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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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The ability to respond to injury is a biological process shared by organisms of different kingdoms that can even result in complete regeneration of a part or structure that was lost . Due to their immobility , multicellular fungi are prey to various predators and are therefore constantly exposed to mechanical damage . ... | The idea of regenerating lost body parts has always fascinated humans due to its impact on human health . Recently , the study of the response to damage has gained importance not only in regenerative medicine , but also in organ transplantation . We have established a microbial model that given its relative simplicity ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"fungal",
"genetics",
"statistics",
"light",
"microscopy",
"fungal",
"structure",
"fungi",
"statistical",
"data",
"confocal",
"laser",
"microscopy",
"mathematics",
"dna",
"replication",
"microscopy",
"genome",
"analysis",
"confocal",
"microscopy",
"dna",
"research",
"an... | 2018 | Danger signals activate a putative innate immune system during regeneration in a filamentous fungus |
Lynch syndrome ( hereditary nonpolypsis colorectal cancer or HNPCC ) is a common cancer predisposition syndrome . Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair ( MMR ) caused by a mutation in one of the mismatch repair genes MLH1 , MSH2 , MSH... | Lynch syndrome ( hereditary nonpolypsis colorectal cancer or HNPCC ) is a common cancer predisposition syndrome . Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair ( MMR ) caused by a mutation in one of the mismatch repair genes MLH1 , MSH2 , MSH... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Dominant Mutations in S. cerevisiae PMS1 Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway |
The immunization with genetically attenuated Leishmania cell lines has been associated to the induction of memory and effector T cell responses against Leishmania able to control subsequent challenges . A Leishmania infantum null mutant for the HSP70-II genes has been described , possessing a non-virulent phenotype . T... | Despite numerous efforts made , a vaccine against leishmaniasis for humans is not available . Attempts based on parasite fractions or selected antigens failed to confer long lasting protection . On the other side , leishmanization , which consists in the inoculation of live virulent parasites in hidden parts of the bod... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"spleen",
"ears",
"immunology",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"animal",
"models",
"preventive",
"medicine",
"developmental",
"biology",
... | 2017 | Vaccination with a Leishmania infantum HSP70-II null mutant confers long-term protective immunity against Leishmania major infection in two mice models |
Since the pioneering work by Julius Adler in the 1960's , bacterial chemotaxis has been predominantly studied as metabolism-independent . All available simulation models of bacterial chemotaxis endorse this assumption . Recent studies have shown , however , that many metabolism-dependent chemotactic patterns occur in b... | Traditionally , bacterial chemotaxis has been treated as metabolism-independent . Under this assumption , dedicated chemotaxis signalling pathways operate independently of metabolic processes . There is however , in various strains of bacteria , growing evidence of metabolism-dependent chemotaxis where metabolism modul... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"microbiology/microbial",
"physiology",
"and",
"metabolism",
"cell",
"biology/chemical",
"biology",
"of",
"the",
"cell",
"computational",
"biology/metabolic",
"networks",
"computational",
"biology/systems",
"biology"
] | 2010 | A Minimal Model of Metabolism-Based Chemotaxis |
Under natural conditions , animals encounter a barrage of sensory information from which they must select and interpret biologically relevant signals . Active sensing can facilitate this process by engaging motor systems in the sampling of sensory information . The echolocating bat serves as an excellent model to inves... | As animals operate in the natural environment , they must detect and process relevant sensory information embedded in complex and noisy signals . One strategy to overcome this challenge is to use active sensing or behavioral adjustments to extract sensory information from a selected region of the environment . We studi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"acoustics",
"vocalization",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"ears",
"vertebrates",
"animals",
"mammals",
"animal",
"signaling",
"and",
"communication",
"echoes",
"animal",
"behavior",
"computer",
"vision",
"remote",
"sensing... | 2016 | Action Enhances Acoustic Cues for 3-D Target Localization by Echolocating Bats |
Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings . Structural studies have shown that in many cases , the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its pro... | Despite intense interest and considerable effort , there are few examples of small molecules that directly inhibit protein-protein interactions . Crystal structures of early successes have highlighted the plasticity of the protein surface , as some inhibitor-bound proteins are captured in conformations that are distinc... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations |
Congenital cytomegalovirus ( CMV ) infection is the most common non-hereditary cause of sensorineural hearing loss ( SNHL ) yet the mechanisms of hearing loss remain obscure . Natural Killer ( NK ) cells play a critical role in regulating murine CMV infection via NK cell recognition of the Ly49H cell surface receptor o... | Cytomegalovirus ( CMV ) transmission from an infected mother to her fetus is a leading cause of permanent hearing loss in children , but the contributing processes are not clear . In this report , we utilized a mouse model , which recapitulates many features of congenital CMV mediated childhood hearing loss , to demons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"ears",
"immunology",
"cytomegalovirus",
"infection",
"neuroscience",
"animal",
"models",
"outer",
"hair",
"cells",
"otology",
"inner",
"ear",
"model",
"organisms",
... | 2017 | Natural killer cells attenuate cytomegalovirus-induced hearing loss in mice |
Schistosome parasites cause schistosomiasis , one of the most prevalent parasitemias worldwide affecting humans and animals . Constant pairing of schistosomes is essential for female sexual maturation and egg production , which causes pathogenesis . Female maturation involves signaling pathways controlling mitosis and ... | As one of the most prevalent parasitic infections worldwide , schistosomiasis is caused by blood-flukes of the genus Schistosoma . Pathology coincides with egg production , which is started upon pairing of the dioeciously living adults . A constant pairing contact is required to induce mitoses and differentiation proce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gene",
"networks",
"animal",
"genetics",
"gene",
"regulation",
"microbiology",
"parasitology",
"dna",
"transcription",
"gene",
"function",
"parasite",
"physiology",
"genome",
"analysis",
"tools",
"genome",
"databases",
"molecular",
"genetics",
"microbial",
"growth",
"a... | 2013 | Transcriptome Analyses of Inhibitor-treated Schistosome Females Provide Evidence for Cooperating Src-kinase and TGFβ Receptor Pathways Controlling Mitosis and Eggshell Formation |
Mutations affecting the ribosome lead to several diseases known as ribosomopathies , with phenotypes that include growth defects , cytopenia , and bone marrow failure . Diamond-Blackfan anemia ( DBA ) , for example , is a pure red cell aplasia linked to the mutation of ribosomal protein ( RP ) genes . Here we show the ... | Diseases linked to mutations affecting the ribosome , ribosomopathies , have an exceptionally wide range of phenotypes . However , many ribosomopathies have some features in common including cytopenia and growth defects . Our study aims to clarify the mechanisms behind these common phenotypes . We find that mutations i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"of",
"disease",
"insulin-dependent",
"signal",
"transduction",
"signal",
"transduction",
"developmental",
"biology",
"cell",
"biology",
"molecular",
"development",
"genetics",
"tor",
"signaling",
"biology",
"and",
"life",
"sciences",
"molecular",
"cell",
"b... | 2014 | Ribosomal Protein Mutations Induce Autophagy through S6 Kinase Inhibition of the Insulin Pathway |
Active adult stem cells maintain a bipotential state with progeny able to either self-renew or initiate differentiation depending on extrinsic signals from the surrounding microenvironment . However , the intrinsic gene regulatory networks and chromatin states that allow adult stem cells to make these cell fate choices... | Many adult tissues are maintained throughout life by the dual ability of adult stem cells to produce progeny that either self-renew or differentiate to replace specialized cells lost to turnover or damage . Although signals from the surrounding microenvironment have been shown to regulate the choice between self-renewa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"spermatocytes",
"rna",
"interference",
"cloning",
"cell",
"differentiation",
"germ",
"cells",
"developmental",
"biology",
"stem",
"cells",
"molecular",
"biology",
"techniques",
"epigenetics",
"sperm",
"... | 2019 | DREF Genetically Counteracts Mi-2 and Caf1 to Regulate Adult Stem Cell Maintenance |
Calcium through NMDA receptors ( NMDARs ) is necessary for the long-term potentiation ( LTP ) of synaptic strength; however , NMDARs differ in several properties that can influence the amount of calcium influx into the spine . These properties , such as sensitivity to magnesium block and conductance decay kinetics , ch... | The striatum of the basal ganglia plays a key role in fluent motor control; pathology in this structure causes the motor symptoms of Parkinson's Disease and Huntington's Chorea . A putative cellular mechanism underlying learning of motor control is synaptic plasticity , which is an activity dependent change in synaptic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"and",
"memory",
"developmental",
"neuroscience",
"cellular",
"neuroscience",
"ion",
"channels",
"synaptic",
"plasticity",
"synapses",
"computational",
"neuroscience",
"single",
"neuron",
"function",
"biology",
"neuroscience",
"neurophysiology"
] | 2012 | The Effects of NMDA Subunit Composition on Calcium Influx and Spike Timing-Dependent Plasticity in Striatal Medium Spiny Neurons |
Circadian pacemakers are essential to synchronize animal physiology and behavior with the day∶night cycle . They are self-sustained , but the phase of their oscillations is determined by environmental cues , particularly light intensity and temperature cycles . In Drosophila , light is primarily detected by a dedicated... | In most organisms , intracellular molecular pacemakers called circadian clocks coordinate metabolic , physiological , and behavioral processes during the course of the day . For example , they determine when animals are active or resting . Circadian clocks are self-sustained oscillators , but their free-running period ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"genetics",
"and",
"genomics/gene",
"function"
] | 2009 | A Constant Light-Genetic Screen Identifies KISMET as a Regulator of Circadian Photoresponses |
Tsetse flies are the sole vectors of Trypanosoma brucei parasites that cause sleeping sickness . Our knowledge on the early interface between the infective metacyclic forms and the mammalian host skin is currently highly limited . Glossina morsitans flies infected with fluorescently tagged T . brucei parasites were use... | Sleeping sickness is caused by trypanosomes that are transmitted by the blood feeding tsetse flies . The present study has established an experimental transmission model with fluorescently labeled parasites in mice that allows us to study their fate following natural transmission by a tsetse fly bite . Parasites that a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"ears",
"parasitic",
"diseases",
"animals",
"glossina",
"otology",
"ear",
"infections",
"tsetse",
"fly",
"insect",
"vectors",
"digestive",
"system... | 2016 | The Dermis as a Delivery Site of Trypanosoma brucei for Tsetse Flies |
Two observations about the cortex have puzzled neuroscientists for a long time . First , neural responses are highly variable . Second , the level of excitation and inhibition received by each neuron is tightly balanced at all times . Here , we demonstrate that both properties are necessary consequences of neural netwo... | Two observations about the cortex have puzzled and fascinated neuroscientists for a long time . First , neural responses are highly variable . Second , the level of excitation and inhibition received by each neuron is tightly balanced at all times . Here , we demonstrate that both properties are necessary consequences ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Predictive Coding of Dynamical Variables in Balanced Spiking Networks |
The relationship between chromatin structure and gene expression is a subject of intense study . The universal transcriptional activator Gal4 removes promoter nucleosomes as it triggers transcription , but how it does so has remained obscure . The reverse process , repression of transcription , has often been correlate... | In this paper , we examine activation and repression of transcription of a gene in yeast . This gene , like the typical human gene , is wrapped in DNA-protein packets called nucleosomes . It is widely believed that these condensed packets are unwrapped , in a process called nucleosome removal , as transcription begins ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology"
] | 2008 | Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription |
The aim of this study is to model the association between weekly time series of dengue case counts and meteorological variables , in a high-incidence city of Colombia , applying Bayesian hierarchical dynamic generalized linear models over the period January 2008 to August 2015 . Additionally , we evaluate the model’s s... | Time series analysis of dengue disease case counts are currently employed to establish associations between dengue disease and environmental , socioeconomic and climatic variables and to predict the evolution of dengue epidemics . Nowadays there is acceptance that climatic factors like environmental temperature , rainf... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"atmospheric",
"science",
"geographical",
"locations",
"mathematical",
"models",
"electromagnetic",
"radiation",
"mathematics",
"forecasting",
"statistics",
"(mathematics)",
"atmospheric",
"dynamics",
"humidity",
"research",
"and",
"... | 2017 | Bayesian dynamic modeling of time series of dengue disease case counts |
As the more recent next-generation sequencing ( NGS ) technologies provide longer read sequences , the use of sequencing datasets for complete haplotype phasing is fast becoming a reality , allowing haplotype reconstruction of a single sequenced genome . Nearly all previous haplotype reconstruction studies have focused... | While human and other eukaryotic genomes typically contain two copies of every chromosome , plants , yeast and fish such as salmon can have strictly more than two copies of each chromosome . By running standard genotype calling tools , it is possible to accurately identify the number of “wild type” and “mutant” alleles... | [
"Abstract",
"Introduction",
"Method",
"Results",
"Discussion",
"Discussion"
] | [
"haplotypes",
"biology",
"and",
"life",
"sciences",
"population",
"genetics",
"computational",
"biology",
"evolutionary",
"biology"
] | 2014 | HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data |
The Drosophila Alp/Enigma family protein Zasp52 localizes to myotendinous junctions and Z-discs . It is required for terminal muscle differentiation and muscle attachment . Its vertebrate ortholog ZASP/Cypher also localizes to Z-discs , interacts with α-actinin through its PDZ domain , and is involved in Z-disc mainten... | Muscles are comprised of huge , multinucleated cells that feature a highly organized cytoskeletal architecture consisting of variable numbers of myofibrils , whose formation is not well understood . Each myofibril is an array of sarcomeres , the smallest contractile unit of muscles . The contractile system consists of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunocytochemistry",
"animal",
"genetics",
"genetic",
"mutation",
"protein",
"interactions",
"gene",
"function",
"developmental",
"biology",
"organism",
"development",
"molecular",
"development",
"molecular",
"genetics",
"morphogenesis",
"sequence",
"analysis",
"cytochemist... | 2013 | Alp/Enigma Family Proteins Cooperate in Z-Disc Formation and Myofibril Assembly |
Sleep contributes to cognitive functioning and is sufficient to alter brain morphology and function . However , mechanisms underlying sleep regulation remain poorly understood . In mammals , tumor necrosis factor-alpha ( TNFα ) is known to regulate sleep , and cytokine expression may represent an evolutionarily ancient... | Every animal sleeps , from fruit flies to humans . However , the function of sleep is still currently unknown . Identifying conserved mechanisms of sleep regulation in evolutionarily ancient organisms may help us to understand the function of sleep . Therefore , we have examined whether Eiger , the homologue of the cyt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"sleep",
"deprivation",
"immune",
"physiology",
"cytokines",
"rna",
"interference",
"sleep",
"astrocytes",
"immunology",
"vertebrates",
"neuroscience",
"macroglial",
"cells",
"animals"... | 2018 | Astrocyte expression of the Drosophila TNF-alpha homologue, Eiger, regulates sleep in flies |
Bacterial secondary metabolites are widely used as antibiotics , anticancer drugs , insecticides and food additives . Attempts to engineer their biosynthetic gene clusters ( BGCs ) to produce unnatural metabolites with improved properties are often frustrated by the unpredictability and complexity of the enzymes that s... | Bacterial secondary metabolites mediate a broad range of microbe-microbe and microbe-host interactions , and are widely used in human medicine , agriculture and manufacturing . Despite recent advances in synthetic biology , efforts to engineer their biosynthetic genes for the production of unnatural variants are frustr... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biotechnology",
"biochemistry",
"secondary",
"metabolism",
"genomics",
"genome",
"evolution",
"genetics",
"synthetic",
"biology",
"biosynthesis",
"biology",
"and",
"life",
"sciences",
"comparative",
"genomics",
"computational",
"biology",
"evolutionary",
"biology",
"microb... | 2014 | A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis |
DNA double-strand breaks ( DSBs ) can be repaired by homologous recombination ( HR ) , which can involve Holliday junction ( HJ ) intermediates that are ultimately resolved by nucleolytic enzymes . An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase , but little is known... | Coordination of DNA repair with cell cycle progression and apoptosis is a central task of the DNA damage response machinery . A key intermediate of recombinational repair and meiotic recombination , first proposed in 1964 , involves four-stranded DNA structures . These intermediates have to be resolved upon completion ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/recombination",
"genetics",
"and",
"genomics/gene",
"discovery",
"molecular",
"biology/dna",
"repair"
] | 2010 | The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair |
The effectiveness of rabies vaccination in both humans and animals is determined by the presence of virus neutralizing antibodies ( VNAs ) . The Rapid Fluorescent Focus Inhibition Test ( RFFIT ) is the method traditionally used for detection and quantification of VNAs . It is a functional in vitro test for assessing th... | The potency of rabies vaccine is demonstrated by the presence of virus neutralizing antibodies ( VNAs ) in serum . It is critical to evaluate immunologic status of individuals who work directly with rabies virus ( RABV ) ( laboratorians ) or at high risk of infection due to interaction with animals ( veterinarians and ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"nuclear",
"staining",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"tropical",
"diseases",
"microbiology",
"light",
"microscopy",
"green",
"fluorescent",
"protein",
"viruses",
... | 2018 | A high throughput neutralization test based on GFP expression by recombinant rabies virus |
Although the growth factor ( GF ) signaling guiding renal branching is well characterized , the intracellular cascades mediating GF functions are poorly understood . We studied mitogen-activated protein kinase ( MAPK ) pathway specifically in the branching epithelia of developing kidney by genetically abrogating the pa... | Development of the ureter and collecting ducts of the kidney requires extensive growth and branching of an epithelial tube , the ureteric bud . While many genes that control this process are known , the intracellular signaling pathways that underlie renal morphogenesis remain poorly understood . The cellular changes th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cadherins",
"mitosis",
"developmental",
"biology",
"cell",
"division",
"cell",
"adhesion",
"adhesion",
"molecules",
"molecular",
"development",
"cell",
"migration",
"biology",
"molecular",
"cell",
"biology",
"morphogenesis",
"cell",
"differentiation",
"cyclins"
] | 2014 | Mitogen-Activated Protein Kinase (MAPK) Pathway Regulates Branching by Remodeling Epithelial Cell Adhesion |
Antivenom is the treatment of choice for snakebite , which annually kills an estimated 32 , 000 people in sub-Saharan Africa and leaves approximately 100 , 000 survivors with permanent physical disabilities that exert a considerable socioeconomic burden . Over the past two decades , the high costs of the most polyspeci... | Snakebite is one of the most under-researched , under-resourced high morbidty/high mortality NTDs , as reflected by the fact that many of the antivenoms used to treat snakebite victims in sub-Saharan Africa are of uncertain and untested efficacy . This Kenya case study is the first examination of the preclinical effica... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"toxins",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"animals",
"toxicology",
"toxic",
"agents",
"vaccines",
"cobras",
"reptile... | 2017 | Preclinical antivenom-efficacy testing reveals potentially disturbing deficiencies of snakebite treatment capability in East Africa |
Helminth infections affect more than a third of the world’s population . Despite very broad phylogenetic differences among helminth parasite species , a systemic Th2 host immune response is typically associated with long-term helminth infections , also known as the “helminth effect” . Many investigations have been carr... | Many studies have been conducted to understand the immune modulatory effects in helminth infections . To determine whether there is a common transcriptomic signature characteristic of the helminth effect , we performed a comprehensive meta-analysis of publicly available gene expression datasets . The results revealed a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"helminths",
"gene",
"regulation",
"immunology",
"parasitic",
"diseases",
"animals",
"mathematics",
"statistics",
"(mathematics)",
"research",
"and",
"analysis",
"metho... | 2016 | Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections |
Flavivirus and Filovirus infections are serious epidemic threats to human populations . Multi-genome comparative analysis of these evolving pathogens affords a view of their essential , conserved sequence elements as well as progressive evolutionary changes . While phylogenetic analysis has yielded important insights ,... | Flaviviruses , including Zika and Dengue viruses , and Filoviruses , including Ebola and Marburg viruses , are significant global public health threats . Genetic surveillance of viral isolates provides important insights into the origin of outbreaks , reveals lineage heterogeneity and diversification , and facilitates ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"and",
"discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"viruses",
"genomic",
"databases",
"filoviruses",
"rna",
"viruses",
"genome",
"analysis",
"microbial",
"genomics",
"research",
"and",
"analysis",
"methods... | 2017 | Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution |
Several recent large clinical trials evaluated HIV vaccine candidates that were based on recombinant adenovirus serotype 5 ( rAd-5 ) vectors expressing HIV-derived antigens . These vaccines primarily elicited T-cell responses , which are known to be critical for controlling HIV infection . In the current study , we pre... | The HIV epidemic is a major global health challenge leading to more than 1 . 8 million deaths annually , and despite significant efforts , the search for an efficacious and safe vaccine continues . Several candidate vaccines were designed to elicit CD8+ T-cell responses and were based on using recombinant Adenovirus se... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"clinical",
"research",
"design",
"clinical",
"immunology",
"clinical",
"trials",
"meta-analyses",
"immune",
"response"
] | 2013 | HIV-1 Vaccine-Induced T-Cell Reponses Cluster in Epitope Hotspots that Differ from Those Induced in Natural Infection with HIV-1 |
Analyses of gene expression profiles in evolutionarily diverse organisms have revealed a role for microRNAs in tuning tissue-specific gene expression . Here , we show that the relatively abundant and constitutively expressed miR-58 family of microRNAs sharply defines the tissue-specific expression of the broadly transc... | MicroRNAs are small , noncoding RNAs that act post-transcriptionally to inhibit expression of their target mRNAs . Gene expression studies of microRNAs and their target transcripts in diverse organisms have suggested that microRNAs may function to shape patterns of tissue expression . In this paper , we show that the m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Tissue Expression Pattern of PMK-2 p38 MAPK Is Established by the miR-58 Family in C. elegans |
Many species rely on olfaction to navigate towards food sources or mates . Olfactory navigation is a challenging task since odor environments are typically turbulent . While time-averaged odor concentration varies smoothly with the distance to the source , instaneous concentrations are intermittent and obtaining stable... | Navigating towards a food source or mating partner based on an animals’ sense of smell is a difficult task due to the complex spatiotemporal distribution of odor molecules . The most basic aspect of this task is the acquisition of samples from the environment . It is clear that odor concentration does not vary smoothly... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"classical",
"mechanics",
"chemical",
"compounds",
"fluid",
"mechanics",
"quantum",
"tunneling",
"neuroscience",
"organic",
"compounds",
"turbulence",
"probability",
"distribution",
"animal",
"behavior",
"mathematics",
"odorants",
"materials",
"science",
"zoology",
"quantum... | 2018 | Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location? |
Substrate dephosphorylation by the cyclin-dependent kinase ( Cdk ) -opposing phosphatase , Cdc14 , is vital for many events during budding yeast mitotic exit . Cdc14 is sequestered in the nucleolus through inhibitory binding to Net1 , from which it is released in anaphase following Net1 phosphorylation . Initial Net1 p... | During the cell cycle , a specific sequence of events leads to the formation of two daughter cells from one mother cell . Progression through the cell cycle is tightly controlled , with events occurring in the right place at the right time . Exactly how this is achieved is still being elucidated . In budding yeast , th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"and",
"Materials"
] | [
"signal",
"transduction",
"fungi",
"feedback",
"regulation",
"cell",
"biology",
"mechanisms",
"of",
"signal",
"transduction",
"cell",
"cycle",
"and",
"cell",
"division",
"biology",
"and",
"life",
"sciences",
"cell",
"processes",
"saccharomyces",
"cerevisiae",
"sacchar... | 2015 | Nur1 Dephosphorylation Confers Positive Feedback to Mitotic Exit Phosphatase Activation in Budding Yeast |
The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA . Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6 , but it wa... | In all organisms , diverse classes of RNA perform a wide range of functions , including programing of protein synthesis , transcriptional and post-transcriptional regulation of gene expression and forming key structural and functional components for pre-mRNA splicing , ribosome synthesis and translation . In consequenc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Availability",
"of",
"data",
"and",
"materials"
] | [
"transfer",
"rna",
"small",
"nucleolar",
"rnas",
"chemical",
"bonding",
"chemical",
"characterization",
"vesicles",
"gene",
"regulation",
"messenger",
"rna",
"cellular",
"structures",
"and",
"organelles",
"physical",
"chemistry",
"research",
"and",
"analysis",
"methods"... | 2017 | Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex |
Ischemic stroke is the second leading cause of death worldwide . Only one moderately effective therapy exists , albeit with contraindications that exclude 90% of the patients . This medical need contrasts with a high failure rate of more than 1 , 000 pre-clinical drug candidates for stroke therapies . Thus , there is a... | Stroke is the second leading cause of death worldwide . Today , only one approved therapy exists—a drug that breaks down blood clots—the effectiveness of which is moderate , and it can only be used in about 10% of patients because of contraindications . New therapeutic strategies that are translatable to humans and mor... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"physiology/cardiovascular",
"physiology",
"and",
"circulation",
"neurological",
"disorders/cerebrovascular",
"disease",
"non-clinical",
"medicine/research",
"methods",
"pharmacology/drug",
"development",
"cardiovascular",
"disorders/cardiovascular",
"pharmacology",
"genetics",
"and"... | 2010 | Post-Stroke Inhibition of Induced NADPH Oxidase Type 4 Prevents Oxidative Stress and Neurodegeneration |
During the last 20 years , the epidemiology of Japanese encephalitis virus ( JEV ) has changed significantly in its endemic regions due to the gradual displacement of the previously dominant genotype III ( GIII ) with clade b of GI ( GI-b ) . Whilst there is only limited genetic difference distinguishing the two GI cla... | Japanese encephalitis virus ( JEV ) is a zoonotic flavivirus , which is primarily transmitted by Culex species mosquitoes and a leading cause of pediatric encephalitis in Asia . JEV is also an important public health threat to countries outside the endemic region because collections of Cx . quinquefasciatus from around... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"japanese",
"encephalitis",
"virus",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"geographical",
"locations",
"microbiology",
"vector-borne",
"diseases",
"vertebrates",
"saliva",
"a... | 2016 | Differential Infectivities among Different Japanese Encephalitis Virus Genotypes in Culex quinquefasciatus Mosquitoes |
Zambia is endemic for Taenia solium taeniosis and cysticercosis . In this single-centered , cross-sectional , community-based study , the role of neurocysticercosis ( NCC ) as a cause of epilepsy was examined . People with epilepsy ( PWE , n = 56 ) were identified in an endemic area using a screening questionnaire foll... | Neurocysticercosis , an infection caused by the larval stage of Taenia solium ( the pork tapeworm ) , is a preventable and treatable disease and one of the main causes of epilepsy in low-income countries . Studies in Zambia have indicated high endemicity of T . solium in rural communities where a high prevalence of epi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Prevalence of Neurocysticercosis in People with Epilepsy in the Eastern Province of Zambia |
A bivalent killed whole cell oral cholera vaccine has been found to be safe and efficacious for five years in the cholera endemic setting of Kolkata , India , when given in a two dose schedule , two weeks apart . A randomized controlled trial revealed that the immune response was not significantly increased following t... | The five year efficacy results of the bivalent , killed whole cell oral cholera vaccine was shown to offer 65% protection in cholera endemic Kolkata . Currently , two oral cholera vaccines ( OCV ) are prequalified by the World Health Organization: the whole cell recombinant cholera toxin B subunit vaccine ( Dukoral ) ,... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Flexibility of Oral Cholera Vaccine Dosing—A Randomized Controlled Trial Measuring Immune Responses Following Alternative Vaccination Schedules in a Cholera Hyper-Endemic Zone |
Dihydropyridines ( DHPs ) are L-type calcium channel ( Cav1 ) blockers prescribed to treat several diseases including hypertension . Cav1 channels normally exist in three states: a resting closed state , an open state that is triggered by membrane depolarization , followed by a non-conducting inactivated state that is ... | L-type calcium channels are important drug targets because they regulate many physiological processes throughout the body . For example , L-type calcium channels regulate cardiac myocytes and vascular smooth muscle contraction . Antagonists are therefore commonly used to lower blood pressure and treat other related ail... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"physiology/cardiovascular",
"physiology",
"and",
"circulation",
"non-clinical",
"medicine",
"pharmacology/drug",
"resistance",
"physiology/muscle",
"and",
"connective",
"tissue",
"physiology/neuronal",
"signaling",
"mechanisms",
"chemical",
"biology"
] | 2008 | A Genetic Screen for Dihydropyridine (DHP)-Resistant Worms Reveals New Residues Required for DHP-Blockage of Mammalian Calcium Channels |
Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs . However , it can be difficult to decipher the basis of changes in chromatin organization and their functional effect on gene expression . Here , we present a large-scale comparative g... | Divergence in gene regulation plays a major role in organismal evolution . Evidence suggests that changes in the packaging of eukaryotic genomes into chromatin can underlie the evolution of divergent gene expression patterns . Here , we explore the role of chromatin structure in regulatory evolution by whole-genome mea... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/nuclear",
"structure",
"and",
"function",
"mol... | 2010 | The Role of Nucleosome Positioning in the Evolution of Gene Regulation |
The Sonic hedgehog ( Shh ) signaling pathway regulates developmental , homeostatic , and repair processes throughout the body . In the skin , touch domes develop in tandem with primary hair follicles and contain sensory Merkel cells . The developmental signaling requirements for touch dome specification are largely unk... | Sonic hedgehog ( Shh ) is one of a limited set of signaling molecules that cells use to drive organ formation during development and tissue regeneration after birth . How Shh signaling achieves different biological effects in the same tissue is incompletely understood . Touch domes are unique sensory structures in the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"skin",
"merkel",
"cells",
"medicine",
"and",
"health",
"sciences",
"integumentary",
"system",
"epithelial",
"cells",
"developmental",
"signaling",
"epidermis",
"research",
"and",
"analysis",
"methods",
"specimen",
"preparation",
"and",
"treatment",
"staining",
"hair",
... | 2016 | A Cascade of Wnt, Eda, and Shh Signaling Is Essential for Touch Dome Merkel Cell Development |
Cholera remains a substantial health burden in Asia and Africa particularly in resource poor settings . The standard procedures to identify the etiological organism V . cholerae are isolation from microbiological culture from stool as well as Polymerase Chain Reaction ( PCR ) . Both the processes are highly lab oriente... | Cholera still remains a burning public health issue in the developing world . Microbiological culture is the gold standard method for cholera diagnosis . However , it requires well equipped laboratories and 24–72 hours’ time for the isolation of pathogens , which may not be feasible for hard to reach areas and during e... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"microbial",
"cultures",
"pathogens",
"vibrio",
"biological",
"cultures",
"tropical",
"diseases",
"microbiology",
"geographical",
"locations",
"immunology",
"dia... | 2019 | Field evaluation of a locally produced rapid diagnostic test for early detection of cholera in Bangladesh |
Calcium responses have been observed as spikes of the whole-cell calcium concentration in numerous cell types and are essential for translating extracellular stimuli into cellular responses . While there are several suggestions for how this encoding is achieved , we still lack a comprehensive theory . To achieve this g... | Upon stimulation a large number of cell types respond with transient increases of the intracellular calcium concentration , which often take the form of repetitive spikes . It is therefore believed that calcium spikes play a central role in cellular signal transduction . A critical feature of these calcium spikes is th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"carbachol",
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"paracrine",
"signaling",
"drugs",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"endocrine",
"physiology",
"probability",
"distribution",
"math... | 2017 | A Bayesian approach to modelling heterogeneous calcium responses in cell populations |
Dengue is a major public health problem in tropical and subtropical regions; however , under-reporting of cases to national surveillance systems hinders accurate knowledge of disease burden and costs . Laboratory-confirmed dengue cases identified through the Nicaraguan Pediatric Dengue Cohort Study ( PDCS ) were compar... | National public health and epidemiology programs are often tasked with tracking certain infectious diseases , but many barriers lead to under-reporting . In tropical and subtropical countries where dengue fever is endemic , under-reporting may be due to misdiagnosis , limitations of the WHO case classification , and la... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/epidemiology",
"infectious",
"diseases/viral",
"infections",
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2010 | High Dengue Case Capture Rate in Four Years of a Cohort Study in Nicaragua Compared to National Surveillance Data |
Dengue infection ranks as one of the most significant viral diseases of the globe . Currently , there is no specific vaccine or antiviral therapy for prevention or treatment . Monocytes/macrophages are the principal target cells for dengue virus and are responsible for disseminating the virus after its transmission . D... | Prevention and treatment of dengue infection remain a serious global public health priority . Extensive efforts are required toward the development of vaccines and discovery of potential therapeutic compounds against the dengue viruses . Dengue virus entry is a critical step for virus reproduction and establishes the i... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"medicine",
"public",
"health",
"and",
"epidemiology",
"small",
"molecules",
"microbiology",
"host-pathogen",
"interaction",
"developmental",
"biology",
"emerging",
"infectious",
"diseases",
"microbial",
"growth",
"and",
"development",
"applied",
"microbiol... | 2011 | Inhibition of Dengue Virus Entry and Multiplication into Monocytes Using RNA Interference |
Transcription of the Neurospora crassa circadian clock gene frequency ( frq ) is an essential process in the negative feedback loop that controls circadian rhythms . WHITE COLLAR 1 ( WC-1 ) and WHITE COLLAR 2 ( WC-2 ) forms the WC complex ( WCC ) that is the main activator of frq transcription by binding to its promote... | Circadian clocks , which measure time on a scale of approximately 24 hours , are generated by a cell-autonomous circadian oscillator comprised of autoregulatory feedback loops . In the Neurospora crassa circadian oscillator , WHITE COLLAR complex ( WCC ) actives transcription of the frequency ( frq ) gene . FRQ inhibit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"gene",
"regulation",
"regulatory",
"proteins",
"messenger",
"rna",
"dna-binding",
"proteins",
"circadian",
"oscillators",
"transcription",
"factors",
"chronobiology",
"molecular",
"biology",
"techniques",
"research",
"and",
"analysis",
"methods",
"transc... | 2018 | Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus |
Visceral leishmaniasis ( VL ) is a disease caused by two known vector-borne parasite species ( Leishmania donovani , L . infantum ) , transmitted to man by phlebotomine sand flies ( species: Phlebotomus and Lutzomyia ) , resulting in ≈50 , 000 human fatalities annually , ≈67% occurring on the Indian subcontinent . Indo... | Visceral leishmaniasis is a disease caused by a virulent vector-borne parasite transmitted to man by phlebotomine sand flies . Fipronil-based drugs , administered to cattle orally , provide a potential means of sand fly control by permeating in cattle blood and being excreted in cattle feces , targeting adult females f... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"livestock",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"insect",
"metamorphosis",
"ruminants",
"demography",
"vertebrates",
"sand",
"flies",
"animals",
"mammals",
"developmental",
"biology",
"pupae",
"population",
"biology",
"infectiou... | 2016 | Visceral Leishmaniasis on the Indian Subcontinent: Modelling the Dynamic Relationship between Vector Control Schemes and Vector Life Cycles |
The circadian clock controls many physiological processes in higher plants and causes a large fraction of the genome to be expressed with a 24h rhythm . The transcripts encoding the RNA-binding proteins AtGRP7 ( Arabidopsis thaliana Glycine Rich Protein 7 ) and AtGRP8 oscillate with evening peaks . The circadian clock ... | The circadian clock organizes the day in the life of a plant by causing 24h rhythms in gene expression . For example , the core clockwork of the model plant Arabidopsis thaliana causes the transcripts encoding the RNA-binding proteins AtGRP7 and AtGRP8 to undergo high amplitude oscillations with a peak at the end of th... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"systems",
"biology",
"model",
"organisms",
"plant",
"and",
"algal",
"models",
"mathematics",
"theoretical",
"biology",
"plant",
"biology",
"regulatory",
"networks",
"biology",
"computational",
"biology",
"signaling",
"networks",
"nonlinear",
"dynamics",
"genetics",
"an... | 2013 | A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana |
Enhanced root hair production , which increases the root surface area for nutrient uptake , is a typical adaptive response of plants to phosphate ( Pi ) starvation . Although previous studies have shown that ethylene plays an important role in root hair development induced by Pi starvation , the underlying molecular me... | Phytohormone ethylene has previously been known to play an important role in mediating root hair development induced by phosphate starvation; however , the underlying molecular mechanism is not understood . Using combined molecular , genetic , and genomic approaches , we identify a group of genes that affect root hair ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"anatomy",
"chemical",
"compounds",
"ethylene",
"signaling",
"cascade",
"ethylene",
"gene",
"regulation",
"regulatory",
"proteins",
"brassica",
"dna-binding",
"proteins",
"organic",
"compounds",
"hormones",
"root",
"hairs",
"mutation",
"plant",
"science",
"mode... | 2016 | The Molecular Mechanism of Ethylene-Mediated Root Hair Development Induced by Phosphate Starvation |
The parameters involved in human cytomegalovirus ( HCMV ) latent infection in CD14 ( + ) and CD34 ( + ) cells remain poorly identified . Using next generation sequencing we deduced the transcriptome of HCMV latently infected CD14 ( + ) and CD34 ( + ) cells in experimental as well as natural latency settings . The gene ... | Human cytomegalovirus ( HCMV ) is a ubiquitous herpesvirus where infection is usually subclinical . HCMV initial infection is followed by the establishment of latency in CD34 ( + ) myeloid cells and CD14 ( + ) monocytes . Primary infection or reactivation from latency can be associated with significant morbidity and mo... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases"
] | 2013 | Cis and Trans Acting Factors Involved in Human Cytomegalovirus Experimental and Natural Latent Infection of CD14 (+) Monocytes and CD34 (+) Cells |
In the rice blast fungus Magnaporthe oryzae , the cAMP-PKA pathway regulates surface recognition , appressorium turgor generation , and invasive growth . However , deletion of CPKA failed to block appressorium formation and responses to exogenous cAMP . In this study , we generated and characterized the cpk2 and cpkA c... | The cAMP-PKA signaling pathway plays a critical role in regulating various cellular processes in eukaryotic cells in response to extracellular cues . In the rice blast fungus , this important pathway is involved in surface recognition , appressorium morphogenesis , and infection . However , the exact role of PKA is not... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"gene",
"regulation",
"fungal",
"structure",
"fungi",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"gene",
"types",
"appressoria",
"plant",
"pathology",
"molecular",
"biology",
"techniques",
"mutagenesis",
"and",
"g... | 2017 | PKA activity is essential for relieving the suppression of hyphal growth and appressorium formation by MoSfl1 in Magnaporthe oryzae |
Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands . Experimental structure determination of such complexes at atomic resolution , however , can be time-consuming and costly . Computational methods for structure prediction of protein/ligand complexes , p... | Structure-based drug design has become a powerful tool in modern drug discovery pipelines . A critical prerequisite is a structure of the target protein close to its ligand bound conformation which is often difficult to determine experimentally . In many cases , a structure of the unbound receptor is available , but co... | [
"Abstract",
"Introduction"
] | [
"biophysics/theory",
"and",
"simulation",
"biophysics/biomacromolecule-ligand",
"interactions",
"computational",
"biology/protein",
"structure",
"prediction",
"computational",
"biology/molecular",
"dynamics",
"biochemistry/drug",
"discovery"
] | 2010 | Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations |
Group A streptococcus ( GAS; Streptococcus pyogenes ) is a common pathogen that invades non-phagocytic human cells via endocytosis . Once taken up by cells , it escapes from the endocytic pathway to the cytoplasm , but here it is contained within a membrane-bound structure termed GAS-containing autophagosome-like vacuo... | Autophagy has become one of the leading edge subjects in science . Autophagy occurs when a cell eats some of its cellular components and digests them . These cellular components may include cytosol and organelles as well as bacteria that has invaded the cell . Thus , autophagy plays an important role in killing pathoge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology"
] | 2009 | An Initial Step of GAS-Containing Autophagosome-Like Vacuoles Formation Requires Rab7 |
Unique purine-rich mRNA sequences embedded in the coding sequences of a distinct group of gammaherpesvirus maintenance proteins underlie the ability of the latently infected cell to minimize immune recognition . The Epstein-Barr virus nuclear antigen , EBNA1 , a well characterized lymphocryptovirus maintenance protein ... | Viruses establishing persistent latent infections have evolved various mechanisms to avoid immune surveillance . The Epstein-Barr virus-encoded nuclear antigen , EBNA1 , expressed in all EBV-associated malignancies , modulates its own protein levels at quantities sufficient to maintain viral infection but low enough so... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"antigen",
"processing",
"and",
"recognition",
"epstein-barr",
"virus",
"infectious",
"mononucleosis",
"immunology",
"biology",
"viral",
"diseases",
"immune",
"response"
] | 2012 | Messenger RNA Sequence Rather than Protein Sequence Determines the Level of Self-synthesis and Antigen Presentation of the EBV-encoded Antigen, EBNA1 |
Rapid bone destruction often leads to permanent joint dysfunction in patients with septic arthritis , which is mainly caused by Staphylococcus aureus ( S . aureus ) . Staphylococcal cell wall components are known to induce joint inflammation and bone destruction . Here , we show that a single intra-articular injection ... | Rapid bone destruction often leads to permanent joint dysfunction in septic arthritis , which is mainly caused by S . aureus . Despite advances in the use of antibiotics , permanent reductions in joint function occur in up to 50% of patients , who may also need joint replacement surgery . Additional challenge is posed ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"rheumatology",
"knee",
"joints",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"diagnostic",
"radiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"staphylococcus",
"aureus",
"magnetic",
"r... | 2019 | The YIN and YANG of lipoproteins in developing and preventing infectious arthritis by Staphylococcus aureus |
Chagas disease , caused by Trypanosoma cruzi , is endemic in Latin America and an emerging infectious disease in the US and Europe . We have shown TcG1 , TcG2 , and TcG4 antigens elicit protective immunity to T . cruzi in mice and dogs . Herein , we investigated antigenicity of the recombinant proteins in humans to det... | Chagas disease is the most common cause of congestive heart failure related deaths among young adults in the endemic areas of South and Central America and Mexico . Diagnosis and treatment of T . cruzi infection has remained difficult and challenging after 100 years of its identification . In >95% of human cases , T . ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"biomarker",
"epidemiology",
"clinical",
"laboratory",
"sciences",
"diagnostic",
"medicine",
"chagas",
"disease",
"epidemiology",
"neglected",
"tropical",
"diseases",
"epidemiological",
"method... | 2013 | Antigenicity and Diagnostic Potential of Vaccine Candidates in Human Chagas Disease |
An important follow-up step after genetic markers are found to be associated with a disease outcome is a more detailed analysis investigating how the implicated gene or chromosomal region and an established environment risk factor interact to influence the disease risk . The standard approach to this study of gene–envi... | Many common diseases result from a complex interplay of genetic and environmental risk factors . It is important to study the potential genetic and environmental risk factors jointly in order to achieve a better understanding of the mechanisms underlying disease development . The standard single-marker approach that st... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"computer",
"science"
] | 2012 | A Flexible Bayesian Model for Studying Gene–Environment Interaction |
Meningococcal meningitis is a major health problem in the “African Meningitis Belt” where recurrent epidemics occur during the hot , dry season . In Niger , a central country belonging to the Meningitis Belt , reported meningitis cases varied between 1 , 000 and 13 , 000 from 2003 to 2009 , with a case-fatality rate of... | Meningococcal meningitis ( MM ) is an infection of the meninges caused by a bacterium , Neisseria meningitidis , transmitted through respiratory and throat secretions . It can cause brain damage and results in death in 5–15% of cases . Large epidemics of MM occur almost every year in sub-Saharan Africa during the hot ,... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"geography",
"public",
"health",
"and",
"epidemiology",
"computer",
"science",
"epidemiology",
"earth",
"sciences",
"public",
"health",
"geoinformatics",
"human",
"geography"
] | 2012 | Analysing Spatio-Temporal Clustering of Meningococcal Meningitis Outbreaks in Niger Reveals Opportunities for Improved Disease Control |
Eastern Equine Encephalitis ( EEE ) ( Togaviridae , Alphavirus ) is a highly pathogenic mosquito-borne arbovirus that circulates in an enzootic cycle involving Culiseta melanura mosquitoes and wild Passeriformes birds in freshwater swamp habitats . Recently , the northeastern United States has experienced an intensific... | Eastern equine encephalitis ( EEE ) is a highly pathogenic mosquito-borne virus responsible for outbreaks of severe disease in humans and equines , causing high mortality and neurological impairment in most survivors . In the past , human disease outbreaks in the northeastern United States occurred intermittently; howe... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"population",
"genetics",
"genomic",
"library",
"construction",
"animals",
"invertebrate",
"genomics",
"genome",
"analysis",
"dna",
"construction",
"molecular",
"biology",
"techniques",
"population",
"biology",
"in... | 2018 | Population genomics of Culiseta melanura, the principal vector of Eastern equine encephalitis virus in the United States |
The type 2 immune response is the central mechanism of disease progression in schistosomiasis , but the signals that induce it after infection remain elusive . Aberrant microRNA ( miRNA ) expression is a hallmark of human diseases including schistosomiasis , and targeting the deregulated miRNA can mitigate disease outc... | Schistosomiasis is a serious but neglected tropical infectious disease . Hepatic fibrosis caused by lodged eggs from the parasite is the primary cause of morbidity and mortality from this disease . Type 2 immune response , featured by the T helper 2 cell associated cytokines such as IL-4 and IL-13 , is the central regu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"schistosoma",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"helminths",
"gene",
"regulation",
"tropical",
"diseases",
"fibrosis",
"parasitic",
"diseases",
"animals",
"liver",
"diseases",
"collagens",
"animal",
"models",
"developmental",
"biology",
"micrornas... | 2018 | Down-regulation of microRNA-203-3p initiates type 2 pathology during schistosome infection via elevation of interleukin-33 |
The plant hormone auxin plays a critical role in regulating various aspects of plant growth and development , and the spatial accumulation of auxin within organs , which is primarily attributable to local auxin biosynthesis and polar transport , is largely responsible for lateral organ morphogenesis and the establishme... | Auxin is a key plant hormone and the spatial accumulation of auxin is essential for lateral organ morphogenesis and gravitropic responses in higher plants . However , the various mechanisms through which spatial auxin accumulation is regulated remain to be fully elucidated . Here , we identify a gain-of-function mutant... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The Arabidopsis IDD14, IDD15, and IDD16 Cooperatively Regulate Lateral Organ Morphogenesis and Gravitropism by Promoting Auxin Biosynthesis and Transport |
Trachoma , caused by Chlamydia trachomatis ( Ct ) , is the leading infectious cause of blindness . Sequence-based analysis of the multiple strains typically present in endemic communities may be informative for epidemiology , transmission , response to treatment , and understanding the host response . Conjunctival and ... | Trachoma is an important cause of blindness resulting from transmission of the bacterium Chlamydia trachomatis . One way to understand better how this infection is transmitted and how the human immune system controls it is to study the strains of bacteria associated with infection . Comparing strains before and after t... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"ophthalmology/eye",
"infections",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/bacterial",
"infections",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2008 | Chlamydia trachomatis ompA Variants in Trachoma: What Do They Tell Us? |
Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression . A commonly used method for this purpose is a top-down approach based on clustering the netw... | Gene co-expression networks unite genes with similar expression patterns . From these networks , gene co-expression modules can be identified . A specific family of transcription factor ( s ) may regulate the genes within a co-expression module . Thus , module identification is important to decipher the gene regulatory... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways |
Differential DNA methylation is an essential epigenetic signal for gene regulation , development , and disease processes . We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types . A total of 28 , 626 subclones were seq... | Epigenetics is defined as the inheritance of changes in gene function without changing the DNA sequence . Epigenetic signals comprise methylation of cytosine bases of the DNA and chemical modifications of the histone proteins . DNA methylation plays important roles in development and disease processes . To investigate ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/histone",
"modification",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/genome",
"projects",
"molecular",
"biology/dna",
"methylation",
"genetics",
"and",
"genomics/epi... | 2009 | DNA Methylation Analysis of Chromosome 21 Gene Promoters at Single Base Pair and Single Allele Resolution |
Malaria , dengue fever , and filariasis are three of the most common mosquito-borne diseases worldwide . Malaria and lymphatic filariasis can occur as concomitant human infections while also sharing common mosquito vectors . The overall prevalence and health significance of malaria and filariasis have made them top pri... | Malaria and lymphatic filariasis are two of the most important mosquito-borne parasitic diseases worldwide , which can occur as concomitant human infections . The Anopheles sinensis mosquito is the most common malaria and lymphatic filariasis vector in Southeast Asia . Disease-vector control is an important part of the... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"arthropoda",
"public",
"and",
"occupational",
"health",
"invertebrates",
"disease",
"vectors",
"mosquitoes",
"medicine",
"and",
"health",
"sciences",
"infectious",
"diseases",
"helminth",
"infections",
"filariasis",
"epidemiology",
"global",
"health",
"biology",
"and",
... | 2014 | Multiple Resistances and Complex Mechanisms of Anopheles sinensis Mosquito: A Major Obstacle to Mosquito-Borne Diseases Control and Elimination in China |
During animal development , cellular morphogenesis plays a fundamental role in determining the shape and function of tissues and organs . Identifying the components that regulate and drive morphogenesis is thus a major goal of developmental biology . The four-celled tip of the Caenorhabditis elegans male tail is a simp... | Morphogenesis is a process in which cells change their shape and position to give rise to mature structures . Elucidation of the molecular basis of morphogenesis and its regulation would be a major step towards understanding organ formation and functionality . We focus on a powerful model for morphogenesis , the four-c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"genetics",
"biology",
"morphogenesis",
"gene",
"networks",
"genetics",
"and",
"genomics"
] | 2011 | A Bow-Tie Genetic Architecture for Morphogenesis Suggested by a Genome-Wide RNAi Screen in Caenorhabditis elegans |
Cystic echinococcosis ( CE ) is a chronic , complex and neglected disease caused by the larval stage of Echinococcus granulosus . The effects of this neglect have a stronger impact in remote rural areas whose inhabitants have no chances of being diagnosed and treated properly without leaving their jobs and travelling l... | Cystic echinococcosis ( CE ) is an important and widespread disease that affects sheep , cattle , and humans living in areas where sheep and cattle are raised . CE is highly endemic in rural sections of Rio Negro , Argentina , where our group is based . However , it requires continuous monitoring of both populations wi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"global",
"health"
] | 2012 | Early Diagnosis, Treatment and Follow-Up of Cystic Echinococcosis in Remote Rural Areas in Patagonia: Impact of Ultrasound Training of Non-Specialists |
Emerging evidence has shown microRNAs ( miRNAs ) play an important role in human disease research . Identifying potential association among them is significant for the development of pathology , diagnose and therapy . However , only a tiny portion of all miRNA-disease pairs in the current datasets are experimentally va... | Identification of miRNA-disease associations is considered as an important step for the development of diagnose and therapy . Computational methods contribute to discovering the potential disease-related miRNAs . Based on the assumption that functionally related miRNAs tend to be involved disease , the model of LMTRDA ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"and",
"discussion",
"Conclusion"
] | [
"medicine",
"and",
"health",
"sciences",
"linguistics",
"statistics",
"natural",
"antisense",
"transcripts",
"gene",
"regulation",
"cancers",
"and",
"neoplasms",
"social",
"sciences",
"oncology",
"hematologic",
"cancers",
"and",
"related",
"disorders",
"micrornas",
"mat... | 2019 | LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities |
The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years . Using unbiased molecular dynamics with the OPEP coarse-grained potential , we focus here on the onset of aggregation in a 20-mer system . With a total of 16 . 9... | Protein aggregation plays an important pathological role in numerous neurodegenerative diseases such as Alzheimer's , Parkinson's , Creutzfeldt-Jakob , the Prion disease and diabetes mellitus . In most cases , misfolded proteins are involved and aggregate irreversibly to form highly ordered insoluble macrostructures , ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results/Discussion"
] | [
"physics",
"biochemistry",
"biochemistry",
"simulations",
"proteins",
"biophysics",
"simulations",
"chemistry",
"biology",
"computational",
"chemistry",
"biophysics",
"thermodynamics",
"physical",
"chemistry"
] | 2012 | Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence |
Vector-borne transmission of Trypanosoma cruzi is seen exclusively in the Americas where an estimated 8 million people are infected with the parasite . Significant research in southern Peru has been conducted to understand T . cruzi infection and vector control , however , much less is known about the burden of infecti... | Chagas disease causes significant morbidity and mortality throughout Central and South America . The epidemiology and control of this disease is subject to unique regional particularities , including the behavior and ecology of the local insect vector species . Significant resources have been allocated towards research... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Prevalence and Transmission of Trypanosoma cruzi in People of Rural Communities of the High Jungle of Northern Peru |
Many mosquito species are naturally polymorphic for their abilities to transmit parasites , a feature which is of great interest for controlling vector-borne disease . Aedes aegypti , the primary vector of dengue and yellow fever and a laboratory model for studying lymphatic filariasis , is genetically variable for its... | Within mosquito populations , genetic differences between individuals affect their ability to transmit human diseases such as malaria , dengue fever , and lymphatic filariasis . In the mosquito Aedes aegypti , some individuals are genetically resistant to Brugia malayi , a mosquito-vectored parasite that causes a debil... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response |
The late onset of neurodegeneration in humans indicates that the survival and function of cells in the nervous system must be maintained throughout adulthood . In the optic lamina of the adult Drosophila , the photoreceptor axons are surrounded by multiple types of glia . We demonstrated that the adult photoreceptors a... | Degeneration of the nervous system can be viewed as a failure to maintain cell survival or function in the nervous system . The late onset of neurodegeneration in humans indicates that the cell survival in the nervous system must be maintained throughout our lives . Neuronal survival is maintained by neurotrophic facto... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Maintenance of Glia in the Optic Lamina Is Mediated by EGFR Signaling by Photoreceptors in Adult Drosophila |
Measles remains a significant childhood disease , and is associated with a transient immune suppression . Paradoxically , measles virus ( MV ) infection also induces robust MV-specific immune responses . Current hypotheses for the mechanism underlying measles immune suppression focus on functional impairment of lymphoc... | Measles is associated with a transient immune suppression , resulting in increased susceptibility to opportunistic infections . Indeed , the main causes of measles mortality are secondary infections in the respiratory and digestive tract . Although measles is associated with lymphopenia , depletion of lymphocytes has o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"immune",
"cells",
"immunity",
"to",
"infections",
"immunology",
"immune",
"suppression",
"microbiology",
"animal",
"models",
"histology",
"adaptive",
"immunity",
"model",
"organisms",
"immune",
"defense",
"animal",
"models",
"of",
"infection",
"infectious",... | 2012 | Measles Immune Suppression: Lessons from the Macaque Model |
Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis , the main causative agent of tuberculosis , resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine . The continuous and ever increasing appearance of multi-drug resistant mycobacteria necessitat... | Mycobacterium tuberculosis ( MTB ) , the causative agent of TB , is a dramatically successful pathogen that poses a considerable challenge for modern medicine . The increase in multi-drug resistant TB necessitates the identification of novel drug targets and drugs with new mechanisms of action . In this work , we devel... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"sequence",
"analysis",
"systems",
"biology",
"biochemistry",
"genomics",
"biology",
"computational",
"biology",
"comparative",
"genomics",
"proteomics",
"pharmacogenomics"
] | 2011 | Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosis |
Candida albicans is a major life-threatening human fungal pathogen . Host defence against systemic Candida infection relies mainly on phagocytosis of fungal cells by cells of the innate immune system . In this study , we have employed video microscopy , coupled with sophisticated image analysis tools , to assess the co... | Host defence against systemic candidiasis relies mainly on the ingestion and elimination of fungal cells by cells of the innate immune system , especially neutrophils and macrophages . Here we have used live cell video microscopy coupled with sophisticated image analysis to generate a temporal and spatial analysis in u... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mycology",
"immune",
"cells",
"immunology",
"biology",
"microbiology"
] | 2012 | Stage Specific Assessment of Candida albicans Phagocytosis by Macrophages Identifies Cell Wall Composition and Morphogenesis as Key Determinants |
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology . We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements , which is based on the concept of “su... | The behavior of organisms is based on the concerted action occurring on an astonishing range of scales from the molecular to the organismal level . Molecular properties control the function of a cell , while cell ensembles form tissues and organs , which work together as an organism . In order to understand and charact... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells |
The human double-homeodomain retrogene DUX4 is expressed in the testis and epigenetically repressed in somatic tissues . Facioscapulohumeral muscular dystrophy ( FSHD ) is caused by mutations that decrease the epigenetic repression of DUX4 in somatic tissues and result in mis-expression of this transcription factor in ... | Transposable elements ( TEs ) are found in most genomes , and many TEs create extra copies of themselves in new genomic locations by a process called retrotransposition . TEs are often thought of as genomic parasites that must be suppressed , because retrotransposition can cause great harm to their host organism . Howe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | DUX4 Binding to Retroelements Creates Promoters That Are Active in FSHD Muscle and Testis |
Stimulus-specific adaptation ( SSA ) occurs when neurons decrease their responses to frequently-presented ( standard ) stimuli but not , or not as much , to other , rare ( deviant ) stimuli . SSA is present in all mammalian species in which it has been tested as well as in birds . SSA confers short-term memory to neuro... | We present a possible mechanism for the way auditory cortex emphasizes stimuli that are deviant within a regular , repetitive sequence . This enhancement is strong and widespread in auditory cortex , but not in its major thalamic input , the ventral division of the medial geniculate body . In contrast with previous mod... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"auditory",
"cortex",
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"neural",
"networks",
"nervous",
"system",
"membrane",
"potential",
"brain",
"electrophysiology",
"neuroscience",
"computational",
"neuroscience",
"mood",
"disorders",
"neuronal",
"tuni... | 2017 | Stimulus-specific adaptation in a recurrent network model of primary auditory cortex |
Glioblastoma , the most common primary malignant brain tumor , is incurable with current therapies . Genetic and molecular analyses demonstrate that glioblastomas frequently display mutations that activate receptor tyrosine kinase ( RTK ) and Pi-3 kinase ( PI3K ) signaling pathways . In Drosophila melanogaster , activa... | Glioblastomas , the most common primary brain tumor , harbor mutations in receptor tyrosine kinases ( RTKs ) , such as EGFR , and components of the Pi-3 kinase ( PI3K ) signaling pathway . However , the genes that act downstream of RTK and PI3K signaling to drive glioblastoma remain unclear . To investigate the genetic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cancer",
"genetics",
"signaling",
"in",
"selected",
"disciplines",
"neuroscience",
"model",
"organisms",
"oncogenic",
"signaling",
"biology",
"phospholipid",
"signaling",
"cascade",
"signal",
"transduction",
"genetic",
"screens",
"genetics",
"molecular",
"cell",
"biology... | 2013 | A Kinome-Wide RNAi Screen in Drosophila Glia Reveals That the RIO Kinases Mediate Cell Proliferation and Survival through TORC2-Akt Signaling in Glioblastoma |
Cryptochromes are a class of flavoprotein blue-light signaling receptors found in plants , animals , and humans that control plant development and the entrainment of circadian rhythms . In plant cryptochromes , light activation is proposed to result from photoreduction of a protein-bound flavin chromophore through intr... | Vision in animals is generally associated with light-sensitive rhodopsin pigments located in the eyes . However , animals ranging from flies to humans also possess ancient visual receptors known as cryptochromes in multiple cell types . In this work , we study the mechanism of light sensing in two representative animal... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"biophysics",
"molecular",
"biology"
] | 2008 | Human and Drosophila Cryptochromes Are Light Activated by Flavin Photoreduction in Living Cells |
In development , lineage-restricted transcription factors simultaneously promote differentiation while repressing alternative fates . Molecular dissection of this process has been challenging as transcription factor loci are regulated by many trans-acting factors functioning through dispersed cis elements . It is not u... | Different cell types are formed and maintained by proteins called transcription factors that directly bind to specific DNA sequences to activate or repress gene expression . While numerous DNA sequences bound by transcription factors are established , many questions remain unanswered regarding how they function at spec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/epigenetics",
"developmental",
"biology/developmental",
"molecular",
"mechanisms",
"molecular",
"biology/transcription",
"initiation",
"and",
"activation",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2010 | A Single cis Element Maintains Repression of the Key Developmental Regulator Gata2 |
Crimean-Congo hemorrhagic fever ( CCHF ) is a severe tick-borne disease well recognized through Europe and Asia where diagnostic tests and medical surveillance are available . However , it is largely neglected in Africa , especially in the tropical rainforest of Central Africa where only sporadic human cases have been ... | Crimean-Congo hemorrhagic fever virus ( CCHFV ) is transmitted to humans through tick-bite or contact with infected blood or tissues from livestock , the main vertebrate hosts in a peri-domestic natural cycle . With numerous outbreaks , a high case fatality rate ( 3%–30% ) and a high risk for nosocomial transmission , ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion"
] | [
"emerging",
"infectious",
"diseases",
"virology",
"emerging",
"viral",
"diseases",
"biology",
"microbiology",
"viral",
"evolution"
] | 2011 | Re-Emergence of Crimean-Congo Hemorrhagic Fever Virus in Central Africa |
Cell cycle control is modified at meiosis compared to mitosis , because two divisions follow a single DNA replication event . Cyclin-dependent kinases ( CDKs ) promote progression through both meiosis and mitosis , and a central regulator of their activity is the APC/C ( Anaphase Promoting Complex/Cyclosome ) that is e... | In the life cycle of sexual organisms , a specialized cell division—meiosis—reduces the number of chromosomes from two sets ( 2n , diploid ) to one set ( n , haploid ) , while fertilization restores the original chromosome number . Meiosis reduces ploidy because it consists of two cellular divisions following a single ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"plant",
"biology",
"genetics",
"biology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | OSD1 Promotes Meiotic Progression via APC/C Inhibition and Forms a Regulatory Network with TDM and CYCA1;2/TAM |
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes . More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered . Due to limitations of experimental approaches , computational t... | Structures of protein-RNA complexes are important for characterization of biological processes . The number of experimentally determined protein-RNA complexes is limited . Thus modeling of these complexes is important . Reliable structural predictions of proteins and their complexes are provided by comparative modeling... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion"
] | [
"sequencing",
"techniques",
"protein",
"interactions",
"protein",
"structure",
"prediction",
"protein",
"structure",
"molecular",
"biology",
"techniques",
"rna",
"alignment",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"rna",
"structure",
"protein",
... | 2016 | Template-Based Modeling of Protein-RNA Interactions |
Genomic time series data generated by evolve-and-resequence ( E&R ) experiments offer a powerful window into the mechanisms that drive evolution . However , standard population genetic inference procedures do not account for sampling serially over time , and new methods are needed to make full use of modern experimenta... | A growing number of experimental biologists are generating “evolve-and-resequence” ( E&R ) data in which the genomes of an experimental population are repeatedly sequenced over time . The resulting time series data provide important new insights into the dynamics of evolution . This type of analysis has only recently b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution |
Elevated levels of acute-phase serum amyloid A ( A-SAA ) cause amyloidosis and are a risk factor for atherosclerosis and its clinical complications , type 2 diabetes , as well as various malignancies . To investigate the genetic basis of A-SAA levels , we conducted the first genome-wide association study on baseline A-... | An elevated level of acute-phase serum amyloid A ( A-SAA ) , a sensitive marker of the acute inflammatory state with high heritability estimates , causes amyloidosis and is a risk factor for atherosclerosis and its clinical complications , type 2 diabetes , as well as various malignancies . This study describes the fir... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"discovery",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system"
] | 2010 | Genome-Wide Association Study Identifies Two Novel Regions at 11p15.5-p13 and 1p31 with Major Impact on Acute-Phase Serum Amyloid A |
For ethical and logistical reasons , population-genetic studies of parasites often rely on the non-invasive sampling of offspring shed from their definitive hosts . However , if the sampled offspring are naturally derived from a small number of parents , then the strong family structure can result in biased population-... | Genetic epidemiology uses genetic data to uncover patterns of disease processes . To acquire data for these analyses , individual pathogens are collected and scored at genetic markers , and the resultant data are analyzed to infer biological patterns about the pathogen populations . In lieu of invasive sampling of adul... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Non-Invasive Sampling of Schistosomes from Humans Requires Correcting for Family Structure |
A major obstacle to understanding neural coding and computation is the fact that experimental recordings typically sample only a small fraction of the neurons in a circuit . Measured neural properties are skewed by interactions between recorded neurons and the “hidden” portion of the network . To properly interpret neu... | No experiment in neuroscience can record from more than a tiny fraction of the total number of neurons present in a circuit . This severely complicates measurement of a network’s true properties , as unobserved neurons skew measurements away from what would be measured if all neurons were observed . For example , the m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"neural",
"networks",
"decision",
"making",
"nervous",
"system",
"membrane",
"potential",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"cognitive",
"psychology",
"cognition",
"network",
"analys... | 2018 | Predicting how and when hidden neurons skew measured synaptic interactions |
During the 2014 Ebola Virus Disease ( EVD ) epidemic , the Ebola-Tx trial evaluated the use of convalescent plasma ( CP ) in Guinea . The effectiveness of plasmapheresis trials depends on the recruitment of plasma donors . This paper describes what motivated or deterred EVD survivors to donate CP , providing insights f... | During the 2014 West-African Ebola Virus Disease epidemic , the Ebola-Tx clinical trial in Guinea aimed to determine whether the administration of Ebola antibodies from the blood plasma of Ebola survivors could increase Ebola patients’ survival rate . Ebola-Tx was the first trial to solicit and evaluate blood-product d... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusion"
] | [
"guinea",
"medicine",
"and",
"health",
"sciences",
"clinical",
"laboratory",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"education",
"pathogens",
"sociology",
"geographical",
"locations",
"tropical",
"diseases",
"social",
"sciences",
"eb... | 2018 | What motivates Ebola survivors to donate plasma during an emergency clinical trial? The case of Ebola-Tx in Guinea |
The human blood fluke Schistosoma mansoni causes intestinal schistosomiasis , a widespread neglected tropical disease . Infection of freshwater snails Biomphalaria spp . is an essential step in the transmission of S . mansoni to humans , although the physiological interactions between the parasite and its obligate snai... | Schistosoma mansoni is one of four major species of human blood flukes that , together , infect over 250 million people worldwide . Transmission of S . mansoni to humans requires infection of freshwater intermediate host snails , Biomphalaria spp . , in order to complete its life cycle . The B . glabrata embryonic ( Bg... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"schistosoma",
"invertebrates",
"schistosoma",
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"medicine",
"and",
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"reactive",
"oxygen",
"species",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"helminths",
"immunology",
"membrane",
"potential",
"el... | 2017 | H+ channels in embryonic Biomphalaria glabrata cell membranes: Putative roles in snail host-schistosome interactions |
Endogenous small RNAs ( sRNAs ) and Argonaute proteins are ubiquitous regulators of gene expression in germline and somatic tissues . sRNA-Argonaute complexes are often expressed in gametes and are consequently inherited by the next generation upon fertilization . In Caenorhabditis elegans , 26G-RNAs are primary endoge... | Small RNAs ( sRNAs ) and their partner Argonaute proteins regulate the expression of target RNAs . When sperm and egg meet upon fertilization , a diverse set of proteins and RNA , including sRNA-Argonaute complexes , is passed on to the developing progeny . Thus , these two players are important to initiate specific ge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"rna",
"interference",
"caenorhabditis",
"gene",
"regulation",
"animals",
"invertebrate",
"genomics",
"animal",
"models",
"age",
"groups",
"developmental",
"biology",
"caenorhabditis",
"elegans",
"model",
"organisms",
"genome",
"analysis",
"experimental",
... | 2019 | Maternal and zygotic gene regulatory effects of endogenous RNAi pathways |
Functional magnetic resonance imaging ( fMRI ) , with blood oxygenation level-dependent ( BOLD ) contrast , is a widely used technique for studying the human brain . However , it is an indirect measure of underlying neuronal activity and the processes that link this activity to BOLD signals are still a topic of much de... | Functional magnetic resonance imaging ( fMRI ) , with blood oxygenation level-dependent ( BOLD ) contrast , is a widely used technique for studying the human brain . However , the relationship between neuronal activity and blood flow , the basis of fMRI , is still under much debate . A growing body of evidence from ani... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"applied",
"mathematics",
"biology",
"computational",
"biology",
"nonlinear",
"dynamics",
"biophysics",
"neuroscience"
] | 2011 | Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI |
Rapidly characterizing the amplitude and variability in transmissibility of novel human influenza strains as they emerge is a key public health priority . However , comparison of early estimates of the basic reproduction number during the 2009 pandemic were challenging because of inconsistent data sources and methods .... | The ability to rapidly and reliably characterize novel strains of influenza in terms of their transmissibility is crucial for health planners: without good estimates for key parameters it is not possible to identify the appropriate strength of interventions or the spatial optimization of interventions based on variabil... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"population",
"modeling",
"influenza",
"infectious",
"disease",
"modeling",
"biology",
"viral",
"diseases",
"computational",
"biology"
] | 2013 | Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations |
Dengue is the world's most important mosquito-borne viral illness . Successful future management of this disease requires an understanding of the population dynamics of the vector , especially in the context of changing climates . Our capacity to predict future dynamics is reflected in our ability to explain the signif... | Dengue transmission has not always been confined to tropical areas . In some cases , this has been due to a reduced geographic range of the mosquitoes that are able to carry dengue viruses . In Australia , Aedes aegypti mosquitoes once occurred throughout temperate , drier parts of the country but are now restricted to... | [
"Abstract",
"Introduction",
"Methods",
"Discussion"
] | [
"infectious",
"diseases/viral",
"infections",
"ecology/population",
"ecology"
] | 2010 | The Extinction of Dengue through Natural Vulnerability of Its Vectors |
With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies , the chance to identify sub-networks involved in coordinated processing increases . Sequences of synchronous spike events ( SSEs ) constitute one type of such coordinated spiking that propagates ac... | Neurons in the cerebral cortex are highly interconnected . However , the mechanisms of coordinated processing in the neuronal network are not yet understood . Theoretical studies have proposed synchronized electrical impulses ( spikes ) propagating between groups of nerve cells as a basis of cortical processing . Indee... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"applied",
"mathematics",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"simulation",
"and",
"modeling",
"algorithms",
"probability",
"distribution",
"mathematics",
"convo... | 2016 | ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains |
Schistosomiasis is one of the most disabling neglected tropical diseases , ranking second in terms of years lived with disability . While treatment with the drug praziquantel can have immediate beneficial effects , reinfection can occur rapidly if people are in contact with cercaria-infested water . Water treatment for... | Schistosomiasis control currently focuses on preventive chemotherapy ( PC ) with praziquantel , which is effective , safe , and inexpensive . However , this treatment does not prevent subsequent reinfection . As schistosomiasis control targets become more ambitious and move towards elimination , interest is increasing ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"ultraviolet",
"radiation",
"helminths",
"tropical",
"diseases",
"database",
"searching",
"light",
"parasitic",
"diseases",
"animals",
"electromagnetic",
"radiation",
"neglect... | 2018 | The effectiveness of water treatment processes against schistosome cercariae: A systematic review |
Thrombocytopenia is a hallmark of dengue infection , and bleeding is a dreaded complication of dengue fever . Prophylactic platelet transfusion has been used to prevent bleeding in the management of dengue fever , although the evidence for its benefit is lacking . In adult dengue patients with platelet count <20 , 000/... | Thrombocytopenia is one of the most prominent clinical features in dengue infection . This may manifest clinically as bleeding , which carries significant morbidity and mortality . For many years , clinicians have given dengue patients platelet transfusion in a bid to increase their platelet counts to prevent hemorrhag... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"clinical",
"laboratory",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"blood",
"counts",
"immunology",
"tropical",
"diseases",
"preventive",
"medicine",
"signs",
"and",
"symptom... | 2016 | Potential Harm of Prophylactic Platelet Transfusion in Adult Dengue Patients |
Place cells in the mammalian hippocampus signal self-location with sparse spatially stable firing fields . Based on observation of place cell activity it is possible to accurately decode an animal’s location . The precision of this decoding sets a lower bound for the amount of information that the hippocampal populatio... | Being able to accurately self-localize is critical for most motile organisms . In mammals , place cells in the hippocampus appear to be a central component of the brain network responsible for this ability . In this work we recorded the activity of a population of hippocampal neurons from freely moving rodents and carr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"machine",
"learning",
"algorithms",
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"applied",
"mathematics",
"membrane",
"potential",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
"simulati... | 2019 | Efficient neural decoding of self-location with a deep recurrent network |
Dengue is prevalent among Malaysia's indigenous peoples , known as the Orang Asli , and it poses a serious health threat to them . The study aims to look at the socio-demographic factors , health beliefs , and knowledge about dengue and its association to dengue prevention practices among Orang Asli communities in Peni... | Dengue poses a threat to everyone worldwide , including the Orang Asli community in Peninsular Malaysia . Social demographic , knowledge and behavioral factors are essential aspects to control and prevent dengue . This study is aimed to examine these factors and their association with dengue prevention practices . A cr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Practices of Dengue Fever Prevention and the Associated Factors among the Orang Asli in Peninsular Malaysia |
A key function of the Vpu protein of HIV-1 is the targeting of newly-synthesized CD4 for proteasomal degradation . This function has been proposed to occur by a mechanism that is fundamentally distinct from the cellular ER-associated degradation ( ERAD ) pathway . However , using a combination of genetic , biochemical ... | HIV-1 devotes two accessory proteins , Nef and Vpu , to the task of removing the viral receptor , CD4 , from the cell surface . Whereas Nef delivers surface CD4 for degradation in lysosomes , Vpu targets newly-made CD4 in the endoplasmic reticulum for degradation by cytosolic proteasomes . This latter process was thoug... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/membranes",
"and",
"sorting",
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"virology/virulence",
"factors",
"and",
"mechanisms"
] | 2010 | Multilayered Mechanism of CD4 Downregulation by HIV-1 Vpu Involving Distinct ER Retention and ERAD Targeting Steps |
Vertebrate genes often play functionally distinct roles in different subsets of cells; however , tools to study the cell-specific function of gene products are poorly developed . Therefore , we have established a novel mouse model that enables the visualization and manipulation of defined subpopulations of neurons . To... | In mammals , many genes execute a unique set of distinctive and common functions in different cell types . Strategies to address these individual roles often involve the generation of series of transgenic animals . Here , we present a novel approach that combines a single transgenic mouse line with tissue-specific tran... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"embryology",
"developmental",
"neuroscience",
"neural",
"circuit",
"formation",
"axon",
"guidance",
"molecular",
"development",
"biology",
"neuroscience",
"pattern",
"formation",
"cell",
"fate",
"determination"
] | 2011 | A Novel Approach to Selectively Target Neuronal Subpopulations Reveals Genetic Pathways That Regulate Tangential Migration in the Vertebrate Hindbrain |
Kaposi’s sarcoma associated herpesvirus ( KSHV ) infection stabilizes hypoxia inducible factors ( HIFs ) . The interaction between KSHV encoded factors and HIFs plays a critical role in KSHV latency , reactivation and associated disease phenotypes . Besides modulation of large-scale signaling , KSHV infection also repr... | Hypoxia inducible factors ( HIFs ) play a critical role in survival and growth of cancerous cells , in addition to modulating cellular metabolism . Kaposi’s sarcoma associated herpesvirus ( KSHV ) infection stabilizes HIFs . Several factors encoded by KSHV are known to interact with up or downstream targets of HIFs . H... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"sequencing",
"techniques",
"cell",
"physiology",
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"oxygen",
"pathogens",
"microbiology",
"cell",
"metabolism",
"glucose",
"metabolism",
"viruses",
"dna",
... | 2018 | Metabolic reprogramming of Kaposi’s sarcoma associated herpes virus infected B-cells in hypoxia |
Instrumental responses are hypothesized to be of two kinds: habitual and goal-directed , mediated by the sensorimotor and the associative cortico-basal ganglia circuits , respectively . The existence of the two heterogeneous associative learning mechanisms can be hypothesized to arise from the comparative advantages th... | When confronted with different alternatives , animals can respond either based on their pre-established habits , or by considering the short- and long-term consequences of each option . Whereas habitual decision making is fast , goal-directed thinking is a time-consuming task . Instead , habits are inflexible after bei... | [
"Abstract",
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"control",
"engineering",
"computer",
"science",
"behavioral",
"neuroscience",
"control",
"systems",
"computational",
"neuroscience",
"biology",
"neuroscience"
] | 2011 | Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes |
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