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X chromosome inactivation in eutherian mammals has been thought to be tightly controlled , as expected from a mechanism that compensates for the different dosage of X-borne genes in XX females and XY males . However , many X genes escape inactivation in humans , inactivation of the X in marsupials is partial , and the ...	Dosage compensation is a mechanism that restores the expression of X chromosome genes back to their original level when Y homologues lose function . In placental and marsupial mammals this is achieved by upregulating the single X in males . The carry-through of overexpression to females would result in functional tetra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "biology", "genomics" ]	2013	Independent Evolution of Transcriptional Inactivation on Sex Chromosomes in Birds and Mammals
Caenorhabditis elegans vulval development provides an important paradigm for studying the process of cell fate determination and pattern formation during animal development . Although many genes controlling vulval cell fate specification have been identified , how they orchestrate themselves to generate a robust and in...	Systems biology aims to gain a system-level understanding of living systems . To achieve such an understanding , we need to establish the methodologies and techniques to understand biological systems in their full complexity . One such attempt is to use methods designed for the construction and analysis of complex comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "caenorhabditis", "cell", "biology", "developmental", "biology", "computational", "biology" ]	2007	Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development
All eukaryotes have the ability to detect and respond to environmental and hormonal signals . In many cases these signals evoke cellular changes that are incompatible and must therefore be orchestrated by the responding cell . In the yeast Saccharomyces cerevisiae , hyperosmotic stress and mating pheromones initiate si...	All cells can detect and respond to signals in their environment . The ability to interpret these signals with accuracy is needed for proper growth and differentiation . Moreover , cells must prioritize responses when confronted with competing signals . However the molecular mechanisms that govern signal prioritization...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "mechanisms", "of", "signal", "transduction", "microbiology", "feeback", "regulation", "cell", "differentiation", "developmental", "biology", "model", "organisms", "crosstalk", "mapk", "signaling", "cascades", "stress", "signaling", "cas...	2012	Checkpoints in a Yeast Differentiation Pathway Coordinate Signaling during Hyperosmotic Stress
Peroxiredoxins are a family of antioxidant enzymes critically involved in cellular defense and signaling . Particularly , yeast peroxiredoxin Tsa1p is thought to play a role in the maintenance of genome integrity , but the underlying mechanism is not understood . In this study , we took a genetic approach to investigat...	Peroxiredoxins are a family of antioxidant enzymes highly conserved from yeast to human . Loss of peroxiredoxin in mice can lead to severe anemia and malignant tumors , but the underlying cause is not understood . One way to derive new knowledge of peroxiredoxins is through genetic analysis in yeast . We have shown tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/gene", "function" ]	2009	Loss of Yeast Peroxiredoxin Tsa1p Induces Genome Instability through Activation of the DNA Damage Checkpoint and Elevation of dNTP Levels
Completion of early stages of retrovirus infection depends on the cell cycle . While gammaretroviruses require mitosis for proviral integration , lentiviruses are able to replicate in post-mitotic non-dividing cells . Resting cells such as naive resting T lymphocytes from peripheral blood cannot be productively infecte...	Naive quiescent CD4-positive T cells or monocytes that are in the G0 stage of the cell cycle cannot be productively infected by retroviruses in vitro , but the molecular basis of this restriction remains poorly understood . In this report , we demonstrate that incoming foamy retroviruses remain around the centrosome as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "cell", "biology", "microbiology", "virology" ]	2007	Centrosomal Latency of Incoming Foamy Viruses in Resting Cells
The pathogenesis of bacteraemia after challenge with one million pneumococci of three isogenic variants was investigated . Sequential analyses of blood samples indicated that most episodes of bacteraemia were monoclonal events providing compelling evidence for a single bacterial cell bottleneck at the origin of invasiv...	Decades of research on bacterial sepsis have been devoted to analysing the steps that lead from a local event , either carriage or a localised infection , to systemic disease . Our work analyses in depth the events determining systemic infection by one of the main human pathogens , Streptococcus pneumoniae . Consistent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "microbial", "metabolism", "infectious", "diseases", "microbial", "mutation", "streptococci", "microbial", "evolution", "microbial", "pathogens", "host-pathogen", "interaction", "biology", "microbiology", "infectious", "disease", "modeling...	2014	The Role of Host and Microbial Factors in the Pathogenesis of Pneumococcal Bacteraemia Arising from a Single Bacterial Cell Bottleneck
Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat ( NLR ) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation , triggering a rapid , localized cell death called a hypersensitive response ( HR ) . Three domains are recog...	The plant hypersensitive defense response ( HR ) is a rapid , localized cell death , usually occurring upon the recognition of specific pathogen-encoded molecules and consequent activation of nucleotide binding-leucine rich repeat ( NLR ) proteins . Rp1-D21 , a naturally-occurring mutant caused by the recombination of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Molecular and Functional Analyses of a Maize Autoactive NB-LRR Protein Identify Precise Structural Requirements for Activity
To help learn how phytopathogens feed from their hosts , genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated . This identified 453 genes from 19 families . Comparisons with a necrotrophic oomycete , Pythium ultimum var . ultimum , and a hemibiotrophic fun...	Little is known of how plant pathogens adapt to different growth conditions and host tissues . To understand the interaction between the filamentous eukaryotic microbe Phytophthora infestans and its potato and tomato hosts , we mined the genome for genes encoding proteins involved in nutrient uptake and measured their ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "anatomy", "oomycetes", "medicine", "and", "health", "sciences", "chemical", "compounds", "microbiology", "nitrates", "fungi", "plant", "science", "nutrition", "crops", "potato", "plants", "vegetables", "crop", "science", "gene", "expression", "chemistry", "t...	2016	Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis
Because of the development of resistance in trypanosomes to trypanocidal drugs , the livelihood of millions of livestock keepers in sub-Saharan Africa is threatened now more than ever . The existing compounds have become virtually useless and pharmaceutical companies are not keen on investing in the development of new ...	African Animal Trypanosomiasis causes the death of 3 million head of cattle each year . The annual economic losses as a result of the disease are estimated to be 4 . 5 billion US dollars . Trypanosomes are transmitted by tsetse flies and can infect a wide range of hosts from wildlife to domestic animals . This study is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2010	Chemosensitization of Trypanosoma congolense Strains Resistant to Isometamidium Chloride by Tetracyclines and Enrofloxacin
Transmembrane channel proteins play pivotal roles in maintaining the homeostasis and responsiveness of cells and the cross-membrane electrochemical gradient by mediating the transport of ions and molecules through biological membranes . Therefore , computational methods which , given a set of 3D coordinates , can autom...	Transmembrane channel proteins are responsible for the transport of ions and molecules through biological membranes and are pivotal for the physiology of the cell . In fact , their incorrect functioning is involved or related to several diseases ( diabetes , myotonia , Parkinson's disease , etc . ) . Moreover , their s...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "computational", "biology/macromolecular", "structure", "analysis" ]	2009	PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure
Calcineurin governs stress survival , sexual differentiation , and virulence of the human fungal pathogen Cryptococcus neoformans . Calcineurin is activated by increased Ca2+ levels caused by stress , and transduces signals by dephosphorylating protein substrates . Herein , we identified and characterized calcineurin s...	Calcineurin is a Ca2+/calmodulin-dependent protein phosphatase essential for stress survival , sexual development , and virulence of the human fungal pathogen Cryptococcus neoformans and other major pathogenic fungi of global human health relevance . However , no calcineurin substrates are known in pathogenic fungi . E...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "classical", "mechanics", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "microbiology", "sexual", "reproduction", "mechanical", "stress", "enzym...	2016	Calcineurin Targets Involved in Stress Survival and Fungal Virulence
Reward-modulated spike-timing-dependent plasticity ( STDP ) has recently emerged as a candidate for a learning rule that could explain how behaviorally relevant adaptive changes in complex networks of spiking neurons could be achieved in a self-organizing manner through local synaptic plasticity . However , the capabil...	A major open problem in computational neuroscience is to explain how learning , i . e . , behaviorally relevant modifications in the central nervous system , can be explained on the basis of experimental data on synaptic plasticity . Spike-timing-dependent plasticity ( STDP ) is a rule for changes in the strength of an...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "neuroscience/animal", "cognition", "neuroscience/theoretical", "neuroscience" ]	2008	A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback
Bacterial microcompartments ( BMCs ) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism . All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci , or operons . To enable the ident...	Some enzymatic transformations have undesirable side reactions , produce toxic or volatile intermediates , or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space , as in the membrane-bound organelles of eukaryotes . Recently , it was discovered tha...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "bacterial", "genomics", "genetics", "biology", "and", "life", "sciences", "genomics", "computational", "biology", "microbial", "genomics" ]	2014	A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
How pathogenic bacteria infect and kill their host is currently widely investigated . In comparison , the fate of pathogens after the death of their host receives less attention . We studied Bacillus thuringiensis ( Bt ) infection of an insect host , and show that NprR , a quorum sensor , is active after death of the i...	Bacillus thuringiensis ( Bt ) is a well known entomopathogenic bacterium successfully used as a biopesticide for fifty years . The insecticidal properties of Bt are mainly due to specific toxins forming a crystal inclusion associated with the spore . After ingestion by susceptible insect larvae , toxins could induce fa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bacteriology", "small", "molecules", "enzymes", "gene", "regulation", "microbiology", "host-pathogen", "interaction", "molecular", "genetics", "microbial", "growth", "and", "development", "bacterial", "pathogens", "applied", "microbiology", "microbial", "p...	2012	Necrotrophism Is a Quorum-Sensing-Regulated Lifestyle in Bacillus thuringiensis
Previous studies suggest that protective immunity against Schistosoma haematobium is primarily stimulated by antigens from dying worms . Praziquantel treatment kills adult worms , boosting antigen exposure and protective antibody levels . Current schistosomiasis control efforts use repeated mass drug administration ( M...	Urogenital schistosomiasis , caused by schistosome blood flukes , infects more than 100 million people in sub-Saharan Africa . Current control efforts involve regularly treating all school-aged children with the drug praziquantel , which kills schistosome worms . Earlier work by our group suggests that protective immun...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "applied", "mathematics", "immunity", "to", "infections", "immunology", "tropical", "diseases", "parasitic", "diseases", "mathematics", "population", "modeling", "negl...	2014	Predicted Impact of Mass Drug Administration on the Development of Protective Immunity against Schistosoma haematobium
The conformational dynamics of proteins is rarely used in methodologies used to predict the impact of genetic mutations due to the paucity of three-dimensional protein structures as compared to the vast number of available sequences . Until now a three-dimensional ( 3D ) structure has been required to predict the confo...	Proteins are dynamic machines that undergo atomic fluctuations , side chain rotations , and collective domain movements that are required for biological function . There is , therefore , a need for quantitative metrics that capture the dynamic fluctuations per position to understand the critical role of protein dynamic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "crystal", "structure", "split-decomposition", "method", "condensed", "matter", "physics", "multiple", "alignment", "calculation", "protein", "structure", "prediction", "protein", "structure", "crystallography", "structural", "genomics", "research", "and", "analysis", "meth...	2018	Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs
Microbes have an astonishing capacity to transform their environments . Yet , the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species . Such enhanced metabolic capaci...	Microbes constantly change their environment , consuming some compounds from their surroundings and secreting others . This microbial activity plays a crucial role in many important environmental cycles , ultimately making all life possible . These processes , however , are often not accomplished by a single species bu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "computer", "and", "information", "sciences", "ecosystem", "modeling", "ecology", "network", "analysis", "biology", "and", "life", "sciences", "metabolic", "networks", "computational", "biology", "microbial", "ecology" ]	2014	Emergent Biosynthetic Capacity in Simple Microbial Communities
Neurons are particularly vulnerable to perturbations in endo-lysosomal transport , as several neurological disorders are caused by a primary deficit in this pathway . In this report , we used positional cloning to show that the spontaneously occurring neurological mutation teetering ( tn ) is a single nucleotide substi...	Endocytic trafficking involves the internalization , endosomal sorting and lysosomal degradation of cell surface cargo . Many factors involved in endosomal sorting in mammalian cells have been identified , and mutations in these components are associated with a variety of neurological disorders . While the function of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Motor and Sensory Deficits in the teetering Mice Result from Mutation of the ESCRT Component HGS
During thrombosis , thrombin generates fibrin , however fibrin reversibly binds thrombin with low affinity E-domain sites ( KD = 2 . 8 μM ) and high affinity γ’-fibrin sites ( KD = 0 . 1 μM ) . For blood clotting on collagen/tissue factor ( 1 TF-molecule/μm2 ) at 200 s-1 wall shear rate , high μM-levels of intraclot th...	During blood clotting events , a complex series of reaction are involved . Simulation gives insights to the concentration of different enzymes which are at too low of concentration to be detected . However , the models are often large and difficult to solve for clotting under flow conditions . With a thin film approxim...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "fibrinogen", "fibrin", "cardiovascular", "medicine", "thrombosis", "elution", "platelets", "glycoproteins", "research", "and", "analysis", "methods", "separation", "processes", "coagulation", ...	2019	Reduced model to predict thrombin and fibrin during thrombosis on collagen/tissue factor under venous flow: Roles of γ’-fibrin and factor XIa
Aspergillus fumigatus is an environmental fungus that causes invasive aspergillosis ( IA ) in immunocompromised patients . Although -CC-chemokine receptor-2 ( CCR2 ) and Ly6C-expressing inflammatory monocytes ( CCR2+Mo ) and their derivatives initiate adaptive pulmonary immune responses , their role in coordinating inn...	Despite the significant impact of fungal infections to human health our understanding of immunity to these pathogens remains incomplete . Human mycoses are associated with high morbidity and mortality , even with modern antifungal therapies . Aspergillus fumigatus is the most common etiologic agent of invasive aspergil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "aspergillosis", "immune", "cells", "monocytes", "immunity", "innate", "immunity", "immune", "defense", "immunology", "immunity", "to", "infections", "biology", "fungal", "diseases" ]	2014	Inflammatory Monocytes Orchestrate Innate Antifungal Immunity in the Lung
There is unequivocal evidence in the literature that epidemics adversely affect the livelihoods of individuals , households and communities . However , evidence in the literature is dominated by the socioeconomic impacts of HIV/AIDS and malaria , while evidence on the impact of the Ebola virus disease ( EVD ) on househ...	Epidemics such as HIV/AIDS , malaria and Ebola virus disease ( EVD ) may adversely impact the livelihoods of the society affected by the epidemics . Nonetheless , the mechanism behind the effects of the epidemics may differ depending on different factors , such as the transmission mechanisms , latency , and mortality r...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "social", "epidemiology", "farms", "crops", "africa", "agricultural", "production", "crop", "science", "epidemiology",...	2018	The impact of the Ebola virus disease (EVD) epidemic on agricultural production and livelihoods in Liberia
We use stochastic neural field theory to analyze the stimulus-dependent tuning of neural variability in ring attractor networks . We apply perturbation methods to show how the neural field equations can be reduced to a pair of stochastic nonlinear phase equations describing the stochastic wandering of spontaneously for...	A topic of considerable current interest concerns the neural mechanisms underlying the suppression of cortical variability following the onset of a stimulus . Since trial-by-trial variability and noise correlations are known to affect the information capacity of neurons , such suppression could improve the accuracy of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "perturbation", "theory", "neural", "networks", "neuroscience", "learning", "and", "memory", "cognitive", "neuroscience", "mathematics", "cognition", "network", "analysis", "algebra", "memory", "interneurons", "quantum", "mechanics", "neuronal", "tuning", "computer", "and...	2019	Stochastic neural field model of stimulus-dependent variability in cortical neurons
The malaria parasite Plasmodium falciparum exports several hundred proteins into the infected erythrocyte that are involved in cellular remodeling and severe virulence . The export mechanism involves the Plasmodium export element ( PEXEL ) , which is a cleavage site for the parasite protease , Plasmepsin V ( PMV ) . Th...	To survive within human red blood cells , malaria parasites must export a catalog of proteins that remodel the host cell and its surface . This enables parasites to acquire nutrients from outside the cell and to modify the cell surface in order to evade host defenses . Protein export involves proteolytic cleavage of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "enzymology", "microbiology", "plasmodium", "falciparum", "chemical", "biology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "ge...	2014	Inhibition of Plasmepsin V Activity Demonstrates Its Essential Role in Protein Export, PfEMP1 Display, and Survival of Malaria Parasites
Up to 1 . 45 billion people currently suffer from soil transmitted helminth infection , with the largest burden occurring in Africa and Asia . Safe and cost effective deworming treatment exists , but there is a debate about mass distribution of this treatment in high prevalence settings . While the World Health Organiz...	Mass deworming is recommended by the World Health Organization for health benefits to communities where soil-transmitted helminth infection is endemic . In addition to health benefits , several recent studies find long run educational or economic benefits for cohorts dewormed as children . In this paper , treatment and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "education", "sociology", "geographical", "locations", "social", "sciences", "numeracy", "uganda", "neuroscience", "parasitic", "diseases", "pediatrics", "age", "groups", "academic", "skills", "research", "design", "c...	2019	The long run impact of early childhood deworming on numeracy and literacy: Evidence from Uganda
Co-occurrence of malaria and filarial worm parasites has been reported , but little is known about the interaction between filarial worm and malaria parasites with the same Anopheles vector . Herein , we present data evaluating the interaction between Wuchereria bancrofti and Anopheles punctulatus in Papua New Guinea (...	The parasites that cause malaria and human lymphatic filariasis are both transmitted by mosquitoes , and often times in areas where these two diseases are co-endemic , mosquitoes in the genus Anopheles transmit both parasites . Currently , it is unknown how parasite transmission is effected when malaria and filarial wo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "microbiology/parasitology", "immunology/innate", "immunity" ]	2011	Filarial Worms Reduce Plasmodium Infectivity in Mosquitoes
Although the tprK gene of Treponema pallidum are thought to play a critical role in the pathogenesis of syphilis , the profile of variations in tprK during the development of human syphilis infection have remained unclear . Through next-generation sequencing , we compared the tprK gene of 14 secondary syphilis patients...	Antigenic variation of the TprK antigen has been acknowledged to explain the persistence of Treponema pallidum in the host , however , the profile of variations in tprK during the development of human syphilis infection has not been well characterized . Here , we performed next-generation sequencing to compare the vari...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "urology", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "antigenic", "variation", "treponematoses", "bacterial", ...	2019	Insights into the genetic variation profile of tprK in Treponema pallidum during the development of natural human syphilis infection
Histone lysine ( K ) residues , which are modified by methyl- and acetyl-transferases , diversely regulate RNA synthesis . Unlike the ubiquitously activating effect of histone K acetylation , the effects of histone K methylation vary with the number of methyl groups added and with the position of these groups in the hi...	Histone methylation regulates gene expression and can have drastic consequences for health if the process is defective . Histone lysine demethylases ( KDMs ) counteract the activity of methyl-transferases and remove methyl group ( s ) from histones . KDM3A is a H3K9me2/1 demethylase that performs diverse functions via ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "dna-binding", "proteins", "histones", "histone", "modification" ]	2014	Specific Phosphorylation of Histone Demethylase KDM3A Determines Target Gene Expression in Response to Heat Shock
Sox10 is a dynamically regulated transcription factor gene that is essential for the development of neural crest–derived and oligodendroglial populations . Developmental genes often require multiple regulatory sequences that integrate discrete and overlapping functions to coordinate their expression . To identify Sox10...	The neural crest is a population of embryonic migratory stem cells . They form atop the future spinal cord and migrate throughout developing embryos and form many different cells , including the epidermal pigment cells , bone cells in the head , and nerve cells of the peripheral nervous system . In this study , we stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology/molecular", "development", "genetics", "and", "genomics/genetics", "of", "disease", "neuroscience/neurodevelopment", "genetics", "and", "genomics/functional", "genomics" ]	2008	Identification of Neural Crest and Glial Enhancers at the Mouse Sox10 Locus through Transgenesis in Zebrafish
Integrins may undergo large conformational changes during activation , but the dynamic processes and pathways remain poorly understood . We used molecular dynamics to simulate forced unbending of a complete integrin αVβ3 ectodomain in both unliganded and liganded forms . Pulling the head of the integrin readily induced...	Proteins can regulate their functions via conformational changes . One example is integrins , which are transmembrane receptors mediating cell-cell and cell-matrix adhesions . Inactive integrins may assume a bent conformation with low affinities for ligands unable to support adhesions . Intracellular or extracellular s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "cell", "biology/cell", "adhesion", "biophysics/theory", "and", "simulation" ]	2011	Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3
Piriformospora indica is an endophytic fungus that colonizes roots of many plant species and promotes growth and resistance to certain plant pathogens . Despite its potential use in agriculture , little is known on the molecular basis of this beneficial plant-fungal interaction . In a genetic screen for plants , which ...	Like many root-colonizing microbes , the primitive Basidiomycete fungus Piriformospora indica colonizes the roots of many plant species and promotes their growth . The lack of host specificity suggests that the plant response to this endopyhte is based on general signalling processes . In a genetic screen for Arabidops...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "biology", "molecular", "cell", "biology" ]	2011	The OXI1 Kinase Pathway Mediates Piriformospora indica-Induced Growth Promotion in Arabidopsis
Scorpion venom induces systemic inflammation characterized by an increase in cytokine release and chemokine production . There have been few experimental studies assessing the effects of scorpion venom on adipose tissue function in vivo . To study the adipose tissue inflammation ( ATI ) induced by Androctonus australis...	Androctonus australis hector ( Aah ) is the scorpion most frequently causing serious human envenomation . In Algeria , Aah is responsible for approximately 50 , 000 cases of scorpion envenomation per year . The Aah sting causes multi-system failure that may be fatal; the manifestations include cardiopulmonary abnormali...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2012	TNF-α Involvement in Insulin Resistance Induced by Experimental Scorpion Envenomation
We present a new approach to the handling and interrogating of large flow cytometry data where cell status and function can be described , at the population level , by global descriptors such as distribution mean or co-efficient of variation experimental data . Here we link the “real” data to initialise a computer simu...	One of the key challenges facing cell biologists today is understanding the influence of molecular controls in shaping and controlling cell growth and proliferation . There is growing recognition that abnormal progression through the cell cycle and the associated effects on the growth of cell populations has a major im...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics", "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology", "physics/interdisciplinary", "physics" ]	2010	Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations
Paramutation involves homologous sequence communication that leads to meiotically heritable transcriptional silencing . We demonstrate that mop2 ( mediator of paramutation2 ) , which alters paramutation at multiple loci , encodes a gene similar to Arabidopsis NRPD2/E2 , the second-largest subunit of plant-specific RNA ...	How an individual's genes are activated or silenced is an essential question impacting all fields of biology . Usually gene expression patterns , i . e . , which genes are on and which are off in different tissues and during development , are highly reproducible; and those patterns are efficiently reset in the next gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics" ]	2009	A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes
Over 200 million people have , and another 600 million are at risk of contracting , schistosomiasis , one of the major neglected tropical diseases . Transmission of this infection , which is caused by helminth parasites of the genus Schistosoma , depends upon the release of parasite eggs from the human host . However ,...	Schistosomes are parasitic worms that infect hundreds of millions of people in developing countries . They cause disease by virtue of the fact that the eggs that they produce , which are intended for release from the host in order to allow transmission of infection , can become trapped in target organs such as the live...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "animals", "in", "vitro", "infectious", "diseases", "microbiology" ]	2007	TGF-β Signaling Controls Embryo Development in the Parasitic Flatworm Schistosoma mansoni
Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes . They consist of an autocatalytic intron RNA ( a “ribozyme” ) and an intron-encoded reverse transcriptase , which function together to promote intron integration into new DNA sites by a mechanism termed...	Mobile group II introns are bacterial retrotransposons that are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes . They consist of an autocatalytic intron RNA ( a ribozyme ) and an intron-encoded reverse transcriptase , which together promote intron mobility to new DNA sites by a mechanism...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation
Establishment of sister chromatid cohesion is coupled to DNA replication , but the underlying molecular mechanisms are incompletely understood . DDX11 ( also named ChlR1 ) is a super-family 2 Fe-S cluster-containing DNA helicase implicated in Warsaw breakage syndrome ( WABS ) . Herein , we examined the role of DDX11 in...	Chromosomes are DNA molecules that contain the genetic information . During replication , the two sister DNA molecules covered by proteins ( sister chromatids ) are held together by many copies of a ring-like protein complex named cohesin , in a process called sister-chromatid cohesion . Before a cell divides , the coh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "hela", "cells", "enzymes", "cell", "cycle", "and", "cell", "division", "gene", "regulation", "biological", "cultures", "cell", "processes", "enzymology", "dna", "helicases", "chromatids", "dna", "replication", "cell", "cultures", "sequence", "motif", "analysis", "d...	2018	Interaction of the Warsaw breakage syndrome DNA helicase DDX11 with the replication fork-protection factor Timeless promotes sister chromatid cohesion
The neuronal system underlying learning , generation and recognition of song in birds is one of the best-studied systems in the neurosciences . Here , we use these experimental findings to derive a neurobiologically plausible , dynamic , hierarchical model of birdsong generation and transform it into a functional model...	How do birds communicate via their songs ? Investigating this question may not only lead to a better understanding of communication via birdsong , but many believe that the answer will also give us hints about how humans decode speech from complex sound wave modulations . In birds , the output and neuronal responses of...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "circuit", "models", "motor", "systems", "nonlinear", "dynamics", "mathematics", "neural", "networks", "computational", "neuroscience", "biology", "computational", "biology", "sensory", "systems", "neuroscience", "neurophysiology", "coding", "mechanisms" ]	2011	A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs
CpG islands ( CGIs ) are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters . As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation , we devised a CGI enrichment method based on nonmethylated CpG affinity chromatogr...	The human genome contains about 22 , 000 genes , each encoding one of the proteins required for human life . A particular cell type ( e . g . , blood , skin , etc . ) expresses a specific subset of protein genes and silences the remainder . To shed light on the mechanisms that cause genes to be activated or shut down ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics" ]	2008	A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci
Triatoma dimidiata , currently the major Central American vector of Trypanosoma cruzi , the parasite that causes Chagas disease , inhabits caves throughout the region . This research investigates the possibility that cave dwelling T . dimidiata might transmit the parasite to humans and links the blood meal sources of c...	Caves have enduring appeal to humans , and their lure in Central America includes tourism , religious ceremonies and shelter . The major Chagas disease vector in this region , Triatoma dimidiata , inhabits caves throughout its range . We challenge the assumption that cave-dwelling vectors are not important for human tr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "parasitic", "protozoans", "plant", "science", "protozoans", "plant", "pathology", "population", "biology", "genetic", "epidemiology", "infecti...	2014	Hunting, Swimming, and Worshiping: Human Cultural Practices Illuminate the Blood Meal Sources of Cave Dwelling Chagas Vectors (Triatoma dimidiata) in Guatemala and Belize
Plants defend themselves against pathogens by activating an array of immune responses . Unfortunately , immunity programs may also cause unintended collateral damage to the plant itself . The quantitative disease resistance gene ACCELERATED CELL DEATH 6 ( ACD6 ) serves to balance growth and pathogen resistance in natur...	Plants defend themselves against pathogens by activating immune responses . Unfortunately , these can cause unintended collateral damage to the plant itself . Nevertheless , some wild plants have genetic variants that confer a low threshold for the activation of immunity . While these enable a plant to respond particul...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "brassica", "alleles", "plant", "science", "model", "organisms", "signs", "and", "symptoms", "experimental", "organism", "systems", "plants", "arab...	2018	Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene
The HLA ( Human Leukocyte Antigens ) genes are well-documented targets of balancing selection , and variation at these loci is associated with many disease phenotypes . Variation in expression levels also influences disease susceptibility and resistance , but little information exists about the regulation and populatio...	The level at which a gene is expressed can have important influence on the phenotype of an organism , including its predisposition to develop diseases . One way to estimate gene expression is by quantifying the abundance of RNA . RNA-seq has become the method of choice to provide such estimates at the genomewide scale ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "variant", "genotypes", "alleles", "genetic", "mapping", "genome", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "sequence", "alignment", "bioinformatics", "gene", "expression", "genetic", "loci", ...	2019	Expression estimation and eQTL mapping for HLA genes with a personalized pipeline
Human infection with Bwamba virus ( BWAV ) and the closely related Pongola virus ( PGAV ) , as well as Nyando virus ( NDV ) , are important causes of febrile illness in Africa . However , despite seroprevalence studies that indicate high rates of infection in many countries , these viruses remain relatively unknown and...	Bunyavirus infections cause febrile illnesses of varying severity worldwide; however , despite their public health importance most remain relatively unstudied . In order to clarify the genetic relationships among African orthobunyaviruses associated with human infection , we have sequenced multiple strains of Bwamba ( ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "organismal", "evolution", "comparative", "sequence", "analysis", "medicine", "and", "health", "sciences", "viral", "classification", "emerging", "viral", "diseases", "vector-borne", "diseases", "microbiology", "viruses", "microbial", "evolution"...	2014	Molecular Characterization of Human Pathogenic Bunyaviruses of the Nyando and Bwamba/Pongola Virus Groups Leads to the Genetic Identification of Mojuí dos Campos and Kaeng Khoi Virus
Treponema pallidum subsp . pertenue ( TPE ) is the causative agent of yaws , a multistage disease endemic in tropical regions in Africa , Asia , Oceania , and South America . To date , seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin ( CDC-2 , CDC 2575 , Gauthier ...	Treponema pallidum subsp . pertenue ( TPE ) is the causative agent of yaws , a multi-stage disease that is endemic in tropical regions of Africa , Asia , Oceania , and South America . TPE belongs to the pathogenic treponemes and causes several human and animal infections . Whole genome sequences of two TPE strains isol...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "sequence", "assembly", "tools", "membrane", "proteins", "outer", "membrane", "proteins", "genome", "analysis", "sequence", "motif", "analysis", "cellular...	2018	Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes
Mycobacterium tuberculosis ( Mtb ) impairs dendritic cell ( DC ) functions and induces suboptimal antigen-specific CD4 T cell immune responses that are poorly protective . Mucosal T-helper cells producing IFN-γ ( Th1 ) and IL-17 ( Th17 ) are important for protecting against tuberculosis ( TB ) , but the mechanisms by w...	Tuberculosis ( TB ) remains a serious global health problem and understanding how to induce protective immunity to M . tuberculosis ( Mtb ) remains a major challenge . While antigen-specific CD4 T cells and IFN-γ are important for controlling Mtb infection , they are not sufficient for protecting against TB . We need i...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "t", "helper", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "tropical", "diseases", "cell-mediated", "immunity", "cloning", "bacterial", "disease...	2017	Engaging the CD40-CD40L pathway augments T-helper cell responses and improves control of Mycobacterium tuberculosis infection
Uterine smooth muscle cells remain quiescent throughout most of gestation , only generating spontaneous action potentials immediately prior to , and during , labor . This study presents a method that combines transcriptomics with biophysical recordings to characterise the conductance repertoire of these cells , the ‘co...	A well-known problem in electrophysiologal modeling is that the parameters of the gating kinetics of the ion channels cannot be uniquely determined from observed behavior at the cellular level . One solution is to employ simplified “macroscopic” currents that mimic the behavior of aggregates of distinct entities at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "voltage-gated", "ion", "channels", "uterus", "calcium-activated", "potassium", "channels", "medicine", "and", "health", "sciences", "reproductive", "system", "membrane", "potential", "electrophysiology", "neuroscience", "ion", "channels", "cellular", "structures", "and", ...	2016	Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells
In the peripheral nervous system ( PNS ) myelinating Schwann cells synthesize large amounts of myelin protein zero ( P0 ) glycoprotein , an abundant component of peripheral nerve myelin . In humans , mutations in P0 cause the demyelinating Charcot-Marie-Tooth 1B ( CMT1B ) neuropathy , one of the most diffused genetic d...	Charcot-Marie-Tooth neuropathies are a large family of peripheral nerve disorders , showing extensive clinical and genetic heterogeneity . Although strong advances have been made in the identification of genes and mutations involved , effective therapies are still lacking . Intracellular retention of abnormal proteins ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Schwann cells ER-associated degradation contributes to myelin maintenance in adult nerves and limits demyelination in CMT1B mice
Treatment and morbidity control of schistosomiasis relies on a single drug , praziquantel . Hence , there is a pressing need to develop additional therapeutics against schistosomiasis . The antimalarial drug mefloquine shows antischistosomal activity in animal models and clinical trials , which calls for further invest...	The antimalarial drug mefloquine shows activity against blood flukes that cause the disease schistosomiasis . In animal studies it has been found that a mefloquine-praziquantel combination kills blood flukes more effectively than praziquantel alone . Combining praziquantel with another drug might therefore increase eff...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "infectious", "diseases", "schistosomiasis", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases" ]	2014	Praziquantel, Mefloquine-Praziquantel, and Mefloquine-Artesunate-Praziquantel against Schistosoma haematobium: A Randomized, Exploratory, Open-Label Trial
Hepatitis C virus ( HCV ) infection is a leading cause of liver disease worldwide . The HCV RNA genome is translated into a single polyprotein . Most of the cleavage sites in the non-structural ( NS ) polyprotein region are processed by the NS3/NS4A serine protease . The vital NS2-NS3 cleavage is catalyzed by the NS2 a...	Hepatitis C virus ( HCV ) replicates its genome in close association to cellular membranes which serve as assembly site of multi-subunit replication complexes . The process of replication complex maturation must be properly controlled to prevent the non-functional maturation/assembly of these complexes . In this proces...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Conserved NS3 Surface Patch Orchestrates NS2 Protease Stimulation, NS5A Hyperphosphorylation and HCV Genome Replication
Identifying biomarkers for tuberculosis ( TB ) is an ongoing challenge in developing immunological correlates of infection outcome and protection . Biomarker discovery is also necessary for aiding design and testing of new treatments and vaccines . To effectively predict biomarkers for infection progression in any dise...	Tuberculosis ( TB ) is a disease that is caused by infection after inhaling the bacterium Mycobacterium tuberculosis . Not everyone infected with TB bacteria becomes sick . As a result , two TB-related conditions have been categorized: latent TB infection ( not sick but still harboring the bacteria ) and active TB dise...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "granulomas", "immunology", "tropical", "diseases", "biomarkers", "bacterial", "diseases", "cytotoxic", "t", "cells", "bacteria", "infectious", "diseases", "white", "blood"...	2016	Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome
Collaboration between heterogeneous pattern recognition receptors ( PRRs ) leading to synergistic coordination of immune response is important for the host to fight against invading pathogens . Although complement receptor 3 ( CR3 ) and Dectin-1 are major PRRs to detect fungi , crosstalk between these two receptors in ...	The incidence of life-threatening fungal infections is increasing during the last decades . A better understanding of the interactions between fungal pathogen and its host cell is important to the development of new therapeutic strategies against fungal infections . Dimorphic fungus Histoplasma capsulatum becomes disse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	CR3 and Dectin-1 Collaborate in Macrophage Cytokine Response through Association on Lipid Rafts and Activation of Syk-JNK-AP-1 Pathway
Dyskeratosis congenita ( DC ) is a heterogeneous inherited bone marrow failure and cancer predisposition syndrome in which germline mutations in telomere biology genes account for approximately one-half of known families . Hoyeraal Hreidarsson syndrome ( HH ) is a clinically severe variant of DC in which patients also ...	Patients with dyskeratosis congenita ( DC ) , a rare inherited disease , are at very high risk of developing cancer and bone marrow failure . The clinical features of DC include nail abnormalities , skin discoloration , and white spots in the mouth . Patients with Hoyeraal-Hreidarsson syndrome ( HH ) have symptoms of D...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Recessive Founder Mutation in Regulator of Telomere Elongation Helicase 1, RTEL1, Underlies Severe Immunodeficiency and Features of Hoyeraal Hreidarsson Syndrome
It was recently reported that the recBC mutants of Escherichia coli , deficient for DNA double-strand break ( DSB ) repair , have a decreased copy number of their terminus region . We previously showed that this deficit resulted from DNA loss after post-replicative breakage of one of the two sister-chromosome termini a...	The Escherichia coli recBC mutant , deficient for DNA double-strand break ( DSB ) repair , shows a viability defect and a specific deficit in the level of chromosome terminus DNA sequences . We previously showed that this deficit results from heritable terminus DNA loss , owing to cell-division dependent DSBs in the ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chromosome", "structure", "and", "function", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "replication", "forms", "of", "dna", "circular", "dna", "dna", "homologous", "recombination", "chromosome", "biology", "genetic", "loci", "biochemis...	2018	Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome
Diphthamide is a highly modified histidine residue in eukaryal translation elongation factor 2 ( eEF2 ) that is the target for irreversible ADP ribosylation by diphtheria toxin ( DT ) . In Saccharomyces cerevisiae , the initial steps of diphthamide biosynthesis are well characterized and require the DPH1-DPH5 genes . H...	Diphthamide is an unusual modified amino acid found uniquely in a single protein , eEF2 , which is required for cells to synthesize new proteins . The name refers to its target function for eEF2 inactivation by diphtheria toxin , the disease-inducing agent produced by the pathogen Corynebacterium diphtheriae . Why cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biochemistry", "computer", "science", "model", "organisms", "molecular", "cell", "biology", "genetics", "chemistry", "biology", "genomics", "microbiology", "genetics", "and", "genomics", "toxicology" ]	2013	The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network
Barrier epithelia that are persistently exposed to microbes have evolved potent immune tools to eliminate such pathogens . If mechanisms that control Drosophila systemic responses are well-characterized , the epithelial immune responses remain poorly understood . Here , we performed a genetic dissection of the cascades...	Invertebrates solely rely on innate immune responses for defense against microbial infections . Taking advantage of its powerful genetics , the fly Drosophila melanogaster has been extensively used as a model system to dissect the molecular mechanisms that control innate immunity . This work led to the discovery of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "immunity", "innate", "immunity", "immunology", "biology" ]	2011	Toll-8/Tollo Negatively Regulates Antimicrobial Response in the Drosophila Respiratory Epithelium
MicroRNAs ( miRNAs ) are small non-coding RNAs that regulate gene expression by binding to partially complementary regions within the 3’UTR of their target genes . Computational methods play an important role in target prediction and assume that the miRNA “seed region” ( nt 2 to 8 ) is required for functional targeting...	microRNAs are small RNA molecules that regulate biological processes by binding to the 3’UTR of a gene and their dysregulation is associated with several diseases . Computationally predicting these targets remains a challenge as they only partially match their target and so there can be hundreds of targets for a single...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "transfection", "learning", "neural", "networks", "engineering", "and", "technology", "gene", "regulation", "social", "sciences", "neuroscience", "learning", "and", "memory", "artificial", "neural", "networks", "micrornas", "cognitive", "psychology", "mathematics", "nucle...	2018	miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
In West Africa , envenoming by saw-scaled or carpet vipers ( Echis ocellatus ) causes great morbidity and mortality , but there is a crisis in supply of effective and affordable antivenom ( ISRCTN01257358 ) . In a randomised , double-blind , controlled , non-inferiority trial , “EchiTAb Plus-ICP” ( ET-Plus ) equine ant...	Snake bite threatens millions of poor rural folk throughout Africa . In Nigeria , as in many countries of sub-Saharan Africa , it takes a terrible toll on human life and limb . Over the years , the news for those exposed to snake bite has been generally bad: withdrawal of antivenom manufacturers , increasing cost and ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/occupational", "and", "industrial", "medicine" ]	2010	Randomised Controlled Double-Blind Non-Inferiority Trial of Two Antivenoms for Saw-Scaled or Carpet Viper (Echis ocellatus) Envenoming in Nigeria
The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols ( TAGs ) . To describe the genetic basis of the Rhodococcus oleaginous metabolism , we sequenced and perform...	Biofuels research is focused on understanding the energy-related metabolic capabilities of a broad range of biological species . To this end we sequenced the genome of Rhodococcus opacus PD630 , a bacterium that accumulates close to 80% of its cellular dry weight in oil , a rare trait in the prokaryotic and eukaryotic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "lipids", "enzymes", "genetics", "biology", "genomics", "microbiology", "metabolism", "genetics", "and", "genomics" ]	2011	Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development
Amyloid-like inclusions have been associated with Huntington's disease ( HD ) , which is caused by expanded polyglutamine repeats in the Huntingtin protein . HD patients exhibit a high incidence of cardiovascular events , presumably as a result of accumulation of toxic amyloid-like inclusions . We have generated a Dros...	Huntington's disease ( HD ) is associated with amyloid-like inclusions in the brain and heart , and accumulation of amyloid protein is associated with neurodegeneration and cardiomyopathy . Recent studies suggest that HD patients show increased susceptibility to cardiac failure . However , the mechanisms by which disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Huntington's Disease Induced Cardiac Amyloidosis Is Reversed by Modulating Protein Folding and Oxidative Stress Pathways in the Drosophila Heart
The trafficking of primordial germ cells ( PGCs ) across multiple embryonic structures to the nascent gonads ensures the transmission of genetic information to the next generation through the gametes , yet our understanding of the mechanisms underlying PGC migration remains incomplete . Here we identify a role for the ...	Egg and sperm derive from precursors in the early embryo called primordial germ cells ( PGCs ) . The mechanisms underlying the migration of PGCs through the embryo to the forming gonads remain unclear . In a genetic screen , we identified a role for the receptor Ror2 and its ligand Wnt5a in promoting PGC colonization o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "embryology", "organism", "development", "stem", "cells", "embryonic", "stem", "cells", "genetic", "screens", "genetics", "organogenesis", "biology", "genetics", "and", "genomics" ]	2011	Ror2 Enhances Polarity and Directional Migration of Primordial Germ Cells
A century after its discovery , Chagas disease still represents a major neglected tropical threat . Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field . The purpose of this study was to evaluate the performance of PCR methods in detectio...	A century after its discovery , Chagas disease , caused by the parasite Trypanosoma cruzi , still represents a major neglected tropical threat . Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field . The polymerase chain reaction ( PCR ) h...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "molecular", "biology", "microbiology/parasitology" ]	2011	International Study to Evaluate PCR Methods for Detection of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients
Neuronal activity is mediated through changes in the probability of stochastic transitions between open and closed states of ion channels . While differences in morphology define neuronal cell types and may underlie neurological disorders , very little is known about influences of stochastic ion channel gating in neuro...	The activity of neurons in the brain is mediated through changes in the probability of random transitions between open and closed states of ion channels . Since differences in morphology define distinct types of neuron and may underlie neurological disorders , it is important to understand how morphology influences the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal", "signaling", "mechanisms", "biophysics/theory", "and", "simulation", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes
Defining the mechanisms of Mycobacterium tuberculosis ( Mtb ) persistence in the host macrophage and identifying mycobacterial factors responsible for it are keys to better understand tuberculosis pathogenesis . The emerging picture from ongoing studies of macrophage deactivation by Mtb suggests that ingested bacilli s...	Mycobacterium tuberculosis ( Mtb ) is a very successful intracellular pathogen that infects lung macrophages . Its resistance to intracellular killing has been linked to the development of pulmonary tuberculosis ( TB ) in humans . Thus , understanding the mechanism by which Mycobacterium tuberculosis ( Mtb ) persists i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "host-pathogen", "interaction", "biology", "microbiology" ]	2013	Mycobacterium tuberculosis Nucleoside Diphosphate Kinase Inactivates Small GTPases Leading to Evasion of Innate Immunity
Many animal organs are composed largely or entirely of polarized epithelial tubes , and the formation of complex organ systems , such as the digestive or vascular systems , requires that separate tubes link with a common polarity . The Caenorhabditis elegans digestive tract consists primarily of three interconnected tu...	Tubes composed of epithelial cells are universal building blocks of animal organs , and complex organs typically contain multiple interconnected tubes , such as in the digestive tract or vascular system . The nematode Caenorhabditis elegans provides a simple genetic system to study how tubes form and link . Understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Cell Interactions and Patterned Intercalations Shape and Link Epithelial Tubes in C. elegans
Plague , a zoonosis caused by Yersinia pestis , is found in Asia and the Americas , but predominantly in Africa , with the island of Madagascar reporting almost one third of human cases worldwide . Plague's occurrence is affected by local climate factors which in turn are influenced by large-scale climate phenomena suc...	Plague is a vector-borne bacterial infection with rodents and their fleas as its principal hosts . Transmission to humans occurs via the bite of an infected flea . In the highlands of Madagascar , plague is endemic and more than one hundred human cases are reported every year . Global climate is known to affect many in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "plant", "science", "yersinia", "global", "health", "plant", "pathology", "n...	2014	A Non-Stationary Relationship between Global Climate Phenomena and Human Plague Incidence in Madagascar
Functional MRI ( fMRI ) studies have traditionally relied on intersubject normalization based on global brain morphology , which cannot establish proper functional correspondence between subjects due to substantial intersubject variability in functional organization . Here , we reliably identified a set of discrete , h...	No two individuals are alike . The size , shape , position , and connectivity patterns of brain functional regions can vary drastically between individuals . While interindividual differences in functional organization are well recognized , to date , standard procedures for functional neuroimaging research still rely o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "methods", "and", "resources", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "social", "sciences", "problem", "solving", "neuroscience", "magnetic", "resonance", "imaging", "co...	2019	Performing group-level functional image analyses based on homologous functional regions mapped in individuals
Buruli ulcer is a chronic painless skin disease caused by Mycobacterium ulcerans . The local nerve damage induced by M . ulcerans invasion is similar to the nerve damage evoked by the injection of mycolactone in a Buruli ulcer mouse model . In order to elucidate the mechanism of this nerve damage , we tested and compar...	Buruli ulcer is a chronic skin disease caused by Mycobacterium ulcerans , and the disease is characterized by the painless nature of its lesion . Similar to leprosy , loss of pain often hinders the patients from taking proper medical care , resulting in gross deformities . A toxic lipid mycolactone produced from Mycoba...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "endothelial", "cells", "cell", "processes", "immunology", "tropical", "diseases", "macroglial", "cells", "fibroblasts", "toxic...	2017	Mycolactone cytotoxicity in Schwann cells could explain nerve damage in Buruli ulcer
Australia uses a protocol combining human rabies immunoglobulin ( HRIG ) and rabies vaccine for post-exposure prophylaxis ( PEP ) of rabies and Australian bat lyssavirus ( ABLV ) , with the aim of achieving an antibody titre of ≥0 . 5 IU/ml , as per World Health Organization ( WHO ) guidelines , as soon as possible . W...	In Australia , the administration of rabies post-exposure prophylaxis ( PEP ) occurs for potentially exposed returned travellers from endemic regions or for potential local exposure to Australian Bat Lyssavirus . For Australian tourists , delays in commencing PEP or not receiving HRIG or all recommended doses of vaccin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "vaccines", "medicine", "vaccination", "infectious", "diseases", "rabies", "clinical", "immunology", "immunity", "travel-associated", "diseases", "neglected", "tropical", "diseases", "immunology" ]	2013	Using Serology to Assist with Complicated Post-Exposure Prophylaxis for Rabies and Australian Bat Lyssavirus
While acute lung injury ( ALI ) contributes significantly to critical illness , it resolves spontaneously in many instances . The majority of patients experiencing ALI require mechanical ventilation . Therefore , we hypothesized that mechanical ventilation and concomitant stretch-exposure of pulmonary epithelia could a...	Acute lung injury is a devastating lung disease caused by injuries or acute infections to the lung . In patients it manifests itself as acute respiratory distress syndrome . Severe pulmonary edema and uncontrolled lung inflammation are typical symptoms of acute lung injury , which make it hard for patients to breath ef...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	HIF1A Reduces Acute Lung Injury by Optimizing Carbohydrate Metabolism in the Alveolar Epithelium
The Pseudomonas syringae acetyltransferase HopZ1a is delivered into host cells by the type III secretion system to promote bacterial growth . However , in the model plant host Arabidopsis thaliana , HopZ1a activity results in an effector-triggered immune response ( ETI ) that limits bacterial proliferation . HopZ1a-tri...	All plants must ward off potentially infectious microbes , and those grown in large-scale crop operations are especially vulnerable to the rapid spread of disease by successful pathogens . Although many bacteria and fungi can supress plant immune responses by producing specialized virulence proteins called ‘effectors’ ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "interactions", "brassica", "plant", "physiology", "plasmid", "construction", "fungi", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "plant", "pathology", "sequence", "motif", "analysis", "molecular", "biology", "techniques", ...	2019	Perturbations of the ZED1 pseudokinase activate plant immunity
Abscission is the final step of cytokinesis that involves the cleavage of the intercellular bridge connecting the two daughter cells . Recent studies have given novel insight into the spatiotemporal regulation and molecular mechanisms controlling abscission in cultured yeast and human cells . The mechanisms of abscissi...	Cytokinesis , the final step of cell division , concludes with a process termed abscission , during which the two daughter cells physically separate . In spite of their importance , the molecular machineries controlling abscission are poorly characterized especially in the context of living metazoan tissues . Here we p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	ALIX and ESCRT-III Coordinately Control Cytokinetic Abscission during Germline Stem Cell Division In Vivo
DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation . The “genetic switch” of bacteriophage λ determines whether a prophage stays incorporated in the E . coli chromosome or enters the lytic cycle of phage propagation and cell lysis . Past studies have shown that long-range ...	One mechanism cells use to regulate gene expression is DNA looping , whereby two distant DNA sites are brought together by regulatory proteins . The looping then either enhances interactions between other regulatory proteins bound at the separate sites or brings those regulatory proteins close to RNA polymerase at the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nucleic", "acids", "gene", "regulation", "genetics", "gene", "expression", "dna", "molecular", "genetics", "biology", "computational", "biology", "molecular", "cell", "biology", "synthetic", "biology", "biophysics", "dna", "transcription" ]	2013	Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells
Thermal adaptation is essential in all organisms . In yeasts , the heat shock response is commanded by the heat shock transcription factor Hsf1 . Here we have integrated unbiased genetic screens with directed molecular dissection to demonstrate that multiple signalling cascades contribute to thermal adaptation in the p...	Candida albicans is one of the most persistent yeast pathogens known to man , causing frequent mucosal infections ( thrush ) in otherwise healthy individuals , and potentially fatal bloodstream infections in immunocompromised patients . C . albicans colonises warm-blooded animals and occupies thermally buffered niches ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "signal", "transduction", "mycology", "signaling", "in", "cellular", "processes", "model", "organisms", "molecular", "cell", "biology", "cellular", "stress", "responses", "cell", "biology", "microbial", "pathogens", "yeast", "and", "fungal", "models", "biology", "micr...	2012	Hsp90 Orchestrates Transcriptional Regulation by Hsf1 and Cell Wall Remodelling by MAPK Signalling during Thermal Adaptation in a Pathogenic Yeast
Chronic Chagas disease presents several different clinical manifestations ranging from asymptomatic to severe cardiac and/or digestive clinical forms . Several studies have demonstrated that immunoregulatory mechanisms are important processes for the control of the intense immune activity observed in the chronic phase ...	Chagas disease is a parasitic infection caused by protozoan Trypanosoma cruzi that affects approximately 11 million people in Latin America . The involvement of the host's immune response on the development of severe forms of Chagas disease has not been fully elucidated . Studies on the immune response against T . cruz...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immunity", "to", "infections" ]	2009	Profile of Central and Effector Memory T Cells in the Progression of Chronic Human Chagas Disease
Two theoretical models dominate current understanding of actin-based propulsion: microscopic polymerization ratchet model predicts that growing and writhing actin filaments generate forces and movements , while macroscopic elastic propulsion model suggests that deformation and stress of growing actin gel are responsibl...	There are two major ideas about how actin networks generate force against an obstacle: one is that the force comes directly from the elongation and bending of individual actin filaments against the surface of the obstacle; the other is that a growing actin gel can build up stress around the obstacle to squeeze it forwa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "actin", "filaments", "biophysic", "al", "simulations", "biology", "cell", "mechanics", "computational", "biology", "biophysics", "biomechanics" ]	2012	Mesoscopic Model of Actin-Based Propulsion
Bacterial spores play an important role in disease initiation , transmission and persistence . In some species , the exosporium forms the outermost structure of the spore and provides the first point of contact between the spore and the environment . The exosporium may also be involved in spore adherence , protection a...	Clostridium sordellii is a lethal pathogen in humans and animals and its spores are critical for initiating infection . Outer spore proteins in Bacillus and Clostridium species are important for spore fitness and pathogenesis , however , equivalent proteins in C . sordellii have not been identified and their role is un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "gut", "bacteria", "animal", "models", "of", "disease", "microbiology", "animal", "models", "mutation", "model", "organisms", "gastroenterology", "and", "hepatology", "experimental", "organism", "systems", "bacter...	2018	Clostridium sordellii outer spore proteins maintain spore structural integrity and promote bacterial clearance from the gastrointestinal tract
HIV-1 assembly and release are believed to occur at the plasma membrane in most host cells with the exception of primary macrophages , for which exclusive budding at late endosomes has been reported . Here , we applied a novel ultrastructural approach to assess HIV-1 budding in primary macrophages in an immunomarker-in...	Macrophages are one of the major target cells for HIV-1 infection and play an important role in viral pathogenesis . Previous studies indicated that the pathway of HIV-1 particle morphogenesis is distinct in primary human macrophages , and this has been suggested to play a role in viral persistence . Early reports indi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "infectious", "diseases", "cell", "biology", "virology", "immunology", "homo", "(human)" ]	2007	HIV-1 Buds Predominantly at the Plasma Membrane of Primary Human Macrophages
Specialized endocrine cells produce and release steroid hormones that govern development , metabolism and reproduction . In order to synthesize steroids , all the genes in the biosynthetic pathway must be coordinately turned on in steroidogenic cells . In Drosophila , the steroid producing endocrine cells are located i...	Steroid hormones play important roles in physiology and disease . These hormones are molecules produced and secreted by endocrine cells in the body and control sexual maturation , metabolism and reproduction . We found transcriptional regulators that underlie the specialized function of endocrine steroid-producing cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "animal", "models", "signal", "transduction", "developmental", "biology", "model", "organisms", "animal", "genetics", "organism", "development", "cell", "biology", "cell", "growth", "gene", "expression", "genetics", "biology", "and", "life", "scien...	2014	Transcriptional Control of Steroid Biosynthesis Genes in the Drosophila Prothoracic Gland by Ventral Veins Lacking and Knirps
Cycles involving covalent modification of proteins are key components of the intracellular signaling machinery . Each cycle is comprised of two interconvertable forms of a particular protein . A classic signaling pathway is structured by a chain or cascade of basic cycle units in such a way that the activated protein i...	Cellular signaling is carried out by a complex network of interactions . A structure that is found commonly in signaling pathways is a sequence of on-off cycles between two states of the same protein , referred to as a cascade . By analyzing and reducing the basic kinetic equations of this system , we have constructed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/signaling", "networks", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/theory", "and", "simulation", "cell", "biology/cell", "signaling" ]	2008	A Hidden Feedback in Signaling Cascades Is Revealed
Long non-coding RNAs regulate various biological processes such as dosage compensation , imprinting , and chromatin organization . HOTAIR , a paradigm of this new class of RNAs , is localized within the human HOXC gene cluster and was shown , in human cells , to regulate HOXD genes in trans via the recruitment of Polyc...	Long non-coding RNAs ( lincRNA ) have recently become a new paradigm for gene regulation via chromatin remodeling in a variety of biological processes , including during embryonic development . HOTAIR , a human lincRNA localized within the HOXC cluster was shown to help silence HOXD cluster genes in trans , through the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "genomics", "evolutionary", "biology", "genetics", "and", "genomics" ]	2011	Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human
In eukaryotes , hundreds of mRNAs are localized by specialized transport complexes . For localization , transcripts are recognized by RNA-binding proteins and incorporated into motor-containing messenger ribonucleoprotein particles ( mRNPs ) . To date , the molecular assembly of such mRNPs is not well understood and mo...	In eukaryotes , the majority of cells are asymmetric and a way to establish such polarity is directional transport of macromolecules along cytoskeletal filaments . Among the cargoes transported , mRNAs play an essential role , as their localized translation contributes significantly to the generation of asymmetry . To ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/morphogenesis", "and", "cell", "biology", "molecular", "biology/translational", "regulation", "molecular", "biology/rna-protein", "interactions", "biochemistry/macromolecular", "assemblies", "and", "machines" ]	2011	A Cytoplasmic Complex Mediates Specific mRNA Recognition and Localization in Yeast
Recent studies have identified thousands of regions in the genome associated with chromatin modifications , which may in turn be affecting gene expression . Existing works have used heuristic methods to investigate the relationships between genome , epigenome , and gene expression , but , to our knowledge , none have e...	Genome-wide association studies ( GWAS ) have revealed that the majority of variants associated with complex disease lie in noncoding regulatory sequences . More recent studies have identified thousands of quantitative trait loci ( QTLs ) associated with chromatin modifications , which in turn are associated with chang...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "dna-binding", "proteins", "social", "sciences", "simulation", "and", "modeling", "probability", "distribution", "mathematics", "genome", "analysis", "epigenetics", "molecular", "genetics", "chromatin", "research", "and", "analysis",...	2018	Methods for fine-mapping with chromatin and expression data
Neurocysticercosis ( NCC ) is an infection of the brain with the larval cyst of the tapeworm , Taenia solium . Cysticidal treatment induces parasite killing resulting in a post inflammatory response and seizures , which generally requires corticosteroid treatment to control inflammation . The nature of this response an...	Infection of the brain with larvae of the tapeworm Taenia solium is called neurocysticercosis ( NCC ) , a disease with varied and serious neurological symptoms . Therapy requires antiparasitic drugs and corticosteroids to prevent seizures caused by treatment due to inflammation around dying parasites . The gene express...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pig", "models", "gene", "regulation", "immunology", "vertebrates", "animals", "mammals"...	2017	TNF-α blockade suppresses pericystic inflammation following anthelmintic treatment in porcine neurocysticercosis
Neuronal excitability relies on inward sodium and outward potassium fluxes during action potentials . To prevent neuronal hyperexcitability , potassium ions have to be taken up quickly . However , the dynamics of the activity-dependent potassium fluxes and the molecular pathways underlying extracellular potassium homeo...	Neural excitability relies on precise inward and outward ionic fluxes . In particular , potassium ions , released by neurons during activity , have to be taken up efficiently to prevent hyperexcitability . Astrocytes , the third element of the synapse , play a prominent role in extracellular potassium homeostasis . Thu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels
Translationally Controlled Tumor Protein ( TCTP ) controls growth by regulating the G1/S transition during cell cycle progression . Our genetic interaction studies show that TCTP fulfills this role by interacting with CSN4 , a subunit of the COP9 Signalosome complex , known to influence CULLIN-RING ubiquitin ligases ac...	During organism development , the correct implementation of organs with unique shape , size and function , is the result of coordinated cellular processes , such as cell proliferation and expansion . Deregulation of these processes affect human health and can lead to severe diseases . While plants and animals have larg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "plant", "anatomy", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "brassica", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "p...	2019	TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals
The oxidative stress theory of aging postulates that aging results from the accumulation of molecular damage caused by reactive oxygen species ( ROS ) generated during normal metabolism . Superoxide dismutases ( SODs ) counteract this process by detoxifying superoxide . It has previously been shown that elimination of ...	In this paper , we examine the oxidative stress theory of aging using C . elegans as a model system . This theory proposes that aging results from the accumulation of molecular damage caused by reactive oxygen species ( ROS ) . To test this theory , we examined the effect of deleting each of the five individual superox...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "developmental", "biology/aging" ]	2009	Deletion of the Mitochondrial Superoxide Dismutase sod-2 Extends Lifespan in Caenorhabditis elegans
Transgenic crops producing insecticidal toxins from Bacillus thuringiensis ( Bt ) are commercially successful in reducing pest damage , yet knowledge of resistance mechanisms that threaten their sustainability is incomplete . Insect resistance to the pore-forming Cry1Ac toxin is correlated with the loss of high-affinit...	Crystal toxin proteins from Bacillus thuringiensis ( Bt ) make ideal bioinsecticides because of their high potency against certain insects and lack of activity against most other species . Transgenic cotton and maize expressing pore-forming Cry1A Bt-toxins are now widely used in agriculture , enabling substantial reduc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "cell", "biology/cellular", "death", "and", "stress", "responses", "biotechnology/plant", "biotechnology", "biochemistry/biomacromolecule-ligand", "interactions" ]	2010	An ABC Transporter Mutation Is Correlated with Insect Resistance to Bacillus thuringiensis Cry1Ac Toxin
Noise is a prevalent and sometimes even dominant aspect of many biological processes . While many natural systems have adapted to attenuate or even usefully integrate noise , the variability it introduces often still delimits the achievable precision across biological functions . This is particularly so for visual phot...	The invertebrate phototransduction system captures and converts environmental light inputs into electrical signals for use in later visual processing . Consequently , one would expect it to be optimised in some way to ensure that only a minimal amount of environmental information is lost during conversion . Confirming ...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "invertebrates", "markov", "models", "particle", "physics", "applied", "mathematics", "social", "sciences", "light", "neuroscience", "animals", "electromagnetic", "radiation", "simulation", "and", "modeling", "algorithms", "photons", "mathematics", "vision", "cellular", "...	2017	Point process analysis of noise in early invertebrate vision
The parasite Entamoeba histolytica is the etiological agent of amoebiasis and phagocytosis plays a key role in virulence of this organism . Signaling pathways involved in activation of cytoskeletal dynamics required for phagocytosis remain to be elucidated . Phagocytosis is initiated with sequential recruitment of EhC2...	E . histolytica is the causative agent of amoebiasis and leads to morbidity and mortality in developing countries . It is known to phagocytose immune and non-immune cells , epithelial tissue , erythrocytes and commensal bacteria . The high rate of phagocytosis in this protist parasite provides a unique system to study ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Entamoeba histolytica, Arp2/3 Complex Is Recruited to Phagocytic Cups through an Atypical Kinase EhAK1
Cholera is the prime example of blood-group-dependent diseases , with individuals of blood group O experiencing the most severe symptoms . The cholera toxin is the main suspect to cause this relationship . We report the high-resolution crystal structures ( 1 . 1–1 . 6 Å ) of the native cholera toxin B-pentamer for both...	Cholera is a severe diarrheal disease that kills a hundred thousand people per year . With climate change , the number of cases is predicted to increase to millions . Individuals with blood group O are particularly at risk . Here we report high-resolution crystal structures of the native cholera toxin of both major bio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "milk", "body", "fluids", "toxins", "pathology", "and", "laboratory", "medicine", "crystal", "structure", "immune", "physiology", "immunology", "tropical", "diseases", "condensed", "matter", "physics", "blood", "groups", "toxic...	2016	High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence
Telomerase , the enzyme that maintains telomeres , preferentially lengthens short telomeres . The S . cerevisiae Pif1 DNA helicase inhibits both telomerase-mediated telomere lengthening and de novo telomere addition at double strand breaks ( DSB ) . Here , we report that the association of the telomerase subunits Est2 ...	Telomerase , the enzyme that maintains telomeres , preferentially lengthens short telomeres . The baker’s yeast Pif1 DNA helicase inhibits both telomerase-mediated lengthening of existing telomeres and the formation of new telomeres at double strand breaks . By virtue of its ATPase activity , Pif1 reduces the level of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Pif1 Helicase, a Negative Regulator of Telomerase, Acts Preferentially at Long Telomeres
Schools of fish and flocks of birds can move together in synchrony and decide on new directions of movement in a seamless way . This is possible because group members constantly share directional information with their neighbors . Although detecting the directionality of other group members is known to be important to ...	Schooling fish exhibit impressive group-level coordination in which multiple individuals move together in a seamless way . This is possible because each individual in the group responds to the movement of other group members . But how many individuals does each fish pay attention to ? Which are the influential neighbor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "velocity", "collective", "animal", "behavior", "fish", "swimming", "medicine", "and", "health", "sciences", "classical", "mechanics", "reaction", "time", "vertebrates", "mathematical", "models", "neuroscience", "biological", "locomotion", "animals", "cognitive", "neurosc...	2017	Identifying influential neighbors in animal flocking
Paracoccidioides brasiliensis causes paracoccidioidomycosis , one of the most prevalent systemic mycosis in Latin America . Thus , understanding the characteristics of the protective immune response to P . brasiliensis is of interest , as it may reveal targets for disease control . The initiation of the immune response...	Paracoccidioides brasiliensis is an etiological agent of paracoccidioidomycosis , one of the most prevalent systemic mycosis in South America , affecting over 10 million people . One of the hallmark features of this fungus is its multinucleated nature , where a single P . brasiliensis cell can have from one to over 50 ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "clinical", "immunology", "genetics", "immunology", "biology", "microbiology", "clinical", "genetics" ]	2013	TLR9 Activation Dampens the Early Inflammatory Response to Paracoccidioides brasiliensis, Impacting Host Survival
In Timor-Leste there have been intermittent and ineffective soil-transmitted helminth ( STH ) deworming programs since 2004 . In a resource-constrained setting , having information on the geographic distribution of STH can aid in prioritising high risk communities for intervention . This study aimed to quantify the env...	The majority of soil-transmitted helminth ( STH ) infections have long-term ramifications on an individual’s health and productivity , contributing to malnutrition , anaemia , and impaired childhood growth . In Timor-Leste there have been intermittent and ineffective STH control programs since 2004 . When resources are...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "helminths", "grasslands", "tropical", "diseases", "hookworms", "geographical", "locations", "plant", "communities", "parasitic", "diseases", "animals", "necator", "am...	2017	An environmental assessment and risk map of Ascaris lumbricoides and Necator americanus distributions in Manufahi District, Timor-Leste
Cell-fate asymmetry in the predivisional cell of Caulobacter crescentus requires that the regulatory protein DivL localizes to the new pole of the cell where it up-regulates CckA kinase , resulting in a gradient of CtrA~P across the cell . In the preceding stage of the cell cycle ( the “stalked” cell ) , DivL is locali...	The aquatic bacterium , Caulobacter crescentus , divides asymmetrically into a non-motile “stalked” cell that stays at its place of birth , and a motile “swarmer” cell that disperses to a different locale . Prior to cell division , the cell passes through a “predivisional” stage , when it has a stalk at its “old” end a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models
Neuropathic pain has been little studied in leprosy . We assessed the prevalence and clinical characteristics of neuropathic pain and the validity of the Douleur Neuropathique 4 questionnaire as a screening tool for neuropathic pain in patients with treated leprosy . The association of neuropathic pain with psychologic...	Neuropathic pain has only recently been recognised as a complication of leprosy . We assessed 101 treated leprosy patients in Mumbai and found that 22 of them had neuropathic pain . The pain occurred as numbness 86% , tingling 68% , and decreased sensation to light touch 81% . This pain was significantly associated wit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "public", "health", "and", "epidemiology", "mental", "health", "science", "policy", "evidence-based", "healthcare", "neurological", "disorders", "anesthesiology", "and", "pain", "management", "infectious", "diseases/bacterial", "infections", "neuroscience" ]	2011	Neuropathic Pain and Psychological Morbidity in Patients with Treated Leprosy: A Cross-Sectional Prevalence Study in Mumbai
TNFα is a pleiotropic pro-inflammatory cytokine with a key role in the activation of the immune system to fight viral infections . Despite its antiviral role , a few viruses might utilize the host produced TNFα to their benefit . Some recent reports have shown that anti-TNFα therapies could be utilized to treat certain...	Tumor necrosis factor alpha ( TNFα ) is one of the main pro-inflammatory cytokines produced in response to a broad type of infections [1] . Although TNFα has a crucial role in protecting the host organism from pathogens , its deregulation can promote susceptibility to pathogens by impairing pathogen clearance and , ult...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "antiviral", "immune", "response", "viral", "transmission", "and", "infection", "cell", "processes", "immunology", "microbiology", "vertebrates", "animals", "animal", "models", "o...	2016	TNFα Impairs Rhabdoviral Clearance by Inhibiting the Host Autophagic Antiviral Response
Cerebral autoregulation ( CA ) is an important vascular control mechanism responsible for relatively stable cerebral blood flow despite changes of systemic blood pressure ( BP ) . Impaired CA may leave brain tissue unprotected against potentially harmful effects of BP fluctuations . It is generally accepted that CA is ...	Cerebral autoregulation is an important mechanism that regulates blood supply to brain tissue to match metabolic demands during daily activities . Impaired cerebral autoregulation increases the dependence of cerebral blood flow on systemic blood pressure , and is associated with fatal outcomes in patients after brain i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "integrative", "physiology", "anatomy", "and", "physiology", "cardiovascular", "mathematics", "circulatory", "physiology", "stroke", "medical", "physics", "biology", "nonlinear", "dynamics", "cardiovascular", "system", "physics", "cerebrovascular", "diseases", "...	2012	A Nonlinear Dynamic Approach Reveals a Long-Term Stroke Effect on Cerebral Blood Flow Regulation at Multiple Time Scales
In laboratory yeast strains with Sir2 and Fob1 function , wild-type NAD+ salvage is required for calorie restriction ( CR ) to extend replicative lifespan . CR does not significantly alter steady state levels of intracellular NAD+ metabolites . However , levels of Sir2 and Pnc1 , two enzymes that sequentially convert N...	Though calorie restriction extends lifespan and healthspan in multiple model organisms , the intrinsic mechanisms remain unclear . In budding yeast Saccharomyces cerevisiae , manipulation of nicotinamide adenine dinucleotide ( NAD+ ) —a central metabolic cofactor—can restrict or extend replicative lifespan , suggesting...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Calorie Restriction-Mediated Replicative Lifespan Extension in Yeast Is Non-Cell Autonomous
Experimental evolution of the plant pathogen Ralstonia solanacearum , where bacteria were maintained on plant lineages for more than 300 generations , revealed that several independent single mutations in the efpR gene from populations propagated on beans were associated with fitness gain on bean . In the present work ...	Among plant pathogens of major economic and food crops , Ralstonia solanacearum , the causal agent of bacterial wilt , is recognized as one of the most destructive plant bacterial diseases . In addition , the emergence of new pathotypes , more aggressive and adapted to new hosts , has been reported . During an evolutio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "organismal", "evolution", "microbiology", "cloning", "plant", "science", "genome", "analysis", "microbial", "evolution", "crops", "plant", "pathology", "molecular", "biology", "techniques", "plants", "research", "and", "analysis", "methods", "legumes", ...	2016	Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum
In nature the prevalence of Leishmania infection in whole sand fly populations can be very low ( <0 . 1% ) , even in areas of endemicity and high transmission . It has long since been assumed that the protozoan parasite Leishmania can manipulate the feeding behavior of its sand fly vector , thus enhancing transmission ...	Leishmaniasis is a human parasitic disease that can result in destructive skin lesions or sometimes in fatal visceral involvement if left untreated . Infections are acquired via the bites of female sand flies , small blood-feeding insects . In this experimental study using mice , we show that Leishmania parasites can m...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "none", "(leishmania)", "microbiology", "mus", "(mouse)", "insects" ]	2007	Leishmania Manipulation of Sand Fly Feeding Behavior Results in Enhanced Transmission

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