when crossing internal barriers . Thus , the interests of parasite and vector may well not be aligned and we can expect the parasite ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Trypanosoma cruzi, Etiological Agent of Chagas Disease, Is Virulent to Its Triatomine Vector Rhodnius prolixus in a Temperature-Dependent Manner
Multiciliated cells of the airways , brain ventricles , and female reproductive tract provide the motive force for mucociliary clearance , cerebrospinal fluid circulation , and ovum transport . Despite their clear importance to human biology and health , the molecular mechanisms underlying multiciliated cell differenti...	Lining the airways , brain ventricles , and oviducts , multicilia are small hair-like structures that beat in a whip-like motion to propel fluids , such as mucus , over cell surfaces . Dysfunction of multicilia arising from genetic perturbations is most prominently associated with a devastating disorder called primary ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "cell", "differentiation", "animal", "models", "membrane", "proteins", "developmental", "biology", "model", "organisms", "respiratory", "system", "experimental", "organism", "systems", "centrioles", "embryos", "trachea"...	2017	Conditional knockout mice for the distal appendage protein CEP164 reveal its essential roles in airway multiciliated cell differentiation
Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species . Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process ...	Pathogens have evolved strategies to invade , replicate and spread within their hosts . On the contrary , vertebrates have developed sophisticated immune defence mechanisms that limit , and ideally clear , the infection . This dynamic interplay between host and pathogens determines the course of the infection and the d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "lymphoid", "organs", "animal", "models", "model", "organisms", "lymphatic", "system", "population", "modeling", "gastroenterology", "and", "hepatology", "research", "an...	2014	Independent Bottlenecks Characterize Colonization of Systemic Compartments and Gut Lymphoid Tissue by Salmonella
Ongoing climate change can alter conditions for plant growth , in turn affecting ecological and social systems . While there have been considerable advances in understanding the physical aspects of climate change , comprehensive analyses integrating climate , biological , and social sciences are less common . Here we u...	Ongoing greenhouse gas emissions can alter climate suitability for plant growth , in turn affecting biological and social systems . Using the latest generation of available climate projections we show that there will be fewer days with suitable climates for plant growth , despite an increase in days above freezing . Th...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[]	2015	Suitable Days for Plant Growth Disappear under Projected Climate Change: Potential Human and Biotic Vulnerability
Genetic makeup of the host plays a significant role in the course and outcome of infection . Inbred strains of mice display a wide range of sensitivities to Listeria monocytogenes infection and thus serve as a good model for analysis of the effect of genetic polymorphism . The outcome of L . monocytogenes infection in ...	Specific variances in an individual's DNA , known as genetic polymorphisms , can play a significant role in determining susceptibility to an infectious disease . To identify the genetic polymorphisms that are associated with resistance to the common human bacterial pathogen L . monocytogenes , we have carried out a ser...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "infectious", "diseases", "in", "vitro", "mus", "(mouse)", "molecular", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	Irf3 Polymorphism Alters Induction of Interferon Beta in Response to Listeria monocytogenes Infection
Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause several neurological disorders including Rett syndrome . The di-nucleotide methyl-CG ( mCG ) is the classical MeCP2 DNA recognition sequence , but additional methylated sequence targets have been reported . Here we show by in vitro and in vivo ana...	Rett Syndrome is a severe neurological disorder found in approximately 1:10 . 000 female births . The gene causing most cases of Rett Syndrome has been identified as methyl-CG binding protein 2 ( MeCP2 ) which is an epigenetic reader protein , classically characterized as binding to CpG methylated ( mCG ) di-nucleotide...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "brain", "nucleotides", "sequence", "motif", "analysis", "epigenetics", "dna", "mammalian", "genomics", "molecular", "biology", "techniques", "dna", "methylation", "chromatin", "research", "and", "analysis", "meth...	2017	MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain
Superantigens ( SAgs ) are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyogenes . They target a large fraction of T cell pools to set in motion a “cytokine storm” with severe and sometimes life-threatening consequences typically encountered in toxic shock syndrome ( TSS ) . Given the rapidity w...	Superantigens ( SAgs ) are toxins produced by Staphylococcus aureus and Streptococcus pyogenes , microbes that are responsible for a multitude of infectious diseases and conditions . Once released , SAgs activate many immune cells , resulting in a massive inflammatory response that is often followed by a state of immun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Statistical", "analyses" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "animal", "models", "developmental",...	2017	MAIT cells launch a rapid, robust and distinct hyperinflammatory response to bacterial superantigens and quickly acquire an anergic phenotype that impedes their cognate antimicrobial function: Defining a novel mechanism of superantigen-induced immunopathology and immunosuppression
HIV-associated neurocognitive disorders ( HAND ) represent a spectrum neurological syndrome that affects up to 25% of patients with HIV/AIDS . Multiple pathogenic mechanisms contribute to the development of HAND symptoms including chronic neuroinflammation and neurodegeneration . Among the factors linked to development...	Host cells employ a myriad of antiviral defense systems but most viruses have developed effective countermeasures . Viruses such as HIV that cause lifelong infections are particularly successful in subverting the host antiviral response . While mitochondria have long been known to be critical hubs for antiviral signali...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "enzymes", "immunology", "microbiology", "enzymology", "retroviruses", "viru...	2017	MicroRNAs upregulated during HIV infection target peroxisome biogenesis factors: Implications for virus biology, disease mechanisms and neuropathology
Genome-wide association studies ( GWAS ) for quantitative traits and disease in humans and other species have shown that there are many loci that contribute to the observed resemblance between relatives . GWAS to date have mostly focussed on discovery of genes or regulatory regions habouring causative polymorphisms , u...	Results from recent genome-wide association studies indicate that for most complex traits , there are many loci that contribute to variation in observed phenotype and that the effect of a single variant ( single nucleotide polymorphism , SNP ) on a phenotype is small . Here , we propose a method that combines the effec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/animal", "genetics" ]	2008	Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data
DNA damage response ( DDR ) and selective autophagy both can be activated by reactive oxygen/nitrogen species ( ROS/RNS ) , and both are of paramount importance in cancer development . The selective autophagy receptor and ubiquitin ( Ub ) sensor p62 plays a key role in their crosstalk . ROS production has been well doc...	Reactive oxygen/nitrogen species ( ROS/RNS ) can induce both DNA damage response ( DDR ) and selective autophagy , which play crucial roles in cancer development . The selective autophagy receptor and ubiquitin ( Ub ) sensor p62 links their crosstalk . However , p62-mediated selective autophagy and its interplay with D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "cell", "processes", "microbiology", "immunoblotting", "organisms...	2019	p62-mediated Selective autophagy endows virus-transformed cells with insusceptibility to DNA damage under oxidative stress
Hepatitis C virus ( HCV ) particles closely mimic human very-low-density lipoproteins ( VLDL ) to evade humoral immunity and to facilitate cell entry . However , the principles that govern HCV association with VLDL components are poorly defined . Using an siRNA screen , we identified ABHD5 ( α/β hydrolase domain contai...	HCV replication is linked to the host lipid metabolism , and virions are secreted as lipo-viro-particles whose density , size and biochemical content resemble VLDL . HCV assembles close to lipid droplets and is released via the secretory pathway , but it remains unclear how it accesses the VLDL assembly pathway . In th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "enzymes", "hepacivirus", "pathogens", "enzymology", "microbiology", "viral", "structure", "viruses", "rna", "viruses", "lipid", "signaling", "research", "and", ...	2016	ABHD5/CGI-58, the Chanarin-Dorfman Syndrome Protein, Mobilises Lipid Stores for Hepatitis C Virus Production
Mosquitoes genetically engineered to be resistant to Plasmodium parasites represent a promising novel approach in the fight against malaria . The insect immune system itself is a source of anti-parasitic genes potentially exploitable for transgenic designs . The Anopheles gambiae thioester containing protein 1 ( TEP1 )...	We examined whether the natural anti-parasitic protein TEP1 can be harnessed to generate malaria resistant mosquitoes . We report the expression pattern of genes of the TEP1 immune pathway and the effects of both exogenous and enhanced endogenous expression of TEP1 on the development of Plasmodium in Anopheles gambiae ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Ethics", "Statement" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "luciferase", "body", "fluids", "immune", "cells", "plasmodium", "enzymes", "immunology", "enzymology", "parasitic", "diseases", "animals", "parasitology", "developmental", ...	2017	Transgenic Expression of the Anti-parasitic Factor TEP1 in the Malaria Mosquito Anopheles gambiae
Bacterial populations co-ordinate gene expression collectively through quorum sensing ( QS ) , a cell-to-cell communication mechanism employing diffusible signal molecules . The LysR-type transcriptional regulator ( LTTR ) protein PqsR ( MvfR ) is a key component of alkyl-quinolone ( AQ ) -dependent QS in Pseudomonas a...	Populations of bacterial cells collectively co-ordinate their activities through cell-to-cell communication via the production and sensing of signal molecules . This is called quorum sensing ( QS ) and in many bacteria , QS controls the expression of virulence genes , the products of which damage host tissues . Consequ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "bacterial", "diseases", "infectious", "diseases", "bacterial", "biofilms", "gram", "negative", "materials", "science", "pseudomonas", "infections", "microbial", "pathogens", "chemistry", "biology", "microbiology", "chemical", "biology", "crystal...	2013	Structural Basis for Native Agonist and Synthetic Inhibitor Recognition by the Pseudomonas aeruginosa Quorum Sensing Regulator PqsR (MvfR)
The functional contribution of CNV to human biology and disease pathophysiology has undergone limited exploration . Recent observations in humans indicate a tentative link between CNV and weight regulation . Smith-Magenis syndrome ( SMS ) , manifesting obesity and hypercholesterolemia , results from a deletion CNV at 1...	Genetic factors play a large role in obesity . However , despite recent technical progress in the search for genetic variants , the identities of causative and contributory genetic factors remain largely unknown . Whereas nucleotide sequence variation has been studied extensively with respect to its potential contribut...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	A Duplication CNV That Conveys Traits Reciprocal to Metabolic Syndrome and Protects against Diet-Induced Obesity in Mice and Men
Severe dengue virus ( DENV ) disease is associated with extensive immune activation , characterized by a cytokine storm . Previously , elevated lipopolysaccharide ( LPS ) levels in dengue were found to correlate with clinical disease severity . In the present cross-sectional study we identified markers of microbial tra...	The pathogenesis of severe dengue virus ( DENV ) infection is still not fully understood . It is hypothesized that it is caused by a cytokine storm as is described in severe sepsis . In the sepsis field , the potent immunostimulator lipopolysaccharide ( LPS ) is proposed to play an important role in the development of ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "dengue", "fever", "neglected", "tropical", "diseases", "dengue", "viral", "diseases", "immune", "response" ]	2013	Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease
Next-generation sequencing has made possible the detection of rare variant ( RV ) associations with quantitative traits ( QT ) . Due to high sequencing cost , many studies can only sequence a modest number of selected samples with extreme QT . Therefore association testing in individual studies can be underpowered . Be...	Next-generation sequencing has greatly expanded our ability to identify missing heritability due to rare variants . In order to increase the power to detect associations , one desirable study design is to combine samples from multiple cohorts for mapping commonly measured traits . However , many current studies sequenc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome", "sequencing", "genome", "analysis", "tools", "genomics", "genetic", "association", "studies", "trait", "locus", "analysis", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2012	A Unified Method for Detecting Secondary Trait Associations with Rare Variants: Application to Sequence Data
Temporal analysis of sound is fundamental to auditory processing throughout the animal kingdom . Echolocating bats are powerful models for investigating the underlying mechanisms of auditory temporal processing , as they show microsecond precision in discriminating the timing of acoustic events . However , the neural b...	We routinely rely on a stopwatch to precisely measure the time it takes for an athlete to reach the finish line . Without the assistance of such a timing device , our measurement of elapsed time becomes imprecise . By contrast , some animals , such as echolocating bats , naturally perform timing tasks with remarkable p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "acoustics", "action", "potentials", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "vertebrates", "social", "sciences", "electrophysiology", "neuroscience", "animals", "mammals", "echoes", "an...	2018	Neural timing of stimulus events with microsecond precision
To evaluate the relative effectiveness of tsetse control methods , their costs need to be analysed alongside their impact on tsetse populations . Very little has been published on the costs of methods specifically targeting human African trypanosomiasis In northern Uganda , a 250 km2 field trial was undertaken using sm...	Sleeping sickness remains a serious threat in Sub-Saharan Africa . The disease is normally controlled by medical screening of the human population and treatment of individuals found to be infected . The disease is transmitted by tsetse flies but vector control is rarely used for control . A major reason given is that i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Costs Of Using “Tiny Targets” to Control Glossina fuscipes fuscipes, a Vector of Gambiense Sleeping Sickness in Arua District of Uganda
A genetic interaction ( GI ) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene . Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network . This provided insights into the mechanisms underlying the robus...	Network biology has focused for years on protein-protein interaction ( PPI ) networks , identifying nodes with central structural functions and modules associated to bioprocesses , phenotypes and diseases . Network biology field moved to a higher level of abstraction , and started characterizing a less intuitive kind o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "genetic", "networks", "protein", "interactions", "caenorhabditis", "protein", "interaction", "networks", "animals", "animal", "models", "molecular", "machines", "caenorhabditis", "elegans", "model", "organisms", "network", "analysis", "genome", "analysis",...	2016	Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways
Many bacteria build biofilm matrices using a conserved exopolysaccharide named PGA or PNAG ( poly-β-1 , 6-N-acetyl-D-glucosamine ) . Interestingly , while E . coli and other members of the family Enterobacteriaceae encode the pgaABCD operon responsible for PGA synthesis , Salmonella lacks it . The evolutionary force dr...	During bacterial evolution , specific traits that optimize the organism’s fitness are selected . The production of exopolysaccharides is widespread among bacteria in which they play a protective shielding role as main constituents of biofilms . In contrast to closely related siblings , Salmonella has lost the capacity ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "biofilms", "exopolysaccharides", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "cellulose", "pathogens", "bile", "microbiology", "operons", "organic", "compounds", "salmon...	2017	Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host
A main determinant of prolonged Trypanosoma brucei infection and transmission and success of the parasite is the interplay between host acquired immunity and antigenic variation of the parasite variant surface glycoprotein ( VSG ) coat . About 0 . 1% of trypanosome divisions produce a switch to a different VSG through ...	Trypanosoma brucei—a deadly parasite of humans and animals—owes its success to its ability to cope with host immunity , and the mechanism it uses to do so is a remarkable example of biological variation . Immune responses that develop against the parasite surface coat are only partially effective against the parasite p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "adaptive", "immunity", "trypanosoma", "microbial", "mutation", "molecular", "cell", "biology", "nucleic", "acids", "immunity", "parasite", "evolution", "genetics", "dna", "recombination", "molecular", "genetics", "protozoology", "biology", "micr...	2013	Mosaic VSGs and the Scale of Trypanosoma brucei Antigenic Variation
The identification of T cell epitopes and their HLA ( human leukocyte antigen ) restrictions is important for applications such as the design of cellular vaccines for HIV . Traditional methods for such identification are costly and time-consuming . Recently , a more expeditious laboratory technique using ELISpot assays...	At the core of the human adaptive immune response is the train-to-kill mechanism in which specialized immune cells are sensitized to recognize small peptides from foreign pathogens ( e . g . , HIV virus ) . Following this sensitization , these cells are then activated to kill other cells that display this same peptide ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "viruses", "infectious", "diseases", "mathematics", "immunology", "computational", "biology" ]	2007	A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
Hard ticks subvert the immune responses of their vertebrate hosts in order to feed for much longer periods than other blood-feeding ectoparasites; this may be one reason why they transmit perhaps the greatest diversity of pathogens of any arthropod vector . Tick-induced immunomodulation is mediated by salivary componen...	Dendritic cells ( DC ) are specialised cells of the vertebrate immune system . DC can sense different types of infectious agents and parasites , and both trigger and help regulate the specific types of immunity needed to eliminate them . We have discovered that the largest and globally most important group of hard tick...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "cytokines", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "immune", "suppression", "microbiology", "host-pathogen", "interaction", "adaptive", "immunity", "immune", "defense", "ticks", "immunoregulat...	2013	Novel Immunomodulators from Hard Ticks Selectively Reprogramme Human Dendritic Cell Responses
Interactions between protein domains and lipid molecules play key roles in controlling cell membrane signalling and trafficking . The pleckstrin homology ( PH ) domain is one of the most widespread , binding specifically to phosphatidylinositol phosphates ( PIPs ) in cell membranes . PH domains must locate specific PIP...	Cell signalling pathways are crucial for many biological processes including cell proliferation and survival . Signalling is governed by a complex network of interactions within the cell , and disruption of signalling can lead to a variety of human diseases . Often , a key event in the signalling cascade is the reversi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "biophysics", "simulations", "biophysics" ]	2012	Finding a Needle in a Haystack: The Role of Electrostatics in Target Lipid Recognition by PH Domains
It is estimated that in Latin America and the Caribbean ( LAC ) at least 13 . 9 million preschool age and 35 . 4 million school age children are at risk of infections by soil-transmitted helminths ( STH ) : Ascaris lumbricoides , Trichuris trichiura and hookworms ( Necator americanus and Ancylostoma duodenale ) . Altho...	Soil-transmitted helminths ( STH ) are part of the group of neglected infectious diseases ( NID ) in Latin America and the Caribbean ( LAC ) , and are associated with several adverse chronic effects on child health . Although control interventions such as periodic administration of anthelmintic drugs , health education...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Update on the Mapping of Prevalence and Intensity of Infection for Soil-Transmitted Helminth Infections in Latin America and the Caribbean: A Call for Action
Pregnancy-associated malaria is caused by Plasmodium falciparum malaria parasites binding specifically to chondroitin sulfate A in the placenta . This sequestration of parasites is a major cause of low birth weight in infants and anemia in the mothers . VAR2CSA , a polymorphic multi-domain protein of the PfEMP1 family ...	Individuals living in areas with high Plasmodium falciparum transmission acquire immunity to malaria over time and adults have markedly reduced risk of getting severe disease . However , pregnant women constitute an important exception , and they become more susceptible to malaria during pregnancy . This so called preg...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "immunology", "plasmodium", "microbiology", "computational", "biology" ]	2008	Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA
Babesia bovis , is a tick borne apicomplexan parasite responsible for important cattle losses globally . Babesia parasites have a complex life cycle including asexual replication in the mammalian host and sexual reproduction in the tick vector . Novel control strategies aimed at limiting transmission of the parasite ar...	Babesia bovis , is a tick borne apicomplexan parasite responsible for important cattle losses globally . Babesia parasites have a complex life cycle including asexual replication in the mammalian host and sexual reproduction in the tick vector . Novel control strategies aimed at limiting transmission of the parasite ar...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "ixodes", "parasitic", "diseases", "animals", "parasitic", "protozoans", "parasitology", "vaccines", "developmental", "biology", "apicomplexa", "protozoans"...	2017	The Babesia bovis hap2 gene is not required for blood stage replication, but expressed upon in vitro sexual stage induction

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