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Thermotherapy is an accepted alternative therapy for new-world cutaneous leishmaniasis , but current heat-delivery modalities are too costly to be made widely available to endemic populations . We adapted a low-cost heat pack named the HECT-CL device that delivers safe , reliable , and renewable conduction heat . 25 pa...	American cutaneous leishmaniasis is an endemic parasitic disease in Peru , with more than a reported thousand cases per year associated with significant disabilities and economic impact . In comparison to old-world cutaneous Leishmaniasis where the infection generally heals on its own , American cutaneous Leishmaniasis...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "leishmaniasis", "medicine", "neglected", "tropical", "diseases", "infectious", "diseases" ]	2013	Novel Low-Cost Thermotherapy for Cutaneous Leishmaniasis in Peru
Chikungunya is an endemo-epidemic infection , which is still considered as an emerging public health problem . The aim of this study was to evaluate in a 65+ population , the accuracy of two chikungunya screening scores that were developed in younger people . It was performed in the Martinique University Hospitals from...	Chikungunya virus is an alpha-virus transmitted by Aedes egyptii or albopictus bites . This infection is still considered as an emerging public health problem . In the acute stage of infection , typical physical signs of Chikungunya virus infection are febrile illness associated with severe and debilitating polyarthral...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "death", "rates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "elderly", "chikungunya", "infection", "demography", "tropical", "diseases", "age", "groups", "signs", "a...	2017	Do Two Screening Tools for Chikungunya Virus Infection that were Developed among Younger Population Work Equally as Well in Patients Aged over 65 Years?
Continuous attractor networks are used to model the storage and representation of analog quantities , such as position of a visual stimulus . The storage of multiple continuous attractors in the same network has previously been studied in the context of self-position coding . Several uncorrelated maps of environments a...	How is your position in an environment represented in the brain , and how does the representation distinguish between multiple environments ? One of the proposed answers relies on continuous attractor neural networks . Consider the web page of your campus map as a network of pixels . Every pixel is a neuron , and nearb...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience" ]	2010	Continuous Attractors with Morphed/Correlated Maps
The accuracy of protein structures , particularly their binding sites , is essential for the success of modeling protein complexes . Computationally inexpensive methodology is required for genome-wide modeling of such structures . For systematic evaluation of potential accuracy in high-throughput modeling of binding si...	Protein-protein interactions play a central role in life processes at the molecular level . The structural information on these interactions is essential for our understanding of these processes and our ability to design drugs to cure diseases . Limitations of experimental techniques to determine the structure of prote...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biophysics/macromolecular", "assemblies", "and", "machines", "biophysics/structural", "genomics", "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/genomics" ]	2010	Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling
Perceptual decision-making relies on the gradual accumulation of noisy sensory evidence . It is often assumed that such decisions are degraded by adding noise to a stimulus , or to the neural systems involved in the decision making process itself . But it has been suggested that adding an optimal amount of noise can , ...	Noise is usually thought of as being detrimental for perception and decision-making , but recent work has revealed that under certain circumstances simple detection performance can be enhanced when an optimal amount of noise is applied to the visual cortex non-invasively using tRNS . Here we asked whether this stochast...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "brain", "social", "sciences", "cerebral", "hemispheres", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "left", "hemisphere", "cognitive", "psychology", "functional", "electrical", ...	2018	Stochastic resonance enhances the rate of evidence accumulation during combined brain stimulation and perceptual decision-making
Taenia solium , a zoonotic infection transmitted between humans and pigs , is considered an emerging infection in Sub-Saharan Africa , yet individual and community-level factors associated with the human infection with the larval stages ( cysticercosis ) are not well understood . This study aims to estimate the magnitu...	Taenia solium is an infection that is transmitted between pigs and humans . Humans may get infected with the larvae of Taenia solium , which results in cysticercosis , an infection common in pig farming communities where there is poor sanitation and free roaming pigs . Most published studies on this infection have incl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Prevalence of and Factors Associated with Human Cysticercosis in 60 Villages in Three Provinces of Burkina Faso
Whipworms and blood flukes combined infect almost one billion people in developing countries . Only a handful of anthelmintic drugs are currently available to treat these infections effectively; there is therefore an urgent need for new generations of anthelmintic compounds . Medicinal plants have presented as a viable...	Schistosomiasis and trichuriasis affects millions of people worldwide and are caused by blood flukes and whipworms , respectively . Only a handful of anthelmintic drugs exist to treat these infections and the pipeline for the next generation of anthelmintic drugs is sparse , precipitating the need for new drug developm...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "parasitic", "diseases", "animals", "nematode", "infections", "animal", "models", "model", "organisms", "pharmaceutics", "medicinal", "p...	2016	Compounds Derived from the Bhutanese Daisy, Ajania nubigena, Demonstrate Dual Anthelmintic Activity against Schistosoma mansoni and Trichuris muris
Livestock populations can be used to study recessive defects caused by deleterious alleles . The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population , especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozyg...	We report a large deletion within the BBS9 gene that induces late fetal mortality in homozygous affected animals in a commercial pig population . This late fetal mortality causes the fetus to become encapsulated and desiccated during the remaining time of the pregnancy , a process called mummification . The unusually h...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "body", "weight", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "vertebrates", "alleles", "animals", "genetic", "mapping", "mammals", "telecommunications", "physiological", "parameters", "birth", "weight", "swine", "gene", "expression", "g...	2018	Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome
To date , the genome-wide association study ( GWAS ) is the primary tool to identify genetic variants that cause phenotypic variation . As GWAS analyses are generally univariate in nature , multivariate phenotypic information is usually reduced to a single composite score . This practice often results in loss of statis...	The genome-wide association study ( GWAS ) is the primary tool to identify genetic variants that cause phenotypic variation . As GWAS methods are generally univariate in nature , multivariate phenotypic information is usually reduced to a single composite score , which frequently results in a considerable loss of stati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "social", "and", "behavioral", "sciences", "quantitative", "traits", "biology", "psychometrics", "psychology", "trait", "locus", "phenotypes", "heredity", "genetic", "association", "studies", "genetics", "human", "genetics", "genet...	2013	TATES: Efficient Multivariate Genotype-Phenotype Analysis for Genome-Wide Association Studies
The pancreaticobiliary ductal system connects the liver and pancreas to the intestine . It is composed of the hepatopancreatic ductal ( HPD ) system as well as the intrahepatic biliary ducts and the intrapancreatic ducts . Despite its physiological importance , the development of the pancreaticobiliary ductal system re...	The liver and pancreas function as exocrine glands that secrete bile and pancreatic juice , respectively , to aid the digestion and absorption of nutrients . These fluids reach the intestine via the pancreaticobiliary ductal system , a complex network of ducts . Despite its pivotal role , the development of this ductal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "zebrafish", "model", "organisms", "genetics", "biology", "morphogenesis", "genetics", "and", "genomics", "gene", "function" ]	2012	sox9b Is a Key Regulator of Pancreaticobiliary Ductal System Development
Mitigation of a severe influenza pandemic can be achieved using a range of interventions to reduce transmission . Interventions can reduce the impact of an outbreak and buy time until vaccines are developed , but they may have high social and economic costs . The non-linear effect on the epidemic dynamics means that su...	In the event of an influenza pandemic which has high mortality and the potential to spread rapidly , such as the 1918–19 pandemic , there are a number of non-pharmaceutical public health control options available to reduce transmission in the community and mitigate the effects of the pandemic . These include reducing s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2011	Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives
Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens , the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered . Experimental infection of jasmonate-deficient and jasmonate-insensitive ...	While many important elements of plant defense signaling have been identified , the function of these defense signaling pathways may mask additional variation in the plant–pathogen interaction , including both pathogen variation and variation in downstream plant defense responses . Jasmonate plant hormones contribute t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "genetics", "and", "genomics/genetics", "of", "disease", "plant", "biology/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression" ]	2010	Deficiencies in Jasmonate-Mediated Plant Defense Reveal Quantitative Variation in Botrytis cinerea Pathogenesis
The essential biological properties of proteins—folding , biochemical activities , and the capacity to adapt—arise from the global pattern of interactions between amino acid residues . The statistical coupling analysis ( SCA ) is an approach to defining this pattern that involves the study of amino acid coevolution in ...	Proteins display the ability to fold , to carry out complex biochemical reactions , and to be adaptive to changing conditions of selection—the essential characteristics contributing to organismal fitness . A major goal is to understand how these properties emerge from the global pattern of interactions between amino ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "split-decomposition", "method", "multiple", "alignment", "calculation", "mathematics", "coevolution", "protein", "sequencing", "algebra", "protein", "structure", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "am...	2016	Evolution-Based Functional Decomposition of Proteins
We show that two host-encoded primary RNAs ( pri-miRs ) and the corresponding microRNA ( miR ) clusters – widely reported to have cell transformation-associated activity – are regulated by EBNA3A and EBNA3C . Utilising a variety of EBV-transformed lymphoblastoid cell lines ( LCLs ) carrying knockout- , revertant- or co...	A relatively unbiased screen of human microRNAs ( miRs ) revealed that in EBV-transformed B cells , a miR cluster , miR-221/miR-222 , that is frequently up-regulated in cancer , is induced by the latent EBV only if the viral nuclear proteins EBNA3A and EBNA3C are both expressed . The same two EBV proteins silence a tum...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Epstein-Barr Virus Proteins EBNA3A and EBNA3C Together Induce Expression of the Oncogenic MicroRNA Cluster miR-221/miR-222 and Ablate Expression of Its Target p57KIP2
It has been proposed that rotavirus infection promotes the progression of genetically-predisposed children to type 1 diabetes , a chronic autoimmune disease marked by infiltration of activated lymphocytes into pancreatic islets . Non-obese diabetic ( NOD ) mice provide a model for the human disease . Infection of adult...	Understanding how viruses contribute to type 1 diabetes development is vital for disease prevention . Infection of children at-risk of diabetes with the gastrointestinal pathogen rotavirus is associated with increased immune responses to pancreatic islets , leading to the proposal that rotavirus infection may accelerat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "cytokines", "b", "cells", "clinical", "immunology", "immunity", "innate", "immunity", "autoimmune", "diseases", "antigen-presenting", "cells", "diabetes", "mellitus", "type", "1", "t", "cells", "viral", "diseas...	2014	Rotavirus Activates Lymphocytes from Non-Obese Diabetic Mice by Triggering Toll-Like Receptor 7 Signaling and Interferon Production in Plasmacytoid Dendritic Cells
Most cellular processes depend on intracellular locations and random collisions of individual protein molecules . To model these processes , we developed algorithms to simulate the diffusion , membrane interactions , and reactions of individual molecules , and implemented these in the Smoldyn program . Compared to the ...	We developed a general-purpose biochemical simulation program , called Smoldyn . It represents proteins and other molecules of interest with point-like particles that diffuse , interact with surfaces , and react , all in continuous space . This high level of detail allows users to investigate spatial organization withi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/synthetic", "biology", "cell", "biology/cell", "signaling", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "biochemistry/theory", "and", "simulation", "computational", "biology/systems", "biology" ]	2010	Detailed Simulations of Cell Biology with Smoldyn 2.1
Spike timing-dependent plasticity ( STDP ) modifies synaptic strengths based on timing information available locally at each synapse . Despite this , it induces global structures within a recurrently connected network . We study such structures both through simulations and by analyzing the effects of STDP on pair-wise ...	The connectivity structure in neural networks reflects , at least in part , the long-term effects of synaptic plasticity mechanisms that underlie learning and memory . In one of the most widespread such mechanisms , spike-timing dependent plasticity ( STDP ) , the temporal order of pre- and postsynaptic spiking across ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "computational", "neuroscience", "biology", "neuroscience" ]	2013	Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity
The inositol trisphosphate receptor ( ) is one of the most important cellular components responsible for oscillations in the cytoplasmic calcium concentration . Over the past decade , two major questions about the have arisen . Firstly , how best should the be modeled ? In other words , what fundamental properties of t...	The inositol trisphosphate receptor ( ) is one of the most important cellular components responsible for calcium oscillations . Over the past decade , two major questions about the have arisen . Firstly , what fundamental properties of the allow it to perform its function ? Secondly , although calcium oscillations are ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells
The ribosomal RNA genes ( rDNA ) comprise a highly repetitive gene cluster . The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome . DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase , which triggers unequ...	Ribosomal RNA genes ( rDNA ) comprise an unstable region of the genome due to their highly repetitive structure and elevated levels of transcription . Collision between transcription and replication machineries of rDNA , which may lead to DNA damage in the form of a double-stranded break , is avoided by the replication...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "damage", "fungi", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "dna", "recombination", "dna", "cell", "nucleus", "cellular", "structures", "and", "organell...	2019	Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
Plant nucleotide-binding leucine-rich repeat ( NB-LRR ) disease resistance ( R ) proteins recognize specific “avirulent” pathogen effectors and activate immune responses . NB-LRR proteins structurally and functionally resemble mammalian Nod-like receptors ( NLRs ) . How NB-LRR and NLR proteins activate defense is poorl...	How plant NB-LRR resistance proteins and the related mammalian Nod-like receptors ( NLRs ) activate defense is poorly understood . Plant and animal immune receptors can function in pairs . Two Arabidopsis nuclear immune receptors , RPS4 and RRS1 , confer recognition of the unrelated bacterial effectors , AvrRps4 and Po...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutation", "plant", "science", "genetic", "screens", "gene", "identification", "and", "analysis", "gene", "expression", "genetics", "plant", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "gene", "function" ]	2014	The Nuclear Immune Receptor RPS4 Is Required for RRS1SLH1-Dependent Constitutive Defense Activation in Arabidopsis thaliana
Little is currently known about dynamic brain networks involved in high-level cognition and their ontological basis . Here we develop a novel Variational Bayesian Hidden Markov Model ( VB-HMM ) to investigate dynamic temporal properties of interactions between salience ( SN ) , default mode ( DMN ) , and central execut...	Characterizing the temporal dynamics of functional interactions between distributed brain regions is of fundamental importance for understanding human brain organization and its development . Progress in the field has been hampered both by a lack of strong computational techniques to investigate brain dynamics and an i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "markov", "models", "neural", "networks", "applied", "mathematics", "random", "variables", "neuroscience", "covariance", "magnetic", "resonanc...	2016	Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling
Hypersensitive response programmed cell death ( HR-PCD ) is a critical feature in plant immunity required for pathogen restriction and prevention of disease development . The precise control of this process is paramount to cell survival and an effective immune response . The discovery of new components that function to...	Control over PCD in plants , like in animals , is central to determining susceptibility or resistance to disease . Yet there is a real paucity in understanding of the biochemical processes that are crucial in determining how PCD is co-ordinated during plant immune responses . Here we demonstrate that a BTB domain prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "plant", "anatomy", "enzymes", "cell", "processes", "enzymology", "microbiology", "plant", "science", "plants", "flowering", "plants", "ligases", "bacteria", "agrobacteria", "physical", "chemistry", "chemical", "properties", "nicotiana", "dimerization", ...	2017	BTB-BACK Domain Protein POB1 Suppresses Immune Cell Death by Targeting Ubiquitin E3 ligase PUB17 for Degradation
The mainstay of toxoplasmosis treatment targets the folate biosynthetic pathways and has not changed for the last 50 years . The activity of these chemotherapeutic agents is restricted to one lifecycle stage of Toxoplasma gondii , they have significant toxicity , and the impending threat of emerging resistance to these...	Toxoplasma gondii is a protozoan parasite that infects at least two thirds of the world human population . Once it infects the human host , it has great predilection for the brain and the retina of the eye . It remains latent until the host's immune system weakens , and then causes organ tissue damage . There are very ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases" ]	2014	Auranofin Is Highly Efficacious against Toxoplasma gondii In Vitro and in an In Vivo Experimental Model of Acute Toxoplasmosis
Clostridium difficile is a Gram-positive spore-former bacterium and the leading cause of nosocomial antibiotic-associated diarrhea that can culminate in fatal colitis . During the infection , C . difficile produces metabolically dormant spores , which persist in the host and can cause recurrence of the infection . The ...	We discovered a mechanism of assembly of the outer most layer of Clostridium difficile spores , the exosporium . While CdeC is conserved in several Peptostreptococcaeace family members , CdeM is unique to C . difficile . We show that two proteins that are rich in cysteine amino acid residues , CdeC and CdeM , are essen...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "bacteriology", "peptostreptococcus", "medicine", "and", "health", "sciences", "gut", "bacteria", "chemical", "compounds", "animal", "models", "of", "disease", "microbiology", "organic", "compounds", "animal", "models", "model", "organisms", "experimental", "organism", ...	2018	Clostridium difficile exosporium cysteine-rich proteins are essential for the morphogenesis of the exosporium layer, spore resistance, and affect C. difficile pathogenesis
Living tissues undergo deformation during morphogenesis . In this process , cells generate mechanical forces that drive the coordinated cell motion and shape changes . Recent advances in experimental and theoretical techniques have enabled in situ measurement of the mechanical forces , but the characterization of mecha...	In order to shape the body of a multicellular organism , cells generate mechanical forces and undergo deformation . Although these forces are being increasingly determined , quantitative characterization of the relation between the deformation and forces at the tissue level remains challenging . To estimate these prope...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "tissue", "mechanics", "fluorescence", "imaging", "mechanical", "properties", "classical", "mechanics", "cell", "cycle", "and", "cell", "division", "cell", "processes", "biomechanics", "developmental", "biology", "molecular", "motors", "actin", "motors", "materials", "s...	2018	Inverse tissue mechanics of cell monolayer expansion
Pulmonary Francisella tularensis and Burkholderia pseudomallei infections are highly lethal in untreated patients , and current antibiotic regimens are not always effective . Activating the innate immune system provides an alternative means of treating infection and can also complement antibiotic therapies . Several na...	Activation of the innate immune system offers an alternative and effective means to counter infection , particularly , in cases when the etiologic agent is unknown , such as a potential bioterrorism attack or when the agent is resistant to antibiotics . Here we report that a natural polysaccharide extract derived from ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "microbiology" ]	2012	Nasal Acai Polysaccharides Potentiate Innate Immunity to Protect against Pulmonary Francisella tularensis and Burkholderia pseudomallei Infections
Plasmodium vivax , one of the five species of Plasmodium parasites that cause human malaria , is responsible for 25–40% of malaria cases worldwide . Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this p...	Plasmodium vivax malaria is a major global public health problem , with nearly 2 . 5 billion people at risk for infection and approximately 132–391 million clinical infections annually . It has a wide geographical range , with a high disease burden in Asia , Central and South America , the Middle East , Oceania , and E...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections
A fundamental , but unanswered question in host-pathogen interactions is the timing , localization and population distribution of virulence gene expression during infection . Here , microarray and in situ single cell expression methods were used to study Vibrio cholerae growth and virulence gene expression during infec...	Most pathogenic microorganisms infect in a stepwise manner: colonization of host surfaces is followed by invasion and injury of host tissues and , late in the infectious process , dissemination to other hosts occurs . During its residence in the host , the pathogen produces essential virulence determinants and often re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics/gene", "expression", "microbiology/microbial", "physiology", "and", "metabolism", "infectious", "diseases/bacterial", "infections", "genetics", "and", "genomics/epigenetics", "microbiology/microbial", "growth", "and", "deve...	2010	A Bistable Switch and Anatomical Site Control Vibrio cholerae Virulence Gene Expression in the Intestine
The West Nile virus ( WNV ) , isolated in 1937 , is an arbovirus ( arthropod-borne virus ) that infects thousands of people each year . Despite its burden on global health , little is known about the virus’ biological and evolutionary dynamics . As several lineages are endemic in West Africa , we obtained the complete ...	The West Nile virus ( WNV ) can cause severe neurological diseases including meningitis , encephalitis , and acute flaccid paralysis . Differences in WNV genetics could play a role in the frequency of neurological symptoms from an infection . For the first time , we observed how geographically similar but genetically d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "invertebrates", "vero", "cells", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "biological", "cultures", "microbiology", "vertebrates", "animals", "viruses", "phylogenetics", "data", "management", "rna", ...	2017	Biological and phylogenetic characteristics of West African lineages of West Nile virus
Opisthorchis viverrini is considered among the most important of the food-borne trematodes due to its strong association with advanced periductal fibrosis and bile duct cancer ( cholangiocarcinoma ) . We investigated the relationship between plasma levels of Interleukin ( IL ) -6 and the risk of developing advanced fib...	O . viverrini is among the few parasites considered a Class 1 carcinogen because of its strong association with bile duct cancer ( cholangiocarcinoma ) . Currently , more than 40 million people are infected with O . viverrini worldwide . Thailand has the highest prevalence of O . viverrini at 10 million people infected...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "diagnostic", "medicine", "clinical", "immunology", "clinical", "research", "design", "epidemiology", "immunology", "biology", "public", "health" ]	2012	Elevated Plasma IL-6 Associates with Increased Risk of Advanced Fibrosis and Cholangiocarcinoma in Individuals Infected by Opisthorchis viverrini
Dialysis patients with chronic renal failure receiving deferoxamine for treating iron overload are uniquely predisposed for mucormycosis , which is most often caused by Rhizopus oryzae . Although the deferoxamine siderophore is not secreted by Mucorales , previous studies established that Rhizopus species utilize iron ...	Deferoxamine is an iron-chelating agent often used to treat patients with acute iron poisoning , such as seen in dialysis patients with chronic renal failure . These patients are uniquely predisposed to a deadly fungal infection , called mucormycosis , because deferoxamine supplies iron that supports growth of fungi ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Fob1 and Fob2 Proteins Are Virulence Determinants of Rhizopus oryzae via Facilitating Iron Uptake from Ferrioxamine
Development is often strongly regulated by interactions among close relatives , but the underlying molecular mechanisms are largely unknown . In eusocial insects , interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes . Here , we begin to characterize the so...	Social interactions are fundamental to all forms of life , from single-celled bacteria to complex plants and animals . Despite their obvious importance , little is known about the molecular causes and consequences of social interactions . In this paper , we study the molecular basis of nurse-larva social interactions t...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Methods" ]	[ "medicine", "and", "health", "sciences", "abdomen", "medical", "personnel", "gene", "regulation", "health", "care", "developmental", "biology", "health", "care", "providers", "genome", "analysis", "genomics", "gene", "expression", "life", "cycles", "evolutionary", "ge...	2019	Transcriptomic basis and evolution of the ant nurse-larval social interactome
Gene duplications are believed to facilitate evolutionary innovation . However , the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct . Here , we study a large family of fungal glucosidase genes that unde...	Darwin's theory of evolution is one of gradual change , yet evolution sometimes takes remarkable leaps . Such evolutionary innovations are often linked to gene duplication through one of three basic scenarios: an extra copy can increase protein levels , different ancestral subfunctions can be split over the copies and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "evolutionary", "biology", "enzymes", "biology", "evolutionary", "processes" ]	2012	Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
Point mutations in TBX1 can recapitulate many of the structural defects of 22q11 deletion syndromes ( 22q11DS ) , usually associated with a chromosomal deletion at 22q1 . 2 . 22q11DS often includes specific cardiac and pharyngeal organ anomalies , but the presence of characteristic craniofacial defects is highly variab...	A range of structural malformations is associated with 22q11 deletion syndrome ( 22q11DS ) , which is usually associated with microdeletions at chromosome 22q11 . 2 . Variable defects in cardiovascular , pharyngeal , and craniofacial structures occur , but the basis for such variability is unknown . Mutations in TBX1 ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "developmental", "biology/organogenesis", "genetics", "and", "genomics/gene", "function", "developmental", "biology/developmental", "molecular", "mechanisms" ]	2009	Chordin Is a Modifier of Tbx1 for the Craniofacial Malformations of 22q11 Deletion Syndrome Phenotypes in Mouse
RNA-DEPENDENT RNA POLYMERASE 6 ( RDR6 ) is a key RNA silencing factor initially characterized in transgene silencing and virus resistance . This enzyme also contributes to the biosynthesis of endogenous short interfering RNAs ( siRNAs ) from non-coding RNAs , transposable elements and protein-coding transcripts . One c...	Virus resistance relies in some plant-viral interactions on the RNA-DEPENDANT RNA POLYMERASE 6 ( RDR6 ) , a major actor of RNA silencing that acts at the post-transcriptional level . Here , we demonstrate that RDR6 also plays a role in basal defense and race-specific resistance . RDR6 and the microRNA miR472 , which ta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "genomics", "immunology", "microbiology", "biology" ]	2014	The Arabidopsis miR472-RDR6 Silencing Pathway Modulates PAMP- and Effector-Triggered Immunity through the Post-transcriptional Control of Disease Resistance Genes
Protozoan parasites infect and kill millions of people worldwide every year , particularly in developing countries where access to clean fresh water is limited . Among the most common are intestinal parasites , including Giardia lamblia and Entamoeba histolytica . These parasites wreak havoc on the epithelium lining th...	Entamoeba histolytica , Giardia lamblia , and Naegleria fowleri pathogens are widespread throughout the world infecting and killing hundreds of thousands of people every year . They are also listed as category B bioterrorism agents by the NIH and the CDC . However , there is a serious unmet need to develop more effecti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "trophozoites", "parasite", "groups", "medicine", "and", "health", "sciences", "giardia", "enzymes", "enzymology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "cysteine", "proteases", "naegleria", "fowleri", "giardia", ...	2017	Larrea tridentata: A novel source for anti-parasitic agents active against Entamoeba histolytica, Giardia lamblia and Naegleria fowleri
Clonorchiasis , one of the most important food-borne trematodiases , affects more than 12 million people in the People’s Republic of China ( P . R . China ) . Spatially explicit risk estimates of Clonorchis sinensis infection are needed in order to target control interventions . Georeferenced survey data pertaining to ...	Clonorchiasis is an important food-borne trematodiases and it has been estimated that more than 12 million people in China are affected . Precise information on where the disease occurs can help to identify priority areas for where control interventions should be implemented . We collected data from recent surveys on c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "china", "tropical", "diseases", "geographical", "locations", "vertebrates", "parasitic", "diseases", "animals", "simulation", "and", "modeling", "trematodes", "freshwater", "fish", "clonorchis", "sine...	2017	Risk mapping of clonorchiasis in the People’s Republic of China: A systematic review and Bayesian geostatistical analysis
The adhesion of Plasmodium falciparum-infected erythrocytes ( IRBC ) to receptors on different host cells plays a divergent yet critical role in determining the progression and outcome of the infection . Based on our ex vivo studies with clinical parasite isolates from adult Thai patients , we have previously proposed ...	Of the several species of malaria parasites that infect humans , disease caused by Plasmodium falciparum is responsible for most of the deaths . The unique pathological finding of this infection is the intense adhesion of infected red blood cells ( IRBC ) in the microcirculation , resulting in obstruction to blood flow...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	CD36 Recruits α5β1 Integrin to Promote Cytoadherence of P. falciparum-Infected Erythrocytes
Genome-wide association studies ( GWAS ) have transformed our understanding of the genetics of complex traits such as autoimmune diseases , but how risk variants contribute to pathogenesis remains largely unknown . Identifying genetic variants that affect gene expression ( expression quantitative trait loci , or eQTLs ...	The human immune system has evolved to protect us from infection and cancer , whilst avoiding damage to healthy tissue . If this complex system goes wrong , immune cells may cause inappropriate inflammation and damage , resulting in clinical disease . Examples include inflammatory bowel disease and autoimmune vasculiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "gastroenterology", "and", "hepatology", "genome", "analysis", "inflammatory", "bowel", "disease", "cytotoxic", ...	2016	Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease
The recent development of whole genome association studies has lead to the robust identification of several loci involved in different common human diseases . Interestingly , some of the strongest signals of association observed in these studies arise from non-coding regions located in very large introns or far away fr...	We describe a new methodology to identify individual differences in the expression of the two copies of one gene . This is achieved by comparing the mRNA level of the two alleles using a heterozygous polymorphism in the transcript as marker . We show that this approach allows an exhaustive survey of cis-acting regulati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/epigenetics", "genetics", "and", ...	2008	Differential Allelic Expression in the Human Genome: A Robust Approach To Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression
Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids . In selenoprotein transcripts , the UGA codon may either represent a translation termination signal or a selenocysteine ( Sec ) codon . Translating UGA to Sec requires selenium and specialize...	The “code book” of protein translation maps 43 = 64 triplets of RNA sequences ( codons ) into 20 canonical amino acids and the stop signal . This code book is universal in almost all organisms on earth . Selenoproteins consist of selenium-containing amino acids–selenocysteines ( Sec ) –that are not among the 20 canonic...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "methods" ]	[ "transfer", "rna", "applied", "mathematics", "messenger", "rna", "protein", "abundance", "simulation", "and", "modeling", "algorithms", "protein", "synthesis", "mathematics", "chemical", "synthesis", "research", "and", "analysis", "methods", "selenium", "proteins", "gen...	2017	A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons
Antibody effector functions , such as antibody-dependent cellular cytotoxicity , complement deposition , and antibody-dependent phagocytosis , play a critical role in immunity against multiple pathogens , particularly in the absence of neutralizing activity . Two modifications to the IgG constant domain ( Fc domain ) r...	Accumulating evidence points to a critical role for non-neutralizing antibody functions in protective immunity against a variety of pathogens , including HIV . Non-neutralizing antibody function is controlled by antibody constant domain interactions with Fc receptors , which itself is regulated via changes in antibody ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "vaccines", "preventive", "medicine", "...	2016	Antigen-Specific Antibody Glycosylation Is Regulated via Vaccination
In the northwest of Ethiopia , at the South Gondar region , there was a visceral leishmaniasis ( VL ) outbreak in 2005 , making the disease a public health concern for the regional health authorities ever since . The knowledge on how the population perceives the disease is essential in order to propose successful contr...	Visceral leishmaniasis ( VL ) is a vector borne disease that can be fatal if left untreated . In northern Ethiopia there was a VL outbreak in 2005 , making the disease a public health challenge ever since . In order to promote the participation of communities in the control of the disease , it is essential to know how ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "behavioral", "and", "social", "aspects", "of", "health", "tropical", "diseases", "social", "sciences", "anthropology", "health", "care", "preventive", "medicine", "global", "health", "neglected", "tropical", "diseases", "infec...	2014	Knowledge, Attitudes and Practices Related to Visceral Leishmaniasis in Rural Communities of Amhara State: A Longitudinal Study in Northwest Ethiopia
The phylum Nematoda is biologically diverse , including parasites of plants and animals as well as free-living taxa . Underpinning this diversity will be commensurate diversity in expressed genes , including gene sets associated specifically with evolution of parasitism . Here we have analyzed the extensive expressed s...	The high-throughput sequencing of messenger RNA from parasitic organisms has permitted large-scale sequence analyses typically reserved for complete genome studies . Such expressed sequence tags ( ESTs ) have previously been generated for 37 species from the phylum Nematoda , of which 35 were from parasitic species . T...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "genetics", "and", "genomics/gene", "discovery", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "infectious", "diseases/helminth", "infections", "evolutionary", "biology/bioinformatics", "computational", "biology/genomics", "genetics", "and", "genomics/...	2008	On the Extent and Origins of Genic Novelty in the Phylum Nematoda
Serological assays for human IgG4 to the Onchocerca volvulus antigen Ov16 have been used to confirm elimination of onchocerciasis in much of the Americas and parts of Africa . A standardized source of positive control antibody ( human anti-Ov16 IgG4 ) will ensure the quality of surveillance data using these tests . A r...	Serological markers such as antibody responses to pathogen-specific antigens are used to inform disease epidemiology in many elimination programs . A major challenge with program-scale serological testing , and with any diagnostic test validation , is access to consistent and unlimited control reagents with which to pr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	A Recombinant Positive Control for Serology Diagnostic Tests Supporting Elimination of Onchocerca volvulus
In order to respond reliably to specific features of their environment , sensory neurons need to integrate multiple incoming noisy signals . Crucially , they also need to compete for the interpretation of those signals with other neurons representing similar features . The form that this competition should take depends...	Perception involves using incoming sensory signals to infer which objects or features are present in the surroundings . To do this , sensory systems must perform two basic operations: ( i ) combination of noisy sensory cues , and ( ii ) competition between different percepts . Here we show that the optimal form of comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "neural", "networks", "social", "sciences", "neuroscience", "signal", "inhibition", "computational", "neuroscience", "neuronal", "tuning", "coding", "mechanisms", "computer", "and", "information", "sciences", "animal", "cells", "sensory", "receptors", "signal", "transduct...	2017	Sensory noise predicts divisive reshaping of receptive fields
Recent single molecule experiments , using either atomic force microscopy ( AFM ) or Förster resonance energy transfer ( FRET ) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures . Topology-based simulation models have been used successfully to generate models for these ...	Multidomain proteins with tandem repeats are abundant in eukaryotic proteins . Recent studies have shown that such domains may have a propensity for forming domain-swapped misfolded species which are stable for long periods , and therefore a potential hazard in the cell . However , for some types of tandem domains , no...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results" ]	[ "simulation", "and", "modeling", "fluorophotometry", "protein", "structure", "thermodynamics", "research", "and", "analysis", "methods", "fluorescence", "resonance", "energy", "transfer", "proteins", "structural", "proteins", "repeated", "sequences", "molecular", "biology",...	2016	Structural Determinants of Misfolding in Multidomain Proteins
Communication between neuronal and glial cells is important for many brain functions . Astrocytes can modulate synaptic strength via Ca2+-stimulated release of various gliotransmitters , including glutamate and ATP . A physiological role of ATP release from astrocytes was suggested by its contribution to glial Ca2+-wav...	Brain function depends on the interaction between two major types of cells: neurons transmitting electrical signals and glial cells , which control cerebral circulation and neuronal homeostasis . There is a growing evidence of the participation of astrocytes in regulating neuronal excitability and synaptic plasticity v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "molecular", "neuroscience", "neurochemistry", "anatomy", "and", "physiology", "electrophysiology", "neuroscience", "homeostatic", "mechanisms", "synaptic", "plasticity", "ion", "channels", "neurotransmitters", "signaling", "pathways", "neurological", "s...	2014	Exocytosis of ATP From Astrocytes Modulates Phasic and Tonic Inhibition in the Neocortex
Transcriptional activation domains ( ADs ) are generally thought to be intrinsically unstructured , but capable of adopting limited secondary structure upon interaction with a coactivator surface . The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such co...	The regulated transcription of eukaryotic genes is governed by gene-specific transcription factors that contain activation domains to stimulate the expression of nearby genes . Activation domains are unable to take up a defined three-dimensional conformation . Nevertheless , as we demonstrate in our study , molecular d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "molecular", "dynamics", "dna", "transcription", "simulation", "and", "modeling", "protein", "sequencing", "sequence", "motif", "analysis", "transactivation", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequ...	2016	Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions
Alcelaphine herpesvirus 1 ( AlHV-1 ) is a γ-herpesvirus ( γ-HV ) belonging to the macavirus genus that persistently infects its natural host , the wildebeest , without inducing any clinical sign . However , cross-transmission to other ruminant species causes a deadly lymphoproliferative disease named malignant catarrha...	The macavirus alcelaphine herpesvirus 1 ( AlHV-1 ) is a γ-herpesvirus ( γ-HV ) that has been first isolated in East-Africa in 1960 from a wildebeest and identified to be the etiological agent of malignant catarrhal fever ( MCF ) in bovine . An interesting aspect of AlHV-1 is that it can persist in wildebeest by remaini...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "transfection", "flow", "cytometry", "innate", "immune", "system", "antigen", "presentation", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "microbiology", "plasmid", "construction", "protein", "synthesis", "dna", "construct...	2017	Macavirus latency-associated protein evades immune detection through regulation of protein synthesis in cis depending upon its glycin/glutamate-rich domain
Apoptosis is an evolutionary conserved cell death mechanism , which requires activation of initiator and effector caspases . The Drosophila initiator caspase Dronc , the ortholog of mammalian Caspase-2 and Caspase-9 , has an N-terminal CARD domain that recruits Dronc into the apoptosome for activation . In addition to ...	Apoptosis is a programmed cell death mechanism which is conserved from flies to humans . Apoptosis is mediated by proteases , termed caspases that cleave cellular proteins and trigger the death of the cell . Activation of caspases is regulated at various levels such as protein-protein interaction for initiator caspases...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "molecular", "probe", "techniques", "cell", "processes", "immunoblotting", "cloning", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", ...	2017	An inhibitory mono-ubiquitylation of the Drosophila initiator caspase Dronc functions in both apoptotic and non-apoptotic pathways
Homolog pairing and crossing over during meiosis I prophase is required for accurate chromosome segregation to form euploid gametes . The repair of Spo11-induced double-strand breaks ( DSB ) using a homologous chromosome template is a major driver of pairing in many species , including fungi , plants , and mammals . In...	Meiosis is the key stage of gametogenesis , when the diploid genome complement is reduced by one half to form haploid gametes for sexual reproduction . Accurate chromosome segregation requires that homologous chromosomes pair , recombine by crossing over , and segregate from one another during the first meiotic divisio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	Multiple Opposing Constraints Govern Chromosome Interactions during Meiosis
Mammalian oocytes are arrested at prophase of the first meiotic division in the primordial follicle pool for months , even years , after birth depending on species , and only a limited number of oocytes resume meiosis , complete maturation , and ovulate with each reproductive cycle . We recently reported that protein p...	Formation of haploid gametes from diploid germ cells requires a specialized reductive cell division known as meiosis . In contrast to male meiosis that takes place continuously , a unique feature of female meiosis in mammals is the long arrest in meiosis I , which lasts up to 50 years in humans . Because the size of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "phosphatases", "germ", "cells", "animal", "models", "dna", "damage", "oocytes", "model", "organis...	2016	Protein Phosphatase 6 Protects Prophase I-Arrested Oocytes by Safeguarding Genomic Integrity
Defining the molecular structure and function of synapses is a central theme in brain research . In Drosophila the Bruchpilot ( BRP ) protein is associated with T-shaped ribbons ( “T-bars” ) at presynaptic active zones ( AZs ) . BRP is required for intact AZ structure and normal evoked neurotransmitter release . By scr...	Neurons communicate through release of neurotransmitters at specialized contacts called synapses . Modulation of synaptic transmission likely underlies all higher brain function including feature abstraction , learning and memory , and cognition . The complex molecular machinery that regulates neurotransmitter release ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/disease", "models", "physiology/cell", "signaling", "genetics", "and", "genomics/gene", "function", "neuroscience/neuronal", "signaling", "mechanisms", "physiology/membranes", "and", "sorting" ]	2009	Bruchpilot in Ribbon-Like Axonal Agglomerates, Behavioral Defects, and Early Death in SRPK79D Kinase Mutants of Drosophila
CDKs ( cyclin-dependent kinases ) associate with different cyclins to form different CDK-complexes that are fundamental for an ordered cell cycle progression , and the coordination of this progression with different aspects of the cellular physiology . During meiosis programmed DNA double-strand breaks ( DSBs ) initiat...	Meiotic division is a cell division process where a single round of DNA replication is followed by two sequential chromosome segregations , the first reductional ( homologous chromosomes separate ) and the second equational ( sister chromatids segregate ) . As a consequence diploid organisms halve ploidy , producing ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "fungi", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "molecular", "biology", "techniques", "mutagenesis", "and", "gene", "deletion", "techniques", "dna",...	2019	CDK contribution to DSB formation and recombination in fission yeast meiosis
In humans , meiotic chromosome segregation errors increase dramatically as women age , but the molecular defects responsible are largely unknown . Cohesion along the arms of meiotic sister chromatids provides an evolutionarily conserved mechanism to keep recombinant chromosomes associated until anaphase I . One attract...	In humans , chromosome segregation errors during meiosis are the leading cause of birth defects and miscarriages . Moreover , as women age , these errors increase dramatically . For accurate segregation during the first meiotic division , homologous chromosomes must remain physically associated until anaphase I . Norma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "developmental", "biology/aging", "genetics", "and", "genomics/chromosome", "biology" ]	2008	Aging Predisposes Oocytes to Meiotic Nondisjunction When the Cohesin Subunit SMC1 Is Reduced
Protein kinase B ( PKB/Akt ) belongs to the AGC superfamily of related serine/threonine protein kinases . It is a key regulator downstream of various growth factors and hormones and is involved in malignant transformation and chemo-resistance . Full-length PKB protein has not been crystallised , thus studying the molec...	A critical protein in cell-signalling pathways , called protein kinase B , regulates many aspects of cell biology from metabolism to proliferation and survival , by modifying other proteins with the addition of a phosphate group . Hence , deregulation of its activity has acute consequences on cell function . Increased ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "computational", "biology", "biophysics", "molecular", "biology" ]	2009	Role of a Novel PH-Kinase Domain Interface in PKB/Akt Regulation: Structural Mechanism for Allosteric Inhibition
Various ascomycete fungi possess sex-specific molecular mechanisms , such as repeat-induced point mutations , meiotic silencing by unpaired DNA , and unusual adenosine-to-inosine RNA editing , for genome defense or gene regulation . Using a combined analysis of functional genetics and deep sequencing of small noncoding...	Control of gene expression by small noncoding RNA ( sRNA ) has recently been highlighted as a significant post-transcriptional regulatory mechanism . To date , researchers have predominantly focused on the identification of microRNA-like RNAs ( milRNAs ) in fungi because microRNAs ( miRNAs ) are key regulators in anima...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "interference", "fungal", "genetics", "gene", "regulation", "developmental", "biology", "fungi", "genome", "analysis", "epigenetics", "morphogenesis", "small", "interfering", "rnas", "mycology", "genetic", "interference", "gene", "expression", "biochemistry", "rna"...	2017	Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum
Animal aging is characterized by progressive , degenerative changes in many organ systems . Because age-related degeneration is a major contributor to disability and death in humans , treatments that delay age-related degeneration are desirable . However , no drugs that delay normal human aging are currently available ...	Age-related degeneration is a fundamental feature of animal biology and an important contributor to human disability and death . However , no medicines have been shown to delay human aging . To identify drugs that delay age-related degeneration , we screened FDA-approved compounds and discovered that the hypertension d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "caenorhabditis", "oxidative", "stress", "microbiology", "animals", "drug", "screening", "animal", "models", "physiological", "processes", "developmental", "biology", "caenorhab...	2016	Angiotensin Converting Enzyme (ACE) Inhibitor Extends Caenorhabditis elegans Life Span
Insufficient licensing of DNA replication origins has been shown to result in genome instability , stem cell deficiency , and cancers . However , it is unclear whether the DNA damage resulting from deficient replication licensing occurs generally or if specific sites are preferentially affected . To map locations of on...	Many RBC micronuclei result from double strand DNA breaks that give rise to acentromeric chromosomal fragments that fail to incorporate into nuclei during mitosis and consequently remain in the cell following enucleation . Here , RBC micronuclear DNA is sequenced ( Mic-Seq ) to define the locations of breaks genome-wid...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Data", "Access" ]	[ "genetic", "networks", "micronuclei", "microbiology", "sequence", "tagged", "site", "analysis", "dna", "replication", "network", "analysis", "protein", "structure", "mammalian", "genomics", "dna", "research", "and", "analysis", "methods", "sequence", "analysis", "comput...	2017	A Signature of Genomic Instability Resulting from Deficient Replication Licensing
AIP56 ( apoptosis-inducing protein of 56 kDa ) is a major virulence factor of Photobacterium damselae piscicida ( Phdp ) , a Gram-negative pathogen that causes septicemic infections , which are among the most threatening diseases in mariculture . The toxin triggers apoptosis of host macrophages and neutrophils through ...	The apoptosis inducing protein of 56 kDa ( AIP56 ) is a key virulence factor secreted by Photobacterium damselae piscicida ( Phdp ) , a Gram-negative bacterium that causes septicaemic infections in economically important marine fish species . It is known that AIP56 induces massive destruction of the phagocytic cells of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2013	The Apoptogenic Toxin AIP56 Is a Metalloprotease A-B Toxin that Cleaves NF-κb P65
Fungal infection has become one of the leading causes of hospital-acquired infections with high mortality rates . Furthermore , drug resistance is common for fungus-causing diseases . Synergistic drug combinations could provide an effective strategy to overcome drug resistance . Meanwhile , synergistic drug combination...	Drug combinations represent a promising strategy for overcoming fungal drug resistance and treating complex diseases . There is an urgent need to establish powerful computational methods for systematic prediction of synergistic drug combination on a large scale . Based on the assumption that principal drugs which obtai...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "antifungals", "drug", "screening", "fungi", "model", "organisms", "pharmacology", "fungal", "pathogens", "research", "and", "a...	2016	NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning
Vibrio cholerae-specific bacteriophages are common features of the microbial community during cholera infection in humans . Phages impose strong selective pressure that favors the expansion of phage-resistant strains over their vulnerable counterparts . The mechanisms allowing virulent V . cholerae strains to defend ag...	Vibrio cholerae is the causative agent of the severe diarrheal disease cholera . V . cholerae is commonly recovered from patient samples with predatory bacteriophages ( phages ) , which impose strong selective pressure favoring phage resistant strains over their vulnerable counterparts . Here , we investigated the acti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "genome", "engineering", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "bacteriophages", "pathogens", "vibrio", "synthetic", "biology", "tropical", "diseases", "microbiology", "s...	2017	A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome
Schistosomiasis is a debilitating neglected tropical disease that infects over 200 million people worldwide . To combat this disease , in 2012 , the World Health Organization announced a goal of reducing and eliminating transmission of schistosomes . Current control focuses primarily on mass drug administration ( MDA )...	Schistosomiasis is a chronic and debilitating disease . Current control focuses primarily on mass drug administration ( MDA ) . We monitored schistosome transmission via fecal egg counts and genetic markers in a school based MDA setting to learn how the intervention was influencing transmission or the targeted schistos...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "biology", "and", "life", "sciences", "population", "biology", "genomics" ]	2014	No Apparent Reduction in Schistosome Burden or Genetic Diversity Following Four Years of School-Based Mass Drug Administration in Mwea, Central Kenya, a Heavy Transmission Area
The coordination of cell proliferation and cell fate determination is critical during development but the mechanisms through which this is accomplished are unclear . We present evidence that the Snail-related transcription factor CES-1 of Caenorhabditis elegans coordinates these processes in a specific cell lineage . C...	Animal development is a complex process and requires the coordination in space and time of various processes . These processes include the controlled production of cells , also referred to as ‘cell proliferation’ , and the adoption by cells of specific fates , also referred to as ‘cell fate determination’ . The observa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Coordination of Cell Proliferation and Cell Fate Determination by CES-1 Snail
We present a novel methodology to construct a Boolean dynamic model from time series metagenomic information and integrate this modeling with genome-scale metabolic network reconstructions to identify metabolic underpinnings for microbial interactions . We apply this in the context of a critical health issue: clindamyc...	The community of bacteria that live in our intestines ( called the “gut microbiome” ) is important to normal intestinal function , and destruction of this community has a causative role in diseases including obesity , diabetes , and even neurological disorders . Clostridum difficile is an opportunistic pathogenic bacte...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
Human African Trypanosomiasis is a devastating disease caused by the parasite Trypanosoma brucei . Trypanosomes live extracellularly in both the tsetse fly and the mammal . Trypanosome surface proteins can directly interact with the host environment , allowing parasites to effectively establish and maintain infections ...	Human African Trypanosomiasis ( HAT ) is a fatal disease caused by African trypanosomes and transmitted by an infected tsetse fly . Presently , there are no vaccines to prevent mammalian infections . Proteins expressed on the trypanosome surface can influence the host environment and allow for their transmission . Pote...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "biology", "microbiology", "molecular", "cell", "biology", "veterinary", "science" ]	2012	Transcript Expression Analysis of Putative Trypanosoma brucei GPI-Anchored Surface Proteins during Development in the Tsetse and Mammalian Hosts
Meiotic recombination plays a critical role in sexual reproduction by creating crossovers between homologous chromosomes . These crossovers , along with sister chromatid cohesion , connect homologs to enable proper segregation at Meiosis I . Recombination is initiated by programmed double strand breaks ( DSBs ) at part...	Sexual reproduction requires that cells deliberately introduce large numbers of double strand breaks into their chromosomes . Repair of these breaks creates physical connections between homologs that promote proper segregation during meiosis . It is critical that segregation not proceed until all the breaks have been f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "meiosis", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "regulatory", "proteins", "cell", "processes", "enzymes", "dna-binding", "proteins", "enzymology", "chromatids", "dna", "transcription", "phosphatases", "transcription", "facto...	2018	Mek1 coordinates meiotic progression with DNA break repair by directly phosphorylating and inhibiting the yeast pachytene exit regulator Ndt80
Because there is considerable variation in gene expression even between closely related species , it is clear that gene regulatory mechanisms evolve relatively rapidly . Because primary sequence conservation is an unreliable proxy for functional conservation of cis-regulatory elements , their assessment must be carried...	Given the importance of gene expression changes in evolution , a better understanding of how they accumulate is desirable . However , gene regulation is a complex biochemical process and it is not a priori clear whether general trends even exist . We systematically addressed this question by testing , in C . elegans , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "caenorhabditis", "gene", "regulation", "animals", "dna", "transcription", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "molecular", "genetics", "morphogenesis", "pattern", "formation", "research", "and"...	2014	Pervasive Divergence of Transcriptional Gene Regulation in Caenorhabditis Nematodes
Type III secretion system 1 ( T3SS1 ) is used by the enteropathogen Salmonella enterica serovar Typhimurium to establish infection in the gut . Effector proteins translocated by this system across the plasma membrane facilitate invasion of intestinal epithelial cells . One such effector , the inositol phosphatase SopB ...	Non-Typhoidal Salmonella are important agents of food borne disease worldwide . These facultative intracellular bacteria use a specialized Type III Secretion ( T3SS1 ) system to invade intestinal epithelial cells . Effector proteins translocated by this system across the eukaryotic plasma membrane induce actin rearrang...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "hela", "cells", "pathogens", "biological", "cultures", "microbiology", "salmonellosis", "epithelial", "cells", "bacterial", "diseases", "s...	2017	A second wave of Salmonella T3SS1 activity prolongs the lifespan of infected epithelial cells
Secondary metabolites , including toxins and melanins , have been implicated as virulence attributes in invasive aspergillosis . Although not definitively proved , this supposition is supported by the decreased virulence of an Aspergillus fumigatus strain , ΔlaeA , that is crippled in the production of numerous seconda...	Patients with suppressed immune systems due to cancer treatments , HIV/AIDS , or organ transplantation are at high risk of infection from microbes . Some of the most deadly infections for such patients arise from a fungal pathogen , Aspergillus fumigatus . This species , like several of its close relatives , can produc...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "secondary", "metabolism", "aspergillus", "fumigatus", "mycotoxin", "fungal", "immunology", "microbiology", "computational", "biology", "pathogenicity", "gene", "expression", "regulation", "genetics", "and", "genomics" ]	2007	Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA
Populations of genetically identical eukaryotic cells show significant cell-to-cell variability in gene expression . However , we lack a good understanding of the origins of this variation . We have found marked cell-to-cell variability in average cellular rates of transcription . We also found marked cell-to-cell vari...	Though pairs of cells may have identical genes , they still show behavioural differences . These cell-to-cell differences may arise from variations in how genes are transcribed and translated by the cellular machinery . Identifying the origins of this variation is important as it helps us understand why genetically ide...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/nuclear", "structure", "and", "function", "cell", "biology/cell", "growth", "and", "division", "cell", "biology", "cell", "biology/plant", "genetics", "and", "gene", "expression", "cell", "biology/chemical", "biology", "of", "the", "cell", "cell", "...	2010	Connecting Variability in Global Transcription Rate to Mitochondrial Variability
The interferon-induced dynamin-like MxA GTPase restricts the replication of influenza A viruses . We identified adaptive mutations in the nucleoprotein ( NP ) of pandemic strains A/Brevig Mission/1/1918 ( 1918 ) and A/Hamburg/4/2009 ( pH1N1 ) that confer MxA resistance . These resistance-associated amino acids in NP di...	Influenza A viruses of avian or swine origin sporadically enter into the human population but do not transmit between individuals . In rare cases , however , they establish a new virus lineage in humans . The mechanisms by which invading viruses overcome the species barrier are not well understood , but multiple adapta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunity", "virology", "innate", "immunity", "biology", "microbiology", "viral", "diseases", "viral", "evolution" ]	2013	Pandemic Influenza A Viruses Escape from Restriction by Human MxA through Adaptive Mutations in the Nucleoprotein
Lymphatic filariasis is a chronic , disabling and often disfiguring condition that principally impacts the world’s poorest people . In addition to the well-recognised physical disability associated with lymphedema and hydrocele , affected people often experience rejection , stigma and discrimination . The resulting emo...	Lymphatic filariasis is a chronic illness that is disabling and often results in disfigurement . Affected people experience rejection , and stigma and discrimination , which can result in significant emotional consequences . Overall functioning and the quality of life of such individuals can be further affected by this...	[ "Abstract", "Introduction", "Methods", "Results", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "health", "care", "filariasis", "neglected", "tropical", "diseases", "lymphatic", "filariasis", "africa", "mood", "d...	2017	Prevalence of depression and associated clinical and socio-demographic factors in people living with lymphatic filariasis in Plateau State, Nigeria
Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy , we mapped estrogen receptor α ( ERα ) binding sites in MCF-7 breast cancer cells . We identified 1 , 234 high confidence binding clusters of which 94% are projected to be bona fide ERα binding regions . Only 5% of the mapped estrog...	Estrogen receptors ( ERs ) play key roles in facilitating the transcriptional effects of hormone functions in target tissues . To obtain a genome-wide view of ERα binding sites , we applied chromatin immunoprecipitation coupled with a cloning and sequencing strategy using chromatin immunoprecipitation pair end-tagging ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "mammals", "computational", "biology", "homo", "(human)", "genetics", "and", "genomics" ]	2007	Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Biological and social networks are composed of heterogeneous nodes that contribute differentially to network structure and function . A number of algorithms have been developed to measure this variation . These algorithms have proven useful for applications that require assigning scores to individual nodes–from ranking...	Decision making in complex societies requires that individuals be aware of the group's collective opinions about themselves and their peers . In previous work , social power , defined as the consensus about an individual's ability to win fights , was shown to affect decisions about conflict intervention . We develop me...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "complex", "systems", "mathematics", "ecology", "applied", "mathematics", "biology", "computational", "biology", "behavioral", "ecology" ]	2013	A Family of Algorithms for Computing Consensus about Node State from Network Data
Maintenance of the correct redox status of iron is functionally important for critical biological processes . Multicopper ferroxidases play an important role in oxidizing ferrous iron , released from the cells , into ferric iron , which is subsequently distributed by transferrin . Two well-characterized ferroxidases , ...	Multi-copper ferroxidases play a critical role in maintaining iron homeostasis in humans . Two well-characterized ferroxidases , ceruloplasmin and hephaestin , facilitate iron transport in different tissues by oxidizing ferrous iron to the ferric form , which is subsequently carried by transferrin . Hephaestin like 1 (...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "integumentary", "system", "molecular", "probe", "techniques", "immunoblotting", "fibroblasts", "animal", "models", "model", "organisms", "animal", "anatomy", "connective", "tissue", "cells", "experimental", "organism", "systems", ...	2019	Biallelic HEPHL1 variants impair ferroxidase activity and cause an abnormal hair phenotype
The secretion of extracellular vesicles ( EVs ) in helminth parasites is a constitutive mechanism that promotes survival by improving their colonization and adaptation in the host tissue . In the present study , we analyzed the production of EVs from supernatants of cultures of Echinococcus granulosus protoscoleces and...	Human cystic echinococcosis , caused by chronic infection with the larval stage of Echinococcus granulosus , affects over 1 million people worldwide . This helminth parasite secretes numerous excretory/secretory products that are in contact with host tissues where it establishes hydatid cysts . In this study , we compr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "vesicles", "immune", "cells", "cestodes", "helminths", "antigen-presenting", "cells", "immunology", "parasitic", "diseases", "animals", "dendritic", "cells", "cellular", "structures", "and", "organelles", "animal"...	2019	Extracellular vesicles from Echinococcus granulosus larval stage: Isolation, characterization and uptake by dendritic cells
Pressure ulcers are costly and life-threatening complications for people with spinal cord injury ( SCI ) . People with SCI also exhibit differential blood flow properties in non-ulcerated skin . We hypothesized that a computer simulation of the pressure ulcer formation process , informed by data regarding skin blood fl...	Pressure ulcers are costly and life-threatening complications for people with spinal cord injury ( SCI ) . To gain insight into the pathogenesis and effective treatment of post-SCI pressure ulcers , we constructed a computer simulation in a hybrid modeling platform which combines both equation- and agent-based models ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biochemical", "simulations", "computer", "science", "computer", "modeling", "immunology", "biology", "computational", "biology", "computerized", "simulations", "immune", "response", "immune", "system" ]	2013	Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury
Density-Enhanced Phosphatase-1 ( DEP-1 ) de-phosphorylates various growth factor receptors and adhesion proteins to regulate cell proliferation , adhesion and migration . Moreover , dep-1/scc1 mutations have been detected in various types of human cancers , indicating a broad tumor suppressor activity . During C . eleg...	The phosphorylation of proteins by kinases is one of the most common post-translational modifications that regulates protein function in a variety of processes . Protein kinases are usually counteracted by specific phosphatases that remove the phosphate groups from proteins . We have undertaken a systematic biochemical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "invertebrates", "rna", "interference", "caenorhabditis", "enzymes", "egfr", "signaling", "enzymology", "animals", "phosphatases", "animal", "models", "membrane", "proteins", "caenorhabditis", "elegans", "integrins", "model", "organisms", "experimental", ...	2017	β-Integrin de-phosphorylation by the Density-Enhanced Phosphatase DEP-1 attenuates EGFR signaling in C. elegans
The circadian clock underlies daily rhythms of diverse physiological processes , and alterations in clock function have been linked to numerous pathologies . To apply chemical biology methods to modulate and dissect the clock mechanism with new chemical probes , we performed a circadian screen of ∼120 , 000 uncharacter...	Most organisms show daily rhythms in physiology , behavior , and metabolism , which may be advantageous because they anticipate environmental changes thus optimize energy metabolism . These rhythms are controlled by the circadian clock , which produces cyclic expression of thousands of output genes . More than a dozen ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "biology", "biochemistry", "molecular", "biology", "cell", "biology" ]	2010	High-Throughput Chemical Screen Identifies a Novel Potent Modulator of Cellular Circadian Rhythms and Reveals CKIα as a Clock Regulatory Kinase
The worldwide burden of snakebite is high , especially in remote regions with lesser accessibility to professional healthcare . Therefore , adequate first aid for snakebite is of the utmost importance . A wide range of different first aid techniques have been described in literature , and are being used in practice . T...	The Belgian Red Cross-Flanders develops first aid guidelines that specifically target laypeople . In the context of updating the first aid guidelines for sub-Saharan Africa , we aimed to summarize the best available evidence for the treatment of snakebite , feasible for laypeople . Of the numerous first aid measures su...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "traditional", "medicine", "medicine", "and", "health", "sciences", "radiochemistry", "toxins", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "vertebrates", "animals", "toxicology", "toxic", "agents", "observational", "studies", "research", "design...	2016	The Treatment of Snake Bites in a First Aid Setting: A Systematic Review
The possibility of using computer simulation and mathematical modeling to gain insight into biological and other complex systems is receiving increased attention . However , it is as yet unclear to what extent these techniques will provide useful biological insights or even what the best approach is . Epstein–Barr viru...	The possibility of using computer simulation and mathematical modeling to gain insight into biological systems is receiving increased attention . However , it is as yet unclear to what extent these techniques will provide useful biological insights or even what the best approach is . Epstein–Barr virus ( EBV ) provides...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "agent", "based", "model", "infectious", "diseases", "epstein-barr", "virus", "computer", "simulation", "pathology", "virology", "immunology", "dynamics", "of", "infection", "computational", "biology" ]	2007	A Virtual Look at Epstein–Barr Virus Infection: Biological Interpretations
Mobile elements comprise close to one half of the mass of the human genome . Only LINE-1 ( L1 ) , an autonomous non-Long Terminal Repeat ( LTR ) retrotransposon , and its non-autonomous partners—such as the retropseudogenes , SVA , and the SINE , Alu—are currently active human retroelements . Experimental evidence show...	SINE retroelement amplification has been extremely successful in the human genome . Although these non-autonomous elements parasitize factors from LINEs , both the human Alu and the cumulative rodent SINEs have generated over one million copies in their respective hosts . Alu-induced mutagenesis is responsible for the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "molecular", "biology" ]	2009	The RNA Polymerase Dictates ORF1 Requirement and Timing of LINE and SINE Retrotransposition
As an advanced approach to identify suitable targeting molecules required for various diagnostic and therapeutic interventions , we developed a procedure to devise peptides with customizable features by an iterative computer-assisted optimization strategy . An evolutionary algorithm was utilized to breed peptides in si...	A clever identification procedure is crucial when peptidic ligands for diagnostic and therapeutic techniques such as in vivo imaging or drug targeting are to be developed . Here , we present a propitious and versatile approach for the discovery of peptide sequences with custom features that is based on an iterative com...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "algorithms", "biochemistry", "computer", "science", "synthetic", "peptide", "biology", "proteomics" ]	2012	Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures
DNA mismatch repair greatly increases genome fidelity by recognizing and removing replication errors . In order to understand how this fidelity is maintained , it is important to uncover the relative specificities of the different components of mismatch repair . There are two major mispair recognition complexes in euka...	DNA mismatch repair is a major pathway that prevents both base substitution and insertion or deletion errors during replication . Most eukaryotes have two recognition complexes , MutSα and MutSβ , homologues of prokaryotic MutS and differing in their affinity for mismatches , with MutSα recognizing base-base mismatches...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Different Roles of Eukaryotic MutS and MutL Complexes in Repair of Small Insertion and Deletion Loops in Yeast
Topoisomerases are enzymes with crucial functions in DNA metabolism . They are ubiquitously present in prokaryotes and eukaryotes and modify the steady-state level of DNA supercoiling . Biochemical analyses indicate that Topoisomerase 3α ( TOP3α ) functions together with a RecQ DNA helicase and a third partner , RMI1/B...	The topoisomerases of the class IA are present in all three eukaryotic kingdoms—plants , fungi , and animals—and are involved in DNA replication and DNA repair . During the course of their action , they introduce transient single-strand nicks into DNA . In higher eukaryotes , two different classes of the enzymes are pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "genetics", "and", "gene", "expression", "molecular", "biology/dna", "replication", "molecular", "biology/chromatin", "structure", "biotechnology/plant", "biotechnology", "computational", "biology/comparative", "sequence", "analysis", "developmental", ...	2008	Topoisomerase 3α and RMI1 Suppress Somatic Crossovers and Are Essential for Resolution of Meiotic Recombination Intermediates in Arabidopsis thaliana
Tumor-induced angiogenesis leads to the development of leaky tumor vessels devoid of structural and morphological integrity . Due to angiogenesis , elevated interstitial fluid pressure ( IFP ) and low blood perfusion emerge as common properties of the tumor microenvironment that act as barriers for drug delivery . In o...	Tumor vessels being very different from their normal counterparts are leaky and lack organization that sustains blood circulation . As a result , insufficient blood supply and high fluid pressure begin to appear inside the tumor which leads to a reduced delivery of drugs within the tumor , especially in tumor center . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "vesicles", "cardiovascular", "physiology", "engineering", "and", "technology", "cancer", "treatment", "clinical", "oncology", "drugs", "chemotherapeutic", "agents", "oncology", "angiogenesis", "developmental", "biology", "clinical",...	2017	Quantifying the effects of antiangiogenic and chemotherapy drug combinations on drug delivery and treatment efficacy
In the absence of vaccines and limitations of currently available chemotherapy , development of safe and efficacious drugs is urgently needed for visceral leishmaniasis ( VL ) that is fatal , if left untreated . Earlier we reported in vitro apoptotic antileishmanial activity of n-hexane fractions of Artemisia annua lea...	Visceral leishmaniasis ( VL ) is a fatal , vector-borne tropical disease that affects the poorest sections of the society . The currently available drugs are toxic , expensive and have severe side effects . The problem is further compounded by emergence of VL-HIV co-infection and occurence of PKDL after apparent cure ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "clinical", "medicine", "clinical", "immunology", "complementary", "and", "alternative", "medicine", "herbal", "medicine", "biology", "and", "life", "sciences", "immunology", "microbiology", "parasitology" ]	2015	Th1-Biased Immunomodulation and Therapeutic Potential of Artemisia annua in Murine Visceral Leishmaniasis
Chlamydia spp . are intracellular obligate bacterial pathogens that infect a wide range of host cells . Here , we show that C . caviae enters , replicates , and performs a complete developmental cycle in Drosophila SL2 cells . Using this model system , we have performed a genome-wide RNA interference screen and identif...	Chlamydia spp . are intracellular bacterial pathogens that infect a wide range of hosts and cause various diseases , including preventable blindness in developing countries , sexually transmitted disease , and pneumonia . Chlamydia spp . are able to establish their replication niche inside the host cell , residing in a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "infectious", "diseases", "cell", "biology", "mammals", "homo", "(human)", "microbiology", "drosophila", "eubacteria" ]	2007	RNAi Screen in Drosophila Cells Reveals the Involvement of the Tom Complex in Chlamydia Infection
The World Health Organization aims for complete morbidity control of fishborne zoonotic trematodes ( FZT ) in endemic areas by 2020 . The main intervention tool for achieving this goal is regular use of preventive chemotherapy by offering praziquantel to those at risk in endemic areas . The purpose of this study was to...	Fishborne zoonotic trematodes ( FZT ) are small parasitic flatworms ( flukes ) living either in the intrahepatic bile ducts or in the intestines of humans and many species of animals and birds . Transmission occurs by eating infected raw freshwater fish . FZT are especially common in Southeast and East Asia . WHO sugge...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "tropical", "diseases", "parasitic", "diseases", "parasitology", "foodborne", "trematodiases", "gastroenterology", "and", "hepatology", "global", "health", "neglected", "tropical", "diseases",...	2014	High Reinfection Rate after Preventive Chemotherapy for Fishborne Zoonotic Trematodes in Vietnam
Fundamental properties of phasic firing neurons are usually characterized in a noise-free condition . In the absence of noise , phasic neurons exhibit Class 3 excitability , which is a lack of repetitive firing to steady current injections . For time-varying inputs , phasic neurons are band-pass filters or slope detect...	Principal brain cells , called neurons , show a tremendous amount of diversity in their responses to driving stimuli . A widely present but understudied class of neurons prefers to respond to high-frequency inputs and neglect slow variations; these cells are called phasic neurons . Although phasic neurons do not normal...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2010	Slope-Based Stochastic Resonance: How Noise Enables Phasic Neurons to Encode Slow Signals
Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine , potato late blight has exemplified this threat . The causal oomycete pathogen , Phytophthora infestans , undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual...	We have documented a dramatic shift in the population of the potato late blight pathogen Phytophthora infestans in northwest Europe in which an invasive and aggressive lineage called 13_A2 has emerged and rapidly displaced other genotypes . The genome of a 13_A2 isolate revealed a high rate of sequence polymorphism and...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "plant", "biology", "population", "dynamics", "genome", "sequencing", "genome", "databases", "plant", "science", "plant", "pathology", "mutation", "databases", "population", "biology", "plant", "genetics", "comparative", "genomics", "...	2012	Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen
The susceptibility of Anopheles mosquitoes to Plasmodium infections relies on complex interactions between the insect vector and the malaria parasite . A number of studies have shown that the mosquito innate immune responses play an important role in controlling the malaria infection and that the strength of parasite c...	During their development in the mosquito vector , Plasmodium parasites undergo complex developmental steps and incur severe bottlenecks . The largest parasite losses occur in the mosquito midgut where robust immune responses are activated . Variability in P . falciparum infection levels indicates that parasite transmis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology", "genetics", "immunology", "biology", "genomics", "evolutionary", "biology", "microbiology", "population", "biology", "genetics", "and", "genomics" ]	2012	Midgut Microbiota of the Malaria Mosquito Vector Anopheles gambiae and Interactions with Plasmodium falciparum Infection
The mosquito Aedes aegypti is the primary vector of dengue virus ( DENV ) infection in humans , and DENV is the most important arbovirus across most of the subtropics and tropics worldwide . The early time periods after infection with DENV define critical cellular processes that determine ultimate success or failure of...	Dengue virus is primarily transmitted by Aedes aegypti mosquitoes . Control of the vector mosquito is the major practice to prevent dengue . However , it is not well known how the virus can infect some mosquito strains but fail to do so with other refractory strains . To address that question , we conducted whole genom...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome", "expression", "analysis", "emerging", "viral", "diseases", "microbiology", "host-pathogen", "interaction", "viral", "vectors", "mechanisms", "of", "resistance", "and", "susceptibility", "emerging", "infectious", "diseases", "viral", "immune", "evasion", "medical...	2011	Global Cross-Talk of Genes of the Mosquito Aedes aegypti in Response to Dengue Virus Infection
Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine . We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue . We hypothesized that these differences in culture s...	Regenerative medicine specialists have been using a type of cell commonly found in the skin called the fibroblast because it is easily obtained from skin samples , grows well in culture , and can be manipulated in the laboratory to de-differentiate into a primordial state known as the induced pluripotent stem cell . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "scalp", "biological", "cultures", "fibroblasts", "connective", "tissue", "cells", "genome", "analysis", "epigenetics", "dna", "molecular", "biology", "techniques", "rna", "sequencing", "dna", "methyla...	2016	Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Identifying transcription factors ( TF ) involved in producing a genome-wide transcriptional profile is an essential step in building mechanistic model that can explain observed gene expression data . We developed a statistical framework for constructing genome-wide signatures of TF activity , and for using such signat...	Knowing transcription factors ( TF ) that regulate expression of differentially expressed genes is essential for understanding signaling cascades and regulatory mechanisms that lead to changes in gene expression . We developed methods for constructing gene-level scores ( TREG binding scores ) measuring likelihood that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules
Dengue laboratory diagnosis is essentially based on detection of the virus , its components or antibodies directed against the virus in blood samples . Blood , however , may be difficult to draw in some patients , especially in children , and sampling during outbreak investigations or epidemiological studies may face l...	Dengue is the most important arthropod-borne disease affecting humans and represents a huge public health burden in affected countries . Symptoms are often non-specific hence the need for an early , sensitive and specific diagnosis of dengue for appropriate management as well as for early epidemic detection . Currently...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Value of Routine Dengue Diagnostic Tests in Urine and Saliva Specimens
Sepsis is a frequent complication in critical illness . The mechanisms that are involved in initiation and propagation of the disease are not well understood . Scavenger receptor A ( SRA ) is a membrane receptor that binds multiple polyanions such as oxidized LDL and endotoxin . Recent studies suggest that SRA acts as ...	Trauma and other critical illnesses can progress to septic shock . The mechanisms that result in this progression are not understood . For this reason , there are no proven treatments available , and the mortality rate from sepsis remains quite high . We have found that mice that lack a certain cell surface protein , s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immunology", "biology", "microbiology", "critical", "care", "and", "emergency", "medicine" ]	2012	Scavenger Receptor Class A Plays a Central Role in Mediating Mortality and the Development of the Pro-Inflammatory Phenotype in Polymicrobial Sepsis
Recent reports suggest that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana . Three NF-YC genes ( NF-YC3 , NF-YC4 , and NF-YC9 ) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leu...	Light perception is critically important for the fitness of plants in both natural and agricultural settings . Plants not only use light for photosynthesis , but also as a cue for proper development . As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit . When bl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "anatomy", "plant", "growth", "and", "development", "gene", "regulation", "plant", "embryo", "anatomy", "regulatory", "proteins", "dna-binding", "proteins", "light", "microscopy", "plant", "physiology", "developmental", "biology", "plant", "science", "luminesce...	2016	NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana

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