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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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Outbreaks of infectious diseases require a rapid response from policy makers . The choice of an adequate level of response relies upon available knowledge of the spatial and temporal parameters governing pathogen spread , affecting , amongst others , the predicted severity of the epidemic . Yet , when a new pathogen is... | We consider emerging epidemics , arising , e . g . , when a new pathogen is introduced in a host population . In face of the new threat , crucial control measures have to be implemented quickly , yet prior knowledge of the parameters underlying pathogen spread and transmission is often missing . Predictive modelling ca... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"infectious",
"disease",
"modeling",
"population",
"modeling",
"computational",
"biology"
] | 2014 | Bayesian Analysis for Inference of an Emerging Epidemic: Citrus Canker in Urban Landscapes |
A variety of human diseases are associated with gammaherpesviruses , including neoplasms of lymphocytes ( e . g . Burkitt's lymphoma ) and endothelial cells ( e . g . Kaposi's sarcoma ) . Gammaherpesvirus infections usually result in either a productive lytic infection , characterized by expression of all viral genes a... | Various human diseases are associated with gammaherpesvirus infections , including neoplasms of lymphocytes ( e . g . Burkitt's lymphoma ) and endothelial cells ( e . g . Kaposi's sarcoma ) . Gammaherpesvirus infection of cells usually results in either productive infection that is characterized by new virus production... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/persistence",
"and",
"latency",
"virology/immunodeficiency",
"viruses",
"virology/animal",
"models",
"of",
"infection",
"virology",
"microbiology",
"virology/host",
"invasion",
"and",
"cell",
"entry"
] | 2008 | Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection |
Over 133 , 000 children present to hospitals with Acute Encephalitis Syndrome ( AES ) annually in Asia . Japanese encephalitis ( JE ) accounts for approximately one-quarter of cases; in most cases no pathogen is identified and management is supportive . Although JE is known to result in neurological impairment , few st... | More than 133 , 000 children present annually to hospitals in Asia with clinical features of acute brain infection ( Acute Encephalitis Syndrome [AES] ) . Japanese encephalitis accounts for one-quarter of cases in Asia . With no specific treatments for AES , management is largely supportive . AES commonly causes neurol... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"global",
"health",
"neurology",
"public",
"health",
"pediatrics",
"physiotherapy",
"and",
"rehabilitation"
] | 2013 | The Functional, Social and Economic Impact of Acute Encephalitis Syndrome in Nepal – a Longitudinal Follow-Up Study |
Sporadic Japanese encephalitis ( JE ) cases still have been reported in Zhejiang Province in recent years , and concerns about vaccine cross-protection and population-level immunity have been raised off and on within the public health sphere . Genotype I ( GI ) has replaced GIII as the dominant genotype in Asian countr... | Japanese encephalitis ( JE ) remains one of the most significant public health problems in Asia and the Western Pacific region . A JE viral infection can cause death and severe sequelae . Vaccination is the most effective method for preventing JE currently . After decades of routine vaccination , the number of JE cases... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biogeography",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"immune",
"physiology",
"china",
"immunology",
"population",
"genetics",
"geographical",
"locations",
"vaccines",
"preventive",
"medicine",
"age",
"groups",
"population... | 2016 | Sero-Molecular Epidemiology of Japanese Encephalitis in Zhejiang, an Eastern Province of China |
Interactions between microbial species are sometimes mediated by the exchange of small molecules , secreted by one species and metabolized by another . Both one-way ( commensal ) and two-way ( mutualistic ) interactions may contribute to complex networks of interdependencies . Understanding these interactions constitut... | Microbial metabolism affects biogeochemical cycles and human health . In most natural environments , multiple microbial species interact with each other , forming complex ecosystems whose properties are poorly understood . In an effort to understand inter-microbial interactions , and to explore new metabolic engineerin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/environmental",
"microbiology",
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"computational",
"biology/synthetic",
"biology",
"evolutionary",
"biology/evolutionary",
"ecology",
"microbiology/microbial",
"physiology",
"and",
"metabolism",
... | 2010 | Environments that Induce Synthetic Microbial Ecosystems |
This study aimed to investigate the pharmacology and anti-parasitic efficacy of albendazole–chitosan microspheres ( ABZ-CS-MPs ) for established intraperitoneal infections of Echinococcus multilocularis metacestodes in an experimental murine model . Male outbred Kunming mice infected with E . multilocularis Metacestode... | Alveolar echinococcosis ( AE ) is caused by the metacestode stage of Echinococcus multilocularis and is a rare but life-threatening disease . Albendazole is the most frequently used anti-parasitic drugs in patients infected with AE . However , ABZ has only limited water solubility , and small differences in drug solubi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Efficacy of Albendazole-Chitosan Microsphere-based Treatment for Alveolar Echinococcosis in Mice |
Caenorhabditis elegans SKN-1 ( ortholog of mammalian Nrf1/2/3 ) is critical for oxidative stress resistance and promotes longevity under reduced insulin/IGF-1–like signaling ( IIS ) , dietary restriction ( DR ) , and normal conditions . SKN-1 inducibly activates genes involved in detoxification , protein homeostasis , ... | The nematode C . elegans has proven to be an invaluable organism for elucidating mechanisms that influence aging . Here we used genome-scale RNA interference screening in C . elegans to identify mechanisms that regulate a set of genes that defend against oxygen radicals and other stresses . These genes are activated by... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/post-translational",
"regulation",
"of",
"gene",
"expression",
"molecular",
"biology/transcription",
"initiation",
"and",
"activation",
"genetics",
"and",
"genomics/gene",
"expression",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
... | 2010 | RNAi Screening Implicates a SKN-1–Dependent Transcriptional Response in Stress Resistance and Longevity Deriving from Translation Inhibition |
Invasion of the central nervous system ( CNS ) by African trypanosomes represents a critical step in the development of human African trypanosomiasis . In both clinical cases and experimental mouse infections it has been demonstrated that predisposition to CNS invasion is associated with a type 1 systemic inflammatory ... | African trypanosomiasis ( also known as sleeping sickness ) is caused by the protozoan parasites Trypanosoma brucei rhodesiense and T . b . gambiense . After infection through the bite of the tsetse fly vector , parasites initially disseminate in the blood and lymphatic systems , in what is known as the early or haemol... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Central Nervous System Parasitosis and Neuroinflammation Ameliorated by Systemic IL-10 Administration in Trypanosoma brucei-Infected Mice |
Previous studies on the influence of weather on Aedes aegypti dynamics in Puerto Rico suggested that rainfall was a significant driver of immature mosquito populations and dengue incidence , but mostly in the drier areas of the island . We conducted a longitudinal study of Ae . aegypti in two neighborhoods of the metro... | Previous studies on the influence of weather on Aedes aegypti in Puerto Rico suggested that rainfall influenced mosquito populations and dengue incidence in the drier areas of the island . We studied temporal changes in Ae . aegypti in areas where rainfall is more uniformly distributed throughout the year . Changes in ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"ecology",
"biology",
"population",
"ecology"
] | 2011 | Population Dynamics of Aedes aegypti and Dengue as Influenced by Weather and Human Behavior in San Juan, Puerto Rico |
Ref is an HNH superfamily endonuclease that only cleaves DNA to which RecA protein is bound . The enigmatic physiological function of this unusual enzyme is defined here . Lysogenization by bacteriophage P1 renders E . coli more sensitive to the DNA-damaging antibiotic ciprofloxacin , an example of a phenomenon termed ... | The bacteriophage P1-encoded Ref protein is a novel class of endonuclease , cleaving only DNA to which the bacterial RecA protein is bound . The physiological role of such an enzyme has been entirely enigmatic . In this article , we define Ref as a P1 function that amplifies the lytic cycle under conditions when the ba... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | P1 Ref Endonuclease: A Molecular Mechanism for Phage-Enhanced Antibiotic Lethality |
Oedematous lesions are a less common but more severe form of Mycobacterium ulcerans disease . Misdiagnosis as bacterial cellulitis can lead to delays in treatment . We report the first comprehensive descriptions of the clinical features and risk factors of patients with oedematous disease from the Bellarine Peninsula o... | The oedematous form of Buruli ulcer , caused by Mycobacterium ulcerans , is less common representing 7% of cases over a 15 year period in a patient cohort from the Bellarine Peninsula of south-eastern Victoria , Australia . In this study , for oedematous Buruli ulcer cases , fever and pain were usually present and inve... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2014 | Clinical Features and Risk Factors of Oedematous Mycobacterium ulcerans Lesions in an Australian Population: Beware Cellulitis in an Endemic Area |
Malaria is a life-threatening disease spread by mosquitoes . Plasmodium falciparum M1 alanyl aminopeptidase ( PfM1-AAP ) is a promising target for the treatment of malaria . The recently solved crystal structures of PfM1-AAP revealed that the buried active site can be accessed through two channel openings: a short N-te... | Malaria is a tropical disease caused by infections with protozoan parasites of the genius Plasmodium . Currently , the disease results in over 400 , 000 human deaths per year worldwide and future prevention and treatment is at risk due to the rise of drug-resistant parasites . Plasmodium falciparum M1 alanyl aminopepti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"chemical",
"characterization",
"crystal",
"structure",
"electricity",
"condensed",
"matter",
"physics",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"electrostatics",
"protozoans",
"crystallography",
"... | 2018 | Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase |
Infection by DNA viruses can elicit DNA damage responses ( DDRs ) in host cells . In some cases the DDR presents a block to viral replication that must be overcome , and in other cases the infecting agent exploits the DDR to facilitate replication . We find that low multiplicity infection with the autonomous parvovirus... | Infection by DNA viruses can result in the induction of cellular DNA damage responses . These potent responses can present a block to the replication of certain viruses , but can also be utilized by others to their advantage . We show here that autonomous parvoviruses , single-stranded linear DNA viruses that infect ma... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/viral",
"replication",
"and",
"gene",
"regulation",
"virology",
"virology/effects",
"of",
"virus",
"infection",
"on",
"host",
"gene",
"expression",
"molecular",
"biology/dna",
"repair",
"virology/host",
"antiviral",
"responses"
] | 2010 | Parvovirus Minute Virus of Mice Induces a DNA Damage Response That Facilitates Viral Replication |
Approximately 30% of alleles causing genetic disorders generate premature termination codons ( PTCs ) , which are usually associated with severe phenotypes . However , bypassing the deleterious stop codon can lead to a mild disease outcome . Splicing at NAGNAG tandem splice sites has been reported to result in insertio... | Mild disease outcomes associated with premature termination codons can result from at least three different mechanisms , but none of these mechanisms explain the mild phenotype observed in some patients . Subtle differences in alternative transcripts have recently been reported at NAGNAG tandem acceptor motifs , which ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics/bioinformatics",
"genetics",
"and",
"genomics/medical",
"genetics"
] | 2010 | Alternative Splicing at a NAGNAG Acceptor Site as a Novel Phenotype Modifier |
The origin of the bilaterian head is a fundamental question for the evolution of animal body plans . The head of bilaterians develops at the anterior end of their primary body axis and is the site where the brain is located . Cnidarians , the sister group to bilaterians , lack brain-like structures and it is not clear ... | The evolutionary origin of head development is a fundamental question for understanding the evolution of animal body plans . Bilaterally symmetrical animals ( Bilaterians ) have an anterior-posterior ( head-to-tail ) axis , whose anterior end is usually characterized by a nervous system centralization , the brain . Thi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"organism",
"development",
"biology",
"pattern",
"formation",
"evolutionary",
"developmental",
"biology"
] | 2013 | The Bilaterian Head Patterning Gene six3/6 Controls Aboral Domain Development in a Cnidarian |
Previous studies of Ebola Virus Disease ( EVD ) have focused on clinical symptoms and Ebola virus ( EBOV ) cycle threshold ( CT ) values recorded at patient triage . Our study explores EVD symptoms and EBOV CT values from onset of illness to recovery or death in a diverse population of patients . We analyzed clinical c... | Previous studies of Ebola Virus Disease ( EVD ) have focused on clinical symptoms and viral load ( or its proxy of cycle threshold value ) in the blood of patients measured the day they begin medical care . However , this provides a single snapshot of the illness in time and does not indicate how signs/symptoms and cyc... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"geographical",
"locations",
"microbiology",
"pulmonology",
"diarrhea",
"signs",
"and",
"symptoms",
"gastroenterology",
"and",
"hepatology",... | 2017 | The natural history of acute Ebola Virus Disease among patients managed in five Ebola treatment units in West Africa: A retrospective cohort study |
How biochemical and mechanical information are integrated during tissue development is a central question in morphogenesis . In many biological systems , the PIX-GIT complex localises to focal adhesions and integrates both physical and chemical information . We used Drosophila melanogaster egg chamber formation to stud... | A major challenge in biology is to identify the genes and processes that build tissues of correct shape and function . Recently , transmission of mechanical forces through cell adhesions , and control of cell tension via contractile force-generating proteins , have emerged as fundamental to tissue development . Current... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"and",
"materials"
] | [
"invertebrates",
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"focal",
"adhesions",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"molecular",
"motors",
"actin",
"motors",
"experimental",
"... | 2019 | The dPix-Git complex is essential to coordinate epithelial morphogenesis and regulate myosin during Drosophila egg chamber development |
A next generation approach to cancer envisions developing preventative vaccinations to stimulate a person's immune cells , particularly cytotoxic T lymphocytes ( CTLs ) , to eliminate incipient tumors before clinical detection . The purpose of our study is to quantitatively assess whether such an approach would be feas... | An innovative approach to treating cancer envisions developing preventative anti-cancer vaccines to train a person's immune cells to eliminate early-stage tumors close to genesis . The design of such a treatment strategy requires an understanding of the tumor and immune interactions leading to a successful anti-cancer ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"mathematics",
"theoretical",
"biology",
"applied",
"mathematics",
"biology",
"computational",
"biology"
] | 2012 | Modeling Protective Anti-Tumor Immunity via Preventative Cancer Vaccines Using a Hybrid Agent-based and Delay Differential Equation Approach |
Recent studies have shown that a cytoplasmic virus called Leishmaniavirus ( LRV ) is present in some Leishmania species and acts as a potent innate immunogen , aggravating lesional inflammation and development in mice . In humans , the presence of LRV in Leishmania guyanensis and in L . braziliensis was significantly c... | About 80% of leishmaniasis infections result in cutaneous manifestations with a broad symptomatic spectrum , ranging from self-healing localized to disseminated lesions . The mechanism behind these latter aggravated forms of leishmaniasis is still poorly understood . One possible factor is an endosymbiotic RNA virus id... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"enzyme-linked",
"immunoassays",
"immunology",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"animal",
"models",
"preventive",
"medicine",
"model",
"organisms",
"immunologi... | 2017 | Exacerbated Leishmaniasis Caused by a Viral Endosymbiont can be Prevented by Immunization with Its Viral Capsid |
Secretory vesicles in endocrine cells store hormones such as growth hormone ( GH ) and insulin before their release into the bloodstream . The molecular mechanisms governing budding of immature secretory vesicles from the trans-Golgi network ( TGN ) and their subsequent maturation remain unclear . Here , we identify th... | Regulated secretion of peptide hormones , such as growth hormone ( GH ) and insulin , represents a fundamental process in controlling physiological homeostasis . In endocrine cells , hormone-containing vesicles bud from the Golgi apparatus to enable storage and regulated release into the blood stream . Here we show tha... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"pituitary",
"insulin",
"neurochemistry",
"diabetic",
"endocrinology",
"endocrinology",
"membranes",
"and",
"sorting",
"biology",
"molecular",
"cell",
"biology",
"neuroendocrinology",
"metabolism",
"neuroscience",
"hormones"
] | 2013 | PICK1 Deficiency Impairs Secretory Vesicle Biogenesis and Leads to Growth Retardation and Decreased Glucose Tolerance |
Schistosomiasis , one of the world’s greatest human neglected tropical diseases , is caused by parasitic trematodes of the genus Schistosoma . A unique feature of schistosome biology is that the induction of sexual maturation as well as the maintenance of the differentiation status of female reproductive organs and egg... | Schistosomiasis is one of the 17 neglected tropical diseases prioritized by the World Health Organization . It affects hundreds of millions of people in developing countries in the poorest tropical and subtropical regions of the world . Today , essentially a single drug , praziquantel ( PZQ ) , is available to treat th... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"helminths",
"tropical",
"diseases",
"light",
"microscopy",
"parasitic",
"diseases",
"animals",
"germ",
"cells",
"oocytes",
"confocal",
"laser",
"microscopy",
"microscopy",
... | 2016 | Discovery and Characterization of Novel Anti-schistosomal Properties of the Anti-anginal Drug, Perhexiline and Its Impact on Schistosoma mansoni Male and Female Reproductive Systems |
Using transcriptomic and metabolomic measurements from the NCI60 cell line panel , together with a novel approach to integration of molecular profile data , we show that the biochemical pathways associated with tumour cell chemosensitivity to platinum-based drugs are highly coincident , i . e . they describe a consensu... | Resistance to chemotherapy drugs in cancer sufferers is very common . Using a panel of 59 cell lines obtained from different types of cancer we study the links between the genes and metabolites measured in these cells and the resistance the cells show to common cancer drugs containing platinum . In order to combine the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"oncology/oncology",
"agents",
"computational",
"biology",
"computational",
"biology/systems",
"biology"
] | 2011 | Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells |
A metabolome-wide genome-wide association study ( mGWAS ) aims to discover the effects of genetic variants on metabolome phenotypes . Most mGWASes use as phenotypes concentrations of limited sets of metabolites that can be identified and quantified from spectral information . In contrast , in an untargeted mGWAS both i... | Metabolome-wide genome-wide association studies aim to discover how genetic variation affects metabolome traits . Such studies typically follow an acquire-identify-associate procedure: metabolome data are acquired experimentally , metabolites are identified in the experimental data and their concentrations quantified ,... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"protons",
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"nmr",
"spectroscopy",
"urine",
"metabolomics",
"metabolites",
"genome",
"analysis",
"molecular",
"genetics",
"research",
"and",
"analysis",
"methods",
"genomi... | 2017 | Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy |
The mammalian genome is organized into submegabase-sized chromatin domains ( CDs ) including topologically associating domains , which have been identified using chromosome conformation capture-based methods . Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement . ... | The mammalian genome is partitioned into topological chromatin domains ( CDs ) in the living cell nuclei . Gene expression is highly regulated within CDs according to their structure , whereas chromatin itself is highly dynamic . This raises the following question: how is the CD structure in such dynamic chromatin ? We... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"relaxation",
"time",
"hela",
"cells",
"biological",
"cultures",
"geometry",
"mathematics",
"materials",
"science",
"cell",
"cultures",
"epigenetics",
"macromolecules",
"chromatin",
"materials",
"by",
"structure",
"research",
"and",
"analysis",
"methods",
"polymers",
"p... | 2016 | Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells |
Coronaviruses infect animals and humans causing a wide range of diseases . The diversity of coronaviruses in many mammalian species is contributed by relatively high mutation and recombination rates during replication . This dynamic nature of coronaviruses may facilitate cross-species transmission and shifts in tissue ... | Coronaviruses are important pathogens in humans and animals . Although some coronaviruses can cause severe illness in humans and animals with considerable fatality , there is no antiviral drugs available for coronavirus infections . Feline infectious peritonitis ( FIP ) , caused by virulent feline coronavirus , is the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"lymphopenia",
"medicine",
"and",
"health",
"sciences",
"coronaviruses",
"body",
"fluids",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"respiratory",
"infections",
"pathogens",
"sars",
"coronavirus",
"immunology",
"microbiology",
"... | 2016 | Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor |
Despite the low case fatality , Zika virus ( ZIKV ) infection has been associated with microcephaly in infants and Guillain-Barré syndrome . Antiviral and vaccine developments against ZIKV are still ongoing; therefore , in the meantime , preventing the disease transmission is critical . Primarily transmitted by Aedes s... | Male-to-female sexual transmission of ZIKV has been reported more than the other sexual modes . Here we observe the disease progression of ZIKV in the testicular tissue of mouse models by gaining access to interstitial cells , the basement membrane of seminiferous tubule , spermatogenic cells , and sperm . In addition ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"reproductive",
"system",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"oxidative",
"stress",
"pathogens",
"immunology",
"microbiology",
"neurosc... | 2018 | Ebselen alleviates testicular pathology in mice with Zika virus infection and prevents its sexual transmission |
Clostridium difficile is the main cause of antibiotic-associated diarrhea , leading to significant morbidity and mortality and putting considerable economic pressure on healthcare systems . Current knowledge of the molecular basis of pathogenesis is limited primarily to the activities and regulation of two major toxins... | Clostridium difficile is a bacterial pathogen that causes antibiotic-associated diarrhea , which can be fatal . Infections often occur in healthcare facilities , where there is a high population density of susceptible patients with many possible routes of transmission . We currently do not know the functions of molecul... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbial",
"physiology",
"emerging",
"infectious",
"diseases",
"biology",
"microbiology",
"bacterial",
"pathogens",
"gram",
"positive"
] | 2011 | The Clostridium difficile Cell Wall Protein CwpV is
Antigenically Variable between Strains, but Exhibits Conserved
Aggregation-Promoting Function |
Age-related hearing impairment ( ARHI ) , one of the most common sensory disorders , can be mitigated , but not cured or eliminated . To identify genetic influences underlying ARHI , we conducted a genome-wide association study of ARHI in 6 , 527 cases and 45 , 882 controls among the non-Hispanic whites from the Geneti... | Age-related hearing impairment ( ARHI ) is one of the most common sensory disorders . While ARHI effects can be mitigated with current technologies , it cannot be cured or eliminated . It is thus hoped that identification of genetic influences on ARHI may one day lead to curative therapies . Towards this goal , the cur... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"ears",
"african",
"americans",
"variant",
"genotypes",
"genetic",
"mapping",
"ethnicities",
"otology",
"inner",
"ear",
"mathematics",
"statistics",
"(mathematics)",
"genome",
"analysis",
... | 2016 | A Large Genome-Wide Association Study of Age-Related Hearing Impairment Using Electronic Health Records |
Chagas Disease , a WHO- and NIH-designated neglected tropical disease , is endemic in Latin America and an emerging infection in North America and Europe as a result of population moves . Although a major cause of morbidity and mortality due to heart failure , as well as inflicting a heavy economic burden in affected r... | Chagas Disease is the leading cause of heart disease in Latin America and an emerging infection in Europe and North America . The clinical presentation of Chagas Disease arises from infection by the protozoan parasite Trypanosoma cruzi , which leads to progressive cardiomyopathy . No vaccine is available and chemothera... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"parastic",
"protozoans",
"biochemistry",
"lipids",
"trypanosoma",
"emerging",
"infectious",
"diseases",
"small",
"molecules",
"protozoology",
"biology",
"microbiology",
"sterols",
"drug",
"discovery"
] | 2012 | Diverse Inhibitor Chemotypes Targeting Trypanosoma cruzi CYP51 |
A common haplotype on 10q26 influences the risk of age-related macular degeneration ( AMD ) and encompasses two genes , LOC387715 and HTRA1 . Recent data have suggested that loss of LOC387715 , mediated by an insertion/deletion ( in/del ) that destabilizes its message , is causally related with the disorder . Here we s... | Age-related macular degeneration ( AMD ) is the leading blindness cause in western countries . Several genes encoding components of the complement pathway—including CFH , C2/BF , and C3—have been confirmed to be associated with AMD , as well as a region on 10q26 that encompasses two genes . Recent data have suggested t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"discovery",
"ophthalmology/macular",
"disorders",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/complex",
"traits",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomic... | 2010 | Genetic and Functional Dissection of HTRA1 and LOC387715 in Age-Related Macular Degeneration |
In 2013 , the World Health Organization ( WHO ) recognized mycetoma as one of the neglected tropical conditions due to the efforts of the mycetoma consortium . This same consortium formulated knowledge gaps that require further research . One of these gaps was that very few data are available on the epidemiology and tr... | WHO has recognized mycetoma as one of the neglected tropical diseases ( NTDs ) worldwide . Studies indicate infections from soil or possibly mediated by thorn pricks , but no detailed studies have investigated effects of soil type and Acacia distributions on mycetoma in Sudan . Here , we investigated risk factors assoc... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences",
"research",
"and",
"analysis",
"methods"
] | 2014 | Mapping the Potential Risk of Mycetoma Infection in Sudan and South Sudan Using Ecological Niche Modeling |
A number of human infections are characterized by the presence of more than one bacterial species and are defined as polymicrobial diseases . Methods for the analysis of the complex biological interactions in mixed infections with a large number of microorganisms are limited and do not effectively determine the contrib... | Bacterial infections often involve more than one species . The lung disease of cystic fibrosis ( CF ) patients provides examples of polymicrobial infections whereby diverse and dynamic microbial communities are a characteristic of CF airways . The significance of microbe–microbe interactions and the interplay of the co... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology/innate",
"immunity",
"infectious",
"diseases/respiratory",
"infections"
] | 2008 | Discerning the Complexity of Community Interactions Using a Drosophila Model of Polymicrobial Infections |
The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold . This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes . Initial binding to the X is thought to occur at “e... | The genomes of complex organisms encompass hundreds of millions of base pairs of DNA , and regulatory molecules must distinguish specific targets within this vast landscape . In general , regulatory factors find target genes through sequence-specific interactions with the underlying DNA . However , sequence-specific fa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"genetics",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context |
Gauging the systemic effects of non-synonymous single nucleotide polymorphisms ( nsSNPs ) is an important topic in the pursuit of personalized medicine . However , it is a non-trivial task to understand how a change at the protein structure level eventually affects a cell's behavior . This is because complex informatio... | Small changes in protein sequences , such as missense mutations resulting from genetic variations in the genome , can have a large impact on cellular behavior . Consequently , numerous studies have been carried out to evaluate the disease susceptibility of missense mutations by directly analyzing their structural or fu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"protein",
"interactions",
"proteins",
"protein",
"structure",
"biology",
"computational",
"biology",
"biophysics",
"simulations",
"biophysics"
] | 2012 | A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins |
Fasciola hepatica , along with Fasciola gigantica , is the causative agent of fasciolosis , a foodborne zoonotic disease affecting grazing animals and humans worldwide . Pathology is directly related to the release of parasite proteins that facilitate establishment within the host . The dominant components of these exc... | Vaccines for neglected parasitic diseases are of paramount importance . An understanding of the basic biology underpinning target expression within parasite populations is one of the pre-requisites for vaccine discovery and development . Fasciola hepatica causes global disease in humans and their livestock . The pathol... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry/protein",
"chemistry",
"molecular",
"biology/bioinformatics",
"infectious",
"diseases/helminth",
"infections",
"molecular",
"biology",
"genetics",
"and",
"genomics/bioinformatics"
] | 2011 | Towards Delineating Functions within the Fasciola Secreted Cathepsin L Protease Family by Integrating In Vivo Based Sub-Proteomics and Phylogenetics |
Sex chromosomes turn over rapidly in some taxonomic groups , where closely related species have different sex chromosomes . Although there are many examples of sex chromosome turnover , we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution . The sympatr... | Sex is ubiquitous , but sex-determining mechanisms are evolutionarily labile . Even in taxa with genetic sex determination mechanisms , closely related species often have different sex chromosomes . Although there are many examples of such sex chromosome turnover , we know little about the functional roles of sex chrom... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"sequencing",
"organismal",
"evolution",
"evolutionary",
"ecology",
"animal",
"genetics",
"genome",
"evolution",
"chromosome",
"biology",
"genetics",
"comparative",
"genomics",
"biology",
"genomics",
"evolutionary",
"biology",
"genomic",
"evolution",
"evolutionary... | 2014 | Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species |
A large group of viruses rely on low pH to activate their fusion proteins that merge the viral envelope with an endosomal membrane , releasing the viral nucleocapsid . A critical barrier to understanding these events has been the lack of approaches to study virus-cell membrane fusion within acidic endosomes , the natur... | Enveloped viruses are taken up into host cells after they bind to a specific receptor on the cell surface . These viruses are often delivered to specific compartments known as endosomes which have an acid environment that can trigger the virus and endosome membranes to fuse , allowing virus entry into the cell interior... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/host",
"invasion",
"and",
"cell",
"entry"
] | 2011 | Imaging Single Retrovirus Entry through Alternative Receptor Isoforms and Intermediates of Virus-Endosome Fusion |
Respiratory syncytial virus ( RSV ) protein M2-1 functions as an essential transcriptional cofactor of the viral RNA-dependent RNA polymerase ( RdRp ) complex by increasing polymerase processivity . M2-1 is a modular RNA binding protein that also interacts with the viral phosphoprotein P , another component of the RdRp... | Premature termination of transcription by the RNA-dependent RNA polymerase ( RdRp ) complex of respiratory syncytial virus ( RSV ) is prevented by the M2-1 protein . This transcription factor interacts with both RNA and viral phosphoprotein P , the main RdRp cofactor , through a specific “core” domain . Using NMR , we ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"protein",
"interactions",
"viral",
"classification",
"microbiology",
"viral",
"structure",
"rna",
"viruses",
"protein",
"structure",
"proteins",
"structural",
"proteins",
"biology",
"recombinant",
"proteins",
"viral",
"replication",
"complex",
"viral",
"replication",
"bi... | 2012 | Structure and Functional Analysis of the RNA- and Viral Phosphoprotein-Binding Domain of Respiratory Syncytial Virus M2-1 Protein |
Leishmaniasis is a neglected disease produced by the intracellular protozoan parasite Leishmania . In the present study , we show that LABCG2 , a new ATP-binding cassette half-transporter ( ABCG subfamily ) from Leishmania , is involved in parasite virulence . Down-regulation of LABCG2 function upon expression of an in... | Leishmania is a protozoan parasite that infects human macrophages , producing the neglected tropical disease known as leishmaniasis . As is the case for apoptotic cells , transient exposure of phosphatidylserine ( PS ) on the surface of the parasite is required for macrophage engulfment and infection . Although the mec... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"parastic",
"protozoans",
"leishmania",
"protozoology",
"host-pathogen",
"interaction",
"biology",
"microbiology",
"parasitology"
] | 2013 | LABCG2, a New ABC Transporter Implicated in Phosphatidylserine Exposure, Is Involved in the Infectivity and Pathogenicity of Leishmania |
Epstein-Barr virus ( EBV ) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence . Host-cell transcription is perturbed principally through the actions of EBV EBNA 2 , 3A , 3B and 3C , with cellular genes deregulated by specific combinations of these EBNAs through unknown m... | Epstein-Barr virus ( EBV ) is associated with numerous cancers . The ability of the virus to infect B-cells and convert them from short-lived into immortal cells is the key to its cancer-promoting properties . A small number of EBV transcription factors are required for immortalization and act in concert to drive cell ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming |
Considerable evidence now supports the idea that the moderate telomere lengthening produced by recombinational telomere elongation ( RTE ) in a Kluyveromyces lactis telomerase deletion mutant occurs through a roll-and-spread mechanism . However , it is unclear whether this mechanism can account for other forms of RTE t... | Indefinite growth of tumor cells requires a mechanism to maintain telomeres . While most cancers use telomerase for this , some maintain long and heterogeneous telomeres using a recombination-dependent mechanism termed alternative lengthening of telomeres ( ALT ) . What causes ALT and how their long and heterogeneous t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cancer",
"genetics",
"microbiology",
"kluyveromyces",
"lactis",
"telomeres",
"model",
"organisms",
"dna",
"chromosome",
"biology",
"biology",
"molecular",
"biology",
"cell",
"biology",
"nucleic",
"acids",
"genetics",
"yeast",
"and",
"fungal",
"models",
"dna",
"recomb... | 2012 | Long Telomeres Produced by Telomerase-Resistant Recombination Are Established from a Single Source and Are Subject to Extreme Sequence Scrambling |
Vascular extravasation , a key step in systemic infection by hematogenous microbial pathogens , is poorly understood , but has been postulated to encompass features similar to vascular transmigration by leukocytes . The Lyme disease spirochete can cause a variety of clinical manifestations , including arthritis , upon ... | Lyme disease is the most common vector-transmitted infection in North America and Europe . Diverse clinical manifestations of Lyme disease result from the dissemination of the spirochetes causing the disease into a variety of tissue sites . Dissemination results from invasion of the vasculature by the bacteria , follow... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Intravital Imaging of Vascular Transmigration by the Lyme Spirochete: Requirement for the Integrin Binding Residues of the B. burgdorferi P66 Protein |
Upon infection , human adenovirus ( HAdV ) must activate the expression of its early genes to reprogram the cellular environment to support virus replication . This activation is orchestrated in large part by the first HAdV gene expressed during infection , early region 1A ( E1A ) . E1A binds and appropriates component... | Adenovirus typically infects the upper respiratory tract and is one of the viral groups that causes the common cold . The virus itself is unable to reproduce on its own and so must use the infected host cell to produce more virus . Adenovirus reprograms the infected cell using the early gene products . The transcriptio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"rna",
"infectious",
"diseases",
"nucleic",
"acids",
"common",
"cold",
"gene",
"expression",
"genetics",
"gene",
"regulation",
"molecular",
"genetics",
"rna",
"synthesis",
"biology",
"viral",
"diseases",
"chromatin",
"dna",
"transcription",
... | 2013 | Viral Retasking of hBre1/RNF20 to Recruit hPaf1 for Transcriptional Activation |
Phenotypic plasticity is ubiquitous and primarily controlled by interactions between environmental and genetic factors . The migratory locust , a worldwide pest , exhibits pronounced phenotypic plasticity , which is a population density-dependent transition that occurs between the gregarious and solitary phases . Genes... | Phenotypic plasticity refers to the ability of an organism to alter its phenotypes in response to environmental changes . Genetic factors , such as coding and non-coding RNAs , contribute to phenotypic variation . MicroRNAs ( miRNAs ) , which are non-coding RNAs , function as post-transcriptional repressors of gene exp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"interference",
"entomology",
"gene",
"expression",
"genetics",
"biology",
"zoology"
] | 2014 | MicroRNA-133 Inhibits Behavioral Aggregation by Controlling Dopamine Synthesis in Locusts |
Perceptual learning of visual features occurs when multiple stimuli are presented in a fixed sequence ( temporal patterning ) , but not when they are presented in random order ( roving ) . This points to the need for proper stimulus coding in order for learning of multiple stimuli to occur . We examined the stimulus co... | When a person learns to judge several stimuli in succession , like baseball pitches arriving at various speeds and spins , judgments may improve with practice only if these stimuli are presented in a fixed temporal sequence , rather than in a random order . These contrary effects suggest the need for proper stimulus co... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience"
] | 2008 | Stimulus Coding Rules for Perceptual Learning |
Target-based drug discovery must assess many drug-like compounds for potential activity . Focusing on low-molecular-weight compounds ( fragments ) can dramatically reduce the chemical search space . However , approaches for determining protein-fragment interactions have limitations . Experimental assays are time-consum... | In drug discovery , the goal is to identify new compounds to alter the behavior of a protein implicated in disease . With the very large number of small molecules to test , researchers have increasingly studied fragments ( compounds with a small number of atoms ) because there are fewer possibilities to evaluate and th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"applied",
"mathematics",
"algorithms",
"empirical",
"methods",
"research",
"design",
"mathematics",
"protein",
"structure",
"information",
"technology",
"research",
"and",
"analysis",
"methods",
"computer",
"and",
"information",
"sciences",
"proteins",
"chemistry",
"mole... | 2014 | Knowledge-based Fragment Binding Prediction |
Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive , intermediate phenotypes . This phenomenon , called extrinsic postzygotic isolation ( EPI ) , is thought to play a critical role in the early stages of speciation . However , despite its intuitive ... | When two populations adapt to different ecological environments , they may become reproductively incompatible with each other and eventually form distinct species . One form of incompatibility thought to contribute to this process occurs when hybrids between diverging populations are ecologically maladapted . They suff... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology",
"evolutionary",
"biology/evolutionary",
"ecology",
"evolutionary",
"biology/animal",
"behavior"
] | 2010 | Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations |
Lung cancer is the leading cause of cancer-related death worldwide . Aberrant splicing has been implicated in lung tumorigenesis . However , the functional links between splicing regulation and lung cancer are not well understood . Here we identify the RNA-binding protein QKI as a key regulator of alternative splicing ... | Alternative pre-mRNA splicing is a key mechanism for increasing proteomic diversity and modulating gene expression . Emerging evidence indicates that splicing program is frequently deregulated during tumorigenesis , and cancer cells favor to produce protein isoforms that can promote growth and survival . Lung cancer is... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"rna",
"rna",
"processing",
"nucleic",
"acids",
"biology",
"and",
"life",
"sciences"
] | 2014 | The RNA-Binding Protein QKI Suppresses Cancer-Associated Aberrant Splicing |
Biologically detailed single neuron and network models are important for understanding how ion channels , synapses and anatomical connectivity underlie the complex electrical behavior of the brain . While neuronal simulators such as NEURON , GENESIS , MOOSE , NEST , and PSICS facilitate the development of these data-dr... | Computer modeling is becoming an increasingly valuable tool in the study of the complex interactions underlying the behavior of the brain . Software applications have been developed which make it easier to create models of neural networks as well as detailed models which replicate the electrical activity of individual ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/systems",
"biology",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail |
Group II introns are ancient retroelements that significantly shaped the origin and evolution of contemporary eukaryotic genomes . These self-splicing ribozymes share a common ancestor with the telomerase enzyme , the spliceosome machinery as well as the highly abundant spliceosomal introns and non-LTR retroelements . ... | A hallmark of eukaryotic cells is the ability of their numerous introns , sequences that interrupt genes , to generate genetic diversity through the expression of several different protein variants from a single gene . These eukaryotic introns share a common ancestor with bacterial group II introns , which are mobile ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"lactococcus",
"lactis",
"reverse",
"transcriptase-polymerase",
"chain",
"reaction",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"messenger",
"rna",
"microbiology",
"sequence",
"motif",
"analysis",
"molecular",
"biol... | 2018 | Bacterial group II introns generate genetic diversity by circularization and trans-splicing from a population of intron-invaded mRNAs |
Pathogenic yeasts and fungi are an increasing global healthcare burden , but discovery of novel antifungal agents is slow . The mycoparasitic yeast Saccharomycopsis schoenii was recently demonstrated to be able to kill the emerging multi-drug resistant yeast pathogen Candida auris . However , the molecular mechanisms i... | Fungal infections both in humans and in crop plants are on the rise , but novel strategies to combat yeast pathogens are few and far between . The mycoparasitic yeast Saccharomycopsis schoenii has recently been described as being able to physically attack and kill various clinically relevant Candida species , including... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"ecology",
"and",
"environmental",
"sciences",
"chemical",
"compounds",
"fungal",
"genetics",
"salts",
"organic",
"compounds",
"fungi",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"genome",
"analysis",
"amino",
"acids",
"plant",
"p... | 2019 | Multi-omics characterization of the necrotrophic mycoparasite Saccharomycopsis schoenii |
The ability to make optimal decisions depends on evaluating the expected rewards associated with different potential actions . This process is critically dependent on the fidelity with which reward value information can be maintained in the nervous system . Here we directly probe the fidelity of value representation fo... | Many models of learning and decision-making assume that experienced rewards are stored without error . We examined this assumption experimentally: participants first learned an association between different options and rewards in a simple two-alternative choice task . We then asked them to report what reward they expec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"decision",
"making",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"geometry",
"cognitive",
"neuroscience",
"cognitive",
"psychology",
"mathematics",
"probability",
"distribution",
"cognition",
"memory",
"fractals",
"animal",
"cells",
"le... | 2017 | Fidelity of the representation of value in decision-making |
In the male mouse the X and Y chromosomes pair and recombine within the small pseudoautosomal region . Genes located on the unsynapsed segments of the X and Y are transcriptionally silenced at pachytene by Meiotic Sex Chromosome Inactivation ( MSCI ) . The degree to which MSCI is conserved in other vertebrates is curre... | In meiosis , the correct segregation of the homologous chromosomes is assured by the coordination of synapsis ( a pairing mechanism ) and repair of DNA double-strand breaks through homologous recombination . The sex chromosomes represent a challenge to the system , because they are largely comprised of non-homologous s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"model",
"organisms",
"molecular",
"cell",
"biology",
"cell",
"biology",
"chromosome",
"biology",
"gene",
"expression",
"biology",
"evolutionary",
"biology",
"molecular",
"biology"
] | 2012 | Error-Prone ZW Pairing and No Evidence for Meiotic Sex Chromosome Inactivation in the Chicken Germ Line |
The parasitic trematode Schistosoma mansoni is one of the major causative agents of human schistosomiasis , which afflicts 200 million people worldwide . Praziquantel remains the main drug used for schistosomiasis treatment , and reliance on the single therapy has been prompting the search for new therapeutic compounds... | Heme is an essential molecule to most living organisms , but once in a free state it exerts toxic effects . Blood-feeding organisms evolved efficient ways to detoxify free heme derived from hemoglobin digestion . A key mechanism present in some hematophagous organisms consists of the crystallization of heme into a pigm... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"biology/gene",
"expression",
"biochemistry",
"biochemistry/membrane",
"proteins",
"and",
"energy",
"transduction",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses"
] | 2009 | Interference with Hemozoin Formation Represents an Important Mechanism of Schistosomicidal Action of Antimalarial Quinoline Methanols |
Trachoma programs have dramatically reduced the prevalence of the ocular chlamydia that cause the disease . Some have hypothesized that immunity to the infection may be reduced because of program success in reducing the incidence of infection , and transmission may then increase . Longitudinal studies of multiple commu... | Trachoma , caused by repeated infections by the ocular strains of Chlamydia trachomatis , is the most common infectious cause of blindness in the world . Treatment for trachoma includes mass azithromycin treatments to the entire community . To reduce the prevalence of infection , the World Health Organization ( WHO ) a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"complex",
"systems",
"medicine",
"infectious",
"diseases",
"trachoma",
"mathematics",
"population",
"modeling",
"ophthalmology",
"applied",
"mathematics",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"modeling",
"biology",
"computational",
"biology"
] | 2013 | Assessment of Transmission in Trachoma Programs over Time Suggests No Short-Term Loss of Immunity |
Trypanosoma cruzi is the causative agent of Chagas' Disease . The parasite has a complex population structure , with six major evolutionary lineages , some of which have apparently resulted from ancestral hybridization events . Because there are important biological differences between these lineages , strain typing me... | Trypanosoma cruzi , the causative agent of Chagas Disease , infects approximately 8 million people in the Americas , with 200 , 000 new cases reported anually . The disease , in its chronic stage , has different manifestations: mega-colon , mega-esophagus , and cardiomyopathy , among others . The fact that infections b... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"parastic",
"protozoans",
"trypanosoma",
"genetic",
"polymorphism",
"gene",
"identification",
"and",
"analysis",
"genetics",
"molecular",
"genetics",
"biology",
"population",
"genetics",
"microbiology",
"protozoology",
"genetics",
"and",
"genomics"
] | 2012 | A Simple Strain Typing Assay for Trypanosoma cruzi: Discrimination of Major Evolutionary Lineages from a Single Amplification Product |
High Mobility Group B ( HMGB ) proteins are nuclear architectural factors involved in chromatin remodeling and important nuclear events . HMGBs also play key roles outside the cell acting as alarmins or Damage-associated Molecular Patterns ( DAMPs ) . In response to a danger signal these proteins act as immune mediator... | When an infection occurs , the innate immune cells recognize Pathogen Associated Molecular Patterns ( PAMPs ) through their Pattern Recognition Receptors . This triggers an inflammatory response intended to kill the foreign microbe . But inflammation can also be triggered by the recognition of endogenous molecules call... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"inflammatory",
"diseases",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"immune",
"cells",
"immunology",
"tropical",
"diseases",
"parasitic",
... | 2017 | Trypanosoma cruzi High Mobility Group B (TcHMGB) can act as an inflammatory mediator on mammalian cells |
Uropathogenic Escherichia coli ( UPEC ) , the primary causative agent of urinary tract infections , typically express filamentous adhesive organelles called type 1 pili that mediate both bacterial attachment to and invasion of bladder urothelial cells . Several host proteins have previously been identified as receptors... | Strains of bacteria called uropathogenic Escherichia coli ( UPEC ) are the primary cause of urinary tract infections ( UTIs ) , which by some estimates are the second most common type of infectious disease in the world today . UPEC strains typically express hair-like fibers called type 1 pili on their surface that allo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"eukaryotes",
"in",
"vitro",
"infectious",
"diseases",
"microbiology"
] | 2007 | Integrin-Mediated Host Cell Invasion by Type 1–Piliated Uropathogenic Escherichia coli |
We present a comprehensive assessment of genomic diversity in the African-American population by studying three genotyped cohorts comprising 3 , 726 African-Americans from across the United States that provide a representative description of the population across all US states and socioeconomic status . An estimated 82... | Genetic studies of African-Americans identify functional variants , elucidate historical and genealogical mysteries , and reveal basic biology . However , African-Americans have been under-represented in genetic studies , and relatively little is known about nation-wide patterns of genomic diversity in the population .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"hispanic",
"people",
"african",
"americans",
"population",
"genetics",
"census",
"mathematical",
"models",
"ethnicities",
"research",
"design",
"paleontology",
"population",
"biology",
"research",
"and",
"analysis",
"methods",
"random",
"walk",
"geography",
"native",
"... | 2016 | The Great Migration and African-American Genomic Diversity |
Ascaris lumbricoides remains the most common endoparasite in humans , yet there is still very little information available about the immunological principles of protection , especially those directed against larval stages . Due to the natural host-parasite relationship , pigs infected with A . suum make an excellent mo... | Ascaris lumbricoides is the most common intestinal parasite in humans . A . suum is closely related to A . lumbricoides but infects pigs and can be used to study the immune response against larval stages . Most larvae are eliminated from the small intestine between 14 and 21 days after infection in what is called a sel... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | The Intestinal Expulsion of the Roundworm Ascaris suum Is Associated with Eosinophils, Intra-Epithelial T Cells and Decreased Intestinal Transit Time |
Cell polarity is a general cellular process that can be seen in various cell types such as migrating neutrophils and Dictyostelium cells . The Rho small GTP ( guanosine 5′-tri phosphate ) ases have been shown to regulate cell polarity; however , its mechanism of emergence has yet to be clarified . We first developed a ... | Eukaryotic cells such as neutrophils and Dictyostelium cells respond to temporal and spatial gradients of extracellular signals with directional movements . In a migrating cell , specific molecular events take place at the front and back edges . The spatially distinctive molecular accumulation inside cells is known as ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biophysics",
"cell",
"biology",
"none",
"computational",
"biology"
] | 2007 | A Mass Conserved Reaction–Diffusion System Captures Properties of Cell Polarity |
The control of the size of internal tubular organs , such as the lungs or vascular system , is critical for proper physiological activity and to prevent disease or malformations . This control incorporates the intrinsic physical anisotropy of tubes to generate proportionate organs that match their function . The exact ... | The regulation of the size of tubular organs is critical to ensure their physiological activity and to prevent disease and malformations . Here we use the Drosophila tracheal system as a suitable model to investigate the mechanisms underlying size regulation of tubular organs . Different mechanisms were known to contro... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"condensed",
"matter",
"physics",
"light",
"microscopy",
"anisotropy",
"cell",
"polarity",
"developmental",
"biology",
"respiratory",
"system",
"microscopy",
"materials",
"science",
"oils",
"molecular",
"bio... | 2018 | Anisotropic Crb accumulation, modulated by Src42A, is coupled to polarised epithelial tube growth in Drosophila |
The structure and quantitative composition of the cerebral cortex are interrelated with its computational capacity . Empirical data analyzed here indicate a certain hierarchy in local cortical composition . Specifically , neural wire , i . e . , axons and dendrites take each about 1/3 of cortical space , spines and gli... | Cerebral cortex is an outer layer of the brain in mammals , and it plays a critical part in various cognitive processes such as learning , memory , attention , language , and consciousness . The cerebral cortex contains a number of neuroanatomical parameters whose values are essentially conserved across species and bra... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"METHODS"
] | [] | 2015 | Cortical Composition Hierarchy Driven by Spine Proportion Economical Maximization or Wire Volume Minimization |
Constant optogenetic stimulation targeting both pyramidal cells and inhibitory interneurons has recently been shown to elicit propagating waves of gamma-band ( 40–80 Hz ) oscillations in the local field potential of non-human primate motor cortex . The oscillations emerge with non-zero frequency and small amplitude—the... | Optogenetic stimulation is increasingly used as a surrogate for endogenous activity to probe neural dynamics . Our model shows that optogenetic stimulation which predominantly recruits inhibitory neurons can dramatically alter the neural dynamics from type I excitability ( integrators ) to type II excitability ( resona... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"optogenetics",
"bifurcation",
"theory",
"vertebrates",
"electrophysiology",
"neuroscience",
"animals",
"mammals",
"primates",
"systems",
"science",
"mathematics",
"brain",
"mapping",
"bioassays",
"and",
"physiological",
"analysis",
... | 2017 | Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation |
The patch-leaving problem is a canonical foraging task , in which a forager must decide to leave a current resource in search for another . Theoretical work has derived optimal strategies for when to leave a patch , and experiments have tested for conditions where animals do or do not follow an optimal strategy . Never... | Foraging is a ubiquitous animal behavior , performed by organisms as different as worms , birds , rats , and humans . Although the behavior has been extensively studied , it is not known how the brain processes information obtained during foraging activity to make subsequent foraging decisions . We form an evidence acc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"decision",
"making",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"simulation",
"and",
"modeling",
"cognitive",
"neuroscience",
"cognitive",
"psychology",
"animal",
"behavior",
"mathematics",
"cognition",
"memory",
"zoology",
"research",
"and",
"a... | 2019 | Foraging as an evidence accumulation process |
It is well known that Affymetrix microarrays are widely used to predict genome-wide gene expression and genome-wide genetic polymorphisms from RNA and genomic DNA hybridization experiments , respectively . It has recently been proposed to integrate the two predictions by use of RNA microarray data only . Although the a... | One of the ultimate goals of genomics is to explore structural and functional variations of all genes in a genome . High-density oligo-microarray techniques enable prediction of genome-wide gene expression and genome-wide genetic polymorphisms from using RNA and genomic DNA samples , respectively . A recent proposal to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics/statistics",
"computational",
"biology/genomics",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2009 | Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data |
Alveolar echinococcosis ( AE ) is a severe helminth disease affecting humans , which is caused by the fox tapeworm Echinococcus multilocularis . AE represents a serious public health issue in larger regions of China , Siberia , and other regions in Asia . In Europe , a significant increase in prevalence since the 1990s... | Echinococcus multilocularis is a tapeworm of the red fox , which represents a considerable health threat to respectively infected humans . Main endemic areas are located in China , Siberia , and central Europe . Alarmed by an emerging or reemerging situation in Europe , the question of how the parasite gets spatially a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"ecology/evolutionary",
"ecology",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2009 | Genetic Diversity of the Cestode Echinococcus multilocularis in Red Foxes at a Continental Scale in Europe |
Candida albicans strains that are homozygous at the mating type locus ( MTLa or MTLα ) can spontaneously switch at a low frequency from the normal yeast cell morphology ( white ) to an elongated cell type ( opaque ) , which is the mating-competent form of the fungus . The ability to switch reversibly between these two ... | Some strains of the opportunistic fungal pathogen Candida albicans can reversibly switch from the normal yeast morphology ( white ) to an elongated cell type termed opaque , which is the mating-competent form of C . albicans . C . albicans strains first have to become homozygous at the mating type locus to be able to s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/microbial",
"growth",
"and",
"development",
"microbiology/microbial",
"evolution",
"and",
"genomics",
"microbiology/medical",
"microbiology",
"microbiology"
] | 2008 | Environmental Induction of White–Opaque Switching in Candida albicans |
To better characterize the behavior of HIV-1 capsids we developed EURT , for Entry/Uncoating assay based on core-packaged RNA availability and Translation . EURT is an alternative to Blam-Vpr , but as reporter RNA translation relies on core opening , it can be used to study viral capsids behavior . Our study reveals th... | Following viral-to-cellular membrane fusion , the HIV-1 genome is propelled inside the cell as part of an higher order nucleoproteic structure often referred to as viral core , or capsid . Here , we have developed a novel entry/uncoating assay based on the degree of exposure of a virion-packaged mRNA reporter to the tr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"luciferase",
"assay",
"luciferase",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"pathogens",
"microbiology",
"enzymology",
"viral",
"structure",
"biochemical",
"analysis",
"retroviruses",
"viruses",
"immunodeficiency",
... | 2016 | A Novel Entry/Uncoating Assay Reveals the Presence of at Least Two Species of Viral Capsids During Synchronized HIV-1 Infection |
Multiple treatment strategies are available for empiric antibiotic therapy in hospitals , but neither clinical studies nor theoretical investigations have yielded a clear picture when which strategy is optimal and why . Extending earlier work of others and us , we present a mathematical model capturing treatment strate... | For life-threatening infections , antibiotics need to be administered as soon as possible . Because it takes time to acquire data about the disease causing bacteria , the immediate treatment is often empiric . In particular , there are three treatment strategies discussed in the field of empiric treatment: cycling , mi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Acknowledgement"
] | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"linear",
"discriminant",
"analysis",
"drugs",
"microbiology",
"mathematical",
"models",
"optimization",
"antibiotic",
"resistance",
"mathematics",
"pharmaceutics",
"statistics",
"(mathematics)",
"antibiotics",
"pharm... | 2017 | Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies |
Sub-microscopic ( SM ) Plasmodium infections represent transmission reservoirs that could jeopardise malaria elimination goals . A better understanding of the epidemiology of these infections and factors contributing to their occurrence will inform effective elimination strategies . While the epidemiology of SM P . fal... | Light microscopy ( LM ) has been the mainstay of malaria diagnosis for case management and surveillance . The introduction of molecular based diagnostics such as polymerase chain reaction ( PCR ) in the 1990s resulted in increased reporting of Plasmodium infections in communities compared to LM , indicating that sub-mi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences"
] | 2015 | Systematic Review of Sub-microscopic P. vivax Infections: Prevalence and Determining Factors |
IL-13 driven Th2 immunity is indispensable for host protection against infection with the gastrointestinal nematode Nippostronglus brasiliensis . Disruption of CD28 mediated costimulation impairs development of adequate Th2 immunity , showing an importance for CD28 during the initiation of an immune response against th... | CD28 is an important costimulatory molecule , involved in the activation of naive T cells , enhancing cytokine production , preventing T cell anergy and apoptosis . Furthermore , CD28 plays a crucial role in the organisation of secondary lymphoid tissue by assisting in the recruitment of T cells into the B cell follicl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"humoral",
"immunity",
"adaptive",
"immunity",
"immune",
"cells",
"cytokines",
"immunity",
"immune",
"activation",
"immune",
"defense",
"immunology",
"immunity",
"to",
"infections",
"biology",
"immune",
"response",
"immune",
"system"
] | 2014 | Inducible Deletion of CD28 Prior to Secondary Nippostrongylus brasiliensis Infection Impairs Worm Expulsion and Recall of Protective Memory CD4+ T Cell Responses |
Accurate diagnostic techniques for schistosomiasis are essential for prevalence determination and identification of positive patients . A point-of-care test for detecting schistosome circulating cathodic antigen ( POC-CCA ) has been evaluated for its accuracy in different endemic regions . This reagent strip/dipstick b... | Schistosomiasis mansoni is a relevant disease affecting millions of individuals in different countries , in particular countries in Africa , and Brazil . Diagnosis performed by Kato-Katz technique for the detection of eggs in stool and a point-of-care test for circulating cathodic antigen detection in urine ( POC-CCA )... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"helminths",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"parasitology",
"urine",
"neglected",
"tropical",
"diseases",
"research",
"and",
... | 2016 | Improvement of POC-CCA Interpretation by Using Lyophilization of Urine from Patients with Schistosoma mansoni Low Worm Burden: Towards an Elimination of Doubts about the Concept of Trace |
We have developed a powerful experimental framework that combines competitive selection and microarray-based genetic footprinting to comprehensively reveal the genetic basis of bacterial behaviors . Application of this method to Escherichia coli motility identifies 95% of the known flagellar and chemotaxis genes , and ... | Bacteria thrive in a limitless range of extreme environments , accompanied by exotic metabolisms and sophisticated behaviors . However , our modern molecular understanding of bacteria comes from studies of a limited range of phenotypes in a handful of model organisms such as E . coli and Bacillus subtilis . With the av... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics",
"microbiology",
"eubacteria"
] | 2007 | A Comprehensive Genetic Characterization of Bacterial Motility |
Accumulating evidence indicates that miRNAs can be promising diagnostic and/or prognostic markers for various cancers . In this study , we identified a novel miRNA , miR-3607-3p , and its targets in non-small cell lung cancer ( NSCLC ) . The expression of miR-3607-3p was measured and its correlation with patient progno... | We first showed downregulation of miR-3607-3p in NSCLC tissues and demonstrated that miR-3607-3p may act as an independent predictor of overall survival . Serum miR-3607-3p may be a novel marker of patients with NSCLC . We further found that miR-3607-3p possesses the potency to suppress NSCLC growth and metastasis and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"transfection",
"medicine",
"and",
"health",
"sciences",
"luciferase",
"natural",
"antisense",
"transcripts",
"gene",
"regulation",
"enzymes",
"cancers",
"and",
"neoplasms",
"basic",
"cancer",
"research",
"enzymology",
"oncology",
"animal",
"models",
"micrornas",
"model... | 2018 | miR-3607-3p suppresses non-small cell lung cancer (NSCLC) by targeting TGFBR1 and CCNE2 |
We report for the first time the genomics of a nuclear compartment of the eukaryotic cell . 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains ( NADs ) in the linear human genome and identified different gene families and certain satellite repeats as the major building... | It is becoming increasingly clear that the nuclear organization and location of genes in metazoan organisms is not random . Functionally related genes are often found next to each other in the linear genome , and distant DNA elements or DNA regions residing on different chromosomes may reside in specific nuclear compar... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/nucleolus",
"and",
"nuclear",
"bodies",
"genetics",
"and",
"genomics/nuclear",
"structure",
"and",
"function",
"genetics",
"and",
"genomics/bioinformatics",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/epigenetics",
... | 2010 | Initial Genomics of the Human Nucleolus |
Zinc is an essential metal involved in a wide range of biological processes , and aberrant zinc metabolism is implicated in human diseases . The gastrointestinal tract of animals is a critical site of zinc metabolism that is responsible for dietary zinc uptake and distribution to the body . However , the role of the ga... | Zinc is an essential mineral nutrient involved in many physiological processes , and it plays a critical role in human health . Insufficient dietary zinc causes a wide range of health problems , and excess dietary zinc causes toxicity . Furthermore , genetic mutations affecting zinc metabolism have been implicated in a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology",
"genetics",
"biology",
"genomics"
] | 2013 | ttm-1 Encodes CDF Transporters That Excrete Zinc from Intestinal Cells of C. elegans and Act in a Parallel Negative Feedback Circuit That Promotes Homeostasis |
HIV-1 integrates more frequently into transcribed genes , however the biological significance of HIV-1 integration targeting has remained elusive . Using a selective high-throughput chemical screen , we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a s... | HIV-1 integrates more frequently within transcribed host genes , however we do not understand the biological significance of this . We found that a drug called digoxin inhibits wild type HIV-1 more potently than an HIV-1 bearing a single point mutation in the capsid protein . Here we show that digoxin represses HIV-1 g... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"pathogens",
"immunology",
"microbiology",
"enzymology",
"cell",
"metabolism",
"phosphatases... | 2017 | Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation |
There is compelling biological data to suggest that cancer arises from a series of mutations in single target cells , resulting in defects in cell renewal and differentiation processes which lead to malignancy . Because much mutagenic damage is expressed following cell division , more-rapidly renewing tissues could be ... | Cancer is thought to arise from a series of mutations in cells . Because mutations are expressed following cell division , more-rapidly renewing tissues could be at higher risk because of the larger number of divisions . Cairns suggested that tissues may reduce cancer risk by partitioning the dividing cell populations ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"cell",
"division",
"analysis",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"cancer",
"risk",
"factors",
"cancer",
"stem",
"cells",
"cell",
"differentiation",
"oncology",
"developmental",
"biology",
"stem... | 2017 | Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer |
The thymus is a vertebrate-specific organ where T lymphocytes are generated . Genetic programs that lead to thymus development are incompletely understood . We previously screened ethylnitrosourea-induced medaka mutants for recessive defects in thymus development . Here we report that one of those mutants is caused by ... | Medaka , Oryzias latipes , is a small freshwater fish that is useful for studies of forward and reverse genetics . The availability of various inbred strains is the distinct advantage of medaka over zebrafish , especially in studies of the immune system . The thymus is a primary immune organ that is unique to vertebrat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"molecular",
"biology/nucleolus",
"and",
"nuclear",
"bodies",
"developmental",
"biology/organogenesis",
"immunology/genetics",
"of",
"the",
"immune",
"system",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system"
] | 2008 | WDR55 Is a Nucleolar Modulator of Ribosomal RNA Synthesis, Cell Cycle Progression, and Teleost Organ Development |
Neuronal activity differs between wakefulness and sleep states . In contrast , an attractor state , called self-organized critical ( SOC ) , was proposed to govern brain dynamics because it allows for optimal information coding . But is the human brain SOC for each vigilance state despite the variations in neuronal dyn... | Brain activity shows complex dynamics , even in the absence of external stimulation . In fact , most brain activity is generated internally . Therefore , it is crucial to understand the generation principles of internal activity . One hypothesis is that complex brain dynamics emerges from simple local interactions if t... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"physics",
"neural",
"networks",
"computational",
"neuroscience",
"interdisciplinary",
"physics",
"biophysics",
"simulations",
"biology",
"biophysics",
"neuroscience",
"neurophysiology"
] | 2013 | Neuronal Avalanches Differ from Wakefulness to Deep Sleep – Evidence from Intracranial Depth Recordings in Humans |
Studying SIV infection of natural host monkey species , such as sooty mangabeys , has provided insights into the immune changes associated with these nonprogressive infections . Mangabeys maintain immune health despite high viremia or the dramatic CD4 T cell depletion that can occur following multitropic SIV infection ... | SIV infection of sooty mangabeys is generally characterized by maintained CD4 T cell levels and a lack of disease progression despite active virus replication . We have previously shown however , that dramatic loss of CD4 T cells can occur during SIV infection of mangabeys . This study investigates the potential for do... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"medicine",
"infectious",
"diseases",
"immunology",
"biology"
] | 2013 | Multifunctional Double-negative T Cells in Sooty Mangabeys Mediate T-helper Functions Irrespective of SIV Infection |
During a tuberculosis infection and inside lipid-laden foamy macrophages , fatty acids ( FAs ) and sterols are the major energy and carbon source for Mycobacterium tuberculosis . Mycobacteria can be found both inside a vacuole and the cytosol , but how this impacts their access to lipids is not well appreciated . Lipid... | Mycobacterium tuberculosis ( Mtb ) survives the human immune defence mechanisms leading to latent tuberculosis in one third of the world population . The ability to persist latently in human macrophages is due to a remarkable physiological change that is accompanied by a slowdown in replication , low metabolism , and p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"dictyosteliomycota",
"pathogens",
"microbiology",
"neutral",
"lipids",
"experimental",
"organism",
"systems",
"bacteria",
"bacterial",
"pathogens",
"researc... | 2017 | Mycobacterium marinum Degrades Both Triacylglycerols and Phospholipids from Its Dictyostelium Host to Synthesise Its Own Triacylglycerols and Generate Lipid Inclusions |
Molecular signatures are computational or mathematical models created to diagnose disease and other phenotypes and to predict clinical outcomes and response to treatment . It is widely recognized that molecular signatures constitute one of the most important translational and basic science developments enabled by recen... | One of the promises of personalized medicine is to use molecular information to better diagnose , manage , and treat disease . This promise is enabled through the use of molecular signatures that are computational models to predict a phenotype of interest from high-throughput assay data . Many molecular signatures have... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/gene",
"discovery",
"computer",
"science/applications",
"computational",
"biology/systems",
"biology",
"genetics",
"and",
"genomics/gene",
"expression",
"mathematics/statistics",
"genetics",
"and",
"genomics/b... | 2010 | Analysis and Computational Dissection of Molecular Signature Multiplicity |
Sulphur ( S ) is an essential element for all living organisms . The uptake , assimilation and metabolism of S in plants are well studied . However , the regulation of S homeostasis remains largely unknown . Here , we report on the identification and characterisation of the more sulphur accumulation1 ( msa1-1 ) mutant ... | Sulphur is an essential element for all living organisms including plants . Plants take up sulphur from the soil mainly in the form of inorganic sulphate . The uptake of sulphate and assimilation of sulphur have been well studied . However , the regulation of sulphur accumulation in plants remains largely unknown . In ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"plant",
"anatomy",
"chemical",
"compounds",
"salts",
"brassica",
"sulfur",
"organisms",
"plant",
"science",
"model",
"organisms",
"genetically",
"modified",
"plants",
"epigenetics",
"dna",
"molecular",
"biology",
"techniques",
"plants",
"dna",
"methyla... | 2016 | Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana |
Several recent studies have shown that neural activity in vivo tends to be constrained to a low-dimensional manifold . Such activity does not arise in simulated neural networks with homogeneous connectivity and it has been suggested that it is indicative of some other connectivity pattern in neuronal networks . In part... | A network in the brain consists of thousands of neurons . A priori , we expect that the network will have as many degrees of freedom as its number of neurons . Surprisingly , experimental evidence suggests that local brain activity is confined to a subspace spanned by ~10 variables . Here , we employ three established ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"engineering",
"and",
"technology",
"nervous",
"system",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"systems",
"science",
"mathematics",
"computational",
"neuroscience"... | 2019 | Perturbing low dimensional activity manifolds in spiking neuronal networks |
The WRAP53 gene gives rise to a p53 antisense transcript that regulates p53 . This gene also encodes a protein that directs small Cajal body–specific RNAs to Cajal bodies . Cajal bodies are nuclear organelles involved in diverse functions such as processing ribonucleoproteins important for splicing . Here we identify t... | Cajal bodies , discovered more than 100 years ago by Santiago Ramón y Cajal , are sub-organelles found in the nucleus of proliferative cells and neurons . They have been implicated in a variety of nuclear functions including ribonucleoprotein maturation , spliceosome formation , histone mRNA processing , RNA polymerase... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"cell",
"biology"
] | 2010 | WRAP53 Is Essential for Cajal Body Formation and for Targeting the Survival of Motor Neuron Complex to Cajal Bodies |
UV-induced DNA damage causes repression of RNA synthesis . Following the removal of DNA lesions , transcription recovery operates through a process that is not understood yet . Here we show that knocking-out of the histone methyltransferase DOT1L in mouse embryonic fibroblasts ( MEFDOT1L ) leads to a UV hypersensitivit... | Through the deformation of the genomic DNA structure , UV-induced DNA lesions have repressive effect on various nuclear processes including replication and transcription . As a matter of fact , the removal of these lesions is a priority for the cell and takes place at the expense of fundamental cellular processes that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"biology",
"gene",
"function"
] | 2013 | Histone Methyltransferase DOT1L Drives Recovery of Gene Expression after a Genotoxic Attack |
Mucosal HIV-1 transmission is inefficient . However , certain viral and host characteristics may play a role in facilitating HIV acquisition and systemic expansion . Cells expressing high levels of integrin α4β7 have been implicated in favoring the transmission process and the infusion of an anti-α4β7 mAb ( RM-Act-1 ) ... | To successfully infect a new host through the sexual route , HIV needs to travel to anatomical sites distant from the mucosal site of exposure reaching draining lymph nodes and the gut , where it can expand and disseminate . The characteristics of the vaginal mucosal microenvironment that facilitate HIV acquisition are... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"blood",
"cells",
"cell",
"binding",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"cloning",
"animals",
"mamm... | 2016 | A Small Molecule, Which Competes with MAdCAM-1, Activates Integrin α4β7 and Fails to Prevent Mucosal Transmission of SHIV-SF162P3 |
Measles virus ( MV ) is hypothesized to enter the host by infecting epithelial cells of the respiratory tract , followed by viremia mediated by infected monocytes . However , neither of these cell types express signaling lymphocyte activation molecule ( CD150 ) , which has been identified as the receptor for wild-type ... | Measles remains one of the most important causes of childhood mortality in developing countries . The virus is highly infectious and is spread via the respiratory route . According to textbook descriptions , measles virus first infects respiratory epithelial cells , followed by viremia mediated by infected monocytes . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"primates",
"viruses",
"infectious",
"diseases",
"virology",
"immunology",
"homo",
"(human)"
] | 2007 | Predominant Infection of CD150+ Lymphocytes and Dendritic Cells during Measles Virus Infection of Macaques |
Recognizing the actions of others from visual stimuli is a crucial aspect of human perception that allows individuals to respond to social cues . Humans are able to discriminate between similar actions despite transformations , like changes in viewpoint or actor , that substantially alter the visual appearance of a sce... | Recognizing the actions of others from video sequences across changes in viewpoint , gait or illumination is a hallmark of human visual intelligence . A large number of studies have highlighted which areas in the human brain are involved in the processing of biological motion , while others have described how single ne... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"brain",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"perception",
"cognitive",
"psychology",
"cognition",
"brain",
"mapping",
"artificial",
"intelligence",
"memory",
"visi... | 2017 | Invariant recognition drives neural representations of action sequences |
It is widely accepted that MAPK activation in budding and fission yeasts is often associated with negative effects on cell cycle progression , resulting in delay or arrest at a specific stage in the cell cycle , thereby enabling cells to adapt to changing environmental conditions . For instance , activation of the Cell... | Signaling cascades connect changes in the extracellular environment with cellular responses . An obvious target for this signaling is cell cycle machinery , since cells have to integrate outside signals to decide whether to proliferate or not . Here we report that the response to cell wall damage in the fungus Ustilago... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/microbial",
"growth",
"and",
"development",
"microbiology/microbial",
"growth",
"and",
"development",
"developmental",
"biology/microbial",
"growth",
"and",
"development",
"cell",
"biology/cell",
"signaling"
] | 2010 | Activation of the Cell Wall Integrity Pathway Promotes Escape from G2 in the Fungus Ustilago maydis |
Phytoplasmas are insect-transmitted bacterial pathogens that colonize a wide range of plant species , including vegetable and cereal crops , and herbaceous and woody ornamentals . Phytoplasma-infected plants often show dramatic symptoms , including proliferation of shoots ( witch’s brooms ) , changes in leaf shapes and... | Phytoplasmas are parasites of a wide range of plant species and are transmitted by sap-feeding insects , such as leafhoppers . Phytoplasma-infected plants are often easily recognized because of their dramatic symptoms , including shoot proliferations ( witch’s brooms ) and altered leaf shapes , leading to severe econom... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"biotechnology",
"plant",
"anatomy",
"engineering",
"and",
"technology",
"gene",
"regulation",
"regulatory",
"proteins",
"brassica",
"dna-binding",
"proteins",
"plant",
"science",
"model",
"organisms",
"genetically",
"modified",
"plants",
"experimental",
"organism",
"syst... | 2019 | Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize |
The eocyte hypothesis , in which Eukarya emerged from within Archaea , has been boosted by the description of a new candidate archaeal phylum , “Lokiarchaeota” , from metagenomic data . Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins . However , individual phy... | Two scenarios have been proposed to describe the history of cellular life on our planet . For some authors , two lineages emerged from the last universal cellular ancestor , one leading to Bacteria , the other one leading to a common ancestor of Archaea and Eukarya ( Woese’s hypothesis ) , while others suggest that Euk... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"taxonomy",
"microbiology",
"dna-binding",
"proteins",
"phylogenetics",
"data",
"management",
"plant",
"science",
"polymerases",
"phylogenetic",
"analysis",
"genome",
"analysis",
"protein",
"structure",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"co... | 2017 | Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes |
In 2006 there were an estimated 645 , 000 people in Amhara , Ethiopia , with trachomatous trichiasis ( TT ) who needed surgery . Despite an extensive integrated eye care worker training programme ( IECW ) and robust support for TT surgical services , productivity has not reached targets . We investigated why surgeon pr... | Blindness from trachoma is caused by the abrasive effect of trichiasis ( in-turned eyelashes ) . Surgery is performed to correct this anatomical abnormality , and prevent blindness . Despite the progress made in many regions in controlling the active/infectious stages of this disease , the global prevalence of trichias... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"neglected",
"tropical",
"diseases",
"trachoma"
] | 2011 | Clearing the Backlog: Trichiasis Surgeon Retention and Productivity in Northern Ethiopia |
Shewanella oneidensis MR-1 sequentially utilizes lactate and its waste products ( pyruvate and acetate ) during batch culture . To decipher MR-1 metabolism , we integrated genome-scale flux balance analysis ( FBA ) into a multiple-substrate Monod model to perform the dynamic flux balance analysis ( dFBA ) . The dFBA em... | This study integrates two modeling approaches , a Monod kinetic model and genome-scale flux balance analysis , to analyze the dynamic metabolism of an environmentally important bacterium ( S . oneidensis MR-1 ) . The modeling results reveal that MR-1 metabolism is suboptimal for biomass growth , while MR-1 continuously... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biology",
"computational",
"biology",
"microbiology",
"genetics",
"and",
"genomics"
] | 2012 | Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1 |
We proposed a spatially extended model of early events of B cell receptors ( BCR ) activation , which is based on mutual kinase-receptor interactions that are characteristic for the immune receptors and the Src family kinases . These interactions lead to the positive feedback which , together with two nonlinearities re... | B cells are activated in response to binding of appropriate ligands , which induces the aggregation of B cell receptors . The formation of even small clusters containing less than 1% of all the receptors is sufficient for activation . This observation led us to a model in which the receptor cluster serves only as a swi... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"mathematics",
"biology"
] | 2011 | B Cell Activation Triggered by the Formation of the Small Receptor Cluster: A Computational Study |
Helminth infection and malaria remain major causes of ill-health in the tropics and subtropics . There are several shared risk factors ( e . g . , poverty ) , and hence , helminth infection and malaria overlap geographically and temporally . However , the extent and consequences of helminth-Plasmodium co-infection at d... | Parasitic worm infection and malaria are common in tropical and subtropical countries and many people suffer from multiple parasite infections concurrently . It is important to gain knowledge on co-endemicity patterns because such information can help to design and prioritize interventions and control strategies focusi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"plasmodium",
"falciparum",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"pediatrics",
"protozoans",
"plasmodium",
"malariae",
"neglected",
"tropical",
"diseases",
"public",
"and",
"occupational",
"he... | 2014 | Infection and Co-infection with Helminths and Plasmodium among School Children in Côte d’Ivoire: Results from a National Cross-Sectional Survey |
Several sequence based genotyping schemes have been developed for Leptospira spp . The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results . A total of 48 isolates consisting of L . interrogans ( n = 40 ) a... | Two independent multilocus sequence based genotyping schemes ( denoted here as 7L and 6L for schemes with 7 and 6 loci , respectively ) are in use for Leptospira spp . , which has led to uncertainty as to which should be adopted by the scientific community . The purpose of this study was to apply the two schemes to a s... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"molecular",
"genetics",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Comparison of Two Multilocus Sequence Based Genotyping Schemes for Leptospira Species |
Accurate prediction of disease risk based on genetic factors is an important goal in human genetics research and precision medicine . Advanced prediction models will lead to more effective disease prevention and treatment strategies . Despite the identification of thousands of disease-associated genetic variants throug... | Genetic risk prediction plays a significant role in precision medicine . Accurate prediction models could have great impact on disease prevention and treatment strategies . However , prediction accuracies for most complex diseases remain moderate mainly due to the challenges in identifying and quantifying the effects o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"functional",
"genomics",
"genomics",
"statistics",
"diabetes",
"mellitus",
"endocrine",
"disorders",
"coronary",
"heart",
"disease",
"mathematics",
"forecasting",
"statistics",
"(mathematics)... | 2017 | Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction |
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