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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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Quality assessment is essential for the computational prediction and design of RNA tertiary structures . To date , several knowledge-based statistical potentials have been proposed and proved to be effective in identifying native and near-native RNA structures . All these potentials are based on the inverse Boltzmann f... | RNA is an important and versatile macromolecule participating in various biological processes . In addition to experimental approaches , the computational prediction of RNA 3D structures is an alternative and important source of obtaining structural information and insights into their functions . An important part of t... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"and",
"discussion"
] | [
"molecular",
"dynamics",
"neural",
"networks",
"particle",
"physics",
"statistics",
"rna",
"structure",
"prediction",
"neuroscience",
"nucleotides",
"atoms",
"mathematics",
"forecasting",
"composite",
"particles",
"research",
"and",
"analysis",
"methods",
"computer",
"and... | 2018 | RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks |
Varicella-zoster virus ( VZV ) is a neurotropic human alphaherpesvirus that causes varicella upon primary infection , establishes latency in multiple ganglionic neurons , and can reactivate to cause zoster . Live attenuated VZV vaccines are available; however , they can also establish latent infections and reactivate .... | Varicella-zoster virus ( VZV ) , the alphaherpesvirus that typically causes childhood chickenpox and shingles in adults , becomes latent in neurons , thus remaining in the body for a lifetime . Unfortunately , few models are available to study the establishment of VZV latency since the virus infects only humans and est... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"chickenpox",
"shingles",
"viral",
"diseases"
] | 2013 | Three-Dimensional Normal Human Neural Progenitor Tissue-Like Assemblies: A Model of Persistent Varicella-Zoster Virus Infection |
We compared the neutralization sensitivity of early/transmitted HIV-1 variants from patients infected by subtype B viruses at 3 periods of the epidemic ( 1987–1991 , 1996–2000 , 2006–2010 ) . Infectious pseudotyped viruses expressing envelope glycoproteins representative of the viral quasi-species infecting each patien... | Most of the patients develop autologous neutralizing antibodies ( NAbs ) during HIV-1 infection . These NAbs drive the viral evolution and lead to the selection of escape variants at the individual level . The aim of our study was to check if , subsequently to the selective pressure exerted by the individual NAbs respo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"humoral",
"immunity",
"medicine",
"infectious",
"diseases",
"viral",
"immune",
"evasion",
"immunity",
"hiv",
"virology",
"immunology",
"biology",
"microbiology",
"viral",
"diseases",
"viral",
"evolution",
"immunoglobulins"
] | 2013 | Evidence for a Continuous Drift of the HIV-1 Species towards Higher Resistance to Neutralizing Antibodies over the Course of the Epidemic |
Decision-making is usually accompanied by metacognition , through which a decision maker monitors uncertainty regarding a decision and may then consequently revise the decision . These metacognitive processes can occur prior to or in the absence of feedback . However , the neural mechanisms of metacognition remain cont... | Decision-making is often accompanied by a sense of uncertainty regarding the outcome . In many situations , there is no explicit feedback or cue to indicate whether the decision is correct or not . Fortunately , our brain can evaluate decision uncertainty using the internal signals and subsequently make appropriate adj... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cingulate",
"cortex",
"control",
"theory",
"medicine",
"and",
"health",
"sciences",
"decision",
"theory",
"diagnostic",
"radiology",
"functional",
"magnetic",
"resonance",
"imaging",
"decision",
"making",
"engineering",
"and",
"technology",
"prefrontal",
"cortex",
"app... | 2018 | The neural system of metacognition accompanying decision-making in the prefrontal cortex |
The unfolded protein response ( UPR ) regulates cell fate following exposure of cells to endoplasmic reticulum stresses . PERK , a UPR protein kinase , regulates protein synthesis and while linked with cell survival , exhibits activities associated with both tumor progression and tumor suppression . For example , while... | PERK is critical for progression of specific cancers and has provided stimulus for the generation of small molecule PERK inhibitors . Paradoxically , the anti-proliferative and pro-death functions of PERK have potential tumor suppressive qualities . We demonstrate that PERK can function as either a tumor suppressor or ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"cell",
"cycle",
"and",
"cell",
"division",
"cancer",
"treatment",
"cell",
"processes",
"biological",
"cultures",
"cancers",
"and",
"neoplasms",
"epithelial",
"cells",
"oncology",
"cell",
"cultures",
"chromat... | 2016 | PERK Is a Haploinsufficient Tumor Suppressor: Gene Dose Determines Tumor-Suppressive Versus Tumor Promoting Properties of PERK in Melanoma |
Genetic variants in intron 1 of the fat mass– and obesity-associated ( FTO ) gene have been consistently associated with body mass index ( BMI ) in Europeans . However , follow-up studies in African Americans ( AA ) have shown no support for some of the most consistently BMI–associated FTO index single nucleotide polym... | Genetic variants within the fat mass– and obesity-associated ( FTO ) gene are associated with increased risk of obesity . To better understand which specific genetic variant ( s ) in this genetic region is associated with obesity risk , we attempt to genotype or impute all known genetic variants in the region and test ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"genetics",
"population",
"genetics",
"biology",
"human",
"genetics",
"public",
"health",
"genetics",
"and",
"genomics"
] | 2013 | A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study |
APOBEC3G ( A3G ) /APOBEC3F ( A3F ) are two members of APOBEC3 cytidine deaminase subfamily . Although they potently inhibit the replication of vif-deficient HIV-1 , this mechanism is still poorly understood . Initially , A3G/A3F were thought to catalyze C-to-U transitions on the minus-strand viral cDNAs during reverse ... | Cytidine deaminases are host enzymes that remove the amino group from the cytidine base on single-stranded DNA or RNA , resulting in a replacement of the cytidine with a uracil . Such replacement may alter the amino acid–coding sequence of the gene and change protein function . It has been well documented that APOBEC1 ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/immunodeficiency",
"viruses",
"microbiology/medical",
"microbiology",
"microbiology/innate",
"immunity"
] | 2008 | APOBEC3G and APOBEC3F Require an Endogenous Cofactor to Block HIV-1 Replication |
There has been much interest in studying evolutionary games in structured populations , often modeled as graphs . However , most analytical results so far have only been obtained for two-player or linear games , while the study of more complex multiplayer games has been usually tackled by computer simulations . Here we... | Cooperation can be defined as the act of providing fitness benefits to other individuals , often at a personal cost . When interactions occur mainly with neighbors , assortment of strategies can favor cooperation but local competition can undermine it . Previous research has shown that a single coefficient can capture ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"recreation",
"infographics",
"taxonomy",
"applied",
"mathematics",
"population",
"genetics",
"social",
"sciences",
"data",
"management",
"mathematics",
"population",
"biology",
"computer",
"and",
"information",
"sciences",
"games",
"behavior",
"social",
"psychology",
"ev... | 2016 | Evolutionary Games of Multiplayer Cooperation on Graphs |
The evolutionary success of primate lentiviruses reflects their high capacity to mutate and adapt to new host species , immune responses within individual hosts , and , in recent years , antiviral drugs . APOBEC3G ( A3G ) and APOBEC3F ( A3F ) are host cell DNA-editing enzymes that induce extensive HIV-1 mutation that s... | HIV has shown a chameleon-like nature , always changing to adapt to its environment . Defining the factors that drive and regulate genetic changes in HIV over time is key to understanding how HIV causes disease and escapes from the body's immune responses and drug treatment . The diversity of HIV has implications for t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"viruses",
"infectious",
"diseases",
"virology",
"evolutionary",
"biology",
"molecular",
"biology"
] | 2007 | Target Cell APOBEC3C Can Induce Limited G-to-A Mutation in HIV-1 |
Small cell lung cancer ( SCLC ) is an aggressive disease with poor survival . A few sequencing studies performed on limited number of samples have revealed potential disease-driving genes in SCLC , however , much still remains unknown , particularly in the Asian patient population . Here we conducted whole exome sequen... | SCLC patients are initially highly chemo-sensitive with response rates of greater than 80% in both limited and extensive diseases , but suffer uniform disease recurrence or progression in a very short period of time . In the absence of well-defined genomic biomarkers and insights into the resistance mechanism , many ta... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"gene",
"regulation",
"cancer",
"treatment",
"cancers",
"and",
"neoplasms",
"ethnicities",
"oncology",
"dna",
"small",
"interfering",
"rnas",
"chinese",
"people",
"lung",
"and",
"intrathoracic",
"tumors",
"gene",
"expression",
... | 2016 | Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer |
Identifying optimal dosing of antibiotics has proven challenging—some antibiotics are most effective when they are administered periodically at high doses , while others work best when minimizing concentration fluctuations . Mechanistic explanations for why antibiotics differ in their optimal dosing are lacking , limit... | In this era of rising concerns about antibiotic resistance , the rational design of optimal antibiotic treatment regimens remains an important unrealized goal . At this time , the characteristics of antibiotic treatment regimens ( e . g . dosing levels , treatment duration , route of administration ) are determined lar... | [
"Abstract",
"Introduction",
"Results",
"Model",
"1:",
"General",
"Principles",
"of",
"Antibiotic-Target",
"Reaction",
"Kinetics",
"Model",
"2:",
"Onset",
"and",
"End",
"of",
"Antibiotic",
"Action",
"Determine",
"Pharmacodynamic",
"Properties",
"of",
"Ampicillin",
"and... | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"pathogens",
"drugs",
"microbiology",
"developmental",
"biology",
"antibiotic",
"resistance",
"tetracyclines",
"antibiotics",
"pharmacodynami... | 2017 | Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies |
Host defense against the intracellular protozoan parasite Trypanosoma cruzi depends on Toll-like receptor ( TLR ) -dependent innate immune responses . Recent studies also suggest the presence of TLR-independent responses to several microorganisms , such as viruses , bacteria , and fungi . However , the TLR-independent ... | Trypanosoma cruzi is an intracellular protozoan parasite that causes Chagas diseases in humans . Invasion of T . cruzi into the host is sensed by Toll-like receptors ( TLRs ) , which recognize microbial components that are present in microbes but not in the host . TLRs are essential for the initiation of immune respons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/protozoal",
"infections",
"immunology/innate",
"immunity"
] | 2009 | NFATc1 Mediates Toll-Like Receptor-Independent Innate Immune Responses during Trypanosoma cruzi Infection |
Animal circadian clocks are based on multiple oscillators whose interactions allow the daily control of complex behaviors . The Drosophila brain contains a circadian clock that controls rest–activity rhythms and relies upon different groups of PERIOD ( PER ) –expressing neurons . Two distinct oscillators have been func... | Living organisms have evolved circadian clocks that anticipate daily changes in their environment . Their clockwork is fully endogenous , but can be reset by external cues . ( Light is the most efficient cue . ) The circadian neuronal network of the fruit fly ( Drosophila ) brain perceives light through the visual syst... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience",
"genetics",
"and",
"genomics"
] | 2007 | Light Activates Output from Evening Neurons and Inhibits Output from Morning Neurons in the Drosophila Circadian Clock |
The search for genes that regulate stem cell self-renewal and differentiation has been hindered by a paucity of markers that uniquely label stem cells and early progenitors . To circumvent this difficulty we have developed a method that identifies cell-state regulators without requiring any markers of differentiation ,... | The discovery of stem cell regulators is a major goal of biological research , but progress is often limited by a lack of definitive markers capable of distinguishing stem cells from early progenitors . Even in cases where markers have been identified , they often only enrich for certain cell states and do not uniquely... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation |
Genomic rearrangements ( gross chromosomal rearrangements , GCRs ) threatens genome integrity and cause cell death or tumor formation . At the terminus of linear chromosomes , a telomere-binding protein complex , called shelterin , ensures chromosome stability by preventing chromosome end-to-end fusions and regulating ... | Tips of chromosomes , telomeres , are bound and protected by a telomere-binding protein complex called shelterin . Most previous studies focused on shelterin’s telomere-specific role , and its general role in genome maintenance has not been explored extensively . In this study , we first set up an assay measuring the s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"chromosome",
"structure",
"and",
"function",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"cloning",
"telomeres",
"mutation",
"fungi",
"model",
"organisms",
"non-homologous",
"end",
"joining",
"experimental",
"organism",
"systems",
"dna",
"molecul... | 2019 | Telomere-binding proteins Taz1 and Rap1 regulate DSB repair and suppress gross chromosomal rearrangements in fission yeast |
Complete metamorphosis ( Holometaboly ) is a key innovation that underlies the spectacular success of holometabolous insects . Phylogenetic analyses indicate that Holometabola form a monophyletic group that evolved from ancestors exhibiting hemimetabolous development ( Hemimetaboly ) . However , the nature of the chang... | Complete metamorphosis is an evolutionary innovation that has been critical for the success of insects . Phylogenetic relationships reveal that holometabolous insects evolved from ancestors displaying hemimetabolous development . Yet , little is known about the molecular nature of the changes required for such transiti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"insect",
"metamorphosis",
"animals",
"developmental",
"biology",
"animal",
"anatomy",
"nymphs",
"pupae",
"hemimetabolism",
"zoology",
"wings",
"holometabolism",
"insects",
"arthropoda",
"entomology",
"metamorphosis",
"biology",
"and",
"life",
"sciences",
... | 2016 | The Occurrence of the Holometabolous Pupal Stage Requires the Interaction between E93, Krüppel-Homolog 1 and Broad-Complex |
Standard approaches to data analysis in genome-wide association studies ( GWAS ) ignore any potential functional relationships between gene variants . In contrast gene pathways analysis uses prior information on functional structure within the genome to identify pathways associated with a trait of interest . In a secon... | Genes do not act in isolation , but interact in complex networks or pathways . By accounting for such interactions , pathways analysis methods hope to identify aspects of a disease or trait's genetic architecture that might be missed using more conventional approaches . Most existing pathways methods take a univariate ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results"
] | [] | 2013 | Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts |
Viruses have two modes spread in a host body , one is to release infectious particles from infected cells ( global infection ) and the other is to infect directly from an infected cell to an adjacent cell ( local infection ) . Since the mode of spread affects the evolution of life history traits , such as virulence , i... | Viruses such as human immunodeficiency virus and measles virus can spread through physical contact between infected and susceptible cells ( cell-to-cell infection ) , as well as normal cell-free infection through virions . Some experimental evidences support the possibility that high ability of cell-to-cell infection i... | [
"Abstract",
"Results",
"Discussion"
] | [
"organismal",
"evolution",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"applied",
"mathematics",
"microbiology",
"viral",
"structure",
"simulation",
"and",
"modeling",
"viruses",
"algorithms",
"evolutionary",
"comput... | 2018 | The role of spatial heterogeneity in the evolution of local and global infections of viruses |
Trypanosoma brucei is the causative agent of African sleeping sickness . The polyamine biosynthetic pathway has the distinction of being the target of the only clinically proven anti-trypanosomal drug with a known mechanism of action . Polyamines are essential for cell growth , and their metabolism is extensively regul... | Human African trypanosomiasis ( HAT ) is an important vector-borne pathogen . The World Health Organization estimates that more than 50 million people are at risk for the disease , which occurs focally , in remote regions , and periodically reaches epidemic levels . Untreated HAT is always fatal , and the available dru... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry/chemical",
"biology",
"of",
"the",
"cell",
"biochemistry/transcription",
"and",
"translation",
"biochemistry/biocatalysis",
"infectious",
"diseases/protozoal",
"infections"
] | 2008 | Regulated Expression of an Essential Allosteric Activator of Polyamine Biosynthesis in African Trypanosomes |
Bacteria sense and respond to many environmental cues , rewiring their regulatory network to facilitate adaptation to new conditions/niches . Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring . CodY is one such global regulator , controlling express... | Bacterial pathogens sense multiple host-related metabolic signals that alert them of host localization and result in induction of virulence traits . The Gram-positive foodborne pathogen Listeria monocytogenes activates the transcription of its virulence genes in response to low levels of branch-chained amino acids ( BC... | [
"Abstract",
"Introduction",
"Results",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"microbiology",
"dna",
"transcription",
"regulator",
"genes",
"gene",
"types",
"bacterial",
"pathogens",
"medical",
"microbiology",
"gene",
"express... | 2016 | Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes |
In recent years , the East African region has seen an increase in arboviral diseases transmitted by blood-feeding arthropods . Effective surveillance to monitor and reduce incidence of these infections requires the use of appropriate vector sampling tools . Here , trapped skin volatiles on fur from sheep , a known pref... | The East African region is a major epizootic center for endemic and emerging mosquito borne-arboviruses such as Rift Valley fever virus ( RVFV ) , as evidenced by the increasing frequency and magnitude of this disease . The absence of vaccines or prophylactic drugs for most of these diseases emphasizes the need for acc... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"chemistry",
"biology",
"veterinary",
"science",
"agriculture"
] | 2012 | Sheep Skin Odor Improves Trap Captures of Mosquito Vectors of Rift Valley Fever |
Extracting network-based functional relationships within genomic datasets is an important challenge in the computational analysis of large-scale data . Although many methods , both public and commercial , have been developed , the problem of identifying networks of interactions that are most relevant to the given input... | Analysis of high-content genomic data within the context of known networks of interactions of genes can lead to a better understanding of the underlying biological processes . However , finding the networks of interactions that are most relevant to the given data is a challenging task . We present a random walk-based a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/systems",
"biology",
"computational",
"biology/genomics"
] | 2010 | Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data |
The Kaposi sarcoma associated herpesvirus ( KSHV ) latency associated nuclear antigen ( LANA ) is expressed in all KSHV associated malignancies and is essential for maintenance of KSHV genomes in infected cells . To identify kinases that are potentially capable of modifying LANA , in vitro phosphorylation assays were p... | The Kaposi sarcoma associated herpesvirus ( KSHV ) is associated with cancers that have an increased incidence in individuals with compromised immune systems . KSHV expresses a protein , LANA , that is needed to maintain KSHV genomes in infected cells and also promotes the growth of KSHV associated tumors . Kinases reg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology",
"viruses",
"and",
"cancer",
"biology",
"microbiology"
] | 2012 | Phosphorylation of the Chromatin Binding Domain of KSHV LANA |
Acanthamoeba castellanii , which causes keratitis and blindness in under-resourced countries , is an emerging pathogen worldwide , because of its association with contact lens use . The wall makes cysts resistant to sterilizing reagents in lens solutions and to antibiotics applied to the eye . Transmission electron mic... | A half century ago , investigators identified cellulose in the Acanthamoeba cyst wall , which has two layers and conical ostioles that connect them . Here we showed cyst walls contain three large sets of cellulose-binding lectins , which localize to the ectocyst layer ( a Jonah lectin ) or to the endocyst layer and ost... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"chitin",
"trophozoites",
"parasite",
"groups",
"vesicles",
"chemical",
"compounds",
"cellulose",
"organic",
"compounds",
"parasitic",
"protozoans",
"parasitology",
"acanthamoeba",
"apicomplexa",
"protozoans",
"materials",
"science",
"macromolecules",
"cellular",
"structures"... | 2019 | The most abundant cyst wall proteins of Acanthamoeba castellanii are lectins that bind cellulose and localize to distinct structures in developing and mature cyst walls |
Zika virus ( ZIKV ) infection during human pregnancy may cause diverse and serious congenital defects in the developing fetus . Previous efforts to generate animal models of human ZIKV infection and clinical symptoms often involved manipulating mice to impair their Type I interferon ( IFN ) signaling , thereby allowing... | Zika virus ( ZIKV ) infection during human pregnancy may cause severe congenital abnormalities and fetal death . There is currently no licensed vaccine or anti-ZIKV therapeutic to prevent or treat infection and/or disease . To generate an animal model that mimics human ZIKV infections , others have manipulated mice to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blastocysts",
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"animal",
"models",
"of",
"disease",
"biological",
"cultures",
"microbiology",
"animal",
"models",
"viruses",
... | 2018 | Zika virus infection in immunocompetent pregnant mice causes fetal damage and placental pathology in the absence of fetal infection |
The operation of a health care facility , such as a cholera or Ebola treatment center in an emergency setting , results in the production of pathogen-laden wastewaters that may potentially lead to onward transmission of the disease . The research presented here evaluated the design and operation of a novel treatment sy... | When an outbreak of infectious disease occurs in a low-resource setting , the rapid construction of emergency healthcare facilities may significantly reduce mortality . The facilities also result in the generation of large volumes of highly contaminated fecal waste that represents a potential basis for further disease ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [] | 2015 | Minimizing the Risk of Disease Transmission in Emergency Settings: Novel In Situ Physico-Chemical Disinfection of Pathogen-Laden Hospital Wastewaters |
The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins . The molecular mechanisms coordinating the activation of about predicted origins remain poorly understood , partly due to the intrinsic rarity of repli... | Replication is the mechanism by which genomes are duplicated into two exact copies . Genomic stability is under the control of a spatiotemporal program that orchestrates both the positioning and the timing of firing of about 50 , 000 replication starting points , also called replication origins . Replication bubbles fo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"genomics",
"cell",
"biology",
"dna",
"replication",
"nucleic",
"acids",
"genetics",
"biology",
"and",
"life",
"sciences",
"dna",
"epigenetics",
"computational",
"biology",
"molecular",
"cell",
"biology"
] | 2014 | The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells |
Organ development is directed by selector gene networks . Eye development in the fruit fly Drosophila melanogaster is driven by the highly conserved selector gene network referred to as the “retinal determination gene network , ” composed of approximately 20 factors , whose core comprises twin of eyeless ( toy ) , eyel... | Animals develop by using different combinations of simple instructions . The highly conserved retinal determination ( RD ) network is an ancient set of instructions that evolved when multicellular animals first developed primitive eyes . Evidence suggests that this network is re-used throughout evolution to direct the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"cell",
"differentiation",
"biology",
"cell",
"fate",
"determination"
] | 2013 | Dynamic Rewiring of the Drosophila Retinal Determination Network Switches Its Function from Selector to Differentiation |
Human T-cell lymphotropic virus type 1 ( HTLV-1 ) infection can increase the risk of developing skin disorders . This study evaluated the correlation between HTLV-1 proviral load and CD4+ and CD8+ T cells count among HTLV-1 infected individuals , with or without skin disorders ( SD ) associated with HTLV-1 infection [S... | HTLV-1 infection may increase the risk of developing skin disorders . A total of 193 HTLV-1 infected subjects were studied , including asymptomatic carriers and HAM/TSP patients . Of the subjects , 76% had an abnormal skin condition , with a high prevalence both among HTLV-1 asymptomatic carriers and HAM/TSP patients .... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | High Prevalence of Skin Disorders among HTLV-1 Infected Individuals Independent of Clinical Status |
Filarial nematodes currently infect up to 54 million people worldwide , with millions more at risk for infection , representing the leading cause of disability in the developing world . Brugia malayi is one of the causative agents of lymphatic filariasis and remains the only human filarial parasite that can be maintain... | Filarial nematodes currently infect millions of people worldwide and represent a leading cause of disability . Currently available medications are insufficient in reaching elimination of these parasites . Many filarial nematodes , including Brugia malayi , have an Achilles heel of sorts—that is their obligate symbiotic... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"heme",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"parasitic",
"diseases",
"animals",
"wolbachia",
"parasitology",
"invertebrate",
"genomics",
"nematode",
"infections",
"developmental",
"biology",
"brugia",
"bacteria",
"proteins",
"gene",
"expression",
"li... | 2017 | Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq |
In the G1 phase of the cell division cycle , eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of the transcriptional and protein synthetic capacities and building the machinery for chromosome replication . The function of G1 has an early evolutionary origin and is pre... | The study of eukaryotic cell division has overwhelmingly focused on cells from two branches of evolution , fungal and metazoan , with more distant eukaryotes rarely studied . One exception is apicomplexan pathogens where in the last two decades development of genetic models has been rapid . While not a perfect solution... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"model",
"organisms",
"genetics",
"biology",
"genomics",
"microbiology",
"genetics",
"and",
"genomics"
] | 2013 | Discovery of a Splicing Regulator Required for Cell Cycle Progression |
In Deinococcus radiodurans , the extreme resistance to DNA–shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments . The rapid reconstitution of an intact genome is thought to occur through an extended synth... | Deinococcus radiodurans bacterium is among the best-known organisms found to resist extremely high exposures to desiccation and ionizing radiation , both causing extensive DNA double-strand breaks . Because a single unrepaired DNA double-strand break is usually lethal , DNA double-strand breaks are considered as the mo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/dna",
"replication",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
"molecular",
"biology/recombination",
"genetics",
"and",
"genomics/gene",
"function",
"microbiology/microbial",
"growth",
"and",
"development",
"molecular",
"biology/... | 2010 | A Major Role of the RecFOR Pathway in DNA Double-Strand-Break Repair through ESDSA in Deinococcus radiodurans |
Protein chaperones are essential in all domains of life to prevent and resolve protein misfolding during translation and proteotoxic stress . HSP70 family chaperones , including E . coli DnaK , function in stress induced protein refolding and degradation , but are dispensable for cellular viability due to redundant cha... | All living organisms use protein chaperones to prevent proteins from becoming insoluble either spontaneously or during cellular stress that can damage proteins . The HSP70 chaperone DnaK has been well characterized in E . coli and is important for that bacterium to resist protein denaturation from heat , but is dispens... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"mycobacteria",
"proteins",
"protein",
"folding",
"medical",
"microbiology",
"chaperone",
"proteins",
"protein",
"structure",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"bacterial",
"pathogens"
] | 2014 | An Essential Nonredundant Role for Mycobacterial DnaK in Native Protein Folding |
Kaposi’s Sarcoma-associated Herpesvirus ( KSHV ) is the etiologic agent of Kaposi’s Sarcoma ( KS ) . KSHV establishes a predominantly latent infection in the main KS tumor cell type , the spindle cell , which is of endothelial cell origin . KSHV requires the induction of multiple metabolic pathways , including glycolys... | KSHV is the etiologic agent of KS , the most common tumor of AIDS patients worldwide . Currently , there are no therapeutics available to directly treat latent KSHV infection . This study reveals that latent KSHV infection induces endothelial cells to become glutamine addicted , similarly to cancer cells . Extracellula... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Latent KSHV Infected Endothelial Cells Are Glutamine Addicted and Require Glutaminolysis for Survival |
Clinical reports of Zika Virus ( ZIKV ) RNA detection in breast milk have been described , but evidence conflicts as to whether this RNA represents infectious virus . We infected post-parturient AG129 murine dams deficient in type I and II interferon receptors with ZIKV . ZIKV RNA was detected in pup stomach milk clots... | Can Zika virus be transmitted from nursing mothers to their children via breast milk ? Only 4 years have passed since the Zika virus outbreak in Brazil , and much remains to be understood about the transmission and health consequences of Zika infection . To date , some case reports have detected Zika virus RNA in the b... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"milk",
"breast",
"milk",
"body",
"fluids",
"reproductive",
"system",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"biological",
"cultures",
"microbiology",
"diet",
"viruses",
"animal",
"models",
... | 2019 | Detection of Zika virus in mouse mammary gland and breast milk |
Amphimerus sp . is a liver fluke which recently has been shown to have a high prevalence of infection among an indigenous group , Chachi , who reside in a tropical rainforest in the northwestern region of Ecuador . Since it is unknown which animals can act as a reservoir and/or definitive hosts for Amphimerus sp . in t... | Amphimerus sp . is a fluke that infects the bile ducts of its definitive hosts . Recently , it has been shown that an indigenous Amerindian group , the Chachi , living in a rural and remote tropical area of Ecuador , are infected with this parasite . The epidemiology and life cycle of this parasite remains elusive , an... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | High Prevalence of the Liver Fluke Amphimerus sp. in Domestic Cats and Dogs in an Area for Human Amphimeriasis in Ecuador |
The Roseobacter clade is a ubiquitous group of marine α-proteobacteria . To gain insight into the versatile metabolism of this clade , we took a constraint-based approach and created a genome-scale metabolic model ( iDsh827 ) of Dinoroseobacter shibae DFL12T . Our model is the first accounting for the energy demand of ... | The oceans are home to a large variety of microorganisms , which interact in several ways with world-wide metabolic cycles . A representative of an important group of marine bacteria called the Roseobacter clade is Dinoroseobacter shibae . This organism is known to use a variant of photosynthesis to obtain energy from ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae |
Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease that is caused by a novel bunyavirus SFTSV . Currently our knowledge of the host-related factors that influence the pathogenesis of disease is inadequate to allow prediction of fatal outcome . Here we conducted a prospective study of... | SFTS now brings about a substantial global public health concern . Preexisting chronic conditions were thought to increase risk of severe SFTSV infections , however with sparse data mining efforts . In this study , we quantified the frequency of chronic comorbidities in SFTS , estimated their contribution to disease se... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"chemical",
"compounds",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"immunology",
"microbiology",
"carbohydrates",
... | 2019 | Preexisting chronic conditions for fatal outcome among SFTS patients: An observational Cohort Study |
Novel strategies are required to control mosquitoes and the pathogens they transmit . One attractive approach involves maternally inherited endosymbiotic Wolbachia bacteria . After artificial infection with Wolbachia , many mosquitoes become refractory to infection and transmission of diverse pathogens . We evaluated t... | Current methods to control mosquitoes and the pathogens they transmit are ineffective , partly due to insecticide and drug resistance . One novel control method involves exploiting naturally occurring Wolbachia bacteria in insects . Wolbachia are bacterial symbionts that are attractive candidates for mosquito-borne dis... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"environmental",
"impacts",
"immunology",
"microbiology",
"technology",
"regulations",
"parasitic",
"diseases",
"parasitology",
"population",
"biology",
"zoology",
"vete... | 2014 | Wolbachia Enhances West Nile Virus (WNV) Infection in the Mosquito Culex tarsalis |
Mass drug administration ( MDA ) is , and has been , the principal method for the control of the schistosome helminths . Using MDA only is unlikely to eliminate the infection in areas of high transmission and the implementation of other measures such as reduced water contact improved hygiene and sanitation are required... | Nearly 258 million people are infected worldwide by schistosome parasites . The World Health Organization ( WHO ) has set control guidelines to combat the morbidity and mortality induced by infection , defined by reaching ≤5% and ≤1% prevalence of heavy-intensity infections in school-aged children ( SAC ) , respectivel... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Sensitivity",
"analysis",
"and",
"model",
"limitations",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"helminths",
"immunology",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"health",
"care",
"vaccines",
"preventive",
"medicine",
"age",
"groups",
"primates",... | 2019 | Modelling the impact of a Schistosoma mansoni vaccine and mass drug administration to achieve morbidity control and transmission elimination |
Microsporidia comprise a phylum of over 1400 species of obligate intracellular pathogens that can infect almost all animals , but little is known about the host response to these parasites . Here we use the whole-animal host C . elegans to show an in vivo role for ubiquitin-mediated response to the microsporidian speci... | Microbial pathogens have two distinct lifestyles: some pathogens live outside of host cells , and others live inside of host cells and are called intracellular pathogens . Microsporidia are fungal-related intracellular pathogens that can infect all animals , but are poorly understood . We used the roundworm C . elegans... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"invertebrates",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"caenorhabditis",
"immunology",
"microbiology",
"animals"... | 2014 | Ubiquitin-Mediated Response to Microsporidia and Virus Infection in C. elegans |
Zika virus ( ZIKV ) is a little known flavivirus that caused a major outbreak in 2007 , in the South-western Pacific Island of Yap . It causes dengue-like syndromes but with milder symptoms . In Africa , where it was first isolated , ZIKV is mainly transmitted by sylvatic Aedes mosquitoes . The virus has also been isol... | Zika virus ( ZIKV ) is an emerging mosquito-borne zoonotic pathogen that causes dengue-like syndromes . Despite its high epidemic potential , little is known about the virus . Although the isolation of the virus was confined to the African continent , serological evidences have shown the widespread distribution of ZIKV... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"mosquitoes",
"vector",
"biology",
"neglected",
"tropical",
"diseases",
"biology",
"microbiology",
"vectors",
"and",
"hosts",
"viral",
"diseases"
] | 2012 | Oral Susceptibility of Singapore Aedes (Stegomyia) aegypti (Linnaeus) to Zika Virus |
Computational neuroimaging methods aim to predict brain responses ( measured e . g . with functional magnetic resonance imaging [fMRI] ) on the basis of stimulus features obtained through computational models . The accuracy of such prediction is used as an indicator of how well the model describes the computations unde... | Encoding computational models in brain responses measured with fMRI allows testing the algorithmic representations carried out by the neural population within voxels . The accuracy of a model in predicting new responses is used as a measure of the brain validity of the computational model being tested , but the result ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"statistical",
"noise",
"diagnostic",
"radiology",
"functional",
"magnetic",
"resonance",
"imaging",
"data",
"acquisition",
"statistics",
"random",
"variables",
"neuroscience",
"covariance",
"magnetic",
"resonance",
"imaging",
"sim... | 2019 | Methods for computing the maximum performance of computational models of fMRI responses |
Cryptosporidium is a leading cause of moderate-to-severe diarrhea ( MSD ) in young children in Africa . We examined factors associated with Cryptosporidium infection in MSD cases enrolled at the rural western Kenya Global Enteric Multicenter Study ( GEMS ) site from 2008-2012 . At health facility enrollment , stool sam... | Cryptosporidium is an important cause of childhood diarrhea . Research on cryptosporidiosis in countries where it is endemic remains limited; few studies have comprehensively examined risk factors for children in Kenya and similar settings . We examined characteristics associated with Cryptosporidium in children with m... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neonatology",
"children",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"water",
"resources",
"surface",
"water",
"pathology",
"and",
"laboratory",
"medicine",
"maternal",
"health",
"geographical",
"locations",
"cryptosporidium",... | 2018 | Clinical, environmental, and behavioral characteristics associated with Cryptosporidium infection among children with moderate-to-severe diarrhea in rural western Kenya, 2008–2012: The Global Enteric Multicenter Study (GEMS) |
Intuitively , higher intelligence might be assumed to correspond to more efficient information transfer in the brain , but no direct evidence has been reported from the perspective of brain networks . In this study , we performed extensive analyses to test the hypothesis that individual differences in intelligence are ... | Networks of interconnected brain regions coordinate brain activities . Information is processed in the grey matter ( cortex and subcortical structures ) and passed along the network via whitish , fatty-coated fiber bundles , the white matter . Using maps of these white matter tracks , we provided evidence that higher i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/cognitive",
"neuroscience",
"radiology",
"and",
"medical",
"imaging/magnetic",
"resonance",
"imaging",
"computational",
"biology/computational",
"neuroscience"
] | 2009 | Brain Anatomical Network and Intelligence |
Common diseases such as type 2 diabetes are phenotypically heterogeneous . Obesity is a major risk factor for type 2 diabetes , but patients vary appreciably in body mass index . We hypothesized that the genetic predisposition to the disease may be different in lean ( BMI<25 Kg/m2 ) compared to obese cases ( BMI≥30 Kg/... | Individuals with Type 2 diabetes ( T2D ) can present with variable clinical characteristics . It is well known that obesity is a major risk factor for type 2 diabetes , yet patients can vary considerably—there are many lean diabetes patients and many overweight people without diabetes . We hypothesized that the genetic... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"public",
"health",
"and",
"epidemiology",
"diabetes",
"mellitus",
"type",
"2",
"diabetic",
"endocrinology",
"genetic",
"epidemiology",
"molecular",
"epidemiology",
"epidemiology",
"endocrinology",
"diabetes",
"and",
"e... | 2012 | Stratifying Type 2 Diabetes Cases by BMI Identifies Genetic Risk Variants in LAMA1 and Enrichment for Risk Variants in Lean Compared to Obese Cases |
A powerful way to separate signal from noise in biology is to convert the molecular data from individual genes or proteins into an analysis of comparative biological network behaviors . One of the limitations of previous network analyses is that they do not take into account the combinatorial nature of gene interaction... | The systems approach to medicine derives from the idea that diseased cells arise from one or more perturbed biological networks due to the net effect of interactions among multiple molecular agents; by measuring differences in the abundance of biomolecules ( e . g . , mRNA , proteins , metabolites ) we can identify rep... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/gene",
"expression",
"genetics",
"and",
"genomics/gene",
"expression",
"molecular",
"biology/bioinformatics",
"computational",
"biology/signaling",
"networks",
"computational",
"biology",
"computational",
"biology/systems",
"biology"
] | 2010 | Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC) |
Gerodermia osteodysplastica ( GO ) is characterized by skin laxity and early-onset osteoporosis . GORAB , the responsible disease gene , encodes a small Golgi protein of poorly characterized function . To circumvent neonatal lethality of the GorabNull full knockout , Gorab was conditionally inactivated in mesenchymal p... | Gerodermia osteodysplastica ( GO ) is segmental progeroid disorder affecting connective tissues and bone , leading to extreme bone fragility . The cause are loss-of-function mutations in the Golgi protein GORAB , whose function has been only partially unravelled . Using several mouse models and patient-derived primary ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"tibia",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"salts",
"osteoblast",
"differentiation",
"fibroblasts",
"collagens",
"cell",
"differentiation",
"animal",
"models",
"developmental",
"biology",
"model",
"organisms",
"osteoblasts",
"proteoglycans",
... | 2018 | Impaired proteoglycan glycosylation, elevated TGF-β signaling, and abnormal osteoblast differentiation as the basis for bone fragility in a mouse model for gerodermia osteodysplastica |
The 2013–2016 Ebola virus outbreak in West Africa was the largest and deadliest outbreak to date . Here we conducted a serological study to examine the antibody levels in survivors and the seroconversion in close contacts who took care of Ebola-infected individuals , but did not develop symptoms of Ebola virus disease ... | As the causative agent of an often lethal hemorrhagic fever disease in humans and nonhuman primates , Zaire ebolavirus typically causes high fever , severe diarrhea , and vomiting which results in case fatality rates as high as 90% . The 2013–2016 outbreak in West Africa was the largest and most devastating Ebola outbr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"body",
"fluids",
"pathogens",
"immunology",
"sociology",
"microbiology",
"social",
"sciences",
"vertebrates",
"animals",
"mamma... | 2019 | Serological analysis of Ebola virus survivors and close contacts in Sierra Leone: A cross-sectional study |
We develop a new powerful method to reproduce in silico single-molecule manipulation experiments . We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine . We moreover im... | Video game techniques are designed to simulate rigid body dynamics of macroscopic bodies , e . g . characters or vehicles , in a realistic manner . However they are not able to deal with temperature effects , hence they are not able to deal with molecules . In order to extend these powerful techniques to molecular mode... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results/Discussion"
] | [
"physics",
"computer",
"science",
"computer",
"animation",
"biophysic",
"al",
"simulations",
"computing",
"methods",
"biology",
"computational",
"biology",
"biophysics",
"simulations",
"biophysics"
] | 2014 | In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics |
Trypanosoma brucei rhodesiense ( Tbr ) and T . b . gambiense ( Tbg ) , causative agents of Human African Trypanosomiasis ( sleeping sickness ) in Africa , have evolved alternative mechanisms of resisting the activity of trypanosome lytic factors ( TLFs ) , components of innate immunity in human serum that protect again... | Human African Trypanosomiasis , or sleeping sickness , is caused by two different parasites: Trypanosoma brucei gambiense ( Tbg ) and T . b . rhodesiense ( Tbr ) . Each parasite employs a different mechanism to resist trypanosome lytic factor ( TLF ) , the active innate immune component of human serum . In Tbg group 1 ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology",
"haplotypes",
"genetic",
"mutation",
"genetic",
"polymorphism",
"epidemiology",
"genetics",
"population",
"genetics",
"biology",
"population",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Trypanosoma brucei gambiense Group 1 Is Distinguished by a Unique Amino Acid Substitution in the HpHb Receptor Implicated in Human Serum Resistance |
In women , oocytes arrest development at the end of prophase of meiosis I and remain quiescent for years . Over time , the quality and quantity of these oocytes decreases , resulting in fewer pregnancies and an increased occurrence of birth defects . We used the nematode Caenorhabditis elegans to study how oocyte quali... | As women age , the quality of their oocytes declines , causing the eggs they make to have a higher chance of producing a miscarriage or a child with birth defects . We used the roundworm C . elegans to study this problem . We show that oocyte quality declines in these small animals during aging , much as in mammals . F... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"developmental",
"biology/germ",
"cells",
"genetics",
"and",
"genomics/animal",
"genetics",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
"developmental",
"biology/aging",
"developmental",
"biology/developmental",
"molecular",
"mechanisms"
] | 2008 | Apoptosis Maintains Oocyte Quality in Aging Caenorhabditis elegans Females |
Most fungal pathogens of humans display robust protective oxidative stress responses that contribute to their pathogenicity . The induction of enzymes that detoxify reactive oxygen species ( ROS ) is an essential component of these responses . We showed previously that ectopic expression of the heme-containing catalase... | The pathogenic yeast Candida albicans faces multiple challenges within its human host . These include the need to protect itself against the toxic oxidants used by the host to kill invading microbes , and the need to scavenge iron , an essential micronutrient that is limiting in certain tissues . The iron-containing en... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"oxides",
"oxidative",
"stress",
"enzymes",
"pathogens",
"immunology",
"microbiology",
"enzymology",
"animal",
"models",
... | 2017 | Elevated catalase expression in a fungal pathogen is a double-edged sword of iron |
Trachoma , caused by ocular infection with Chlamydia trachomatis , is hyperendemic on the Bijagós Archipelago of Guinea Bissau . An understanding of the risk factors associated with active trachoma and infection on these remote and isolated islands , which are atypical of trachoma-endemic environments described elsewhe... | Trachoma , caused by ocular infection with Chlamydia trachomatis , is the leading infectious cause of blindness worldwide . The World Health Organization elimination strategy includes community mass treatment with oral antibiotics , education regarding hygiene and facial cleanliness and environmental improvements . Pop... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"and",
"occupational",
"health",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"global",
"health",
"epidemiology"
] | 2014 | Risk Factors for Active Trachoma and Ocular Chlamydia trachomatis Infection in Treatment-Naïve Trachoma-Hyperendemic Communities of the Bijagós Archipelago, Guinea Bissau |
Miniature inverted-repeat transposable elements ( MITEs ) are numerically predominant transposable elements in the rice genome , and their activities have influenced the evolution of genes . Very little is known about how MITEs can rapidly amplify to thousands in the genome . The rice MITE mPing is quiescent in most cu... | Transposable elements are major components of eukaryotic genomes , comprising a large portion of the genome in some species . Miniature inverted-repeat transposable elements ( MITEs ) , which belong to the class II DNA transposable elements , are abundant in gene-rich regions , and their copy numbers are very high; the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"breeding",
"mobile",
"genetic",
"elements",
"plant",
"science",
"agronomy",
"cell",
"biology",
"genetic",
"elements",
"genetics",
"transposable",
"elements",
"biology",
"and",
"life",
"sciences",
"dna",
"transposons",
"plant",
"genetics",
"molecular",
"cell"... | 2014 | Early Embryogenesis-Specific Expression of the Rice Transposon Ping Enhances Amplification of the MITE mPing |
Flagella are assembled sequentially from the inside-out with morphogenetic checkpoints that enforce the temporal order of subunit addition . Here we show that flagellar basal bodies fail to proceed to hook assembly at high frequency in the absence of the monotopic protein SwrB of Bacillus subtilis . Genetic suppressor ... | Bacteria build needle-like injectsomes to secrete toxins into host cells and build propeller-like flagella to swim through their environment using a molecular machine called the type III secretion system ( T3SS ) . Both the injectisome and the flagellum are large self-assembling complexes and regulation of the T3SS ens... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Functional Activation of the Flagellar Type III Secretion Export Apparatus |
Orthobunyaviruses such as Cache Valley virus ( CVV ) and Kairi virus ( KRIV ) are important animal pathogens . Periodic outbreaks of CVV have resulted in the significant loss of lambs on North American farms , whilst KRIV has mainly been detected in South and Central America with little overlap in geographical range . ... | Cache Valley and Kairi viruses ( CVV and KRIV; Peribunyaviridae , Orthobunyavirus ) are important animal pathogens of the Americas . In this study we developed reverse genetics systems to study and manipulate viral genomes of both viruses . Viral genomes were mutated to prevent the expression of the NSs protein , a key... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"plasmid",
"construction",
"viruses",
"next-generation",
"sequencing",
"rna",
"viruses",
"genome",
"analysis",
"dna",
"construct... | 2018 | Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas |
Large-scale sequencing efforts have documented extensive genetic variation within the human genome . However , our understanding of the origins , global distribution , and functional consequences of this variation is far from complete . While regulatory variation influencing gene expression has been studied within a ha... | Previous gene expression studies have identified factors influencing population-level variation in gene regulation . However , these efforts have been limited to a small set of well-studied populations . By leveraging the high resolution of RNA sequencing and broad population sampling , we survey the landscape of trans... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"genomics",
"genome",
"analysis",
"gene",
"expression",
"transcriptome",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"genetic",
"engineering"
] | 2014 | Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture |
The role of CpG island methylation in normal development and cell differentiation is of keen interest , but remains poorly understood . We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays . This techni... | About half of all human genes contain a CpG-rich region called a “CpG island” in the 5′ area , often encompassing the promoter and transcription start site of the associated gene . DNA methylation was initially suggested to control tissue-specific gene expression in mammalian cells , but most promoter region CpG island... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"molecular",
"biology",
"developmental",
"biology",
"homo",
"(human)"
] | 2007 | Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters |
Leishmania virulence factors responsible for the complicated epidemiology of the various leishmaniases remain mainly unidentified . This study is a characterization of a gene previously identified as upregulated in two of three overlapping datasets containing putative factors important for Leishmania’s ability to estab... | Leishmaniases are human parasitic diseases caused by several species of insect-transmitted Leishmania . The pathogenic genus Leishmania has close relatives that also colonize the guts of insects but are not able to infect mammalian cells . When the genes and gene expression profiles of pathogenic Leishmania are compare... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"microbiology",
"parasitic",
"diseases",
"protozoan",
"life",
"cycles",
"parasitic",
"protozoans",
"developmental",
"biology",
"prot... | 2017 | A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts |
Oocyte meiotic progression and maternal-to-zygote transition are accompanied by dynamic epigenetic changes . The functional significance of these changes and the key epigenetic regulators involved are largely unknown . Here we show that Setdb1 , a lysine methyltransferase , controls the global level of histone H3 lysin... | During oogenesis , oocytes accumulate transcripts and proteins that support meiotic maturation and early embryogenesis . Although a number of such maternal-effect factors have been identified , our knowledge about the molecular machinery that drives meiotic progression and maternal-to-zygotic transition is still limite... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"meiosis",
"retrotransposons",
"gene",
"regulation",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"germ",
"cells",
"zygotes",
"developmental",
"biology",
"oocytes",
"genetic",
"elements",
"embryos",
"small",
"interfering",
"rnas",
"embryology",
"mo... | 2016 | Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse |
Altered protein homeostasis underlies degenerative diseases triggered by misfolded proteins , including spinal and bulbar muscular atrophy ( SBMA ) , a neuromuscular disorder caused by a CAG/glutamine expansion in the androgen receptor . Here we show that the unfolded protein response ( UPR ) , an ER protein quality co... | In many age-dependent neurodegenerative diseases , the accumulation of misfolded or mutant proteins drives pathogenesis . Several protein quality control pathways have emerged as central regulators of the turnover of these toxic proteins and therefore impact phenotypic severity . In spinal and bulbar muscular atrophy (... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"neurological",
"disorders",
"neurology",
"neurodegenerative",
"diseases"
] | 2011 | Macroautophagy Is Regulated by the UPR–Mediator CHOP and Accentuates the Phenotype of SBMA Mice |
Postembryonic development in Caenorhabditis elegans is a powerful model for the study of the temporal regulation of development and for the roles of microRNAs in controlling gene expression . Stable switch-like changes in gene expression occur during development as stage-specific microRNAs are expressed and subsequentl... | In the nematode roundworm C . elegans , seam cells , a type of adult stem cell , divide in a completely predictable manner throughout post-embryonic development . Study of the control of the timing of these cells’ division and differentiation led to the discovery of the first microRNAs , which are small non-coding RNAs... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The GATA Factor elt-1 Regulates C. elegans Developmental Timing by Promoting Expression of the let-7 Family MicroRNAs |
The CsrRS ( or CovRS ) two component system controls expression of up to 15% of the genome of group A Streptococcus ( GAS ) . While some studies have suggested that the sensor histidine kinase CsrS responds to membrane perturbations as a result of various environmental stresses , other data have implicated the human an... | Group A Streptococcus ( S . pyogenes or GAS ) is exclusively a human pathogen that can inhabit the human throat as a harmless commensal , cause localized , self-limited infection in the form of pharyngitis or strep throat , or invade local tissues or the bloodstream to produce life-threatening disease states such as ne... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"emerging",
"infectious",
"diseases",
"immunity",
"medical",
"microbiology",
"innate",
"immunity",
"immunology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"immune",
"response",
"pathogenesis"
] | 2011 | Signal Transduction through CsrRS Confers an Invasive Phenotype in Group A Streptococcus |
Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago . Examples include processing geospatial data , analyzing -omics data , and running large-scale simulations . Conventional desktop computing cannot handle these tasks when they are large , and high... | Computational biology often requires processing large amounts of data , running many simulations , or other computationally intensive tasks . In this hybrid primer/tutorial , we describe how high-throughput computing ( HTC ) can be used to solve these problems . First , we present an overview of high-throughput computi... | [
"Abstract",
"Introduction",
"HTCondor",
"Materials",
"and",
"methods",
"Sandbox",
"code",
"Examples",
"When",
"not",
"to",
"use",
"HTC",
"Additional",
"resources",
"Conclusion"
] | [
"employment",
"ecology",
"and",
"environmental",
"sciences",
"education",
"social",
"sciences",
"computers",
"neuroscience",
"learning",
"and",
"memory",
"scientists",
"cognition",
"memory",
"information",
"technology",
"data",
"processing",
"science",
"and",
"technology"... | 2018 | Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor |
Little is known about the strains of Trypanosoma cruzi circulating in Central America and specifically in the most important vector in this region , Triatoma dimidiata . Approximately six million people are infected with T . cruzi , the causative agent of Chagas disease , which has the greatest negative economic impact... | Little is known about the strains of the Chagas parasite circulating in Central America . This parasite is responsible for the most serious parasitic disease in Latin America and is presently divided into seven different strains . In Central America , the Chagas parasite is spread mainly by one species of kissing bug b... | [
"Abstract",
"Introduction",
"Materials",
"&",
"methods",
"Results",
"Discussion"
] | [
"geographical",
"locations",
"parasitic",
"protozoans",
"genetic",
"mapping",
"north",
"america",
"protozoans",
"research",
"and",
"analysis",
"methods",
"central",
"america",
"sequence",
"analysis",
"south",
"america",
"bioinformatics",
"sequence",
"alignment",
"people",... | 2017 | The diversity of the Chagas parasite, Trypanosoma cruzi, infecting the main Central American vector, Triatoma dimidiata, from Mexico to Colombia |
Metabolic networks perform some of the most fundamental functions in living cells , including energy transduction and building block biosynthesis . While these are the best characterized networks in living systems , understanding their evolutionary history and complex wiring constitutes one of the most fascinating open... | Metabolism is the network of biochemical reactions that transforms available resources ( “inputs” ) into energy currency and building blocks ( “outputs” ) . Different organisms have different assortments of metabolic pathways and input/output requirements , reflecting their adaptation to specific environments , and to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/metabolic",
"networks",
"computational",
"biology/systems",
"biology",
"physics/interdisciplinary",
"physics"
] | 2010 | Signatures of Arithmetic Simplicity in Metabolic Network Architecture |
Defining the correlates of immune protection conferred by SIVΔnef , the most effective vaccine against SIV challenge , could enable the design of a protective vaccine against HIV infection . Here we provide a comprehensive assessment of immune responses that protect against SIV infection through detailed analyses of ce... | Annually , more than two million people worldwide are infected with HIV , the virus that causes AIDS . Rhesus macaques can be infected with SIV , a close relative and ancestor of HIV , resulting in simian AIDS , recapitulating key aspects of human HIV infection . SIVΔnef , a live attenuated form of SIV , protects rhesu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"enzyme-linked",
"immunoassays",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"preventive",
"medici... | 2016 | Persistent Low-Level Replication of SIVΔnef Drives Maturation of Antibody and CD8 T Cell Responses to Induce Protective Immunity against Vaginal SIV Infection |
Cells assemble numerous types of actomyosin bundles that generate contractile forces for biological processes , such as cytokinesis and cell migration . One example of contractile bundles is a transverse arc that forms via actomyosin-driven condensation of actin filaments in the lamellipodia of migrating cells and exer... | Contractile networks and bundles generate mechanical forces required for various cellular processes , particularly cell division and migration . In many of these processes , networks are structurally reorganized into bundles by the activity of molecular motors . During this morphological transformation , filaments cons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"stiffness",
"cell",
"motility",
"mechanical",
"properties",
"actin",
"filaments",
"classical",
"mechanics",
"molecular",
"motors",
"actin",
"motors",
"materials",
"science",
"damage",
"mechanics",
"motor",
"proteins",
"dynamic",
"actin",
"filaments",
"buckling",
"polym... | 2017 | Morphological Transformation and Force Generation of Active Cytoskeletal Networks |
To replicate in mammalian hosts , bacterial pathogens must acquire iron . The majority of iron is coordinated to the protoporphyrin ring of heme , which is further bound to hemoglobin . Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin . Bacillus anthracis , the causat... | Pathogenic bacteria need to acquire host iron to replicate during infection . Approximately 80% of mammalian iron is associated with a small molecule termed heme , most of which is bound to circulating hemoglobin and involved in O2 transport in red cells . Bacteria secrete proteins , termed hemophores , to acquire the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2012 | Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore |
High tropical species diversity is often attributed to evolutionary dynamics over long timescales . It is possible , however , that latitudinal variation in diversification begins when divergence occurs within species . Phylogeographic data capture this initial stage of diversification in which populations become geogr... | The causes of high tropical species diversity remain contentious and disputed . Recent studies have shown that latitudinal differences in speciation and extinction rates give rise to high tropical diversity . However , it is unclear if this gradient is the product of population-level , species-level , or clade-level pr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biogeography",
"taxonomy",
"ecology",
"and",
"environmental",
"sciences",
"mitochondrial",
"dna",
"atmospheric",
"science",
"population",
"genetics",
"species",
"delimitation",
"data",
"management",
"speciation",
"paleontology",
"forms",
"of",
"dna",
"dna",
"population",... | 2017 | A latitudinal phylogeographic diversity gradient in birds |
High-order epistasis—where the effect of a mutation is determined by interactions with two or more other mutations—makes small , but detectable , contributions to genotype-fitness maps . While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories , the evolutionary co... | A key goal for evolutionary biologists is understanding why one evolutionary trajectory is taken rather than others . This requires understanding how individual mutations , as well as interactions between them , determine the accessibility of evolutionary pathways . We used a robust statistical analysis to reveal inter... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"epistasis",
"physics",
"sound",
"waves",
"mutation",
"substitution",
"mutation",
"point",
"mutation",
"fitness",
"epistasis",
"acoustics",
"mathematics",
"statistics",
"(mathematics)",
"confidence",
"intervals",
"heredity",
"genetics",
"biology",
"and",
"life",
"sciences... | 2017 | High-order epistasis shapes evolutionary trajectories |
X-linked myotubular myopathy ( XLMTM ) is a congenital disorder caused by mutations of the myotubularin gene , MTM1 . Myotubularin belongs to a large family of conserved lipid phosphatases that include both catalytically active and inactive myotubularin-related proteins ( i . e . , “MTMRs” ) . Biochemically , catalytic... | Congenital myopathies are a group of heredity diseases characterized by muscle weakness and impaired locomotion that manifest in both children and adults . X-linked myotubular myopathy ( XLMTM ) is a subtype of congenital myopathy that predominantly affects males and is caused by mutations in the myotubularin ( MTM1 ) ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2013 | Loss of Catalytically Inactive Lipid Phosphatase Myotubularin-related Protein 12 Impairs Myotubularin Stability and Promotes Centronuclear Myopathy in Zebrafish |
Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types . However , synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge ... | After years of community efforts , many experimental and computational approaches have been developed and applied for functional annotation of the human genome , yet proper annotation still remains challenging , especially in non-coding regions . As complex disease research rapidly advances , increasing evidence sugges... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"functional",
"genomics",
"immune",
"cells",
"neurodegenerative",
"diseases",
"immunology",
"human",
"genomics",
"genome",
"analysis",
"genome",
"annotation",
"alzheimer",
... | 2017 | Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease |
All-trans retinoic acid ( ATRA ) is instrumental to male germ cell differentiation , but its mechanism of action remains elusive . To address this question , we have analyzed the phenotypes of mice lacking , in spermatogonia , all rexinoid receptors ( RXRA , RXRB and RXRG ) or all ATRA receptors ( RARA , RARB and RARG ... | Differentiation of spermatozoa from immature germ cells , called spermatogonia , critically depends on retinoic acid ( ATRA ) , the active metabolite of vitamin A that acts though binding to nuclear receptors called RXR and RAR . To understand the mechanism by which ATRA control germ cell differentiation , we generated... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Retinoic Acid Receptors Control Spermatogonia Cell-Fate and Induce Expression of the SALL4A Transcription Factor |
It has been recently hypothesized that many of the signals detected in genome-wide association studies ( GWAS ) to T2D and other diseases , despite being observed to common variants , might in fact result from causal mutations that are rare . One prediction of this hypothesis is that the allelic associations should be ... | Single rare causal alleles and/or collections of multiple rare alleles have been suggested to create “synthetic associations” with common variants in genome-wide association studies ( GWAS ) . This model predicts that associations with common variants will not be consistent across populations . In this study , we exami... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"public",
"health",
"and",
"epidemiology/epidemiology",
"genetics",
"and",
"genomics",
"diabetes",
"and",
"endocrinology/type",
"2",
"diabetes"
] | 2010 | Consistent Association of Type 2 Diabetes Risk Variants Found in Europeans in Diverse Racial and Ethnic Groups |
During oogenesis , the egg prepares for fertilization and early embryogenesis . As a consequence , vesicle transport is very active during vitellogenesis , and oocytes are an outstanding system to study regulators of membrane trafficking . Here , we combine zebrafish genetics and the oocyte model to identify the molecu... | Oocytes of egg laying animals frequently represent the biggest cell type of a species . The size of the egg is a consequence of active transport processes , e . g . the import of yolk proteins , which results in the massive storage of vesicles . In addition , secretory vesicles termed cortical granules are stored in th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"physiology",
"animal",
"genetics",
"vertebrates",
"animals",
"osteichthyes",
"animal",
"models",
"developmental",
"biology",
"model",
"organisms",
"organism",
"development",
"molecular",
"genetics",
"research",
"and",
"analysis",
"methods",
"fishes",
"organogenes... | 2014 | Souffle/Spastizin Controls Secretory Vesicle Maturation during Zebrafish Oogenesis |
Human infection by malarial parasites of the genus Plasmodium begins with the bite of an infected Anopheles mosquito . Current estimates place malaria mortality at over 650 , 000 individuals each year , mostly in African children . Efforts to reduce disease burden can benefit from the development of mathematical models... | We report a new mathematical model of the progression , within a human host , of a malaria infection caused by the parasite Plasmodium falciparum . This model incorporates probability distributions for the key parameters of infection and transmission so that model outputs match the entire range of observed responses in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"mathematics",
"tropical",
"diseases",
"(non-neglected)",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"plasmodium",
"malariae",
"applied",
"mathematics",
"population",
"biology",
"biology",
"malaria",
"parasitic",
"diseases"
... | 2013 | Malaria's Missing Number: Calculating the Human Component of R0 by a Within-Host Mechanistic Model of Plasmodium falciparum Infection and Transmission |
Many biological problems involve the response to multiple perturbations . Examples include response to combinations of many drugs , and the effects of combinations of many mutations . Such problems have an exponentially large space of combinations , which makes it infeasible to cover the entire space experimentally . T... | Sometimes a combination of drugs works much better than each drug alone . Finding such drug cocktails is a pressing challenge in order to combat drug resistance and to improve drug effects . However , it is impossible to test all combinations of multiple drug experimentally . Therefore , researchers are looking for com... | [
"Abstract",
"Introduction",
"Results",
"Estimating",
"triplet",
"interactions",
"requires",
"an",
"accurate",
"null",
"model",
"Discussion",
"Methods"
] | [
"antimicrobials",
"deletion",
"mutation",
"medicine",
"and",
"health",
"sciences",
"microbial",
"mutation",
"statistical",
"noise",
"statistics",
"drugs",
"microbiology",
"mathematical",
"models",
"mutation",
"antibiotic",
"resistance",
"mathematics",
"antibiotics",
"artifi... | 2019 | Noise-precision tradeoff in predicting combinations of mutations and drugs |
How a stimulus or a task alters the spontaneous dynamics of the brain remains a fundamental open question in neuroscience . One of the most robust hallmarks of task/stimulus-driven brain dynamics is the decrease of variability with respect to the spontaneous level , an effect seen across multiple experimental condition... | Task- or stimulus-related changes of brain dynamics have been the subject of intense investigation during the last years . One of the most robust hallmarks of task/stimulus-driven brain dynamics , as measured using diverse recording techniques , is the decrease of variability with respect to the spontaneous level . Thi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling |
Scavenger receptor class B type 1 ( SR-B1 ) and low-density lipoprotein receptor ( LDLR ) are known to be involved in entry of hepatitis C virus ( HCV ) , but their precise roles and their interplay are not fully understood . In this study , deficiency of both SR-B1 and LDLR in Huh7 cells was shown to impair the entry ... | Hepatitis C virus ( HCV ) utilizes several receptors to enter hepatocytes , including scavenger receptor class B type 1 ( SR-B1 ) receptor and low-density lipoprotein receptor ( LDLR ) . HCV particles interact with lipoprotein and apolipoproteins to form complexes termed lipoviroparticles . Several reports have shown t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"binding",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"molecular",
"probe",
"techniques",
"hepacivirus",
"pathogens",
"gene",
"regulation",
"vector-borne",
"diseases",
"microbiology",
"immunoblottin... | 2016 | Lipoprotein Receptors Redundantly Participate in Entry of Hepatitis C Virus |
Dengue is one of the most serious and rapidly spreading arboviral diseases in the world . Despite many acute febrile illnesses in Ethiopia , the burden of illness due to dengue in the country is largely unknown . Thus , the present study aimed to provide the first baseline data on seroprevalence and associated risk fac... | Despite dengue is currently one of the leading causes of arboviral diseases in the globe , it is unrecognized and underreported in Africa , particularly in Ethiopia . Thus , we conducted a cross-sectional study among febrile patients who were attending health institutions to document seroprevalence and associated risk ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"dengue",
"virus",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"geographical",
"locations",
"microbiology",
"tropical",
"diseases"... | 2018 | A serologic study of dengue in northwest Ethiopia: Suggesting preventive and control measures |
Spinocerebellar ataxia type 2 ( SCA2 ) is an autosomal dominant disorder with progressive degeneration of cerebellar Purkinje cells ( PCs ) and other neurons caused by expansion of a glutamine ( Q ) tract in the ATXN2 protein . We generated BAC transgenic lines in which the full-length human ATXN2 gene was transcribed ... | Spinocerebellar ataxia type 2 ( SCA2 ) is an inherited neurodegenerative disorder leading to predominant loss of Purkinje cells in the cerebellum and impairment of motor coordination . The mutation is expansion of a protein domain consisting of a stretch of glutamine amino acids . We generated a mouse model of SCA2 con... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Ataxin-2 Regulates RGS8 Translation in a New BAC-SCA2 Transgenic Mouse Model |
Extracellular bacteria , such as Pseudomonas aeruginosa and Klebsiella pneumoniae , have been reported to induce autophagy; however , the role and machinery of infection-induced autophagy remain elusive . We show that the pleiotropic Src kinase Lyn mediates phagocytosis and autophagosome maturation in alveolar macropha... | It is vital to establish the mechanistic basis for initiation of host defenses and immune responses that are required to eliminate bacterial infection . This line of inquiry will increase knowledge of bacterial pathogenesis and uncover new insights that can enhance design and effectiveness of novel therapeutics . We de... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | Lyn Delivers Bacteria to Lysosomes for Eradication through TLR2-Initiated Autophagy Related Phagocytosis |
Dengue is a leading cause of fever and mimics other acute febrile illnesses ( AFI ) . In 2009 , the World Health Organization ( WHO ) revised criteria for clinical diagnosis of dengue . The new WHO 2009 classification of dengue divides suspected cases into three categories: dengue without warning signs , dengue with wa... | Dengue is an important cause of acute fever in the tropics that is difficult to distinguish from other common etiologies of fever . The World Health Organization ( WHO ) revised criteria for the clinical diagnosis and classification of acute dengue in 2009 . The performance of these criteria has not been widely evaluat... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
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"sciences",
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"medical",
"doctors",
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"and",
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"diseases",
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"health",
"care",
"throat",
"health",
"care",
"providers",
"signs",
... | 2018 | Evaluation of the WHO 2009 classification for diagnosis of acute dengue in a large cohort of adults and children in Sri Lanka during a dengue-1 epidemic |
While in Northern hemisphere countries , the pandemic H1N1 virus ( H1N1pdm ) was introduced outside of the typical influenza season , Southern hemisphere countries experienced a single wave of transmission during their 2009 winter season . This provides a unique opportunity to compare the spread of a single virus in di... | Although relatively mild , the 2009 H1N1 pandemic reminded us once again of the on-going threat posed by novel respiratory viruses and the need for understanding better how such pathogens emerge and spread . From April to September 2009 , countries in temperate regions of the Southern hemisphere experienced large epide... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"global",
"health",
"infectious",
"disease",
"control",
"epidemiological",
"methods",
"infectious",
"disease",
"modeling"
] | 2011 | Transmission Characteristics of the 2009 H1N1 Influenza Pandemic: Comparison of 8 Southern Hemisphere Countries |
Loss of heterozygosity ( LOH ) at tumor suppressor loci is a major contributor to cancer initiation and progression . Both deletions and mitotic recombination can lead to LOH . Certain chromosomal loci known as common fragile sites are susceptible to DNA lesions under replication stress , and replication stress is prev... | Loss of heterozygosity ( LOH ) at tumor-suppressor genes contributes to cancer , and deletions resulting in LOH are frequently observed in tumor cells at certain chromosomal regions known as common fragile sites . LOH can also result from repair of DNA damage by mitotic recombination , if the homologous chromosome rath... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Fragile Site Instability in Saccharomyces cerevisiae Causes Loss of Heterozygosity by Mitotic Crossovers and Break-Induced Replication |
The history of Chagas disease control in Peru and many other nations is marked by scattered and poorly documented vector control campaigns . The complexities of human migration and sporadic control campaigns complicate evaluation of the burden of Chagas disease and dynamics of Trypanosoma cruzi transmission . We conduc... | The historically rural problem of Chagas disease is increasing in urban areas in Latin America . Peri-rural development may play a critical role in the urbanization of Chagas disease and other parasitic infections . We conducted a cross-sectional study in an urbanizing rural area in southern Peru , and we encountered a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2011 | A History of Chagas Disease Transmission, Control, and Re-Emergence in Peri-Rural La Joya, Peru |
The Gram negative bacterium Vibrio cholerae is the causative agent of the secretory diarrheal disease cholera , which has traditionally been classified as a noninflammatory disease . However , several recent reports suggest that a V . cholerae infection induces an inflammatory response in the gastrointestinal tract ind... | Although several reports describe an inflammatory component of the diarrheal disease cholera , the innate immune response to V . cholerae and its impact on the pathogenesis of the disease is poorly understood . In the present study we can link the presence of host neutrophils with a colonization defect of a V . cholera... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gram",
"negative",
"immunity",
"innate",
"immunity",
"microbial",
"pathogens",
"host-pathogen",
"interaction",
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2013 | Vibrio cholerae Evades Neutrophil Extracellular Traps by the Activity of Two Extracellular Nucleases |
Enterovirus 71 ( EV71 ) causes life-threatening epidemics in Asia and can be phylogenetically classified into three major genogroups ( A∼C ) including 11 genotypes ( A , B1∼B5 , and C1∼C5 ) . Recently , EV71 epidemics occurred cyclically in Taiwan with different genotypes . In recent years , human studies using post-in... | Enterovirus 71 ( EV71 ) has caused several life-threatening epidemics in children in the Asia-Pacific region since 1997 . EV71 has one single serotype as measured using hyper-immune animal antisera but can be phylogenetically classified into three major genogroups ( A , B and C ) and eleven genotypes ( A , B1–B5 , and ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"emerging",
"infectious",
"diseases",
"epidemiology",
"biology",
"and",
"life",
"sciences",
"microbiology",
"viral",
"diseases"
] | 2014 | Monitoring Antigenic Variations of Enterovirus 71: Implications for Virus Surveillance and Vaccine Development |
DNA cytosine methylation is involved in the regulation of gene expression during development and its deregulation is often associated with disease . Mammalian genomes are predominantly methylated at CpG dinucleotides . Unmethylated CpGs are often associated with active regulatory sequences while methylated CpGs are oft... | DNA methylation mainly occurs at CpG dinucleotides and strongly influences gene expression during development . Deregulation of DNA methylation is often associated with disease . In mammalian genomes , unmethylated CpG dinucleotides are generally associated with active regulatory sequences , while methylated CpGs are o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"chemical",
"compounds",
"immunology",
"nucleotides",
"organic",
"compounds",
"dna",
"transcription",
"germ",
"cells",
"pyrimidines",
"epigenetics",
"dna",
"dna",
"methylation",
"chromatin",
... | 2019 | Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus |
Nigeria has a significant burden of lymphatic filariasis ( LF ) caused by the parasite Wuchereria bancrofti . A major concern to the expansion of the LF elimination programme is the risk of serious adverse events ( SAEs ) associated with the use of ivermectin in areas co-endemic with Loa filariasis . To better understa... | Nigeria is estimated to have the highest burden of lymphatic filariasis ( LF ) , a disease also known as elephantiasis , which is transmitted by mosquitoes and caused by the parasite Wuchereria bancrofti . The National LF Elimination Programme is planning to scale up the elimination programme through mass drug administ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"mosquitoes",
"soil-transmitted",
"helminths",
"filariasis",
"elephantiasis",
"tropical",
"diseases",
"(non-neglected)",
"global",
"health",
"neglected",
"tropical",
"diseases",
"loiasis",
"onchocerciasis",
"parasitic",
"diseases",
"malar... | 2013 | Lymphatic Filariasis in Nigeria; Micro-stratification Overlap Mapping (MOM) as a Prerequisite for Cost-Effective Resource Utilization in Control and Surveillance |
Immunity to Plasmodium falciparum ( Pf ) malaria is only acquired after years of repeated infections and wanes rapidly without ongoing parasite exposure . Antibodies are central to malaria immunity , yet little is known about the B-cell biology that underlies the inefficient acquisition of Pf-specific humoral immunity ... | Plasmodium falciparum ( Pf ) is a mosquito-borne parasite that causes over 500 million cases of malaria annually , one million of which result in death , primarily among African children . The development of an effective malaria vaccine would be a critical step toward the control and eventual elimination of this diseas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"immunology/immunomodulation",
"immunology/immune",
"response",
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"immunology",
"infectious",
"diseases/protozoal",
"infections",
... | 2010 | The Plasmodium falciparum-Specific Human Memory B Cell Compartment Expands Gradually with Repeated Malaria Infections |
Self-organized criticality is an attractive model for human brain dynamics , but there has been little direct evidence for its existence in large-scale systems measured by neuroimaging . In general , critical systems are associated with fractal or power law scaling , long-range correlations in space and time , and rapi... | Systems in a critical state are poised on the cusp of a transition between ordered and random behavior . At this point , they demonstrate complex patterning of fluctuations at all scales of space and time . Criticality is an attractive model for brain dynamics because it optimizes information transfer , storage capacit... | [
"Abstract",
"Introduction",
"Methods",
"and",
"Materials",
"Discussion"
] | [
"physics/interdisciplinary",
"physics",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2009 | Broadband Criticality of Human Brain Network Synchronization |
Most genetic variants associated with disease occur within regulatory regions of the genome , underscoring the importance of defining the mechanisms underlying differences in regulation of gene expression between individuals . We discovered a pair of co-regulated , divergently oriented transcripts , AQY2 and ncFRE6 , t... | Large-scale genome profiling studies have revealed that disease-associated variants occur most frequently within regulatory regions of DNA . In order to connect variants ( genotypes ) to expression profiles ( phenotypes ) , it is necessary to have a thorough understanding of the mechanisms underlying transcriptional re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity |
Coordinated replication of eukaryotic genomes is intrinsically asymmetric , with continuous leading strand synthesis preceding discontinuous lagging strand synthesis . Here we provide two types of evidence indicating that , in fission yeast , these two biosynthetic tasks are performed by two different replicases . Firs... | It is important to understand the architecture of the DNA replication machinery and whether this is common to all organisms . Recent work in Saccharomyces cerevisiae has genetically assigned specific DNA polymerases to leading and lagging strand DNA synthesis , Polε and Polε respectively . In this manuscript , we use a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"model",
"organisms",
"genetics",
"biology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | The Major Roles of DNA Polymerases Epsilon and Delta at the Eukaryotic Replication Fork Are Evolutionarily Conserved |
Information processing in the human brain arises from both interactions between adjacent areas and from distant projections that form distributed brain systems . Here we map interactions across different spatial scales by estimating the degree of intrinsic functional connectivity for the local ( ≤14 mm ) neighborhood d... | Information processing in the human brain arises from both interactions between adjacent brain areas and from distant projections that form distributed systems . Here we estimated functional connectivity profiles in the human brain using a novel approach to map the regional balance between local and distant functional ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/cognitive",
"neuroscience",
"neurological",
"disorders/cognitive",
"neurology",
"and",
"dementia",
"neurological",
"disorders/neuroimaging",
"computational",
"biology/computational",
"neuroscience",
"neurological",
"disorders/neuropsychiatric",
"disorders",
"neuroscience/... | 2010 | The Organization of Local and Distant Functional Connectivity in the Human Brain |
Imprinted genes display biased expression of paternal and maternal alleles and are only found in mammals and flowering plants . Compared to several hundred imprinted genes that are functionally characterized in mammals , very few imprinted genes were confirmed in plants and even fewer of them have been functionally inv... | Imprinted genes are only found in mammals and flowering plants , and they express with parent-of-origin-specific patterns . Unlike in mammals , only a few imprinted genes was identified and functionally characterized in plants , and almost all of them encode nuclear proteins . Here , we identified NUWA as a new type of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"plant",
"anatomy",
"plant",
"growth",
"and",
"development",
"plant",
"embryo",
"anatomy",
"ovules",
"brassica",
"endosperm",
"developmental",
"biology",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"mitochondria",
"bioenergetics",
"e... | 2017 | A Novel Imprinted Gene NUWA Controls Mitochondrial Function in Early Seed Development in Arabidopsis |
Somatic migration of Toxocara canis- and T . cati-larvae in humans may cause neurotoxocarosis ( NT ) when larvae accumulate and persist in the central nervous system ( CNS ) . Host- or parasite-induced immunoregulatory processes contribute to the pathogenesis; however , detailed data on involvement of bioactive lipid m... | Neurotoxocarosis ( NT ) is induced by larvae of the zoonotic roundworms Toxocara canis and T . cati migrating and persisting in the central nervous system of paratenic hosts , and may be accompanied by severe neurological symptoms . Toxocara spp . are known to modulate the hosts’ immune response , but data concerning i... | [
"Abstract",
"Introduction",
"Material",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"brain",
"developmental",
"biology",
"metabolites",
"signs",
"and",
"symptoms",
"cerebellum",
"lipids",
"inflammation",
"lipid",
"mediators",
"cerebrum",
"metabolic",
"p... | 2019 | Multiplex profiling of inflammation-related bioactive lipid mediators in Toxocara canis- and Toxocara cati-induced neurotoxocarosis |
Severe dengue infection often has unpredictable clinical progressions and outcomes . Obesity may play a role in the deterioration of dengue infection due to stronger body immune responses . Several studies found that obese dengue patients have a more severe presentation with a poorer prognosis . However , the associati... | Dengue fever , an Aedes mosquito-borne viral infection , is a self-limiting or asymptomatic viral infection . In its severe form , severe dengue , the symptoms include organ failure , life-threatening bleeding , and shock . Patients with obesity were found to be at higher risks of developing complications and severe de... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion",
"Conclusion"
] | [
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"database",
"searching",
"pediatrics",
"physiological",
"parameters",
"nutrition",
"mathematics",
"statistics",
"(mathematics)",
"obesity",
"neglected",
"tropical",
"diseases",
"pediatric",
... | 2018 | The association between obesity and dengue severity among pediatric patients: A systematic review and meta-analysis |
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