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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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Active DNA demethylation plays crucial roles in the regulation of gene expression in both plants and animals . In Arabidopsis thaliana , active DNA demethylation is initiated by the ROS1 subfamily of 5-methylcytosine-specific DNA glycosylases via a base excision repair mechanism . Recently , IDM1 and IDM2 were shown to... | DNA cytosine methylation ( 5-methylcytosine , 5-meC ) plays important roles in genome organization , genomic imprinting , transposon silencing and gene expression . DNA methylation patterns are dynamically controlled by methylation and demethylation reactions during development and reproduction in eukaryotes . In Arabi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Regulation of Active DNA Demethylation by a Methyl-CpG-Binding Domain Protein in Arabidopsis thaliana |
Animal control measures in Latin America have decreased the incidence of urban human rabies transmitted by dogs and cats; currently most cases of human rabies are transmitted by bats . In 2004–2005 , rabies outbreaks in populations living in rural Brazil prompted widespread vaccination of exposed and at-risk population... | Animal control measures have decreased the incidence of human rabies in urban regions of Latin America . Currently , most cases of human rabies occur in rural areas and are transmitted by bats . In 2004–2005 , rabies outbreaks affecting populations living in remote areas of Brazil prompted the widespread vaccination of... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"tropical",
"diseases",
"microbiology",
"vertebrates",
"animals",
"mammals",
"vaccines",
"preventive",
... | 2016 | Persistence of Rabies Virus-Neutralizing Antibodies after Vaccination of Rural Population following Vampire Bat Rabies Outbreak in Brazil |
We carried out an admixture analysis of a sample comprising 1 , 019 individuals from all the provinces of Cuba . We used a panel of 128 autosomal Ancestry Informative Markers ( AIMs ) to estimate the admixture proportions . We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in... | Cuba is the largest island of the Greater Antilles and its most populous country . The post-Columbian history of the Caribbean has been marked by the encounter of people from different continents . Here , we present an admixture analysis of 1 , 019 individuals from all the provinces of Cuba , using autosomal , mtDNA an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"haplotypes",
"medicine",
"and",
"health",
"sciences",
"genetic",
"polymorphism",
"genetic",
"association",
"studies",
"epidemiology",
"genetics",
"biology",
"and",
"life",
"sciences",
"population",
"genetics",
"gene",
"flow",
"human",
"genetics",
"evolutionary",
"biolo... | 2014 | Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers |
Lyme disease , caused by Borrelia burgdorferi , is a vector-borne illness that requires the bacteria to adapt to distinctly different environments in its tick vector and various mammalian hosts . Effective colonization ( acquisition phase ) of a tick requires the bacteria to adapt to tick midgut physiology . Successful... | Borrelia burgdorferi , the Lyme disease agent , exploits a multifaceted enzootic cycle that requires a tick vector for successful transmission between mammalian hosts . Two different regulatory systems control genes that are required to complete this infective cycle . The Hk1/Rrp1 two-component system affects genes req... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"microbiology",
"developmental",
"biology",
"nymphs",
"bacteria",
"bacterial",
"pathogens",
"borrelia",
"burgd... | 2016 | Two Different Virulence-Related Regulatory Pathways in Borrelia burgdorferi Are Directly Affected by Osmotic Fluxes in the Blood Meal of Feeding Ixodes Ticks |
We observe and quantify wave-like characteristics of amoeboid migration . Using the amoeba Dictyostelium discoideum , a model system for the study of chemotaxis , we demonstrate that cell shape changes in a wave-like manner . Cells have regions of high boundary curvature that propagate from the leading edge toward the ... | Migration of cells on surfaces and through tissues is an important part of life , from the amazingly coordinated migration of cells during development to the uncontrollable migration of metastatic cancer cells . Here we investigate the physics of cell migration with the goal of gaining new insights into how cells move ... | [
"Abstract",
"Introduction",
"Results",
"Materials",
"and",
"Methods"
] | [
"physics",
"model",
"organisms",
"protozoan",
"models",
"biology",
"microbiology",
"biophysics"
] | 2012 | Cell Shape Dynamics: From Waves to Migration |
Chronic Chagas cardiomyopathy ( CCC ) , a life-threatening inflammatory dilated cardiomyopathy , affects 30% of the approximately 8 million patients infected by Trypanosoma cruzi . Even though the Th1 T cell-rich myocarditis plays a pivotal role in CCC pathogenesis , little is known about the factors controlling inflam... | Chronic Chagas cardiomyopathy ( CCC ) is an inflammatory heart disease that affects millions in Latin America , and in growing numbers in USA and Europe . Survival among CCC patients is shorter than among patients with cardiomyopathy of non-inflammatory etiology . This suggests that the inflammatory cell influx plays a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"gene",
"expression",
"genetics",
"immunology",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Myocardial Chemokine Expression and Intensity of Myocarditis in Chagas Cardiomyopathy Are Controlled by Polymorphisms in CXCL9 and CXCL10 |
Loxoscelism is the designation given to clinical symptoms evoked by Loxosceles spider's bites . Clinical manifestations include skin necrosis with gravitational spreading and systemic disturbs . The venom contains several enzymatic toxins . Herein , we describe the cloning , expression , refolding and biological evalua... | Accidents involving brown spiders ( Loxosceles genus ) are reported throughout the world . South and Southeast of Brazil are endemic areas for this spider . Loxosceles bites commonly trigger local signs as swelling , erythema , hemorrhage and the hallmark symptom: a dermonecrotic lesion with gravitational spreading . S... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"medicine",
"dermatology",
"inflammatory",
"diseases",
"enzymes",
"immunology",
"toxicology",
"toxic",
"agents",
"glycobiology",
"histology",
"proteoglycans",
"glycoproteins",
"sequence",
"analysis",
"proteins",
"extracellular",
"matrix",
"connective",
"tissue",... | 2013 | A Novel Hyaluronidase from Brown Spider (Loxosceles intermedia) Venom (Dietrich's Hyaluronidase): From Cloning to Functional Characterization |
Unlike most bacteria , Vibrio cholerae harbors two distinct , nonhomologous circular chromosomes ( chromosome I and II ) . Many features of chromosome II are plasmid-like , which raised questions concerning its chromosomal nature . Plasmid replication and segregation are generally not coordinated with the bacterial cel... | During proliferation , DNA synthesis , chromosome segregation , and cell division must be coordinated to ensure the stable inheritance of the genetic material . In eukaryotes , this is achieved by checkpoint mechanisms that delay certain steps until others are completed . No such temporal separation exists in bacteria ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/dna",
"repair",
"molecular",
"biology/recombination",
"microbiology/microbial",
"evolution",
"and",
"genomics",
"microbiology"
] | 2008 | FtsK-Dependent Dimer Resolution on Multiple Chromosomes in the Pathogen Vibrio cholerae |
Protein-coding genes in eukaryotes are interrupted by introns , but intron densities widely differ between eukaryotic lineages . Vertebrates , some invertebrates and green plants have intron-rich genes , with 6–7 introns per kilobase of coding sequence , whereas most of the other eukaryotes have intron-poor genes . We ... | In eukaryotes , protein-coding genes are interrupted by non-coding introns . The intron densities widely differ , from 6–7 introns per kilobase of coding sequence in vertebrates , some invertebrates and plants , to only a few introns across the entire genome in many unicellular forms . We applied a robust statistical m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer",
"science",
"biology"
] | 2011 | A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes |
Olfactory sensory neurons choose to express a single odorant receptor ( OR ) from a large gene repertoire and extend axons to reproducible , OR-specific locations within the olfactory bulb . This developmental process produces a topographically organized map of odorant experience in the brain . The axon guidance mechan... | Assembling the brain circuitry responsible for our sense of olfaction is a formidable task . The sensory neurons that detect odorants in the nasal epithelium , the olfactory sensory neurons , choose to express a single odorant receptor from a large gene repertoire . Sensory neurons that choose a particular odorant rece... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"fish",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"vertebrates",
"neuroscience",
"animals",
"dna",
"transcription",
"animal",
"models",
"osteichthyes",
"model",
"organisms",
"experimental",
"organism",
"systems",
"transcription",
"factors",
... | 2018 | Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons |
Antibiotic-resistant Salmonella enterica serovar Paratyphi A , the agent of paratyphoid A fever , poses an emerging public health dilemma in endemic areas of Asia and among travelers , as there is no licensed vaccine . Integral to our efforts to develop a S . Paratyphi A vaccine , we addressed the role of flagella as a... | Salmonella enterica serovar Paratyphi A is a pathogen that causes a systemic disease that is marked by serious complications and , if untreated , high mortality . The study of S . Paratyphi A pathogenesis and vaccine development has been extremely challenging since S . Paratyphi A is human host-restricted and no approp... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"humoral",
"immunity",
"medicine",
"genetic",
"mutation",
"immunity",
"to",
"infections",
"immunology",
"microbiology",
"bacterial",
"diseases",
"adaptive",
"immunity",
"infectious",
"disease",
"control",
"bacterial",
"pathogens",
"immunizations",
"infectious",
"diseases",
... | 2011 | Cell-Associated Flagella Enhance the Protection Conferred by Mucosally-Administered Attenuated Salmonella Paratyphi A Vaccines |
Siderophore biosynthesis by the highly lethal mould Aspergillus fumigatus is essential for virulence , but non-existent in humans , presenting a rare opportunity to strategize therapeutically against this pathogen . We have previously demonstrated that A . fumigatus excretes fusarinine C and triacetylfusarinine C to ca... | Patients with suppressed immune systems due to cancer treatments , HIV/AIDS , organ transplantation , or genetic disorders are at high risk of infection with the ubiquitously present fungal pathogen Aspergillus fumigatus . Treatments for this disease , collectively termed invasive aspergillosis , are often not successf... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"biochemistry",
"infectious",
"diseases",
"yeast",
"and",
"fungi",
"eukaryotes",
"microbiology",
"mus",
"(mouse)",
"genetics",
"and",
"genomics"
] | 2007 | Distinct Roles for Intra- and Extracellular Siderophores during Aspergillus fumigatus Infection |
Human malaria parasite species were originally acquired from other primate hosts and subsequently became endemic , then spread throughout large parts of the world . A major zoonosis is now occurring with Plasmodium knowlesi from macaques in Southeast Asia , with a recent acceleration in numbers of reported cases partic... | Extraordinary phases of pathogen evolution may occur during an emerging zoonosis , potentially involving adaptation to human hosts , with changes in patterns of virulence and transmission . In a large population genetic survey , we show that the malaria parasite Plasmodium knowlesi in humans is an admixture of two high... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Admixture in Humans of Two Divergent Plasmodium knowlesi Populations Associated with Different Macaque Host Species |
Visna/Maedi , or ovine progressive pneumonia ( OPP ) as it is known in the United States , is an incurable slow-acting disease of sheep caused by persistent lentivirus infection . This disease affects multiple tissues , including those of the respiratory and central nervous systems . Our aim was to identify ovine genet... | Ovine lentivirus targets the host immune system and causes persistent retroviral infections affecting millions of sheep worldwide . In primates , lentivirus resistance is attributed to mutant virus coreceptors that are not expressed . In sheep , some animals are resistant to lentivirus infection despite repeated exposu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"veterinary",
"diseases",
"veterinary",
"epidemiology",
"epidemiology",
"genetics",
"molecular",
"genetics",
"biology",
"genetics",
"and",
"genomics",
"veterinary",
"science"
] | 2012 | Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations |
Vibrio vulnificus causes highly lethal bacterial infections in which the Multifunctional Autoprocessing Repeats-in-Toxins ( MARTX ) toxin product of the rtxA1 gene is a key virulence factor . MARTX toxins are secreted proteins up to 5208 amino acids in size . Conserved MARTX N- and C-terminal repeat regions work in con... | The bacterium Vibrio vulnificus causes highly lethal infections in susceptible individuals exposed to contaminated water or seafood . V . vulnificus produces a MARTX toxin , which plays a significant role in bacterial virulence . The large MARTX toxin has numerous functional regions that have been characterized in vitr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"toxins",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"spleen",
"pathogens",
"vibrio",
"cell",
"processes",
"microbiology",
"toxicology",
"toxic",
"agents",
"physiological",
"processes",... | 2017 | The Effector Domain Region of the Vibrio vulnificus MARTX Toxin Confers Biphasic Epithelial Barrier Disruption and Is Essential for Systemic Spread from the Intestine |
Spontaneous sub-cellular calcium release events ( SCRE ) are conjectured to promote rapid arrhythmias associated with conditions such as heart failure and atrial fibrillation: they can underlie the emergence of spontaneous action potentials in single cells which can lead to arrhythmogenic triggers in tissue . The multi... | A loss of the regular rhythm of the beating heart , called arrhythmia , can inhibit its pumping function and even lead to sudden death . Understanding the processes by which normal rhythm is interrupted presents a major yet critical research problem . One challenge is the inherent multi-scale dependence of the electric... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"simulation",
"and",
"modeling",
"probability",
"distribution",
"mathematics",
"cardiac",
"pacing",
"cellular",
"structures",
"and",
"organelles",
... | 2019 | Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation |
Motor control requires the generation of a precise temporal sequence of control signals sent to the skeletal musculature . We describe an experiment that , for good performance , requires human subjects to plan movements taking into account uncertainty in their movement duration and the increase in that uncertainty wit... | Many recent models of motor planning are based on the idea that the CNS plans movements to minimize “costs” intrinsic to motor performance . A minimum variance model would predict that the motor system plans movements that minimize motor error ( as measured by the variance in movement ) subject to the constraint that t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"neuroscience/sensory",
"systems",
"neuroscience/motor",
"systems",
"computational",
"biology/computational",
"neuroscience",
"neuroscience/theoretical",
"neuroscience"
] | 2008 | Optimal Compensation for Temporal Uncertainty in Movement Planning |
The mechanisms by which Regulatory T cells suppress IL-2 production of effector CD4+ T cells in pathological conditions are unclear . A subpopulation of human Treg expresses the ectoenzyme CD39 , which in association with CD73 converts ATP/ADP/AMP to adenosine . We show here that Treg/CD39+ suppress IL-2 expression of ... | Regulatory T cells ( Treg ) represent a subset of T lymphocytes and have a pivotal role in chronic viral infections and cancer by limiting immune activation . It has been shown that Treg are expanded in chronic HIV infected patients . However , the mechanisms of Treg immune-modulator functions are not clearly known . C... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunopathology",
"medicine",
"infectious",
"diseases",
"immune",
"cells",
"immunity",
"hiv",
"immune",
"activation",
"t",
"cells",
"immunity",
"to",
"infections",
"immunology",
"retrovirology",
"and",
"hiv",
"immunopathogenesis",
"biology",
"viral",
"diseases"
] | 2013 | Regulatory T Cells Negatively Affect IL-2 Production of Effector T Cells through CD39/Adenosine Pathway in HIV Infection |
It is widely known that prion strains can mutate in response to modification of the replication environment and we have recently reported that prion mutations can occur in vitro during amplification of vole-adapted prions by Protein Misfolding Cyclic Amplification on bank vole substrate ( bvPMCA ) . Here we exploited t... | Prions are unique infectious agents , consisting of PrPSc , a self-propagating aggregated conformer of the host-encoded prion protein PrPC . Despite the absence of any nucleic acid information , prions exist as distinct strains that share the same amino acid sequence but differ in their conformation . Moreover , prions... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"livestock",
"organismal",
"evolution",
"animal",
"diseases",
"medicine",
"and",
"health",
"sciences",
"ruminants",
"enzymes",
"italian",
"people",
"epitope",
"mapping",
"enzymology",
"vertebrates",
"microbiology",
"animals",
"mammals",
"ethnicities",
"animal",
"prion",
... | 2016 | Isolation of a Defective Prion Mutant from Natural Scrapie |
Schnyder corneal dystrophy ( SCD ) is a rare genetic eye disease characterized by corneal opacification resulted from deposition of excess free cholesterol . UbiA prenyltransferase domain-containing protein-1 ( UBIAD1 ) is an enzyme catalyzing biosynthesis of coenzyme Q10 and vitamin K2 . More than 20 UBIAD1 mutations ... | Schnyder corneal dystrophy ( SCD ) is a rare genetic eye disease caused by deposition of free cholesterol in the cornea . It is closely correlated with mutations in the UbiA prenyltransferase domain-containing protein-1 ( UBIAD1 ) gene , which encodes an enzyme catalyzing biosynthesis of coenzyme Q10 and vitamin K2 . T... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"ocular",
"anatomy",
"animal",
"models",
"model",
"organisms",
"immunoprecipitation",
"experimental",
"organism",
"systems",
"research",
"and",
"analysis",
"methods",
"lipids",
"animal",
"studies",
"proteins",
"ubiquitination",
"... | 2019 | Schnyder corneal dystrophy-associated UBIAD1 mutations cause corneal cholesterol accumulation by stabilizing HMG-CoA reductase |
Chimeric Antigen Receptor ( CAR ) T-cells have emerged as a powerful immunotherapy for various forms of cancer and show promise in treating HIV-1 infection . However , significant limitations are persistence and whether peripheral T cell-based products can respond to malignant or infected cells that may reappear months... | Hematopoietic Stem/Progenitor Cell ( HSPC ) based gene therapy can be used to treat many infectious and genetic diseases . Here , we used an HSPC-based approach to redirect and enhance host immunity against HIV-1 . We engineered HSPCs to carry chimeric antigen receptor ( CAR ) genes that detect and destroy HIV-infected... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"hiv",
"infections",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"immune",
"physiology",
"viral",
"transmission",
"and",
"infection",
"cyt... | 2017 | Long-term persistence and function of hematopoietic stem cell-derived chimeric antigen receptor T cells in a nonhuman primate model of HIV/AIDS |
How organisms determine particular organ numbers is a fundamental key to the development of precise body structures; however , the developmental mechanisms underlying organ-number determination are unclear . In many eudicot plants , the primordia of sepals and petals ( the floral organs ) first arise sequentially at th... | Why do most eudicot flowers have either four or five petals ? This fundamental and attractive problem in botany has been little investigated . Here , we identify the properties responsible for organ-number determination in floral development using mathematical modeling . Earlier experimental and theoretical studies sho... | [
"Abstract",
"Introduction",
"Model",
"Results/Discussion"
] | [] | 2015 | A Dynamical Phyllotaxis Model to Determine Floral Organ Number |
Systematic identification of protein-drug interaction networks is crucial to correlate complex modes of drug action to clinical indications . We introduce a novel computational strategy to identify protein-ligand binding profiles on a genome-wide scale and apply it to elucidating the molecular mechanisms associated wit... | Both the cost to launch a new drug and the attrition rate during the late stage of the drug discovery and development process are increasing . Torcetrapib is a case in point , having been withdrawn from phase III clinical trials after 15 years of development and an estimated cost of US $800 M . Torcetrapib represents a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/literature",
"analysis",
"computational",
"biology/macromolecular",
"structure",
"analysis",
"biotechnology/protein",
"chemistry",
"and",
"proteomics",
"biotechnology/small",
"molecule",
"chemistry",
"cardiovascular",
"disorders/hypertension",
"pharmacology/... | 2009 | Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors |
Eukaryotic cells form stress granules under a variety of stresses , however the signaling pathways regulating their formation remain largely unknown . We have determined that the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 is required for stress granule formation upon glucose deprivation but not heat... | In response to environmental stress , such as nutrient limitations or toxic chemicals , cells must quickly counteract these threats in order to survive . One way cells fight environmental challenges is through the formation of stress granules , which are aggregates of proteins and mRNA within the cytoplasm . Though the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"carbohydrate",
"metabolism",
"chemical",
"compounds",
"dna-binding",
"proteins",
"vertebrates",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
"animals",
"mammals",
"cell",
"signaling",
"fungi",
"model",
"organisms",
"glucose",
"signaling",
... | 2017 | Lysine acetyltransferase NuA4 and acetyl-CoA regulate glucose-deprived stress granule formation in Saccharomyces cerevisiae |
Dorsoventral patterning of the embryonic axis relies upon the mutual antagonism of competing signaling pathways to establish a balance between ventralizing BMP signaling and dorsal cell fate specification mediated by the organizer . In zebrafish , the initial embryo-wide domain of BMP signaling is refined into a morpho... | A complex integration of signaling pathways establishes the body plan of the vertebrate embryo . The dorsal side of the embryo is defined by the organizer , a specialized field of cells that breaks the symmetry of the zebrafish blastula by instructing neighboring cells to adopt dorsal fates based on their proximity . T... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The Integrator Complex Subunit 6 (Ints6) Confines the Dorsal Organizer in Vertebrate Embryogenesis |
Oral infection by Trypanosoma cruzi has been the primary cause of recent outbreaks of acute Chagas' diseases . This route of infection may involve selective binding of the metacyclic trypomastigote surface molecule gp82 to gastric mucin as a first step towards invasion of the gastric mucosal epithelium and subsequent s... | Frequent outbreaks of acute Chagas' disease by food contamination with T . cruzi , characterized by high mortality , have been reported in recent years . In Brazil , oral infection is currently the most important mechanism of T . cruzi transmission . Studies on oral T . cruzi infection in mice have shown that insect-st... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2010 | Role of GP82 in the Selective Binding to Gastric Mucin during Oral Infection with Trypanosoma cruzi |
Kaposi’s sarcoma-associated herpesvirus ( KSHV; human herpesvirus 8 ) belongs to the subfamily of Gammaherpesvirinae and is the etiological agent of Kaposi’s sarcoma as well as of two lymphoproliferative diseases: primary effusion lymphoma and multicentric Castleman disease . The KSHV life cycle is divided into a laten... | The life cycle of Kaposi Sarcoma herpesvirus involves both persistence in a latent form and productive replication to generate new viral particles . How the virus switches between latency and productive ( ‘lytic’ ) replication is only partially understood . Here we show that a viral homologue of interferon regulatory f... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"endothelial",
"cells",
"microbiology",
"epithelial",
"cells",
"viruses",
"protein",
"expression",
"dna",
"viruses",
"molecular",
"biology",
"techni... | 2019 | Kaposi’s sarcoma-associated herpesvirus vIRF2 protein utilizes an IFN-dependent pathway to regulate viral early gene expression |
The Arabidopsis fruit mainly consists of a mature ovary that shows three well defined territories that are pattern elements along the mediolateral axis: the replum , located at the medial plane of the flower , and the valve and the valve margin , both of lateral nature . JAG/FIL activity , which includes the combined f... | There are three main pattern elements in the mediolateral axis of the Arabidopsis fruit . Two of them , the valves and the valve margins , are placed in lateral positions , while the third , called replum , is located in the medial plane of the flower . The replum expresses meristematic genes ( medial factors ) that sp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"growth",
"and",
"development",
"plant",
"biology",
"developmental",
"biology",
"plant",
"science",
"model",
"organisms",
"plants",
"pattern",
"formation",
"arabidopsis",
"thaliana",
"plant",
"genetics",
"biology",
"fruits",
"plant",
"and",
"algal",
"models",... | 2012 | Antagonistic Gene Activities Determine the Formation of Pattern Elements along the Mediolateral Axis of the Arabidopsis Fruit |
The hepatitis C virus ( HCV ) p7 protein is required for infectious virus production via its role in assembly and ion channel activity . Although NMR structures of p7 have been reported , the location of secondary structural elements and orientation of the p7 transmembrane domains differ among models . Furthermore , th... | Hepatitis C virus ( HCV ) infection can lead to significant liver disease and , without a vaccine , continues to pose a significant public health threat . The viral p7 protein is a multifunctional protein that is required for infectious virus production via its role in orchestrating virion assembly and its activity as ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The N-terminal Helical Region of the Hepatitis C Virus p7 Ion Channel Protein Is Critical for Infectious Virus Production |
Ichthyoses are a heterogeneous group of inherited cornification disorders characterized by generalized dry skin , scaling and/or hyperkeratosis . Ichthyosis vulgaris is the most common form of ichthyosis in humans and caused by genetic variants in the FLG gene encoding filaggrin . Filaggrin is a key player in the forma... | The skin undergoes a constant process of self-renewing and keratinocytes migrate from the basal layer of the epidermis to the uppermost layer , the stratum corneum , as they differentiate . A defect in the differentiation of keratinocytes can lead to cornification disorders such as ichthyosis . The most common form of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"skin",
"medicine",
"and",
"health",
"sciences",
"integumentary",
"system",
"immunofluorescence",
"staining",
"enzymes",
"enzymology",
"vertebrates",
"dogs",
"animals",
"mammals",
"protein",
"expression",
"genome",
"analysis",
"epidermis",
"mammalian",
"genomics",
"molecu... | 2017 | A de novo variant in the ASPRV1 gene in a dog with ichthyosis |
Pleuropulmonary Blastoma ( PPB ) is the primary neoplastic manifestation of a pediatric cancer predisposition syndrome that is associated with several diseases including cystic nephroma , Wilms tumor , neuroblastoma , rhabdomyosarcoma , medulloblastoma , and ovarian Sertoli-Leydig cell tumor . The primary pathology of ... | Pleuropulmonary Blastoma ( PPB ) is a pediatric disease that presents with multifocal cystic lung lesions . Familial mutations in DICER1 , an essential gene for microRNA synthesis , predisposes to PPB and other related diseases . Loss or mutation of the second copy of DICER1 in developing airway epithelium is thought t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Fibroblast Growth Factor 9 Regulation by MicroRNAs Controls Lung Development and Links DICER1 Loss to the Pathogenesis of Pleuropulmonary Blastoma |
The cell cycle is the fundamental process of cell populations , it is regulated by environmental cues and by intracellular checkpoints . Cell cycle variability in clonal cell population is caused by stochastic processes such as random partitioning of cellular components to progeny cells at division and random interacti... | All cells in multicellular organisms obey orchestrated sequences of signals to ensure developmental and homeostatic fitness under a variety of external stimuli . However , there also exist self-perpetuating stem-cell populations , the function of which is to provide a steady supply of differentiated progenitors that in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"g1",
"phase",
"cell",
"division",
"analysis",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"population",
"genetics",
"simulation",
"and",
"modeling",
"physiological",
"processes",
"homeostasis",
"effective"... | 2019 | Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells |
Multidrug resistant leprosy , defined as resistance to rifampin , dapsone and fluoroquinolones ( FQ ) , has been described in Mycobacterium leprae . However , the in vivo impact of fluoroquinolone resistance , mainly mediated by mutations in DNA gyrase ( GyrA2GyrB2 ) , has not been precisely assessed . Our objective wa... | Although there is efficient multidrug therapy to cure leprosy , the transmission of M . leprae is still active , leading to 219 , 000 new cases in 2011 . Drug resistant leprosy has been described and may prevent eradication of the disease , notably multidrug resistant defined as resistance to rifampin , dapsone and flu... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Resistance of M. leprae to Quinolones: A Question of Relativity? |
Triatomine bugs are the vectors of Trypanosoma cruzi , the agent of Chagas disease . Vector control has for decades relied upon insecticide spraying , but insecticide resistance has recently emerged in several triatomine populations . One alternative strategy to reduce T . cruzi transmission is paratransgenesis , where... | Triatomines are blood-sucking bugs that transmit Trypanosoma cruzi , the agent of Chagas disease . Insecticide spraying has been very successful at controlling house-infesting bugs , but some triatomines have developed insecticide resistance . One alternative disease-control strategy involves modifying the genomes of b... | [
"Abstract",
"Introduction",
"Material",
"and",
"methods",
"Results",
"Discussion",
"Conclusions"
] | [
"medicine",
"and",
"health",
"sciences",
"gut",
"bacteria",
"microbiome",
"body",
"fluids",
"microbiology",
"parasitic",
"protozoans",
"developmental",
"biology",
"nymphs",
"protozoans",
"bacteria",
"microbial",
"genomics",
"digestive",
"system",
"medical",
"microbiology"... | 2018 | Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation |
Post-kala-azar dermal leishmaniasis ( PKDL ) is a cutaneous complication appearing after treatment of visceral leishmaniasis , and PKDL patients are considered infectious to sand flies and may therefore play a role in the transmission of VL . We estimated the risk and risk factors of PKDL in patients with past VL treat... | Post-kala-azar dermal leishmaniasis ( PKDL ) is a skin disorder seen in patients treated for Leishmania donovani visceral leishmaniasis ( VL ) , a neglected tropical disease that is fatal if left untreated . In the Indian subcontinent , PKDL is seen in 5–10% of all past VL cases and is also reported in some without his... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"leishmaniasis",
"neglected",
"tropical",
"diseases"
] | 2011 | Post-Kala-azar Dermal Leishmaniasis in Nepal: A Retrospective Cohort Study (2000–2010) |
To control and prevent rabies in Latin America , mass dog vaccination campaigns ( MDVC ) are implemented mainly through fixed-location vaccination points: owners have to bring their dogs to the vaccination points where they receive the vaccination free of charge . Dog rabies is still endemic in some Latin-American coun... | In Peru and other dog rabies-affected countries , mass dog vaccination campaigns ( MDVC ) are implemented primarily through fixed-location vaccination points: owners have to bring their dogs to the vaccination points where they receive the vaccination . To stop rabies virus transmission , a high and even dog vaccinatio... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"neighborhoods",
"immunology",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"microbiology",
"social",
"sciences",
"pets",
"and",
... | 2019 | Socio-spatial heterogeneity in participation in mass dog rabies vaccination campaigns, Arequipa, Peru |
The small GTPase Rac is known to be an important regulator of cell polarization , cytoskeletal reorganization , and motility of mammalian cells . In recent microfluidic experiments , HeLa cells endowed with appropriate constructs were subjected to gradients of the small molecule rapamycin leading to synthetic membrane ... | Cell polarization is associated with intracellular gradients of signaling proteins such as Rho GTPases that organize the cytoskeleton in cell motility . We previously observed cells in microfluidic channels and studied their polarization and motility in a simplified ( nearly 1 dimensional ) geometry . There , precise g... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"mathematics",
"applied",
"mathematics",
"regulatory",
"networks",
"biology",
"computational",
"biology",
"signaling",
"networks"
] | 2012 | Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation |
Women comprise a minority of the Science , Technology , Engineering , Mathematics , and Medicine ( STEMM ) workforce . Quantifying the gender gap may identify fields that will not reach parity without intervention , reveal underappreciated biases , and inform benchmarks for gender balance among conference speakers , ed... | In most fields of science , medicine , and technology research , men comprise more than half of the workforce , particularly at senior levels . Most previous work has concluded that the gender gap is smaller today than it was in the past , giving the impression that there will soon be equal numbers of men and women res... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Methods"
] | [
"open",
"science",
"open",
"access",
"publishing",
"employment",
"publication",
"practices",
"engineering",
"and",
"technology",
"bibliometrics",
"sexual",
"and",
"gender",
"issues",
"sociology",
"social",
"sciences",
"careers",
"research",
"and",
"analysis",
"methods",... | 2018 | The gender gap in science: How long until women are equally represented? |
Leprosy is an endemic infectious disease caused by Mycobacterium leprae that predominantly attacks the skin and peripheral nerves , leading to progressive impairment of motor , sensory and autonomic function . Little is known about how this peripheral neuropathy affects corticospinal excitability of handgrip muscles . ... | Leprosy is an endemic disease caused by Mycobacterium leprae that predominantly attacks both skin and peripheral nerves , resulting in persistent distal hand atrophy and the loss of sensory and autonomic functions . In this study , we employ a noninvasive tool named transcranial magnetic stimulation ( TMS ) to map the ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Primary Motor Cortex Representation of Handgrip Muscles in Patients with Leprosy |
The South-to-North Water Diversion ( SNWD ) project is designed to channel fresh water from the Yangtze River north to more industrialized parts of China . An important question is whether future climate change and dispersal via the SNWD may synergistically favor a northward expansion of species involved in hosting and... | The South-to-North Water Diversion ( SNWD ) project is designed to channel fresh water from the Yangtze River north to more industrialized parts of China . An important question is whether future climate change and dispersal via the SNWD may synergistically favor northward expansion of schistosomiasis in China . Our mo... | [
"Abstract",
"Introduction",
"Methodology",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"ecological",
"niches",
"helminths",
"china",
"atmospheric",
"science",
"geographical",
"locations",
"tropical",
"diseases",
"parasitic",
"diseases",
"a... | 2017 | Schistosoma japonicum transmission risk maps at present and under climate change in mainland China |
After more than a decade of steadily declining notifications , the number of reported cholera cases has recently increased in Vietnam . We conducted a matched case-control study to investigate transmission of cholera during an outbreak in Ben Tre , southern Vietnam , and to explore the associated risk factors . Sixty o... | Cholera is a highly contagious , acute diarrheal illness , which poses a profound health threat in many parts of the less developed world . The majority of cases are reported from Sub-Saharan Africa , South-East Asia , and the Americas ( i . e . , Haiti ) where infections are primarily transmitted through ingestion of ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"surface",
"water",
"water",
"resources",
"pathology",
"and",
"laboratory",
"medicine",
"rivers",
"pathogens",
"vibrio",
"tropical",
"diseases",
"microbiology",
"geographical",
"loca... | 2017 | Cholera returns to southern Vietnam in an outbreak associated with consuming unsafe water through iced tea: A matched case-control study |
Envenomation of humans by snakes is a complex and continuously evolving medical emergency , and treatment is made that much more difficult by the diverse biochemical composition of many venoms . Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation ... | This work demonstrates that full-length venom protein messenger RNAs are present in secreted venoms and can be used to acquire full-length protein sequences of toxins from both front-fanged ( Elapidae , Viperidae ) and rear-fanged ( Colubridae ) snake venoms , eliminating the need to use venom glands . Full-length tran... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"toxins",
"pathology",
"and",
"laboratory",
"medicine",
"split-decomposition",
"method",
"vertebrates",
"animals",
"toxicology",
"toxic",
"agents",
"multiple",
"alignment",
"calculation",
"reptiles",
"fo... | 2016 | Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution |
RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions ( HJs ) respectively . In addition to their action in the last steps of homologous recombination , they process HJs made by replication fork reversal , a reaction which occurs at inactivated replication forks by the annealing of b... | DNA replication is the process by which DNA strands are copied to ensure the transmission of the genetic material to daughter cells . Chromosome replication is not a continuous process but is subjected to accidental arrests , owing to the encounter of obstacles or to the dysfunctioning of a replication protein . In bac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"molecular",
"biology/dna",
"replication",
"molecular",
"biology/recombination",
"biochemistry/protein",
"chemistry",
"genetics",
"and",
"genomics/chromosome",
"biology",
"biochemistry/replication",
"and",
"repair",
"genetics",
"and",
"genomics/gene",
"function",
"microbiology/mi... | 2008 | ruvA Mutants That Resolve Holliday Junctions but Do Not Reverse Replication Forks |
Upon cell adhesion , talin physically couples the cytoskeleton via integrins to the extracellular matrix , and subsequent vinculin recruitment is enhanced by locally applied tensile force . Since the vinculin binding ( VB ) sites are buried in the talin rod under equilibrium conditions , the structural mechanism of how... | For cell survival , most eukaryotic cells need to be mechanically anchored to their environment . This is done by transmembrane proteins , including integrins , which externally bind to the extracellular matrix and on the cell interior to the contractile cytoskeleton via scaffolding proteins . One essential scaffolding... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biophysics",
"cell",
"biology",
"mammals",
"computational",
"biology"
] | 2008 | How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism |
Most biological processes accelerate with temperature , for example cell division . In contrast , the circadian rhythm period is robust to temperature fluctuation , termed temperature compensation . Temperature compensation is peculiar because a system-level property ( i . e . , the circadian period ) is stable under v... | Circadian rhythms govern the timing of many physiological events . Mysteriously , the period of the rhythm is robust to temperature although the underlying biochemical reactions usually accelerate with temperature , a paradox that has remained unsolved for more than 60 years . Experiments conducted over the last few de... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"ecology",
"and",
"environmental",
"sciences",
"messenger",
"rna",
"electromagnetic",
"radiation",
"circadian",
"oscillators",
"chronobiology",
"ecological",
"metrics",
"gene",
"expression",
"luminescence",
"physics",
"circadian",
"rhythms",
"biochemistry",
"genetic",
"osci... | 2017 | Temperature–amplitude coupling for stable biological rhythms at different temperatures |
Cdc7p-Dbf4p is a conserved protein kinase required for the initiation of DNA replication . The Dbf4p regulatory subunit binds Cdc7p and is essential for Cdc7p kinase activation , however , the N-terminal third of Dbf4p is dispensable for its essential replication activities . Here , we define a short N-terminal Dbf4p r... | Cdc7p-Dbf4p is a two-subunit enzyme required to copy the genetic material present on every chromosome in a process termed DNA replication . Dbf4p is an essential regulatory subunit of this enzyme that likely directs the Cdc7p subunit to its targets within the cell . We found that Dbf4p physically interacts with another... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/dna",
"replication",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/cancer",
"genetics",
"molecular",
"biology/chromatin",
"structure",
"molecular",
"biology/dna",
"repair"
] | 2009 | Cdc7p-Dbf4p Regulates Mitotic Exit by Inhibiting Polo Kinase |
Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics . However , to date most methods have shown sub-optimal performance under realistic demographic scenarios . Moreover , over the past decade there has been a renewed interest in determining ... | The genetic basis of recent adaptation can be uncovered from genomic patterns of variation , which are perturbed in predictable ways when a beneficial mutation “sweeps” through a population . However , the detection of such “selective sweeps” is complicated by demographic events , such as population expansion , which c... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cognitive",
"science",
"engineering",
"and",
"technology",
"demography",
"population",
"genetics",
"neuroscience",
"simulation",
"and",
"modeling",
"decision",
"analysis",
"management",
"engineering",
"artificial",
"intelligence",
"population",
"biology",
"research",
"and"... | 2016 | S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning |
The complex life cycle of the parasitic nematode Strongyloides stercoralis leads to either developmental arrest of infectious third-stage larvae ( iL3 ) or growth to reproductive adults . In the free-living nematode Caenorhabditis elegans , analogous determination between dauer arrest and reproductive growth is governe... | Strongyloides stercoralis is a parasitic nematode that infects hundreds of millions of people worldwide . The infectious form of S . stercoralis is a developmentally arrested third-stage larva ( iL3 ) ; once inside the host , the iL3 activates and develops into an adult parasitic female . First-stage larvae ( L1 ) excr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2016 | Regulation of Life Cycle Checkpoints and Developmental Activation of Infective Larvae in Strongyloides stercoralis by Dafachronic Acid |
Memories are stored and consolidated as a result of a dialogue between the hippocampus and cortex during sleep . Neurons active during behavior reactivate in both structures during sleep , in conjunction with characteristic brain oscillations that may form the neural substrate of memory consolidation . In the hippocamp... | Our memories are consolidated while we sleep through a bidirectional exchange of information between two brain areas called cortex and hippocampus . Neurons that were active in behavioral tasks reactivate again in both structures during sleep in a process of linking and modifying memories from the short term storage of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"sleep",
"membrane",
"potential",
"brain",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
"physiological",
"processes",
"ganglion",
"cells",
"cognition",
"memory",
"... | 2016 | Hippocampal CA1 Ripples as Inhibitory Transients |
Glioblastoma ( GB ) is a highly invasive and lethal brain tumor due to its universal recurrence . Although it has been suggested that the electroneutral Na+-K+-Cl− cotransporter 1 ( NKCC1 ) can play a role in glioma cell migration , the precise mechanism by which this ion transporter contributes to GB aggressiveness re... | Treatment of many cancers has been hampered by the invasive ability of tumor cells . A notable example is brain cancer , which is incurable due to its invasiveness and resulting high tumor recurrence after surgical resection . Here , we analyze further the function of NKCC1 , an ion transporter that is known to regulat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"medicine",
"neurological",
"disorders",
"neurology",
"surgery",
"biology",
"molecular",
"cell",
"biology"
] | 2012 | Regulation of Brain Tumor Dispersal by NKCC1 Through a Novel Role in Focal Adhesion Regulation |
Self-organized criticality refers to the spontaneous emergence of self-similar dynamics in complex systems poised between order and randomness . The presence of self-organized critical dynamics in the brain is theoretically appealing and is supported by recent neurophysiological studies . Despite this , the neurobiolog... | The intricate relationship between structural brain connectivity and functional brain activity is an important and intriguing research area . Brain structure ( the pattern of neuroanatomical connections ) is thought to strongly influence and constrain brain function ( the pattern of neuronal activations ) . Concurrentl... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neuroanatomy",
"neural",
"networks",
"computational",
"neuroscience",
"biology",
"neuroscience"
] | 2011 | Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons |
Toll-like receptor ( TLR ) ligands are being considered as adjuvants for the induction of antigen-specific immune responses , as in the design of vaccines . Polyriboinosinic-polyribocytoidylic acid ( poly I:C ) , a synthetic double-stranded RNA ( dsRNA ) , is recognized by TLR3 and other intracellular receptors . Poly ... | Novel adjuvants that facilitate the induction of strong cellular immunity could be of help in the design of vaccine strategies to combat infections such as HIV or tuberculosis . Our immune cells possess archaic receptors recognizing structures of infectious pathogens , and the interaction of these receptors with their ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/immunity",
"to",
"infections",
"virology/vaccines"
] | 2009 | Synthetic Double-Stranded RNAs Are Adjuvants for the Induction of T Helper 1 and Humoral Immune Responses to Human Papillomavirus in Rhesus Macaques |
Canine rabies is one of the most important and feared zoonotic diseases in the world . In some regions rabies elimination is being successfully coordinated , whereas in others rabies is endemic and continues to spread to uninfected areas . As epidemics emerge , both accepted and contentious control methods are used , a... | Canine rabies continues to cause tens of thousands of horrific deaths worldwide , primarily in Asia and Africa . Momentum is building towards development of a global elimination strategy for canine rabies , but questions remain over how best to eliminate rabies epidemics . This paper uses data generated from the recent... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"disease",
"mapping",
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"rabies",
"veterinary",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"zoonotic",
"diseases",
"spatial",
"epidemiology",
"population",
"biology",
"bi... | 2013 | Designing Programs for Eliminating Canine Rabies from Islands: Bali, Indonesia as a Case Study |
The bacteriophage φ29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of a portal motor complex . Several mechanical models for the generation of these high forces by the motor complex predict coupling of DNA translocation to rotation of the head-tail connector dodecamer ... | The life cycles of many viruses include a self-assembly stage in which a powerful molecular motor packs the DNA genome into the virus's preformed shell ( the capsid ) . Biochemical and biophysical studies have identified essential components of the packaging machinery and measured various characteristics of the packagi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viruses",
"biochemistry",
"virology",
"biophysics",
"molecular",
"biology"
] | 2007 | Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage φ29 Capsids |
Expression quantitative trait loci ( eQTL ) studies have generated large amounts of data in different organisms . The analyses of these data have led to many novel findings and biological insights on expression regulations . However , the role of epistasis in the joint regulation of multiple genes has not been explored... | eQTL studies collect both gene expression and genotype data , and they are highly informative as to how genes regulate expressions . Although much progress has been made in the analysis of such data , most studies have considered one marker at a time . As a result , those markers with weak marginal yet strong interacti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genetics",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2013 | Statistical Analysis Reveals Co-Expression Patterns of Many Pairs of Genes in Yeast Are Jointly Regulated by Interacting Loci |
Lichtheimia species are the second most important cause of mucormycosis in Europe . To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales , we report the full genome sequence of L . corymbifera and compared it to the genome of Rhizopus oryzae , the most commo... | Lichtheimia species are ubiquitous saprophytic fungi , which cause life-threating infections in humans . In contrast to the mucoralean pathogen R . oryzae , Lichtheimia species belong to the ancient mucoralean lineages . We determined the genome of L . corymbifera ( formerly Mycocladus corymbifer ex Absidia corymbifera... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"organismal",
"evolution",
"medicine",
"and",
"health",
"sciences",
"genome",
"evolution",
"pathology",
"and",
"laboratory",
"medicine",
"microbiology",
"genome",
"sequencing",
"genomic",
"databases",
"phylogenetics",
"fungi",
"fungal",
"evolut... | 2014 | Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina) |
Toll-like receptors ( TLRs ) are sentinel receptors of the innate immune system . TLR4 detects bacterial lipopolysaccharide ( LPS ) and TLR5 detects bacterial flagellin . A common human nonsense polymorphism , TLR5:c . 1174C>T , results in a non-functional TLR5 protein . Individuals carrying this variant have decreased... | Toll-like receptors ( TLRs ) are important receptors of the innate immune system . TLR4 detects bacterial lipopolysaccharide ( LPS ) and TLR5 detects bacterial flagellin . A common human polymorphism in TLR5 encodes a shortened protein and blunts the immune response to flagellin . Individuals carrying this variant have... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"bacteriology",
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"luciferase",
"body",
"fluids",
"immune",
"physiology",
"cytokines",
"immune",
"cells",
"enzymes",
"melioidosis",
"immunology",
"microbiology",
"enzymology",
"immune... | 2019 | Flagellin-independent effects of a Toll-like receptor 5 polymorphism in the inflammatory response to Burkholderia pseudomallei |
In this study , we developed a mouse model of type 2 diabetes mellitus ( T2DM ) using streptozotocin and nicotinamide and identified factors that increase susceptibility of T2DM mice to infection by Mycobacterium tuberculosis ( Mtb ) . All Mtb-infected T2DM mice and 40% of uninfected T2DM mice died within 10 months , w... | In the current study , we employed an experimentally induced type 2 diabetes mellitus ( T2DM ) model in wild type C57BL/6 mice and investigated the immune response to Mycobacterium tuberculosis ( Mtb ) infection . We found that natural killer ( NK ) and CD11c+ cell interactions in Mtb-infected T2DM mice led to increase... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"immune",
"cells",
"immunology",
"tropical",
"diseases",
"diabetes",
"mellitus",
"animal",
"models",
"bacterial",
"diseas... | 2016 | NK-CD11c+ Cell Crosstalk in Diabetes Enhances IL-6-Mediated Inflammation during Mycobacterium tuberculosis Infection |
Nipah virus ( NiV ) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins . The G glycoprotein attaches to cell receptors , triggering the fusion ( F ) glycoprotein to execute membrane fusion . Here we report the first crystal structure of the pre-fusion form of the Ni... | Paramyxoviruses infect host cells through the coordinated functions of two envelope glycoproteins . The G glycoprotein attaches to cell receptors triggering the fusion ( F ) glycoprotein to execute membrane fusion . The crystal structure of the NiV-F protein has not been reported . Additionally , many molecular details... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly |
Synaptic plasticity is considered to play a crucial role in the experience-dependent self-organization of local cortical networks . In the absence of sensory stimuli , cerebral cortex exhibits spontaneous membrane potential transitions between an UP and a DOWN state . To reveal how cortical networks develop spontaneous... | Information processing by the brain relies crucially on neuronal circuits . Therefore , clarifying the structure of the brain circuitry is a crucial step towards understanding how the brain processes information . In particular , the cerebral cortex occupies a large portion of the brain in primates and humans , so the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience",
"neuroscience/theoretical",
"neuroscience"
] | 2008 | Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model |
In tsetse flies , nutrients for intrauterine larval development are synthesized by the modified accessory gland ( milk gland ) and provided in mother's milk during lactation . Interference with at least two milk proteins has been shown to extend larval development and reduce fecundity . The goal of this study was to pe... | Tsetse flies are the sole vector for African trypanosomes , causative agents of sleeping sickness in humans and nagana in cattle . Transcriptome and proteome analyses were utilized to examine the underlying mechanisms of tsetse lactation that occur during each reproductive cycle . These analyses revealed a dramatic shi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"genomics",
"functional",
"genomics",
"entomology",
"proteins",
"genome",
"analysis",
"transcriptome",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"proteomics",
"computational",
"biology",
"zoology",
"parasitology"
] | 2014 | A Novel Highly Divergent Protein Family Identified from a Viviparous Insect by RNA-seq Analysis: A Potential Target for Tsetse Fly-Specific Abortifacients |
Chromosome conformation capture ( 3C ) techniques have revealed many fascinating insights into the spatial organization of genomes . 3C methods typically provide information about chromosomal contacts in a large population of cells , which makes it difficult to draw conclusions about the three-dimensional organization ... | Spatial interactions between distant genomic regions are of fundamental importance in gene regulation and other nuclear processes . Recent chromatin crosslinking ( “Hi-C” ) experiments probe the spatial organization of chromosomes on a genome-wide scale to an extent that was previously unattainable . These experiments ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chromosome",
"structure",
"and",
"function",
"mathematics",
"statistics",
"(mathematics)",
"protein",
"structure",
"epigenetics",
"structural",
"genomics",
"chromatin",
"research",
"and",
"analysis",
"methods",
"sex",
"chromosomes",
"chromosome",
"biology",
"proteins",
"... | 2016 | Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data |
Post-translational modifications of histone proteins modulate the binding of transcription regulators to chromatin . Studies in Drosophila have shown that the phosphorylation of histone H3 at Ser10 ( H3S10ph ) by JIL-1 is required specifically during early transcription elongation . 14-3-3 proteins bind H3 only when ph... | Activation of gene expression is thought to be regulated mainly at the level of transcription initiation . Nevertheless , many genes in Drosophila and vertebrates contain RNA polymerase that has started transcription but is paused 30–40 bp from the initiation site . Activation of these genes may thus be regulated by re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/transcription",
"elongation",
"molecular",
"biology/histone",
"modification",
"molecular",
"biology/chromatin",
"structure"
] | 2010 | 14-3-3 Mediates Histone Cross-Talk during Transcription Elongation in Drosophila |
The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants . Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses . Controlling the expression level of OsAP2-39 which inc... | Hormones play an important role in controlling plant growth and development through a dynamic and complicated set of interactions . ABA and GA are well-known as antagonistic partners although the mechanism through which this occurs still needs further elucidation . In this project , we found that a transcription factor... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology/plant",
"growth",
"and",
"development",
"plant",
"biology/plant",
"genetics",
"and",
"gene",
"expression",
"plant",
"biology/plant",
"biochemistry",
"and",
"physiology"
] | 2010 | The APETALA-2-Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic Acid and Gibberellin in Rice |
Evolutionary and ecosystem dynamics are often treated as different processes –operating at separate timescales– even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions . A recent long-term field experiment has explicitly shown that communities of competing plant species can e... | Population ecology and evolutionary biology have been traditionally studied as separate disciplines , even if feedbacks between community and evolutionary processes are known to exist , having been empirically characterized in recent years in different types of communities ( from microbes to plants and vertebrates ) , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"community",
"ecology",
"ecological",
"metrics",
"ecology",
"and",
"environmental",
"sciences",
"ecological",
"niches",
"species",
"diversity",
"ecology",
"species",
"delimitation",
"phenotypes",
"speciation",
"genetics",
"biology",
"and",
"life",
"sciences",
"theoretical... | 2016 | Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities |
Transposable elements ( TEs ) make up the majority of many plant genomes . Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation . To dissect the interplay of siRNA–mediated regulation and TE evolution , and to examine how TE differences affect nearby gene exp... | Transposable elements ( TEs ) are selfish DNA sequences . Together with their immobilized derivatives , they account for a large fraction of eukaryotic genomes . TEs can affect nearby gene activity , either directly by disrupting regulatory sequences or indirectly through the host mechanisms used to prevent TE prolifer... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"transposons",
"genomics",
"molecular",
"cell",
"biology",
"plant",
"science",
"genome",
"evolution",
"plant",
"evolution",
"plant",
"biology",
"plant",
"genomics",
"biology",
"computational",
"biology",
"epigenomics",
"molecular",
"biology",
"genetics",
"and",
"genomic... | 2013 | Transposon Variants and Their Effects on Gene Expression in Arabidopsis |
Formation of centromeric heterochromatin in fission yeast requires the combined action of chromatin modifying enzymes and small RNAs derived from centromeric transcripts . Positive feedback mechanisms that link the RNAi pathway and the Clr4/Suv39h1 histone H3K9 methyltransferase complex ( Clr-C ) result in requirements... | Centromeres are the chromosomal regions that promote chromosome movement during cell division . They consist of repetitive DNA sequences that are packaged into heterochromatin . Disruption of centromeric heterochromatin leads to chromosome loss that can result in miscarriages and genetic disorders . We have sought to d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/histone",
"modification",
"molecular",
"biology/rna-protein",
"interactions",
"molecular",
"biology/centromeres",
"molecular",
"biology/chromosome",
"structure",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/epigenetics",
... | 2010 | Continuous Requirement for the Clr4 Complex But Not RNAi for Centromeric Heterochromatin Assembly in Fission Yeast Harboring a Disrupted RITS Complex |
Recent information has revealed the functional diversity and importance of mitochondria in many cellular processes including orchestrating the innate immune response . Intriguingly , several infectious agents , such as Toxoplasma , Legionella , and Chlamydia , have been reported to grow within vacuoles surrounded by ho... | Recent discoveries have revealed the remarkable functional diversity of mitochondria in roles other than energy production , including an integral role for mitochondria and their dynamics in the regulation of the innate immune response . Interestingly , host mitochondria are recruited to the membranes that surround cer... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"model",
"organisms",
"cell",
"biology",
"evolutionary",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"molecular",
"cell",
"biology",
"research",
"and",
"analysis",
"methods"
] | 2014 | Toxoplasma Effector MAF1 Mediates Recruitment of Host Mitochondria and Impacts the Host Response |
Chagas disease is a neglected tropical disease . About 6 to 8 million people are chronically infected and 10% to 15% develop irreversible gastrointestinal disorders , including megaesophagus . Treatment focuses on improving symptoms , and isosorbide and nifedipine may be used for this purpose . We conducted a systemati... | Chagas disease is a chronic neglected tropical disease that has increased in prevalence in the last decade . About 10% of chronically infected patients develop the digestive form of the disease . Megaesophagus is a common manifestation , and symptoms include difficulty or discomfort in swallowing and regurgitation . Tr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"statistics",
"laryngology",
"metaanalysis",
"tropical",
"diseases",
"parasitic",
"diseases",
"headaches",
"dysphagia",
"physiological",
"processes",
"mathematics",
"signs",
"and",
"sym... | 2018 | Isosorbide and nifedipine for Chagas' megaesophagus: A systematic review and meta-analysis |
Brucellosis is endemic in the bovine population in India and causes a loss of US$ 3·4 billion to the livestock industry besides having a significant human health impact . We developed a stochastic simulation model to estimate the impact of three alternative vaccination strategies on the prevalence of Brucella infection... | Brucellosis is an endemic zoonosis in India and recent studies demonstrate that the disease results in a median loss of US$ 3 . 43 billion in livestock populations . Lack of resources to compensate farmers and a ban on cow slaughter means that test and slaughter policy to control brucellosis cannot be implemented in In... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"united",
"states",
"livestock",
"medicine",
"and",
"health",
"sciences",
"immunology",
"tropical",
"diseases",
"geographical",
"locations",
"india",
"brucellosis",
"north",
"america",
"preventive",
"medicine",
"bacterial",
"diseases",
"vaccines",
"neglected",
"tropical",... | 2018 | Cost-benefit analysis of intervention policies for prevention and control of brucellosis in India |
Noma ( cancrum oris ) , a neglected tropical disease , rapidly disintegrates the hard and soft tissue of the face and leads to severe disfiguration and high mortality . The disease is poorly understood . We aimed to estimate risk factors for diagnosed noma to better guide existing prevention and treatment strategies us... | Noma or cancrum oris is an orofacial gangrene that rapidly disintegrates the hard and soft tissue of the face . Little is known about noma as most cases live in underserved , difficult to reach locations . There is a dearth of literature on the risk factors for the development of noma . Médecins Sans Frontières ( MSF )... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"neonatology",
"children",
"medicine",
"and",
"health",
"sciences",
"maternal",
"health",
"immunology",
"tropical",
"diseases",
"health",
"care",
"pediatrics",
"preventive",
"medicine",
"bacterial",
"diseases",
"age",
"groups",
"women's",
"health",
"... | 2018 | Risk factors for diagnosed noma in northwest Nigeria: A case-control study, 2017 |
The US2-11 region of human and rhesus cytomegalovirus encodes a conserved family of glycoproteins that inhibit MHC-I assembly with viral peptides , thus preventing cytotoxic T cell recognition . Since HCMV lacking US2-11 is no longer able to block assembly and transport of MHC-I , we examined whether this is also obser... | To avoid immune detection by cytotoxic T lymphocytes , viruses interfere with antigen presentation by major histocompatibility complex class I ( MHC-I ) molecules . We have discovered a unique cytomegaloviral protein that interferes with the biosynthesis of MHC-I heavy chains and was thus termed viral inhibitor of heav... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/antigen",
"processing",
"and",
"recognition",
"immunology/immunomodulation",
"virology/animal",
"models",
"of",
"infection",
"virology",
"virology/immune",
"evasion",
"molecular",
"biology/translational",
"regulation"
] | 2008 | Signal Peptide-Dependent Inhibition of MHC Class I Heavy Chain Translation by Rhesus Cytomegalovirus |
Salt stress is one of the major abiotic factors that affect the metabolism , growth and development of plants , and soybean [Glycine max ( L . ) Merr . ] germination is sensitive to salt stress . Thus , to ensure the successful establishment and productivity of soybeans in saline soil , the genetic mechanisms of salt t... | Soil salinity can seriously threaten soybean growth and development and seed germination is a key phase in the soybean growth cycle . Thus , understanding the genetic mechanism of salt tolerance at the germination stage is very important for improving the salt tolerance of soybean at the germination stage . An analysis... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"plant",
"anatomy",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"integumentary",
"system",
"quantitative",
"trait",
"loci",
"plant",
"physiology",
"genetic",
"mapping",
"plant",
"scienc... | 2019 | A cation diffusion facilitator, GmCDF1, negatively regulates salt tolerance in soybean |
Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum ( LGM ) . However , the routes and genetic composition of these postglacial migrants remain unclear . We sequenced the genomes , up to 57× coverage , of seven hunter-gatherers excavated across Scandi... | The Scandinavian peninsula was the last part of Europe to be colonized after the Last Glacial Maximum . The migration routes , cultural networks , and the genetic makeup of the first Scandinavians remain elusive and several hypotheses exist based on archaeology , climate modeling , and genetics . By analyzing the genom... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"geologic",
"time",
"population",
"genetics",
"geographical",
"locations",
"social",
"sciences",
"ethnicities",
"archaeology",
"effective",
"population",
"size",
"geology",
"genome",
"analysis",
"mesolithic",
"period",
"paleontology",
"paleogenetics",
"population",
"biology... | 2018 | Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation |
Hepatitis C virus ( HCV ) is a major cause of end-stage liver diseases . With 3–4 million new HCV infections yearly , a vaccine is urgently needed . A better understanding of virus escape from neutralizing antibodies and their corresponding epitopes are important for this effort . However , for viral isolates with high... | Worldwide hepatitis C virus ( HCV ) is one of the leading causes of chronic liver diseases , including cirrhosis and cancer . Treatment accessibility is limited and development of a preventive vaccine has proven difficult , partly due to the high mutation rate of the virus . Recent studies of HCV antibody neutralizatio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"microbial",
"mutation",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"hepacivirus",
"pathogens",
"immunology",
"microbiology",
"viral",
"structure",
"viruses",
"mutation",
"substitution",
"mutation",
"rna"... | 2017 | Applying antibody-sensitive hypervariable region 1-deleted hepatitis C virus to the study of escape pathways of neutralizing human monoclonal antibody AR5A |
Microscopy , being relatively easy to perform at low cost , is the universal diagnostic method for detection of most globally important parasitic infections . As quality control is hard to maintain , misdiagnosis is common , which affects both estimates of parasite burdens and patient care . Novel techniques for high-r... | There is a need to develop diagnostic methods for parasitic infections specifically designed for use in resource-deficient situations . Worm infections are common in many poor countries and even if repeated treatment can be arranged at low cost , diagnostics and identification of treatment failures demand resources not... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | On-Chip Imaging of Schistosoma haematobium Eggs in Urine for Diagnosis by Computer Vision |
Domains are modules within proteins that can fold and function independently and are evolutionarily conserved . Here we compared the usage and distribution of protein domain families in the free-living proteomes of Archaea , Bacteria and Eukarya and reconstructed species phylogenies while tracing the history of domain ... | Proteins are made up of well-packed structural units referred to as domains . Domain structure in proteins is responsible for protein function and is evolutionarily conserved . Here we report global patterns of protein domain gain and loss in the three superkingdoms of life . We reconstructed phylogenetic trees using d... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genomics",
"genome",
"evolution",
"biology",
"computational",
"biology"
] | 2014 | Global Patterns of Protein Domain Gain and Loss in Superkingdoms |
Since the beginnings of domestication , the craniofacial architecture of the domestic dog has morphed and radiated to human whims . By beginning to define the genetic underpinnings of breed skull shapes , we can elucidate mechanisms of morphological diversification while presenting a framework for understanding human c... | As a result of selective breeding practices , modern dogs display a multitude of head shapes . Breeds such as the Pug and Bulldog popularize one of these morphologies , termed “brachycephaly . ” A short , upward-pointing snout , a massive and rounded head , and an underbite typify brachycephalic breeds . Here , we have... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"animal",
"genetics",
"genetic",
"mutation",
"gene",
"function",
"animal",
"models",
"genome",
"sequencing",
"developmental",
"biology",
"model",
"organisms",
"mutation",
"types",
"skeletal",
"development",
"morphogenesis",
"biolog... | 2012 | Variation of BMP3 Contributes to Dog Breed Skull Diversity |
The prefrontal cortex is centrally involved in a wide range of cognitive functions and their impairment in psychiatric disorders . Yet , the computational principles that govern the dynamics of prefrontal neural networks , and link their physiological , biochemical and anatomical properties to cognitive functions , are... | Computational network models are an important tool for linking physiological and neuro-dynamical processes to cognition . However , harvesting network models for this purpose may less depend on how much biophysical detail is included , but more on how well the model can capture the functional network physiology . Here ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"prefrontal",
"cortex",
"membrane",
"potential",
"brain",
"electrophysiology",
"neuroscience",
"ganglion",
"cells",
"network",
"analysis",
"interneurons",
"computer",
"and",
"informatio... | 2016 | A Detailed Data-Driven Network Model of Prefrontal Cortex Reproduces Key Features of In Vivo Activity |
Prostate cancer patients often have increased levels of psychological stress or anxiety , but the molecular mechanisms underlying the interaction between psychological stress and prostate cancer as well as therapy resistance have been rarely studied and remain poorly understood . Recent reports show that stress inhibit... | Psychological stress and anxiety are often experienced by prostate cancer patients , but the underlying mechanisms of interactions between psychological stress and cancer development , as well as drug resistance , are unclear . Here , we employed a systems biology approach to study interactions between stress-activated... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers a Synergism Pattern Switch in Drug Combination Therapy |
Recently available cancer sequencing data have revealed a complex view of the cancer genome containing a multitude of mutations , including drivers responsible for cancer progression and neutral passengers . Measuring selection in cancer and distinguishing drivers from passengers have important implications for develop... | Darwinian evolution in cancer is responsible for the emergence of malignant traits in initially benign tumors . As tumor cells divide , they accumulate new mutations and while most of them are “passengers” which do not confer any selective growth advantage , “driver” mutations endow cells with traits that contribute to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cancer",
"genomics",
"medicine",
"and",
"health",
"sciences",
"cancer",
"genetics",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"basic",
"cancer",
"research",
"oncology",
"mutation",
"probability",
"distribution",
"mathematics",
"computer",
"and"... | 2019 | On measuring selection in cancer from subclonal mutation frequencies |
Originally a binary classifier , Lot Quality Assurance Sampling ( LQAS ) has proven to be a useful tool for classification of the prevalence of Schistosoma mansoni into multiple categories ( ≤10% , >10 and <50% , ≥50% ) , and semi-curtailed sampling has been shown to effectively reduce the number of observations needed... | The control of schistosomiasis calls for rapid and reliable classification tools . This study evaluates the performance of one such tool , Lot Quality Assurance Sampling ( LQAS ) for assessing the prevalence of S . mansoni in African schoolchildren . We outline the design considerations and introduce novel sequential s... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"medicine",
"infectious",
"diseases",
"schistosomiasis",
"public",
"health",
"and",
"epidemiology",
"mathematics",
"statistics",
"biostatistics",
"child",
"health",
"parasitic",
"diseases"
] | 2012 | Multiple Category-Lot Quality Assurance Sampling: A New Classification System with Application to Schistosomiasis Control |
Cryptococcus neoformans ( Cn ) , the major causative agent of human fungal meningoencephalitis , replicates within phagolysosomes of infected host cells . Despite more than a half-century of investigation into host-Cn interactions , host factors that mediate infection by this fungal pathogen remain obscure . Here , we ... | Cryptococcus neoformans is a facultative intracellular fungal pathogen that causes cryptococcosis in both immunocompromised and immunocompetent individuals worldwide . Initial infection usually occurs in the lungs , but the fungus can disseminate to other organs . The pathogen shows a predilection to the central nervou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases"
] | 2011 | Functional Analysis of Host Factors that Mediate the Intracellular Lifestyle of Cryptococcus neoformans |
Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors ( TFs ) . When TFs are bound to active regulatory regions , they displace canonical nucleosomes , making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chroma... | The functional expression of all genes is regulated by proteins , namely transcription factors that bind to specific areas of DNA known as regulatory regions . Whereas most DNA in our genome is normally bound by other proteins ( histones ) and packaged into units called nucleosomes , a specific subset of tissue-specifi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling |
By following the evolution of populations that are initially genetically homogeneous , much can be learned about core biological principles . For example , it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection . Unfortunately , in multicell... | A consequence of an increasingly interconnected world is the spread of species outside their native range—a phenomenon with potentially dramatic impacts on ecosystem services . Using population genomics , we can robustly infer dynamics of colonization and successful population establishment . We have compared hundred g... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Methods"
] | [
"biotechnology",
"taxonomy",
"population",
"genetics",
"brassica",
"mutation",
"phylogenetics",
"data",
"management",
"model",
"organisms",
"substitution",
"mutation",
"plant",
"science",
"methylation",
"phylogenetic",
"analysis",
"experimental",
"organism",
"systems",
"gen... | 2018 | The rate and potential relevance of new mutations in a colonizing plant lineage |
Prions propagate as multiple strains in a wide variety of mammalian species . The detection of all such strains by a single ultrasensitive assay such as Real Time Quaking-induced Conversion ( RT-QuIC ) would facilitate prion disease diagnosis , surveillance and research . Previous studies have shown that bank voles , a... | Prion diseases are neurodegenerative disorders that propagate as multiple strains in a variety of mammalian species . The detection of all such prion types by a single ultrasensitive assay , such as the Real Time Quaking-induced Conversion ( RT-QuIC ) assay , would facilitate prion disease diagnosis , surveillance , an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Bank Vole Prion Protein As an Apparently Universal Substrate for RT-QuIC-Based Detection and Discrimination of Prion Strains |
Synaptic interactions between neurons of the human cerebral cortex were not directly studied to date . We recorded the first dataset , to our knowledge , on the synaptic effect of identified human pyramidal cells on various types of postsynaptic neurons and reveal complex events triggered by individual action potential... | We recorded the first connections , to our knowledge , between human nerve cells and reveal that a subset of interactions is so strong that some presynaptic cells are capable of eliciting action potentials in the postsynaptic target neurons . Interestingly , these strong connections selectively link pyramidal cells usi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience",
"physiology"
] | 2008 | Complex Events Initiated by Individual Spikes in the Human Cerebral Cortex |
Salmonella enterica serovar Typhimurium ( S . Tm ) is a cause of food poisoning accompanied with gut inflammation . Although mucosal inflammation is generally thought to be protective against bacterial infection , S . Tm exploits the inflammation to compete with commensal microbiota , thereby growing up to high densiti... | For proteins residing outside the bacterial cytoplasm , transport is an essential step for adequate function . The twin-arginine translocation ( Tat ) system enables the transport of folded proteins across the cytoplasmic membrane in prokaryotes . It has recently become clear that this system plays a pivotal role in th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"cell",
"cycle",
"and",
"cell",
"division",
"drugs",
"immunology",
"bile",
"cell",
"processes",
"light",
"microscopy",
"microbiology",
"salmonell... | 2018 | Tat-exported peptidoglycan amidase-dependent cell division contributes to Salmonella Typhimurium fitness in the inflamed gut |
Ryanodine receptors ( RyRs ) are ion channels that regulate muscle contraction by releasing calcium ions from intracellular stores into the cytoplasm . Mutations in skeletal muscle RyR ( RyR1 ) give rise to congenital diseases such as central core disease . The absence of high-resolution structures of RyR1 has limited ... | Ryanodine receptors ( RyRs ) are ion channels present in the membranes of an intracellular calcium storage organelle , the sarcoplasmic reticulum . Nerve impulse triggers the opening of RyR channels , thus increasing the cytoplasmic calcium levels , which subsequently leads to muscle contraction . Congenital mutations ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/molecular",
"dynamics",
"biochemistry/membrane",
"proteins",
"and",
"energy",
"transduction",
"cardiovascular",
"disorders",
"biophysics/membrane",
"proteins",
"and",
"energy",
"transduction"
] | 2009 | A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1) |
Interactions of proteins regulate signaling , catalysis , gene expression and many other cellular functions . Therefore , characterizing the entire human interactome is a key effort in current proteomics research . This challenge is complicated by the dynamic nature of protein-protein interactions ( PPIs ) , which are ... | Protein-protein-interactions ( PPIs ) participate in virtually all biological processes . However , the PPI map is not static but the pairs of proteins that interact depends on the type of cell , the subcellular localization and modifications of the participating proteins , among many other factors . Therefore , it is ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"protein",
"interactions",
"influenza",
"signaling",
"pathways",
"alzheimer",
"disease",
"infectious",
"diseases",
"proteins",
"regulatory",
"networks",
"biology",
"dementia",
"systems",
"biology",
"biochemistry",
"signal",
"transduction",
"neurological",
"disor... | 2013 | Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions |
A large amount of short interfering RNA ( vsiRNA ) is generated from plant viruses during infection , but the function , structure and biogenesis of these is not understood . We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation based array approach . The profil... | Viral RNA is processed into short RNAs in plants , which guide a complex to the viral RNA and cause cleavage of the viral RNA . We profiled Cymbidium ringspot virus ( CymRSV ) derived short RNAs using three different methods . Profiling of viral short interfering RNAs revealed a different sequence bias for the 454 and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"plant",
"biology/plant-biotic",
"interactions",
"virology/host",
"antiviral",
"responses"
] | 2010 | Structural and Functional Analysis of Viral siRNAs |
Anaplastic Lymphoma Kinase ( Alk ) is a Receptor Tyrosine Kinase ( RTK ) activated in several cancers , but with largely unknown physiological functions . We report two unexpected roles for the Drosophila ortholog dAlk , in body size determination and associative learning . Remarkably , reducing neuronal dAlk activity ... | Neurofibromatosis-1 ( NF1 ) syndrome is a common ( 1/3 , 000 births ) genetic disorder affecting multiple organ systems , including the nervous system . Its clinical features include short stature , learning disabilities , and several types of benign and malignant tumors . NF1 is caused by mutations that inactivate the... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"animal",
"models",
"molecular",
"neuroscience",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"drosophila",
"melanogaster",
"model",
"organisms",
"genetics",
"signaling",
"pathways",
"biology",
"neuroscience",
"learning",
"and",
"memory",
"genetics",
"and",
"... | 2011 | The Receptor Tyrosine Kinase Alk Controls Neurofibromin Functions in Drosophila Growth and Learning |
In budding yeast , asymmetric cell division yields a larger mother and a smaller daughter cell , which transcribe different genes due to the daughter-specific transcription factors Ace2 and Ash1 . Cell size control at the Start checkpoint has long been considered to be a main regulator of the length of the G1 phase of ... | Asymmetric cell division is a universal mechanism for generating differentiated cells . The progeny of such divisions can often display differential cell cycle regulation . This study addresses how differential regulation of gene expression in the progeny of a single division can alter cell cycle control . In budding y... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/cell",
"differentiation",
"cell",
"biology/cell",
"growth",
"and",
"division"
] | 2009 | Daughter-Specific Transcription Factors Regulate Cell Size Control in Budding Yeast |
The cellular endosomal sorting complex required for transport ( ESCRT ) machinery is involved in membrane budding processes , such as multivesicular biogenesis and cytokinesis . In HIV-infected cells , HIV-1 hijacks the ESCRT machinery to drive HIV release . Early in the HIV-1 assembly process , the ESCRT-I protein Tsg... | Viruses hijack the cellular machinery to complete their life cycle . In the case of HIV-1 , the endosomal sorting complex required for transport ( ESCRT ) is recruited by nascent viruses to release themselves from infected cells . Currently , there has been an intense amount of research on how the ESCRT machinery induc... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Super-Resolution Imaging of ESCRT-Proteins at HIV-1 Assembly Sites |
The development of rapid serodiagnostic tests for sleeping sickness and other diseases caused by kinetoplastids relies on the affordable production of parasite-specific recombinant antigens . Here , we describe the production of recombinant antigens from Trypanosoma brucei gambiense ( T . b . gambiense ) in the related... | The development of rapid serodiagnostic tests for African sleeping sickness and other diseases caused by kinetoplastids relies in part on the affordable production of parasite-specific recombinant antigens . The majority of cases of sleeping sickness are caused by the parasite Trypanosoma brucei gambiense ( T . b . gam... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Expression of Trypanosoma brucei gambiense Antigens in Leishmania tarentolae. Potential for Use in Rapid Serodiagnostic Tests (RDTs) |
Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge , as cells are dynamic , chemically diverse , and fragile . A case in point is the cell membrane , which is too small to be seen directly with optical microscopy and provides little observational contr... | The structure and organization of the cell membrane are central to many biological functions , and although they have been extensively studied , there is still much that we don’t understand . A wealth of detailed information has been obtained from studies of model lipid membranes . However , these systems are often hig... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neutron",
"scattering",
"pathology",
"and",
"laboratory",
"medicine",
"particle",
"physics",
"pathogens",
"bacillus",
"microbiology",
"prokaryotic",
"models",
"experimental",
"organism",
"systems",
"lipid",
"structure",
"molecular... | 2017 | The in vivo structure of biological membranes and evidence for lipid domains |
CD8+ T cells play an important role in controlling of HIV and SIV infections . However , these cells are largely excluded from B cell follicles where HIV and SIV producing cells concentrate during chronic infection . It is not known , however , if antigen-specific CD8+ T cells are excluded gradually as pathogenesis pro... | A paucity of SIV-specific CD8+ T cells in lymphoid follicles and complete absence within most follicular germinal centers during early infection may set the stage for the establishment of persistent chronic infection . | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"hiv",
"infections",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency",
"viruses",
"lymph",
"nodes",
"rna",... | 2019 | Low levels of SIV-specific CD8+ T cells in germinal centers characterizes acute SIV infection |
Genome-wide association studies ( GWAS ) have in recent years discovered thousands of associated markers for hundreds of phenotypes . However , associated loci often only explain a relatively small fraction of heritability and the link between association and causality has yet to be uncovered for most loci . Rare causa... | Genome-wide association studies ( GWAS ) , based on the hypothesis that common genetic variation underlies complex diseases , have found many sites in the genome associated with complex diseases . However , both the fraction of variation explained by these sites and the number of studies identifying causal variants rem... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genetic",
"polymorphism",
"genetics",
"population",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics"
] | 2012 | Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation |
CD4 T cells are critical for control of persistent infections; however , the key signals that regulate CD4 T help during chronic infection remain incompletely defined . While several studies have addressed the role of inhibitory receptors and soluble factors such as PD-1 and IL-10 , significantly less work has addresse... | The natural rodent pathogen LCMV clone 13 causes a persistent viral infection in mice and has successfully predicted several immunological factors that are relevant to human chronic viral infection such as HIV . LCMV clone 13 infection is ultimately controlled by cell-mediated and humoral immune responses by day 60–90 ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | GITR Intrinsically Sustains Early Type 1 and Late Follicular Helper CD4 T Cell Accumulation to Control a Chronic Viral Infection |
The centrality-lethality rule , which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential , suggests that the topological prominence of a protein in a protein interaction network may be a good predictor of its biological importance . Even though the correlatio... | Analysis of protein interaction networks in the budding yeast Saccharomyces cerevisiae has revealed that a small number of proteins , the so-called hubs , interact with a disproportionately large number of other proteins . Furthermore , many hub proteins have been shown to be essential for survival of the cell—that is ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/systems",
"biology"
] | 2008 | Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality |
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