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The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin , dynein , and myosin . Although much is known about how single motors function , there is significant evidence that cargos in vivo are carried by m...	The spatial organization of living cells depends upon a transportation system consisting of molecular motor proteins that act like porters carrying cargos along filaments that are analogous to roads . The breakdown of this transportation system has been associated with neurodegenerative diseases such as Alzheimer's and...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "physics", "biophysic", "al", "simulations", "biophysics", "theory", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2011	How Molecular Motors Are Arranged on a Cargo Is Important for Vesicular Transport
Enterovirus 71 ( EV71 ) is the major causative pathogen of hand , foot , and mouth disease ( HFMD ) . Its pathogenicity is not fully understood , but innate immune evasion is likely a key factor . Strategies to circumvent the initiation and effector phases of anti-viral innate immunity are well known; less well known i...	Enterovirus 71 ( EV71 ) is the causative pathogen of hand , foot , and mouth disease ( HFMD ) . Since the 2008 outbreak of HFMD in Fuyang , Anhui province , China , HFMD has been a severe public health concern affecting children . The major obstacle hindering HFMD prevention and control efforts is the lack of targeted ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "immune", "evasion", "virology", "biology", "microbiology" ]	2013	Enterovirus 71 Protease 2Apro Targets MAVS to Inhibit Anti-Viral Type I Interferon Responses
Chromosome congression and segregation in C . elegans oocytes depend on a complex of conserved proteins that forms a ring around the center of each bivalent during prometaphase; these complexes are then removed from chromosomes at anaphase onset and disassemble as anaphase proceeds . Here , we uncover mechanisms underl...	Most cells have two sets of chromosomes , one from each parent . Meiosis is a specialized form of cell division where chromosomes are duplicated once and segregated twice , in order to generate eggs ( oocytes ) or sperm with only one copy of every chromosome . This is necessary so that fertilization will produce an emb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna", "interference", "microtubules", "anaphase", "metaphase", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "germ", "cells", "oocytes", "sumoylation", "epigenetics", "tubulins", "cellular", "structures", "and", "organelles",...	2018	Dynamic SUMO remodeling drives a series of critical events during the meiotic divisions in Caenorhabditis elegans
Depletion of Wolbachia endosymbionts of human pathogenic filariae using 4–6 weeks of doxycycline treatment can lead to permanent sterilization and adult filarial death . We investigated the anti-Wolbachia drug candidate ABBV-4083 in the Litomosoides sigmodontis rodent model to determine Wolbachia depletion kinetics wit...	Onchocerciasis and lymphatic filariasis represent debilitating neglected tropical diseases that are caused by parasitic filarial nematodes . Current efforts to eliminate onchocerciasis are hampered by the lack of drugs that lead to permanent sterilization of the adult worms or provide a macrofilaricidal effect , i . e ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "body", "fluids", "drugs", "tropical", "diseases", "microbiology", "parasitic", "diseases", "wolbachia", "antimalarials", "nematode", "infections", "developmental", "biology", "filariasis", "pharmaceutics", "antibio...	2019	In vivo kinetics of Wolbachia depletion by ABBV-4083 in L. sigmodontis adult worms and microfilariae
There is a worldwide upscale in mass drug administration ( MDA ) programs to control the morbidity caused by soil-transmitted helminths ( STHs ) : Ascaris lumbricoides , Trichuris trichiura and hookworm . Although anthelminthic drugs which are used for MDA are supplied by two pharmaceutical companies through donation ,...	Soil-transmitted helminths ( STHs ) infect millions of children worldwide . To fight STH , large-scale de-worming programs are implemented in which anthelmintic drugs ( either albendazole ( ABZ ) or mebendazole ( MEB ) ) are administered . However , there is a wide range of other brands , which are even more accessible...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Assessment of Efficacy and Quality of Two Albendazole Brands Commonly Used against Soil-Transmitted Helminth Infections in School Children in Jimma Town, Ethiopia
Modeling the local absorption and retention patterns of membrane-permeant small molecules in a cellular context could facilitate development of site-directed chemical agents for bioimaging or therapeutic applications . Here , we present an integrative approach to this problem , combining in silico computational models ...	We have developed an integrative , cell-based modeling approach to facilitate the design and discovery of chemical agents directed to specific sites of action within a living organism . Here , a computational , multiscale transport model of the lung was adapted to enable virtual screening of small molecules targeting t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "computer", "science", "medicinal", "chemistry", "computer", "modeling", "drugs", "and", "devices", "chemistry", "biology", "computational", "biology", "chemical", "biology" ]	2012	A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes
Th9 cells are a subset of CD4+ T cells that express the protoypical cytokine , IL-9 . Th9 cells are known to effect protective immunity in animal models of intestinal helminth infections . However , the role of Th9 cells in human intestinal helminth infections has never been examined . To examine the role of Th9 cells ...	Strongyloides stercoralis is a common intestinal parasite affecting about 50–100 million people worldwide . It is characterized by a complex lifecycle involving both free- living and parasitic stages and the clinical manifestations range from asymptomatic infection to multi-organ failure . It has the propensity to caus...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	IL-10- and TGFβ-mediated Th9 Responses in a Human Helminth Infection
Schistosoma mansoni do not have de novo purine pathways and rely on purine salvage for their purine supply . It has been demonstrated that , unlike humans , the S . mansoni is able to produce adenine directly from adenosine , although the enzyme responsible for this activity was unknown . In the present work we show th...	The huge challenge in parasitic chemotherapy development is finding a specific compound to attack the parasite organisms without damaging their host . Schistosoma mansoni , which is the causative agent of schistosomiasis , is one of the major health concerns in the developing world . Purine bases are essential for orga...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "glycosylamines", "crystal", "structure", "chemical", "compounds", "phosphates", "helminths", "enzymes", "condensed", "matter", "physics", "enzymology", "nucleotides", "animals", "organic", "compounds", "purines", "c...	2016	Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5’-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway
Vaccinia mature virus requires A26 envelope protein to mediate acid-dependent endocytosis into HeLa cells in which we hypothesized that A26 protein functions as an acid-sensitive membrane fusion suppressor . Here , we provide evidence showing that N-terminal domain ( aa1-75 ) of A26 protein is an acid-sensitive region ...	Vaccinia virus is a complex large DNA virus with a large number of viral membrane proteins to facilitate cell entry . Although it is well established that vaccinia mature virus uses endocytosis to enter cells , it remains unclear how it triggers membrane fusion in the acidic environment of endosomes . Recently , we hyp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "microbial", "mutation", "poxviruses", "pathology", "and", "laboratory", "medicine", "crystal", "structure", "viral", "transmission", "and", "infection", "pathogens", "condensed", "matter", "physics", "micro...	2019	Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH
Morphological changes are critical for host colonisation in plant pathogenic fungi . These changes occur at specific stages of their pathogenic cycle in response to environmental signals and are mediated by transcription factors , which act as master regulators . Histone deacetylases ( HDACs ) play crucial roles in reg...	Many pathogenic fungi need to undergo morphological changes in order to infect their hosts . Typically , pathogenic fungi switch from a non-pathogenic yeast-like form to a polarised pathogenic filament . This morphological switch is regulated genetically and is triggered by specific environmental conditions . Histone d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Hos2 Histone Deacetylase Controls Ustilago maydis Virulence through Direct Regulation of Mating-Type Genes
Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution . We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor , teosinte , using deep RNA sequencing in F1 hybrid and parent inbred line...	Modification of cis regulatory elements to produce differences in gene expression level , localization , and timing is an important mechanism by which organisms evolve divergent adaptations . To examine gene regulatory change during the domestication of maize from its wild progenitor , teosinte , we assessed allele-spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "plant", "genetics", "biology", "and", "life", "sciences", "genomics", "evolutionary", "biology", "evolutionary", "genetics" ]	2014	The Role of cis Regulatory Evolution in Maize Domestication
The trematode Fasciola hepatica is responsible for chronic zoonotic infection globally . Despite causing a potent T-helper 2 response , it is believed that potent immunomodulation is responsible for rendering this host reactive non-protective host response thereby allowing the parasite to remain long-lived . We have pr...	Parasitic worms , helminths , can cause long-lived chronic infection in many hosts that they infection . The liver fluke , Fasciola hepatica , is one such parasite causing global infection of both humans and animals . F . hepatica exerts an influence over the immune system such that it avoids effector mechanisms and pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "parasitic", "diseases", "fibroblasts", "connective", "tissue", "cells", "white", "blood", "cells", "parasitic", "intestinal", "di...	2016	A Trematode Parasite Derived Growth Factor Binds and Exerts Influences on Host Immune Functions via Host Cytokine Receptor Complexes
A large fraction of human genes are regulated by genetic variation near the transcribed sequence ( cis-eQTL , expression quantitative trait locus ) , and many cis-eQTLs have implications for human disease . Less is known regarding the effects of genetic variation on expression of distant genes ( trans-eQTLs ) and their...	Expression quantitative trait locus ( eQTL ) studies have demonstrated that human genes can be regulated by genetic variation residing close to the gene ( cis-eQTLs ) or in a distant region or on a different chromosome ( trans-eQTLs ) . While cis-eQTL variants are likely to affect transcription factor binding or chroma...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gene", "regulatory", "networks", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians
Identifying gene-gene interaction is a hot topic in genome wide association studies . Two fundamental challenges are: ( 1 ) how to smartly identify combinations of variants that may be associated with the trait from astronomical number of all possible combinations; and ( 2 ) how to test epistatic interaction when all p...	Genes do not operate in vacuum . They interact with each other in many ways . Therefore , to figure out genetic causes of disease by case-control association studies , it is important to take interactions into account . There are two fundamental challenges in interaction-focused analysis . The first is the number of po...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "algorithms", "genome-wide", "association", "studies", "computer", "and", "information", "sciences", "mathematics", "statistics", "(mathematics)", "gene", "regulatory", "networks", "genome", "analysis", "genetics", "applied", "mathematics", "biology", "and", "life", "scie...	2014	AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects
Cognitive skills undergo protracted developmental changes resulting in proficiencies that are a hallmark of human cognition . One skill that develops over time is the ability to problem solve , which in turn relies on cognitive control and attention abilities . Here we use a novel multimodal neurocognitive network-base...	The human brain undergoes significant maturational changes between childhood and adulthood that are thought to enable increasingly sophisticated thoughts and behaviors . One of the skills that we develop over time is the ability to problem solve , which relies in turn on the ability to control our attention and success...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cognitive", "neuroscience", "psychology", "neuroanatomy", "mental", "health", "signal", "processing", "biology", "neuroscience", "neuroimaging", "engineering" ]	2012	Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model
The consumption of a vertebrate blood meal by adult female mosquitoes is necessary for their reproduction , but it also presents significant physiological challenges to mosquito osmoregulation and metabolism . The renal ( Malpighian ) tubules of mosquitoes play critical roles in the initial processing of the blood meal...	The Asian tiger mosquito Aedes albopictus is a vector of several medically-important arboviruses and one of the most invasive mosquito species in the world . Existing control measures for mosquitoes are presently being challenged by the emergence of resistance to insecticides that target the nervous system . Thus , it ...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "anatomy", "cell", "biology", "entomology", "renal", "physiology", "physiology", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "molecular", "genetics", "renal", "system", "molecular", "cell", "biology", "zoology" ]	2014	Transcriptomic Evidence for a Dramatic Functional Transition of the Malpighian Tubules after a Blood Meal in the Asian Tiger Mosquito Aedes albopictus
Human T lymphotropic Virus type 1 ( HTLV-1 ) is the etiological agent of Adult T cell Leukemia/Lymphoma ( ATLL ) and HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis ( HAM/TSP ) . Both CD4+ T-cells and dendritic cells ( DCs ) infected with HTLV-1 are found in peripheral blood from HTLV-1 carriers . We previous...	Human T-Lymphotropic Virus type 1 ( HTLV-1 ) is the etiological agent of Adult T-cell Leukemia/Lymphoma ( ATLL ) and HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis ( HAM/TSP ) . In chronically infected patients , the provirus is mainly detected in the CD4+ T-cell population . However , beside lymphocytes , H...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "vesicles", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "antigen-presenting", "cells", "immunology", "microbiology", "enzymology", ...	2017	Dendritic cell maturation, but not type I interferon exposure, restricts infection by HTLV-1, and viral transmission to T-cells
High-throughput sequencing has enabled genetic screens that can rapidly identify mutations that occur during experimental evolution . The presence of a mutation in an evolved lineage does not , however , constitute proof that the mutation is adaptive , given the well-known and widespread phenomenon of genetic hitchhiki...	Experimental evolution allows us to observe evolution in real time . New advances in genome sequencing make it trivial to discover the mutations that have arisen in evolved cultures; however , linking those mutations to particular adaptive traits remains difficult . We evaluated the fitness impacts of thousands of sing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "deletion", "mutation", "mutation", "fungi", "model", "organisms", "fungal", "evolution", "research", "and", "analysis", "methods", "saccharomyces", "mycology", "evolutionary", "genetics", "yeast", "point", "mutation", "genetic", "screens", "gene", "identification", "an...	2016	High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations
Transposable elements ( TEs ) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing . The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low...	Transposable elements comprise a substantial portion of many eukaryotic genomes . These mobile fragments of DNA can directly mutate genes through insertions into coding regions but may also affect the gene regulation through nearby insertions . There is evidence that the majority of transposable elements are epigenetic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "epigenetics", "biology", "genetics", "and", "genomics" ]	2012	Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons
One of the striking findings of comparative developmental genetics was that expression patterns of core transcription factors are extraordinarily conserved in bilaterians . However , it remains unclear whether cis-regulatory elements of their target genes also exhibit common signatures associated with conserved embryon...	Regional identity in embryos is defined by a few specific transcription factors that activate a large number of target genes through binding to common tags in regulatory sequences . In chordates it is unclear if such tags can be identified in the cis-regulatory regions of regionally expressed genes . To address this qu...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/transcriptional", "regulation", "developmental", "biology/developmental", "evolution", "developmental", "biology/pattern", "formation", "develo...	2010	A cis-Regulatory Signature for Chordate Anterior Neuroectodermal Genes
Bluetongue virus ( BTV ) causes hemorrhagic disease in economically important livestock . The BTV genome is organized into ten discrete double-stranded RNA molecules ( S1-S10 ) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly . To substanti...	Bluetongue virus ( BTV ) is an economically important pathogen of ruminants that belongs to a group of viruses whose genome consists of multiple segments of double-stranded RNA . In order for the virus to synthesize viable and infectious progeny , a precise set of the 10 newly replicated BTV segments must be selected f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity
Enteropathogenic E . coli ( EPEC ) is a human pathogen that causes acute and chronic pediatric diarrhea . The hallmark of EPEC infection is the formation of attaching and effacing ( A/E ) lesions in the intestinal epithelium . Formation of A/E lesions is mediated by genes located on the pathogenicity island locus of en...	Enteropathogenic E . coli ( EPEC ) causes diarrhea and generates the attaching and effacing ( A/E ) lesion in human gut epithelium . A/E lesion formation requires the locus of enterocyte effacement ( LEE ) in the bacterial genome , which encodes a protein injection system delivering the translocated intimin receptor ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "transport", "medicine", "and", "health", "sciences", "biopsy", "hela", "cells", "biological", "cultures", "cell", "processes", "surgical", "and", "invasive", "medical", "procedures", "epithelial", "cells", "mutation", "cell", "cultures", "molecular", "biol...	2017	Attaching and effacing (A/E) lesion formation by enteropathogenic E. coli on human intestinal mucosa is dependent on non-LEE effectors
Identifying regulatory mechanisms that influence inflammation in metabolic tissues is critical for developing novel metabolic disease treatments . Here , we investigated the role of microRNA-146a ( miR-146a ) during diet-induced obesity in mice . miR-146a is reduced in obese and type 2 diabetic patients and our results...	Obesity and metabolic disease are on the rise throughout the world , creating a need for research into the interaction between diet and genetics . It is known that chronic inflammation contributes to obesity , but it is not well understood how inflammation and inflammatory genes are controlled to prevent obesity . Here...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "inflammatory", "diseases", "body", "weight", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "diet", "physiological", "parameters", "signs", "and", "symptoms", "nutrition", "obe...	2019	Anti-inflammatory microRNA-146a protects mice from diet-induced metabolic disease
Although leprosy is largely curable with multidrug therapy , incomplete treatment limits therapeutic effectiveness and is an important obstacle to disease control . To inform efforts to improve treatment completion rates , we aimed to identify the geographic and socioeconomic factors associated with leprosy treatment d...	While the leprosy new case detection has been decreasing worldwide since the introduction of multidrug therapy ( MDT ) in the 1980s , treatment default remains an important risk factor for leprosy-associated disability and an obstacle to disease control and elimination . Treatment default occurs when an individual with...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "salaries", "engineering", "and", "technology", "sewage", "tropical", "diseases", "geographical", "locations", "social", "sciences", "social", "geography", "health", "care", "ethnicities", "bacterial", "diseases", "neglected", "t...	2019	Geographic and socioeconomic factors associated with leprosy treatment default: An analysis from the 100 Million Brazilian Cohort
Adhesion governs to a large extent the mechanical interaction between a cell and its microenvironment . As initial cell spreading is purely adhesion driven , understanding this phenomenon leads to profound insight in both cell adhesion and cell-substrate interaction . It has been found that across a wide variety of cel...	How cells spread on a newly encountered surface is an important issue , since it hints at how cells interact physically with the specific material in general . It has been shown before that many cell types have very similar early spreading behavior . This observation has been linked to the mechanical nature of the phen...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[]	2013	Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model
Oral transmission of Trypanosoma cruzi , the causative agent of Chagas disease , is the most important route of infection in Brazilian Amazon and Venezuela . Other South American countries have also reported outbreaks associated with food consumption . A recent study showed the importance of parasite contact with oral ...	Oral transmission of Trypanosoma cruzi associated with food/beverage consumption is presently an important route of infection in Brazil and Venezuela . Colombia , Bolivia , Argentina and Ecuador have also reported to have acute cases of Chagas disease transmission through the oral route . Significant studies about this...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "parasitic", "diseases", "parasitic", "protozoans", "electromagnetic", "radiation", "bioluminescence", "imaging", "optical", "analysis", "respiratory", "system", "lymph", "nodes", "protozoans", "lympha...	2017	Unraveling Chagas disease transmission through the oral route: Gateways to Trypanosoma cruzi infection and target tissues
Hantaan virus ( HTNV ) causes a severe lethal haemorrhagic fever with renal syndrome ( HFRS ) in humans . Despite a limited understanding of the pathogenesis of HFRS , the importance of the abundant production of pro-inflammatory cytokines has been widely recognized . Interleukin 33 ( IL-33 ) has been demonstrated to p...	Hantaan virus ( HTNV ) causes human hemorrhagic fever with renal syndrome ( HFRS ) with a mortality rate of approximately 15% in Asia . At present , the primary treatment for HFRS is limited to critical care management and the use of anti-viral drugs , such as Ribavirin . However , the cytokine storm at the acute phase...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	IL-33/ST2 Correlates with Severity of Haemorrhagic Fever with Renal Syndrome and Regulates the Inflammatory Response in Hantaan Virus-Infected Endothelial Cells
The glycosphingolipid isoglobotrihexosylceramide , or isogloboside 3 ( iGb3 ) , is believed to be critical for natural killer T ( NKT ) cell development and self-recognition in mice and humans . Furthermore , iGb3 may represent an important obstacle in xenotransplantation , in which this lipid represents the only other...	Identification of endogenous antigens that regulate natural killer T ( NKT ) cell development and function is a major goal in immunology . Originally the glycosphingolipid , iGb3 , was suggested to be the main endogenous ligand in both mice and humans . However , recent studies have challenged this hypothesis . From a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology" ]	2008	Humans Lack iGb3 Due to the Absence of Functional iGb3-Synthase: Implications for NKT Cell Development and Transplantation
Epigenetic mechanisms suppress the transcription of transposons and DNA repeats; however , this suppression can be transiently released under prolonged heat stress . Here we show that the Arabidopsis thaliana imprinted gene SDC , which is silent during vegetative growth due to DNA methylation , is activated by heat and...	In plants , expression of certain imprinted genes is restricted to embryo nourishing tissue , the endosperm . Since these genes are silenced by epigenetic mechanisms during vegetative growth , it has been assumed that they have no role in this phase of the plant life cycle . Here , we report on heat-mediated release of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "plant", "science" ]	2014	Heat-Induced Release of Epigenetic Silencing Reveals the Concealed Role of an Imprinted Plant Gene
Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where , both for inference and for assessing prediction uncertainties , it is essential to characterize the system behavior globally in the parameter space . However , current methods based on...	In various scientific domains , in particular in systems biology , dynamic mathematical models of increasing complexity are being developed and analyzed to study biochemical reaction networks . A major challenge in dealing with such models is the uncertainty in parameters such as kinetic constants; how to efficiently a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks
Nucleic acid sensing by cells is a key feature of antiviral responses , which generally result in type-I Interferon production and tissue protection . However , detection of double-stranded RNAs in virus-infected cells promotes two concomitant and apparently conflicting events . The dsRNA-dependent protein kinase ( PKR...	Nucleic acids detection by multiple molecular sensors results in type-I interferon production , which protects cells and tissues from viral infections . At the intracellular level , the detection of double-stranded RNA by one of these sensors , the dsRNA-dependent protein kinase also leads to the profound inhibition of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Induction of GADD34 Is Necessary for dsRNA-Dependent Interferon-β Production and Participates in the Control of Chikungunya Virus Infection
Chagas disease is a neglected disease caused by the intracellular parasite Trypanosoma cruzi . Around 30% of the infected patients develop chronic cardiomyopathy or megasyndromes , which are high-cost morbid conditions . Immune response against myocardial self-antigens and exacerbated Th1 cytokine production has been a...	Chagas disease is caused by the intracellular parasite Trypanosoma cruzi . This infection has been considered one of the most neglected diseases and affects several million people in the Central and South America . Around 30% of the infected patients develop digestive and cardiac forms of the disease . Most patients ar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "immunology/immunity", "to", "infections", "immunology/immune", "response", "infectious", "diseases/protozoal", "infections" ]	2010	IL-17 Produced during Trypanosoma cruzi Infection Plays a Central Role in Regulating Parasite-Induced Myocarditis
Mycetoma is caused by the subcutaneous inoculation of filamentous fungi or aerobic filamentous bacteria that form grains in the tissue . The purpose of this study is to describe the epidemiologic , clinic , laboratory , and therapeutic characteristics of patients with mycetoma at the Oswaldo Cruz Foundation in Rio de J...	Mycetoma is a major health problem in tropical areas and is prevalent among people of low socio-economic status . As in many other regions of the world , the incidence and prevalence of mycetoma in Brazil is unknown . This study describes some aspects of mycetoma patients in 24 years of experience at the National Insti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "and", "review", "of", "the", "literature" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "mycetoma", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "surgical", "and", "invasive", "medical", "procedures", "acremonium", "nocardia", "signs", ...	2017	Review of 21 cases of mycetoma from 1991 to 2014 in Rio de Janeiro, Brazil
Despite decades of community-based mass drug administration ( MDA ) for neglected tropical diseases , it remains an open question as to what constitutes the best combination of community medicine distributors ( CMDs ) for achieving high ( >65%/75% ) treatment rates within a village . Routine community-based MDA was eva...	Community-based mass drug administration ( MDA ) uses volunteers within at-risk communities to distribute preventive chemotherapies en masse for neglected tropical diseases . Treatment rates achieved by community medicine distributors ( CMDs ) vary widely and can undermine morbidity control . We studied routine communi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "behavioral", "and", "social", "aspects", "of", "health", "sociology", "tropical", "diseases", "social", "sciences", "anthropology", "parasitic", "diseases", "filariasis", "pharmaceutics", "global", "health", "neglected", "tropic...	2019	The division of labour between community medicine distributors influences the reach of mass drug administration: A cross-sectional study in rural Uganda
The improved characterisation of risk factors for rheumatoid arthritis ( RA ) suggests they could be combined to identify individuals at increased disease risks in whom preventive strategies may be evaluated . We aimed to develop an RA prediction model capable of generating clinically relevant predictive data and to de...	Rheumatoid arthritis ( RA ) is a common , incurable disease with major individual and health service costs . Preventing its development is therefore an important goal . Being able to predict who will develop RA would allow researchers to look at ways to prevent it . Many factors have been found that increase someone's ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Predicting the Risk of Rheumatoid Arthritis and Its Age of Onset through Modelling Genetic Risk Variants with Smoking
Mass drug administration ( MDA ) treatment of active trachoma with antibiotic is recommended to be initiated in any district where the prevalence of trachoma inflammation , follicular ( TF ) is ≥10% in children aged 1–9 years , and then to continue for at least three annual rounds before resurvey . In The Gambia the PR...	Trachoma , caused by infection with a bacterium ( chlamydia ) is controlled by mass drug administration ( MDA ) , which is recommended yearly for districts in which a trachoma problem has been found to exist . The decision , after several rounds , that MDA is no longer needed is currently based on clinical signs of tra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[]	2015	Costs of Testing for Ocular Chlamydia trachomatis Infection Compared to Mass Drug Administration for Trachoma in The Gambia: Application of Results from the PRET Study
Complex trait genome-wide association studies ( GWAS ) provide an efficient strategy for evaluating large numbers of common variants in large numbers of individuals and for identifying trait-associated variants . Nevertheless , GWAS often leave much of the trait heritability unexplained . We hypothesized that some of t...	Despite the striking success of genome-wide association studies in identifying genetic loci associated with common complex traits and diseases , much of the heritable risk for these traits and diseases remains unexplained . A higher resolution investigation of the genome through sequencing studies is expected to clarif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "sequencing", "genomics", "heredity", "genetics", "biology", "quantitative", "traits", "genetics", "and", "genomics", "complex", "traits" ]	2011	Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability
The integration of experimental data into genome-scale metabolic models can greatly improve flux predictions . This is achieved by restricting predictions to a more realistic context-specific domain , like a particular cell or tissue type . Several computational approaches to integrate data have been proposed—generally...	Recent methodological developments have facilitated the integration of high-throughput data into genome-scale models to obtain context-specific metabolic reconstructions . A unique solution to this data integration problem often may not be guaranteed , leading to a multitude of context-specific predictions equally conc...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "carbohydrate", "metabolism", "metabolic", "networks", "brassica", "glucose", "metabolism", "optimization", "model", "organisms", "mathematics", "network", "analysis", "experimental", "organism", "systems", "plants", "thermodynamics", "research", "and", "analysis", "methods...	2017	On the effects of alternative optima in context-specific metabolic model predictions
Trachoma is a fibrotic disease of the conjunctiva initiated by Chlamydia trachomatis infection . This blinding disease affects over 40 million people worldwide yet the mechanisms underlying its pathogenesis remain poorly understood . We have investigated host microRNA ( miR ) expression in health ( N ) and disease ( co...	Trachoma is a debilitating disease that affects 40 million people worldwide . It can cause progressive fibrosis of the upper eyelid and blindness , yet the mechanism is poorly understood . We have investigated the expression of short sequences of genetic material ( microRNA ) that regulate gene expression . We screened...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "gene", "networks", "rna", "interference", "gene", "regulation", "immunology", "gene", "function", "bacterial", "diseases", "neglected", "tropical", "diseases", "epigenetics", "molecular", "genetics", "signaling", "pathways", "infectious", "diseases", "inflamm...	2013	Conjunctival MicroRNA Expression in Inflammatory Trachomatous Scarring
Recombination between co-infecting poxviruses provides an important mechanism for generating the genetic diversity that underpins evolution . However , poxviruses replicate in membrane-bound cytoplasmic structures known as factories or virosomes . These are enclosed structures that could impede DNA mixing between co-in...	Recombination plays a critical role in DNA repair and also creates the genetic diversity that underpins evolution . This has important implications for viruses , since recombination may create new pathogens with new infectious properties . It has long been known that hybrids can be recovered from cells co-infected with...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "probe", "techniques", "dna-binding", "proteins", "microbiology", "viruses", "dna", "replication", "dna", "viruses", "dna", "molecular", "biology", "techniques", "microbial", "genetics", "gel", "electrophoresis", "research", "and", "analysis", "methods", "e...	2016	Live-Cell Imaging of Vaccinia Virus Recombination
Type I interferons ( IFN-I ) broadly control innate immunity and are typically transcriptionally induced by Interferon Regulatory Factors ( IRFs ) following stimulation of pattern recognition receptors within the cytosol of host cells . For bacterial infection , IFN-I signaling can result in widely variant responses , ...	Type I interferons ( IFN-I ) broadly stimulate innate immunity against viral , bacterial and parasitic pathogens . Many bacterial pathogens induce IFN-I through phosphorylation of Interferon Regulatory Factor 3 ( IRF-3 ) allowing it to bind promoters containing Interferon Stimulated Response Elements ( ISRE ) which inc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2012	Opposing Roles for Interferon Regulatory Factor-3 (IRF-3) and Type I Interferon Signaling during Plague
Apoptosis is a highly regulated cell death mechanism involved in many physiological processes . A key component of extrinsically activated apoptosis is the death receptor Fas which , on binding to its cognate ligand FasL , oligomerize to form the death-inducing signaling complex . Motivated by recent experimental data ...	Many prominent diseases , most notably cancer , arise from an imbalance between the rates of cell growth and death in the body . This is often due to mutations that disrupt a cell death program called apoptosis . Here , we focus on the extrinsic pathway of apoptotic activation which is initiated upon detection of an ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/cell", "signaling", "mathematics", "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/systems", "biology" ]	2010	Bistability in Apoptosis by Receptor Clustering
How cells establish and dynamically change polarity are general questions in cell biology . Cells of the rod-shaped bacterium Myxococcus xanthus move on surfaces with defined leading and lagging cell poles . Occasionally , cells undergo reversals , which correspond to an inversion of the leading-lagging pole polarity a...	Most cells are spatially organized with proteins localizing to specific regions . The ability of cells to polarize facilitates many processes including motility . Myxococcus xanthus cells move in the direction of their long axis and occasionally change direction of movement by undergoing reversals . Similarly to eukary...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "evolutionary", "biology", "microbiology", "gtpase", "signaling", "microbial", "evolution", "signaling", "in", "cellular", "processes", "comparative", "genomics", "biology", "evolutionary", "genetics", "signal", "transduction", "genomics", "molecular", "cell...	2012	A Response Regulator Interfaces between the Frz Chemosensory System and the MglA/MglB GTPase/GAP Module to Regulate Polarity in Myxococcus xanthus
Tropical pathogens often cause febrile illnesses in humans and are responsible for considerable morbidity and mortality . The similarities in clinical symptoms provoked by these pathogens make diagnosis difficult . Thus , early , rapid and accurate diagnosis will be crucial in patient management and in the control of t...	Tropical diseases consist of a group of debilitating and fatal infections that occur primarily in rural and urban settings of tropical and subtropical countries . While the primary indices of an infection are mostly the presentation of clinical signs and symptoms , outcomes due to an infection with tropical pathogens a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacteriology", "infectious", "diseases", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "medical", "microbiology", "virology", "molecular", "probe", "techniques", "biology", "and", "life", "sciences", "molecular", "biology", "techniques", "microbiolog...	2014	An Integrated Lab-on-Chip for Rapid Identification and Simultaneous Differentiation of Tropical Pathogens
Yaws is an infectious , debilitating and disfiguring disease of poverty that mainly affects children in rural communities in tropical areas . In Cameroon , mass-treatment campaigns carried out in the 1950s reduced yaws to such low levels that it was presumed the disease was eradicated . In 2010 , an epidemiological stu...	Yaws is an infectious and disfiguring disease of poverty primarily affecting children in rural communities in tropical areas . Yaws is easily treated by a single dose of antibiotics and is on the World Health Organization’s eradication list . Yaws was thought eradicated in the Cameroon in the 1950s following aggressive...	[ "Abstract", "Introduction", "Methods", "Results", "Observations", "of", "the", "distribution", "of", "yaws", "in", "Bankim", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "health", "care", "treponematoses", "bacterial", "diseases", "age", "g...	2017	Yaws resurgence in Bankim, Cameroon: The relative effectiveness of different means of detection in rural communities
In most eukaryotes , the prophase of the first meiotic division is characterized by a high level of homologous recombination between homologous chromosomes . Recombination events are not distributed evenly within the genome , but vary both locally and at large scale . Locally , most recombination events are clustered i...	In most sexually reproducing species , during meiosis a high level of recombination between homologous chromosomes is induced . These events are not evenly distributed in the genome but clustered in small regions called hotspots . The genetic factors controlling their activity in mammals are still poorly understood . W...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mus", "(mouse)", "molecular", "biology", "developmental", "biology" ]	2007	Cis- and Trans-Acting Elements Regulate the Mouse Psmb9 Meiotic Recombination Hotspot
Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades . This hypothesis predicts , among other things , rapid rates of morphological evolution during the early history of major groups , as lineages invade disparate ecological niches . However , few studies of adapti...	Animals display huge morphological and ecological diversity . One possible explanation of how this diversity evolved is the "niche filling" model of adaptive radiation—under which evolutionary rates are highest early in the evolution of a group , as lineages diversify to fill disparate ecological niches . We studied pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "paleozoology", "paleobiology", "vertebrate", "paleontology", "earth", "sciences", "paleontology", "biology", "and", "life", "sciences", "evolutionary", "theory", "evolutionary", "biology", "evolutionary", "processes" ]	2014	Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage
The proper assembly of the synaptonemal complex ( SC ) between homologs is critical to ensure accurate meiotic chromosome segregation . The SC is a meiotic tripartite structure present from yeast to humans , comprised of proteins assembled along the axes of the chromosomes and central region ( CR ) proteins that bridge...	Meiosis is a two-part cell division program that ensures the formation of haploid gametes ( e . g . eggs and sperm ) , which can then reconstitute a species' ploidy through fertilization . A critical step towards accomplishing this task is the accurate segregation of homologous chromosomes away from each other during m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "genetics", "and", "genomics/chromosome", "biology", "cell", "biology/nuclear", "structure", "and", "function" ]	2009	A Yeast Two-Hybrid Screen for SYP-3 Interactors Identifies SYP-4, a Component Required for Synaptonemal Complex Assembly and Chiasma Formation in Caenorhabditis elegans Meiosis
The ability of innate immune cells to sense and respond to impending danger varies by anatomical location . The liver is considered tolerogenic but is still capable of mounting a successful immune response to clear various infections . To understand whether hepatic immune cells tune their response to different infectio...	The ability of human pathogens , like HBV , HCV or Plasmodium spp . to infect the liver might be influenced by its tolerogenic features . However , hepatic tolerance is not absolute since protective immunity can be triggered . Our goal was to define how to deliberately elicit an intrahepatic protective immune response ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "immunology", "medicine", "and", "health", "sciences" ]	2014	Toll-Like Receptor 8 Agonist and Bacteria Trigger Potent Activation of Innate Immune Cells in Human Liver
Vector arthropods control arbovirus replication and spread through antiviral innate immune responses including RNA interference ( RNAi ) pathways . Arbovirus infections have been shown to induce the exogenous small interfering RNA ( siRNA ) and Piwi-interacting RNA ( piRNA ) pathways , but direct antiviral activity by ...	A number of orthobunyaviruses such as Oropouche virus , La Crosse virus and Schmallenberg virus are important global human or animal pathogens transmitted by arthropod vectors . Further understanding of the antiviral control mechanisms in arthropod vectors is key to developing novel prevention strategies based on preve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "luciferase", "rna", "interference", "gene", "regulation", "enzymes", "microbiology", "enzymology", "animals", "viruses", "epigenetics", "molecular", "biology", "techniques", "rna", "seq...	2017	The Antiviral RNAi Response in Vector and Non-vector Cells against Orthobunyaviruses
Species often encounter , and adapt to , many patches of similar environmental conditions across their range . Such adaptation can occur through convergent evolution if different alleles arise in different patches , or through the spread of shared alleles by migration acting to synchronize adaptation across the species...	Often , a large species range will include patches where the species differs because it has adapted to locally differing conditions . For instance , rock pocket mice are often found with a coat color that matches the rocks they live in , these color differences are controlled genetically , and mice that don’t match the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "Methods" ]	[]	2015	Convergent Evolution During Local Adaptation to Patchy Landscapes
Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly abundant in many environments . Owing to their capability to utilize solar energy and atmospheric carbon dioxide for growth , cyanobacteria are increasingly recognized as a prolific resource for the synthesis of valuable chemicals and v...	Phototrophic microorganisms hold great promises as a resource to generate high-value products and biofuels using only atmospheric carbon dioxide , light , and some minerals . In particular cyanobacteria , the only known prokaryotes capable of oxygen-evolving photosynthesis , have attracted recent attention as a possibl...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "systems", "biology", "biochemistry", "theoretical", "biology", "biology", "computational", "biology", "marine", "biology" ]	2013	Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803
A striking feature of vascular plants is the regular arrangement of lateral organs on the stem , known as phyllotaxis . The most common phyllotactic patterns can be described using spirals , numbers from the Fibonacci sequence and the golden angle . This rich mathematical structure , along with the experimental reprodu...	How living organisms affected by natural , stochastic variability achieve regular developmental patterns is a challenging question in biology . A fitting field of investigation is provided by phyllotaxis , the regular arrangements of lateral organs such as leaves or flowers on the stem of vascular plants , as visible o...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "physics", "systems", "biology", "developmental", "biology", "plant", "science", "condensed-matter", "physics", "organism", "development", "mathematics", "theoretical", "biology", "plant", "biology", "biology", "computational", "biology", "biophysics", "nonlinear", "dynamic...	2012	Noise and Robustness in Phyllotaxis
The Direct Agglutination Test ( DAT ) has a high diagnostic accuracy and remains , in some geographical areas , part of the diagnostic algorithm for Visceral Leishmaniasis ( VL ) . However , subjective interpretation of results introduces potential for inter-reader variation . We report an assessment of inter-laborator...	Until the 1990's accurate Visceral Leishmaniasis ( VL ) diagnosis necessitated parasitological confirmation by microscopy or culture of the blood , bone-marrow , lymph nodes or spleen . These techniques are invasive and splenic aspirates are associated with a risk of serious bleeding . This has led to the development o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "diagnostic", "medicine", "leishmaniasis", "protozoan", "infections", "parasitic", "diseases" ]	2012	Leishmaniasis Direct Agglutination Test: Using Pictorials as Training Materials to Reduce Inter-Reader Variability and Improve Accuracy
Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens , leading to identifiable signatures of balancing selection . To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum , we generated paired-end short-read sequences of parasites in clinical...	The memory component of acquired immune responses selects for distinctive patterns of polymorphism in genes encoding important target antigens of pathogens . These are detectable by surveying for evidence of balancing selection , as previously illustrated in analyses of genes encoding malaria parasite antigens that are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "parasite", "evolution", "population", "genetics", "immunology", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "plasmodium", "falciparum", "parasitology", "genome", "sequencing", "adaptive", "immunity", "infectious", "diseases", "genetic...	2012	Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites
Eukaryotic organelles evolve to support the lifestyle of evolutionarily related organisms . In the fungi , filamentous Ascomycetes possess dense-core organelles called Woronin bodies ( WBs ) . These organelles originate from peroxisomes and perform an adaptive function to seal septal pores in response to cellular wound...	In the kingdom Fungi , tubular cells called hyphae grow by tip extension and lateral branching to produce an interconnected multicellular syncytium and this unique cellular architecture is especially suited to foraging , long distance transport , and invasive growth . Major groups of fungi have independently evolved ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "cell", "biology", "microbiology/microbial", "evolution", "and", "genomics", "cell", "biology/microbial", "growth", "and", "development", "microbiology", "evolutionary", "biology", "evolutionary", "biology/morpho...	2009	A Tether for Woronin Body Inheritance Is Associated with Evolutionary Variation in Organelle Positioning
Future infectious disease epidemics are likely to disproportionately affect countries with weak health systems , exacerbating global vulnerability . To decrease the severity of epidemics in these settings , lessons can be drawn from the Ebola outbreak in West Africa . There is a dearth of literature on public perceptio...	To decrease the severity of epidemics in countries with under-developed health system capacity to control outbreaks , lessons can be drawn from the Ebola outbreak in West Africa . This is the first study , to our knowledge , to use qualitative research methods to understand community members’ perceptions of using the E...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "health", "services", "research", "engineering", "and", "technology", "transportation", "pathogens", "tropical", "diseases", "geographical", "locations", "microbiology", "ebola", "hemor...	2016	Fears and Misperceptions of the Ebola Response System during the 2014-2015 Outbreak in Sierra Leone
New strategies to combat the global scourge of schistosomiasis may be revealed by increased understanding of the mechanisms by which the obligate snail host can resist the schistosome parasite . However , few molecular markers linked to resistance have been identified and characterized in snails . Here we test six inde...	Aquatic snails transmit schistosome blood flukes , causing a parasitic disease second only to malaria in its global health impact . The mechanisms by which some snails naturally resist infection are poorly understood , but if characterized could enable protocols to interfere with transmission of the disease . Here we i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni
Fungal pathologies are seen in immunocompromised and healthy humans . C-type lectins expressed on immature dendritic cells ( DC ) recognize fungi . We report a novel dorsal pseudopodial protrusion , the “fungipod” , formed by DC after contact with yeast cell walls . These structures have a convoluted cell-proximal end ...	Yeasts are normal microbial commensals of humans and a significant source of opportunistic infections , especially in immunocompromised individuals . We report a novel cellular protrusive structure , the fungipod , which participates in the host-microbe interaction between human immature dendritic cells ( DC ) and yeas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "infectious", "diseases/fungal", "infections", "microbiology/innate", "immunity", "immunology/innate", "immunity", "cell", "biology/cytoskeleton" ]	2010	A Novel Pseudopodial Component of the Dendritic Cell Anti-Fungal Response: The Fungipod
Scale-free networks are generically defined by a power-law distribution of node connectivities . Vastly different graph topologies fit this law , ranging from the assortative , with frequent similar-degree node connections , to a modular structure . Using a metric to determine the extent of modularity , we examined the...	The protein interaction network or interactome emerged as a powerful descriptor in the large-scale phenotypic studies of the post-genomic era . A major concern in such analysis is the integration of interactomic information with other phenotypic descriptors such as expression profile , co-localization , developmental p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Supporting", "Information" ]	[ "yeast", "and", "fungi", "computational", "biology", "biophysics", "genetics", "and", "genomics", "saccharomyces" ]	2007	Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network
Human T-Cell Lymphotropic Virus Type 1 ( HTLV-1 ) is the etiological agent of adult T-cell leukemia ( ATL ) and HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . It has been estimated that 10–20 million people are infected worldwide , but no successful treatment is available . Recently , the epide...	Human T-cell lymphotropic virus type 1 ( HTLV-1 ) is the causative agent of Adult T-Cell Leukemia/Lymphoma ( ATL ) , the Tropical Spastic Paraparesis/HTLV-1-associated Myelopathy ( TSP/HAM ) and other inflammatory diseases , including dermatitis , uveitis , and myositis . It is estimated that 2–8% of the infected perso...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/sexually", "transmitted", "diseases", "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/viral", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "disease...	2011	Genetic Characterization of Human T-Cell Lymphotropic Virus Type 1 in Mozambique: Transcontinental Lineages Drive the HTLV-1 Endemic
The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented . This broad range of functions is achieved through specific structures that have been ( presumably ) optimized through evolution . State-of-the-art methods , such as McCaskill's ...	Evolution is a central concept in biology . This phenomenon can be observed at all levels of the organization of life—from single molecules to multicellular organisms . Here , we focus our attention on the implication of evolution at the level of nucleic acid sequences . In this context , RNA sequences presumably have ...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "computational", "biology", "biophysics/rna", "structure" ]	2008	Efficient Algorithms for Probing the RNA Mutation Landscape
Containment of Mycobacterium tuberculosis ( Mtb ) infection requires T cell recognition of infected macrophages . Mtb has evolved to tolerate , evade , and subvert host immunity . Despite a vigorous and sustained CD8+ T cell response during Mtb infection , CD8+ T cells make limited contribution to protection . Here , w...	Immunodominant antigens elicit a large majority of T cells during an infection , and it is presumed that these T cells go on to recognize infected cells . Immunodominant antigens produced by Mycobacterium tuberculosis ( Mtb ) have been incorporated into vaccines , but whether T cells specific for these antigens recogni...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "antigen-presenting", "cells", "immunology", "microbiology", "developmental", "biology", "clinical", "medicine", "cytotoxic", "t", "cells", "microbial", "growth", "and", "development", "bacter...	2018	Mycobacterium tuberculosis-specific CD4+ and CD8+ T cells differ in their capacity to recognize infected macrophages
Crimean-Congo hemorrhagic fever virus ( CCHFV ) causes severe acute human disease with lethal outcome . The knowledge about the immune response for this human health threat is highly limited . In this study , we have screened the glycoprotein of CCHFV for novel linear B-cell epitopic regions using a microarray approach...	Crimean-Congo hemorrhagic fever ( CCHF ) is a widespread disease caused by a tick-borne virus belonging to the genus Orthonairovirus of the Nairoviridae family . The virus is responsible for outbreaks of severe viral hemorrhagic fever with a case fatality rate of approximately 30% . The CCHF virus is transmitted to peo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "turkey", "(country)", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "crimean-congo", "hemorrhagic", "fever", "immunology", "tropical", "diseases", "geographical", "locations",...	2018	Epitope-mapping of the glycoprotein from Crimean-Congo hemorrhagic fever virus using a microarray approach
Sequence-specific transcription factors ( TFs ) are critical for specifying patterns and levels of gene expression , but target DNA elements are not sufficient to specify TF binding in vivo . In eukaryotes , the binding of a TF is in competition with a constellation of other proteins , including histones , which packag...	Many Transcription Factors ( TFs ) have been shown to bind DNA in a sequence-specific manner . However , only a sub-set of possible binding sites are occupied in vivo , and it remains unclear how TFs discriminate between sequences of equal predicted binding affinity . We set out to determine how a specific TF , Heat Sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/chromatin", "structure", "molecular", "biology/transcription", "initiation", "and", "activation" ]	2010	Chromatin Landscape Dictates HSF Binding to Target DNA Elements
Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending , wrapping or bridging DNA . The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative bacteria is a DNA bridging protein and can structure DNA by binding to two separate DNA duplexes ...	The Histone-like Nucleoid Structuring protein ( H-NS ) occurs in enterobacteria , such as Salmonella typhimurium and Escherichia coli , and structures DNA by forming filaments along DNA duplexes . Several nucleotide sequences have been identified to which H-NS binds with high affinity . Yet , obtaining highly detailed ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "chemical", "bonding", "molecular", "dynamics", "dna-binding", "proteins", "sequence", "motif", "analysis", "dna", "dna", "structure", "molecular", "biology", "techniques", "hydrogen", "bonding", "research", "and", "analysis", "methods", "phy...	2019	Predicting the mechanism and rate of H-NS binding to AT-rich DNA
Non-malaria febrile illnesses such as bacterial bloodstream infections ( BSI ) are a leading cause of disease and mortality in the tropics . However , there are no reliable , simple diagnostic tests for identifying BSI or other severe non-malaria febrile illnesses . We hypothesized that different infectious agents resp...	In the tropics , malaria is commonly attributed to be the cause of most childhood fevers , while in fact this condition is more commonly caused by other pathogens that are clinically indistinguishable from malaria . These so-called non-malaria febrile illnesses include bacterial bloodstream infections , which are assoc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "bile", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "metabolomics", "protozoans", "metabolites", "malarial", "parasites", "hematology", "biochemistry", "diagnostic", ...	2016	Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach
Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets . Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment . In systems with many nearly matched targets , rapid and stringent formation of ...	Protein folding and the binding of sequence dependent proteins to DNA are examples of self-assembling systems in which the binding energy varies continuously throughout the interaction . Previous theoretical work has highlighted the importance of dividing the interaction into separate stages characterized by interactio...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "bacteriology", "protein", "interactions", "dna-binding", "proteins", "microbiology", "database", "searching", "bacterial", "genetics", "microbial", "genetics", "sequence", "similarity", "searching", "thermodynamics", "microbial", "genomics", "research", "and", "analysis", ...	2017	Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA
Alternative splicing is known to remodel protein-protein interaction networks ( “interactomes” ) , yet large-scale determination of isoform-specific interactions remains challenging . We present a domain-based method to predict the isoform interactome from the reference interactome . First , we construct the domain-res...	Protein-protein interaction networks have been extensively used in systems biology to study the role of proteins in cell function and disease . However , current network biology studies typically assume that one gene encodes one protein isoform , ignoring the effect of alternative splicing . Alternative splicing allows...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "protein", "interactions", "protein", "interaction", "networks", "cell", "processes", "alternative", "splicing", "mathematics", "forecasting", "statistics", "(mathematics)", "network", "analysis", "genome", "analysis", "research", "and", "analysis", "meth...	2017	Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing
The three major soil-transmitted helminths ( STH ) Ascaris lumbricoides , Trichuris trichiura and Necator americanus/Ancylostoma duodenale are among the most widespread parasites worldwide . Despite the global expansion of preventive anthelmintic treatment , standard operating procedures to monitor anthelmintic drug ef...	Soil-transmitted helminths ( roundworms , whipworms and hookworms ) infect millions of children in ( sub ) tropical countries , resulting in malnutrition , growth stunting , intellectual retardation and cognitive deficits . Currently , there is a need to closely monitor anthelmintic drug efficacy and to develop standar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/global", "health", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "public", "health", "and", "epidemiolog...	2011	Assessment of the Anthelmintic Efficacy of Albendazole in School Children in Seven Countries Where Soil-Transmitted Helminths Are Endemic
In India , dengue disease is emerging as the most important vector borne public health problem due to rapid and unplanned urbanization , high human density and week management of the disease . Clinical cases are grossly underreported and not much information is available on prevalence and incidence of the disease . A c...	Dengue disease , transmitted through the bite of DENV infected mosquitoes , is an increasing health problem in the Asian subcontinent , including India . Dengue ranges from mild undifferentiated fever to circulatory shock and potentially death . Clinical disease gives an incomplete picture of the magnitude of dengue , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "geographical", "locations", "microbiology", "india", "viruses", "vaccines", "age"...	2018	Stratified sero-prevalence revealed overall high disease burden of dengue but suboptimal immunity in younger age groups in Pune, India
Epigenetic mechanisms are emerging as one of the major factors of the dynamics of gene expression in the human malaria parasite , Plasmodium falciparum . To elucidate the role of chromatin remodeling in transcriptional regulation associated with the progression of the P . falciparum intraerythrocytic development cycle ...	Malaria is a devastating parasitic disease caused by the protozoan protist Plasmodium falciparum . The complex life cycle of P . falciparum comprises various morphological and functionally distinct forms and is completed in two different hosts . Various regulatory mechanisms are employed by these parasites to complete ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "systems", "biology", "functional", "genomics", "model", "organisms", "biology", "genomics", "microbiology", "genetics", "and", "genomics", "parasitology", "parasite", "physiology" ]	2013	Dynamic Epigenetic Regulation of Gene Expression during the Life Cycle of Malaria Parasite Plasmodium falciparum
The Fanconi anemia ( FA ) -BRCA pathway mediates repair of DNA interstrand crosslinks . The FA core complex , a multi-subunit ubiquitin ligase , participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins , FANCD2 and FANCI ( or the ID complex ) . However , the regulation of the FA cor...	Fanconi anemia is a genetic disease characterized by bone marrow failure , congenital malformations and cancer predisposition . Cells derived from Fanconi anemia patients have a dysfunctional FA-BRCA pathway and are deficient in the repair of a specific form of DNA damage , DNA interstrand-crosslinks , that are induced...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2
Msb2 is a sensor protein in the plasma membrane of fungi . In the human fungal pathogen C . albicans Msb2 signals via the Cek1 MAP kinase pathway to maintain cell wall integrity and allow filamentous growth . Msb2 doubly epitope-tagged in its large extracellular and small cytoplasmic domain was efficiently cleaved duri...	Microbial pathogens are attacked by antimicrobial peptides ( AMPs ) produced by the human host . AMPs kill pathogens and recruit immune cells to the site of infection . In defense , the human fungal pathogen Candida albicans continuously cleaves and secretes a glycoprotein fragment of the surface protein Msb2 , which p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "fungal", "diseases" ]	2012	Msb2 Shedding Protects Candida albicans against Antimicrobial Peptides
Gene expression data generated systematically in a given system over multiple time points provides a source of perturbation that can be leveraged to infer causal relationships among genes explaining network changes . Previously , we showed that food intake has a large impact on blood gene expression patterns and that t...	Peripheral blood is the most readily accessible human tissue for clinical studies and experimental research more generally . Large-scale molecular profiling technologies have enabled measurements of mRNA expression on the scale of whole genomes . Understanding the relationships between human blood gene expression profi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/population", "genetics", "computational", "biology/systems", "biology", "computational", "biology/transcriptional", "regulation" ]	2010	Characterizing Dynamic Changes in the Human Blood Transcriptional Network
The range of the Asian tiger mosquito Aedes albopictus is expanding globally , raising the threat of emerging and re-emerging arbovirus transmission risks including dengue and chikungunya . Its detection in Papua New Guinea's ( PNG ) southern Fly River coastal region in 1988 and 1992 placed it 150 km from mainland Aust...	The range of the Asian tiger mosquito Aedes albopictus is expanding globally , raising the threat of emerging and re-emerging arbovirus transmission risks , including chikungunya and dengue . Detection of Ae . albopictus in southern Papua New Guinea ( PNG ) in 1988 and 1992 placed it 150 km from mainland Australia . In...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "mosquitoes", "vector", "biology", "biology", "microbiology", "vectors", "and", "hosts" ]	2013	Tracing the Tiger: Population Genetics Provides Valuable Insights into the Aedes (Stegomyia) albopictus Invasion of the Australasian Region
Seminal fluid proteins have been shown to play important roles in male reproductive success , but the mechanisms for this regulation remain largely unknown . In Caenorhabditis elegans , sperm differentiate from immature spermatids into mature , motile spermatozoa during a process termed sperm activation . For C . elega...	Sexual reproduction requires the generation of highly specialized gametes , eggs and sperm , that must encounter one another and fuse together to form a zygote . Males provide not only sperm but also seminal fluid , which contains a variety of factors that promote male fertility through effects on sperm and on female p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "cell", "differentiation", "germ", "cells", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "molecular", "development", "signaling", "in", "cellular", "processes", "fertilization", "biology", "molecu...	2011	TRY-5 Is a Sperm-Activating Protease in Caenorhabditis elegans Seminal Fluid
The dengue virus ( DV ) is an important human pathogen from the Flavivirus genus , whose genome- and antigenome RNAs start with the strictly conserved sequence pppAG . The RNA-dependent RNA polymerase ( RdRp ) , a product of the NS5 gene , initiates RNA synthesis de novo , i . e . , without the use of a pre-existing pr...	The 5′- and 3′-ends of RNA virus genomes have evolved towards efficient replication , translation , and escape from defense mechanisms of the host cell . Little is known about how RNA viruses conserve or restore the correct ends of their genomes . The Flavivirus genus of positive-strand RNA viruses contains important h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "viral", "enzymes", "biology", "microbiology" ]	2012	Molecular Basis for Nucleotide Conservation at the Ends of the Dengue Virus Genome
The ATP binding cassette ( ABC ) proteins are a family of membrane transporters and regulatory proteins responsible for diverse and critical cellular process in all organisms . To date , there has been no attempt to investigate this class of proteins in the infectious parasite Trichomonas vaginalis . We have utilized a...	The parasite Trichomonas vaginalis infects in excess of 100 million people per year , and is a contributory factor to enhanced transmission rates of HIV , the causative virus in AIDS . As such , T . vaginalis infection is an important public health concern . Understanding the biology of the organism is important to det...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "parasitic", "diseases", "biological", "transport", "sequence", "analysis", "infectious", "diseases", "proteins", "membranes", "and", "sorting", "biology", "biochemistry", "cell", "biology", "transmembrane", "transport", "proteins", "computational", "biology", ...	2012	The ATP-Binding Cassette Proteins of the Deep-Branching Protozoan Parasite Trichomonas vaginalis
The emerging disease Buruli ulcer is treated with streptomycin and rifampicin and surgery if necessary . Frequently other antibiotics are used during treatment . Information on prescribing behavior of antibiotics for suspected secondary infections and for prophylactic use was collected retrospectively . Of 185 patients...	Buruli ulcer ( BU ) is a neglected , emerging disease caused by Mycobacterium ulcerans . BU usually starts as a nodule , papule , plaque , or oedema . When left alone , the lesion breaks open and a typical painless ulcer with undermined edges appears which can progress to a large necrotic lesion . BU is treated with an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "buruli", "ulcer", "socioeconomic", "aspects", "of", "health", "public", "health", "and", "epidemiology", "drugs", "and", "devices", "global", "health", "drug", "policy", "neglected", "tropical", "diseases", "public", "health" ]	2013	Towards Rational Use of Antibiotics for Suspected Secondary Infections in Buruli Ulcer Patients
Flow cytometry is the prototypical assay for multi-parameter single cell analysis , and is essential in vaccine and biomarker research for the enumeration of antigen-specific lymphocytes that are often found in extremely low frequencies ( 0 . 1% or less ) . Standard analysis of flow cytometry data relies on visual iden...	The use of flow cytometry to count antigen-specific T cells is essential for vaccine development , monitoring of immune-based therapies and immune biomarker discovery . Analysis of such data is challenging because antigen-specific cells are often present in frequencies of less than 1 in 1 , 000 peripheral blood mononuc...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "adaptive", "immunity", "immune", "cells", "mathematics", "clinical", "immunology", "immunity", "immunologic", "subspecialties", "statistics", "t", "cells", "immunoassays", "immunology", "biology", "biostatistics", "immunologic", "techniques", "tumor", "immunolo...	2013	Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
The cyclic AMP-dependent protein kinase A signaling pathway plays a major role in regulating plant infection by the rice blast fungus Magnaporthe oryzae . Here , we report the identification of two novel genes , MoSOM1 and MoCDTF1 , which were discovered in an insertional mutagenesis screen for non-pathogenic mutants o...	Magnaporthe oryzae , the causal agent of rice blast disease , is an important model fungal pathogen for understanding the molecular basis of plant-fungus interactions . In M . oryzae , the conserved cAMP/PKA signaling pathway has been demonstrated to be crucial for regulating infection-related morphogenesis and pathoge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "microbiology", "host-pathogen", "interaction", "gene", "function", "fungi", "microbial", "growth", "and", "development", "fungal", "reproduction", "mycology", "gene", "expression", "microbial", "pathogens", "biology", "pathogenesis", "molecular", "...	2011	Two Novel Transcriptional Regulators Are Essential for Infection-related Morphogenesis and Pathogenicity of the Rice Blast Fungus Magnaporthe oryzae
Understanding how binding events modulate functional motions of multidomain proteins is a major issue in chemical biology . We address several aspects of this problem by analyzing the differential dynamics of αvβ3 integrin bound to wild type ( wtFN10 , agonist ) or high affinity ( hFN10 , antagonist ) mutants of fibron...	Interactions between proteins are at the basis of all biological processes in the cell . In this context , the study of conformational responses of protein receptors to the binding of endogenous ligands may be a source of inspiration for the design of small molecule modulators that permit to control such biological pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "comparative", "sequence", "analysis", "chemical", "characterization", "crystal", "structure", "electricity", "condensed", "matter", "physics", "integrins", "electrostatics", "sequence", "motif", "analysis", "crystallography", "cellular", "structures", "and", "organelles", ...	2017	High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design
Leptospirosis is a worldwide prevalent zoonosis and chronic kidney disease ( CKD ) is a leading global disease burden . Because of pathophysiological changes in the kidney , it has been suggested that these conditions may be associated . However , the extent of this interaction has not been synthetized . We aimed to sy...	Leptospirosis is an infection that can affect the kidneys acutely , though it seems that even after the acute infection there could be risk of a long-term impaired kidney function . The evidence on this matter is sparse and limited , thus the need to comprehensively seek , synthetize and appraise the available scientif...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chronic", "kidney", "disease", "tropical", "diseases", "biomarkers", "bacterial", "diseases", "crops", "neglected", "tropical", "diseases", "medical", "risk", "factors", "kidneys", "plants", "veterinary", "science", "research", ...	2019	Leptospirosis as a risk factor for chronic kidney disease: A systematic review of observational studies
Many persistent viral infections are characterized by a hypofunctional T cell response and the upregulation of negative immune regulators . These events occur days after the initiation of infection . However , the very early host-virus interactions that determine the establishment of viral persistence remain poorly unc...	Lymphocytic Choriomenengitis Virus ( LCMV ) is an important model for the investigation of the pathogenesis of persistent viral infections . As with humans infected with hepatitis C and Human Immunodeficiency Virus-1 , adult mice persistently infected with immunosuppressive strains of LCMV express high levels of negati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "evasion", "viral", "immune", "evasion", "viral", "persistence", "and", "latency", "viral", "transmission", "and", "infection", "virology", "biology", "and", "life", "sciences", "immunology", "immune", "suppression", "microbiology", "immune", "response" ]	2015	Early Virus-Host Interactions Dictate the Course of a Persistent Infection
Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication . Several of the co-opted host factors bind to the viral RNA , which plays multiple roles , including mRNA function , as an assembly platform for the viral replicase ( VRC ) , template for RNA syn...	Genome-wide screens for host factors affecting tombusvirus replication in yeast indicated that subverted cellular RNA helicases likely play major roles in virus replication . Tombusviruses do not code for their own helicases and they might recruit host RNA helicases to aid their replication in infected cells . Accordin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "microbiology", "agriculture" ]	2014	The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication
Trypanosoma brucei brucei infects livestock , with severe effects in horses and dogs . Mouse strains differ greatly in susceptibility to this parasite . However , no genes controlling these differences were mapped . We studied the genetic control of survival after T . b . brucei infection using recombinant congenic ( R...	Trypanosoma brucei are extracellular protozoa transmitted to mammalian host by the tsetse fly . They developed several mechanisms that subvert host's immune defenses . Therefore analysis of genes affecting host's resistance to infection can reveal critical aspects of host-parasite interactions . Trypanosoma brucei bruc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "animal", "genetics", "genetics", "biology", "microbiology", "host-pathogen", "interaction", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2011	Genetic Control of Resistance to Trypanosoma brucei brucei Infection in Mice
Ethiopia is assumed to have the highest burden of podoconiosis globally , but the geographical distribution and environmental limits and correlates are yet to be fully investigated . In this paper we use data from a nationwide survey to address these issues . Our analyses are based on data arising from the integrated m...	Podoconiosis is a neglected tropical disease that results in swelling of the lower legs and feet . It is common among barefoot individuals with prolonged contact with irritant soils of volcanic origin . The disease causes significant social and economic burden . The disease can be prevented by consistent shoe wearing a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Mapping and Modelling the Geographical Distribution and Environmental Limits of Podoconiosis in Ethiopia
Whole Genome Shotgun ( WGS ) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems , both from the taxonomic and functional point of view . Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possib...	Microbial communities are highly complex ecosystems , harboring a high taxonomic diversity , rapidly varying in time . Focusing on the functional traits of microorganisms instead of species offers an interesting and complementary insight since quite often , owing to environmental selection pressure , traits are less va...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "ecology", "and", "environmental", "sciences", "metagenomics", "functional", "genomics", "metabolites", "microbial", "ecosystems", "ecology", "ecosystems", "metabolic", "processes", "genetics", "biology", "and", "life", "sciences", "genomics", "ecosystem", ...	2016	Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota
Post-mitotic cell separation is one of the most prominent events in the life cycle of eukaryotic cells , but the molecular underpinning of this fundamental biological process is far from being concluded and fully characterized . We use budding yeast Saccharomyces cerevisiae as a model and demonstrate AMN1 as a major ge...	Separation of mother and daughter cells after mitosis in eukaryotes enacts various functional and/or developmental needs and has significant medical and industrial implications . How this cellular behaviour is regulated is far from being concluded . We report here a novel Amn1 mediated post-mitotic cell separation in a...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "cell", "cycle", "and", "cell", "division", "cell", "processes", "mitosis", "fungi", "model", "organisms", "experimental", "organism", "systems", "protein", "structure", "rna", "alignment", "saccharomyces", "research", "and", "analysis", "methods", "sequence", "analys...	2018	Amn1 governs post-mitotic cell separation in Saccharomyces cerevisiae
In order to proceed through their life cycle , Leishmania parasites switch between sandflies and mammals . The flagellated promastigote cells transmitted by the insect vector are phagocytized by macrophages within the mammalian host and convert into the amastigote stage , which possesses a rudimentary flagellum only . ...	Leishmania parasites are responsible for the disease leishmaniasis . They are spread through sandflies . The primary hosts are mammals , including humans . They occur in two different morphological forms . The flagellated promastigotes live in the gut of the sandfly vector . After transmission to the mammalian host the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "cell", "biology/cell", "growth", "and", "division", "cell", "biology/microbial", "growth", "and", "development", "biochemistry/macromolecular", "assemblies", "and", "machines", "infectious", "diseases/protozoal", "i...	2010	Characterization of a Subunit of the Outer Dynein Arm Docking Complex Necessary for Correct Flagellar Assembly in Leishmania donovani
Thermodynamic measurements of ion binding to the Streptomyces lividans K+ channel were carried out using isothermal titration calorimetry , whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography . Here we use these assays to show that the ion radius ...	The exquisite selectivity of potassium ion ( K+ ) channels in cellular membranes allows them to pass K+ ions while restricting the closely related sodium ( Na+ ) ions , and thereby maintain the electrical potential across cellular membranes . In this study , we address the fundamental question: how does the K+ channel ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "in", "vitro", "biophysics", "neuroscience" ]	2007	Structural and Thermodynamic Properties of Selective Ion Binding in a K+ Channel
Axonal transport of synaptic vesicles ( SVs ) is a KIF1A/UNC-104 mediated process critical for synapse development and maintenance yet little is known of how SV transport is regulated . Using C . elegans as an in vivo model , we identified SAM-4 as a novel conserved vesicular component regulating SV transport . Process...	Most cellular components of neurons are synthesized in the cell body and must be transported great distances to form synapses at the ends of axons and dendrites . Neurons use a specialized axonal transport system consisting of microtubule cytoskeletal tracks and numerous molecular motors to shuttle specific cargo to sp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "specimen", "preparation", "and", "treatment", "neurobiology", "of", "disease", "and", "regeneration", "mechanical", "treatment", "of", "specimens", "medicine", "and", "health", "sciences", "specimen", "disruption", "anatomy", "neural", "homeostasis", "electroporation", ...	2014	The Vesicle Protein SAM-4 Regulates the Processivity of Synaptic Vesicle Transport
The fight against cancer is hindered by its highly heterogeneous nature . Genome-wide sequencing studies have shown that individual malignancies contain many mutations that range from those commonly found in tumor genomes to rare somatic variants present only in a small fraction of lesions . Such rare somatic variants ...	The analysis of somatic variants in sequenced tumor samples is important for understanding the molecular disruptions that underlie the vast differences in individual cancer phenotypes or response to treatment . In order to understand which somatic mutations are functionally important for the initiation or progression o...	[ "Abstract", "Introduction", "Materials", "&", "methods", "Results", "Discussion" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "basic", "cancer", "research", "oncology", "genomic", "databases", "mutation", "genome", "analysis", "mutation", "databases", "research", "and", "analysis", "methods", "sequence", "analysis", "bioinformatics...	2017	Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples
The ability of HIV to establish a long-lived latent infection within resting CD4+ T cells leads to persistence and episodic resupply of the virus in patients treated with antiretroviral therapy ( ART ) , thereby preventing eradication of the disease . Protein kinase C ( PKC ) modulators such as bryostatin 1 can activat...	HIV can persist for many years in a latent ( non-expressing ) state in individuals treated with antiretroviral therapy , and these latently-infected cells represent a major barrier to curing HIV infection . One potential approach to eliminating the reservoir cells is to induce them to express viral proteins while maint...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "spleen", "pathogens", "antiviral", "therapy", "immunology", "microbiology", "retroviruses", "viruses...	2017	In vivo activation of latent HIV with a synthetic bryostatin analog effects both latent cell "kick" and "kill" in strategy for virus eradication
Mouse Ikbkap gene encodes IKAP—one of the core subunits of Elongator—and is thought to be involved in transcription . However , the biological function of IKAP , particularly within the context of an animal model , remains poorly characterized . We used a loss-of-function approach in mice to demonstrate that Ikbkap is ...	The process of meiosis is responsible for gamete formation and ensures that offspring will inherit a complete set of chromosomes from each parent . Errors arising during this process generally result in spontaneous abortions , birth defects , or infertility . Many genes that are essential in regulating meiosis have als...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "chromosome", "biology", "genetics", "epigenetics", "biology", "genomics" ]	2013	Ikbkap/Elp1 Deficiency Causes Male Infertility by Disrupting Meiotic Progression
Protein-DNA interactions play important roles in regulations of many vital cellular processes , including transcription , translation , DNA replication and recombination . Sequence variants occurring in these DNA binding proteins that alter protein-DNA interactions may cause significant perturbations or complete abolis...	Developing methods for accurate prediction of effects of amino acid substitutions on protein-DNA interactions is important for a wide range of biomedical applications such as understanding disease-causing mechanism of missense mutations and guiding protein engineering . Very few methods have been developed for predicti...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "deletion", "mutation", "protein", "interactions", "crystal", "structure", "condensed", "matter", "physics", "mutation", "substitution", "mutation", "protein", "structure", "mutation", "databases", "crystallography", "research", "and", "analysis", "methods", "sequence", "...	2018	PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions
An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis . Here , the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification . We re-sequenced the 14 , 000 annotated exon...	Here we show that tiny DNA lesions can be found in huge amounts of DNA sequence data , similar to finding a needle in a haystack . These lesions identify many new candidates for disease genes associated with birth defects , infertility , and growth . Further , our data suggest that we know very little about what mammal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/molecular", "evolution", "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "genetics",...	2009	Discovery of Candidate Disease Genes in ENU–Induced Mouse Mutants by Large-Scale Sequencing, Including a Splice-Site Mutation in Nucleoredoxin
HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution . Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution . HIV’s most rapidly evolving protein is its envelope ( Env ) . Here we use deep mutational scanning to experim...	HIV is infamous for the rapid evolution of its surface protein , Env . The ability to measure the effects of all mutations to Env under defined selection pressures in the lab would open the door to better understanding the factors that shape this evolution . However , this is a daunting experimental task since there ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "microbial", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "pathogens", "biological", "cultures", "microbiology", "retroviruses", "viruses", "immunodeficiency", "virus...	2016	Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture
The presence of aspartic protease inhibitor in filarial parasite Brugia malayi ( Bm-Aspin ) makes it interesting to study because of the fact that the filarial parasite never encounters the host digestive system . Here , the aspartic protease inhibition kinetics of Bm-Aspin and its NMR structural characteristics have b...	Filariasis is a parasitic infectious tropical disease caused by thread like filarial nematodes . These worms occupy the lymph nodes and in chronic cases they lead to the disease “elephantiasis . ” Over 120 million people have already been affected by it , and 40 million are seriously disfigured by this disease . These ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "protein", "interactions", "proteins", "protein", "structure", "biology", "chemical", "biology", "drug", "discovery" ]	2014	A Structural Biology Approach to Understand Human Lymphatic Filarial Infection

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