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Human Group IIA secreted phospholipase A2 ( hGIIA ) is an acute phase protein with bactericidal activity against Gram-positive bacteria . Infection models in hGIIA transgenic mice have suggested the importance of hGIIA as an innate defense mechanism against the human pathogens Group A Streptococcus ( GAS ) and Group B ...	The human immune system is capable of killing invading bacteria by secreting antimicrobial proteins . Cationic human Group IIA secreted phospholipase A2 ( hGIIA ) is especially effective against Gram-positive bacteria by degrading the bacterial membrane . HGIIA requires binding to negatively charged surface structures ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "gram", "positive", "bacteria", "cell", "walls", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "light", "microscopy", "bacterial", "diseases", "group", "b", "streptococcal", "infection...	2018	Streptococcal Lancefield polysaccharides are critical cell wall determinants for human Group IIA secreted phospholipase A2 to exert its bactericidal effects
An important goal of cancer genomic research is to identify the driving pathways underlying disease mechanisms and the heterogeneity of cancers . It is well known that somatic genome alterations ( SGAs ) affecting the genes that encode the proteins within a common signaling pathway exhibit mutual exclusivity , in which...	An important goal of studying cancer genomics is to identify critical pathways that , when perturbed by somatic genomic alterations ( SGAs ) such as somatic mutations , copy number alterations and epigenomic alterations , cause cancers and underlie different clinical phenotypes . In this study , we present a framework ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets
Bacterial pathogens often employ two-component systems ( TCSs ) , typically consisting of a sensor kinase and a response regulator , to control expression of a set of virulence genes in response to changing host environments . In Staphylococcus aureus , the SaeRS TCS is essential for in vivo survival of the bacterium ....	A bacterial pathogen Staphylococcus aureus uses the SaeRS two-component system to control the production of multiple toxins , resulting in a wide range of diseases in human . The sensor kinase SaeS is a member of the intramembrane-sensing histidine kinases ( IM-HKs ) that lacks a sensory domain and harbors a simple N-t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Extracytoplasmic Linker Peptide of the Sensor Protein SaeS Tunes the Kinase Activity Required for Staphylococcal Virulence in Response to Host Signals
Tick-borne zoonoses in the Order Rickettsiales and Legionellales cause infections that often manifest as undifferentiated fevers that are not easy to distinguish from other causes of acute febrile illnesses clinically . This is partly attributed to difficulty in laboratory confirmation since convalescent sera , specifi...	Tick-borne zoonoses caused by pathogens in the Order Rickettsiales and Legionellales are significant causes of morbidity and mortality in many parts of the world . In recent times , incidences of zoonotic diseases have increased due to the changing climate , cross-border movement of tick-infested animals as well as adv...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "domestic", "animals", "geographical", "locations", "microbiology", "vertebrates", "parasitic", "diseases", "animals", "mammals", "rickettsi...	2018	Tick-borne zoonoses in the Order Rickettsiales and Legionellales in Iran: A systematic review
Reassortment is fundamental to the evolution of influenza viruses and plays a key role in the generation of epidemiologically significant strains . Previous studies indicate that reassortment is restricted by segment mismatch , arising from functional incompatibilities among components of two viruses . Additional facto...	Reassortment is the process by which influenza viruses , which carry RNA genomes comprising eight segments , exchange genetic material . Reassortment of the genome segments of two differing influenza strains has the potential to vastly increase the diversity of circulating influenza viruses . Despite its importance to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology" ]	2013	Influenza Virus Reassortment Occurs with High Frequency in the Absence of Segment Mismatch
All of our perceptual experiences arise from the activity of neural populations . Here we study the formation of such percepts under the assumption that they emerge from a linear readout , i . e . , a weighted sum of the neurons’ firing rates . We show that this assumption constrains the trial-to-trial covariance struc...	This article deals with the interpretation of neural activities during perceptual decision-making tasks , where animals must assess the value of a sensory stimulus and take a decision on the basis of their percept . A “standard model” for these tasks has progressively emerged , whence the animal’s percept and subsequen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain
Planaria continue to blossom as a model system for understanding all aspects of regeneration . They provide an opportunity to understand how the replacement of missing tissues from preexisting adult tissue is orchestrated at the molecular level . When amputated along any plane , planaria are capable of regenerating all...	Understanding the genetic basis of tissue regeneration ( remaking ) from adult structures is an important long-term goal for biomedical science . The widespread nature of regenerative phenomena in different animals allows us to study evolution's answers to coordinating this process . We use the relatively simple and ex...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "developmental", "biology/stem", "cells", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "developmental", "biology...	2010	The TALE Class Homeobox Gene Smed-prep Defines the Anterior Compartment for Head Regeneration
Fruits and seeds are the major food source on earth . Both derive from the gynoecium and , therefore , it is crucial to understand the mechanisms that guide the development of this organ of angiosperm species . In Arabidopsis , the gynoecium is composed of two congenitally fused carpels , where two domains: medial and ...	Most of our food comes from fruits and seeds , derived from a fertilized gynoecium . Therefore , understanding the mechanisms that control gynoecium development is of crucial importance . The Arabidopsis gynoecium has two fused carpels , with a medial domain between them , and a lateral domain consisting of the carpel ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "medicine", "and", "health", "sciences", "reproductive", "system", "gene", "regulation", "regulatory", "proteins", "brassica", "dna-binding", "proteins", "hormones", "plant", "science", "model", "organisms", "plant", "hormones", "experimental", "orga...	2017	The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions . However the complexity of these large metabolic networks often hinders their ...	Reduced models are used commonly to understand the metabolism of organisms and to integrate experimental data for many different studies such as physiology , fluxomics and metabolomics . Without consistent or clear criteria on how these reduced models are actually developed , it is difficult to ensure that they reflect...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusion", "Materials", "and", "methods" ]	[ "cell", "physiology", "chemical", "compounds", "ketones", "metabolic", "networks", "enzymology", "cell", "metabolism", "pyruvate", "metabolites", "network", "analysis", "enzyme", "chemistry", "amino", "acid", "metabolism", "purine", "metabolism", "computer", "and", "inf...	2017	redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
Metazoans display remarkable conservation of gene families , including growth factors , yet somehow these genes are used in different ways to generate tremendous morphological diversity . While variations in the magnitude and spatio-temporal aspects of signaling by a growth factor can generate different body patterns ,...	How a limited number of conserved growth factors such as Wnts generate diverse bodies throughout the animal kingdom is a fundamental question in developmental and evolutionary biology . Diversity is thought to arise in part through variations in the strength and location of growth factor signaling . How the signaling p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "molecular", "cell", "biology", "genetics", "biology", "evolutionary", "biology", "neuroscience", "genetics", "and", "genomics" ]	2013	Neurons Refine the Caenorhabditis elegans Body Plan by Directing Axial Patterning by Wnts
The virulence of Francisella tularensis , the etiological agent of tularemia , relies on an atypical type VI secretion system ( T6SS ) encoded by a genomic island termed the Francisella Pathogenicity Island ( FPI ) . While the importance of the FPI in F . tularensis virulence is clearly established , the precise role o...	Francisella tularensis is a highly pathogenic bacterium causing tularemia . Its ability to cause disease is linked to its ability to replicate in the macrophage cytosol . The intracellular life cycle of Francisella is controlled by a type VI secretion system ( T6SS ) , which is thought to inject effectors into the host...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "bacteriology", "protein", "transport", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "immunology", "cell", "processes", "microbiology", "organic", "compo...	2016	Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence
The RIG-I-like receptor ( RLR ) pathway is essential for detecting cytosolic viral RNA to trigger the production of type I interferons ( IFNα/β ) that initiate an innate antiviral response . Through systematic assessment of a wide variety of genomics data , we discovered 10 molecular signatures of known RLR pathway com...	Viruses pose a continuous threat to human health , even though our immune systems have evolved to neutralize invading viruses . As part of the innate immune system , the RIG-I-like receptors ( RLRs ) are essential for detecting viruses during infection . Recognition of viral RNA by the RLRs triggers an antiviral respon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response
Protein subcellular localization is a major determinant of protein function . However , this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments , and therefore it has limited applications in quantitative protein function analyses . Here , we present ...	Proteins are fundamental building blocks of cells . They perform a variety of biological functions , many of which are essential to the vitality and normal functioning of cells . Proteins have to be located at the appropriate regions inside a cell to perform their functions . Therefore , when proteins change their loca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "genome", "analysis", "tools", "subcellular", "organelles", "image", "cytometry", "molecular", "cell", "biology", "image", "processing", "cytometry", "signal", "processing", "biology", "genomics", "evolutionary", "biology", "computational", "biol...	2014	Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins
Brucella are facultative intracellular bacteria that chronically infect humans and animals causing brucellosis . Brucella are able to invade and replicate in a broad range of cell lines in vitro , however the cells supporting bacterial growth in vivo are largely unknown . In order to identify these , we used a Brucella...	Brucella are facultative intracellular bacteria chronically infecting humans and animals causing brucellosis , one of the most common zoonotic disease worldwide which can result in infertility and chronic debilitating disease . The cells supporting Brucella growth in vivo remain largely unknown . In order to identify t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "immunology", "biology" ]	2012	In Situ Microscopy Analysis Reveals Local Innate Immune Response Developed around Brucella Infected Cells in Resistant and Susceptible Mice
Visceral leishmaniasis ( VL ) , with the squeal of Post-kala-azar dermal leishmaniasis ( PKDL ) , is a global threat for health . Studies have shown sodium stibogluconate ( SSG ) resistance in VL patients with chronic arsenic exposure . Here , we assessed the association between arsenic exposure and risk of developing ...	Post-kala-azar dermal leishmaniasis ( PKDL ) is a sequela of visceral leishmaniasis ( VL ) that appears after patients have apparently been cured of visceral leishmaniasis; even been reported in patients without a history of VL . Previous clinical and epidemiological data ascertains the main risk factor associated with...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "tropical", "diseases", "parasitic", "diseases", "geoinformatics", "urine", "signs", "and", "symptoms", "pharmaceuti...	2016	Chronic Arsenic Exposure and Risk of Post Kala-azar Dermal Leishmaniasis Development in India: A Retrospective Cohort Study
Bone morphogenetic protein ( BMP ) gradients provide positional information to direct cell fate specification , such as patterning of the vertebrate ectoderm into neural , neural crest , and epidermal tissues , with precise borders segregating these domains . However , little is known about how BMP activity is regulate...	A subset of cells in the ectoderm of vertebrate embryos becomes the neural crest , which contributes to the bones and cartilage of the adult face . The neural crest arises in a location between the epidermis , which becomes the future skin , and the neural plate , which becomes the future central nervous system . Throu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling", "developmental", "biology/pattern", "formation", "developmental", "biology/cell", "differentiation", "developmental", "biology/molecular",...	2011	SNW1 Is a Critical Regulator of Spatial BMP Activity, Neural Plate Border Formation, and Neural Crest Specification in Vertebrate Embryos
The neglected tropical diseases ( NTDs ) cause significant morbidity and mortality worldwide . Due to the growth in international travel and immigration , NTDs may be diagnosed in countries of the western world , but there has been no specific focus in the literature on imported NTDs . Retrospective study of a cohort o...	Neglected Tropical Diseases ( NTDs ) have been targeted due to their prevalence and the burden of disease they cause globally , but there has been no significant focus in the literature on the subject of NTDs as a group in immigrants and travelers , and no specific studies on the emerging phenomenon of imported NTDs . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/screening", "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "dise...	2010	Neglected Tropical Diseases outside the Tropics
The energy efficiency of neural signal transmission is important not only as a limiting factor in brain architecture , but it also influences the interpretation of functional brain imaging signals . Action potential generation in mammalian , versus invertebrate , axons is remarkably energy efficient . Here we demonstra...	Conserving energy is essential to life . The brain , while only 2% of the body mass , uses an astounding 20% of its energy . It has long been assumed that this large energy consumption was due to the need to generate the electrical signals through which brain cells communicate: the action potentials . However , recent ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cellular", "neuroscience", "ion", "channels", "computational", "neuroscience", "single", "neuron", "function", "biology", "neuroscience" ]	2012	Warm Body Temperature Facilitates Energy Efficient Cortical Action Potentials
Muscle fiber size is activity-dependent and clinically important in ageing , bed-rest , and cachexia , where muscle weakening leads to disability , prolonged recovery times , and increased costs . Inactivity causes muscle wasting by triggering protein degradation and may simultaneously prevent protein synthesis . Durin...	Most genes are transcribed into mRNA and then translated into proteins that function in various cellular processes . Initiation of mRNA translation is thus a fundamental control point in gene expression . Working in a zebrafish model , we have found that muscle activity ( or inactivity ) can differentially regulate the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	eIF4EBP3L Acts as a Gatekeeper of TORC1 In Activity-Dependent Muscle Growth by Specifically Regulating Mef2ca Translational Initiation
In the context of recent arbovirus epidemics , questions about the frequency of simultaneous infection of patients with different arbovirus species have been raised . In 2014 , a major Chikungunya virus ( CHIKV ) epidemic impacted the Caribbean and South America . As part of ongoing screening of schoolchildren presenti...	Chikungunya virus ( CHIKV ) was the cause of a major epidemic in Haiti from May through August , 2014 , as the disease swept through the Caribbean and South and Central America . During the time-period of the epidemic , our group was monitoring a cohort of children in semi-rural Haiti , using molecular and virology met...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "alphaviruses", "viruses", "phylogenetics", "data", "management", "chikungunya"...	2018	Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014
Mokola virus ( MOKV ) appears to be exclusive to Africa . Although the first isolates were from Nigeria and other Congo basin countries , all reports over the past 20 years have been from southern Africa . Previous phylogenetic studies analyzed few isolates or used partial gene sequence for analysis since limited seque...	According to the World Health Organization , rabies is considered both a neglected zoonotic and tropical disease . Among all the lyssavirus species known to exist today , Mokola virus is unique and appears to be exclusive to Africa . In contrast to all other known virus species in the genus Lyssavirus of the family Rha...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Diversity and Epidemiology of Mokola Virus
Epidermal keratinocytes form a highly organized stratified epithelium and sustain a competent barrier function together with dermal and hematopoietic cells . The Notch signaling pathway is a critical regulator of epidermal integrity . Here , we show that keratinocyte-specific deletion of total Notch signaling triggered...	Skin is the largest organ of the body , forming an elaborate barrier that prevents water loss and protects the internal environment from outside invaders . When this barrier is compromised , keratinocytes , keratin-producing epidermal cells , alert and recruit the immune cells to the site of the breach as part of an ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "dermatology", "developmental", "biology", "cell", "biology", "immunology", "hematology" ]	2008	Notch-Deficient Skin Induces a Lethal Systemic B-Lymphoproliferative Disorder by Secreting TSLP, a Sentinel for Epidermal Integrity
The Onchocerca ochengi adult implant and Brugia malayi microfilariemic Severe-Combined Immunodeficient ( SCID ) mouse models are validated screens to measure macrofilaricidal and microfilaricidal activities of candidate onchocerciasis drugs . The purpose of this study was to assess whether 5 daily sub-cutaneous ( s . c...	Onchocerciasis , caused by the filarial parasitic worm , Onchocerca volvulus , is a major cause of infection-related blindness and skin disease and is targeted for elimination . Current drugs are not optimal in all patient populations and a short-course cure would accelerate elimination . Flubendazole is used to treat ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "drug", "absorption", "body", "fluids", "onchocerca", "volvulus", "helminths", "tropical", "diseases", "parasitic", "diseases", "animals", "onchocerca", "brugia", "neglected", "tropical", "diseases", "pharmacology"...	2019	Short-course, oral flubendazole does not mediate significant efficacy against Onchocerca adult male worms or Brugia microfilariae in murine infection models
With the global distribution , morbidity , and mortality associated with tick and louse-borne relapsing fever spirochetes , it is important to understand the dynamics of vector colonization by the bacteria and transmission to the host . Tick-borne relapsing fever spirochetes are blood-borne pathogens transmitted throug...	Relapsing fever spirochetes cause recurrent febrile episodes , rigors , nausea , vomiting , malaise , and pregnancy complications , and are a leading cause of hospital admissions in regions of Africa . Routes of pathogen transmission include crushed human body lice and feces , or through bites by Ornithodoros spp . of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "borrelia", "infection", "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "tropical", "diseases" ]	2014	Transmission Dynamics of Borrelia turicatae from the Arthropod Vector
HIV-prevalence , as well as incidence of zoonotic parasitic diseases like cystic echinococcosis , has increased in the Kyrgyz Republic due to fundamental socio-economic changes after the breakdown of the Soviet Union . The possible impact on morbidity and mortality caused by Toxoplasma gondii infection in congenital to...	A serological study on toxoplasmosis was undertaken in a rural and urban population in Kyrgyzstan . The observed seroprevalence was adjusted because of differences between age and gender stratifications in the study group compared to population census figures . This gave an estimated seroprevalence in rural and urban p...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "socioeconomic", "aspects", "of", "health", "public", "health", "and", "epidemiology", "zoonoses", "disease", "ecology", "neglected", "tropical", "diseases", "infectious", "disease", "modeling", "parasitic", "dis...	2013	Toxoplasma gondii Infection in Kyrgyzstan: Seroprevalence, Risk Factor Analysis, and Estimate of Congenital and AIDS-Related Toxoplasmosis
Schistosomiasis ( bilharzia ) is a chronic and potentially deadly parasitic disease that affects millions of people in ( sub ) tropical areas . An important partial immunity to Schistosoma infections does develop in disease endemic areas , but this takes many years of exposure and maturation of the immune system . Ther...	Schistosomes are parasitic worms that cause chronic and potentially deadly disease in millions of people in ( sub ) tropical areas . An important partial immunity to infection does develop but this takes many years of exposure and multiple infections . Therefore , children are far more susceptible to re-infection after...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology" ]	2012	Differential Anti-Glycan Antibody Responses in Schistosoma mansoni-Infected Children and Adults Studied by Shotgun Glycan Microarray
We have demonstrated that vaccination with pDNA encoding cysteine proteinase Type II ( CPA ) and Type I ( CPB ) with its unusual C-terminal extension ( CTE ) can partially protect BALB/c mice against cutaneous leishmanial infection . Unfortunately , this protection is insufficient to completely control infection withou...	Cutaneous leishmaniasis ( CL ) is the most common form of leishmaniasis with an annual incidence of approximately 2 million cases and is endemic in 88 countries , including Iran . CL's continued spread , along with rather ineffectual treatments and drug-resistant variants emergence has increased the need for advanced p...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "materials", "science", "nanotechnology", "leishmaniasis", "immunology", "biology", "parasitic", "diseases", "immune", "response" ]	2011	C-Terminal Domain Deletion Enhances the Protective Activity of cpa/cpb Loaded Solid Lipid Nanoparticles against Leishmania major in BALB/c Mice
Turnip yellow mosaic virus ( TYMV ) - a member of the alphavirus-like supergroup of viruses - serves as a model system for positive-stranded RNA virus membrane-bound replication . TYMV encodes a precursor replication polyprotein that is processed by the endoproteolytic activity of its internal cysteine proteinase domai...	Positive-stranded RNA viruses are ultimate parasites . In order to replicate their genome , they first need to invade a host cell and , with usually very limited viral genetic material , subvert the host's molecular machinery . Turnip yellow mosaic virus ( TYMV ) is an excellent model system for studying positive-stran...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "enzyme", "structure", "protein", "interactions", "proteins", "virology", "enzymes", "protein", "structure", "viral", "enzymes", "host-pathogen", "interaction", "biology", "microbiology", "viral", "replication", "complex", "viral", "replication" ]	2013	A Compact Viral Processing Proteinase/Ubiquitin Hydrolase from the OTU Family
As proteins are synthesized , the nascent polypeptide must pass through a negatively charged exit tunnel . During this stage , positively charged stretches can interact with the ribosome walls and slow the translation . Therefore , charged polypeptides may be important factors that affect protein expression . To determ...	Which factors shape the sequence of amino acids that will form a protein ? The biochemical features of amino acids , such as their charge and hydrophobicity , are important drivers of protein tridimensional folding , which creates interaction sites for binding other molecules and directs proteins to specific cellular c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "compounds", "messenger", "rna", "organic", "compounds", "polyribosomes", "fungi", "model", "organisms", "experimental", "organism", "systems", "basic", "amino", "acids", "amino", "acids", "molecular", "biology", "techniques", "cellular", "structures", "and"...	2017	Protein charge distribution in proteomes and its impact on translation
Dengue virus ( DENV ) is the most common mosquito-borne flavivirus; it can either cause mild dengue fever or the more severe dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) . One of the characteristic features of DHF/DSS is vascular leakage; although DENV nonstructural protein 1 ( NS1 ) has been prov...	Dengue is a viral disease transmitted by mosquitoes . The symptoms of dengue are often mild; however , severe dengue is one of the leading causes of hospitalization and death among children in Asian and Latin American countries . A symptom of severe dengue is vascular leakage , which can result in fluid accumulation , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "endothelial", "cells", "cell", "processes", "permeability", "immunology", "tropical", "diseases", "epithelial", "cells", "p...	2016	Dengue Virus Nonstructural Protein 1 Induces Vascular Leakage through Macrophage Migration Inhibitory Factor and Autophagy
The majority of cilia are formed and maintained by the highly conserved process of intraflagellar transport ( IFT ) . Mutations in IFT genes lead to ciliary structural defects and systemic disorders termed ciliopathies . Here we show that the severely truncated sensory cilia of hypomorphic IFT mutants in C . elegans tr...	Cilia are ‘antenna-like’ structures that are present on nearly all cell types in animals . These structures are important for sensing and signaling external cues to the cell . Most cilia are formed by a protein transport process called ‘intraflagellar transport’ or IFT . Mutations in IFT genes result in severe cilia de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "microtubules", "caenorhabditis", "neuroscience", "animals", "animal", "models", "physiological", "processes", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "organism", "development", ...	2016	Structural and Functional Recovery of Sensory Cilia in C. elegans IFT Mutants upon Aging
No investigations have been undertaken of risk factors for intensity of soil-transmitted helminth ( STH ) infection in Timor-Leste . This study provides the first analysis of risk factors for intensity of STH infection , as determined by quantitative PCR ( qPCR ) , examining a broad range of water , sanitation and hygi...	We present a detailed analysis of WASH , environmental and demographic factors associated with intensity of STH infection in Manufahi District , Timor-Leste , using qPCR . Investigation of risk factors for intensity of STH infection is rarely undertaken , and prior analyses have used microscopic-based eggs per gram of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "surface", "water", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "necator", "americanus", "health", "c...	2017	Water, Sanitation and Hygiene (WASH) and environmental risk factors for soil-transmitted helminth intensity of infection in Timor-Leste, using real time PCR
West Nile virus ( WNV ) exists in nature as a genetically diverse population of competing genomes . This high genetic diversity and concomitant adaptive plasticity has facilitated the rapid adaptation of WNV to North American transmission cycles and contributed to its explosive spread throughout the New World . WNV is ...	West Nile virus ( WNV ) was introduced into New York state in 1999 and has since spread across the Americas . It is transmitted in nature between adult female mosquitoes and birds and occasionally infects humans and horses . Within the host , WNV exists as a diverse assortment of closely related mutants . WNV populatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "virology/virus", "evolution", "and", "symbiosis", "virology/emerging", "viral", "diseases", "virology/host", "antiviral", "responses"...	2009	RNAi Targeting of West Nile Virus in Mosquito Midguts Promotes Virus Diversification
The computational and cognitive properties of neural systems are often thought to be implemented in terms of their ( stochastic ) network dynamics . Hence , recovering the system dynamics from experimentally observed neuronal time series , like multiple single-unit recordings or neuroimaging data , is an important step...	Neuronal dynamics mediate between the physiological and anatomical properties of a neural system and the computations it performs , in fact may be seen as the ‘computational language’ of the brain . It is therefore of great interest to recover from experimentally recorded time series , like multiple single-unit or neur...	[ "Abstract", "Introduction", "Results", "Discussion", "Models", "and", "methods" ]	[ "neural", "networks", "applied", "mathematics", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "algorithms", "cognitive", "neuroscience", "systems", "science", "mathematics", "cognition", "algebra", "memory", "research", "and", "analysis", ...	2017	A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements
Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment . Compared to the control of flowering before and after winter by the vernalization and day length pathways , mechanisms that delay or promote flowering during a transient cool or warm period , ...	Plants control their flowering time in response to the temperatures of their environment , e . g . in response to the experience of winter or in response to cold and warm ambient temperatures experienced during spring . The knowledge about the evolutionary adaptation of plants to changing ambient temperatures is at pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M
Homologous recombination provides a mechanism of DNA double-strand break repair ( DSBR ) that requires an intact , homologous template for DNA synthesis . When DNA synthesis associated with DSBR is convergent , the broken DNA strands are replaced and repair is accurate . However , if divergent DNA synthesis is establis...	DNA double-strand breaks are accurately repaired by homologous recombination . This accuracy is ensured by copying the correct genetic information present on a second unbroken copy of the DNA , normally a sister chromosome that is generated during DNA replication . This implies that DNA synthesis occurring during recom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nucleic", "acid", "synthesis", "enzymes", "enzymology", "dna", "replication", "agarose", "gel", "electrophoresis", "dna", "gel", "electrophoresis", "dna", "synthesis", "chemical", "synthesis", "research", "and", "analysis", "methods", "electrophoretic", "techniques", "...	2016	RecG Directs DNA Synthesis during Double-Strand Break Repair
Transmission lies at the interface of human immunodeficiency virus type 1 ( HIV-1 ) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution . In the absence of comprehensive direct comparative analyses of the evol...	Since its discovery three decades ago , the HIV epidemic has unfolded into one of the most devastating pandemics in human history . When HIV replication cannot be completely inhibited , the fast-evolving retrovirus continuously evades intra-host immune and drug selective pressure , but diversifies according to more neu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "microbiology", "immunodeficiency", "viruses", "phylogenetics", "microbial", "evolution", "software", "design", "hiv", "epidemiology", "infectious", "diseases", "com...	2014	The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates
General results from statistical learning theory suggest to understand not only brain computations , but also brain plasticity as probabilistic inference . But a model for that has been missing . We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons...	Synaptic connectivity between neurons in the brain and the efficacies ( “weights” ) of these synaptic connections are thought to encode the long-term memory of an organism . But a closer look at their molecular implementation , as well as imaging experiments over longer periods of time , have shown that synaptic connec...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Network Plasticity as Bayesian Inference
Cystic fibrosis ( CF ) is associated with chronic bacterial airway infections leading to lung insufficiency and decreased life expectancy . Staphylococcus aureus is one of the most prevalent pathogens isolated from the airways of CF patients . Mucoid colony morphology has been described for Pseudomonas aeruginosa , the...	Staphylococcus aureus is one of the most common pathogens isolated from the airways of cystic fibrosis ( CF ) patients . In this study , we identified unusual mucoid S . aureus isolates in 8 of 313 ( 2 . 5% ) CF patients . All mucoid isolates carried a 5 bp deletion upstream of the ica operon , which resulted in increa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biofilms", "blood", "cells", "deletion", "mutation", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "operons", "staphylo...	2016	Dynamic in vivo mutations within the ica operon during persistence of Staphylococcus aureus in the airways of cystic fibrosis patients
The global migration patterns of influenza viruses have profound implications for the evolutionary and epidemiological dynamics of the disease . We developed a novel approach to reconstruct the genetic history of human influenza A ( H3N2 ) collected worldwide over 1998 to 2009 and used it to infer the global network of...	Infections by the influenza A virus show highly seasonal patterns in temperate regions . Winter is flu season . Over the course of the autumn and winter , a small number of initial infections grow to encompass a significant proportion of the population . At the end of the winter , infection disappears . It has been sug...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/bioinformatics", "infectious", "diseases/viral", "infections" ]	2010	Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)
Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology . At the largest phylogenetic scales , the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependen...	Species richness varies by many orders of magnitude across the evolutionary "tree of life . " Some groups , like beetles and flowering plants , contain nearly incomprehensible species diversity , but the overwhelming majority of groups contain far fewer species . Many processes presumably contribute to this variation i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phylogenetics", "speciation", "biology", "evolutionary", "biology", "evolutionary", "systematics", "evolutionary", "processes" ]	2012	Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life
Naturally circulating lentiviruses are abundant in African primate species today , yet their origins and history of transmitting between hosts remain obscure . As a means to better understand the age of primate lentiviruses , we analyzed primate genomes for signatures of lentivirus-driven evolution . Specifically , we ...	The emergence of AIDS in the late 20th century has provoked studies to better understand the evolutionary history of viruses and the factors that govern their spread . Pandemic human immunodeficiency virus-type 1 ( HIV-1 ) , which currently infects 34 million people worldwide , emerged following the transmission of a l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "virology", "biology", "microbiology", "host-pathogen", "interaction", "viral", "evolution" ]	2013	Convergence and Divergence in the Evolution of the APOBEC3G-Vif Interaction Reveal Ancient Origins of Simian Immunodeficiency Viruses
Chromosome segregation is fundamental to all cells , but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious . Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole , binds to a ParB-decorated ch...	Reliable chromosome segregation is crucial to all dividing cells . In some bacteria , segregation has been found to occur in a rather counterintuitive way: the chromosome attaches to a filament bundle and erodes it by causing depolymerization of the filaments . Moreover , unlike eukaryotic cells , bacteria do not use m...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "motility", "microbiology", "mitosis", "prokaryotic", "models", "model", "organisms", "cell", "division", "biophysics", "simulations", "theoretical", "biology", "chromosome", "biology", "caulobacter", "crescentus", "biophysics", "theory", "biology", "biophysics", ...	2011	Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis
Delphinids produce large numbers of short duration , broadband echolocation clicks which may be useful for species classification in passive acoustic monitoring efforts . A challenge in echolocation click classification is to overcome the many sources of variability to recognize underlying patterns across many detectio...	Health of marine mammal populations is often considered an indicator of overall marine ecosystem health and resilience , particularly in highly-impacted regions such as the Gulf of Mexico . Marine mammal populations are difficult to monitor given the many challenges of observing animals at sea ( e . g . weather , limit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gulf", "of", "mexico", "acoustics", "medicine", "and", "health", "sciences", "vertebrates", "neuroscience", "marine", "biology", "animals", "mammals", "animal", "signaling", "and", "communication", "animal", "behavior", "pilot", "whales", "bodies", "of", "water", "...	2017	Automated classification of dolphin echolocation click types from the Gulf of Mexico
Mycobacterium tuberculosis ( Mtb ) uses efficient strategies to evade the eradication by professional phagocytes , involving—as recently confirmed—escape from phagosomal confinement . While Mtb determinants , such as the ESX-1 type VII secretion system , that contribute to this phenomenon are known , the host cell fact...	The intracellular fate of the agent of the human tuberculosis agent in phagocytes is a question of great biological relevance . Among the mycobacterial survival strategies , the escape of Mycobacterium tuberculosis from phagosomes has been subject of scientific debate for a long time . However , technically improved me...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Cytosolic Access of Mycobacterium tuberculosis: Critical Impact of Phagosomal Acidification Control and Demonstration of Occurrence In Vivo
Recent experiments revealed that the fruit fly Drosophila melanogaster has a dedicated mechanism for forgetting: blocking the G-protein Rac leads to slower and activating Rac to faster forgetting . This active form of forgetting lacks a satisfactory functional explanation . We investigated optimal decision making for a...	The dominant perception of forgetting in science and society is that it is a nuisance in achieving better memory performance . However , recent experiments in the fruit fly show that the forgetting rate is biochemically adapted to the environment , raising doubts that slower forgetting per se is a desirable feature . H...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "learning", "and", "memory", "biology", "and", "life", "sciences" ]	2014	A Normative Theory of Forgetting: Lessons from the Fruit Fly
A fundamental question in biology is how sharp boundaries of gene expression form precisely in spite of biological variation/noise . Numerous mechanisms position gene expression domains across fields of cells ( e . g . morphogens ) , but how these domains are refined remains unclear . In some cases , domain boundaries ...	In many developing systems , chemical gradients control the formation of segmental domains of gene expression , specifying distinct domains that go on to form different tissues and structures , in a concentration-dependent manner . These gradients are noisy however , raising the question of how sharply delineated bound...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "brain", "vertebrates", "animals", "simulation", "and", "modeling", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "hindbrain", "experimental", "organism", "systems", "...	2017	Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains
Rabies is a vaccine-preventable viral zoonosis belonging to the group of neglected tropical diseases . Exposure to a rabid animal may result in a fatal acute encephalitis if effective post-exposure prophylaxis is not provided . Rabies occurs worldwide , but its burden is disproportionately high in developing countries ...	Rabies has been known as a deadly disease in Nepal for decades , but information on epidemiology , impact and control remains scattered . We collected and summarized information from a variety of sources , including scientific literature and government agencies . Only little original research has been conducted on the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "microbiology", "animals", "mammals", "dogs", "viruses", "preventive", "medicine", "vaccin...	2016	Epidemiology, Impact and Control of Rabies in Nepal: A Systematic Review
Animal African trypanosomosis is a major threat to the economic development and human health in sub-Saharan Africa . Trypanosoma congolense infections represent the major constraint in livestock production , with anemia as the major pathogenic lethal feature . The mechanisms underlying anemia development are ill define...	Bovine African trypanosomosis is a parasitic disease of veterinary importance that adversely affects the public health and economic development of sub-Saharan Africa . Anemia is a major cause of death associated with this disease . Yet , the mechanisms underlying anemia development are not elucidated , which hampers th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "immune", "cells", "spleen", "immunology", "parasitic", "diseases", "hemodilution", "reticulocytes", "anemia", "bone", "marrow", "cells", "physiological", "processes", ...	2016	MIF-Mediated Hemodilution Promotes Pathogenic Anemia in Experimental African Trypanosomosis
Fungal plant pathogens are persistent and global food security threats . To invade their hosts they often form highly specialized infection structures , known as appressoria . The cAMP/ PKA- and MAP kinase-signaling cascades have been functionally delineated as positive-acting pathways required for appressorium develop...	Many fungal pathogens destroy important crops by first gaining entrance to the host using specialized appressorial cells . Understanding the molecular mechanisms that control appressorium formation could provide new routes for managing severe plant diseases . Here , we describe a previously unknown regulatory pathway t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	GATA-Dependent Glutaminolysis Drives Appressorium Formation in Magnaporthe oryzae by Suppressing TOR Inhibition of cAMP/PKA Signaling
Plasmodium ovale is comprised of two genetically distinct subspecies , P . ovale curtisi and P . ovale wallikeri . Although P . ovale subspecies are similar based on morphology and geographical distribution , allelic differences indicate that P . ovale curtisi and P . ovale wallikeri are genetically divergent . Additio...	Humans can be infected with five malaria parasite species: Plasmodium falciparum , P . vivax , P . malariae , P . knowlesi , and P . ovale . Although the vast majority of malaria morbidity and mortality worldwide can be attributed to P . falciparum , non-falciparum malaria parasites can also cause clinical disease . Re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Characterization of Plasmodium ovale curtisi and P. ovale wallikeri in Western Kenya Utilizing a Novel Species-specific Real-time PCR Assay
Gametes are the source and carrier of genetic information , essential for the propagation of all sexually reproducing organisms . Male gametes are derived from a progenitor stem cell population called spermatogonial stem cells ( SSCs ) . SSCs give rise to male gametes through the coordination of two essential processes...	Sexually reproducing organisms require gametes–sperm and eggs–for the perpetuation of life and transmission of genetic information between generations . Male gametes ( sperm ) arise from a dedicated population of stem cells known as spermatogonial stem cells ( SSCs ) . Identification of factors involved in SSC maintena...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "reproductive", "system", "rna", "interference", "helminths", "animals", "spermatogonia", "cell", "differentiation", "germ", "cells", "developmental", "biology", "epigenetics"...	2016	NF-YB Regulates Spermatogonial Stem Cell Self-Renewal and Proliferation in the Planarian Schmidtea mediterranea
Patients with valvulopathy have the highest risk to develop infective endocarditis ( IE ) , although the relationship between valvulopathy and IE is not clearly understood . Q fever endocarditis , an IE due to Coxiella burnetii , is accompanied by immune impairment . Patients with valvulopathy exhibited increased level...	Infective endocarditis ( IE ) is a problem of public health that still causes high mortality despite antibiotic treatments . Most of the patients who develop an IE have pre-existing cardiac lesions , although the relationship between IE and valvulopathy is not clearly understood . We showed here that patients with valv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "cell", "biology/gene", "expression", "cardiovascular", "disorders/valvular", "disease" ]	2008	The Uptake of Apoptotic Cells Drives Coxiella burnetii Replication and Macrophage Polarization: A Model for Q Fever Endocarditis
Biophysically detailed models of single cells are difficult to fit to real data . Recent advances in imaging techniques allow simultaneous access to various intracellular variables , and these data can be used to significantly facilitate the modelling task . These data , however , are noisy , and current approaches to ...	Cellular imaging techniques are maturing at a great pace , but are still plagued by high levels of noise . Here , we present two methods for smoothing individual , noisy traces . The first method fits a full , biophysically accurate description of the cell under study to the noisy data . This allows both smoothing of t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physiology/neuronal", "signaling", "mechanisms", "biophysics/experimental", "biophysical", "methods", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "neuroscience/theoretical", "neuroscience" ]	2009	Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings
Soluble circulating proteins play an important role in the regulation of mating behavior in Drosophila melanogaster . However , how these factors signal through the blood–brain barrier ( bbb ) to interact with the sex-specific brain circuits that control courtship is unknown . Here we show that male identity of the blo...	Complex behaviors such as mating behavior are controlled by the brain . Ensembles of brain cells work in networks to ensure proper behavior at the right time . While the state of these cells plays an important role in whether and how the behavior is displayed , information from outside the brain is also required . Ofte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "signal", "transduction", "drosophila", "melanogaster", "animal", "genetics", "model", "organisms", "molecular", "cell", "biology", "behavioral", "neuroscience", "genetics", "signaling", "pathways", "biology", "neuroscience", "genetics", "and", "genomi...	2013	Sex-Specific Signaling in the Blood–Brain Barrier Is Required for Male Courtship in Drosophila
The viral Tax oncoprotein plays a key role in both Human T-cell lymphotropic virus type 1 ( HTLV-1 ) -replication and HTLV-1-associated pathologies , notably adult T-cell leukemia . Tax governs the transcription from the viral 5’LTR , enhancing thereby its own expression , via the recruitment of dimers of phosphorylate...	Human T-cell lymphotropic virus type 1 ( HTLV-1 ) is the only human retrovirus associated to a cancer . Indeed , HTLV-1 is responsible for adult T-cell leukemia , an aggressive malignant proliferation of CD4+ T lymphocytes . The regulatory protein Tax governs HTLV-1 transcription from the 5’LTR , driving expression of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "transfection", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "immunology", "public", "policy", "microbiology", "social", "sciences", "organic", "compound...	2017	Hijacking of the O-GlcNAcZYME complex by the HTLV-1 Tax oncoprotein facilitates viral transcription
Taenia solium , a zoonotic parasite that is endemic in most developing countries where pork is consumed , is recognised as the main cause of acquired epilepsy in these regions . T . solium has been reported in almost all of the neighboring countries of Democratic Republic of Congo ( DRC ) but data on the current preval...	Taenia solium is a parasite that can affect both humans and pigs , causing important economic losses in pig production and being the main cause of acquired epilepsy in endemic areas . However , the parasite has been neglected in many African countries and particularly in the Democratic Republic of Congo ( DRC ) , where...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology" ]	2010	Taenia solium Cysticercosis in the Democratic Republic of Congo: How Does Pork Trade Affect the Transmission of the Parasite?
The role of regulatory T cells ( Tregs ) in vaccination has been poorly investigated . We have reported that vaccination with ex vivo-generated dendritic-cells ( DC ) loaded with HIV-lipopeptides ( LIPO-5-DC vaccine ) in HIV-infected patients was well tolerated and highly immunogenic . These responses and their relatio...	Highly active antiretroviral therapy ( HAART ) has considerably decreased AIDS-related mortality and morbidity in recent years . Nevertheless , the search for effective vaccine to combat HIV is in the limelight of modern medical research . In clinical trial settings , T-cell responses are routinely measured following v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Decreased HIV-Specific T-Regulatory Responses Are Associated with Effective DC-Vaccine Induced Immunity
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry ( MALDI-TOF MS ) has recently emerged in the field of entomology as a promising method for the identification of arthropods and the detection of associated pathogens . An experimental model of Ctenocephalides felis ( cat fleas ) infected with ...	Fleas are known vectors of human infectious diseases . Identification of fleas and their associated pathogens is essential for the prevention of flea-borne diseases . Currently , the morphological identification of arthropods based on dichotomous keys , as well as molecular techniques , are the most common approaches f...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "borrelia", "infection", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "animals", "bacterial", "diseases", "fleas", "infectious", "disease", "control", "bacteria", "...	2018	Detection of Bartonella spp. in fleas by MALDI-TOF MS
Gammaherpesviruses , including the human pathogens Epstein-Barr virus ( EBV ) and Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , establish lifelong latent infection in B cells and are associated with a variety of tumors . In addition to protein coding genes , these viruses encode numerous microRNAs ( miRNAs ) withi...	Gammaherpesviruses , including the human pathogens Epstein-Barr virus ( EBV ) and Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , establish lifelong infections and are associated with a variety of tumors . These viruses encode numerous molecules called microRNAs ( miRNAs ) within their genomes , which target and sup...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "natural", "antisense", "transcripts", "gene", "regulation", "pathogens", "immunology", "messenger", "rna", "microbiology", "fibroblasts", "viruse...	2019	Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery
Noroviruses are the most common cause of viral gastroenteritis . An increase in the number of globally reported norovirus outbreaks was seen the past decade , especially for outbreaks caused by successive genogroup II genotype 4 ( GII . 4 ) variants . Whether this observed increase was due to an upswing in the number o...	Noroviruses , known as the viruses that cause the ‘stomach flu’ or as the ‘cruise ship virus’ , cause sporadic cases and large outbreaks of gastrointestinal illness in humans . An increase in norovirus outbreaks was reported globally around 2002 . Doubts remained as to whether this increase was real , or caused by impr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "virology/emerging", "viral", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infectio...	2010	Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants
Recent experimental evidence suggests that coordinated expression of ion channels plays a role in constraining neuronal electrical activity . In particular , each neuronal cell type of the crustacean stomatogastric ganglion exhibits a unique set of positive linear correlations between ionic membrane conductances . Thes...	Most motor neurons receive input from the brain before transmitting to the muscle , resulting in a muscle contraction . In some cases , a small group of motor neurons can act independently to control rhythmic muscle contractions . Locomotion in mammals is thought to arise , in a large part , due to neuronal networks of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "neuroscience/motor", "systems", "computational", "biology/computational", "neuroscience", "cell", "biology/neuronal", "signaling", "mechanisms", "neuroscience/neural", "homeostasis", "neuroscience/theoretical", "neur...	2010	Conductance Ratios and Cellular Identity
The intestine is a common site for a variety of pathogenic infections . Helminth infections continue to be major causes of disease worldwide , and are a significant burden on health care systems . Lysine methyltransferases are part of a family of novel attractive targets for drug discovery . SETD7 is a member of the Su...	The gastrointestinal tract is a common site for infection by a variety of pathogens . For example , gut-dwelling parasitic worms currently infect over a billion people , mostly in developing nations . Deworming strategies have been shown to improve physical and intellectual development of infected children , but curren...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immunology", "cell-mediated", "immunity", "parasitic", "diseases", "infectious", "disease", "immunology", "clinical", "medicine", "gastroenterology", "and", "hepatology", "digestive", "system", "gene", "expression", "gastrointestina...	2016	Intestinal Epithelial Cell-Intrinsic Deletion of Setd7 Identifies Role for Developmental Pathways in Immunity to Helminth Infection
Heterogeneous mosquito biting results in different individuals in a population receiving an uneven number of bites . This is a feature of many vector-borne disease systems that , if understood , could guide preventative control efforts toward individuals who are expected to contribute most to pathogen transmission . We...	We studied the biting habits of Aedes aegypti , the principal vector of dengue virus , to determine why certain people are bitten more often by this day-active mosquito . Over one year in dengue-endemic Iquitos , Peru , we collected blood fed mosquitoes from 19 households . Mosquito blood meals were then matched to hou...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "zoology", "entomology", "biology" ]	2014	Determinants of Heterogeneous Blood Feeding Patterns by Aedes aegypti in Iquitos, Peru
The ortholog conjecture posits that orthologous genes are functionally more similar than paralogous genes . This conjecture is a cornerstone of phylogenomics and is used daily by both computational and experimental biologists in predicting , interpreting , and understanding gene functions . A recent study , however , c...	Today's exceedingly high speed of genome sequencing , compared with the generally slow pace of functional assay , means that the functions of most genes identified from genome sequences will be annotated only through computational prediction . The primary source of information for this prediction is the functions of or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "genomics", "functional", "genomics", "evolutionary", "biology", "bio-ontologies", "genomic", "evolution", "biology", "computational", "biology", "comparative", "genomics", "evolutionary", "genetics", "genetics", "and", "genomics" ]	2012	The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data
This article reviews essential topics of canine visceral leishmaniasis ( CVL ) due to Leishmania infantum infection . It focuses on the current serological and molecular diagnostic methods used in epidemiological research and veterinary clinics to diagnose CVL and includes new point-of-care ( POC ) tests under developm...	Dogs are the principal reservoir hosts of L . infantum and consequently play a critical role in the transmission cycle of urban VL , which also affects humans . This review provides updated information on important topics such as diagnostic tests and dog treatments that improve dog health and decrease their transmissio...	[ "Abstract", "Introduction", "Methods", "The", "utility", "of", "standard", "and", "newer", "rapid", "diagnostic", "tests", "in", "the", "clinic", "and", "in", "the", "field", "Impact", "of", "treatment", "on", "dog", "infectiousness", "Are", "prevention", "and",...	[ "kala-azar", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "dogs", "parasitic", "protozoans", "animals", "mammals", "review", "protozo...	2018	Canine visceral leishmaniasis: Diagnosis and management of the reservoir living among us
Humans have been shown to combine noisy sensory information with previous experience ( priors ) , in qualitative and sometimes quantitative agreement with the statistically-optimal predictions of Bayesian integration . However , when the prior distribution becomes more complex than a simple Gaussian , such as skewed or...	The process of decision making involves combining sensory information with statistics collected from prior experience . This combination is more likely to yield ‘statistically optimal’ behavior when our prior experiences conform to a simple and regular pattern . In contrast , if prior experience has complex patterns , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cognitive", "neuroscience", "cognition", "decision", "making", "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "cognitive", "science", "neuroscience" ]	2014	On the Origins of Suboptimality in Human Probabilistic Inference
The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity , but have proved to be challenging to study directly in experiments and simulations . Rational strategies to suppress the formation of toxic amyloid oligomers require a better understanding of the mechanisms by which they are gener...	A number of normally soluble proteins can form amyloid structures in a process associated with neurodegenerative diseases such as Alzheimer's and Parkinson's diseases . Mature amyloid structures consist of large fibrils containing thousands of individual proteins aggregated into linear nanostructures; there is increasi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular", "mechanics", "macromolecular", "assemblies", "chemistry", "biology", "computational", "chemistry", "biophysics", "simulations", "biophysics" ]	2012	Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations
The surface proteins hemagglutinin ( HA ) and neuraminidase ( NA ) of human influenza A virus evolve under selection pressures to escape adaptive immune responses and antiviral drug treatments . In addition to these external selection pressures , some mutations in HA are known to affect the adaptive landscape of NA , a...	The fitness of an organism depends on the coordinated function of many genes . Thus , how a mutation in one gene affects fitness often depends on what mutations are present in other genes . This dependence is called “genetic interaction” or “epistasis” . The prevalence and type of such interactions are not well underst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Coordinated Evolution of Influenza A Surface Proteins
Infections caused by dengue virus are a major cause of morbidity and mortality in tropical and subtropical regions of the world . Factors that control transition from mild forms of disease such as dengue fever ( DF ) to more life-threatening forms such as dengue hemorrhagic fever ( DHF ) are poorly understood . Consequ...	While the majority of patients who exhibit febrile dengue infection recover within a week , a small proportion of the patients progress to develop severe symptoms that can be life-threatening if not managed in a hospital setting . Because there is no method to accurately identify this subgroup of patients , many dengue...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "diagnostic", "medicine", "emerging", "infectious", "diseases", "dengue", "fever", "neglected", "tropical", "diseases", "dengue", "biology", "microbiology", "viral", "diseases" ]	2012	Serum Proteome and Cytokine Analysis in a Longitudinal Cohort of Adults with Primary Dengue Infection Reveals Predictive Markers of DHF
The larva of cestodes belonging to the Echinococcus granulosus sensu lato ( s . l . ) complex causes cystic echinococcosis ( CE ) . It is a globally distributed zoonosis with significant economic and public health impact . The most immunogenic and specific Echinococcus-genus antigen for human CE diagnosis is antigen B ...	Cystic echinococcosis ( CE ) , a worldwide-spread zoonosis , affects livestock mammals and humans with significant economic and public health impact . It is caused by the infection with the larva of cestodes belonging to Echinococcus granulosus complex , a series of parasite species with preference for different hosts ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "immune", "physiology", "apolipoproteins", "helminths", "immunology", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "echinococcus", "mammals", "neglected", "tropical", "disea...	2017	Characterisation of Antigen B Protein Species Present in the Hydatid Cyst Fluid of Echinococcus canadensis G7 Genotype
Heavy glycosylation of the envelope ( Env ) surface subunit , gp120 , is a key adaptation of HIV-1; however , the precise effects of glycosylation on the folding , conformation and dynamics of this protein are poorly understood . Here we explore the patterns of HIV-1 Env gp120 glycosylation , and particularly the enric...	Heavy glycosylation of the envelope surface subunit , gp120 , is a key adaptation of HIV-1 , however , the precise effects of glycosylation on the folding , conformation and dynamics of this protein are poorly understood . The network of glycans on gp120 is of particular interest with regards to vaccine design , becaus...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "disulfide", "bonds", "retroviruses", "viruses", "immunodeficiency", "viruses", "rna", "viruses", "glycosylation", "an...	2016	Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein
Finding a multidimensional potential landscape is the key for addressing important global issues , such as the robustness of cellular networks . We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch . This was realized by explicitly constructing the steady stat...	Cellular networks are at the heart of systems biology at present . To understand how cellular networks function in these highly fluctuating environments , a global approach is needed . Here we provide a global framework , in terms of potential landscapes , for studying the gene regulatory networks in the presence of th...	[ "Abstract", "Introduction", "Methods", "and", "Materials", "Results", "Discussion" ]	[ "oncology", "mathematics", "none", "cell", "biology", "computational", "biology" ]	2007	Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch
The 8-aminoquinoline antimalarials , the only drugs which prevent relapse of vivax and ovale malaria ( radical cure ) , cause dose-dependent oxidant haemolysis in individuals with glucose-6-phosphate dehydrogenase ( G6PD ) deficiency . Patients with <30% and <70% of normal G6PD activity are not given standard regimens ...	More than half of the malaria outside of Sub-Saharan Africa is caused by the parasite Plasmodium vivax which is characterised by multiple relapses of malaria from parasites which persist in the liver . The only drugs which prevent these relapses ( radical cure ) are the 8-aminoquinolines primaquine and tafenoquine , an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "maternal", "health", "obstetrics", "and", "gynecology", "plasmodium", "drugs", "variant", "genotypes", "tropical", "diseases", "parasitic", "diseases", "anemia", "parasitic", "protozoans", "parasitology", "...	2018	Implications of current therapeutic restrictions for primaquine and tafenoquine in the radical cure of vivax malaria
Infection of mammalian cells by the strictly intracellular pathogens Chlamydiae requires adhesion and internalization of the infectious Elementary Bodies ( EBs ) . The components of the latter step were unknown . Here , we identify Chlamydia pneumoniae Pmp21 as an invasin and EGFR as its receptor . Modulation of EGFR s...	The obligate intracellular bacterial pathogen Chlamydia pneumoniae is an important cause of human and animal diseases and can infect various cell types . The molecular mechanisms of chlamydial adhesion to and invasion of human cells are not well defined . Recently we identified Pmp21 and other members of the family of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "host-pathogen", "interaction", "biology", "microbiology", "molecular", "cell", "biology", "bacterial", "pathogens" ]	2013	The Chlamydia pneumoniae Invasin Protein Pmp21 Recruits the EGF Receptor for Host Cell Entry
Smc5/6 , a member of the conserved SMC family of complexes , is essential for growth in most organisms . Its exact functions in a mitotic cell cycle are controversial , as chronic Smc5/6 loss-of-function alleles produce varying phenotypes . To circumvent this issue , we acutely depleted Smc5/6 in budding yeast and dete...	Smc5/6 belongs to the SMC ( Structural Maintenance of Chromosomes ) family of protein complexes , all of which are highly conserved and critical for genome maintenance . To address the roles of Smc5/6 during growth , we rapidly depleted its subunits in yeast and found the main acute effect to be defective ribosomal DNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "probe", "techniques", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "fungi", "sumoylation", "dna", "replication", "dna", "molecular", "biology", "techniques", "synthesis", "phase", "gel", "electrophoresis", "li...	2018	Acute Smc5/6 depletion reveals its primary role in rDNA replication by restraining recombination at fork pausing sites
In this paper , we compared the efficacy of observation based modeling approach using a genetic algorithm with the regular statistical analysis as an alternative methodology in plant research . Preliminary experimental data on in vitro rooting was taken for this study with an aim to understand the effect of charcoal an...	Trials to find out the best combination of factors that contribute to the desired response takes up the chunk of time and resources in any plant tissue culture laboratory . The output of such experiments is analysed statistically to come to a conclusion . However , without prior statistical modifications , the results ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "plant", "anatomy", "applied", "mathematics", "lateral", "roots", "genetic", "algorithms", "simulation", "and", "modeling", "algorithms", "regression", "analysis", "analysis", "of", "variance", "plant", "science", "mathematics", "statistics", "(mathematics)", "artificial"...	2018	Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach
In multispecies microbial communities , the exchange of signals such as acyl-homoserine lactones ( AHL ) enables communication within and between species of Gram-negative bacteria . This process , commonly known as quorum sensing , aids in the regulation of genes crucial for the survival of species within heterogeneous...	In nature , bacteria are commonly found in spatially heterogeneous mixtures . Within these environments , multiple species communicate using chemical signals , and crosstalk often governs the activities of microbial populations , including interactions with the host system , forming biofilms , and bioluminescence . Und...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "gene", "regulation", "pathogens", "microbiology", "signaling", "networks", "pseudomonas", "aeruginosa", "crosstalk", "(biology)", "network", "analys...	2017	Quantifying the strength of quorum sensing crosstalk within microbial communities
The function of Toll pathway defense against bacterial infection has been well established in shrimp , however how this pathway responds to viral infection is still largely unknown . In this study , we report the Toll4-Dorsal-AMPs cascade restricts the white spot syndrome virus ( WSSV ) infection of shrimp . A total of...	The TLR pathway mediated antiviral immune response is well identified in mammals , yet , Toll pathway governing this protection in invertebrates remains unknown . In the present study , we uncover that a shrimp Toll4 from a total of nine Tolls in L . vannamei confers resistance to WSSV thought inducing the NF-κB transc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "phosphorylation", "shrimp", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "rna", "interference", "viral", "transmission", "and", "infection", "immunology", "microbiology", "animals", "animal", "models", "drosophila", "me...	2018	RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Sleep and wakefulness are greatly influenced by various physiological and psychological factors , but the neuronal elements responsible for organizing sleep-wake behavior in response to these factors are largely unknown . In this study , we report that a subset of neurons in the lateral hypothalamic area ( LH ) express...	Adjusting sleep-wake behavior in response to environmental and physiological challenges may not only be of protective value , but can also be vital for the survival of the organism . For example , while it is crucial to increase wake to explore a novel environment to search for potential threats and food sources , it i...	[ "Abstract", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "optogenetics", "sleep", "social", "sciences", "vertebrates", "mice", "neuroscience", "animals", "mammals", "physiological", "processes", "signs", "and", "symptoms", "brain", "mapping...	2019	Lateral hypothalamic neurotensin neurons promote arousal and hyperthermia
Leishmaniasis , a human parasitic disease with manifestations ranging from cutaneous ulcerations to fatal visceral infection , is caused by several Leishmania species . These protozoan parasites replicate as extracellular , flagellated promastigotes in the gut of a sandfly vector and as amastigotes inside the parasitop...	Leishmaniasis is a parasitic disease caused by more than 20 species of the genus Leishmania that affects about 12 million people throughout the world and for which there is not an effective vaccine . Depending on the Leishmania species , clinical manifestation of the disease varies from self-resolving skin lesions to l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Amastin Knockdown in Leishmania braziliensis Affects Parasite-Macrophage Interaction and Results in Impaired Viability of Intracellular Amastigotes
Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal , such as the concentration of a ligand , to sites that generate the appropriate output signal , such as enzymatic activity . This information transdu...	We developed the new information theory-based analysis framework presented here , NbIT analysis , for the study of allosteric mechanisms in biomolecular systems from Molecular Dynamics trajectories . The illustrative application of NbIT to the analysis of the occluded state in the bacterial transporter LeuT , produced ...	[ "Abstract", "Introduction", "Methods", "Results" ]	[ "physics", "computational", "chemistry", "mathematics", "statistical", "mechanics", "statistics", "(mathematics)", "chemistry", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology", "biophysics" ]	2014	NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
Although CD4+ Foxp3+ T cells are largely described in the regulation of CD4+ T cell responses , their role in the suppression of CD8+ T cell priming is much less clear . Because the induction of CD8+ T cells during experimental infection with Trypanosoma cruzi is remarkably delayed and suboptimal , we raised the hypoth...	CD8+ T lymphocytes mediate immunity to intracellular pathogens by killing infected cells . However , some pathogens are able to evade the response of CD8+ T cells and , thus , establish chronic infections . This is the case of Trypanosoma cruzi , the protozoan parasite that causes Chagas disease . Here , we investigate...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "spleen", "immunology", "parasitic", "protozoans", "developmental", "biology", "protozoans", "molecular", "development", "cyt...	2016	A Human Trypanosome Suppresses CD8+ T Cell Priming by Dendritic Cells through the Induction of Immune Regulatory CD4+ Foxp3+ T Cells
The immunologic findings that most consistently correlate with resistance in human schistosomiasis are high levels of IgE and low levels of IgG4 . We have genotyped gene and promoter polymorphisms of cytokines associated with regulation of these isotypes in a cohort of men occupationally exposed to Schistosoma mansoni ...	Approximately 200 million people have schistosomiasis in parts of Africa , South America , the Middle East , the Caribbean and Asia . Several studies of multiple treatments and reinfections indicate that some people develop resistance to reinfection . Of all the immunologic findings associated with such studies , the m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/genetics", "of", "the", "immune", "system", "immunology", "immunology/immunity", "to", "infections" ]	2009	Association of the Gene Polymorphisms IFN-γ +874, IL-13 −1055 and IL-4 −590 with Patterns of Reinfection with Schistosoma mansoni
The ubiquitin proteasome system regulates meiotic recombination in yeast through its association with the synaptonemal complex , a ‘zipper’-like structure that holds homologous chromosome pairs in synapsis during meiotic prophase I . In mammals , the proteasome activator subunit PA200 targets acetylated histones for de...	Proteins within the cells that are unnecessary or damaged are degraded by a large protein complex named the proteasome . The proteins to be degraded are marked by a small protein called ubiquitin . The addition of a small modification ( acetyl group ) to some proteins also promotes their degradation by the proteasome ....	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "cell", "death", "spermatocytes", "metaphase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "germ", "cells", "extraction", "techniques", "sperm", "research", "and", "analysis", "methods", "spermatids", "prophase", "protei...	2019	The PSMA8 subunit of the spermatoproteasome is essential for proper meiotic exit and mouse fertility
Inflammasome is an intracellular protein complex that serves as cytosolic pattern recognition receptor ( PRR ) to engage with pathogens and to process cytokines of the interleukin-1 ( IL-1 ) family into bioactive molecules . It has been established that interleukin-1β ( IL-1β ) is important to host defense against Hist...	Histoplasma capsulatum is a dimorphic fungal pathogen . The microconidia and hyphal elements are breathed in and transform to become yeasts in the lungs . Histoplasmosis occurs worldwide and endemic in mid-western United States . The infection is primarily in the lungs that can become disseminated and cause fatal disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "cells", "pathology", "and", "laboratory", "medicine", "redox", "signaling", "pathogens", "antigen-presenting", "cells", "immunology", "microbiology", "immune", "receptor", "signaling", "o...	2017	Dectin-2 is a primary receptor for NLRP3 inflammasome activation in dendritic cell response to Histoplasma capsulatum
Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs . We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolut...	We set out to trace the evolutionary history of an RNA binding protein and how its interactions with targets change over evolution . Identifying this natural history is a step toward understanding the critical differences between organisms and how gene expression programs are rewired during evolution . Using bioinforma...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
The ability of Staphylococcus aureus and other pathogens to consume glucose is critical during infection . However , glucose consumption increases the cellular demand for manganese sensitizing S . aureus to host-imposed manganese starvation . The current investigations were undertaken to elucidate how S . aureus copes ...	Pathogens , such as Staphylococcus aureus and Salmonella species , must be able to consume glucose in order to cause infection . However , glycolysis can increase the need for manganese and sensitize invaders to the manganese-withholding defense of the host , known as nutritional immunity . How pathogens manage these c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "manganese", "enzymes", "pathogens", "metabolic", "processes", "microbiology", "enzymology", "glucose", "metabolism", "staphylococcus", "aureus", "glycolysis...	2019	Metal-independent variants of phosphoglycerate mutase promote resistance to nutritional immunity and retention of glycolysis during infection
Deeply sampled community genomic ( metagenomic ) datasets enable comprehensive analysis of heterogeneity in natural microbial populations . In this study , we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related ...	Communities of microbes in nature consist of a large number of distinct individuals . The variation in DNA sequence between these individuals contains a record of the evolutionary processes that have shaped each community . In most environments , however , the high number of distinct species makes obtaining information...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2008	Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation
Human Long interspersed element-1 ( L1 ) retrotransposons contain an internal RNA polymerase II promoter within their 5′ untranslated region ( UTR ) and encode two proteins , ( ORF1p and ORF2p ) required for their mobilization ( i . e . , retrotransposition ) . The evolutionary success of L1 relies on the continuous re...	Long interspersed element-1 ( L1 ) sequences comprise about 17% of the human genome reference sequence . The average human genome contains about 100 active L1s that mobilize throughout the genome by a “copy and paste” process termed retrotransposition . Active L1s encode two proteins ( ORF1p and ORF2p ) . ORF1p and ORF...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "transfection", "luciferase", "enzymes", "messenger", "rna", "enzymology", "plasmid", "construction", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "dna", "construction", "research", "and", "analysis", "methods", "sequence", "analysis", "sequence"...	2018	Spliced integrated retrotransposed element (SpIRE) formation in the human genome
Oral microbiota contribute to health and disease , and their disruption may influence the course of oral diseases . Here , we used pyrosequencing to characterize the oral bacteriome and mycobiome of 12 HIV-infected patients and matched 12 uninfected controls . The number of bacterial and fungal genera in individuals ra...	Oral microbiota contribute to health and disease , and their disruption may influence the course of oral diseases like oral candidiasis . Here we identify the core oral mycobiome ( COM ) and core oral bacteriome ( COB ) in HIV-infected and uninfected individuals , and demonstrate that the COM differs between these two ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "mycology", "medical", "microbiology", "fungal", "diseases", "biology", "microbiology", "bacterial", "pathogens" ]	2014	Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic Fungi
Mosquito-borne chikungunya virus ( CHIKV ) is a positive-sense , single-stranded RNA virus from the genus Alphavirus , family Togaviridae , which causes fever , rash and severe persistent polyarthralgia in humans . Since there are currently no FDA licensed vaccines or antiviral therapies for CHIKV , the development of ...	With the adaptation of chikungunya virus ( CHIKV ) to transmission by the Aedes albopictus mosquito , a pandemic has occurred resulting in four to six million human infections , and the virus continues to become endemic in new regions , most recently in the Caribbean . CHIKV can cause debilitating polyarthralgia , last...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunopathology", "animal", "models", "of", "infection", "viral", "vaccines", "virulence", "factors", "and", "mechanisms", "emerging", "infectious", "diseases", "virology", "emerging", "viral", "diseases", "immunology", "host-pathogen", "interaction", "biology", "microbi...	2014	Deliberate Attenuation of Chikungunya Virus by Adaptation to Heparan Sulfate-Dependent Infectivity: A Model for Rational Arboviral Vaccine Design
Given the option , humans and other animals elect to distribute their time between work and leisure , rather than choosing all of one and none of the other . Traditional accounts of partial allocation have characterised behavior on a macroscopic timescale , reporting and studying the mean times spent in work or leisure...	Dividing limited time between work and leisure when both are attractive is a common everyday decision . Rather than doing one exclusively , humans and other animals distribute their time between both . Traditional explanations of this phenomenon have studied the macroscopic average times spent in both . By contrast , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "psychology", "ecology", "and", "environmental", "sciences", "social", "sciences", "economic", "models", "labor", "economics", "ecology", "behavior", "ecological", "economics", "biology", "and", "life", "sciences", "microeconomics", "computational", "biology", "neuroscien...	2014	Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure
It has been proposed that interactions between mammalian chromosomes , or transchromosomal interactions ( also known as kissing chromosomes ) , regulate gene expression and cell fate determination . Here we aimed to identify novel transchromosomal interactions in immune cells by high-resolution genome-wide chromosome c...	It is a widely held belief that , in the darkness of the nucleus , strands of DNA that make up different chromosomes frequently meet to ‘kiss’ . These kisses , or transchromosomal interactions , are thought to be important for the expression of genes and thus cell development . Here , we aimed to identify novel transch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "immunology", "cytotoxic", "t", "cells", "white", "blood", "cells", "animal", "cells", "chromosome", "biology", "gene", "expression", "t", "cells", "antibody-producin...	2018	Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development
Staphylococcus aureus asymptomatically colonises the anterior nares , but the host and bacterial factors that facilitate colonisation remain incompletely understood . The S . aureus surface protein ClfB has been shown to mediate adherence to squamous epithelial cells in vitro and to promote nasal colonisation in both m...	Staphylococcus aureus is an important human commensal , present permanently in the noses of about 20% of the population and representing a significant risk factor for infection . The host and bacterial factors that facilitate nasal colonisation remain to be fully characterised . S . aureus adheres to the squamous epith...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "host-pathogen", "interaction" ]	2012	Nasal Colonisation by Staphylococcus aureus Depends upon Clumping Factor B Binding to the Squamous Epithelial Cell Envelope Protein Loricrin
Viruses encode suppressors of cell death to block intrinsic and extrinsic host-initiated death pathways that reduce viral yield as well as control the termination of infection . Cytomegalovirus ( CMV ) infection terminates by a caspase-independent cell fragmentation process after an extended period of continuous virus ...	Cellular suicide is an effective host defense mechanism to control viral infection . Host cells encode proteins that induce infected cell death while viruses encode proteins that prevent death and facilitate viral replication . Human cytomegalovirus encodes vMIA to suppress host-initiated death pathways . Cytomegalovir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/host", "antiviral", "responses", "microbiology/innate", "immunity", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2008	HtrA2/Omi Terminates Cytomegalovirus Infection and Is Controlled by the Viral Mitochondrial Inhibitor of Apoptosis (vMIA)
Protein phosphatase 2A ( PP2A ) plays a major role in dephosphorylating the targets of the major mitotic kinase Cdk1 at mitotic exit , yet how it is regulated in mitotic progression is poorly understood . Here we show that mutations in either the catalytic or regulatory twins/B55 subunit of PP2A act as enhancers of gwl...	Progression through mitosis requires the addition of phosphate groups onto specific proteins by enzymes collectively known as mitotic protein kinases . At the end of mitosis , these phosphates are removed by protein phosphatases . Whereas we know quite a lot about the mitotic protein kinases , we know much less about t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "mitosis", "drosophila", "melanogaster", "animal", "genetics", "model", "organisms", "molecular", "cell", "biology", "cell", "division", "cell", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2011	Suppression of Scant Identifies Endos as a Substrate of Greatwall Kinase and a Negative Regulator of Protein Phosphatase 2A in Mitosis
Humans frequently need to allocate resources across multiple time-steps . Economic theory proposes that subjects do so according to a stable set of intertemporal preferences , but the computational demands of such decisions encourage the use of formally less competent heuristics . Few empirical studies have examined dy...	People often have to trade-off their present wellbeing against their future wellbeing , for example whether to go to an expensive restaurant today or put the money towards a future holiday . Many studies have examined how people make such trade-offs . However , the majority have done so by analyzing choices between one...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief
Leishmania parasites infect macrophages , cells that play an important role in organismal iron homeostasis . By expressing ferroportin , a membrane protein specialized in iron export , macrophages release iron stored intracellularly into the circulation . Iron is essential for the intracellular replication of Leishmani...	Infection with the protozoan parasite Leishmania causes significant human disease in many parts of the world , particularly in the Middle East , India and South America . The parasite is transmitted by sand flies , which are difficult to control and are becoming increasingly common in urban areas . With domestic dogs s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2014	Leishmania-Mediated Inhibition of Iron Export Promotes Parasite Replication in Macrophages
Disrupting either the DNA annealing factor RAD52 or the A-family DNA polymerase POLQ can cause synthetic lethality with defects in BRCA1 and BRCA2 , which are tumor suppressors important for homology-directed repair of DNA double-strand breaks ( DSBs ) , and protection of stalled replication forks . A likely mechanism ...	We have examined the role of two factors , RAD52 and POLQ , in genome maintenance pathways . While these factors are biochemically distinct , they are both synthetic lethal with loss of the BRCA1 and BRCA2 tumor suppressor genes , and hence are emerging therapeutic targets . Furthermore , RAD52 and POLQ have been impli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "gene", "regulation", "immunology", "cancer", "risk", "factors", "cloning", "nucleotides", "oncology", "dna", "replication", "genetic", "annealing", "molecular", "bi...	2019	Distinct roles of RAD52 and POLQ in chromosomal break repair and replication stress response

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