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Sample records for model linking viral

  1. Molecular modeling and conformational analysis of native and refolded viral genome-linked protein of cardamom mosaic virus.

    PubMed

    Jebasingh, T; Jose, M; Yadunandam, A Kasin; Backiyarani, S; Srividhya, K V; Krishnaswamy, S; Usha, R

    2011-10-01

    The viral genome-linked protein (VPg) of Potyviruses is covalently attached to the 5' end of the genomic RNA. Towards biophysical characterization, the VPg coding region of Cardamom mosaic virus (CdMV) was amplified from the cDNA and expressed in E. coli. Most of the expressed VPg aggregated as inclusion bodies that were solubilized with urea and refolded with L-arginine hydrochloride. The various forms of CdMV VPg (native, denatured and refolded) were purified and the conformational variations between these forms were observed with fluorescence spectroscopy. Native and refolded CdMV VPg showed unordered secondary structure in the circular dichroism (CD) spectrum. The model of CdMV VPg was built based on the crystal structure of phosphotriesterase (from Pseudomonas diminuta), which had the maximum sequence homology with VPg to identify the arrangement of conserved amino acids in the protein to study the functional diversity of VPg. This is the first report on the VPg of CdMV, which is classified as a new member of the Macluravirus genus of the Potyviridae family. PMID:22165292

  2. Molecular modeling and conformational analysis of native and refolded viral genome-linked protein of cardamom mosaic virus.

    PubMed

    Jebasingh, T; Jose, M; Yadunandam, A Kasin; Backiyarani, S; Srividhya, K V; Krishnaswamy, S; Usha, R

    2011-10-01

    The viral genome-linked protein (VPg) of Potyviruses is covalently attached to the 5' end of the genomic RNA. Towards biophysical characterization, the VPg coding region of Cardamom mosaic virus (CdMV) was amplified from the cDNA and expressed in E. coli. Most of the expressed VPg aggregated as inclusion bodies that were solubilized with urea and refolded with L-arginine hydrochloride. The various forms of CdMV VPg (native, denatured and refolded) were purified and the conformational variations between these forms were observed with fluorescence spectroscopy. Native and refolded CdMV VPg showed unordered secondary structure in the circular dichroism (CD) spectrum. The model of CdMV VPg was built based on the crystal structure of phosphotriesterase (from Pseudomonas diminuta), which had the maximum sequence homology with VPg to identify the arrangement of conserved amino acids in the protein to study the functional diversity of VPg. This is the first report on the VPg of CdMV, which is classified as a new member of the Macluravirus genus of the Potyviridae family.

  3. Molecular piracy: the viral link to carcinogenesis.

    PubMed

    Flaitz, C M; Hicks, M J

    1998-11-01

    The vast majority of the human experience with viral infections is associated with acute symptoms, such as malaise, fever, chills, rhinitis and diarrhea. With this acute or lytic phase, the immune system mounts a response and eliminates the viral agent while acquiring antibodies to that specific viral subtype. With latent or chronic infections, the viral agent becomes incorporated into the human genome. Viral agents capable of integration into the host's genetic material are particularly dangerous and may commandeer the host's ability to regulate normal cell growth and proliferation. The oncogenic viruses may immortalize the host cell, and facilitate malignant transformation. Cell growth and proliferation may be enhanced by viral interference with tumor suppressor gene function (p53 and pRb). Viruses may act as vectors for mutated proto-oncogenes (oncogenes). Overexpression of these oncogenes in viral-infected cells interferes with normal cell function and allows unregulated cell growth and proliferation, which may lead to malignant transformation and tumour formation. Development of oral neoplasms, both benign and malignant, has been linked to several viruses. Epstein-Barr virus is associated with oral hairy leukoplakia, lymphoproliferative disease, lymphoepithelial carcinoma, B-cell lymphomas, and nasopharyngeal carcinoma. Human herpesvirus-8 has been implicated in all forms of Kaposi's sarcoma, primary effusion lymphomas, multiple myeloma, angioimmunoblastic lymphadenopathy, and Castleman's disease. Human herpesvirus-6 has been detected in lymphoproliferative disease, lymphomas, Hodgkin's disease, and oral squamous cell carcinoma. The role of human papillomavirus in benign (squamous papilloma, focal epithelial hyperplasia, condyloma acuminatum, verruca vulgaris), premalignant (oral epithelial dysplasia), and malignant (squamous cell carcinoma) neoplasms within the oral cavity is well recognized. Herpes simplex virus may participate as a cofactor in oral squamous

  4. Modeling Viral Capsid Assembly

    PubMed Central

    2014-01-01

    I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened. PMID:25663722

  5. Viral kinetic modeling: state of the art

    SciTech Connect

    Canini, Laetitia; Perelson, Alan S.

    2014-06-25

    Viral kinetic modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how viral kinetic modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viral replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, viral kinetic modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. In conclusion, we expect that viral kinetic modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.

  6. Viral kinetic modeling: state of the art

    DOE PAGES

    Canini, Laetitia; Perelson, Alan S.

    2014-06-25

    Viral kinetic modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how viral kinetic modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viralmore » replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, viral kinetic modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. In conclusion, we expect that viral kinetic modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.« less

  7. Viral kinetic modeling: state of the art.

    PubMed

    Canini, Laetitia; Perelson, Alan S

    2014-10-01

    Viral kinetic (VK) modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how VK modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viral replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, VK modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. We expect that VK modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.

  8. Links between recognition and degradation of cytoplasmic viral RNA in innate immune response.

    PubMed

    Oshiumi, Hiroyuki; Mifsud, Edin J; Daito, Takuji

    2016-03-01

    Recognition and degradation of viral RNA are essential for antiviral innate immune responses. Cytoplasmic viral RNA is recognized by retinoic acid-inducible gene I (RIG-I)-like receptors, which trigger type I interferon (IFN) production. Secreted type I IFN activates ubiquitously expressed type I IFN receptor and induces IFN-stimulated genes (ISGs). To suppress viral replication, several nucleases degrade viral RNA. RNase L is an ISG with endonuclease activity that degrades viral RNA, producing small RNA that activates RIG-I, resulting in the amplification of type I IFN production. Moreover, recent studies have elucidated novel links between viral RNA recognition and degradation. The RNA exosome is a protein complex that includes nucleases and is essential for host and viral RNA decay. Although the small RNAs produced by the RNA exosome do not activate RIG-I, several accessory factors of the RNA exosome promote RIG-I activation. Zinc-finger antiviral protein (ZAP) is an accessory factor that recognizes viral RNA and promotes viral RNA degradation via the RNA exosome. ZAPS is an alternative splicing form of ZAP and promotes RIG-I oligomerization and ATPase activity, resulting in RIG-I activation. DDX60 is another cofactor involved in the viral RNA degradation via the RNA exosome. The DDX60 protein promotes RIG-I signaling in a cell-type specific manner. These observations imply that viral RNA degradation and recognition are linked to each other. In this review, I discuss the links between recognition and degradation of viral RNA. PMID:26643446

  9. Animal Models for Viral Hemorrhagic Fever.

    PubMed

    Falzarano, Darryl; Bente, Dennis A

    2014-04-01

    Viral hemorrhagic fever can be caused by one of a diverse group of viruses that come from four different families of RNA viruses. Disease severity can vary from mild self-limiting febrile illness to severe disease characterized by high fever, high-level viremia, increased vascular permeability that can progress to shock, multi-organ failure, and death. Despite the urgent need, effective treatments and preventative vaccines are currently lacking for the majority of these viruses. A number of factors preclude the effective study of these diseases in humans including the high virulence of the agents involved, the sporadic nature of outbreaks of these viruses which are typically in geographically isolated areas with underserviced diagnostic capabilities, and the requirements for high level bio-containment. As a result, animal models that accurately mimic human disease are essential for advancing our understanding of the pathogenesis of viral hemorrhagic fevers. Moreover, animal models for viral hemorrhagic fevers are necessary to test vaccines and therapeutic intervention strategies. Here, we present an overview of the animal models that have been established for each of the hemorrhagic fever viruses and identify which aspects of human disease are modeled. Furthermore, we discuss how experimental design considerations, such as choice of species and virus strain as well as route and dose of inoculation, have an influence on animal model development. We also bring attention to some of the pitfalls that need to be avoided when extrapolating results from animal models. This article is protected by copyright. All rights reserved.

  10. Gene Expression Profiles Link Respiratory Viral Infection, Platelet Response to Aspirin, and Acute Myocardial Infarction

    PubMed Central

    Cyr, Derek D.; Lucas, Joseph E.; Zaas, Aimee K.; Woods, Christopher W.; Newby, L. Kristin; Kraus, William E.; Ginsburg, Geoffrey S.

    2015-01-01

    Background Influenza infection is associated with myocardial infarction (MI), suggesting that respiratory viral infection may induce biologic pathways that contribute to MI. We tested the hypotheses that 1) a validated blood gene expression signature of respiratory viral infection (viral GES) was associated with MI and 2) respiratory viral exposure changes levels of a validated platelet gene expression signature (platelet GES) of platelet function in response to aspirin that is associated with MI. Methods A previously defined viral GES was projected into blood RNA data from 594 patients undergoing elective cardiac catheterization and used to classify patients as having evidence of viral infection or not and tested for association with acute MI using logistic regression. A previously defined platelet GES was projected into blood RNA data from 81 healthy subjects before and after exposure to four respiratory viruses: Respiratory Syncytial Virus (RSV) (n=20), Human Rhinovirus (HRV) (n=20), Influenza A virus subtype H1N1 (H1N1) (n=24), Influenza A Virus subtype H3N2 (H3N2) (n=17). We tested for the change in platelet GES with viral exposure using linear mixed-effects regression and by symptom status. Results In the catheterization cohort, 32 patients had evidence of viral infection based upon the viral GES, of which 25% (8/32) had MI versus 12.2% (69/567) among those without evidence of viral infection (OR 2.3; CI [1.03-5.5], p=0.04). In the infection cohorts, only H1N1 exposure increased platelet GES over time (time course p-value = 1e-04). Conclusions A viral GES of non-specific, respiratory viral infection was associated with acute MI; 18% of the top 49 genes in the viral GES are involved with hemostasis and/or platelet aggregation. Separately, H1N1 exposure, but not exposure to other respiratory viruses, increased a platelet GES previously shown to be associated with MI. Together, these results highlight specific genes and pathways that link viral infection

  11. Spatiotemporal modelling of viral infection dynamics

    NASA Astrophysics Data System (ADS)

    Beauchemin, Catherine

    Viral kinetics have been studied extensively in the past through the use of ordinary differential equations describing the time evolution of the diseased state in a spatially well-mixed medium. However, emerging spatial structures such as localized populations of dead cells might affect the spread of infection, similar to the manner in which a counter-fire can stop a forest fire from spreading. In the first phase of the project, a simple two-dimensional cellular automaton model of viral infections was developed. It was validated against clinical immunological data for uncomplicated influenza A infections and shown to be accurate enough to adequately model them. In the second phase of the project, the simple two-dimensional cellular automaton model was used to investigate the effects of relaxing the well-mixed assumption on viral infection dynamics. It was shown that grouping the initially infected cells into patches rather than distributing them uniformly on the grid reduced the infection rate as only cells on the perimeter of the patch have healthy neighbours to infect. Use of a local epithelial cell regeneration rule where dead cells are replaced by healthy cells when an immediate neighbour divides was found to result in more extensive damage of the epithelium and yielded a better fit to experimental influenza A infection data than a global regeneration rule based on division rate of healthy cell. Finally, the addition of immune cell at the site of infection was found to be a better strategy at low infection levels, while addition at random locations on the grid was the better strategy at high infection level. In the last project, the movement of T cells within lymph nodes in the absence of antigen, was investigated. Based on individual T cell track data captured by two-photon microscopy experiments in vivo, a simple model was proposed for the motion of T cells. This is the first step towards the implementation of a more realistic spatiotemporal model of HIV than

  12. Type I Interferons link viral infection to enhanced epithelial turnover and repair

    PubMed Central

    Sun, Lulu; Miyoshi, Hiroyuki; Origanti, Sofia; Nice, Timothy J.; Barger, Alexandra C.; Manieri, Nicholas A.; Fogel, Leslie A.; French, Anthony R.; Piwnica-Worms, David; Piwnica-Worms, Helen; Virgin, Herbert W.; Lenschow, Deborah J.; Stappenbeck, Thaddeus S.

    2014-01-01

    Summary The host immune system functions constantly to maintain chronic commensal and pathogenic organisms in check. The consequences of these immune responses on host physiology are as yet unexplored, and may have long-term implications in health and disease. We show that chronic viral infection increased epithelial turnover in multiple tissues, and the antiviral cytokines Type I interferons (IFNs) mediates this response. Using a murine model with persistently elevated Type I IFNs in the absence of exogenous viral infection, the Irgm1-/- mouse, we demonstrate that Type I IFNs act through non-epithelial cells, including macrophages, to promote increased epithelial turnover and wound repair. Downstream of Type I IFN signaling, the highly related IFN-stimulated genes Apolipoprotein L9a and b activate epithelial proliferation through ERK activation. Our findings demonstrate that the host immune response to chronic viral infection has systemic effects on epithelial turnover through a myeloid-epithelial circuit. PMID:25482432

  13. The oncogenic potential of BK-polyomavirus is linked to viral integration into the human genome.

    PubMed

    Kenan, Daniel J; Mieczkowski, Piotr A; Burger-Calderon, Raquel; Singh, Harsharan K; Nickeleit, Volker

    2015-11-01

    It has been suggested that BK-polyomavirus is linked to oncogenesis via high expression levels of large T-antigen in some urothelial neoplasms arising following kidney transplantation. However, a causal association between BK-polyomavirus, large T-antigen expression and oncogenesis has never been demonstrated in humans. Here we describe an investigation using high-throughput sequencing of tumour DNA obtained from an urothelial carcinoma arising in a renal allograft. We show that a novel BK-polyomavirus strain, named CH-1, is integrated into exon 26 of the myosin-binding protein C1 gene (MYBPC1) on chromosome 12 in tumour cells but not in normal renal cells. Integration of the BK-polyomavirus results in a number of discrete alterations in viral gene expression, including: (a) disruption of VP1 protein expression and robust expression of large T-antigen; (b) preclusion of viral replication; and (c) deletions in the non-coding control region (NCCR), with presumed alterations in promoter feedback loops. Viral integration disrupts one MYBPC1 gene copy and likely alters its expression. Circular episomal BK-polyomavirus gene sequences are not found, and the renal allograft shows no productive polyomavirus infection or polyomavirus nephropathy. These findings support the hypothesis that integration of polyomaviruses is essential to tumourigenesis. It is likely that dysregulation of large T-antigen, with persistent over-expression in non-lytic cells, promotes cell growth, genetic instability and neoplastic transformation.

  14. Bio-mathematical models of viral dynamics to tailor antiviral therapy in chronic viral hepatitis

    PubMed Central

    Brunetto, Maurizia Rossana; Colombatto, Piero; Bonino, Ferruccio

    2009-01-01

    The simulation of the dynamics of viral infections by mathematical equations has been applied successfully to the study of viral infections during antiviral therapy. Standard models applied to viral hepatitis describe the viral load decline in the first 2-4 wk of antiviral therapy, but do not adequately simulate the dynamics of viral infection for the following period. The hypothesis of a constant clearance rate of the infected cells provides an unrealistic estimation of the time necessary to reach the control or the clearance of hepatitis B virus (HBV)/hepatitis C virus (HCV) infection. To overcome the problem, we have developed a new multiphasic model in which the immune system activity is modulated by a negative feedback caused by the infected cells reduction, and alanine aminotransferase kinetics serve as a surrogate marker of infected-cell clearance. By this approach, we can compute the dynamics of infected cells during the whole treatment course, and find a good correlation between the number of infected cells at the end of therapy and the long-term virological response in patients with chronic hepatitis C. The new model successfully describes the HBV infection dynamics far beyond the third month of antiviral therapy under the assumption that the sum of infected and non-infected cells remains roughly constant during therapy, and both target and infected cells concur in the hepatocyte turnover. In clinical practice, these new models will allow the development of simulators of treatment response that will be used as an “automatic pilot” for tailoring antiviral therapy in chronic hepatitis B as well as chronic hepatitis C patients. PMID:19195054

  15. Contribution of N-linked glycans on HSV-2 gB to cell–cell fusion and viral entry

    SciTech Connect

    Luo, Sukun; Hu, Kai; He, Siyi; Wang, Ping; Zhang, Mudan; Huang, Xin; Du, Tao; Zheng, Chunfu; Liu, Yalan; Hu, Qinxue

    2015-09-15

    HSV-2 is the major cause of genital herpes and its infection increases the risk of HIV-1 acquisition and transmission. HSV-2 glycoprotein B together with glycoproteins D, H and L are indispensable for viral entry, of which gB, as a class III fusogen, plays an essential role. HSV-2 gB has seven potential N-linked glycosylation (N-CHO) sites, but their significance has yet to be determined. For the first time, we systematically analyzed the contributions of N-linked glycans on gB to cell–cell fusion and viral entry. Our results demonstrated that, of the seven potential N-CHO sites on gB, mutation at N390, N483 or N668 decreased cell–cell fusion and viral entry, while mutation at N133 mainly affected protein expression and the production of infectious virus particles by blocking the transport of gB from the endoplasmic reticulum to Golgi. Our findings highlight the significance of N-linked glycans on HSV-2 gB expression and function. - Highlights: • N-linked glycan at N133 is important for gB intracellular trafficking and maturation. • N-linked glycans at N390, N483 and N668 on gB are necessary for optimal cell–cell fusion. • N-linked glycans at N390, N483 and N668 on gB are necessary for optimal viral entry.

  16. Slice Culture Modeling of Central Nervous System (CNS) Viral Infection

    PubMed Central

    Dionne, Kalen R.; Tyler, Kenneth L.

    2016-01-01

    The complexity of the central nervous system (CNS) is not recapitulated in cell culture models. Thin slicing and subsequent culture of CNS tissue has become a valued means to study neuronal and glial biology within the context of the physiologically relevant tissue milieu. Modern membrane-interface slice culturing methodology allows straightforward access to both CNS tissue and feeding medium, enabling experimental manipulations and analyses that would otherwise be impossible in vivo. CNS slices can be successfully maintained in culture for up to several weeks for investigation of evolving pathology and long-term intervention in models of chronic neurologic disease. Herein, membrane-interface slice culture models for studying viral encephalitis and myelitis are detailed, with emphasis on the use of these models for investigation of pathogenesis and evaluation of novel treatment strategies. We describe techniques to (1) generate brain and spinal cord slices from rodent donors, (2) virally infect slices, (3) monitor viral replication, (4) assess virally induced injury/apoptosis, (5) characterize “CNS-specific” cytokine production, and (6) treat slices with cytokines/pharmaceuticals. Although our focus is on CNS viral infection, we anticipate that the described methods can be adapted to address a wide range of investigations within the fields of neuropathology, neuroimmunology, and neuropharmacology. PMID:23975824

  17. Modeling HIV persistence, the latent reservoir, and viral blips

    PubMed Central

    Rong, Libin; Perelson, Alan S.

    2009-01-01

    HIV-1 eradication from infected individuals has not been achieved with the use of highly active antiretroviral therapy (HAART) for a prolonged period of time. The cellular reservoir for HIV-1 in resting memory CD4+ T cells remains a major obstacle to viral elimination. The reservoir does not decay significantly over long periods of time but is able to release replication-competent HIV-1 upon cell activation. Residual ongoing viral replication may likely occur in many patients because low levels of virus can be detected in plasma by sensitive assays and transient episodes of viremia, or HIV-1 blips, are often observed in patients even with successful viral suppression for many years. Here we review our current knowledge of the factors contributing to viral persistence, the latent reservoir, and blips, and mathematical models developed to explore them and their relationships. We show how mathematical modeling can help improve our understanding of HIV-1 dynamics in patients on HAART and of the quantitative events underlying HIV-1 latency, reservoir stability, low-level viremic persistence, and emergence of intermittent viral blips. We also discuss treatment implications related to these studies. PMID:19539630

  18. Open loop model for WDM links

    NASA Astrophysics Data System (ADS)

    D, Meena; Francis, Fredy; T, Sarath K.; E, Dipin; Srinivas, T.; K, Jayasree V.

    2014-10-01

    Wavelength Division Multiplexing (WDM) techniques overfibrelinks helps to exploit the high bandwidth capacity of single mode fibres. A typical WDM link consisting of laser source, multiplexer/demultiplexer, amplifier and detectoris considered for obtaining the open loop gain model of the link. The methodology used here is to obtain individual component models using mathematical and different curve fitting techniques. These individual models are then combined to obtain the WDM link model. The objective is to deduce a single variable model for the WDM link in terms of input current to system. Thus it provides a black box solution for a link. The Root Mean Square Error (RMSE) associated with each of the approximated models is given for comparison. This will help the designer to select the suitable WDM link model during a complex link design.

  19. Visualization of minute centers of viral infection in unfixed cell cultures by an enzyme-linked antibody assay.

    PubMed

    Smith, K O; Kennell, W L; Lamm, D L

    1981-01-01

    Enzyme-linked antibody was used to treat unfixed herpesvirus-infected human fetal lung cell cultures in a mode which permitted the visualizing of local sites of infection. Foci containing as few as 20 herpesvirus-infected cells produced sufficient viral mass to be easily detectable by this method. 'Clouds' or 'plumes' of colored reaction product diffused into the substrate overlay, accumulated above and around each focus of infection and allowed quantitation of the number of foci in a culture. The number of minute centers of viral infection determined by the enzyme-linked antibody method corresponded almost exactly with values obtained by fluorescence microscopy. Quantitation of herpes simplex infectivity by focus assay was possible within only 17 h after culture inoculation, well before cytopathic effects were visible macroscopically. The technique was also applied to demonstrate measles and mumpsvirus plaques (infectious centers) in Vero cell cultures.

  20. Viral Genome-Linked Protein (VPg) Is Essential for Translation Initiation of Rabbit Hemorrhagic Disease Virus (RHDV)

    PubMed Central

    Zhu, Jie; Wang, Binbin; Miao, Qiuhong; Tan, Yonggui; Li, Chuanfeng; Chen, Zongyan; Guo, Huimin; Liu, Guangqing

    2015-01-01

    Rabbit hemorrhagic disease virus (RHDV), the causative agent of rabbit hemorrhagic disease, is an important member of the caliciviridae family. Currently, no suitable tissue culture system is available for proliferating RHDV, limiting the study of the pathogenesis of RHDV. In addition, the mechanisms underlying RHDV translation and replication are largely unknown compared with other caliciviridae viruses. The RHDV replicon recently constructed in our laboratory provides an appropriate model to study the pathogenesis of RHDV without in vitro RHDV propagation and culture. Using this RHDV replicon, we demonstrated that the viral genome-linked protein (VPg) is essential for RHDV translation in RK-13 cells for the first time. In addition, we showed that VPg interacts with eukaryotic initiation factor 4E (eIF4E) in vivo and in vitro and that eIF4E silencing inhibits RHDV translation, suggesting the interaction between VPg and eIF4E is involved in RHDV translation. Our results support the hypothesis that VPg serves as a novel cap substitute during the initiation of RHDV translation. PMID:26599265

  1. Viral Genome-Linked Protein (VPg) Is Essential for Translation Initiation of Rabbit Hemorrhagic Disease Virus (RHDV).

    PubMed

    Zhu, Jie; Wang, Binbin; Miao, Qiuhong; Tan, Yonggui; Li, Chuanfeng; Chen, Zongyan; Guo, Huimin; Liu, Guangqing

    2015-01-01

    Rabbit hemorrhagic disease virus (RHDV), the causative agent of rabbit hemorrhagic disease, is an important member of the caliciviridae family. Currently, no suitable tissue culture system is available for proliferating RHDV, limiting the study of the pathogenesis of RHDV. In addition, the mechanisms underlying RHDV translation and replication are largely unknown compared with other caliciviridae viruses. The RHDV replicon recently constructed in our laboratory provides an appropriate model to study the pathogenesis of RHDV without in vitro RHDV propagation and culture. Using this RHDV replicon, we demonstrated that the viral genome-linked protein (VPg) is essential for RHDV translation in RK-13 cells for the first time. In addition, we showed that VPg interacts with eukaryotic initiation factor 4E (eIF4E) in vivo and in vitro and that eIF4E silencing inhibits RHDV translation, suggesting the interaction between VPg and eIF4E is involved in RHDV translation. Our results support the hypothesis that VPg serves as a novel cap substitute during the initiation of RHDV translation. PMID:26599265

  2. Stochastical modeling for Viral Disease: Statistical Mechanics and Network Theory

    NASA Astrophysics Data System (ADS)

    Zhou, Hao; Deem, Michael

    2007-04-01

    Theoretical methods of statistical mechanics are developed and applied to study the immunological response against viral disease, such as dengue. We use this theory to show how the immune response to four different dengue serotypes may be sculpted. It is the ability of avian influenza, to change and to mix, that has given rise to the fear of a new human flu pandemic. Here we propose to utilize a scale free network based stochastic model to investigate the mitigation strategies and analyze the risk.

  3. Bovine viral diarrhea virus antigen detection across whole cattle hides using two antigen-capture enzyme-linked immunosorbent assays.

    PubMed

    Vander Ley, Brian L; Ridpath, Julia F; Sweiger, Shaun H

    2012-05-01

    Bovine viral diarrhea virus is a costly disease of cattle that can be controlled by vaccination, biosecurity, and removal of persistently infected cattle. Development and proficiency testing of assays to identify persistently infected cattle requires substantial quantities of known positive- and negative-sample material. The objective of this study was to determine what sections of bovine skin contained Bovine viral diarrhea virus antigen. Two commercially available antigen-capture enzyme-linked immunoassays were used to test subsamples representing the entire skin of 3 persistently infected calves. Both assays detected Bovine viral diarrhea virus antigen in the samples indicated for use by assay protocol. However, one assay identified all subsamples as positive, while the second assay identified 64.4% of subsamples as positive. These results show that use of samples other than those specified by the assay protocol must be validated for each individual assay. In this study, alternative sample sites and use of the entire hide for proficiency testing would be acceptable for only one of the assays tested.

  4. On Modeling Viral Diffusion in Heterogeneous Wireless Networks

    NASA Astrophysics Data System (ADS)

    Nguyen, Hoai-Nam; Shinoda, Yoichi

    Smart phones and computers now are able to co-work in a wireless environment where malware can propagate. Although many investigations have modeled the spread of malware, little has been done to take into account different characteristics of items to see how they affect disease diffusion in an ad hoc network. We have therefore developed a novel framework, consisting of two models, which consider diversity of objects as well as interactions between their different classes. Our framework is able to produce a huge result space thus makes it appropriate to describe many viral proliferating scenarios. Additionally, we have developed a formula to calculate the possible average number of newly infected devices in the considered system. An important contribution of our work is the comprehension of item diversity, which states that a mixture of device types causes a bigger malware spread as the number of device types in the network increases.

  5. Linking host prokaryotic physiology to viral lifestyle dynamics in a temperate freshwater lake (Lake Pavin, France).

    PubMed

    Palesse, S; Colombet, J; Pradeep Ram, A S; Sime-Ngando, T

    2014-11-01

    In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and

  6. Linking host prokaryotic physiology to viral lifestyle dynamics in a temperate freshwater lake (Lake Pavin, France).

    PubMed

    Palesse, S; Colombet, J; Pradeep Ram, A S; Sime-Ngando, T

    2014-11-01

    In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and

  7. Semantically linking in silico cancer models.

    PubMed

    Johnson, David; Connor, Anthony J; McKeever, Steve; Wang, Zhihui; Deisboeck, Thomas S; Quaiser, Tom; Shochat, Eliezer

    2014-01-01

    Multiscale models are commonplace in cancer modeling, where individual models acting on different biological scales are combined within a single, cohesive modeling framework. However, model composition gives rise to challenges in understanding interfaces and interactions between them. Based on specific domain expertise, typically these computational models are developed by separate research groups using different methodologies, programming languages, and parameters. This paper introduces a graph-based model for semantically linking computational cancer models via domain graphs that can help us better understand and explore combinations of models spanning multiple biological scales. We take the data model encoded by TumorML, an XML-based markup language for storing cancer models in online repositories, and transpose its model description elements into a graph-based representation. By taking such an approach, we can link domain models, such as controlled vocabularies, taxonomic schemes, and ontologies, with cancer model descriptions to better understand and explore relationships between models. The union of these graphs creates a connected property graph that links cancer models by categorizations, by computational compatibility, and by semantic interoperability, yielding a framework in which opportunities for exploration and discovery of combinations of models become possible. PMID:25520553

  8. Semantically Linking In Silico Cancer Models

    PubMed Central

    Johnson, David; Connor, Anthony J; McKeever, Steve; Wang, Zhihui; Deisboeck, Thomas S; Quaiser, Tom; Shochat, Eliezer

    2014-01-01

    Multiscale models are commonplace in cancer modeling, where individual models acting on different biological scales are combined within a single, cohesive modeling framework. However, model composition gives rise to challenges in understanding interfaces and interactions between them. Based on specific domain expertise, typically these computational models are developed by separate research groups using different methodologies, programming languages, and parameters. This paper introduces a graph-based model for semantically linking computational cancer models via domain graphs that can help us better understand and explore combinations of models spanning multiple biological scales. We take the data model encoded by TumorML, an XML-based markup language for storing cancer models in online repositories, and transpose its model description elements into a graph-based representation. By taking such an approach, we can link domain models, such as controlled vocabularies, taxonomic schemes, and ontologies, with cancer model descriptions to better understand and explore relationships between models. The union of these graphs creates a connected property graph that links cancer models by categorizations, by computational compatibility, and by semantic interoperability, yielding a framework in which opportunities for exploration and discovery of combinations of models become possible. PMID:25520553

  9. Cell-Free versus Cell-to-Cell Infection by Human Immunodeficiency Virus Type 1 and Human T-Lymphotropic Virus Type 1: Exploring the Link among Viral Source, Viral Trafficking, and Viral Replication.

    PubMed

    Dutartre, Hélène; Clavière, Mathieu; Journo, Chloé; Mahieux, Renaud

    2016-09-01

    Human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus type 1 (HTLV-1) are complex retroviruses mainly infecting CD4(+) T lymphocytes. In addition, antigen-presenting cells such as dendritic cells (DCs) are targeted in vivo by both viruses, although to a lesser extent. Interaction of HIV-1 with DCs plays a key role in viral dissemination from the mucosa to CD4(+) T lymphocytes present in lymphoid organs. While similar mechanisms may occur for HTLV-1 as well, most HTLV-1 data were obtained from T-cell studies, and little is known regarding the trafficking of this virus in DCs. We first compared the efficiency of cell-free versus cell-associated viral sources of both retroviruses at infecting DCs. We showed that both HIV-1 and HTLV-1 cell-free particles are poorly efficient at productively infecting DCs, except when DC-SIGN has been engaged. Furthermore, while SAMHD-1 accounts for restriction of cell-free HIV-1 infection, it is not involved in HTLV-1 restriction. In addition, cell-free viruses lead mainly to a nonproductive DC infection, leading to trans-infection of T-cells, a process important for HIV-1 spread but not for that of HTLV-1. Finally, we show that T-DC cell-to-cell transfer implies viral trafficking in vesicles that may both increase productive infection of DCs ("cis-infection") and allow viral escape from immune surveillance. Altogether, these observations allowed us to draw a model of HTLV-1 and HIV-1 trafficking in DCs.

  10. Frequency dependence and viral diversity imply chaos in an HIV model

    NASA Astrophysics Data System (ADS)

    Iwami, Shingo; Nakaoka, Shinji; Takeuchi, Yasuhiro

    2006-11-01

    In this paper, we consider the effect of viral diversity on the human immune system with frequency dependent rate of proliferation of CTLs (cytotoxic T-lymphocytes) and rate of elimination of infected cells by CTLs. We show that the interior equilibrium of our model can become unstable without viral diversity and we observe stable periodic orbits. Furthermore, our mathematical models suggest that viral diversity produces strange attractors.

  11. Comparison of five bacteriophages as models for viral aerosol studies.

    PubMed

    Turgeon, Nathalie; Toulouse, Marie-Josée; Martel, Bruno; Moineau, Sylvain; Duchaine, Caroline

    2014-07-01

    Bacteriophages are perceived to be good models for the study of airborne viruses because they are safe to use, some of them display structural features similar to those of human and animal viruses, and they are relatively easy to produce in large quantities. Yet, only a few studies have investigated them as models. It has previously been demonstrated that aerosolization, environmental conditions, and sampling conditions affect viral infectivity, but viral infectivity is virus dependent. Thus, several virus models are likely needed to study their general behavior in aerosols. The aim of this study was to compare the effects of aerosolization and sampling on the infectivity of five tail-less bacteriophages and two pathogenic viruses: MS2 (a single-stranded RNA [ssRNA] phage of the Leviviridae family), Φ6 (a segmented double-stranded RNA [dsRNA] phage of the Cystoviridae family), ΦX174 (a single-stranded DNA [ssDNA] phage of the Microviridae family), PM2 (a double-stranded DNA [dsDNA] phage of the Corticoviridae family), PR772 (a dsDNA phage of the Tectiviridae family), human influenza A virus H1N1 (an ssRNA virus of the Orthomyxoviridae family), and the poultry virus Newcastle disease virus (NDV; an ssRNA virus of the Paramyxoviridae family). Three nebulizers and two nebulization salt buffers (with or without organic fluid) were tested, as were two aerosol sampling devices, a liquid cyclone (SKC BioSampler) and a dry cyclone (National Institute for Occupational Safety and Health two-stage cyclone bioaerosol sampler). The presence of viruses in collected air samples was detected by culture and quantitative PCR (qPCR). Our results showed that these selected five phages behave differently when aerosolized and sampled. RNA phage MS2 and ssDNA phage ΦX174 were the most resistant to aerosolization and sampling. The presence of organic fluid in the nebulization buffer protected phages PR772 and Φ6 throughout the aerosolization and sampling with dry cyclones. In this

  12. Comparison of Five Bacteriophages as Models for Viral Aerosol Studies

    PubMed Central

    Turgeon, Nathalie; Toulouse, Marie-Josée; Martel, Bruno; Moineau, Sylvain

    2014-01-01

    Bacteriophages are perceived to be good models for the study of airborne viruses because they are safe to use, some of them display structural features similar to those of human and animal viruses, and they are relatively easy to produce in large quantities. Yet, only a few studies have investigated them as models. It has previously been demonstrated that aerosolization, environmental conditions, and sampling conditions affect viral infectivity, but viral infectivity is virus dependent. Thus, several virus models are likely needed to study their general behavior in aerosols. The aim of this study was to compare the effects of aerosolization and sampling on the infectivity of five tail-less bacteriophages and two pathogenic viruses: MS2 (a single-stranded RNA [ssRNA] phage of the Leviviridae family), Φ6 (a segmented double-stranded RNA [dsRNA] phage of the Cystoviridae family), ΦX174 (a single-stranded DNA [ssDNA] phage of the Microviridae family), PM2 (a double-stranded DNA [dsDNA] phage of the Corticoviridae family), PR772 (a dsDNA phage of the Tectiviridae family), human influenza A virus H1N1 (an ssRNA virus of the Orthomyxoviridae family), and the poultry virus Newcastle disease virus (NDV; an ssRNA virus of the Paramyxoviridae family). Three nebulizers and two nebulization salt buffers (with or without organic fluid) were tested, as were two aerosol sampling devices, a liquid cyclone (SKC BioSampler) and a dry cyclone (National Institute for Occupational Safety and Health two-stage cyclone bioaerosol sampler). The presence of viruses in collected air samples was detected by culture and quantitative PCR (qPCR). Our results showed that these selected five phages behave differently when aerosolized and sampled. RNA phage MS2 and ssDNA phage ΦX174 were the most resistant to aerosolization and sampling. The presence of organic fluid in the nebulization buffer protected phages PR772 and Φ6 throughout the aerosolization and sampling with dry cyclones. In this

  13. Stable cytotoxic T cell escape mutation in hepatitis C virus is linked to maintenance of viral fitness.

    PubMed

    Uebelhoer, Luke; Han, Jin-Hwan; Callendret, Benoit; Mateu, Guaniri; Shoukry, Naglaa H; Hanson, Holly L; Rice, Charles M; Walker, Christopher M; Grakoui, Arash

    2008-01-01

    Mechanisms by which hepatitis C virus (HCV) evades cellular immunity to establish persistence in chronically infected individuals are not clear. Mutations in human leukocyte antigen (HLA) class I-restricted epitopes targeted by CD8(+) T cells are associated with persistence, but the extent to which these mutations affect viral fitness is not fully understood. Previous work showed that the HCV quasispecies in a persistently infected chimpanzee accumulated multiple mutations in numerous class I epitopes over a period of 7 years. During the acute phase of infection, one representative epitope in the C-terminal region of the NS3/4A helicase, NS3(1629-1637), displayed multiple serial amino acid substitutions in major histocompatibility complex (MHC) anchor and T cell receptor (TCR) contact residues. Only one of these amino acid substitutions at position 9 (P9) of the epitope was stable in the quasispecies. We therefore assessed the effect of each mutation observed during in vivo infection on viral fitness and T cell responses using an HCV subgenomic replicon system and a recently developed in vitro infectious virus cell culture model. Mutation of a position 7 (P7) TCR-contact residue, I1635T, expectedly ablated the T cell response without affecting viral RNA replication or virion production. In contrast, two mutations at the P9 MHC-anchor residue abrogated antigen-specific T cell responses, but additionally decreased viral RNA replication and virion production. The first escape mutation, L1637P, detected in vivo only transiently at 3 mo after infection, decreased viral production, and reverted to the parental sequence in vitro. The second P9 variant, L1637S, which was stable in vivo through 7 years of follow-up, evaded the antigen-specific T cell response and did not revert in vitro despite being less optimal in virion production compared to the parental virus. These studies suggest that HCV escape mutants emerging early in infection are not necessarily stable, but are

  14. A Mathematical Model of T1D Acceleration and Delay by Viral Infection.

    PubMed

    Moore, James R; Adler, Fred

    2016-03-01

    Type 1 diabetes (T1D) is often triggered by a viral infection, but the T1D prevalence is rising among populations that have a lower exposure to viral infection. In an animal model of T1D, the NOD mouse, viral infection at different ages may either accelerate or delay disease depending on the age of infection and the type of virus. Viral infection may affect the progression of T1D via multiple mechanisms: triggering inflammation, bystander activation of self-reactive T-cells, inducing a competitive immune response, or inducing a regulatory immune response. In this paper, we create mathematical models of the interaction of viral infection with T1D progression, incorporating each of these four mechanisms. Our goal is to understand how each viral mechanism interacts with the age of infection. The model predicts that each viral mechanism has a unique pattern of interaction with disease progression. Viral inflammation always accelerates disease, but the effect decreases with age of infection. Bystander activation has little effect at younger ages and actually decreases incidence at later ages while accelerating disease in mice that do get the disease. A competitive immune response to infection can decrease incidence at young ages and increase it at older ages, with the effect decreasing over time. Finally, an induced Treg response decreases incidence at any age of infection, but the effect decreases with age. Some of these patterns resemble those seen experimentally. PMID:27030351

  15. O-linked GlcNAcylation elevated by HPV E6 mediates viral oncogenesis.

    PubMed

    Zeng, Qinghua; Zhao, Rui-Xun; Chen, Jianfeng; Li, Yining; Li, Xiang-Dong; Liu, Xiao-Long; Zhang, Wei-Ming; Quan, Cheng-Shi; Wang, Yi-Shu; Zhai, Ying-Xian; Wang, Jian-Wei; Youssef, Mariam; Cui, Rutao; Liang, Jiyong; Genovese, Nicholas; Chow, Louise T; Li, Yu-Lin; Xu, Zhi-Xiang

    2016-08-16

    High-risk human papillomaviruses (HPVs) are causative agents of anogenital cancers and a fraction of head and neck cancers. The mechanisms involved in the progression of HPV neoplasias to cancers remain largely unknown. Here, we report that O-linked GlcNAcylation (O-GlcNAc) and O-GlcNAc transferase (OGT) were markedly increased in HPV-caused cervical neoplasms relative to normal cervix, whereas O-GlcNAcase (OGA) levels were not altered. Transduction of HPV16 oncogene E6 or E6/E7 into mouse embryonic fibroblasts (MEFs) up-regulated OGT mRNA and protein, elevated the level of O-GlcNAc, and promoted cell proliferation while reducing cellular senescence. Conversely, in HPV-18-transformed HeLa cervical carcinoma cells, inhibition of O-GlcNAc with a low concentration of a chemical inhibitor impaired the transformed phenotypes in vitro. We showed that E6 elevated c-MYC via increased protein stability attributable to O-GlcNAcylation on Thr58. Reduction of HPV-mediated cell viability by a high concentration of O-GlcNAc inhibitor was partially rescued by elevated c-MYC. Finally, knockdown of OGT or O-GlcNAc inhibition in HeLa cells or in TC-1 cells, a mouse cell line transformed by HPV16 E6/E7 and activated K-RAS, reduced c-MYC and suppressed tumorigenesis and metastasis. Thus, we have uncovered a mechanism for HPV oncoprotein-mediated transformation. These findings may eventually aid in the development of effective therapeutics for HPV-associated malignancies by targeting aberrant O-GlcNAc.

  16. O-linked GlcNAcylation elevated by HPV E6 mediates viral oncogenesis.

    PubMed

    Zeng, Qinghua; Zhao, Rui-Xun; Chen, Jianfeng; Li, Yining; Li, Xiang-Dong; Liu, Xiao-Long; Zhang, Wei-Ming; Quan, Cheng-Shi; Wang, Yi-Shu; Zhai, Ying-Xian; Wang, Jian-Wei; Youssef, Mariam; Cui, Rutao; Liang, Jiyong; Genovese, Nicholas; Chow, Louise T; Li, Yu-Lin; Xu, Zhi-Xiang

    2016-08-16

    High-risk human papillomaviruses (HPVs) are causative agents of anogenital cancers and a fraction of head and neck cancers. The mechanisms involved in the progression of HPV neoplasias to cancers remain largely unknown. Here, we report that O-linked GlcNAcylation (O-GlcNAc) and O-GlcNAc transferase (OGT) were markedly increased in HPV-caused cervical neoplasms relative to normal cervix, whereas O-GlcNAcase (OGA) levels were not altered. Transduction of HPV16 oncogene E6 or E6/E7 into mouse embryonic fibroblasts (MEFs) up-regulated OGT mRNA and protein, elevated the level of O-GlcNAc, and promoted cell proliferation while reducing cellular senescence. Conversely, in HPV-18-transformed HeLa cervical carcinoma cells, inhibition of O-GlcNAc with a low concentration of a chemical inhibitor impaired the transformed phenotypes in vitro. We showed that E6 elevated c-MYC via increased protein stability attributable to O-GlcNAcylation on Thr58. Reduction of HPV-mediated cell viability by a high concentration of O-GlcNAc inhibitor was partially rescued by elevated c-MYC. Finally, knockdown of OGT or O-GlcNAc inhibition in HeLa cells or in TC-1 cells, a mouse cell line transformed by HPV16 E6/E7 and activated K-RAS, reduced c-MYC and suppressed tumorigenesis and metastasis. Thus, we have uncovered a mechanism for HPV oncoprotein-mediated transformation. These findings may eventually aid in the development of effective therapeutics for HPV-associated malignancies by targeting aberrant O-GlcNAc. PMID:27482104

  17. Mathematical models of immune effector responses to viral infections: Virus control versus the development of pathology

    NASA Astrophysics Data System (ADS)

    Wodarz, Dominik

    2005-12-01

    This article reviews mathematical models which have investigated the importance of lytic and non-lytic immune responses for the control of viral infections. Lytic immune responses fight the virus by killing infected cells, while non-lytic immune responses fight the virus by inhibiting viral replication while leaving the infected cell alive. The models suggest which types or combinations of immune responses are required to resolve infections which vary in their characteristics, such as the rate of viral replication and the rate of virus-induced target cell death. This framework is then applied to persistent infections and viral evolution. It is investigated how viral evolution and antigenic escape can influence the relative balance of lytic and non-lytic responses over time, and how this might correlate with the transition from an asymptomatic infection to pathology. This is discussed in the specific context of hepatitis C virus infection.

  18. An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load.

    PubMed

    Herbeck, Joshua T; Mittler, John E; Gottlieb, Geoffrey S; Mullins, James I

    2014-06-01

    Trends in HIV virulence have been monitored since the start of the AIDS pandemic, as studying HIV virulence informs our understanding of HIV epidemiology and pathogenesis. Here, we model changes in HIV virulence as a strictly evolutionary process, using set point viral load (SPVL) as a proxy, to make inferences about empirical SPVL trends from longitudinal HIV cohorts. We develop an agent-based epidemic model based on HIV viral load dynamics. The model contains functions for viral load and transmission, SPVL and disease progression, viral load trajectories in multiple stages of infection, and the heritability of SPVL across transmissions. We find that HIV virulence evolves to an intermediate level that balances infectiousness with longer infected lifespans, resulting in an optimal SPVL∼4.75 log10 viral RNA copies/mL. Adaptive viral evolution may explain observed HIV virulence trends: our model produces SPVL trends with magnitudes that are broadly similar to empirical trends. With regard to variation among studies in empirical SPVL trends, results from our model suggest that variation may be explained by the specific epidemic context, e.g. the mean SPVL of the founding lineage or the age of the epidemic; or improvements in HIV screening and diagnosis that results in sampling biases. We also use our model to examine trends in community viral load, a population-level measure of HIV viral load that is thought to reflect a population's overall transmission potential. We find that community viral load evolves in association with SPVL, in the absence of prevention programs such as antiretroviral therapy, and that the mean community viral load is not necessarily a strong predictor of HIV incidence.

  19. Structural and metabolic studies of O-linked fucose-containing proteins of normal and virally-transformed rat fibroblasts

    SciTech Connect

    Morton, P.A.

    1985-01-01

    Previous studies in this laboratory have demonstrated that cultured human and rodent cells contain a series of low molecular weight glycosylated amino acids of unusual structure, designated amino acid fucosides. The incorporation of radiolabelled-fucose into one of these components, designated FL4a (glucosylfucosylthreonine), is markedly-reduced in transformed epithelial and fibroblastic cells. The authors have examined fucose-labelled normal and virally-transformed rat fibroblast cell lines for glycoproteins which might be precursors to amino acid fucosides. Using milk alkaline/borohydride treatment (the beta-elimination reaction) to release O-linked oligosaccharides from proteins, they have isolated and partially characterized two low M/sub r/ reaction products (designated DS-ol and TS-ol) released from macromolecular cell material. The identity of one of these components (DS-ol, glucosylfucitol) suggested the existence in these cells of a direct protein precursor to FL4a. They examined fucose-labelled macromolecular cell material for proteins which release DS-ol (DS-proteins.). Using gel filtration chromatography and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) with subsequent autoradiography, they have observed DS-proteins which appear to exhibit a broad molecular weight size range, and are also present in culture medium from normal and transformed cells. The findings suggest that mammalian cells contain DS-proteins and TS-proteins with a novel carbohydrate-peptide linkage wherein L-fucose is O-linked to a polypeptide backbone. Metabolic studies were undertaken to examine both the relationship between DS-protein and FL4a and the biochemical basis for the decreased level of FL4a and the biochemical basis for the decreased level of FL4a observed in transformed cells.

  20. Use of hydrophilic extra-viral domain of canine distemper virus H protein for enzyme-linked immunosorbent assay development

    PubMed Central

    Cho, Ki-hyun; Kim, Jeongmi; Yoo, Hyun-ah; Kim, Dae-hee; Park, Seung-yong; Song, Chang-seon; Choi, In-soo

    2014-01-01

    Simple methods for measuring the levels of serum antibody against canine distemper virus (CDV) would assist in the effective vaccination of dogs. To develop an enzyme-linked immunosorbent assay (ELISA) specific for CDV, we expressed hydrophilic extra-viral domain (HEVD) protein of the A75/17-CDV H gene in a pET 28a plasmid-based Escherichia (E.) coli vector system. Expression was confirmed by dot and Western blotting. We proposed that detection of E. coli-expressed H protein might be conformation-dependent because intensities of the reactions observed with these two methods varied. The H gene HEVD protein was further purified and used as an antigen for an ELISA. Samples from dogs with undetectable to high anti-CDV antibody titers were analyzed using this HEVD-specific ELISA and a commercial CDV antibody detection kit (ImmunoComb). Levels of HEVD antigenicity measured with the assays and immunochromatography correlated. These data indicated that the HEDV protein may be used as antigen to develop techniques for detecting antibodies against CDV. PMID:25234325

  1. Modeling viral and drug kinetics: hepatitis C virus treatment with pegylated interferon alfa-2b.

    PubMed

    Powers, Kimberly A; Dixit, Narendra M; Ribeiro, Ruy M; Golia, Preeti; Talal, Andrew H; Perelson, Alan S

    2003-01-01

    Administration of peginterferon alfa-2b plus ribavirin results in an early hepatitis C virus (HCV) RNA decay followed by an increase as the drug concentration declines between doses. Upon administration of the next dose 1 week later, the same pattern is observed. We have incorporated pharmacokinetic/pharmacodynamic analysis into a model of viral dynamics to describe the effect that changes in drug concentration and effectiveness can have on viral levels. To illustrate the relationship between pharmacokinetics and viral dynamics, we fit the model to data from four HCV/human immunodeficiency virus co-infected patients, and obtained good agreement with the measured serum HCV RNA levels. We were able to account for the observed increases in HCV RNA, and estimate virion and drug half-lives that are in agreement with previous reports. Models incorporating pharmacokinetics are needed to correctly interpret viral load changes and estimate drug effectiveness in treatment protocols using peginterferon alfa-2b. PMID:12934163

  2. Hydrodynamics of linked sphere model swimmers.

    PubMed

    Alexander, G P; Pooley, C M; Yeomans, J M

    2009-05-20

    We describe in detail the hydrodynamics of a simple model of linked sphere swimmers. We calculate the asymptotic form of both the time averaged flow field generated by a single swimmer and the interactions between swimmers in a dilute suspension, showing how each depends on the parameters describing the swimmer and its swimming stroke. We emphasize the importance of time reversal symmetry in determining the far field flow around a swimmer and show that the interactions between swimmers are highly dependent on the relative phase of their swimming strokes. PMID:21825517

  3. Hydrodynamics of linked sphere model swimmers

    NASA Astrophysics Data System (ADS)

    Alexander, G. P.; Pooley, C. M.; Yeomans, J. M.

    2009-05-01

    We describe in detail the hydrodynamics of a simple model of linked sphere swimmers. We calculate the asymptotic form of both the time averaged flow field generated by a single swimmer and the interactions between swimmers in a dilute suspension, showing how each depends on the parameters describing the swimmer and its swimming stroke. We emphasize the importance of time reversal symmetry in determining the far field flow around a swimmer and show that the interactions between swimmers are highly dependent on the relative phase of their swimming strokes.

  4. Use of viral infections in animal models to assess changes in the immune system.

    PubMed Central

    Kern, E R

    1982-01-01

    Viral infections in animal models appear to be ideal systems for determining toxicity to the immune system by environmental substances. Since many viral infections that are utilized in animals produce systemic disease, these models provide an opportunity to evaluate the interaction between virus and components of host resistance. In these infections it is possible to delineate the role of antibody, interferon, cell-mediated immunity, neutrophils and macrophages in response to infection. A change in any of these components responsible for resistance to a particular virus may be correlated with an alteration of mortality an pathogenesis of the viral infection. Three experimental viral infections in mice that are potential candidates for use in determining immunotoxicity are discussed in terms of the response of individual components of resistance to infection and how changes in there components result in alterations of viral pathogenesis. The resistance to encephalomyocarditis virus infection in mice appears to be primarily mediated by antibody and interferon while with herpes simplex virus, infections are mainly controlled through cell-mediated immunity, macrophages, and possible interferon. Cellular immunity also appears to be primarily responsible for resistance to cytomegalovirus infections. Therefore, it is important in the use of these systems for evaluating immunotoxicity to define the pathogenesis of the viral infection and the specific host responses to these infections and to be able to correlate a change in host resistance with an alteration of the viral infection. PMID:6174323

  5. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

    NASA Astrophysics Data System (ADS)

    Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

    2013-12-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

  6. An accurate two-phase approximate solution to the acute viral infection model

    SciTech Connect

    Perelson, Alan S

    2009-01-01

    During an acute viral infection, virus levels rise, reach a peak and then decline. Data and numerical solutions suggest the growth and decay phases are linear on a log scale. While viral dynamic models are typically nonlinear with analytical solutions difficult to obtain, the exponential nature of the solutions suggests approximations can be found. We derive a two-phase approximate solution to the target cell limited influenza model and illustrate the accuracy using data and previously established parameter values of six patients infected with influenza A. For one patient, the subsequent fall in virus concentration was not consistent with our predictions during the decay phase and an alternate approximation is derived. We find expressions for the rate and length of initial viral growth in terms of the parameters, the extent each parameter is involved in viral peaks, and the single parameter responsible for virus decay. We discuss applications of this analysis in antiviral treatments and investigating host and virus heterogeneities.

  7. How Can Viral Dynamics Models Inform Endpoint Measures in Clinical Trials of Therapies for Acute Viral Infections?

    PubMed Central

    Cori, Anne; de Wolf, Frank; Anderson, Roy M.

    2016-01-01

    Acute viral infections pose many practical challenges for the accurate assessment of the impact of novel therapies on viral growth and decay. Using the example of influenza A, we illustrate how the measurement of infection-related quantities that determine the dynamics of viral load within the human host, can inform investigators on the course and severity of infection and the efficacy of a novel treatment. We estimated the values of key infection-related quantities that determine the course of natural infection from viral load data, using Markov Chain Monte Carlo methods. The data were placebo group viral load measurements collected during volunteer challenge studies, conducted by Roche, as part of the oseltamivir trials. We calculated the values of the quantities for each patient and the correlations between the quantities, symptom severity and body temperature. The greatest variation among individuals occurred in the viral load peak and area under the viral load curve. Total symptom severity correlated positively with the basic reproductive number. The most sensitive endpoint for therapeutic trials with the goal to cure patients is the duration of infection. We suggest laboratory experiments to obtain more precise estimates of virological quantities that can supplement clinical endpoint measurements. PMID:27367230

  8. Manipulating 3D-Printed and Paper Models Enhances Student Understanding of Viral Replication

    ERIC Educational Resources Information Center

    Couper, Lisa; Johannes, Kristen; Powers, Jackie; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Understanding key concepts in molecular biology requires reasoning about molecular processes that are not directly observable and, as such, presents a challenge to students and teachers. We ask whether novel interactive physical models and activities can help students understand key processes in viral replication. Our 3D tangible models are…

  9. ModeLang: a new approach for experts-friendly viral infections modeling.

    PubMed

    Wasik, Szymon; Prejzendanc, Tomasz; Blazewicz, Jacek

    2013-01-01

    Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces communication problems because biologists do not have sufficient knowledge to understand mathematical description of the models, and mathematicians do not have sufficient knowledge to define and verify these models. In many areas of systems biology, this problem has already been solved; however, in some of these areas there are still certain problematic aspects. The goal of the presented research was to facilitate this cooperation by designing seminatural formal language for describing viral infection models that will be easy to understand for biologists and easy to use by mathematicians and computer scientists. The ModeLang language was designed in cooperation with biologists and its computer implementation was prepared. Tests proved that it can be successfully used to describe commonly used viral infection models and then to simulate and verify them. As a result, it can make cooperation between biologists and mathematicians modeling viral infections much easier, speeding up computational verification of formulated hypotheses.

  10. Dysplastic Hepatocytes Develop Nuclear Inclusions in a Mouse Model of Viral Hepatitis

    PubMed Central

    Thakur, Priyanka; Lamoke, Folami; Chaffin, Joanna M.; Bartoli, Manuela; Lee, Jeffrey R.; Duncan, Michael B.

    2014-01-01

    Viral hepatitis resulting in chronic liver disease is an important clinical challenge and insight into the cellular processes that drive pathogenesis will be critical in order to develop new diagnostic and therapeutic options. Nuclear inclusions in viral and non-viral hepatitis are well documented and have diagnostic significance in some disease contexts. However, the origins and functional consequences of these nuclear inclusions remain elusive. To date the clinical observation of nuclear inclusions in viral and non-viral hepatitis has not been explored at depth in murine models of liver disease. Herein, we report that in a transgenic model of hepatitis B surface antigen mediated hepatitis, murine hepatocytes exhibit nuclear inclusions. Cells bearing nuclear inclusions were more likely to express markers of cell proliferation. We also established a correlation between these inclusions and oxidative stress. N-acetyl cysteine treatment effectively reduced oxidative stress levels, relieved endoplasmic reticulum (ER) stress, and the number of nuclear inclusions we observed in the transgenic mice. Our results suggest that the presence of nuclear inclusions in hepatocytes correlates with oxidative stress and cellular proliferation in a model of antigen mediated hepatitis. PMID:24932583

  11. Rodent models of HAND and drug abuse: exogenous administration of viral protein(s) and cocaine.

    PubMed

    Yao, Honghong; Buch, Shilpa

    2012-06-01

    Humans and chimpanzees are the natural hosts for HIV. Non-human primate models of SIV/SHIV infection in rhesus, cynomologus and pigtail macaques have been used extensively as excellent model systems for pathogenesis and vaccine studies. However, owing to the variability of disease progression in infected macaques, a phenomenon identical to humans, coupled with their prohibitive costs, there exists a critical need for the development of small-animal models in which to study the untoward effects of HIV-1 infection. Owing to the fact that rodents are not the natural permissive hosts for lentiviral infection, development of small animal models for studying virus infection has used strategies that circumvent the steps of viral entry and infection. Such strategies involve overexpression of toxic viral proteins, SCID mice engrafted with the human PBLs or macrophages, and EcoHIV chimeric virus wherein the gp120 of HIV-1 was replaced with the gp80 of the ecotropic murine leukemia virus. Additional strategy that is often used by investigators to study the toxic effect of viral proteins involves direct stereotactic injection of the viral protein(s) into specific brain regions. The present report is a compilation of the applications of direct administration of Tat into the striatum to mimic the effects of the viral neurotoxin in the CNS. Added advantage of this model is that it is also amenable to repeated intraperitoneal cocaine injections, thereby allowing the study of the additive/synergistic effects of both the viral protein and cocaine. Such a model system recapitulates aspects of HAND in the context of drug abuse. PMID:22447295

  12. Rainfall-runoff model for prediction of waterborne viral contamination in a small river catchment

    NASA Astrophysics Data System (ADS)

    Gelati, E.; Dommar, C.; Lowe, R.; Polcher, J.; Rodó, X.

    2013-12-01

    We present a lumped rainfall-runoff model aimed at providing useful information for the prediction of waterborne viral contamination in small rivers. Viral contamination of water bodies may occur because of the discharge of sewage effluents and of surface runoff over areas affected by animal waste loads. Surface runoff is caused by precipitation that cannot infiltrate due to its intensity and to antecedent soil water content. It may transport animal feces to adjacent water bodies and cause viral contamination. We model streamflow by separating it into two components: subsurface flow, which is produced by infiltrated precipitation; and surface runoff. The model estimates infiltrated and non-infiltrated precipitation and uses impulse-response functions to compute the corresponding fractions of streamflow. The developed methodologies are applied to the Glafkos river, whose catchment extends for 102 km2 and includes the city of Patra. Streamflow and precipitation observations are available at a daily time resolution. Waterborne virus concentration measurements were performed approximately every second week from the beginning of 2011 to mid 2012. Samples were taken at several locations: in river water upstream of Patras and in the urban area; in sea water at the river outlet and approximately 2 km south-west of Patras; in sewage effluents before and after treatment. The rainfall-runoff model was calibrated and validated using observed streamflow and precipitation data. The model contribution to waterborne viral contamination prediction was benchmarked by analyzing the virus concentration measurements together with the estimated surface runoff values. The presented methodology may be a first step towards the development of waterborne viral contamination alert systems. Predicting viral contamination of water bodies would benefit sectors such as water supply and tourism.

  13. A statistical model for telecommunication link design

    NASA Technical Reports Server (NTRS)

    Yuen, J. H.

    1975-01-01

    An evaluation is conducted of the current telecommunication link design technique and a description is presented of an alternative method, called the probability distribution method (PDM), which is free of the disadvantages of the current technique while retaining its advantages. The PDM preserves the simplicity of the design control table (DCT) format. The use of the DCT as a management design control tool is continued. The telecommunication link margin probability density function used presents the probability of achieving any particular value of link performance. It is, therefore, possible to assess the performance risk and other tradeoffs.

  14. Bovine viral diarrhea virus antigen detection across whole cattle hides using two antigen-capture enzyme-linked immunosorbent assays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine viral diarrhea virus is a costly disease of cattle that can be controlled by vaccination, biosecurity, and removal of persistently infected cattle. Development and proficiency testing of assays to identify persistently infected cattle substantial quantities of known positive and negative samp...

  15. Viral Decay Kinetics in the Highly Active Antiretroviral Therapy-Treated Rhesus Macaque Model of AIDS

    PubMed Central

    Deere, Jesse D.; Higgins, Joanne; Cannavo, Elda; Villalobos, Andradi; Adamson, Lourdes; Fromentin, Emilie; Schinazi, Raymond F.; Luciw, Paul A.; North, Thomas W.

    2010-01-01

    To prevent progression to AIDS, persons infected with human immunodeficiency virus type 1 (HIV-1) must remain on highly active antiretroviral therapy (HAART) indefinitely since this modality does not eradicate the virus. The mechanisms involved in viral persistence during HAART are poorly understood, but an animal model of HAART could help elucidate these mechanisms and enable studies of HIV-1 eradication strategies. Due to the specificity of non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) for HIV-1, we have used RT-SHIV, a chimeric virus of simian immunodeficiency virus with RT from HIV-1. This virus is susceptible to NNRTIs and causes an AIDS-like disease in rhesus macaques. In this study, two groups of HAART-treated, RT-SHIV-infected macaques were analyzed to determine viral decay kinetics. In the first group, viral loads were monitored with a standard TaqMan RT-PCR assay with a limit of detection of 50 viral RNA copies per mL. Upon initiation of HAART, viremia decayed in a bi-phasic manner with half-lives of 1.7 and 8.5 days, respectively. A third phase was observed with little further decay. In the second group, the macaques were followed longitudinally with a more sensitive assay utilizing ultracentrifugation to concentrate virus from plasma. Bi-phasic decay of viral RNA was also observed in these animals with half-lives of 1.8 and 5.8 days. Viral loads in these animals during a third phase ranged from 2–58 RNA copies/mL, with little decay over time. The viral decay kinetics observed in these macaques are similar to those reported for HIV-1 infected humans. These results demonstrate that low-level viremia persists in RT-SHIV-infected macaques despite a HAART regimen commonly used in humans. PMID:20668516

  16. Global Analysis of Viral Infection in an Archaeal Model System

    PubMed Central

    Maaty, Walid S.; Steffens, Joseph D.; Heinemann, Joshua; Ortmann, Alice C.; Reeves, Benjamin D.; Biswas, Swapan K.; Dratz, Edward A.; Grieco, Paul A.; Young, Mark J.; Bothner, Brian

    2012-01-01

    to viral infection, demonstrates the power of quantitative two-dimensional differential gel electrophoresis and ABPP using 2D gel compatible fluorescent dyes. PMID:23233852

  17. Using experimental human influenza infections to validate a viral dynamic model and the implications for prediction.

    PubMed

    Chen, S C; You, S H; Liu, C Y; Chio, C P; Liao, C M

    2012-09-01

    The aim of this work was to use experimental infection data of human influenza to assess a simple viral dynamics model in epithelial cells and better understand the underlying complex factors governing the infection process. The developed study model expands on previous reports of a target cell-limited model with delayed virus production. Data from 10 published experimental infection studies of human influenza was used to validate the model. Our results elucidate, mechanistically, the associations between epithelial cells, human immune responses, and viral titres and were supported by the experimental infection data. We report that the maximum total number of free virions following infection is 10(3)-fold higher than the initial introduced titre. Our results indicated that the infection rates of unprotected epithelial cells probably play an important role in affecting viral dynamics. By simulating an advanced model of viral dynamics and applying it to experimental infection data of human influenza, we obtained important estimates of the infection rate. This work provides epidemiologically meaningful results, meriting further efforts to understand the causes and consequences of influenza A infection.

  18. Hepatitis C virus evasion of adaptive immune responses: a model for viral persistence.

    PubMed

    Burke, Kelly P; Cox, Andrea L

    2010-07-01

    Hepatitis C virus (HCV) infects over 170 million people worldwide and is a leading cause of cirrhosis and hepatocellular carcinoma. Approximately 20% [corrected] of those acutely infected clear the infection, whereas the remaining 80% [corrected] progress to chronic infection. Hepatitis C thus provides a model in which successful and unsuccessful responses can be compared to better understand the human response to viral infection. Our laboratory studies the strategies by which HCV evades the adaptive immune response. This review describes the impact of viral mutation on T cell recognition, the role of cell surface inhibitory receptors in recognition of HCV, and the development of antibodies that neutralize HCV infection. Understanding what constitutes an effective immune response in the control of HCV may enable the development of prophylactic and therapeutic vaccines for HCV and other chronic viral infections.

  19. Viral dynamics model with CTL immune response incorporating antiretroviral therapy.

    PubMed

    Wang, Yan; Zhou, Yicang; Brauer, Fred; Heffernan, Jane M

    2013-10-01

    We present two HIV models that include the CTL immune response, antiretroviral therapy and a full logistic growth term for uninfected CD4+ T-cells. The difference between the two models lies in the inclusion or omission of a loss term in the free virus equation. We obtain critical conditions for the existence of one, two or three steady states, and analyze the stability of these steady states. Through numerical simulation we find substantial differences in the reproduction numbers and the behaviour at the infected steady state between the two models, for certain parameter sets. We explore the effect of varying the combination drug efficacy on model behaviour, and the possibility of reconstituting the CTL immune response through antiretroviral therapy. Furthermore, we employ Latin hypercube sampling to investigate the existence of multiple infected equilibria. PMID:22930342

  20. A probability cellular automaton model for hepatitis B viral infections.

    PubMed

    Xiao, Xuan; Shao, Shi-Huang; Chou, Kuo-Chen

    2006-04-01

    The existing models of hepatitis B virus (HBV) infection dynamics are based on the assumption that the populations of viruses and cells are uniformly mixed. However, the real virus infection system is actually not homogeneous and some spatial factors might play a nontrivial role in governing the development of HBV infection and its outcome. For instance, the localized populations of dead cells might adversely affect the spread of infection. To consider this kind of inhomogeneous feature, a simple 2D (dimensional) probability Cellular Automaton model was introduced to study the dynamic process of HBV infection. The model took into account the existence of different types of HBV infectious and non-infectious particles. The simulation results thus obtained showed that the Cellular Automaton model could successfully account for some important features of the disease, such as its wide variety in manifestation and its age dependency. Meanwhile, the effects of the model's parameters on the dynamical process of the infection were also investigated. It is anticipated that the Cellular Automaton model may be extended to serve as a useful vehicle for studying, among many other complicated dynamic biological systems, various persistent infections with replicating parasites.

  1. Transgenic models of Alzheimer's disease: better utilization of existing models through viral transgenesis.

    PubMed

    Platt, Thomas L; Reeves, Valerie L; Murphy, M Paul

    2013-09-01

    Animal models have been used for decades in the Alzheimer's disease (AD) research field and have been crucial for the advancement of our understanding of the disease. Most models are based on familial AD mutations of genes involved in the amyloidogenic process, such as the amyloid precursor protein (APP) and presenilin 1 (PS1). Some models also incorporate mutations in tau (MAPT) known to cause frontotemporal dementia, a neurodegenerative disease that shares some elements of neuropathology with AD. While these models are complex, they fail to display pathology that perfectly recapitulates that of the human disease. Unfortunately, this level of pre-existing complexity creates a barrier to the further modification and improvement of these models. However, as the efficacy and safety of viral vectors improves, their use as an alternative to germline genetic modification is becoming a widely used research tool. In this review we discuss how this approach can be used to better utilize common mouse models in AD research. This article is part of a Special Issue entitled: Animal Models of Disease.

  2. A Highly Intensified ART Regimen Induces Long-Term Viral Suppression and Restriction of the Viral Reservoir in a Simian AIDS Model

    PubMed Central

    Della Corte, Alessandro; Collins, Matt; Yalley-Ogunro, Jake; Greenhouse, Jack; Iraci, Nunzio; Acosta, Edward P.; Barreca, Maria Letizia; Lewis, Mark G.; Savarino, Andrea

    2012-01-01

    Stably suppressed viremia during ART is essential for establishing reliable simian models for HIV/AIDS. We tested the efficacy of a multidrug ART (highly intensified ART) in a wide range of viremic conditions (103–107 viral RNA copies/mL) in SIVmac251-infected rhesus macaques, and its impact on the viral reservoir. Eleven macaques in the pre-AIDS stage of the disease were treated with a multidrug combination (highly intensified ART) consisting of two nucleosidic/nucleotidic reverse transcriptase inhibitors (emtricitabine and tenofovir), an integrase inhibitor (raltegravir), a protease inhibitor (ritonavir-boosted darunavir) and the CCR5 blocker maraviroc. All animals stably displayed viral loads below the limit of detection of the assay (i.e. <40 RNA copies/mL) after starting highly intensified ART. By increasing the sensitivity of the assay to 3 RNA copies/mL, viral load was still below the limit of detection in all subjects tested. Importantly, viral DNA resulted below the assay detection limit (<2 copies of DNA/5*105 cells) in PBMCs and rectal biopsies of all animals at the end of the follow-up, and in lymph node biopsies from the majority of the study subjects. Moreover, highly intensified ART decreased central/transitional memory, effector memory and activated (HLA-DR+) effector memory CD4+ T-cells in vivo, in line with the role of these subsets as the main cell subpopulations harbouring the virus. Finally, treatment with highly intensified ART at viral load rebound following suspension of a previous anti-reservoir therapy eventually improved the spontaneous containment of viral load following suspension of the second therapeutic cycle, thus leading to a persistent suppression of viremia in the absence of ART. In conclusion, we show, for the first time, complete suppression of viral load by highly intensified ART and a likely associated restriction of the viral reservoir in the macaque AIDS model, making it a useful platform for testing potential cures for

  3. A pharmacokinetic/viral kinetic model to evaluate the treatment effectiveness of danoprevir against chronic HCV

    DOE PAGES

    Canini, Laetitia; Chatterjee, Anushree; Guedj, Jeremie; Lemenuel-Diot, Annabelle; Brennan, Barbara; Smith, Patrick F.; Perelson, Alan S.

    2014-10-16

    Background—Viral kinetic models have proven useful to characterize treatment effectiveness during HCV therapy with interferon (IFN) or with direct acting antivirals (DAAs). Methods—We use a pharmacokinetic/viral kinetic (PK/VK) model to describe HCV RNA kinetics during treatment with danoprevir, a protease inhibitor. In a phase 1 study, danoprevir monotherapy was administered for 14 days in ascending doses ranging from 200 to 600 mg per day to 40 patients of whom 32 were treatment-naïve and 8 were non-responders to prior PEG-IFN-α/ribavirin treatment. Results—In most patients, a biphasic decline of HCV RNA during therapy was observed. A two-compartment PK model and a VKmore » model that considered treatment effectiveness to vary with the predicted danoprevir concentration inside the second compartment provided a good fit to the viral load data. A time-varying effectiveness model was also used to fit the viral load data. We found the antiviral effectiveness increased in a dose-dependent manner, with a 14-day time-averaged effectiveness of 0.95 at the lowest dose (100 mg bid) and 0.99 at the highest dose (200 mg tid). Prior IFN non-responders exhibited a 14-day time-averaged effectiveness of 0.98 (300 mg bid). Finally, the second phase decline showed two different behaviors, with 30% of patients exhibiting a rapid decline of HCV RNA, comparable to that seen with other protease inhibitors (>0.3 d-1), whereas the viral decline was slower in the other patients. Conclusions—Our results are consistent with the modest SVR rates from the INFORM-SVR study where patients were treated with a combination of mericitabine and ritonavir-boosted danoprevir.« less

  4. A pharmacokinetic/viral kinetic model to evaluate the treatment effectiveness of danoprevir against chronic HCV

    SciTech Connect

    Canini, Laetitia; Chatterjee, Anushree; Guedj, Jeremie; Lemenuel-Diot, Annabelle; Brennan, Barbara; Smith, Patrick F.; Perelson, Alan S.

    2014-10-16

    Background—Viral kinetic models have proven useful to characterize treatment effectiveness during HCV therapy with interferon (IFN) or with direct acting antivirals (DAAs). Methods—We use a pharmacokinetic/viral kinetic (PK/VK) model to describe HCV RNA kinetics during treatment with danoprevir, a protease inhibitor. In a phase 1 study, danoprevir monotherapy was administered for 14 days in ascending doses ranging from 200 to 600 mg per day to 40 patients of whom 32 were treatment-naïve and 8 were non-responders to prior PEG-IFN-α/ribavirin treatment. Results—In most patients, a biphasic decline of HCV RNA during therapy was observed. A two-compartment PK model and a VK model that considered treatment effectiveness to vary with the predicted danoprevir concentration inside the second compartment provided a good fit to the viral load data. A time-varying effectiveness model was also used to fit the viral load data. We found the antiviral effectiveness increased in a dose-dependent manner, with a 14-day time-averaged effectiveness of 0.95 at the lowest dose (100 mg bid) and 0.99 at the highest dose (200 mg tid). Prior IFN non-responders exhibited a 14-day time-averaged effectiveness of 0.98 (300 mg bid). Finally, the second phase decline showed two different behaviors, with 30% of patients exhibiting a rapid decline of HCV RNA, comparable to that seen with other protease inhibitors (>0.3 d-1), whereas the viral decline was slower in the other patients. Conclusions—Our results are consistent with the modest SVR rates from the INFORM-SVR study where patients were treated with a combination of mericitabine and ritonavir-boosted danoprevir.

  5. Modeling the winter-to-summer transition of prokaryotic and viral abundance in the Arctic Ocean.

    PubMed

    Winter, Christian; Payet, Jérôme P; Suttle, Curtis A

    2012-01-01

    One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations.

  6. Protective Role of the Cholinergic Anti-Inflammatory Pathway in a Mouse Model of Viral Myocarditis

    PubMed Central

    Jing-Lin, Zhao; Wen-Wu, Zhang; Xue-Si, Chen; Xing-Xing, Chen; Yue-Chun, Li

    2014-01-01

    Background Activation of the cholinergic anti-inflammatory pathway, which relies on the α7nAchR (alpha 7 nicotinic acetylcholine receptor), has been shown to decrease proinflammatory cytokines. This relieves inflammatory responses and improves the prognosis of patients with experimental sepsis, endotoxemia, ischemia/reperfusion injury, hemorrhagic shock, pancreatitis, arthritis and other inflammatory syndromes. However, whether the cholinergic anti-inflammatory pathway has an effect on acute viral myocarditis has not been investigated. Here, we studied the effects of the cholinergic anti-inflammatory pathway on acute viral myocarditis. Methodology/Principal Findings In a coxsackievirus B3 murine myocarditis model (Balb/c), nicotine and methyllycaconitine were used to stimulate and block the cholinergic anti-inflammatory pathway, respectively. Relevant signal pathways were studied to compare their effects on myocarditis, survival rate, histopathological changes, ultrastructural changes, and cytokine levels. Nicotine treatments significantly improved survival rate, attenuated myocardial lesions, and downregulated the expression of TNF-α and IL-6. Methyllycaconitine decreased survival rate, aggravated myocardial lesions, and upregulated the expression of TNF-α and IL-6. In addition, levels of the signaling protein phosphorylated STAT3 were higher in the nicotine group and lower in the methyllycaconitine group compared with the untreated myocarditis group. Conclusions/Significance These results show that nicotine protects mice from CVB3-induced viral myocarditis and that methyllycaconitine aggravates viral myocarditis in mice. Because nicotine is a α7nAchR agonist and methyllycaconitine is a α7nAchR antagonist, we conclude that α7nAchR activation increases the phosphorylation of STAT3, reduces the expression of TNF-α and IL-6, and, ultimately, alleviates viral myocarditis. We also conclude that blocking α7nAchR reduces the phosphorylation of STAT3, increases

  7. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.

    PubMed

    Hurwitz, Bonnie L; Westveld, Anton H; Brum, Jennifer R; Sullivan, Matthew B

    2014-07-22

    Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). Although protein clustering techniques provide a significant advance by helping organize this unknown metagenomic sequence space, they typically use only ∼75% of the data and rely on assembly methods not yet tuned for naturally occurring sequence variation. Here, we introduce an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. Application to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly delineated by photic zone and revealed that geographic region, depth, and proximity to shore were significant predictors of community structure. Within subsets of this dataset, depth, season, and oxygen concentration were significant drivers of viral community structure at a single open ocean station, whereas variability along onshore-offshore transects was driven by oxygen concentration in an area with an oxygen minimum zone and not depth or proximity to shore, as might be expected. Together these results demonstrate that this highly scalable approach using complete metagenomic network-based comparisons can both test and generate hypotheses for ecological investigation of viral and microbial communities in nature.

  8. Hepatitis B viral clearance studies using duck virus model.

    PubMed

    Long, Z; Sun, C S; White, E M; Horowitz, B; Sito, A F

    1993-01-01

    We have shown data to suggest that the in vivo duck hepatitis B virus system represents an excellent animal model system for the study of hepatitis B virus. Because of the similarity of DHBV to human HBV (including comparable results in virus inactivation studies), the high level of sensitivity of the DHBV assay, and the rapidity, ease, and relative low cost of obtaining results, we propose that the in vivo DHBV titration system be used as a model for human HBV in process validation studies. Data generated in such validation studies have, in fact, been submitted by a number of blood products manufacturers to the U.S. F.D.A. in support of IND applications.

  9. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes.

    PubMed

    Shekhar, Karthik; Ruberman, Claire F; Ferguson, Andrew L; Barton, John P; Kardar, Mehran; Chakraborty, Arup K

    2013-12-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses. PMID:24483484

  10. Encephalomyocarditis virus 3C protease: efficient cell-free expression from clones which link viral 5' noncoding sequences to the P3 region.

    PubMed Central

    Parks, G D; Duke, G M; Palmenberg, A C

    1986-01-01

    All picornaviral peptides are derived by progressive posttranslational cleavage of a giant precursor polyprotein. Translation of encephalomyocarditis virus (EMC) RNA in rabbit reticulocyte extracts produces active viral peptides, including protease 3C, which is responsible for many cleavage reactions within the processing cascade. DNA plasmids containing 5' noncoding sequences of EMC linked to other portions of the viral genome were constructed and transcribed into RNA. Like virion RNA, the clone-derived transcripts directed efficient protein translation in vitro. The 5'-linked constructions may represent examples of a general method for cell-free expression of any cloned gene segment. One construction produced a self-cleaving P3 region precursor, which contained active 3C protease. A genetically engineered insertion within the 3C sequences eliminated endogenous self-cleavage activity without altering the ability of the P3 peptide to serve as substrate in bimolecular reactions with added 3C. Another plasmid encoding the L-VP0 portion of the capsid region was used to demonstrate that scission between the leader peptide (L) and capsid protein VP0 can be catalyzed by 3C. The enzyme responsible for this step was previously unidentified. A rapid purification scheme for isolation of 3C from EMC-infected HeLa cells is also presented. Images PMID:3021972

  11. Evaluating sludge minimization caused by predation and viral infection based on the extended activated sludge model No. 2d.

    PubMed

    Hao, Xiaodi; Wang, Qilin; Cao, Yali; van Loosdrecht, Mark C M

    2011-10-15

    The Activated Sludge Model No. 2d (ASM2d) was extended to incorporate the processes of both predation and viral infection. The extended model was used to evaluate the contributions of predation and viral infection to sludge minimization in a sequencing batch reactor (SBR) system enriching polyphosphate-accumulating organisms (PAOs). Three individual decay processes formulated according to the general model rules were used in the extended model. The model was firstly calibrated and validated by different experimental results. It was used to evaluate the potential extent of predation and viral infection on sludge minimization. Simulations indicate that predation contributes roughly two times more to sludge minimization than viral infection in the SBR system enriching PAOs. The sensitivity analyses of the selected key parameters reveal that there are thresholds on both predation and viral infection rates, if they are too large a minimal sludge retention time is obtained and the effluent quality is deteriorating. Due to the thresholds, the contributions of predation and viral infection to sludge minimization are limited to a maximal extent of about 21% and 9%, respectively. However, it should be noted that the parameters concerning predation and viral infection were not calibrated separately by independent experiment in our study due to the lack of an effective method, especially for the parameters regarding viral infection. Therefore, it is essential to better evaluate these parameters in the future.

  12. Cross-link guided molecular modeling with ROSETTA.

    PubMed

    Kahraman, Abdullah; Herzog, Franz; Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

    2013-01-01

    Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods. PMID:24069194

  13. Use of a three-dimensional humanized liver model for the study of viral gene vectors.

    PubMed

    Wagner, Anke; Röhrs, Viola; Materne, Eva-Maria; Hiller, Thomas; Kedzierski, Radoslaw; Fechner, Henry; Lauster, Roland; Kurreck, Jens

    2015-10-20

    Reconstituted three-dimensional (3D) liver models obtained by engrafting hepatic cells into an extracellular matrix (ECM) are valuable tools to study tissue regeneration, drug action and toxicology ex vivo. The aim of the present study was to establish a system for the functional investigation of a viral vector in a 3D liver model composed of human HepG2 cells on a rat ECM. An adeno-associated viral (AAV) vector expressing the Emerald green fluorescent protein (EmGFP) and a short hairpin RNA (shRNA) directed against human cyclophilin b (hCycB) was injected into the portal vein of 3D liver models. Application of the vector did not exert toxic effects, as shown by analysis of metabolic parameters. Six days after transduction, fluorescence microscopy analysis of EmGFP production revealed widespread distribution of the AAV vectors. After optimization of the recellularization and transduction conditions, averages of 55 and 90 internalized vector genomes per cell in two replicates of the liver model were achieved, as determined by quantitative PCR analysis. Functionality of the AAV vector was confirmed by efficient shRNA-mediated knockdown of hCycB by 70-90%. Our study provides a proof-of-concept that a recellularized biological ECM provides a valuable model to study viral vectors ex vivo. PMID:26356676

  14. Use of a three-dimensional humanized liver model for the study of viral gene vectors.

    PubMed

    Wagner, Anke; Röhrs, Viola; Materne, Eva-Maria; Hiller, Thomas; Kedzierski, Radoslaw; Fechner, Henry; Lauster, Roland; Kurreck, Jens

    2015-10-20

    Reconstituted three-dimensional (3D) liver models obtained by engrafting hepatic cells into an extracellular matrix (ECM) are valuable tools to study tissue regeneration, drug action and toxicology ex vivo. The aim of the present study was to establish a system for the functional investigation of a viral vector in a 3D liver model composed of human HepG2 cells on a rat ECM. An adeno-associated viral (AAV) vector expressing the Emerald green fluorescent protein (EmGFP) and a short hairpin RNA (shRNA) directed against human cyclophilin b (hCycB) was injected into the portal vein of 3D liver models. Application of the vector did not exert toxic effects, as shown by analysis of metabolic parameters. Six days after transduction, fluorescence microscopy analysis of EmGFP production revealed widespread distribution of the AAV vectors. After optimization of the recellularization and transduction conditions, averages of 55 and 90 internalized vector genomes per cell in two replicates of the liver model were achieved, as determined by quantitative PCR analysis. Functionality of the AAV vector was confirmed by efficient shRNA-mediated knockdown of hCycB by 70-90%. Our study provides a proof-of-concept that a recellularized biological ECM provides a valuable model to study viral vectors ex vivo.

  15. Emergence of viral diseases: mathematical modeling as a tool for infection control, policy and decision making.

    PubMed

    Louz, Derrick; Bergmans, Hans E; Loos, Birgit P; Hoeben, Rob C

    2010-08-01

    Mathematical modeling can be used for the development and implementation of infection control policy to combat outbreaks and epidemics of communicable viral diseases. Here an outline is provided of basic concepts and approaches used in mathematical modeling and parameterization of disease transmission. The use of mathematical models is illustrated, using the 2001 UK foot-and-mouth disease (FMD) epidemic, the 2003 global severe acute respiratory syndrome (SARS) epidemic, and human influenza pandemics, as examples. This provides insights in the strengths, limitations, and weaknesses of the various models, and demonstrates their potential for supporting policy and decision making. PMID:20218764

  16. Emergence of viral diseases: mathematical modeling as a tool for infection control, policy and decision making.

    PubMed

    Louz, Derrick; Bergmans, Hans E; Loos, Birgit P; Hoeben, Rob C

    2010-08-01

    Mathematical modeling can be used for the development and implementation of infection control policy to combat outbreaks and epidemics of communicable viral diseases. Here an outline is provided of basic concepts and approaches used in mathematical modeling and parameterization of disease transmission. The use of mathematical models is illustrated, using the 2001 UK foot-and-mouth disease (FMD) epidemic, the 2003 global severe acute respiratory syndrome (SARS) epidemic, and human influenza pandemics, as examples. This provides insights in the strengths, limitations, and weaknesses of the various models, and demonstrates their potential for supporting policy and decision making.

  17. Model of influenza A virus infection: dynamics of viral antagonism and innate immune response.

    PubMed

    Fribourg, M; Hartmann, B; Schmolke, M; Marjanovic, N; Albrecht, R A; García-Sastre, A; Sealfon, S C; Jayaprakash, C; Hayot, F

    2014-06-21

    Viral antagonism of host responses is an essential component of virus pathogenicity. The study of the interplay between immune response and viral antagonism is challenging due to the involvement of many processes acting at multiple time scales. Here we develop an ordinary differential equation model to investigate the early, experimentally measured, responses of human monocyte-derived dendritic cells to infection by two H1N1 influenza A viruses of different clinical outcomes: pandemic A/California/4/2009 and seasonal A/New Caledonia/20/1999. Our results reveal how the strength of virus antagonism, and the time scale over which it acts to thwart the innate immune response, differs significantly between the two viruses, as is made clear by their impact on the temporal behavior of a number of measured genes. The model thus sheds light on the mechanisms that underlie the variability of innate immune responses to different H1N1 viruses.

  18. PD-1 Blockage Reverses Immune Dysfunction and Hepatitis B Viral Persistence in a Mouse Animal Model

    PubMed Central

    Tzeng, Horng-Tay; Tsai, Hwei-Fang; Liao, Hsiu-Jung; Lin, Yi-Jiun; Chen, Lieping; Chen, Pei-Jer; Hsu, Ping-Ning

    2012-01-01

    Persistent hepatitis B viral (HBV) infection results in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Recent studies in animal models of viral infection indicate that the interaction between the inhibitory receptor, programmed death (PD)-1, on lymphocytes and its ligand (PD-L1) play a critical role in T-cell exhaustion by inducing T-cell inactivation. High PD-1 expression levels by peripheral T-lymphocytes and the possibility of improving T-cell function by blocking PD-1-mediated signaling confirm the importance of this inhibitory pathway in inducing T-cell exhaustion. We studied T-cell exhaustion and the effects of PD-1 and PD-L1 blockade on intrahepatic infiltrating T-cells in our recently developed mouse model of HBV persistence. In this mouse animal model, we demonstrated that there were increased intrahepatic PD-1-expressing CD8+ and CD4+ T cells in mice with HBV persistence, but PD-1 upregulation was resolved in mice which had cleared HBV. The Intrahepatic CD8+ T-cells expressed higher levels of PD-1 and lower levels of CD127 in mice with HBV persistence. Blockade of PD-1/PD-L1 interactions increased HBcAg-specific interferon (IFN)-γ production in intrahepatic T lymphocytes. Furthermore, blocking the interaction of PD-1 with PD-L1 by an anti-PD-1 monoclonal antibody (mAb) reversed the exhausted phenotype in intrahepatic T lymphocytes and viral persistence to clearance of HBV in vivo. Our results indicated that PD-1 blockage reverses immune dysfunction and viral persistence of HBV infection in a mouse animal model, suggesting that the anti-PD-1 mAb might be a good therapeutic candidate for chronic HBV infection. PMID:22761734

  19. Links between soil modelling and proximal sensing

    NASA Astrophysics Data System (ADS)

    Aitkenhead, Matt; McBratney, Alex; Minasny, Budiman

    2015-04-01

    Proximal sensing of soils can provide valuable information for soil modelling, by providing baseline data and validating model predictions through direct observation of soil characteristics. A wide range of soil parameters can be estimated using proximal sensing of soils (PSS), often simultaneously using single hand-held systems, of which there are many types. The benefits for soil modelling include direct observation of modelled parameters, rapid assessment in field conditions and digital data acquisition, making the transfer of information to soil models relatively straightforward. This is an active area of development, with research into improved methods of field-based capture of soil parameters directly relevant for soil modelling. A number of challenges exist, including the removal of or accounting for the effects of field conditions (e.g. soil moisture and structure), and the development of libraries of data that will allow calibration models to be produced. We present an overview of PSS as it relates to soil modelling, including equipment types, calibration approaches, cloud-based processing, soil parameters and processes estimated using PSS, and opportunities and challenges for the future. We also identify and discuss the possibilities for integration of modelling and proximal sensing within precision agriculture/precision land management.

  20. The stability analysis of a general viral infection model with distributed delays and multi-staged infected progression

    NASA Astrophysics Data System (ADS)

    Wang, Jinliang; Liu, Shengqiang

    2015-01-01

    We investigate an in-host model with general incidence and removal rate, as well as distributed delays in virus infections and in productions. By employing Lyapunov functionals and LaSalle's invariance principle, we define and prove the basic reproductive number R0 as a threshold quantity for stability of equilibria. It is shown that if R0 > 1 , then the infected equilibrium is globally asymptotically stable, while if R0 ⩽ 1 , then the infection free equilibrium is globally asymptotically stable under some reasonable assumptions. Moreover, n + 1 distributed delays describe (i) the time between viral entry and the transcription of viral RNA, (ii) the n - 1 -stage time needed for activated infected cells between viral RNA transcription and viral release, and (iii) the time necessary for the newly produced viruses to be infectious (maturation), respectively. The model can describe the viral infection dynamics of many viruses such as HIV-1, HCV and HBV.

  1. Modeling viral coevolution: HIV multi-clonal persistence and competition dynamics

    NASA Astrophysics Data System (ADS)

    Bagnoli, F.; Liò, P.; Sguanci, L.

    2006-07-01

    The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have not yet been understood. We present a model of HIV quasispecies competition, which describes the conditions of viral quasispecies coexistence under different immune system conditions. Our model incorporates both T and B cells responses, and we show that the role of B cells is important and additive to that of T cells. Simulations of coinfection (simultaneous infection) and superinfection (delayed secondary infection) scenarios in the early stages (days) and in the late stages of the infection (years) are in agreement with emerging molecular biology findings. The immune response induces a competition among similar phenotypes, leading to differentiation (quasispeciation), escape dynamics and complex oscillations of viral strain abundance. We found that the quasispecies dynamics after superinfection or coinfection has time scales of several months and becomes even slower when the immune system response is weak. Our model represents a general framework to study the speed and distribution of HIV quasispecies during disease progression, vaccination and therapy.

  2. Integrated Population Pharmacokinetic/Viral Dynamic Modeling of Lopinavir/Ritonavir in HIV-1 Treatment Naïve Patients

    PubMed Central

    Wang, Kun; D'Argenio, David Z.; Acosta, Edward P.; Sheth, Anandi N.; Delille, Cecile; Lennox, Jeffrey L.; Kerstner-Wood, Corenna; Ofotokun, Ighovwerha

    2014-01-01

    Background Lopinavir (LPV)/ritonavir (RTV) co-formulation (LPV/RTV) is a widely used protease inhibitor (PI) based regimen to treat HIV-infection. As with all PIs, the trough concentration (Ctrough) is a primary determinant of response, but the optimum exposure remains poorly defined. The primary objective was to develop an integrated LPV population pharmacokinetic model to investigate the influence of α-1-acid glycoprotein (AAG) and link total and free LPV exposure to pharmacodynamic changes in HIV-1 RNA and assess viral dynamic and drug efficacy parameters. Methods Data from 35 treatment-naïve HIV-infected patients initiating therapy with LPV/RTV 400/100 mg orally twice daily across two studies were used for model development and simulations using ADAPT. Total LPV (LPVt) and RTV concentrations were measured by high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection. Free LPV (LPVf) concentrations were measured using equilibrium dialysis and mass spectrometry. Results LPVt typical value of clearance (CLLPVt/F) was 4.73 L/h and distribution volume (VLPVt/F) was 55.7 L. Clearance (CLLPVf/F) and distibution volume (Vf/F) for LPVf were 596 L/h and 6370 L, respectively. Virion clearance rate was 0.0350 h-1. Simulated LPVLPVt Ctrough at 90% (EC90) and 95% (EC95) maximum response were 316 and 726 ng/mL, respectively. Conclusion The pharmacokinetic/pharmacodynamic model provides a useful tool to quantitatively describe the relationship between LPV/RTV exposure and viral response. This comprehensive modeling and simulation approach could be used as a surrogate assessment of ARV where adequate early phase dose-ranging studies are lacking in order to define target trough concentrations and possibly refine dosing recommendations. PMID:24311282

  3. COMPARING AND LINKING PLUMES ACROSS MODELING APPROACHES

    EPA Science Inventory

    River plumes carry many pollutants, including microorganisms, into lakes and the coastal ocean. The physical scales of many stream and river plumes often lie between the scales for mixing zone plume models, such as the EPA Visual Plumes model, and larger-sized grid scales for re...

  4. A VGI data integration framework based on linked data model

    NASA Astrophysics Data System (ADS)

    Wan, Lin; Ren, Rongrong

    2015-12-01

    This paper aims at the geographic data integration and sharing method for multiple online VGI data sets. We propose a semantic-enabled framework for online VGI sources cooperative application environment to solve a target class of geospatial problems. Based on linked data technologies - which is one of core components of semantic web, we can construct the relationship link among geographic features distributed in diverse VGI platform by using linked data modeling methods, then deploy these semantic-enabled entities on the web, and eventually form an interconnected geographic data network to support geospatial information cooperative application across multiple VGI data sources. The mapping and transformation from VGI sources to RDF linked data model is presented to guarantee the unique data represent model among different online social geographic data sources. We propose a mixed strategy which combined spatial distance similarity and feature name attribute similarity as the measure standard to compare and match different geographic features in various VGI data sets. And our work focuses on how to apply Markov logic networks to achieve interlinks of the same linked data in different VGI-based linked data sets. In our method, the automatic generating method of co-reference object identification model according to geographic linked data is discussed in more detail. It finally built a huge geographic linked data network across loosely-coupled VGI web sites. The results of the experiment built on our framework and the evaluation of our method shows the framework is reasonable and practicable.

  5. Evaluation of viral-lysate enzyme-linked immunosorbent assay kits for detecting human immunodeficiency virus (type 1) infections using human sera standardized by quantitative western blotting.

    PubMed

    Hardy, C T; Damrow, T A; Villareal, D B; Kenny, G E

    1992-06-01

    The first generation of proprietary reagents for detecting antibodies to the Human Immunodeficiency Virus Type 1 (HIV-1) by enzyme-linked immunosorbent assay (ELISA) used as antigen partially purified virus from cell culture lysates. These tests, which are still in use, may vary in their antibody measurement capabilities if different proportions of the viral polypeptides are present in the viral lysate mixtures. We determined the quantities of antibodies in the serum of persons infected with HIV-1 by dilution analysis using 3 ELISA kits: Abbott [A], Du Pont [D], Genetic Systems [G]. The proportionate antibody titres of each serum to p24gag and gp160env/120env were established by quantitative Western blotting. Serum antibody titres were high, frequently over 1:10,000, a result observed both by ELISA and Western blot. For Kit D, sera with high proportions of antibody to p24gag produced antibody titration curves with steep slopes whereas shallower slopes were found in sera with high proportions of antibody to gp160env. In contrast, Kit A gave steeper slopes with sera enriched for gp160env antibodies. Kit G gave results with slopes intermediate between Kits A and D. Serum antibody titres differed between kits depending upon the proportion and concentration of antibodies in a given serum to gp160env and p24gag. The findings that both the concentration and proportion of antibodies to specific viral polypeptides in human sera markedly affect the signal intensity produced by proprietary ELISAs suggest the need for several control sera which reflect the diversity of human serum responses. Standardization of human reference sera by quantitative Western blotting will assist in evaluation and quality control of ELISA tests.

  6. A nationwide database linking information on the hosts with sequence data of their virus strains: A useful tool for the eradication of bovine viral diarrhea (BVD) in Switzerland.

    PubMed

    Stalder, Hanspeter; Hug, Corinne; Zanoni, Reto; Vogt, Hans-Rudolf; Peterhans, Ernst; Schweizer, Matthias; Bachofen, Claudia

    2016-06-15

    Pestiviruses infect a wide variety of animals of the order Artiodactyla, with bovine viral diarrhea virus (BVDV) being an economically important pathogen of livestock globally. BVDV is maintained in the cattle population by infecting fetuses early in gestation and, thus, by generating persistently infected (PI) animals that efficiently transmit the virus throughout their lifetime. In 2008, Switzerland started a national control campaign with the aim to eradicate BVDV from all bovines in the country by searching for and eliminating every PI cattle. Different from previous eradication programs, all animals of the entire population were tested for virus within one year, followed by testing each newborn calf in the subsequent four years. Overall, 3,855,814 animals were tested from 2008 through 2011, 20,553 of which returned an initial BVDV-positive result. We were able to obtain samples from at least 36% of all initially positive tested animals. We sequenced the 5' untranslated region (UTR) of more than 7400 pestiviral strains and compiled the sequence data in a database together with an array of information on the PI animals, among others, the location of the farm in which they were born, their dams, and the locations where the animals had lived. To our knowledge, this is the largest database combining viral sequences with animal data of an endemic viral disease. Using unique identification tags, the different datasets within the database were connected to run diverse molecular epidemiological analyses. The large sets of animal and sequence data made it possible to run analyses in both directions, i.e., starting from a likely epidemiological link, or starting from related sequences. We present the results of three epidemiological investigations in detail and a compilation of 122 individual investigations that show the usefulness of such a database in a country-wide BVD eradication program.

  7. Simple Indirect Enzyme-Linked Immunosorbent Assay to Detect Antibodies Against Bovine Viral Diarrhea Virus, Based on Prokaryotically Expressed Recombinant MBP-NS3 Protein

    PubMed Central

    Mahmoodi, Pezhman; Seyfi Abad Shapouri, Masoud Reza; Ghorbanpour, Masoud; Haji Hajikolaei, Mohammad Rahim; Lotfi, Mohsen; Pourmahdi Boroujeni, Mahdi; Daghari, Maryam

    2015-01-01

    Background: Bovine viral diarrhea (BVD) is an economically important disease of cattle distributed worldwide. Diagnosis of BVD relies on laboratory-based detection of its viral causing agent or virus specific antibodies and the most common laboratory method for this purpose is Enzyme-Linked Immunosorbent Assay (ELISA). Objectives: The current study was aimed to develop a simple indirect ELISA to detect antibodies against Bovine Viral Diarrhea Virus (BVDV) in the sera of infected cattle. Materials and Methods: A new simple indirect ELISA method was developed to detect BVDV infection by prokaryotically (Escherichia coli, BL21 strain) expressed recombinant whole nonstructural protein 3 (NS3) of BVDV (NADL strain). Four hundred bovine serum samples were evaluated by the newly developed NS3-ELISA and virus neutralization test (VNT) as the gold standard method to diagnose BVD. Among these samples, 289 sera had been previously tested by a commercial ELISA kit. Results: Statistical analyses showed a very high correlation between the results of the developed NS3-ELISA and VNT (kappa coefficient = 0.935, P < 0.001), with the relative sensitivity and specificity of 94% and 98.8%, respectively. There was also a high correlation between the results of NS3-ELISA and the commercial ELISA kit (kappa coefficient = 0.802, P < 0.001) with the relative sensitivity and specificity of 90.72% and 91.15%, respectively. Conclusions: The newly developed simple indirect ELISA showed high sensitivity and specificity with respect to VNT. Developing such a simple, sensitive, and specific ELISA which is much less expensive than the available commercial ELISA kits can improve the detection of BVDV infections, help to eliminate the disease from herds, and decrease economic losses caused by this disease. PMID:25964844

  8. Loopholes and missing links in protein modeling.

    PubMed

    Rossi, Karen A; Weigelt, Carolyn A; Nayeem, Akbar; Krystek, Stanley R

    2007-09-01

    This paper provides an unbiased comparison of four commercially available programs for loop sampling, Prime, Modeler, ICM, and Sybyl, each of which uses a different modeling protocol. The study assesses the quality of results and examines the relative strengths and weaknesses of each method. The set of loops to be modeled varied in length from 4-12 amino acids. The approaches used for loop modeling can be classified into two methodologies: ab initio loop generation (Modeler and Prime) and database searches (Sybyl and ICM). Comparison of the modeled loops to the native structures was used to determine the accuracy of each method. All of the protocols returned similar results for short loop lengths (four to six residues), but as loop length increased, the quality of the results varied among the programs. Prime generated loops with RMSDs <2.5 A for loops up to 10 residues, while the other three methods met the 2.5 A criteria at seven-residue loops. Additionally, the ability of the software to utilize disulfide bonds and X-ray crystal packing influenced the quality of the results. In the final analysis, the top-ranking loop from each program was rarely the loop with the lowest RMSD with respect to the native template, revealing a weakness in all programs to correctly rank the modeled loops.

  9. Shuttle/TDRSS modelling and link simulation study

    NASA Technical Reports Server (NTRS)

    Braun, W. R.; Mckenzie, T. M.; Biederman, L.; Lindsey, W. C.

    1979-01-01

    A Shuttle/TDRSS S-band and Ku-band link simulation package called LinCsim was developed for the evaluation of link performance for specific Shuttle signal designs. The link models were described in detail and the transmitter distortion parameters or user constraints were carefully defined. The overall link degradation (excluding hardware degradations) relative to an ideal BPSK channel were given for various sets of user constraint values. The performance sensitivity to each individual user constraint was then illustrated. The effect of excessive Spacelab clock jitter on the return link BER performance was also investigated as was the problem of subcarrier recovery for the K-band Shuttle return link signal.

  10. Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model.

    PubMed

    Otte, Anna; Marriott, Anthony C; Dreier, Carola; Dove, Brian; Mooren, Kyra; Klingen, Thorsten R; Sauter, Martina; Thompson, Katy-Anne; Bennett, Allan; Klingel, Karin; van Riel, Debby; McHardy, Alice C; Carroll, Miles W; Gabriel, Gülsah

    2016-06-24

    There is increasing evidence that 2009 pandemic H1N1 influenza viruses have evolved after pandemic onset giving rise to severe epidemics in subsequent waves. However, it still remains unclear which viral determinants might have contributed to disease severity after pandemic initiation. Here, we show that distinct mutations in the 2009 pandemic H1N1 virus genome have occurred with increased frequency after pandemic declaration. Among those, a mutation in the viral hemagglutinin was identified that increases 2009 pandemic H1N1 virus binding to human-like α2,6-linked sialic acids. Moreover, these mutations conferred increased viral replication in the respiratory tract and elevated respiratory droplet transmission between ferrets. Thus, our data show that 2009 H1N1 influenza viruses have evolved after pandemic onset giving rise to novel virus variants that enhance viral replicative fitness and respiratory droplet transmission in a mammalian animal model. These findings might help to improve surveillance efforts to assess the pandemic risk by emerging influenza viruses.

  11. Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model

    PubMed Central

    Otte, Anna; Marriott, Anthony C.; Dreier, Carola; Dove, Brian; Mooren, Kyra; Klingen, Thorsten R.; Sauter, Martina; Thompson, Katy-Anne; Bennett, Allan; Klingel, Karin; van Riel, Debby; McHardy, Alice C.; Carroll, Miles W.; Gabriel, Gülsah

    2016-01-01

    There is increasing evidence that 2009 pandemic H1N1 influenza viruses have evolved after pandemic onset giving rise to severe epidemics in subsequent waves. However, it still remains unclear which viral determinants might have contributed to disease severity after pandemic initiation. Here, we show that distinct mutations in the 2009 pandemic H1N1 virus genome have occurred with increased frequency after pandemic declaration. Among those, a mutation in the viral hemagglutinin was identified that increases 2009 pandemic H1N1 virus binding to human-like α2,6-linked sialic acids. Moreover, these mutations conferred increased viral replication in the respiratory tract and elevated respiratory droplet transmission between ferrets. Thus, our data show that 2009 H1N1 influenza viruses have evolved after pandemic onset giving rise to novel virus variants that enhance viral replicative fitness and respiratory droplet transmission in a mammalian animal model. These findings might help to improve surveillance efforts to assess the pandemic risk by emerging influenza viruses. PMID:27339001

  12. Multi-Scale Modeling of Cross-Linked Nanotube Materials

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Odegard, G. M.; Herzog, M. N.; Gates, T. S.; Fay, C. C.

    2005-01-01

    The effect of cross-linking single-walled carbon nanotubes on the Young's modulus of a nanotube-reinforced composite is modeled with a multi-scale method. The Young's modulus is predicted as a function of nanotube volume fraction and cross-link density. In this method, the constitutive properties of molecular representative volume elements are determined using molecular dynamics simulation and equivalent-continuum modeling. The Young's modulus is subsequently calculated for cross-linked nanotubes in a matrix which consists of the unreacted cross-linking agent. Two different cross-linking agents are used in this study, one that is short and rigid (Molecule A), and one that is long and flexible (Molecule B). Direct comparisons between the predicted elastic constants are made for the models in which the nanotubes are either covalently bonded or not chemically bonded to the cross-linking agent. At a nanotube volume fraction of 10%, the Young's modulus of Material A is not affected by nanotube crosslinking, while the Young's modulus of Material B is reduced by 64% when the nanotubes are cross-linked relative to the non-cross-linked material with the same matrix.

  13. Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus.

    PubMed

    Mathur, Chhavi; Savithri, Handanahal S

    2012-10-12

    Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity.

  14. Development and evaluation of a blocking enzyme-linked immunosorbent assay and virus neutralization assay to detect antibodies to viral hemorrhagic septicemia virus

    USGS Publications Warehouse

    Wilson, Anna; Goldberg, Tony; Marcquenski, Susan; Olson, Wendy; Goetz, Frederick; Hershberger, Paul; Hart, Lucas M.; Toohey-Kurth, Kathy

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) is a target of surveillance by many state and federal agencies in the United States. Currently, the detection of VHSV relies on virus isolation, which is lethal to fish and indicates only the current infection status. A serological method is required to ascertain prior exposure. Here, we report two serologic tests for VHSV that are nonlethal, rapid, and species independent, a virus neutralization (VN) assay and a blocking enzyme-linked immunosorbent assay (ELISA). The results show that the VN assay had a specificity of 100% and sensitivity of 42.9%; the anti-nucleocapsid-blocking ELISA detected nonneutralizing VHSV antibodies at a specificity of 88.2% and a sensitivity of 96.4%. The VN assay and ELISA are valuable tools for assessing exposure to VHSV.

  15. Development and Evaluation of a Blocking Enzyme-Linked Immunosorbent Assay and Virus Neutralization Assay To Detect Antibodies to Viral Hemorrhagic Septicemia Virus

    PubMed Central

    Wilson, Anna; Goldberg, Tony; Marcquenski, Susan; Olson, Wendy; Goetz, Frederick; Hershberger, Paul; Hart, Lucas

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) is a target of surveillance by many state and federal agencies in the United States. Currently, the detection of VHSV relies on virus isolation, which is lethal to fish and indicates only the current infection status. A serological method is required to ascertain prior exposure. Here, we report two serologic tests for VHSV that are nonlethal, rapid, and species independent, a virus neutralization (VN) assay and a blocking enzyme-linked immunosorbent assay (ELISA). The results show that the VN assay had a specificity of 100% and sensitivity of 42.9%; the anti-nucleocapsid-blocking ELISA detected nonneutralizing VHSV antibodies at a specificity of 88.2% and a sensitivity of 96.4%. The VN assay and ELISA are valuable tools for assessing exposure to VHSV. PMID:24429071

  16. Evaluation of disease and viral biomarkers as triggers for therapeutic intervention in respiratory mousepox - an animal model of smallpox.

    PubMed

    Parker, Scott; Chen, Nanhai G; Foster, Scott; Hartzler, Hollyce; Hembrador, Ed; Hruby, Dennis; Jordan, Robert; Lanier, Randall; Painter, George; Painter, Wesley; Sagartz, John E; Schriewer, Jill; Mark Buller, R

    2012-04-01

    The human population is currently faced with the potential use of natural or recombinant variola and monkeypox viruses as biological weapons. Furthermore, the emergence of human monkeypox in Africa and its expanding environs poses a significant natural threat. Such occurrences would require therapeutic and prophylactic intervention with antivirals to minimize morbidity and mortality of exposed populations. Two orally-bioavailable antivirals are currently in clinical trials; namely CMX001, an ether-lipid analog of cidofovir with activity at the DNA replication stage and ST-246, a novel viral egress inhibitor. Both of these drugs have previously been evaluated in the ectromelia/mousepox system; however, the trigger for intervention was not linked to a disease biomarker or a specific marker of virus replication. In this study we used lethal, intranasal, ectromelia virus infections of C57BL/6 and hairless SKH1 mice to model human disease and evaluate exanthematous rash (rash) as an indicator to initiate antiviral treatment. We show that significant protection can be provided to C57BL/6 mice by CMX001 or ST-246 when therapy is initiated on day 6 post infection or earlier. We also show that significant protection can be provided to SKH1 mice treated with CMX001 at day 3 post infection or earlier, but this is four or more days before detection of rash (ST-246 not tested). Although in this model rash could not be used as a treatment trigger, viral DNA was detected in blood by day 4 post infection and in the oropharyngeal secretions (saliva) by day 2-3 post infection - thus providing robust and specific markers of virus replication for therapy initiation. These findings are discussed in the context of current respiratory challenge animal models in use for the evaluation of poxvirus antivirals.

  17. Extended model of restricted beam for FSO links

    NASA Astrophysics Data System (ADS)

    Poliak, Juraj; Wilfert, Otakar

    2012-10-01

    Modern wireless optical communication systems in many aspects overcome wire or radio communications. Their advantages are license-free operation and broad bandwidth that they offer. The medium in free-space optical (FSO) links is the atmosphere. Operation of outdoor FSO links struggles with many atmospheric phenomena that deteriorate phase and amplitude of the transmitted optical beam. This beam originates in the transmitter and is affected by its individual parts, especially by the lens socket and the transmitter aperture, where attenuation and diffraction effects take place. Both of these phenomena unfavourable influence the beam and cause degradation of link availability, or its total malfunction. Therefore, both of these phenomena should be modelled and simulated, so that one can judge the link function prior to the realization of the system. Not only the link availability and reliability are concerned, but also economic aspects. In addition, the transmitted beam is not, generally speaking, circularly symmetrical, what makes the link simulation more difficult. In a comprehensive model, it is necessary to take into account the ellipticity of the beam that is restricted by circularly symmetrical aperture where then the attenuation and diffraction occur. General model is too computationally extensive; therefore simplification of the calculations by means of analytical and numerical approaches will be discussed. Presented model is not only simulated using computer, but also experimentally proven. One can then deduce the ability of the model to describe the reality and to estimate how far can one go with approximations, i.e. limitations of the model are discussed.

  18. ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS

    PubMed Central

    MIAO, HONGYU; XIA, XIAOHUA; PERELSON, ALAN S.; WU, HULIN

    2011-01-01

    Ordinary differential equations (ODE) are a powerful tool for modeling dynamic processes with wide applications in a variety of scientific fields. Over the last 2 decades, ODEs have also emerged as a prevailing tool in various biomedical research fields, especially in infectious disease modeling. In practice, it is important and necessary to determine unknown parameters in ODE models based on experimental data. Identifiability analysis is the first step in determing unknown parameters in ODE models and such analysis techniques for nonlinear ODE models are still under development. In this article, we review identifiability analysis methodologies for nonlinear ODE models developed in the past one to two decades, including structural identifiability analysis, practical identifiability analysis and sensitivity-based identifiability analysis. Some advanced topics and ongoing research are also briefly reviewed. Finally, some examples from modeling viral dynamics of HIV, influenza and hepatitis viruses are given to illustrate how to apply these identifiability analysis methods in practice. PMID:21785515

  19. Manipulators with flexible links: A simple model and experiments

    NASA Technical Reports Server (NTRS)

    Shimoyama, Isao; Oppenheim, Irving J.

    1989-01-01

    A simple dynamic model proposed for flexible links is briefly reviewed and experimental control results are presented for different flexible systems. A simple dynamic model is useful for rapid prototyping of manipulators and their control systems, for possible application to manipulator design decisions, and for real time computation as might be applied in model based or feedforward control. Such a model is proposed, with the further advantage that clear physical arguments and explanations can be associated with its simplifying features and with its resulting analytical properties. The model is mathematically equivalent to Rayleigh's method. Taking the example of planar bending, the approach originates in its choice of two amplitude variables, typically chosen as the link end rotations referenced to the chord (or the tangent) motion of the link. This particular choice is key in establishing the advantageous features of the model, and it was used to support the series of experiments reported.

  20. Viral Hemorrhagic Fevers

    MedlinePlus

    ... Related Links About VSPB (Viral Special Pathogens Branch) File Formats Help: How do I view different file formats (PDF, DOC, PPT, MPEG) on this site? Adobe PDF file Microsoft PowerPoint file Microsoft Word file Microsoft Excel ...

  1. Skew-normal/independent linear mixed models for censored responses with applications to HIV viral loads

    PubMed Central

    Bandyopadhyay, Dipankar; Lachos, Victor H.; Castro, Luis M.; Dey, Dipak K.

    2012-01-01

    Often in biomedical studies, the routine use of linear mixed-effects models (based on Gaussian assumptions) can be questionable when the longitudinal responses are skewed in nature. Skew-normal/elliptical models are widely used in those situations. Often, those skewed responses might also be subjected to some upper and lower quantification limits (viz. longitudinal viral load measures in HIV studies), beyond which they are not measurable. In this paper, we develop a Bayesian analysis of censored linear mixed models replacing the Gaussian assumptions with skew-normal/independent (SNI) distributions. The SNI is an attractive class of asymmetric heavy-tailed distributions that includes the skew-normal, the skew-t, skew-slash and the skew-contaminated normal distributions as special cases. The proposed model provides flexibility in capturing the effects of skewness and heavy tail for responses which are either left- or right-censored. For our analysis, we adopt a Bayesian framework and develop a MCMC algorithm to carry out the posterior analyses. The marginal likelihood is tractable, and utilized to compute not only some Bayesian model selection measures but also case-deletion influence diagnostics based on the Kullback-Leibler divergence. The newly developed procedures are illustrated with a simulation study as well as a HIV case study involving analysis of longitudinal viral loads. PMID:22685005

  2. Transposon mouse models to elucidate the genetic mechanisms of hepatitis B viral induced hepatocellular carcinoma

    PubMed Central

    Chiu, Amy P; Tschida, Barbara R; Lo, Lilian H; Moriarity, Branden S; Rowlands, Dewi K; Largaespada, David A; Keng, Vincent W

    2015-01-01

    The major type of human liver cancer is hepatocellular carcinoma (HCC), and there are currently many risk factors that contribute to this deadly disease. The majority of HCC occurrences are associated with chronic hepatitis viral infection, and hepatitis B viral (HBV) infection is currently a major health problem in Eastern Asia. Elucidating the genetic mechanisms associated with HBV-induced HCC has been difficult due to the heterogeneity and genetic complexity associated with this disease. A repertoire of animal models has been broadly used to study the pathophysiology and to develop potential treatment regimens for HBV-associated HCC. The use of these animal models has provided valuable genetic information and has been an important contributor to uncovering the factors involved in liver malignant transformation, invasion and metastasis. Recently, transposon-based mouse models are becoming more widely used in liver cancer research to interrogate the genome by forward genetics and also used to validate genes rapidly in a reverse genetic manner. Importantly, these transposon-based rapid reverse genetic mouse models could become crucial in testing potential therapeutic agents before proceeding to clinical trials in human. Therefore, this review will cover the use of transposon-based mouse models to address the problems of liver cancer, especially HBV-associated HCC occurrences in Asia. PMID:26576100

  3. Modelling and analysis of dynamics of viral infection of cells and of interferon resistance

    NASA Astrophysics Data System (ADS)

    Getto, Ph.; Kimmel, M.; Marciniak-Czochra, A.

    2008-08-01

    Interferons are active biomolecules, which help fight viral infections by spreading from infected to uninfected cells and activate effector molecules, which confer resistance from the virus on cells. We propose a new model of dynamics of viral infection, including endocytosis, cell death, production of interferon and development of resistance. The novel element is a specific biologically justified mechanism of interferon action, which results in dynamics different from other infection models. The model reflects conditions prevailing in liquid cultures (ideal mixing), and the absence of cells or virus influx from outside. The basic model is a nonlinear system of five ordinary differential equations. For this variant, it is possible to characterise global behaviour, using a conservation law. Analytic results are supplemented by computational studies. The second variant of the model includes age-of-infection structure of infected cells, which is described by a transport-type partial differential equation for infected cells. The conclusions are: (i) If virus mortality is included, the virus becomes eventually extinct and subpopulations of uninfected and resistant cells are established. (ii) If virus mortality is not included, the dynamics may lead to extinction of uninfected cells. (iii) Switching off the interferon defense results in a decrease of the sum total of uninfected and resistant cells. (iv) Infection-age structure of infected cells may result in stabilisation or destabilisation of the system, depending on detailed assumptions. Our work seems to constitute the first comprehensive mathematical analysis of the cell-virus-interferon system based on biologically plausible hypotheses.

  4. Combination therapy including CpG oligodeoxynucleotides and entecavir induces early viral response and enhanced inhibition of viral replication in a woodchuck model of chronic hepadnaviral infection.

    PubMed

    Meng, Zhongji; Zhang, Xiaoyong; Pei, Rongjuan; Zhang, Ejuan; Kemper, Thekla; Vollmer, Jörg; Davis, Heather L; Glebe, Dieter; Gerlich, Wolfram; Roggendorf, Michael; Lu, Mengji

    2016-01-01

    CpG oligodeoxynucleotides (ODNs) stimulate immune cells via TLR9 and are potentially useful immunomodulators for the treatment of chronic viral infections. In the present study, different classes of CpGs were tested for their capacities for innate immune activation and antiviral activities in the woodchuck model. A class P CpG ODN was found to stimulate interferon (IFN) production in woodchuck peripheral blood mononuclear cells (PBMCs) in vitro, and following subcutaneous administration in vivo, it was observed to induce IFN and MxA expression in woodchuck PBMCs. Combination treatment with CpG ODN and entecavir (ETV) led to effective suppression of the woodchuck hepatitis virus (WHV) load in the woodchucks, with early viral responses and inhibition of replication. The woodchuck hepatitis surface antigen (WHsAg) serum concentrations were strongly decreased by CpG and ETV together but not by either agent alone, indicating synergistic effects. However, viral control post-treatment was still transient, similar to that observed with ETV alone. Significantly elevated levels of serum aspartate aminotransferase (AST) but not of alanine aminotransferase (ALT) in some of the woodchucks receiving CpG ODN were noted, but these increases were resolved before the completion of treatment and were not associated with an elevated serum bilirubin level or coagulation disorders, suggesting the absence of a significant safety concern. PMID:26585244

  5. Modelling the role of immunity in reversion of viral antigenic sites.

    PubMed

    Chan, Carmen H S; Sanders, Lloyd P; Tanaka, Mark M

    2016-03-01

    Antigenic sites in viral pathogens exhibit distinctive evolutionary dynamics due to their role in evading recognition by host immunity. Antigenic selection is known to drive higher rates of non-synonymous substitution; less well understood is why differences are observed between viruses in their propensity to mutate to a novel or previously encountered amino acid. Here, we present a model to explain patterns of antigenic reversion and forward substitution in terms of the epidemiological and molecular processes of the viral population. We develop an analytical three-strain model and extend the analysis to a multi-site model to predict characteristics of observed sequence samples. Our model provides insight into how the balance between selection to escape immunity and to maintain viability is affected by the rate of mutational input. We also show that while low probabilities of reversion may be due to either a low cost of immune escape or slowly decaying host immunity, these two scenarios can be differentiated by the frequency patterns at antigenic sites. Comparison between frequency patterns of human influenza A (H3N2) and human RSV-A suggests that the increased rates of antigenic reversion in RSV-A is due to faster decaying immunity and not higher costs of escape. PMID:26723535

  6. Viral Hepatitis

    MedlinePlus

    ... Public Home » For Veterans and the Public Viral Hepatitis Menu Menu Viral Hepatitis Viral Hepatitis Home For ... the Public Veterans and Public Home How is Hepatitis C Treated? Find the facts about the newest ...

  7. Binding sites for the herpes simplex virus immediate-early protein ICP4 impose an increased dependence on viral DNA replication on simple model promoters located in the viral genome.

    PubMed

    Koop, K E; Duncan, J; Smiley, J R

    1993-12-01

    We examined the ability of binding sites for the herpes simplex virus immediate-early protein ICP4 to alter the regulation of closely linked promoters by placing strong ICP4 binding sites upstream or downstream of simple TATA promoters in the intact viral genome. We found that binding sites strongly reduced the levels of expression at early times postinfection and that this effect was partially overcome after the onset of viral DNA replication. These data confirm that DNA-bound ICP4 can inhibit the activity of a closely linked promoter and raise the possibility that ICP4 binding sites contribute to temporal regulation during infection.

  8. Unique N-linked glycosylation of CasBrE Env influences its stability, processing, and viral infectivity but not its neurotoxicity.

    PubMed

    Renszel, Krystal M; Traister, Russell S; Lynch, William P

    2013-08-01

    The envelope protein (Env) from the CasBrE murine leukemia virus (MLV) can cause acute spongiform neurodegeneration analogous to that induced by prions. Upon central nervous system (CNS) infection, Env is expressed as multiple isoforms owing to differential asparagine (N)-linked glycosylation. Because N-glycosylation can affect protein folding, stability, and quality control, we explored whether unique CasBrE Env glycosylation features could influence neurovirulence. CasBrE Env possesses 6/8 consensus MLV glycosylation sites (gs) but is missing gs3 and gs5 and contains a putative site (gs*). Twenty-nine mutants were generated by modifying these three sites, individually or in combination, to mimic the amino acid sequence in the nonneurovirulent Friend 57 MLV. Three basic viral phenotypes were observed: replication defective (dead; titer < 1 focus-forming unit [FFU]/ml), replication compromised (RC) (titer = 10(2) to 10(5) FFU/ml); and wild-type-like (WTL) (titer > 10(5) FFU/ml). Env protein was undetectable in dead mutants, while RC and WTL mutants showed variations in Env expression, processing, virus incorporation, virus entry, and virus spread. The newly introduced gs3 and gs5 sites were glycosylated, whereas gs* was not. Six WTL mutants tested in mice showed no clear attenuation in disease onset or severity versus controls. Furthermore, three RC viruses tested by neural stem cell (NSC)-mediated brainstem dissemination also induced acute spongiosis. Thus, while unique N-glycosylation affected structural features of Env involved in protein stability, proteolytic processing, and virus assembly and entry, these changes had minimal impact on CasBrE Env neurotoxicity. These findings suggest that the Env protein domains responsible for spongiogenesis represent highly stable elements upon which the more variable viral functional domains have evolved.

  9. Link Prediction in Weighted Networks: A Weighted Mutual Information Model

    PubMed Central

    Zhu, Boyao; Xia, Yongxiang

    2016-01-01

    The link-prediction problem is an open issue in data mining and knowledge discovery, which attracts researchers from disparate scientific communities. A wealth of methods have been proposed to deal with this problem. Among these approaches, most are applied in unweighted networks, with only a few taking the weights of links into consideration. In this paper, we present a weighted model for undirected and weighted networks based on the mutual information of local network structures, where link weights are applied to further enhance the distinguishable extent of candidate links. Empirical experiments are conducted on four weighted networks, and results show that the proposed method can provide more accurate predictions than not only traditional unweighted indices but also typical weighted indices. Furthermore, some in-depth discussions on the effects of weak ties in link prediction as well as the potential to predict link weights are also given. This work may shed light on the design of algorithms for link prediction in weighted networks. PMID:26849659

  10. Link Prediction in Weighted Networks: A Weighted Mutual Information Model.

    PubMed

    Zhu, Boyao; Xia, Yongxiang

    2016-01-01

    The link-prediction problem is an open issue in data mining and knowledge discovery, which attracts researchers from disparate scientific communities. A wealth of methods have been proposed to deal with this problem. Among these approaches, most are applied in unweighted networks, with only a few taking the weights of links into consideration. In this paper, we present a weighted model for undirected and weighted networks based on the mutual information of local network structures, where link weights are applied to further enhance the distinguishable extent of candidate links. Empirical experiments are conducted on four weighted networks, and results show that the proposed method can provide more accurate predictions than not only traditional unweighted indices but also typical weighted indices. Furthermore, some in-depth discussions on the effects of weak ties in link prediction as well as the potential to predict link weights are also given. This work may shed light on the design of algorithms for link prediction in weighted networks.

  11. Fine Mapping of Loci on BTA2 and BTA26 Associated with Bovine Viral Diarrhea Persistent Infection and Linked with Bovine Respiratory Disease in Cattle

    PubMed Central

    Zanella, Ricardo; Casas, Eduardo; Snowder, Gary; Neibergs, Holly L.

    2011-01-01

    Bovine respiratory disease (BRD) is considered to be the most costly infectious disease in the cattle industry. Bovine viral diarrhea virus (BVDV) is one of the pathogens involved with the BRD complex of disease. BVDV infection also negatively impacts cow reproduction and calf performance. Loci associated with persistently infected animals (BVD-PI) and linked with BRD have previously been identified near 14 Mb on bovine chromosome 2 (BTA2) and 15.3 Mb on bovine chromosome 26 (BTA26). The objective of this study was to refine the loci associated with BVD-PI and linked with BRD. Association testing for BVD-PI was performed on a population of 65 BVD-PI calves, 51 of their dams, and 60 unaffected calves (controls) with 142 single nucleotide polymorphisms (SNPs) on BTA2 and 173 SNPs on BTA26. Comparisons were made between BVD-PI calves and controls calves and the dams of BVD-PI calves and controls calves. For the linkage analysis of BRD, the same markers were used to genotype two half-sib families consisting of the sires and 72 BRD positive and 148 BRD negative offspring. Using an allelic chi-square test, 11 loci on BTA2 and 8 loci on BTA26 were associated with the dams of the BVD-PI calves (P < 0.05) and 4 loci on BTA2 and 11 loci on BTA26 were associated with BVD-PI calves. This demonstrates that although some of the loci on BTA2 and BTA26 are jointly involved in the fetal and dam response to BVD-PI infection, there are loci that are solely associated with the maternal or fetal susceptibility to disease. One locus on BTA2 and two loci on BTA26 were found to be linked (P < 0.05) with BRD. The regions linked with BRD were also associated with BVD-PI demonstrating that both the broad (BRD) and narrow (BVD-PI) definition of disease identified shared genomic regions as important in disease susceptibility. These results further refined the loci associated with BVD-PI and linked with BRD. PMID:22303376

  12. Link community detection using generative model and nonnegative matrix factorization.

    PubMed

    He, Dongxiao; Jin, Di; Baquero, Carlos; Liu, Dayou

    2014-01-01

    Discovery of communities in complex networks is a fundamental data analysis problem with applications in various domains. While most of the existing approaches have focused on discovering communities of nodes, recent studies have shown the advantages and uses of link community discovery in networks. Generative models provide a promising class of techniques for the identification of modular structures in networks, but most generative models mainly focus on the detection of node communities rather than link communities. In this work, we propose a generative model, which is based on the importance of each node when forming links in each community, to describe the structure of link communities. We proceed to fit the model parameters by taking it as an optimization problem, and solve it using nonnegative matrix factorization. Thereafter, in order to automatically determine the number of communities, we extend the above method by introducing a strategy of iterative bipartition. This extended method not only finds the number of communities all by itself, but also obtains high efficiency, and thus it is more suitable to deal with large and unexplored real networks. We test this approach on both synthetic benchmarks and real-world networks including an application on a large biological network, and compare it with two highly related methods. Results demonstrate the superior performance of our approach over competing methods for the detection of link communities.

  13. Linking knowledge and action through mental models of sustainable agriculture.

    PubMed

    Hoffman, Matthew; Lubell, Mark; Hillis, Vicken

    2014-09-01

    Linking knowledge to action requires understanding how decision-makers conceptualize sustainability. This paper empirically analyzes farmer "mental models" of sustainability from three winegrape-growing regions of California where local extension programs have focused on sustainable agriculture. The mental models are represented as networks where sustainability concepts are nodes, and links are established when a farmer mentions two concepts in their stated definition of sustainability. The results suggest that winegrape grower mental models of sustainability are hierarchically structured, relatively similar across regions, and strongly linked to participation in extension programs and adoption of sustainable farm practices. We discuss the implications of our findings for the debate over the meaning of sustainability, and the role of local extension programs in managing knowledge systems.

  14. Economic risk analysis model for bovine viral diarrhea virus biosecurity in cow-calf herds.

    PubMed

    Smith, Rebecca L; Sanderson, Michael W; Jones, Rodney; N'Guessan, Yapo; Renter, David; Larson, Robert; White, Brad J

    2014-03-01

    A stochastic model was designed to calculate the cost-effectiveness of biosecurity strategies for bovine viral diarrhea virus (BVDV) in cow-calf herds. Possible sources of BVDV introduction considered were imported animals, including the calves of pregnant imports, and fenceline contact with infected herds, including stocker cattle raised in adjacent pastures. Spread of BVDV through the herd was modeled with a stochastic SIR model. Financial consequences of BVDV, including lost income, treatment costs, and the cost of biosecurity strategies, were calculated for 10 years, based on the risks of a herd with a user-defined import profile. Results indicate that importing pregnant animals and stockers increased the financial risk of BVDV. Strategic testing in combination with vaccination most decreased the risk of high-cost outbreaks in most herds. The choice of a biosecurity strategy was specific to the risks of a particular herd.

  15. Link performance model for filter bank based multicarrier systems

    NASA Astrophysics Data System (ADS)

    Petrov, Dmitry; Oborina, Alexandra; Giupponi, Lorenza; Stitz, Tobias Hidalgo

    2014-12-01

    This paper presents a complete link level abstraction model for link quality estimation on the system level of filter bank multicarrier (FBMC)-based networks. The application of mean mutual information per coded bit (MMIB) approach is validated for the FBMC systems. The considered quality measure of the resource element for the FBMC transmission is the received signal-to-noise-plus-distortion ratio (SNDR). Simulation results of the proposed link abstraction model show that the proposed approach is capable of estimating the block error rate (BLER) accurately, even when the signal is propagated through the channels with deep and frequent fades, as it is the case for the 3GPP Hilly Terrain (3GPP-HT) and Enhanced Typical Urban (ETU) models. The FBMC-related results of link level simulations are compared with cyclic prefix orthogonal frequency division multiplexing (CP-OFDM) analogs. Simulation results are also validated through the comparison to reference publicly available results. Finally, the steps of link level abstraction algorithm for FBMC are formulated and its application for system level simulation of a professional mobile radio (PMR) network is discussed.

  16. Synthesis and characterization of new 5-linked pinoresinol lignin models.

    PubMed

    Yue, Fengxia; Lu, Fachuang; Sun, Runcang; Ralph, John

    2012-12-14

    Pinoresinol structures, featuring a β-β'-linkage between lignin monomer units, are important in softwood lignins and in dicots and monocots, particularly those that are downregulated in syringyl-specific genes. Although readily detected by NMR spectroscopy, pinoresinol structures largely escaped detection by β-ether-cleaving degradation analyses presumably due to the presence of the linkages at the 5 positions, in 5-5'- or 5-O-4'-structures. In this study, which is aimed at helping better understand 5-linked pinoresinol structures by providing the required data for NMR characterization, new lignin model compounds were synthesized through biomimetic peroxidase-mediated oxidative coupling reactions between pre-formed (free-phenolic) coniferyl alcohol 5-5'- or 5-O-4'-linked dimers and a coniferyl alcohol monomer. It was found that such dimers containing free-phenolic coniferyl alcohol moieties can cross-couple with the coniferyl alcohol producing pinoresinol-containing trimers (and higher oligomers) in addition to other homo- and cross-coupled products. Eight new lignin model compounds were obtained and characterized by NMR spectroscopy, and one tentatively identified cross-coupled β-O-4'-product was formed from a coniferyl alcohol 5-O-4'-linked dimer. It was demonstrated that the 5-5'- and 5-O-4'-linked pinoresinol structures could be readily differentiated by using heteronuclear multiple-bond correlation (HMBC) NMR spectroscopy. With appropriate modification (etherification or acetylation) to the newly obtained model compounds, it would be possible to identify the 5-5'- or 5-O-4'-linked pinoresinol structures in softwood lignins by 2D HMBC NMR spectroscopic methods. Identification of the cross-coupled dibenzodioxocin from a coniferyl alcohol 5-5'-linked moiety suggested that thioacidolysis or derivatization followed by reductive cleavage (DFRC) could be used to detect and identify whether the coniferyl alcohol itself undergoes 5-5'-cross-linking during

  17. Synthesis and characterization of new 5-linked pinoresinol lignin models.

    PubMed

    Yue, Fengxia; Lu, Fachuang; Sun, Runcang; Ralph, John

    2012-12-14

    Pinoresinol structures, featuring a β-β'-linkage between lignin monomer units, are important in softwood lignins and in dicots and monocots, particularly those that are downregulated in syringyl-specific genes. Although readily detected by NMR spectroscopy, pinoresinol structures largely escaped detection by β-ether-cleaving degradation analyses presumably due to the presence of the linkages at the 5 positions, in 5-5'- or 5-O-4'-structures. In this study, which is aimed at helping better understand 5-linked pinoresinol structures by providing the required data for NMR characterization, new lignin model compounds were synthesized through biomimetic peroxidase-mediated oxidative coupling reactions between pre-formed (free-phenolic) coniferyl alcohol 5-5'- or 5-O-4'-linked dimers and a coniferyl alcohol monomer. It was found that such dimers containing free-phenolic coniferyl alcohol moieties can cross-couple with the coniferyl alcohol producing pinoresinol-containing trimers (and higher oligomers) in addition to other homo- and cross-coupled products. Eight new lignin model compounds were obtained and characterized by NMR spectroscopy, and one tentatively identified cross-coupled β-O-4'-product was formed from a coniferyl alcohol 5-O-4'-linked dimer. It was demonstrated that the 5-5'- and 5-O-4'-linked pinoresinol structures could be readily differentiated by using heteronuclear multiple-bond correlation (HMBC) NMR spectroscopy. With appropriate modification (etherification or acetylation) to the newly obtained model compounds, it would be possible to identify the 5-5'- or 5-O-4'-linked pinoresinol structures in softwood lignins by 2D HMBC NMR spectroscopic methods. Identification of the cross-coupled dibenzodioxocin from a coniferyl alcohol 5-5'-linked moiety suggested that thioacidolysis or derivatization followed by reductive cleavage (DFRC) could be used to detect and identify whether the coniferyl alcohol itself undergoes 5-5'-cross-linking during

  18. Linking knowledge and action through mental models of sustainable agriculture

    PubMed Central

    Hoffman, Matthew; Lubell, Mark; Hillis, Vicken

    2014-01-01

    Linking knowledge to action requires understanding how decision-makers conceptualize sustainability. This paper empirically analyzes farmer “mental models” of sustainability from three winegrape-growing regions of California where local extension programs have focused on sustainable agriculture. The mental models are represented as networks where sustainability concepts are nodes, and links are established when a farmer mentions two concepts in their stated definition of sustainability. The results suggest that winegrape grower mental models of sustainability are hierarchically structured, relatively similar across regions, and strongly linked to participation in extension programs and adoption of sustainable farm practices. We discuss the implications of our findings for the debate over the meaning of sustainability, and the role of local extension programs in managing knowledge systems. PMID:25157158

  19. Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

    SciTech Connect

    Mathur, Chhavi; Savithri, Handanahal S.

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer Pepper vein banding potyvirus VPg harbors Walker motifs. Black-Right-Pointing-Pointer VPg exhibits ATPase activity in the presence of NIa-Pro. Black-Right-Pointing-Pointer Plausible structural and functional interplay between VPg and NIa-Pro. Black-Right-Pointing-Pointer Functional relevance of prolonged presence of VPg-Pro during infection. -- Abstract: Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity.

  20. A model to study viral and cytokine involvement in Sjögren's syndrome.

    PubMed

    Clark, D A; Lamey, P J; Jarrett, R F; Onions, D E

    1994-01-01

    To investigate mechanisms that may be important in the pathogenesis of Sjögren's syndrome (SS) we developed a protocol for the growth of salivary gland epithelial cells in culture. We examined the effect that viral infection has on the cellular location of the autoantigen La. Autoantibodies to La are common in SS and it has been proposed that viral infection may result in cell membrane expression of La. Co-expression of MHC class II molecules in infected cells could lead to the presentation of La peptides to the immune system. Advenovirus infection of salivary gland epithelial cells resulted in an altered nuclear staining of La. Treatment with interferon-gamma resulted in the expression of La in the cell cytoplasm and HLA-DR molecules at the cell surface. These findings suggest that a cytokine-driven mechanism may generate an autoimmune response to La in SS. Using the polymerase chain reaction (PCR) we tested salivary gland epithelial cell cultures for the presence of human herpesvirus-6 (HHV-6) and Epstein-Barr virus (EBV). Only HHV-6 was detected in 2 of 10 salivary gland epithelial cell cultures although the presence of HHV-6 was not associated with SS. Primary salivary gland cultures may prove useful as an in vitro model to study mechanisms of autoimmunity in SS. PMID:7999958

  1. Application of a patient-derived xenograft model in cytolytic viral activation therapy for nasopharyngeal carcinoma.

    PubMed

    Hsu, Cheng-Lung; Kuo, Yung-Chia; Huang, Yenlin; Huang, Yin-Cheng; Lui, Kar-Wai; Chang, Kai-Ping; Lin, Tung-Liang; Fan, Hsien-Chi; Lin, An-Chi; Hsieh, Chia-Hsun; Lee, Li-Yu; Wang, Hung-Ming; Li, Hsin-Pai; Chang, Yu-Sun

    2015-10-13

    Nasopharyngeal carcinoma (NPC) is an Epstein Barr virus (EBV)-related malignancy in which the tumor microenvironment plays a pivotal role in tumor progression. Here, we developed two patient-derived xenograft (PDX) mouse lines from engrafted NPC metastatic tumors. Positive staining for EBV-encoded small RNAs confirmed that these tumors harbored EBV, and gene expression profile analyses further showed that the PDX was highly similar to the primary parent tumor. In vivo drug screening using the PDX system demonstrated that gemcitabine had the best antitumor effect among the tested drugs. The donor of this PDX also showed excellent responsiveness to gemcitabine treatment. The combination of gemcitabine and valproic acid exerted synergistic antitumor effects. Further addition of ganciclovir to this two-drug combination regimen enhanced cytolytic viral activation, yielding the best antitumor response among tested regimens. Treatment with this three-drug combination regimen decreased plasma EBV-DNA load, tumor viral concentration, and the number of viable tumor cells to a greater extent than the two-drug gemcitabine and valproic acid combination. These results highlight the value of PDX models in the development of EBV-targeted strategies to treat NPC.

  2. Model selection for athermal cross-linked fiber networks.

    PubMed

    Shahsavari, A; Picu, R C

    2012-07-01

    Athermal random fiber networks are usually modeled by representing each fiber as a truss, a Euler-Bernoulli or a Timoshenko beam, and, in the case of cross-linked networks, each cross-link as a pinned, rotating, or welded joint. In this work we study the effect of these various modeling options on the dependence of the overall network stiffness on system parameters. We conclude that Timoshenko beams can be used for the entire range of density and beam stiffness parameters, while the Euler-Bernoulli model can be used only at relatively low network densities. In the high density-high bending stiffness range, strain energy is stored predominantly in the axial and shear deformation modes, while in the other extreme range of parameters, the energy is stored in the bending mode. The effect of the model size on the network stiffness is also discussed. PMID:23005468

  3. Single photon time transfer link model for GNSS satellites

    NASA Astrophysics Data System (ADS)

    Vacek, Michael; Michalek, Vojtech; Peca, Marek; Prochazka, Ivan; Blazej, Josef

    2015-05-01

    The importance of optical time transfer serving as a complement to traditional microwave links, has been attested for GNSSes and for scientific missions. Single photon time transfer (SPTT) is a process, allowing to compare (subtract) time readings of two distant clocks. Such a comparison may be then used to synchronize less accurate clock to a better reference, to perform clock characterization and calibration, to calculate mean time out of ensemble of several clocks, displaced in space. The single-photon time transfer is well established in field of space geodesy, being supported by passive retro-reflectors within space segment of five known GNSSes. A truly two-way, active terminals work aboard of Jason-2 (T2L2) - multiphoton operation, GNSS Beidou (Compass) - SPTT, and are going to be launched within recent ACES project (ELT) - SPTT, and GNSS GLONASS - multiphoton operation. However, there is still missing comprehensive theoretical model of two-way (using satellite receiver and retroreflector) SPTT link incorporating all crucial parameters of receiver (both ground and space segment receivers), transmitter, atmosphere effects on uplink and downlink path, influence of retroreflector. The input to calculation of SPTT link performance will be among others: link budget (distance, power, apertures, beam divergence, attenuation, scattering), propagating medium (atmosphere scintillation, beam wander, etc.), mutual Tx/Rx velocity, wavelength. The SPTT model will be evaluated without the properties of real components. These will be added in the further development. The ground-to-space SPTT link performance of typical scenarios are modeled. This work is a part of the ESA study "Comparison of optical time-transfer links."

  4. An individual-based model of rabbit viral haemorrhagic disease on European wild rabbits (Oryctolagus cuniculus)

    USGS Publications Warehouse

    Fa, John E.; Sharples, Colin M.; Bell, Diana J.; DeAngelis, Donald L.

    2001-01-01

    We developed an individual-based model of Rabbit Viral Hemorrhagic Disease (RVHD) for European wild rabbits (Oryctolagus cuniculus L.), representing up to 1000 rabbits in four hectares. Model output for productivity and recruitment matched published values. The disease was density-dependent and virulence affected outcome. Strains that caused death after several days produced greater overall mortality than strains in which rabbits either died or recovered very quickly. Disease effect also depended on time of year. We also elaborated a larger scale model representing 25 km2 and 100,000+ rabbits, split into a number of grid-squares. This was a more traditional model that did not represent individual rabbits, but employed a system of dynamic equations for each grid-square. Disease spread depended on probability of transmission between neighboring grid-squares. Potential recovery from a major population crash caused by the disease relied on disease virulence and frequency of recurrence. The model's dependence on probability of disease transmission between grid-squares suggests the way that the model represents the spatial distribution of the population affects simulation. Although data on RVHD in Europe are lacking, our models provide a basis for describing the disease in realistic detail and for assessing influence of various social and spatial factors on spread.

  5. Modeling Viral Infectious Diseases and Development of Antiviral Therapies Using Human Induced Pluripotent Stem Cell-Derived Systems

    PubMed Central

    Trevisan, Marta; Sinigaglia, Alessandro; Desole, Giovanna; Berto, Alessandro; Pacenti, Monia; Palù, Giorgio; Barzon, Luisa

    2015-01-01

    The recent biotechnology breakthrough of cell reprogramming and generation of induced pluripotent stem cells (iPSCs), which has revolutionized the approaches to study the mechanisms of human diseases and to test new drugs, can be exploited to generate patient-specific models for the investigation of host–pathogen interactions and to develop new antimicrobial and antiviral therapies. Applications of iPSC technology to the study of viral infections in humans have included in vitro modeling of viral infections of neural, liver, and cardiac cells; modeling of human genetic susceptibility to severe viral infectious diseases, such as encephalitis and severe influenza; genetic engineering and genome editing of patient-specific iPSC-derived cells to confer antiviral resistance. PMID:26184286

  6. Modeling Viral Infectious Diseases and Development of Antiviral Therapies Using Human Induced Pluripotent Stem Cell-Derived Systems.

    PubMed

    Trevisan, Marta; Sinigaglia, Alessandro; Desole, Giovanna; Berto, Alessandro; Pacenti, Monia; Palù, Giorgio; Barzon, Luisa

    2015-07-01

    The recent biotechnology breakthrough of cell reprogramming and generation of induced pluripotent stem cells (iPSCs), which has revolutionized the approaches to study the mechanisms of human diseases and to test new drugs, can be exploited to generate patient-specific models for the investigation of host-pathogen interactions and to develop new antimicrobial and antiviral therapies. Applications of iPSC technology to the study of viral infections in humans have included in vitro modeling of viral infections of neural, liver, and cardiac cells; modeling of human genetic susceptibility to severe viral infectious diseases, such as encephalitis and severe influenza; genetic engineering and genome editing of patient-specific iPSC-derived cells to confer antiviral resistance.

  7. A murine model of coxsackievirus A16 infection for anti-viral evaluation.

    PubMed

    Liu, Qingwei; Shi, Jinping; Huang, Xulin; Liu, Fei; Cai, Yicun; Lan, Ke; Huang, Zhong

    2014-05-01

    Coxsackievirus A16 (CA16) is one of the main causative agents of hand, foot and mouth disease (HFMD), which is a common infectious disease in children. CA16 infection may lead to severe nervous system damage and even death in humans. However, study of the pathogenesis of CA16 infection and development of vaccines and anti-viral agents are hindered partly by the lack of an appropriate small animal model. In the present study, we developed and characterized a murine model of CA16 infection. We show that neonatal mice are susceptible to CA16 infection via intraperitoneal inoculation. One-day-old mice infected with 2×10(6)TCID50 of CA16/SZ05 strain consistently exhibited clinical signs, including reduced mobility, and limb weakness and paralysis. About 57% of the mice died within 14days after infection. Significant damage in the brainstem, limb muscles and intestines of the infected mice in the moribund state was observed by histological examination, and the presence of CA16 in neurons of the brainstem was demonstrated by immunohistochemical staining with a CA16-specific polyclonal antibody, strongly suggesting the involvement of the central nervous system in CA16 infection. Analysis of virus titers in various organs/tissues collected at 3, 6 and 9days post-infection, showed that skeletal muscle was the major site of virus replication at the early stage of infection, while the virus mainly accumulated in the brain at the late stage. In addition, susceptibility of mice to CA16 infection was found to be age dependent. Moreover, different CA16 strains could exhibit varied virulence in vivo. Importantly, we demonstrated that post-exposure treatment with an anti-CA16 monoclonal antibody fully protected mice against lethal CA16 infection. Collectively, these results indicate the successful development of a CA16 infection mouse model for anti-viral evaluation. PMID:24583030

  8. Viral Disease Networks?

    NASA Astrophysics Data System (ADS)

    Gulbahce, Natali; Yan, Han; Vidal, Marc; Barabasi, Albert-Laszlo

    2010-03-01

    Viral infections induce multiple perturbations that spread along the links of the biological networks of the host cells. Understanding the impact of these cascading perturbations requires an exhaustive knowledge of the cellular machinery as well as a systems biology approach that reveals how individual components of the cellular system function together. Here we describe an integrative method that provides a new approach to studying virus-human interactions and its correlations with diseases. Our method involves the combined utilization of protein - protein interactions, protein -- DNA interactions, metabolomics and gene - disease associations to build a ``viraldiseasome''. By solely using high-throughput data, we map well-known viral associated diseases and predict new candidate viral diseases. We use microarray data of virus-infected tissues and patient medical history data to further test the implications of the viral diseasome. We apply this method to Epstein-Barr virus and Human Papillomavirus and shed light into molecular development of viral diseases and disease pathways.

  9. Model updating in flexible-link multibody systems

    NASA Astrophysics Data System (ADS)

    Belotti, R.; Caneva, G.; Palomba, I.; Richiedei, D.; Trevisani, A.

    2016-09-01

    The dynamic response of flexible-link multibody systems (FLMSs) can be predicted through nonlinear models based on finite elements, to describe the coupling between rigid- body and elastic behaviour. Their accuracy should be as high as possible to synthesize controllers and observers. Model updating based on experimental measurements is hence necessary. By taking advantage of the experimental modal analysis, this work proposes a model updating procedure for FLMSs and applies it experimentally to a planar robot. Indeed, several peculiarities of the model of FLMS should be carefully tackled. On the one hand, nonlinear models of a FLMS should be linearized about static equilibrium configurations. On the other, the experimental mode shapes should be corrected to be consistent with the elastic displacements represented in the model, which are defined with respect to a fictitious moving reference (the equivalent rigid link system). Then, since rotational degrees of freedom are also represented in the model, interpolation of the experimental data should be performed to match the model displacement vector. Model updating has been finally cast as an optimization problem in the presence of bounds on the feasible values, by also adopting methods to improve the numerical conditioning and to compute meaningful updated inertial and elastic parameters.

  10. Tailored delivery of analgesic ziconotide across a blood brain barrier model using viral nanocontainers

    NASA Astrophysics Data System (ADS)

    Anand, Prachi; O'Neil, Alison; Lin, Emily; Douglas, Trevor; Holford, Mandë

    2015-08-01

    The blood brain barrier (BBB) is often an insurmountable obstacle for a large number of candidate drugs, including peptides, antibiotics, and chemotherapeutic agents. Devising an adroit delivery method to cross the BBB is essential to unlocking widespread application of peptide therapeutics. Presented here is an engineered nanocontainer for delivering peptidic drugs across the BBB encapsulating the analgesic marine snail peptide ziconotide (Prialt®). We developed a bi-functional viral nanocontainer based on the Salmonella typhimurium bacteriophage P22 capsid, genetically incorporating ziconotide in the interior cavity, and chemically attaching cell penetrating HIV-Tat peptide on the exterior of the capsid. Virus like particles (VLPs) of P22 containing ziconotide were successfully transported in several BBB models of rat and human brain microvascular endothelial cells (BMVEC) using a recyclable noncytotoxic endocytic pathway. This work demonstrates proof in principle for developing a possible alternative to intrathecal injection of ziconotide using a tunable VLP drug delivery nanocontainer to cross the BBB.

  11. Tailored delivery of analgesic ziconotide across a blood brain barrier model using viral nanocontainers

    PubMed Central

    Anand, Prachi; O’Neil, Alison; Lin, Emily; Douglas, Trevor; Holford, Mandë

    2015-01-01

    The blood brain barrier (BBB) is often an insurmountable obstacle for a large number of candidate drugs, including peptides, antibiotics, and chemotherapeutic agents. Devising an adroit delivery method to cross the BBB is essential to unlocking widespread application of peptide therapeutics. Presented here is an engineered nanocontainer for delivering peptidic drugs across the BBB encapsulating the analgesic marine snail peptide ziconotide (Prialt®). We developed a bi-functional viral nanocontainer based on the Salmonella typhimurium bacteriophage P22 capsid, genetically incorporating ziconotide in the interior cavity, and chemically attaching cell penetrating HIV-Tat peptide on the exterior of the capsid. Virus like particles (VLPs) of P22 containing ziconotide were successfully transported in several BBB models of rat and human brain microvascular endothelial cells (BMVEC) using a recyclable noncytotoxic endocytic pathway. This work demonstrates proof in principle for developing a possible alternative to intrathecal injection of ziconotide using a tunable VLP drug delivery nanocontainer to cross the BBB. PMID:26234920

  12. Complex dynamic behavior in a viral model with delayed immune response

    NASA Astrophysics Data System (ADS)

    Wang, Kaifa; Wang, Wendi; Pang, Haiyan; Liu, Xianning

    2007-02-01

    The rich dynamics of a viral infection model is studied under the assumption that the immune response is retarded. It is shown that if the basic reproductive ratio of the virus is less than one, the infection-free equilibrium is globally asymptotically stable. Analytical and numerical results show that if the basic reproductive ratio of the virus is greater than one, the combined effect of the strength of the lytic component, the time delay of the immune response and the birth rate of susceptible host cells is to create a rich dynamics, which includes the occurrence of stable periodic solutions and chaotic dynamical behavior. The route from periodic oscillations to chaos is investigated. These results can be used to explain irregular real time series data on the immune state of patients.

  13. Tailored delivery of analgesic ziconotide across a blood brain barrier model using viral nanocontainers.

    PubMed

    Anand, Prachi; O'Neil, Alison; Lin, Emily; Douglas, Trevor; Holford, Mandë

    2015-01-01

    The blood brain barrier (BBB) is often an insurmountable obstacle for a large number of candidate drugs, including peptides, antibiotics, and chemotherapeutic agents. Devising an adroit delivery method to cross the BBB is essential to unlocking widespread application of peptide therapeutics. Presented here is an engineered nanocontainer for delivering peptidic drugs across the BBB encapsulating the analgesic marine snail peptide ziconotide (Prialt®). We developed a bi-functional viral nanocontainer based on the Salmonella typhimurium bacteriophage P22 capsid, genetically incorporating ziconotide in the interior cavity, and chemically attaching cell penetrating HIV-Tat peptide on the exterior of the capsid. Virus like particles (VLPs) of P22 containing ziconotide were successfully transported in several BBB models of rat and human brain microvascular endothelial cells (BMVEC) using a recyclable noncytotoxic endocytic pathway. This work demonstrates proof in principle for developing a possible alternative to intrathecal injection of ziconotide using a tunable VLP drug delivery nanocontainer to cross the BBB. PMID:26234920

  14. Varying initial-link and terminal-link durations in concurrent-chains schedules: a comparison of three models.

    PubMed

    Mazur, James E

    2004-06-30

    In Experiment 1, pigeons responded on concurrent-chains schedules with equal variable-interval schedules as initial links and fixed delays to food as terminal links. One terminal-link delay was always three times as long as the other. As terminal-link delays increased, response percentages on the key with the shorter terminal link increased according to a curvilinear function. This result supported the predictions of the hyperbolic value-added model and the contextual-choice theory but not delay-reduction theory. In Experiment 2, the terminal links were always delays of 2s and 12s, followed by food, and the durations of the initial links varied across conditions. As initial-link durations increased, pigeons' response percentages on the key with the shorter terminal link decreased, but toward an asymptote greater than 50%, indicating a continued preference for the shorter terminal link with very long initial links. This result was more consistent with the predictions of the hyperbolic-value added model than with those of the contextual-choice model or of delay-reduction theory.

  15. UAS Modeling of the Communication Links Study Results

    NASA Technical Reports Server (NTRS)

    Birr, Richard B.; Girgis, Nancy; Murray, Jennifer

    2011-01-01

    The Federal Aviation Administration (FAA) is the authority that grants access into, and operations within, the National Airspace System (NAS) for all aircraft, including Unmanned Aircraft Systems (UAS). The safe operation of UAS in the NAS must be assured if the full potential of UAS is to be realized and supported by the public and Congress. This report analyzed the communication systems that are needed for the safe operations of UAS in the NAS. Safe operations can be defined as the availability of the required links to carry the information to control the UAS and the return links to allow controllers to know where the UAS is at any given moment as well as how it is performing. This report is the end result of work performed jointly between the FAA and National Aeronautics and Space Administration (NASA)/Kennedy Space Center (NASA KSC). The work was done in support of the Radio Technical Commission for Aeronautics (RTCA) Special Committee 203 (SC-203) Control and Communications Working Group. The RTCA is a federal advisory committee to the FAA. Though the work was not under the direction of the working group, a large part of the specific values used in the simulations came from the working group. Specifically, all of the radio links were modeled based on the formulation completed by the working group. This report analyzed three scenarios from RTCA SC-203 that represent how a UAS would operate in the NAS. Each scenario was created using the Satellite Tool Kit (STK) modeling and simulation tool. The flight paths of the UAS were generated and the UAS dynamics were likewise modeled. Then each communication asset such as transmitters, receivers, and antennas were modeled and placed on the appropriate UAS, satellite, or Control Station (CS). After that, the radio links were analyzed for signal strength and antenna blockage, and the overall link performance was analyzed in detail. The goal was to obtain 99.9% availability on all of the radio communication links. In order

  16. Viral Entry into Cells

    NASA Astrophysics Data System (ADS)

    D'Orsogna, Maria R.

    2010-09-01

    Successful viral infection of a healthy cell requires complex host-pathogen interactions. In this talk we focus on the dynamics specific to the HIV virus entering a eucaryotic cell. We model viral entry as a stochastic engagement of receptors and coreceptors on the cell surface. We also consider the transport of virus material to the cell nucleus by coupling microtubular motion to the concurrent biochemical transformations that render the viral material competent for nuclear entry. We discuss both mathematical and biological consequences of our model, such as the formulation of an effective integrodifferential boundary condition embodying a memory kernel and optimal timing in maximizing viral probabilities.

  17. Viral persistence, latent reservoir, and blips: a review on HIV-1 dynamics and modeling during HAART and related treatment implications

    SciTech Connect

    Rong, Libin; Perelson, Alan

    2008-01-01

    HIV-1 eradication from infected individuals has not been achieved with the use of highly active antiretroviral therapy (HAART) for a prolonged period of time. The cellular reservoir for HIV-1 in resting memory CD4{sup +} T cells remains a major obstacle to viral elimination. The reservoir does not decay significantly over long periods of time as is able to release replication competent HIV-1 upon cell activation. Residual ongoing viral replication may likely occur in many patients because low levels of virus can be detected in plasma by sensitive assays and transient episodes of viremia, or HIV-1 blips, are often observed in patients even with successful viral suppression for many years. Here we review our current knowledge of the factors contributing to viral persistence, the latent reservoir, and blips, and mathematical models developed to explore them and their relationships. We show how mathematical modeling can help improve our understanding of HIV-1 dynamics in patients on HAART and the quantitative events underlying HIV-1 latency, reservoir stability, low-level viremic persistence, and emergence of intermittent viral blips. We also discuss treatment implications related to these studies.

  18. Bench-to-bedside review: Rare and common viral infections in the intensive care unit – linking pathophysiology to clinical presentation

    PubMed Central

    Stollenwerk, Nicholas; Harper, Richart W; Sandrock, Christian E

    2008-01-01

    Viral infections are common causes of respiratory tract disease in the outpatient setting but much less common in the intensive care unit. However, a finite number of viral agents cause respiratory tract disease in the intensive care unit. Some viruses, such as influenza, respiratory syncytial virus (RSV), cytomegalovirus (CMV), and varicella-zoster virus (VZV), are relatively common. Others, such as adenovirus, severe acute respiratory syndrome (SARS)-coronavirus, Hantavirus, and the viral hemorrhagic fevers (VHFs), are rare but have an immense public health impact. Recognizing these viral etiologies becomes paramount in treatment, infection control, and public health measures. Therefore, a basic understanding of the pathogenesis of viral entry, replication, and host response is important for clinical diagnosis and initiating therapeutic options. This review discusses the basic pathophysiology leading to clinical presentations in a few common and rare, but important, viruses found in the intensive care unit: influenza, RSV, SARS, VZV, adenovirus, CMV, VHF, and Hantavirus. PMID:18671826

  19. Viral pneumonia.

    PubMed

    Greenberg, S B

    1991-09-01

    Viral pneumonias are common in infants and young children but rare in adults. Respiratory syncytial virus (RSV) and para-influenza viruses are the most frequent viral pathogens in infants and children. Influenza virus types A and B account for over one half of viral pneumonias in adults. Immunocompromised hosts are susceptible to pneumonias caused by cytomegalovirus (CMV) and other herpesviruses, as well as rubeola and adenovirus. Diagnosis of viral pneumonia depends on appropriate viral cultures and acute and convalescent sera for specific antibodies. Superinfection with bacteria is common in adults. Anti-viral therapy is available for several respiratory viruses. Ribavirin, amantadine/rimantadine, interferon alpha, and acyclovir are antiviral drugs that may be of benefit in treatment and prophylaxis. Prevention of viral pneumonia will depend upon improved viral immunization practices.

  20. Loci on Bos taurus chromosome 2 and Bos taurus chromosome 26 are linked with bovine respiratory disease and associated with persistent infection of bovine viral diarrhea virus.

    PubMed

    Neibergs, H; Zanella, R; Casas, E; Snowder, G D; Wenz, J; Neibergs, J S; Moore, D

    2011-04-01

    The objective of this study was to identify loci linked with bovine respiratory disease (BRD) and subsequently to determine if these same loci were associated with bovine viral diarrhea virus persistent infection (BVD-PI) in affected calves or their dams. A genome-wide linkage study using 312 microsatellites was conducted to identify loci linked with BRD in a Brahman × Hereford sire half-sib family. Disease incidence was recorded from birth to slaughter by daily monitoring. Linkage was suggestive for a QTL on BTA2 (F = 7.31, P = 0.007) and BTA26 (F = 10.46, P = 0.001). Six and 7 markers were added and genotyped between 110 and 126 cM on BTA2 and between 42 and 72 cM on BTA26, respectively, in the intervals where linkage was found. These markers were used to reevaluate the Brahman × Hereford family and to evaluate 3 additional crossbred half-sib families. Linkage was found with BRD on BTA2 (F = 4.94, P < 0.01), with a peak at 110 cM, and on BTA26 (F = 4.03, P < 0.05), with peaks at 42 and 52 cM. The same markers were then tested for an association with BVD-PI in 1) BVD-PI calves compared with age-matched unaffected calves from the same herd or 2) dams with BVD-PI compared with age-matched unaffected calves. Sixty commercial beef cow-calf herds were tested for BVD-PI, and 79 calves from 8 ranches had BVD-PI. Four of 6 markers were associated (P = 4.8 × 10(-9) to P = 0.01) with BVD-PI on BTA2, and 4 of 7 markers were associated (P = 0.008 to P = 0.04) with BVD-PI on BTA26 when BVD-PI calves were compared with unaffected calves. The comparison of BVD-PI dams with unaffected calves detected associations with BVD-PI for all markers tested on BTA2 (P = 3 × 10(-9) to P = 0.005) and for 3 of 7 markers on BTA26 (P = 1.4 × 10(-6) to P = 0.006).

  1. Viral pneumonia

    MedlinePlus

    ... Names Pneumonia - viral; "Walking pneumonia" - viral Images Lungs Respiratory system References Lee FE, Treanor J. Viral infections. In: Mason RJ, VC Broaddus, Martin TR, et al, eds. Murray and Nadel’s Textbook of Respiratory Medicine . 5th ed. Philadelphia, PA: Saunders Elsevier; 2010: ...

  2. Global stability of a multiple delayed viral infection model with general incidence rate and an application to HIV infection.

    PubMed

    Ji, Yu

    2015-06-01

    In this paper, the dynamical behavior of a viral infection model with general incidence rate and two time delays is studied. By using the Lyapunov functional and LaSalle invariance principle, the global stabilities of the infection-free equilibrium and the endemic equilibrium are obtained. We obtain a threshold of the global stability for the uninfected equilibrium, which means the disease will be under control eventually. These results can be applied to a variety of viral infections of disease that would make it possible to devise optimal treatment strategies. Numerical simulations with application to HIV infection are given to verify the analytical results.

  3. The Cotton Rat Model of Respiratory Viral Infections Pathogenesis and Immunity

    PubMed Central

    Boukhvalova, Marina S.; Prince, Gregory A.; Blanco, Jorge C.G.

    2010-01-01

    Development of successful vaccines against human infectious diseases depends on using appropriate animal models for testing vaccine efficacy and safety. For some viral infections the task is further complicated by the frequently changing genetic make-up of the virus, as in the case of influenza, or by the existence of the little-understood phenomenon of vaccine-enhanced disease, as in the case of respiratory syncytial virus (RSV). The cotton rat S.hispidus has been used for years as an excellent small animal model of the RSV vaccine-enhanced disease. Recently, using cotton rats, we have demonstrated that vaccination against another paramyxovirus, human metapneumovirus (hMPV), can also lead to vaccine-enhanced disease. In addition to the study of paramyxoviruses, S.hispidus presents important advantages for the study of orthomyxoviruses such as influenza. The cotton rat is succeptible to infection with unadapted human influenza strains, and heterosubtypic immunity to influenza can be evoked in S.hispidus. The mechanisms of influenza, RSV, and hMPV pathogenesis and immunity can now be investigated in the cotton rat with the development of species-specific reagents for this animal model. PMID:19394861

  4. Next Generation Respiratory Viral Vaccine System: Advanced and Emerging Bioengineered Human Lung Epithelia Model (HLEM) Organoid Technology

    NASA Technical Reports Server (NTRS)

    Goodwin, Thomas J.; Schneider, Sandra L.; MacIntosh, Victor; Gibbons, Thomas F.

    2010-01-01

    Acute respiratory infections, including pneumonia and influenza, are the S t" leading cause of United States and worldwide deaths. Newly emerging pathogens signaled the need for an advanced generation of vaccine technology.. Human bronchial-tracheal epithelial tissue was bioengineered to detect, identify, host and study the pathogenesis of acute respiratory viral disease. The 3-dimensional (3D) human lung epithelio-mesechymal tissue-like assemblies (HLEM TLAs) share characteristics with human respiratory epithelium: tight junctions, desmosomes, microvilli, functional markers villin, keratins and production of tissue mucin. Respiratory Syntial Virus (RSV) studies demonstrate viral growth kinetics and membrane bound glycoproteins up to day 20 post infection in the human lung-orgainoid infected cell system. Peak replication of RSV occurred on day 10 at 7 log10 particles forming units per ml/day. HLEM is an advanced virus vaccine model and biosentinel system for emergent viral infectious diseases to support DoD global surveillance and military readiness.

  5. Modeling chronic hepatitis B or C virus infection during antiviral therapy using an analogy to enzyme kinetics: long-term viral dynamics without rebound and oscillation.

    PubMed

    Takayanagi, Toshiaki

    2013-12-01

    The basic model for chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infection during therapy enables us to analyze short-term viral kinetics. However, the model is not useful for analyzing long-term viral kinetics. Here, I suggest a new model that was obtained by introducing Michaelis-Menten kinetics into the basic model. The new model can exhibit long-term viral kinetics without rebound and oscillation, unlike the basic model. The value of the parameter K in the new model is analogous to the Michaelis constant Km and is predicted to be approximately less than 10(10)/ml.

  6. HIV-1 progression links with viral genetic variability and subtype, and patient's HLA type: analysis of a Nairobi-Kenyan cohort.

    PubMed

    Abidi, Syed Hani; Shahid, Aniqa; Lakhani, Laila S; Shah, Reena; Okinda, Nancy; Ojwang, Peter; Abbas, Farhat; Rowland-Jones, Sarah; Ali, Syed

    2014-02-01

    In a Nairobi-Kenyan cohort of 50 HIV-1 positive patients, we analysed the prevalence of HIV-1 subtypes and human leucocyte antigen (HLA) alleles. From this cohort, 33 patients were selected for the analysis of HIV-1 infection progression markers (i.e. CD4 cell counts and viral loads) and their association with HIV-1 genetic variability and subtype, and patient's HLA type. HIV-1 gag genetic variability, analysed using bioinformatics tools, showed an inverse relationship with CD4 cell count whereas with viral load that relationship was direct. Certain HLA types and viral subtypes were also found to associate with patients' viral load. Associations between disease parameters and the genetic makeup of the host and virus may be crucial in determining the outcome of HIV-1 infection. PMID:24142198

  7. Groundwater Pollution Source Identification using Linked ANN-Optimization Model

    NASA Astrophysics Data System (ADS)

    Ayaz, Md; Srivastava, Rajesh; Jain, Ashu

    2014-05-01

    Groundwater is the principal source of drinking water in several parts of the world. Contamination of groundwater has become a serious health and environmental problem today. Human activities including industrial and agricultural activities are generally responsible for this contamination. Identification of groundwater pollution source is a major step in groundwater pollution remediation. Complete knowledge of pollution source in terms of its source characteristics is essential to adopt an effective remediation strategy. Groundwater pollution source is said to be identified completely when the source characteristics - location, strength and release period - are known. Identification of unknown groundwater pollution source is an ill-posed inverse problem. It becomes more difficult for real field conditions, when the lag time between the first reading at observation well and the time at which the source becomes active is not known. We developed a linked ANN-Optimization model for complete identification of an unknown groundwater pollution source. The model comprises two parts- an optimization model and an ANN model. Decision variables of linked ANN-Optimization model contain source location and release period of pollution source. An objective function is formulated using the spatial and temporal data of observed and simulated concentrations, and then minimized to identify the pollution source parameters. In the formulation of the objective function, we require the lag time which is not known. An ANN model with one hidden layer is trained using Levenberg-Marquardt algorithm to find the lag time. Different combinations of source locations and release periods are used as inputs and lag time is obtained as the output. Performance of the proposed model is evaluated for two and three dimensional case with error-free and erroneous data. Erroneous data was generated by adding uniformly distributed random error (error level 0-10%) to the analytically computed concentration

  8. Defining Scenarios: Linking Integrated Models, Regional Concerns, and Stakeholders

    NASA Astrophysics Data System (ADS)

    Hartmann, H. C.; Stewart, S.; Liu, Y.; Mahmoud, M.

    2007-05-01

    Scenarios are important tools for long-term planning, and there is great interest in using integrated models in scenario studies. However, scenario definition and assessment are creative, as well as scientific, efforts. Using facilitated creative processes, we have worked with stakeholders to define regionally significant scenarios that encompass a broad range of hydroclimatic, socioeconomic, and institutional dimensions. The regional scenarios subsequently inform the definition of local scenarios that work with context-specific integrated models that, individually, can address only a subset of overall regional complexity. Based on concerns of stakeholders in the semi-arid US Southwest, we prioritized three dimensions that are especially important, yet highly uncertain, for long-term planning: hydroclimatic conditions (increased variability, persistent drought), development patterns (urban consolidation, distributed rural development), and the nature of public institutions (stressed, proactive). Linking across real-world decision contexts and integrated modeling efforts poses challenges of creatively connecting the conceptual models held by both the research and stakeholder communities.

  9. Evidence for differential viral oncolytic efficacy in an in vitro model of epithelial ovarian cancer metastasis.

    PubMed

    Tong, Jessica G; Valdes, Yudith Ramos; Barrett, John W; Bell, John C; Stojdl, David; McFadden, Grant; McCart, J Andrea; DiMattia, Gabriel E; Shepherd, Trevor G

    2015-01-01

    Epithelial ovarian cancer is unique among most carcinomas in that metastasis occurs by direct dissemination of malignant cells traversing throughout the intraperitoneal fluid. Accordingly, we test new therapeutic strategies using an in vitro three-dimensional spheroid suspension culture model that mimics key steps of this metastatic process. In the present study, we sought to uncover the differential oncolytic efficacy among three different viruses-Myxoma virus, double-deleted vaccinia virus, and Maraba virus-using three ovarian cancer cell lines in our metastasis model system. Herein, we demonstrate that Maraba virus effectively infects, replicates, and kills epithelial ovarian cancer (EOC) cells in proliferating adherent cells and with slightly slower kinetics in tumor spheroids. Myxoma virus and vaccinia viruses infect and kill adherent cells to a much lesser extent than Maraba virus, and their oncolytic potential is almost completely attenuated in spheroids. Myxoma virus and vaccinia are able to infect and spread throughout spheroids, but are blocked in the final stages of the lytic cycle, and oncolytic-mediated cell killing is reactivated upon spheroid reattachment. Alternatively, Maraba virus has a remarkably reduced ability to initially enter spheroid cells, yet rapidly infects and spreads throughout spheroids generating significant cell killing effects. We show that low-density lipoprotein receptor expression in ovarian cancer spheroids is reduced and this controls efficient Maraba virus binding and entry into infected cells. Taken together, these results are the first to implicate the potential impact of differential viral oncolytic properties at key steps of ovarian cancer metastasis.

  10. Assessing pneumococcal meningitis association with viral respiratory infections and antibiotics: insights from statistical and mathematical models.

    PubMed

    Opatowski, Lulla; Varon, Emmanuelle; Dupont, Claire; Temime, Laura; van der Werf, Sylvie; Gutmann, Laurent; Boëlle, Pierre-Yves; Watier, Laurence; Guillemot, Didier

    2013-08-01

    Pneumococcus is an important human pathogen, highly antibiotic resistant and a major cause of bacterial meningitis worldwide. Better prevention requires understanding the drivers of pneumococcal infection incidence and antibiotic susceptibility. Although respiratory viruses (including influenza) have been suggested to influence pneumococcal infections, the underlying mechanisms are still unknown, and viruses are rarely considered when studying pneumococcus epidemiology. Here, we propose a novel mathematical model to examine hypothetical relationships between Streptococcus pneumoniae meningitis incidence (SPMI), acute viral respiratory infections (AVRIs) and antibiotic exposure. French time series of SPMI, AVRI and penicillin consumption over 2001-2004 are analysed and used to assess four distinct virus-bacteria interaction submodels, ascribing the interaction on pneumococcus transmissibility and/or pathogenicity. The statistical analysis reveals strong associations between time series: SPMI increases shortly after AVRI incidence and decreases overall as the antibiotic-prescription rate rises. Model simulations require a combined impact of AVRI on both pneumococcal transmissibility (up to 1.3-fold increase at the population level) and pathogenicity (up to threefold increase) to reproduce the data accurately, along with diminished epidemic fitness of resistant pneumococcal strains causing meningitis (0.97 (0.96-0.97)). Overall, our findings suggest that AVRI and antibiotics strongly influence SPMI trends. Consequently, vaccination protecting against respiratory virus could have unexpected benefits to limit invasive pneumococcal infections.

  11. The Effects of Simulated Weightlessness on Susceptibility to Viral and Bacterial Infections Using a Murine Model

    NASA Technical Reports Server (NTRS)

    Gould, C. L.

    1985-01-01

    Certain immunological responses may be compromised as a result of changes in environmental conditions, such as the physiological adaptation to and from the weightlessness which occurs during space flight and recovery. A murine antiorthostatic model was developed to simulate weightlessness. Using this model, the proposed study will determine if differences in susceptibility to viral and bacterial infections exist among mice suspended in an antiorthostatic orientation to simulate weightlessness, mice suspended in an orthostatic orientation to provide a stressful situation without the condition of weightlessness simulation, and non-suspended control mice. Inbred mouse strains which are resistant to the diabetogenic effects of the D variant of encephalomyocarditis virus (EMC-D) and the lethal effects of Salmonella typhimurium will be evaluated. Glucose tolerance tests will be performed on all EMC-D-infected and non-infected control groups. The incidence of EMC-D-induced diabetes and the percentage survival of S. typhimurium-infected animals will be determined in each group. An additional study will determine the effects of simulated weightlessness on murine responses to exogenous interferon.

  12. Optimization model for UV-Riboflavin corneal cross-linking

    NASA Astrophysics Data System (ADS)

    Schumacher, S.; Wernli, J.; Scherrer, S.; Bueehler, M.; Seiler, T.; Mrochen, M.

    2011-03-01

    Nowadays UV-cross-linking is an established method for the treatment of keraectasia. Currently a standardized protocol is used for the cross-linking treatment. We will now present a theoretical model which predicts the number of induced crosslinks in the corneal tissue, in dependence of the Riboflavin concentration, the radiation intensity, the pre-treatment time and the treatment time. The model is developed by merging the difussion equation, the equation for the light distribution in dependence on the absorbers in the tissue and a rate equation for the polymerization process. A higher concentration of Riboflavin solution as well as a higher irradiation intensity will increase the number of induced crosslinks. However, performed stress-strain experiments which support the model showed that higher Riboflavin concentrations (> 0.125%) do not result in a further increase in stability of the corneal tissue. This is caused by the inhomogeneous distribution of induced crosslinks throughout the cornea due to the uneven absorption of the UV-light. The new model offers the possibility to optimize the treatment individually for every patient depending on their corneal thickness in terms of efficiency, saftey and treatment time.

  13. Modeling of Long-Range Atmospheric Lasercom Links Between Static and Mobile Platforms

    SciTech Connect

    Scharlemann, E T; Breitfeller, E F; Henderson, J R; Kallman, J S; Morris, J R; Ruggiero, A J

    2003-07-29

    We describe modeling and simulation of long-range terrestrial laser communications links between static and mobile platforms. Atmospheric turbulence modeling, along with pointing, tracking and acquisition models are combined to provide an overall capability to estimate communications link performance.

  14. Linking the Weather Generator with Regional Climate Model

    NASA Astrophysics Data System (ADS)

    Dubrovsky, Martin; Farda, Ales; Skalak, Petr; Huth, Radan

    2013-04-01

    One of the downscaling approaches, which transform the raw outputs from the climate models (GCMs or RCMs) into data with more realistic structure, is based on linking the stochastic weather generator with the climate model output. The present contribution, in which the parametric daily surface weather generator (WG) M&Rfi is linked to the RCM output, follows two aims: (1) Validation of the new simulations of the present climate (1961-1990) made by the ALADIN-Climate Regional Climate Model at 25 km resolution. The WG parameters are derived from the RCM-simulated surface weather series and compared to those derived from weather series observed in 125 Czech meteorological stations. The set of WG parameters will include statistics of the surface temperature and precipitation series (including probability of wet day occurrence). (2) Presenting a methodology for linking the WG with RCM output. This methodology, which is based on merging information from observations and RCM, may be interpreted as a downscaling procedure, whose product is a gridded WG capable of producing realistic synthetic multivariate weather series for weather-ungauged locations. In this procedure, WG is calibrated with RCM-simulated multi-variate weather series in the first step, and the grid specific WG parameters are then de-biased by spatially interpolated correction factors based on comparison of WG parameters calibrated with gridded RCM weather series and spatially scarcer observations. The quality of the weather series produced by the resultant gridded WG will be assessed in terms of selected climatic characteristics (focusing on characteristics related to variability and extremes of surface temperature and precipitation). Acknowledgements: The present experiment is made within the frame of projects ALARO-Climate (project P209/11/2405 sponsored by the Czech Science Foundation), WG4VALUE (project LD12029 sponsored by the Ministry of Education, Youth and Sports of CR) and VALUE (COST ES 1102

  15. Viral infection

    PubMed Central

    Puigdomènech, Isabel; de Armas-Rillo, Laura; Machado, José-David

    2011-01-01

    Viruses have developed different survival strategies in host cells by crossing cell-membrane compartments, during different steps of their viral life cycle. In fact, the non-regenerative viral membrane of enveloped viruses needs to encounter the dynamic cell-host membrane, during early steps of the infection process, in which both membranes fuse, either at cell-surface or in an endocytic compartment, to promote viral entry and infection. Once inside the cell, many viruses accomplish their replication process through exploiting or modulating membrane traffic, and generating specialized compartments to assure viral replication, viral budding and spreading, which also serve to evade the immune responses against the pathogen. In this review, we have attempted to present some data that highlight the importance of membrane dynamics during viral entry and replicative processes, in order to understand how viruses use and move through different complex and dynamic cell-membrane structures and how they use them to persist. PMID:21966556

  16. Does Viral Tropism Play a Role in Heterosexual Transmission of HIV? Findings in the SIV–Rhesus Macaque Model

    PubMed Central

    MILLER, CHRISTOPHER J.

    2009-01-01

    Substantial effort is being directed toward generating vaccines that can prevent the heterosexual transmission of HIV-1. If “Selection” for specific variants during sexual intercourse occurs, then vaccines should be designed to prevent transmission of these specific viruses. Using the SIV–rhesus macaque model to test the hypothesis that specific HIV genotypes are more efficient at producing infection by sexual transmission, it was possible to demonstrate that the genotypic determinants that permit SIV or SHIV to produce systemic infection differ depending on the route of virus inoculation. This finding supports the conclusion that there is selection for viral genotypes during sexual transmission of HIV. However, the ability of a virus to grow in rhesus macaque monocyte-derived macrophages in vitro does not predict the outcome of intravaginal inoculation with that virus. We did find that after intravenous inoculation all the vaginally transmitting viruses produced plasma antigenemia and high levels of plasma viral RNA. In contrast, although the nontransmitting viruses infect rhesus macaques after intravenous inoculation, the infection that occurs after intravenous inoculation is characterized by a lack of viral antigen in plasma and low levels of plasma viral RNA. On the basis of these results, it is clear that viruses which are adapted to replicate to high levels in vivo are transmitted by vaginal inoculation. This principle may also apply to the transmission of HIV in humans. PMID:9581889

  17. Model of Atmospheric Links on Optical Communications from High Altitude

    NASA Technical Reports Server (NTRS)

    Subich, Christopher

    2004-01-01

    Optical communication links have the potential to solve many of the problems of current radio and microwave links to satellites and high-altitude aircraft. The higher frequency involved in optical systems allows for significantly greater signal bandwidth, and thus information transfer rate, in excess of 10 Gbps, and the highly directional nature of laser-based signals eliminates the need for frequency-division multiplexing seen in radio and microwave links today. The atmosphere, however, distorts an optical signal differently than a microwave signal. While the ionosphere is one of the most significant sources of noise and distortion in a microwave or radio signal, the lower atmosphere affects an optical signal more significantly. Refractive index fluctuations, primarily caused by changes in atmospheric temperature and density, distort the incoming signal in both deterministic and nondeterministic ways. Additionally, suspended particles, such as those in haze or rain, further corrupt the transmitted signal. To model many of the atmospheric effects on the propagating beam, we use simulations based on the beam-propagation method. This method, developed both for simulation of signals in waveguides and propagation in atmospheric turbulence, separates the propagation into a diffraction and refraction problem. The diffraction step is an exact solution, within the limits of numerical precision, to the problem of propagation in free space, and the refraction step models the refractive index variances over a segment of the propagation path. By applying refraction for a segment of the propagation path, then diffracting over that same segment, this method forms a good approximation to true propagation through the atmospheric medium. Iterating over small segments of the total propagation path gives a good approximation to the problem of propagation over the entire path. Parameters in this model, such as initial beam profile and atmospheric constants, are easily modified in a

  18. Integrative modelling reveals mechanisms linking productivity and plant species richness.

    PubMed

    Grace, James B; Anderson, T Michael; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M; Pärtel, Meelis; Bakker, Jonathan D; Buckley, Yvonne M; Crawley, Michael J; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Hector, Andy; Knops, Johannes M H; MacDougall, Andrew S; Melbourne, Brett A; Morgan, John W; Orrock, John L; Prober, Suzanne M; Smith, Melinda D

    2016-01-21

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems. PMID:26760203

  19. Integrative modelling reveals mechanisms linking productivity and plant species richness

    NASA Astrophysics Data System (ADS)

    Grace, James B.; Anderson, T. Michael; Seabloom, Eric W.; Borer, Elizabeth T.; Adler, Peter B.; Harpole, W. Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M.; Pärtel, Meelis; Bakker, Jonathan D.; Buckley, Yvonne M.; Crawley, Michael J.; Damschen, Ellen I.; Davies, Kendi F.; Fay, Philip A.; Firn, Jennifer; Gruner, Daniel S.; Hector, Andy; Knops, Johannes M. H.; MacDougall, Andrew S.; Melbourne, Brett A.; Morgan, John W.; Orrock, John L.; Prober, Suzanne M.; Smith, Melinda D.

    2016-01-01

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

  20. Modeling X-Linked Ancestral Origins in Multiparental Populations

    PubMed Central

    Zheng, Chaozhi

    2015-01-01

    The models for the mosaic structure of an individual’s genome from multiparental populations have been developed primarily for autosomes, whereas X chromosomes receive very little attention. In this paper, we extend our previous approach to model ancestral origin processes along two X chromosomes in a mapping population, which is necessary for developing hidden Markov models in the reconstruction of ancestry blocks for X-linked quantitative trait locus mapping. The model accounts for the joint recombination pattern, the asymmetry between maternally and paternally derived X chromosomes, and the finiteness of population size. The model can be applied to various mapping populations such as the advanced intercross lines (AIL), the Collaborative Cross (CC), the heterogeneous stock (HS), the Diversity Outcross (DO), and the Drosophila synthetic population resource (DSPR). We further derive the map expansion, density (per Morgan) of recombination breakpoints, in advanced intercross populations with L inbred founders under the limit of an infinitely large population size. The analytic results show that for X chromosomes the genetic map expands linearly at a rate (per generation) of two-thirds times 1 – 10/(9L) for the AIL, and at a rate of two-thirds times 1 – 1/L for the DO and the HS, whereas for autosomes the map expands at a rate of 1 – 1/L for the AIL, the DO, and the HS. PMID:25740936

  1. The Viral Polymerase Inhibitor 7-Deaza-2’-C-Methyladenosine Is a Potent Inhibitor of In Vitro Zika Virus Replication and Delays Disease Progression in a Robust Mouse Infection Model

    PubMed Central

    Zmurko, Joanna; Marques, Rafael E.; Schols, Dominique; Verbeken, Erik; Kaptein, Suzanne J.F.; Neyts, Johan

    2016-01-01

    Zika virus (ZIKV) is an emerging flavivirus typically causing a dengue-like febrile illness, but neurological complications, such as microcephaly in newborns, have potentially been linked to this viral infection. We established a panel of in vitro assays to allow the identification of ZIKV inhibitors and demonstrate that the viral polymerase inhibitor 7-deaza-2’-C-methyladenosine (7DMA) efficiently inhibits replication. Infection of AG129 (IFN-α/β and IFN-γ receptor knock-out) mice with ZIKV resulted in acute neutrophilic encephalitis with viral antigens accumulating in neurons of the brain and spinal cord. Additionally, high levels of viral RNA were detected in the spleen, liver and kidney, and levels of IFN-γ and IL-18 were systematically increased in serum of ZIKV-infected mice. Interestingly, the virus was also detected in testicles of infected mice. In line with its in vitro anti-ZIKV activity, 7DMA reduced viremia and delayed virus-induced morbidity and mortality in infected mice, which also validates this small animal model to assess the in vivo efficacy of novel ZIKV inhibitors. Since AG129 mice can generate an antibody response, and have been used in dengue vaccine studies, the model can also be used to assess the efficacy of ZIKV vaccines.   PMID:27163257

  2. The Viral Polymerase Inhibitor 7-Deaza-2'-C-Methyladenosine Is a Potent Inhibitor of In Vitro Zika Virus Replication and Delays Disease Progression in a Robust Mouse Infection Model.

    PubMed

    Zmurko, Joanna; Marques, Rafael E; Schols, Dominique; Verbeken, Erik; Kaptein, Suzanne J F; Neyts, Johan

    2016-05-01

    Zika virus (ZIKV) is an emerging flavivirus typically causing a dengue-like febrile illness, but neurological complications, such as microcephaly in newborns, have potentially been linked to this viral infection. We established a panel of in vitro assays to allow the identification of ZIKV inhibitors and demonstrate that the viral polymerase inhibitor 7-deaza-2'-C-methyladenosine (7DMA) efficiently inhibits replication. Infection of AG129 (IFN-α/β and IFN-γ receptor knock-out) mice with ZIKV resulted in acute neutrophilic encephalitis with viral antigens accumulating in neurons of the brain and spinal cord. Additionally, high levels of viral RNA were detected in the spleen, liver and kidney, and levels of IFN-γ and IL-18 were systematically increased in serum of ZIKV-infected mice. Interestingly, the virus was also detected in testicles of infected mice. In line with its in vitro anti-ZIKV activity, 7DMA reduced viremia and delayed virus-induced morbidity and mortality in infected mice, which also validates this small animal model to assess the in vivo efficacy of novel ZIKV inhibitors. Since AG129 mice can generate an antibody response, and have been used in dengue vaccine studies, the model can also be used to assess the efficacy of ZIKV vaccines.  .

  3. The Viral Polymerase Inhibitor 7-Deaza-2'-C-Methyladenosine Is a Potent Inhibitor of In Vitro Zika Virus Replication and Delays Disease Progression in a Robust Mouse Infection Model.

    PubMed

    Zmurko, Joanna; Marques, Rafael E; Schols, Dominique; Verbeken, Erik; Kaptein, Suzanne J F; Neyts, Johan

    2016-05-01

    Zika virus (ZIKV) is an emerging flavivirus typically causing a dengue-like febrile illness, but neurological complications, such as microcephaly in newborns, have potentially been linked to this viral infection. We established a panel of in vitro assays to allow the identification of ZIKV inhibitors and demonstrate that the viral polymerase inhibitor 7-deaza-2'-C-methyladenosine (7DMA) efficiently inhibits replication. Infection of AG129 (IFN-α/β and IFN-γ receptor knock-out) mice with ZIKV resulted in acute neutrophilic encephalitis with viral antigens accumulating in neurons of the brain and spinal cord. Additionally, high levels of viral RNA were detected in the spleen, liver and kidney, and levels of IFN-γ and IL-18 were systematically increased in serum of ZIKV-infected mice. Interestingly, the virus was also detected in testicles of infected mice. In line with its in vitro anti-ZIKV activity, 7DMA reduced viremia and delayed virus-induced morbidity and mortality in infected mice, which also validates this small animal model to assess the in vivo efficacy of novel ZIKV inhibitors. Since AG129 mice can generate an antibody response, and have been used in dengue vaccine studies, the model can also be used to assess the efficacy of ZIKV vaccines.  . PMID:27163257

  4. Persistence of Viral Reservoirs in Multiple Tissues after Antiretroviral Therapy Suppression in a Macaque RT-SHIV Model

    PubMed Central

    Franks, Tamera; Kiser, Rebecca; Coalter, Vicky; Smedley, Jeremy; Piatak, Michael; Mellors, John W.; Lifson, Jeffrey D.; Ambrose, Zandrea

    2013-01-01

    Although antiretroviral therapy (ART) can suppress HIV-1 replication sufficiently to eliminate measurable plasma viremia, infected cells remain and ensure viral recrudescence after discontinuation of ART. We used a macaque model of HIV-1/AIDS to evaluate the location of infected cells during ART. Twelve macaques were infected with RT-SHIVmne, a SIV containing HIV-1 reverse transcriptase, conferring sensitivity to non-nucleoside reverse transcriptase inhibitors (NNRTIs). Ten to fourteen weeks post-infection, 6 animals were treated with 3 or 4 antiretroviral drugs for 17-20 weeks; 6 control animals remained untreated. Viral DNA (vDNA) and RNA (vRNA) were measured in peripheral blood mononuclear cells (PBMC) and at necropsy in multiple tissues by quantitative PCR and RT-PCR. The majority of virally infected cells were located in lymphoid tissues with variable levels in the gastrointestinal tract of both treated and untreated animals. Tissue viral DNA levels correlated with week 1 plasma viremia, suggesting that tissues that harbor proviral DNA are established within the first week of infection. PBMC vDNA levels did not correlate with plasma viremia or tissue levels of vDNA. vRNA levels were high in lymphoid and gastrointestinal tissues of the untreated animals; animals on ART had little vRNA expressed in tissues and virus could not be cultured from lymph node resting CD4+ cells after 17-20 weeks on ART, indicating little or no ongoing viral replication. Strategies for eradication of HIV-1 will need to target residual virus in ART suppressed individuals, which may not be accurately reflected by frequencies of infected cells in blood. PMID:24367650

  5. Viral meningitis.

    PubMed

    Chadwick, David R

    2005-01-01

    Viruses probably account for most cases of acute meningitis. Viral meningitis is often assumed to be a largely benign disease. For the commonest pathogens causing meningitis, enteroviruses, this is usually the case; however, for many of the other pathogens causing viral meningitis, and for common pathogens in the immunocompromised or infants, viral meningitis is frequently associated with substantial neurological complications and a significant mortality. Diagnostic methods for rapid and accurate identification of pathogens have improved over recent years, permitting more precise and earlier diagnoses. There have been fewer developments in therapies for viral meningitis, and there remain no effective therapies for most pathogens, emphasising the importance of prevention and early diagnosis. This review focuses on the presentation, diagnosis and management of viral meningitis and also covers the prevention of meningitis for pathogens where effective vaccines are available. PMID:16474042

  6. Viral meningitis.

    PubMed

    Chadwick, David R

    2005-01-01

    Viruses probably account for most cases of acute meningitis. Viral meningitis is often assumed to be a largely benign disease. For the commonest pathogens causing meningitis, enteroviruses, this is usually the case; however, for many of the other pathogens causing viral meningitis, and for common pathogens in the immunocompromised or infants, viral meningitis is frequently associated with substantial neurological complications and a significant mortality. Diagnostic methods for rapid and accurate identification of pathogens have improved over recent years, permitting more precise and earlier diagnoses. There have been fewer developments in therapies for viral meningitis, and there remain no effective therapies for most pathogens, emphasising the importance of prevention and early diagnosis. This review focuses on the presentation, diagnosis and management of viral meningitis and also covers the prevention of meningitis for pathogens where effective vaccines are available.

  7. The Linked Dual Representation model of vocal perception and production

    PubMed Central

    Hutchins, Sean; Moreno, Sylvain

    2013-01-01

    The voice is one of the most important media for communication, yet there is a wide range of abilities in both the perception and production of the voice. In this article, we review this range of abilities, focusing on pitch accuracy as a particularly informative case, and look at the factors underlying these abilities. Several classes of models have been posited describing the relationship between vocal perception and production, and we review the evidence for and against each class of model. We look at how the voice is different from other musical instruments and review evidence about both the association and the dissociation between vocal perception and production abilities. Finally, we introduce the Linked Dual Representation (LDR) model, a new approach which can account for the broad patterns in prior findings, including trends in the data which might seem to be countervailing. We discuss how this model interacts with higher-order cognition and examine its predictions about several aspects of vocal perception and production. PMID:24204360

  8. Linking geophysics and soil function modelling - biomass production

    NASA Astrophysics Data System (ADS)

    Krüger, J.; Franko, U.; Werban, U.; Fank, J.

    2012-04-01

    The iSOIL project aims at reliable mapping of soil properties and soil functions with various methods including geophysical, spectroscopic and monitoring techniques. The general procedure contains three steps (i) geophysical monitoring, (ii) generation of soil property maps and (iii) process modelling. The objective of this work is to demonstrate the mentioned procedure with a focus on process modelling. It deals with the dynamics of soil water and the direct influence on crop biomass production. The new module PLUS extends CANDY to simulate crop biomass production based on environmental influences. A soil function modelling with an adapted model parameterisation based on data of ground penetration radar (GPR) and conductivity (EM38) was realized. This study shows an approach to handle heterogeneity of soil properties with geophysical data used for biomass production modelling. The Austrian field site Wagna is characterised by highly heterogenic soil with fluvioglacial gravel sediments. The variation of thickness of topsoil above a sandy subsoil with gravels strongly influences the soil water balance. EM38, mounted on a mobile platform, enables to rapidly scan large areas whereas GPR requires a greater logistical effort. However, GPR can detect exact soil horizon depth between topsoil and subsoil, the combination of both results in a detailed large scale soil map. The combined plot-specific GPR and field site EM38 measurements extends the soil input data and improves the model performance of CANDY PLUS for plant biomass production (Krüger et al. 2011). The example demonstrates how geophysics provides a surplus of data for agroecosystem modelling which identifies and contributes alternative options for agricultural management decisions. iSOIL - "Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping" is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission

  9. Viral Glycoprotein Complex Formation, Essential Function and Immunogenicity in the Guinea Pig Model for Cytomegalovirus.

    PubMed

    Coleman, Stewart; Hornig, Julia; Maddux, Sarah; Choi, K Yeon; McGregor, Alistair

    2015-01-01

    Development of a cytomegalovirus (CMV) vaccine is a major public health priority due to the risk of congenital infection. A key component of a vaccine is thought to be an effective neutralizing antibody response against the viral glycoproteins necessary for cell entry. Species specificity of human CMV (HCMV) precludes direct studies in an animal model. The guinea pig is the only small animal model for congenital cytomegalovirus infection. Analysis of the guinea pig CMV (GPCMV) genome indicates that it potentially encodes homologs to the HCMV glycoproteins (including gB, gH, gL, gM, gN and gO) that form various cell entry complexes on the outside of the virus: gCI (gB); gCII (gH/gL/gO); gCIII (gM/gN). The gB homolog (GP55) has been investigated as a candidate subunit vaccine but little is known about the other homolog proteins. GPCMV glycoproteins were investigated by transient expression studies which indicated that homolog glycoproteins to gN and gM, or gH, gL and gO were able to co-localize in cells and generate respective homolog complexes which could be verified by immunoprecipitation assays. ELISA studies demonstrated that the individual complexes were highly immunogenic in guinea pigs. The gO (GP74) homolog protein has 13 conserved N-glycosylation sites found in HCMV gO. In transient expression studies, only the glycosylated protein is detected but in virus infected cells both N-glycosylated and non-glycosylated gO protein were detected. In protein interaction studies, a mutant gO that lacked N-glycosylation sites had no impact on the ability of the protein to interact with gH/gL which indicated a potential alternative function associated with these sites. Knockout GPCMV BAC mutagenesis of the respective glycoprotein genes (GP55 for gB, GP75 for gH, GP115 for gL, GP100 for gM, GP73 for gN and GP74 for gO) in separate reactions was lethal for virus regeneration on fibroblast cells which demonstrated the essential nature of the GPCMV glycoproteins. The gene

  10. Viral Glycoprotein Complex Formation, Essential Function and Immunogenicity in the Guinea Pig Model for Cytomegalovirus

    PubMed Central

    Maddux, Sarah; Choi, K. Yeon; McGregor, Alistair

    2015-01-01

    Development of a cytomegalovirus (CMV) vaccine is a major public health priority due to the risk of congenital infection. A key component of a vaccine is thought to be an effective neutralizing antibody response against the viral glycoproteins necessary for cell entry. Species specificity of human CMV (HCMV) precludes direct studies in an animal model. The guinea pig is the only small animal model for congenital cytomegalovirus infection. Analysis of the guinea pig CMV (GPCMV) genome indicates that it potentially encodes homologs to the HCMV glycoproteins (including gB, gH, gL, gM, gN and gO) that form various cell entry complexes on the outside of the virus: gCI (gB); gCII (gH/gL/gO); gCIII (gM/gN). The gB homolog (GP55) has been investigated as a candidate subunit vaccine but little is known about the other homolog proteins. GPCMV glycoproteins were investigated by transient expression studies which indicated that homolog glycoproteins to gN and gM, or gH, gL and gO were able to co-localize in cells and generate respective homolog complexes which could be verified by immunoprecipitation assays. ELISA studies demonstrated that the individual complexes were highly immunogenic in guinea pigs. The gO (GP74) homolog protein has 13 conserved N-glycosylation sites found in HCMV gO. In transient expression studies, only the glycosylated protein is detected but in virus infected cells both N-glycosylated and non-glycosylated gO protein were detected. In protein interaction studies, a mutant gO that lacked N-glycosylation sites had no impact on the ability of the protein to interact with gH/gL which indicated a potential alternative function associated with these sites. Knockout GPCMV BAC mutagenesis of the respective glycoprotein genes (GP55 for gB, GP75 for gH, GP115 for gL, GP100 for gM, GP73 for gN and GP74 for gO) in separate reactions was lethal for virus regeneration on fibroblast cells which demonstrated the essential nature of the GPCMV glycoproteins. The gene

  11. Effects of linking a soil-water-balance model with a groundwater-flow model.

    PubMed

    Stanton, Jennifer S; Ryter, Derek W; Peterson, Steven M

    2013-01-01

    A previously published regional groundwater-flow model in north-central Nebraska was sequentially linked with the recently developed soil-water-balance (SWB) model to analyze effects to groundwater-flow model parameters and calibration results. The linked models provided a more detailed spatial and temporal distribution of simulated recharge based on hydrologic processes, improvement of simulated groundwater-level changes and base flows at specific sites in agricultural areas, and a physically based assessment of the relative magnitude of recharge for grassland, nonirrigated cropland, and irrigated cropland areas. Root-mean-squared (RMS) differences between the simulated and estimated or measured target values for the previously published model and linked models were relatively similar and did not improve for all types of calibration targets. However, without any adjustment to the SWB-generated recharge, the RMS difference between simulated and estimated base-flow target values for the groundwater-flow model was slightly smaller than for the previously published model, possibly indicating that the volume of recharge simulated by the SWB code was closer to actual hydrogeologic conditions than the previously published model provided. Groundwater-level and base-flow hydrographs showed that temporal patterns of simulated groundwater levels and base flows were more accurate for the linked models than for the previously published model at several sites, particularly in agricultural areas.

  12. Effects of linking a soil-water-balance model with a groundwater-flow model

    USGS Publications Warehouse

    Stanton, Jennifer S.; Ryter, Derek W.; Peterson, Steven M.

    2013-01-01

    A previously published regional groundwater-flow model in north-central Nebraska was sequentially linked with the recently developed soil-water-balance (SWB) model to analyze effects to groundwater-flow model parameters and calibration results. The linked models provided a more detailed spatial and temporal distribution of simulated recharge based on hydrologic processes, improvement of simulated groundwater-level changes and base flows at specific sites in agricultural areas, and a physically based assessment of the relative magnitude of recharge for grassland, nonirrigated cropland, and irrigated cropland areas. Root-mean-squared (RMS) differences between the simulated and estimated or measured target values for the previously published model and linked models were relatively similar and did not improve for all types of calibration targets. However, without any adjustment to the SWB-generated recharge, the RMS difference between simulated and estimated base-flow target values for the groundwater-flow model was slightly smaller than for the previously published model, possibly indicating that the volume of recharge simulated by the SWB code was closer to actual hydrogeologic conditions than the previously published model provided. Groundwater-level and base-flow hydrographs showed that temporal patterns of simulated groundwater levels and base flows were more accurate for the linked models than for the previously published model at several sites, particularly in agricultural areas.

  13. Linking geophysics and soil function modelling - two examples

    NASA Astrophysics Data System (ADS)

    Krüger, J.; Franko, U.; Werban, U.; Dietrich, P.; Behrens, T.; Schmidt, K.; Fank, J.; Kroulik, M.

    2011-12-01

    iSOIL - "Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping" is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission within the RTD activities of the FP7 Thematic Priority Environment. The iSOIL project aims at reliable mapping of soil properties and soil functions with various methods including geophysical, spectroscopic and monitoring techniques. The general procedure contains three steps (i) geophysical monitoring, (ii) generation of soil property maps and (iii) process modelling. The objective of this work is to demonstrate the methodological procedure on two different examples. Example A focuses on the turnover conditions for soil organic matter (SOM) since many soil functions in a direct or indirect way depend on SOM and SOM depletion is amongst the worst soil threats. Example B deals with the dynamics of soil water and the direct influence on crop biomass production. The applied CANDY model (Franko et al. 1995) was developed to describe dynamics of soil organic matter and mineral nitrogen as well as soil water and temperature. The new module PLUS extends CANDY to simulate crop biomass production based on environmental influences (Krüger et al. 2011). The methodological procedure of example A illustrates a model application for a field site in the Czech Republic using generated soil maps from combined geophysical data. Modelling requires a complete set of soil parameters. Combining measured soil properties and data of geophysical measurements (electrical conductivity and gamma spectrometry) is the basis for digital soil mapping which provided data about clay, silt and sand as well as SOC content. With these data pedotransfer functions produce detailed soil input data (e.g. bulk and particle density, field capacity, wilting point, saturated conductivity) for the rooted soil profile. CANDY calculated different indicators for SOM and gave hints about

  14. Reducing chorioretinal viral counts with intravitreal foscarnet injections in a rabbit model of Herpes simplex virus type-1 retinitis.

    PubMed

    Morin, N J; Delorme, C; Gourde, P; Omar, R F; Désormeaux, A; Tremblay, M J; Beauchamp, D; Rousseau, A; Bergeron, M G

    1999-10-01

    The efficacy of intravitreal foscarnet injections was evaluated in a rabbit model of Herpes simplex virus type-1 (HSV-1) retinitis. In untreated infected animals, viral titration revealed that the optic chiasm, vitreous and chorioretina were positive for HSV-1. On the other hand, foscarnet treatment significantly decreased the viral count in the chorioretina when compared to the untreated group. Immunolocalization of HSV in untreated infected animals clearly showed infected cells in the outer and inner layers of the retina and also in the ciliary body of the eye. Clinical examination by indirect ophthalmoscopy indicated an absence of optic nerve congestion and a lower level of vitritis in foscarnet treated animals compared to the untreated group. It is concluded that intravitreal injections of foscarnet reduced the viral titer in the chorioretina in a rabbit model of HSV-1 retinitis. This route of administration might be valuable for the treatment of CMV retinitis in AIDS patients with sight threatening lesions or intolerance to intravenous anti-CMV drugs.

  15. The effect of alpha 1-blocker, bunazosin on a murine model of congestive heart failure induced by viral myocarditis.

    PubMed

    Yamada, T; Matsumori, A; Okada, I; Tominaga, M; Kawai, C

    1992-11-01

    The purpose of this study was to investigate the therapeutic effect of an alpha 1-blocker, bunazosin, using an experimental murine model of congestive heart failure induced by viral myocarditis. This model is characterized by a high incidence of severe myocarditis and subsequent congestive heart failure, and is suitable for the evaluation of the effect of drugs. To estimate myocardial damage objectively and quantitatively, we used antimyosin monoclonal antibody in addition to histopathological grading. Four-week-old BALB/c mice were inoculated with encephalomyocarditis virus. The mice were injected daily with bunazosin or saline as a placebo from the day of viral inoculation until day 7 (protocol-I) or day 14 (protocol-II), or from day 4 to day 14 (protocol-III). They were then injected with 1.5 microCi of indium-111 labeled antimyosin antibody and were killed 24 h later. The antimyosin cardiac uptake was counted and histopathological grading was performed. The heart-weight to body-weight ratio, left ventricular dimension, histopathological grades and antimyosin cardiac uptake were significantly lower in the bunazosin group than in the placebo group in protocol-II, but not in protocol-I or protocol-III. Bunazosin showed a protective effect against viral myocarditis only when it was started early after infection and continued until the stage of congestive heart failure.

  16. Alterations in favipiravir (T-705) pharmacokinetics and biodistribution in a hamster model of viral hemorrhagic fever.

    PubMed

    Gowen, Brian B; Sefing, Eric J; Westover, Jonna B; Smee, Donald F; Hagloch, Joseph; Furuta, Yousuke; Hall, Jeffery O

    2015-09-01

    Favipiravir (T-705) is a new anti-influenza drug approved for human use in Japan and progressing through Phase 3 clinical trials in the U.S. In addition to its potent inhibitory effects against influenza virus infection, the compound has been shown to be broadly active against RNA viruses from 9 different families, including the Arenaviridae. Several members of the Arenaviridae family of viruses are significant human pathogens that cause viral hemorrhagic fever, a severe systemic syndrome where vascular leak is a cardinal feature. Because arenaviral infections are unlikely to be diagnosed and treated until the illness has progressed to a more advanced state, it is important to understand the effects of the disease state on favipiravir pharmacokinetics (PK) and biodistribution to help guide therapeutic strategy. During acute arenavirus infection in hamsters, we found reduced plasma favipiravir concentrations and altered kinetics of absorption, elimination and time to maximum drug concentration. In addition, the amounts of the favipiravir M1 primary metabolite were higher in the infected animals, suggesting that favipiravir metabolism may favor the formation of this inactive metabolite during viral infection. We also discovered differences in favipiravir and M1 PK parameters associated with arenavirus infection in a number of hamster tissues. Finally, analysis at the individual animal level demonstrated a correlation between reduced plasma favipiravir concentration with increased disease burden as reflected by weight loss and viral load. Our study is the first to show the impact of active viral infection and disease on favipiravir PK and biodistribution, highlighting the need to consider alterations in these parameters when treating individuals with viral hemorrhagic fever of arenavirus or other etiology.

  17. Alterations in favipiravir (T-705) pharmacokinetics and biodistribution in a hamster model of viral hemorrhagic fever

    PubMed Central

    Gowen, Brian B.; Sefing, Eric J.; Westover, Jonna B.; Smee, Donald F.; Hagloch, Joseph; Furuta, Yousuke; Hall, Jeffery O.

    2015-01-01

    Favipiravir (T-705) is a new anti-influenza drug approved for human use in Japan and progressing through Phase 3 clinical trials in the U.S. In addition to its potent inhibitory effects against influenza virus infection, the compound has been shown to be broadly active against RNA viruses from 9 different families, including the Arenaviridae. Several members of the Arenaviridae family of viruses are significant human pathogens that cause viral hemorrhagic fever, a severe systemic syndrome where vascular leak is a cardinal feature. Because arenaviral infections are unlikely to be diagnosed and treated until the illness has progressed to a more advanced state, it is important to understand the effects of the disease state on favipiravir pharmacokinetics (PK) and biodistribution to help guide therapeutic strategy. During acute arenavirus infection in hamsters, we found reduced plasma favipiravir concentrations and altered kinetics of absorption, elimination and time to maximum drug concentration. In addition, the amounts of the favipiravir M1 primary metabolite were higher in the infected animals, suggesting that favipiravir metabolism may favor the formation of this inactive metabolite during viral infection. We also discovered differences in favipiravir and M1 PK parameters associated with arenavirus infection in a number of hamster tissues. Finally, analysis at the individual animal level demonstrated a correlation between reduced plasma favipiravir concentration with increased disease burden as reflected by weight loss and viral load. Our study is the first to show the impact of active viral infection and disease on favipiravir PK and biodistribution, highlighting the need to consider alterations in these parameters when treating individuals with viral hemorrhagic fever of arenavirus or other etiology. PMID:26186980

  18. Implementation of a vibrationally linked chemical reaction model for DSMC

    NASA Technical Reports Server (NTRS)

    Carlson, A. B.; Bird, Graeme A.

    1994-01-01

    A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.

  19. Implementation of a vibrationally linked chemical reaction model for DSMC

    NASA Astrophysics Data System (ADS)

    Carlson, A. B.; Bird, Graeme A.

    1994-04-01

    A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.

  20. Viral Gastroenteritis

    MedlinePlus

    ... stomach, small intestine, and large intestine. Several different viruses can cause viral gastroenteritis, which is highly contagious ... and last for 1 to 3 days. Some viruses cause symptoms that last longer. [ Top ] What are ...

  1. Viral arthritis

    MedlinePlus

    Infectious arthritis - viral ... Ohl CA, Forster D. Infectious arthritis of native joints. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's Principles and Practice of Infectious ...

  2. FSO and radio link attenuation: meteorological models verified by experiment

    NASA Astrophysics Data System (ADS)

    Brazda, Vladimir; Fiser, Ondrej; Svoboda, Jaroslav

    2011-09-01

    Institute of Atmospheric Physics of Czech Academy measures atmospheric attenuation on 60 m experimental FSO link on 830 and 1550 nm for more than three years. Visibility sensors and two 3D sonic anemometers on both transmitting and receiving site, rain gauge and many sensors enabling the refractivity index computation are spaced along the optical link. Meteorological visibility, wind turbulent energy, sonic temperature, structure index and rain rate are correlated with measured attenuation. FSO link attenuation dependence on the above mentioned parameters is analyzed. The paper shows also basic statistical behavior of the long-term FSO signal level and also the simulation of hybrid link techniques.

  3. Viral evolution

    PubMed Central

    Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo

    2012-01-01

    Explaining the origin of viruses remains an important challenge for evolutionary biology. Previous explanatory frameworks described viruses as founders of cellular life, as parasitic reductive products of ancient cellular organisms or as escapees of modern genomes. Each of these frameworks endow viruses with distinct molecular, cellular, dynamic and emergent properties that carry broad and important implications for many disciplines, including biology, ecology and epidemiology. In a recent genome-wide structural phylogenomic analysis, we have shown that large-to-medium-sized viruses coevolved with cellular ancestors and have chosen the evolutionary reductive route. Here we interpret these results and provide a parsimonious hypothesis for the origin of viruses that is supported by molecular data and objective evolutionary bioinformatic approaches. Results suggest two important phases in the evolution of viruses: (1) origin from primordial cells and coexistence with cellular ancestors, and (2) prolonged pressure of genome reduction and relatively late adaptation to the parasitic lifestyle once virions and diversified cellular life took over the planet. Under this evolutionary model, new viral lineages can evolve from existing cellular parasites and enhance the diversity of the world’s virosphere. PMID:23550145

  4. Linking numerical models of lithospheric deformation and magnetotelluric images

    NASA Astrophysics Data System (ADS)

    Sobolev, S. V.

    2012-12-01

    Efficient modeling of geodynamic processes requires constraints from different fields of geosciences. Frequently used are data on crustal structure and composition and their evolution constrained by seismic, gravity and petrological/geochemical studies. However, links between geodynamic modeling and rapidly developing field of magnetotelluric (MT) studies are still insufficient. I'll consider two recent examples of MT observations and geodynamic modeling demonstrating that joint analyses of thermomechanical models of lithospheric deformation and MT images may be useful to understand geodynamic processes. One set of observations is MT data for San Andreas Fault (SAF) in the region close to the SAFOD Site (Becken et al., 2011) that shows high conductivity anomalies in the mantle, that are interpreted as fluid flow feeding creeping part of SAF south of the SAFOD Site. Interestingly, zones of high conductivity do not coincide with the expected zones of the recent active deformation (SAF), but are located to the west of it. Based on thermomechanical model of the evolution of the SAFS in Central and Northern California during the last 20 Mln. years (Popov et al., 2012), I'll demonstrate that high conductivity anomalies precisely coincide with the expected zones of the highest accumulated shear strain. Possible interpretation of this coincidence is that strong preferred orientation of olivine crystals in the highly deformed mantle shear zone causes high permeability of fluids. Another set of observations is MT data showing high conductivity anomalies in the crust of Tibet (Unsworh et al., 2005, Bai et al., 2010) and Pamirs (Sass et al., 2011) that are often interpreted as an evidence for the widely spread partially molten crust. Using 2D thermomechanical models of the collision between India and Eurasia, I'll demonstrate that such structures in the crust cannot appear without delamination of the mantle lithosphere during tectonic shortening. Internal heating of the

  5. Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis.

    PubMed

    Domanskyi, Sergii; Schilling, Joshua E; Gorshkov, Vyacheslav; Libert, Sergiy; Privman, Vladimir

    2016-09-01

    We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of "stiff" equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions. PMID:27608985

  6. Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

    NASA Astrophysics Data System (ADS)

    Domanskyi, Sergii; Schilling, Joshua E.; Gorshkov, Vyacheslav; Libert, Sergiy; Privman, Vladimir

    2016-09-01

    We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of "stiff" equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

  7. Dose-dependent protective effect of nicotine in a murine model of viral myocarditis induced by coxsackievirus B3

    PubMed Central

    Li-Sha, Ge; Jing-Lin, Zhao; Guang-Yi, Chen; Li, Liu; De-Pu, Zhou; Yue-Chun, Li

    2015-01-01

    The alpha 7 nicotinic acetylcholine receptor (alpha7 nAChR) was recently described as an anti-inflammatory target in various inflammatory diseases. The aim of this study was to investigate the dose-related effects of nicotine, an alpha7 nAChR agonist, in murine model of viral myocarditis. BALB/C mice were infected by an intraperitoneally injection with coxsackievirus B3. Nicotine was administered at doses of 0.1, 0.2 or 0.4 mg/kg three times per day for 7 or 14 consecutive days. The effects of nicotine on survival, myocardial histopathological changes, cardiac function, and cytokine levels were studied. The survival rate on day 14 increased in a dose-dependent fashion and was markedly higher in the 0.2 and 0.4 mg/kg nicotine groups than in the infected untreated group. Treatment with high-dose nicotine reduced the myocardial inflammation and improved the impaired left ventricular function in infected mice. The mRNA expressions and protein levels of TNF-α, IL-1β, IL-6, and IL-17A were significantly downregulated in dose-dependent manners in the nicotine treatment groups compared to the infected untreated group. Nicotine dose-dependently reduced the severity of viral myocarditis through inhibiting the production of proinflammatory cytokines. The findings suggest that alpha7 nAChR agonists may be a promising new strategy for patients with viral myocarditis. PMID:26507386

  8. Dose-dependent protective effect of nicotine in a murine model of viral myocarditis induced by coxsackievirus B3.

    PubMed

    Li-Sha, Ge; Jing-Lin, Zhao; Guang-Yi, Chen; Li, Liu; De-Pu, Zhou; Yue-Chun, Li

    2015-10-28

    The alpha 7 nicotinic acetylcholine receptor (alpha7 nAChR) was recently described as an anti-inflammatory target in various inflammatory diseases. The aim of this study was to investigate the dose-related effects of nicotine, an alpha7 nAChR agonist, in murine model of viral myocarditis. BALB/C mice were infected by an intraperitoneally injection with coxsackievirus B3. Nicotine was administered at doses of 0.1, 0.2 or 0.4 mg/kg three times per day for 7 or 14 consecutive days. The effects of nicotine on survival, myocardial histopathological changes, cardiac function, and cytokine levels were studied. The survival rate on day 14 increased in a dose-dependent fashion and was markedly higher in the 0.2 and 0.4 mg/kg nicotine groups than in the infected untreated group. Treatment with high-dose nicotine reduced the myocardial inflammation and improved the impaired left ventricular function in infected mice. The mRNA expressions and protein levels of TNF-α, IL-1β, IL-6, and IL-17A were significantly downregulated in dose-dependent manners in the nicotine treatment groups compared to the infected untreated group. Nicotine dose-dependently reduced the severity of viral myocarditis through inhibiting the production of proinflammatory cytokines. The findings suggest that alpha7 nAChR agonists may be a promising new strategy for patients with viral myocarditis.

  9. Institutional Animal Care and Use Committee Considerations Regarding the Use of Virus-Induced Carcinogenesis and Oncolytic Viral Models.

    PubMed

    Lewis, Stephanie D; Hickman-Davis, Judy M; Bergdall, Valerie K

    2016-01-01

    The use of virus-induced carcinogenesis and oncologic experimental animal models is essential in understanding the mechanisms of cancer development to advance prevention, diagnosis, and treatment methods. The Institutional Animal Care and Use Committee (IACUC) is responsible for both the complex philosophical and practical considerations associated with animal models of cancer. Animal models of cancer carry their own unique issues that require special consideration from the IACUC. Many of the considerations to be discussed apply to cancer models in general; specific issues related to viral carcinogenesis or oncolytic viruses will be specifically discussed as they arise. Responsible animal use integrates good science, humane care, and regulatory compliance. To meet those standards, the IACUC, in conjunction with the research investigator and attending veterinarian, must address a wide range of issues, including animal model selection, cancer model selection, humane end point considerations, experimental considerations, postapproval monitoring, reporting requirements, and animal management and personnel safety considerations.

  10. A cell-based model system links chromothripsis with hyperploidy

    PubMed Central

    Mardin, Balca R; Drainas, Alexandros P; Waszak, Sebastian M; Weischenfeldt, Joachim; Isokane, Mayumi; Stütz, Adrian M; Raeder, Benjamin; Efthymiopoulos, Theocharis; Buccitelli, Christopher; Segura-Wang, Maia; Northcott, Paul; Pfister, Stefan M; Lichter, Peter; Ellenberg, Jan; Korbel, Jan O

    2015-01-01

    A remarkable observation emerging from recent cancer genome analyses is the identification of chromothripsis as a one-off genomic catastrophe, resulting in massive somatic DNA structural rearrangements (SRs). Largely due to lack of suitable model systems, the mechanistic basis of chromothripsis has remained elusive. We developed an integrative method termed “complex alterations after selection and transformation (CAST),” enabling efficient in vitro generation of complex DNA rearrangements including chromothripsis, using cell perturbations coupled with a strong selection barrier followed by massively parallel sequencing. We employed this methodology to characterize catastrophic SR formation processes, their temporal sequence, and their impact on gene expression and cell division. Our in vitro system uncovered a propensity of chromothripsis to occur in cells with damaged telomeres, and in particular in hyperploid cells. Analysis of primary medulloblastoma cancer genomes verified the link between hyperploidy and chromothripsis in vivo. CAST provides the foundation for mechanistic dissection of complex DNA rearrangement processes. PMID:26415501

  11. Optimizing Viral Discovery in Bats

    PubMed Central

    Young, Cristin C. W.; Olival, Kevin J.

    2016-01-01

    Viral discovery studies in bats have increased dramatically over the past decade, yet a rigorous synthesis of the published data is lacking. We extract and analyze data from 93 studies published between 2007–2013 to examine factors that increase success of viral discovery in bats, and specific trends and patterns of infection across host taxa and viral families. Over the study period, 248 novel viruses from 24 viral families have been described. Using generalized linear models, at a study level we show the number of host species and viral families tested best explained number of viruses detected. We demonstrate that prevalence varies significantly across viral family, specimen type, and host taxonomy, and calculate mean PCR prevalence by viral family and specimen type across all studies. Using a logistic model, we additionally identify factors most likely to increase viral detection at an individual level for the entire dataset and by viral families with sufficient sample sizes. Our analysis highlights major taxonomic gaps in recent bat viral discovery efforts and identifies ways to improve future viral pathogen detection through the design of more efficient and targeted sample collection and screening approaches. PMID:26867024

  12. Optimizing Viral Discovery in Bats.

    PubMed

    Young, Cristin C W; Olival, Kevin J

    2016-01-01

    Viral discovery studies in bats have increased dramatically over the past decade, yet a rigorous synthesis of the published data is lacking. We extract and analyze data from 93 studies published between 2007-2013 to examine factors that increase success of viral discovery in bats, and specific trends and patterns of infection across host taxa and viral families. Over the study period, 248 novel viruses from 24 viral families have been described. Using generalized linear models, at a study level we show the number of host species and viral families tested best explained number of viruses detected. We demonstrate that prevalence varies significantly across viral family, specimen type, and host taxonomy, and calculate mean PCR prevalence by viral family and specimen type across all studies. Using a logistic model, we additionally identify factors most likely to increase viral detection at an individual level for the entire dataset and by viral families with sufficient sample sizes. Our analysis highlights major taxonomic gaps in recent bat viral discovery efforts and identifies ways to improve future viral pathogen detection through the design of more efficient and targeted sample collection and screening approaches. PMID:26867024

  13. Linking the M&Rfi Weather Generator with Agrometeorological Models

    NASA Astrophysics Data System (ADS)

    Dubrovsky, Martin; Trnka, Miroslav

    2015-04-01

    Realistic meteorological inputs (representing the present and/or future climates) for the agrometeorological model simulations are often produced by stochastic weather generators (WGs). This contribution presents some methodological issues and results obtained in our recent experiments. We also address selected questions raised in the synopsis of this session. The input meteorological time series for our experiments are produced by the parametric single site weather generator (WG) Marfi, which is calibrated from the available observational data (or interpolated from surrounding stations). To produce meteorological series representing the future climate, the WG parameters are modified by climate change scenarios, which are prepared by the pattern scaling method: the standardised scenarios derived from Global or Regional Climate Models are multiplied by the change in global mean temperature (ΔTG) determined by the simple climate model MAGICC. The presentation will address following questions: (i) The dependence of the quality of the synthetic weather series and impact results on the WG settings. An emphasis will be put on an effect of conditioning the daily WG on monthly WG (presently being one of our hot topics), which aims at improvement of the reproduction of the low-frequency weather variability. Comparison of results obtained with various WG settings is made in terms of climatic and agroclimatic indices (including extreme temperature and precipitation characteristics and drought indices). (ii) Our methodology accounts for the uncertainties coming from various sources. We will show how the climate change impact results are affected by 1. uncertainty in climate modelling, 2. uncertainty in ΔTG, and 3. uncertainty related to the complexity of the climate change scenario (focusing on an effect of inclusion of changes in variability into the climate change scenarios). Acknowledgements: This study was funded by project "Building up a multidisciplinary scientific

  14. An economic model to evaluate the mitigation programme for bovine viral diarrhoea in Switzerland.

    PubMed

    Häsler, B; Howe, K S; Presi, P; Stärk, K D C

    2012-09-15

    Economic analyses are indispensable as sources of information to help policy makers make decisions about mitigation resource use. The aim of this study was to conduct an economic evaluation of the Swiss national mitigation programme for bovine viral diarrhoea virus (BVDV), which was implemented in 2008 and concludes in 2017. The eradication phase of the mitigation programme comprised testing and slaughtering of all persistently infected (PI) animals found. First, the whole population was antigen tested and all PI cattle removed. Since October 2008, all newborn calves have been subject to antigen testing to identify and slaughter PI calves. All mothers of PI calves were retested and slaughtered if the test was positive. Antigen testing in calves and elimination of virus-carriers was envisaged to be conducted until the end of 2011. Subsequently, a surveillance programme will document disease freedom or detect disease if it recurs. Four alternative surveillance strategies based on antibody testing in blood from newborn calves and/or milk from primiparous cows were proposed by Federal Veterinary Office servants in charge of the BVDV mitigation programme. A simple economic spreadsheet model was developed to estimate and compare the costs and benefits of the BVDV mitigation programme. In an independent project, the impact of the mitigation programme on the disease dynamics in the population was simulated using a stochastic compartment model. Mitigation costs accrued from materials, labour, and processes such as handling and testing samples, and recording results. Benefits were disease costs avoided by having the mitigation programme in place compared to a baseline of endemic disease equilibrium. Cumulative eradication costs and benefits were estimated to determine the break-even point for the eradication component of the programme. The margin over eradication cost therefore equalled the maximum expenditure potentially available for surveillance without the net benefit

  15. Viral arthritis

    PubMed Central

    Marks, Michael; Marks, Jonathan L

    2016-01-01

    Acute-onset arthritis is a common clinical problem facing both the general clinician and the rheumatologist. A viral aetiology is though to be responsible for approximately 1% of all cases of acute arthritis with a wide range of causal agents recognised. The epidemiology of acute viral arthritis continues to evolve, with some aetiologies, such as rubella, becoming less common due to vaccination, while some vector-borne viruses have become more widespread. A travel history therefore forms an important part of the assessment of patients presenting with an acute arthritis. Worldwide, parvovirus B19, hepatitis B and C, HIV and the alphaviruses are among the most important causes of virally mediated arthritis. Targeted serological testing may be of value in establishing a diagnosis, and clinicians must also be aware that low-titre autoantibodies, such as rheumatoid factor and antinuclear antibody, can occur in the context of acute viral arthritis. A careful consideration of epidemiological, clinical and serological features is therefore required to guide clinicians in making diagnostic and treatment decisions. While most virally mediated arthritides are self-limiting some warrant the initiation of specific antiviral therapy. PMID:27037381

  16. Lysine directed cross-linking of viral DNA-RNA:DNA hybrid substrate to the isolated RNase H domain of HIV-1 reverse transcriptase.

    PubMed

    Guaitiao, Juan P; Zúñiga, Roberto A; Roth, Monica J; Leon, Oscar

    2004-02-10

    An isolated ribonuclease H domain of HIV-1 reverse transcriptase is capable of specifically removing the tRNA primer within an oligonucleotide mimic. The determinants for substrate specificity are located in a region within the terminal octanucleotide of the acceptor stem of the tRNA. Recognition of the substrate by HIV-1 RNase H was analyzed by the introduction of a cross-linking reagent directed toward lysines on the thymine residue complementary to the scissile bond, facing the major groove of the DNA-RNA:DNA substrate. Cross-linking of the modified substrate to RNase H required the presence of Mn(2+). The Mn(2+) titration of cross-linking paralleled the Mn(2+) requirement for activity. Modified substrate quenched with glycine prior to binding of substrate was efficiently cleaved, whereas the RNA within the cross-linked product was intact. Tryptic digestion of the isolated RNase H-nucleic acid covalent complex revealed a main cross-linked peptide whose N-terminal peptide sequence is VVTLTDTTNQ, indicating that the cross-linked lysine corresponds to Lys476. Cross-linking to K476 was confirmed by analysis of K476C RNase H. Mutation of K476C disrupted the chemical cross-linking while maintaining activity. On the basis of the size of the cross-linker arm, the results indicate that K476 is in closer proximity to the tRNA mimic substrate within the isolated RNase H domain than observed for the RNase H-resistant polypurine tract (PPT) substrate within the HIV-1 RT.

  17. Improving Power System Modeling. A Tool to Link Capacity Expansion and Production Cost Models

    SciTech Connect

    Diakov, Victor; Cole, Wesley; Sullivan, Patrick; Brinkman, Gregory; Margolis, Robert

    2015-11-01

    Capacity expansion models (CEM) provide a high-level long-term view at the prospects of the evolving power system. In simulating the possibilities of long-term capacity expansion, it is important to maintain the viability of power system operation in the short-term (daily, hourly and sub-hourly) scales. Production-cost models (PCM) simulate routine power system operation on these shorter time scales using detailed load, transmission and generation fleet data by minimizing production costs and following reliability requirements. When based on CEM 'predictions' about generating unit retirements and buildup, PCM provide more detailed simulation for the short-term system operation and, consequently, may confirm the validity of capacity expansion predictions. Further, production cost model simulations of a system that is based on capacity expansion model solution are 'evolutionary' sound: the generator mix is the result of logical sequence of unit retirement and buildup resulting from policy and incentives. The above has motivated us to bridge CEM with PCM by building a capacity expansion - to - production cost model Linking Tool (CEPCoLT). The Linking Tool is built to onset capacity expansion model prescriptions onto production cost model inputs. NREL's ReEDS and Energy Examplar's PLEXOS are the capacity expansion and the production cost models, respectively. Via the Linking Tool, PLEXOS provides details of operation for the regionally-defined ReEDS scenarios.

  18. Link Analysis

    NASA Astrophysics Data System (ADS)

    Donoho, Steve

    Link analysis is a collection of techniques that operate on data that can be represented as nodes and links. This chapter surveys a variety of techniques including subgraph matching, finding cliques and K-plexes, maximizing spread of influence, visualization, finding hubs and authorities, and combining with traditional techniques (classification, clustering, etc). It also surveys applications including social network analysis, viral marketing, Internet search, fraud detection, and crime prevention.

  19. Viral potassium channels as a robust model system for studies of membrane-protein interaction.

    PubMed

    Braun, Christian J; Lachnit, Christine; Becker, Patrick; Henkes, Leonhard M; Arrigoni, Cristina; Kast, Stefan M; Moroni, Anna; Thiel, Gerhard; Schroeder, Indra

    2014-04-01

    The viral channel KcvNTS belongs to the smallest K(+) channels known so far. A monomer of a functional homotetramer contains only 82 amino acids. As a consequence of the small size the protein is almost fully submerged into the membrane. This suggests that the channel is presumably sensitive to its lipid environment. Here we perform a comparative analysis for the function of the channel protein embedded in three different membrane environments. 1. Single-channel currents of KcvNTS were recorded with the patch clamp method on the plasma membrane of HEK293 cells. 2. They were also measured after reconstitution of recombinant channel protein into classical planar lipid bilayers and 3. into horizontal bilayers derived from giant unilamellar vesicles (GUVs). The recombinant channel protein was either expressed and purified from Pichia pastoris or from a cell-free expression system; for the latter a new approach with nanolipoprotein particles was used. The data show that single-channel activity can be recorded under all experimental conditions. The main functional features of the channel like a large single-channel conductance (80pS), high open-probability (>50%) and the approximate duration of open and closed dwell times are maintained in all experimental systems. An apparent difference between the approaches was only observed with respect to the unitary conductance, which was ca. 35% lower in HEK293 cells than in the other systems. The reason for this might be explained by the fact that the channel is tagged by GFP when expressed in HEK293 cells. Collectively the data demonstrate that the small viral channel exhibits a robust function in different experimental systems. This justifies an extrapolation of functional data from these systems to the potential performance of the channel in the virus/host interaction. This article is part of a Special Issue entitled: Viral Membrane Proteins-Channels for Cellular Networking. PMID:23791706

  20. Enterovirus 71-induced autophagy increases viral replication and pathogenesis in a suckling mouse model

    PubMed Central

    2014-01-01

    Background We previously reported that Enterovirus 71 (EV71) infection activates autophagy, which promotes viral replication both in vitro and in vivo. In the present study we further investigated whether EV71 infection of neuronal SK-N-SH cells induces an autophagic flux. Furthermore, the effects of autophagy on EV71-related pathogenesis and viral load were evaluated after intracranial inoculation of mouse-adapted EV71 (MP4 strain) into 6-day-old ICR suckling mice. Results We demonstrated that in EV71-infected SK-N-SH cells, EV71 structural protein VP1 and nonstructural protein 2C co-localized with LC3 and mannose-6-phosphate receptor (MPR, endosome marker) proteins by immunofluorescence staining, indicating amphisome formation. Together with amphisome formation, EV71 induced an autophagic flux, which could be blocked by NH4Cl (inhibitor of acidification) and vinblastine (inhibitor of fusion), as demonstrated by Western blotting. Suckling mice intracranially inoculated with EV71 showed EV71 VP1 protein expression (representing EV71 infection) in the cerebellum, medulla, and pons by immunohistochemical staining. Accompanied with these infected brain tissues, increased expression of LC3-II protein as well as formation of LC3 aggregates, autophagosomes and amphisomes were detected. Amphisome formation, which was confirmed by colocalization of EV71-VP1 protein or LC3 puncta and the endosome marker protein MPR. Thus, EV71-infected suckling mice (similar to EV71-infected SK-N-SH cells) also show an autophagic flux. The physiopathological parameters of EV71-MP4 infected mice, including body weight loss, disease symptoms, and mortality were increased compared to those of the uninfected mice. We further blocked EV71-induced autophagy with the inhibitor 3-methyladenine (3-MA), which attenuated the disease symptoms and decreased the viral load in the brain tissues of the infected mice. Conclusions In this study, we reveal that EV71 infection of suckling mice induces an

  1. Linking Student Retention Model with Institutional Planning: The Benefits and Limitations of a Student Matrix Model.

    ERIC Educational Resources Information Center

    Schartman, Laura; Rhee, Byung-Shik

    This study explored the possibility of linking the Luna (1999) student flow matrix model with institutional planning at a comprehensive state institution, investigating how student flow environments were associated with student characteristics such as race, gender, citizenship, class level, entry type, and cumulative grade point average. The study…

  2. Exposure to Electronic Cigarettes Impairs Pulmonary Anti-Bacterial and Anti-Viral Defenses in a Mouse Model

    PubMed Central

    Sussan, Thomas E.; Gajghate, Sachin; Thimmulappa, Rajesh K.; Ma, Jinfang; Kim, Jung-Hyun; Sudini, Kuladeep; Consolini, Nicola; Cormier, Stephania A.; Lomnicki, Slawo; Hasan, Farhana; Pekosz, Andrew; Biswal, Shyam

    2015-01-01

    Electronic cigarettes (E-cigs) have experienced sharp increases in popularity over the past five years due to many factors, including aggressive marketing, increased restrictions on conventional cigarettes, and a perception that E-cigs are healthy alternatives to cigarettes. Despite this perception, studies on health effects in humans are extremely limited and in vivo animal models have not been generated. Presently, we determined that E-cig vapor contains 7x1011 free radicals per puff. To determine whether E-cig exposure impacts pulmonary responses in mice, we developed an inhalation chamber for E-cig exposure. Mice that were exposed to E-cig vapor contained serum cotinine concentrations that are comparable to human E-cig users. E-cig exposure for 2 weeks produced a significant increase in oxidative stress and moderate macrophage-mediated inflammation. Since, COPD patients are susceptible to bacterial and viral infections, we tested effects of E-cigs on immune response. Mice that were exposed to E-cig vapor showed significantly impaired pulmonary bacterial clearance, compared to air-exposed mice, following an intranasal infection with Streptococcus pneumonia. This defective bacterial clearance was partially due to reduced phagocytosis by alveolar macrophages from E-cig exposed mice. In response to Influenza A virus infection, E-cig exposed mice displayed increased lung viral titers and enhanced virus-induced illness and mortality. In summary, this study reports a murine model of E-cig exposure and demonstrates that E-cig exposure elicits impaired pulmonary anti-microbial defenses. Hence, E-cig exposure as an alternative to cigarette smoking must be rigorously tested in users for their effects on immune response and susceptibility to bacterial and viral infections. PMID:25651083

  3. Activating Receptor NKG2D Targets RAE-1-Expressing Allogeneic Neural Precursor Cells in a Viral Model of Multiple Sclerosis

    PubMed Central

    Weinger, Jason G.; Plaisted, Warren C.; Maciejewski, Sonia M.; Lanier, Lewis L.; Walsh, Craig M.; Lane, Thomas E.

    2014-01-01

    Transplantation of major histocompatibility complex (MHC)-mismatched mouse neural precursor cells (NPCs) into mice persistently infected with the neurotropic JHM strain of mouse hepatitis virus (JHMV) results in rapid rejection that is mediated, in part, by T cells. However, the contribution of the innate immune response to allograft rejection in a model of viral-induced neurological disease has not been well defined. Herein, we demonstrate that the natural killer (NK) cell-expressing activating receptor NKG2D participates in transplanted allogeneic NPC rejection in mice persistently infected with JHMV. Cultured NPCs derived from C57BL/6 (H-2b) mice express the NKG2D ligand retinoic acid early precursor transcript (RAE)-1 but expression was dramatically reduced upon differentiation into either glia or neurons. RAE-1+ NPCs were susceptible to NK cell-mediated killing whereas RAE-1- cells were resistant to lysis. Transplantation of C57BL/6-derived NPCs into JHMV-infected BALB/c (H-2d) mice resulted in infiltration of NKG2D+CD49b+ NK cells and treatment with blocking antibody specific for NKG2D increased survival of allogeneic NPCs. Further, transplantation of differentiated RAE-1- allogeneic NPCs into JHMV-infected BALB/c mice resulted in enhanced survival, highlighting a role for the NKG2D:RAE-1 signaling axis in allograft rejection. We also demonstrate that transplantation of allogeneic NPCs into JHMV-infected mice resulted in infection of the transplanted cells suggesting that these cells may be targets for infection. Viral infection of cultured cells increased RAE-1 expression, resulting in enhanced NK cell-mediated killing through NKG2D recognition. Collectively, these results show that in a viral-induced demyelination model, NK cells contribute to rejection of allogeneic NPCs through an NKG2D signaling pathway. PMID:24898518

  4. NCBI viral genomes resource.

    PubMed

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

  5. Protein kinase R reveals an evolutionary model for defeating viral mimicry

    PubMed Central

    Elde, Nels C.; Child, Stephanie J.; Geballe, Adam P.; Malik, Harmit S.

    2008-01-01

    Distinguishing self from non-self is a fundamental biological challenge. Many pathogens exploit the challenge of self discrimination by employing mimicry to subvert key cellular processes including the cell cycle, apoptosis, and cytoskeletal dynamics1-5. Other mimics interfere with immunity6, 7. Poxviruses encode K3L, a mimic of eIF2α, which is the substrate of Protein Kinase R (PKR), an important component of innate immunity in vertebrates8, 9. The PKR-K3L interaction exemplifies the conundrum imposed by viral mimicry. To be effective, PKR must recognize a conserved substrate (eIF2α) while avoiding rapidly evolving substrate mimics like K3L. Using the PKR-K3L system and a combination of phylogenetic and functional analyses, we uncover evolutionary strategies by which host proteins can overcome mimicry. We find that PKR has evolved under dramatic episodes of positive selection in primates. The ability of PKR to evade viral mimics is partly due to positive selection at sites most intimately involved in eIF2α recognition. We also find that adaptive changes on multiple surfaces of PKR produce combinations of substitutions that increase the odds of defeating mimicry. Thus, while it can appear that pathogens gain insurmountable advantages by mimicking cellular components, host factors like PKR can compete in molecular ‘arms races’ with mimics because of remarkable evolutionary flexibility at protein interaction interfaces challenged by mimicry. PMID:19043403

  6. UAS Modeling of the Communication Links Study Results

    NASA Technical Reports Server (NTRS)

    Birr, Richard; Murray, Jennifer; Girgis, nancy

    2011-01-01

    There were many links calculated for this and the other scenarios. The rain was analyzed for 99.9% availability with rain rated of none, 20 mm/hr and 90 mm/hr at a height of 5 km out to 25 NM. This was done for each scenario for LOS and for BLOS links for Scenario 5 and 6. Scenario 1 was a LOS-only scenario. Use of two 3 dB Antennas on both ends. The CS2 was unable to maintain a control RF Link during the flight. The largest access gap periods between object top and bottom UA antennae were caused by terrain (ridges and hills). The CS Antenna was changed to High Gain Directional Antenna, all three CS maintained lock on vehicle. There were RF dropouts between the top and bottom UA antennae caused by aircraft obstructions (fuselage, wings, wheel assembles, etc.). Note that for this study antenna locations were placed on top and bottom center of the UA body. Future study should include actual UA antenna locations on the aircraft providing manufactures are willing to provide information. The importance of CS location(s) was demonstrated for primary or backup CS. With a second backup CS placed in a suitable location the UA was able to maintain an overall RF link. The actual location of both backup CSs required the antenna location to be place 150 ft above ground in order to establish a RF link between the UA and CS.

  7. Viral Hepatitis

    MedlinePlus

    ... with hepatitis? How does a pregnant woman pass hepatitis B virus to her baby? If I have hepatitis B, what does my baby need so that she ... Can I breastfeed my baby if I have hepatitis B? More information on viral hepatitis What is hepatitis? ...

  8. Reactivation of latently infected HIV-1 viral reservoirs and correction of aberrant alternative splicing in the LMNA gene via AMPK activation: Common mechanism of action linking HIV-1 latency and Hutchinson-Gilford progeria syndrome.

    PubMed

    Finley, Jahahreeh

    2015-09-01

    AMPK, a master regulator of cellular metabolism which has been shown to activate PKC-theta (θ) and is essential for T cell activation, may modulate the splicing activities of SRp55 as well as enhance a p32-mediated inhibition of ASF/SF2-induced alternative splicing, potentially correcting aberrant alternative splicing in the LMNA gene and reactivating latent viral HIV-1 reservoirs. Moreover, similar epigenetic modifications and cell cycle regulators also characterize the analogous stages of premature senescence in progeroid cells and latency in HIV-1 infected T cells. AMPK-activating compounds including metformin and resveratrol may thus embody a novel treatment paradigm linking the pathophysiology of HGPS with that of HIV-1 latency.

  9. A novel animal model linking adiposity to altered circadian rhythms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Researchers have provided evidence for a link between obesity and altered circadian rhythms (e.g., shift work, disrupted sleep), but the mechanism for this association is still unknown. Adipocytes possess an intrinsic circadian clock, and circadian rhythms in adipocytokines and adipose tissue metab...

  10. Noncytopathic bovine viral diarrhea virus 2 impairs virus control in a mouse model.

    PubMed

    Seong, Giyong; Lee, Jin-Sol; Lee, Kyung-Hyun; Shin, Seung-Uk; Yoon, Ji Young; Choi, Kyoung-Seong

    2016-02-01

    Bovine viral diarrhea virus (BVDV) is an economically important pathogen that causes development of mild to severe clinical signs in wild and domesticated ruminants. We previously showed that mice could be infected by BVDV. In the present study, we infected mice intraperitoneally with non-cytopathic (ncp) BVDV1 or ncp BVDV2, harvested the blood and organs of the infected mice at days 4, 7, 10 and 14 postinfection (pi), and performed immunohistochemical analyses to confirm BVDV infection. Viral antigens were detected in the spleens of all infected mice from days 4 through 14 and were also found in the mesenteric lymph nodes, gut-associated lymphoid tissue (GALT), heart, kidney, intestine, and bronchus-associated lymphoid tissue (BALT) of some infected mice. In ncp BVDV2-infected mice, flow cytometric analysis revealed markedly fewer CD4(+) and CD8(+) T lymphocytes and lower expression of costimulatory molecules CD80 (B7-1) and CD86 (B7-2) and major histocompatibility complex (MHC) class II (I-A/I-E) than those in ncp BVDV1-infected mice. Production of the cytokines interleukin (IL)-6 and monocyte chemotactic protein (MCP)-1 was higher in the plasma of ncp BVDV2-infected mice than that in that of ncp BVDV1-infected mice. Our results demonstrate that ncp BVDV1 and ncp BVDV2 interact differently with the host innate immune response in vivo. These findings highlight an important distinction between ncp BVDV1 and ncp BVDV2 and suggest that ncp BVDV2 impairs the host's ability to control the infection and enhances virus dissemination.

  11. Modeling and Simulation of a Slider Crank Mechanism with a Flexible Extensible Link

    NASA Astrophysics Data System (ADS)

    Dupac, M.; Noroozi, S.

    In this paper the modelling of a slider-crank mechanism with an extensible flexible link is presented and its dynamical behaviour analyzed. The link flexibility is modelled using extensible rigid links and rotational springs. The equations of motion with and without slider clearance are written. Accurate simulation of the extensible mechanism is performed to study its possible performance and behaviour under the combined effect of different parameters. A dynamic analysis is carried out in order to understand its behaviour under motion reconfiguration.

  12. Viral Space Situational Awareness

    NASA Astrophysics Data System (ADS)

    Gleckler, A.; Butterfield, M. C.

    2012-09-01

    Viral SSA takes advantage of the amateur astronomy community to provide an extremely low-cost and geographically-diverse network of optical SSA sites. In the spirit of programs such as DARPA's Grand Challenge and the National Weather Service's program of providing amateur meteorologists with weather stations linked to a central professional meteorological facility, we form a cooperative bond with a willing community of technically-minded individuals. We term this program "viral" because we will qualify an initial set of astronomers for SSA operation and then use word of mouth in the astronomy community, as well as an outreach program, to pull in new observers. The use of modern remote controlled telescopes allows the incorporation of certified amateur, university, and commercial telescope systems. The availability of the local Viral SSA member for troubleshooting eliminates most significant costs of operating a large network. In this talk, we discuss the key concepts of Viral SSA and the route to a network of 100+ sites in a three year or less timeframe.

  13. Animal models for some important RNA viruses of public health concern in SEARO countries: viral hemorrhagic fever.

    PubMed

    Badole, Sachin L; Yadav, Pragya D; Patil, Dilip R; Mourya, Devendra T

    2015-03-01

    Viral hemorrhagic fevers (VHFs) are major public health problems in the South-East Asia Regional (SEAR) countries. VHFs are a group of illnesses; that are caused by four families of viruses, viz. Arenaviridae, Bunyaviridae, Filoviridae and Flaviviridae. All VHFs have common features: they affect several organs and damage the blood vessels. These symptoms are often accompanied by hemorrhage. To understand pathogenesis, genetic and environmental influence that increase the risk of VHFs, efficacy and safety studies on candidate vaccines and testing of various therapeutic agents, appropriate animal models are essential tools in public and animals health. In the current review, the suitable animal models for Flavivirus [Dengue hemorhagic fever (DHF), Kyasanur forest disease (KFD)]; Bunyavirus [Crimean-Congo hemorrhagic fever (CCHF), Hantavirus fever (HF)]; and Paramyxovirus [Nipah virus fever (NiV)] have been reviewed with specific emphasis on emerging and reemerging viruses in SEAR countries.

  14. Multilevel and Latent Variable Modeling with Composite Links and Exploded Likelihoods

    ERIC Educational Resources Information Center

    Rabe-Hesketh, Sophia; Skrondal, Anders

    2007-01-01

    Composite links and exploded likelihoods are powerful yet simple tools for specifying a wide range of latent variable models. Applications considered include survival or duration models, models for rankings, small area estimation with census information, models for ordinal responses, item response models with guessing, randomized response models,…

  15. A measurement model of medication adherence to highly active antiretroviral therapy and its relation to viral load in HIV-positive adults.

    PubMed

    Llabre, Maria M; Weaver, Kathryn E; Durán, Ron E; Antoni, Michael H; McPherson-Baker, Shvawn; Schneiderman, Neil

    2006-10-01

    This study compared a multiple method measurement model of highly active antiretroviral therapy (HAART) adherence with single-method models to determine optimal validity in predicting HIV viral load. Repeated measures of antiretroviral adherence were collected over a 15-month period using three different measurement methods: a self-report questionnaire, an adherence interview item, and electronic medication monitoring. The participants included HIV-positive men and women (n = 323) who were currently prescribed HAART. Single-factor models composed of multiple measurements over time were developed for each adherence method and HIV viral load. The three adherence methods were then combined in a second order factor measurement model. Structural equation modeling was used to test the models. Mean adherence, defined as percent of doses taken, was 92%, 90%, and 57% by self-report, interview, and electronic monitoring, respectively. Reliability of individual measurements of adherence was low. Four or seven assessments were needed to attain acceptable stability, depending on the method. The second-order factor model of adherence fit the data and explained 45% of the variability in HIV viral load. Models including only one method of assessing adherence explained between 20% and 24% of the variability. Models that included both self-report and electronic monitoring optimized predictive validity. Using at least two different methods of adherence measurement, each assessed at multiple times is recommended to derive reliable and valid measurement of medication adherence, which is predictive of biological outcomes such as HIV viral load.

  16. Viral Exanthem

    MedlinePlus

    ... References/Trusted Links Related diseases: Chickenpox (Varicella) Hand-Foot-and-Mouth Disease Roseola (Sixth Disease) Scarlet Fever View all diseases Community: Discussion Forum Skinmatters Blog ...

  17. Viral Diseases in Zebrafish: What Is Known and Unknown

    PubMed Central

    Crim, Marcus J.; Riley, Lela K.

    2013-01-01

    Naturally occurring viral infections have the potential to introduce confounding variability that leads to invalid and misinterpreted data. Whereas the viral diseases of research rodents are well characterized and closely monitored, no naturally occurring viral infections have been characterized for the laboratory zebrafish (Danio rerio), an increasingly important biomedical research model. Despite the ignorance about naturally occurring zebrafish viruses, zebrafish models are rapidly expanding in areas of biomedical research where the confounding effects of unknown infectious agents present a serious concern. In addition, many zebrafish research colonies remain linked to the ornamental (pet) zebrafish trade, which can contribute to the introduction of new pathogens into research colonies, whereas mice used for research are purpose bred, with no introduction of new mice from the pet industry. Identification, characterization, and monitoring of naturally occurring viruses in zebrafish are crucial to the improvement of zebrafish health, the reduction of unwanted variability, and the continued development of the zebrafish as a model organism. This article addresses the importance of identifying and characterizing the viral diseases of zebrafish as the scope of zebrafish models expands into new research areas and also briefly addresses zebrafish susceptibility to experimental viral infection and the utility of the zebrafish as an infection and immunology model. PMID:23382345

  18. Covalent cross-links in polyampholytic chitosan fibers enhances bone regeneration in a rabbit model.

    PubMed

    Ghosh, Paulomi; Rameshbabu, Arun Prabhu; Das, Dipankar; Francis, Nimmy K; Pawar, Harpreet Singh; Subramanian, Bhuvaneshwaran; Pal, Sagar; Dhara, Santanu

    2015-01-01

    Chitosan fibers were prepared in citric acid bath, pH 7.4 and NaOH solution at pH 13, to form ionotropically cross-linked and uncross-linked fibers, respectively. The fibers formed in citric acid bath were further cross-linked via carbodiimide chemistry; wherein the pendant carboxyl moieties of citric acid were used for new amide bond formation. Moreover, upon covalent cross-linking in the ionically gelled citrate-chitosan fibers, incomplete conversion of the ion pairs to amide linkages took place resulting in the formation of a dual network structure. The dual cross-linked fibers displayed improved mechanical property, higher stability against enzymatic degradation, hydrophobicity and superior bio-mineralization compared to the uncross-linked and native citrate cross-linked fibers. Additionally, upon cyclic loading, the ion pairs in the dual cross-linked fibers dissociated by dissipating energy and reformed during the relaxation period. The twin property of elasticity and energy dissipation mechanism makes the dual cross-linked fiber unique under dynamic mechanical conditions. The differences in the physico-chemical characteristics were reflected in protein adsorption, which in turn influenced the cellular activities on the fibers. Compared to the uncross-linked and ionotropically cross-linked fibers, the dual cross-linked fibers demonstrated higher proliferation and osteogenic differentiation of the MSCs in vitro as well as better osseous tissue regeneration in a rabbit model. PMID:25483844

  19. CXCR4 Signaling Regulates Remyelination by Endogenous Oligodendrocyte Progenitor Cells in a Viral Model of Demyelination

    PubMed Central

    CARBAJAL, KEVIN S.; MIRANDA, JUAN L.; TSUKAMOTO, MICHELLE R.; LANE, THOMAS E.

    2016-01-01

    Following intracranial infection with the neurotropic JHM strain of mouse hepatitis virus (JHMV), susceptible mice will develop widespread myelin destruction that results in pathological and clinical outcomes similar to those seen in humans with the demyelinating disease Multiple Sclerosis (MS). Partial remyelination and clinical recovery occurs during the chronic phase following control of viral replication yet the signaling mechanisms regulating these events remain enigmatic. Here we report the kinetics of proliferation and maturation of oligodendrocyte progenitor cells (OPCs) within the spinal cord following JHMV-induced demyelination and that CXCR4 signaling contributes to the maturation state of OPCs. Following treatment with AMD3100, a specific inhibitor of CXCR4, mice recovering from widespread demyelination exhibit a significant (P < 0.01) increase in the number of OPCs and fewer (P < 0.05) mature oligodendrocytes compared with HBSS-treated animals. These results suggest that CXCR4 signaling is required for OPCs to mature and contribute to remyelination in response to JHMV-induced demyelination. To assess if this effect is reversible and has potential therapeutic benefit, we pulsed mice with AMD3100 and then allowed them to recover. This treatment strategy resulted in increased numbers of mature oligodendrocytes, enhanced remyelination, and improved clinical outcome. These findings highlight the possibility to manipulate OPCs in order to increase the pool of remyelination-competent cells that can participate in recovery. PMID:21830237

  20. Myocardial uptake of antimyosin monoclonal antibody in a murine model of viral myocarditis

    SciTech Connect

    Matsumori, A.; Ohkusa, T.; Matoba, Y.; Okada, I.; Yamada, T.; Kawai, C.; Tamaki, N.; Watanabe, Y.; Yonekura, Y.; Endo, K.

    1989-02-01

    The myocardial uptake of 125I- and 131I-antimyosin monoclonal antibody Fab in experimental myocarditis in BALB/c mice induced by encephalomyocarditis virus was studied. The biodistribution of 125I-antimyosin demonstrated that the highest ratio of radioactivity appears in the heart of infected mice on day 14 (the ratio of percent dose per gram for the organ to percent dose per milliliter for blood; 9.75 +/- 2.79 vs. 1.27 +/- 0.78 at 24 hours in inoculated mice vs. control mice). There was no statistically significant difference between the mean activity ratios of tissues other than the heart in control and inoculated mice. The uptake ratio for the heart increased significantly 3 days after virus inoculation and reached a maximum on day 14 when myocardial lesions were most extensive and prominent. The uptake ratio decreased significantly, but it still remained high compared with controls on day 28 when cellular infiltration had decreased and fibrosis was evident. The scintigraphic images obtained with 131I-antimyosin monoclonal antibody clearly demonstrated that visualization of the heart in experimental myocarditis was possible 24 hours after administration of radiotracer, and localized activity was still observed in the 48-hour image. We conclude that antimyosin monoclonal antibodies localize selectively in the heart from the acute to subacute stage of viral myocarditis. These findings indicate that antimyosin scintigraphy is a reliable noninvasive method for the evaluation of patients suspected of having myocarditis.

  1. Kallikrein 6 Regulates Early CNS Demyelination in a Viral Model of Multiple Sclerosis

    PubMed Central

    Scarisbrick, Isobel A.; Yoon, Hyesook; Panos, Michael; Larson, Nadya; Blaber, Sachiko I.; Blaber, Michael; Rodriguez, Moses

    2012-01-01

    Kallikrein 6 (Klk6) is a secreted serine protease that is elevated in active multiple sclerosis lesions and patient sera. To further evaluate the involvement of Klk6 in chronic progressive demyelinating disease, we determined its expression in the brain and spinal cord of SJL mice infected with Theiler’s murine encephalomyelitis virus (TMEV) and assessed the effects of Klk6-neutralizing antibodies on disease progression. Klk6 RNA expression was elevated in the brain and spinal cord by 7 days post-infection (dpi). Thereafter, Klk6 expression persisted primarily in the spinal cord reaching a peak of 5-fold over controls at mid-chronic stages (60–120 dpi). Significant elevations in Klk6 RNA were also induced in splenocytes stimulated with viral capsid proteins in vitro and in activated THP-1 monocytes. Klk6-neutralizing antibodies reduced TMEV-driven brain and spinal cord pathology and DTH responses when examined at early chronic time points (40 dpi). Reductions in spinal cord pathology included a decrease in activated monocytes/microglia and reductions in the loss of myelin basic protein (MBP). By 180 dpi, pathology scores no longer differed between groups. These findings point to regulatory activities for Klk6 in the development and progression of CNS inflammation and demyelination that can be effectively targeted through the early chronic stages with neutralizing antibody. PMID:22335454

  2. Akabane virus nonstructural protein NSm regulates viral growth and pathogenicity in a mouse model

    PubMed Central

    ISHIHARA, Yukari; SHIODA, Chieko; BANGPHOOMI, Norasuthi; SUGIURA, Keita; SAEKI, Kohei; TSUDA, Shumpei; IWANAGA, Tatsuya; TAKENAKA-UEMA, Akiko; KATO, Kentaro; MURAKAMI, Shin; UCHIDA, Kazuyuki; AKASHI, Hiroomi; HORIMOTO, Taisuke

    2016-01-01

    The biological function of a nonstructural protein, NSm, of Akabane virus (AKAV) is unknown. In this study, we generated a series of NSm deletion mutant viruses by reverse genetics and compared their phenotypes. The mutant in which the NSm coding region was almost completely deleted could not be rescued, suggesting that NSm plays a role in virus replication. We next generated mutant viruses possessing various partial deletions in NSm and identified several regions critical for virus infectivity. All rescued mutant viruses produced smaller plaques and grew inefficiently in cell culture, compared to the wild-type virus. Interestingly, although the pathogenicity of NSm deletion mutant viruses varied in mice depending on their deletion regions and sizes, more than half the mice died following infection with any mutant virus and the dead mice exhibited encephalitis as in wild-type virus-inoculated mice, indicating their neuroinvasiveness. Abundant viral antigens were detected in the brain tissues of dead mice, whereas appreciable antigen was not observed in those of surviving mice, suggesting a correlation between virus growth rate in the brain and neuropathogenicity in mice. We conclude that NSm affects AKAV replication in vitro as well as in vivo and that it may function as a virulence factor. PMID:27181086

  3. A GIS-linked model for the assessment of nitrate contamination in groundwater

    NASA Astrophysics Data System (ADS)

    Lasserre, F.; Razack, M.; Banton, O.

    1999-11-01

    A simple GIS-linked model for groundwater nitrate transport has been developed in the IDRISI GIS environment. The transport model, based on advection transport only, is directly incorporated into a GIS subroutine using the Pascal computing language. This model requires less data than classical approaches and provides a user-friendly model environment. The GIS-model was tested on a 20 km 2 hydrogeologic catchment, particularly vulnerable to agricultural nitrate pollution. The model was coupled with an unsaturated zone transport model (AgriFlux), which simulates water and nitrate fluxes leaving the root zone. The results indicated that the simulated nitrate concentrations were in good agreement with measured values. In order to compare the GIS-linked model with a more complete model, simulations were also performed with MT3D-MODFLOW. The similarities between the results of the two models confirm the validity of the GIS-linked model.

  4. Persistence of viral DNA in the epithelial basal layer suggests a model for papillomavirus latency following immune regression

    PubMed Central

    Maglennon, Gareth Adam; McIntosh, Pauline; Doorbar, John

    2011-01-01

    Rabbit oral papillomavirus (ROPV) causes benign and spontaneously regressing oral lesions in rabbits, and is a useful model of disease associated with low-risk human papillomavirus types. Here we have adapted the ROPV system to study papillomavirus latency. Following lesion regression, ROPV DNA persists at the majority of regressed sites at levels substantially lower than those found in productive papillomas. Spliced viral transcripts were also detected. ROPV persistence in the absence of disease could be demonstrated for a year following infection and lesion-regression. This was not associated with completion of the virus life-cycle or new virion production, indicating that ROPV persists in a latent state. Using novel laser capture microdissection techniques, we could show that the site of latency is a subset of basal epithelial cells at sites of previous experimental infection. We hypothesize that these cells are epithelial stem cells and that reactivation of latency may be a source of recurrent disease. PMID:21492895

  5. Imino sugars inhibit the formation and secretion of bovine viral diarrhea virus, a pestivirus model of hepatitis C virus: Implications for the development of broad spectrum anti-hepatitis virus agents

    PubMed Central

    Zitzmann, Nicole; Mehta, Anand S.; Carrouée, Sandra; Butters, Terry D.; Platt, Frances M.; McCauley, John; Blumberg, Baruch S.; Dwek, Raymond A.; Block, Timothy M.

    1999-01-01

    One function of N-linked glycans is to assist in the folding of glycoproteins by mediating interactions of the lectin-like chaperone proteins calnexin and calreticulin with nascent glycoproteins. These interactions can be prevented by inhibitors of the α-glucosidases, such as N-butyl-deoxynojirimycin (NB-DNJ) and N-nonyl-DNJ (NN-DNJ), and this causes some proteins to be misfolded and retained within the endoplasmic reticulum (ER). We have shown previously that the NN-DNJ-induced misfolding of one of the hepatitis B virus (HBV) envelope glycoproteins prevents the formation and secretion of virus in vitro and that this inhibitor alters glycosylation and reduces the viral levels in an animal model of chronic HBV infection. This led us to investigate the effect of glucosidase inhibitors on another ER-budding virus, bovine viral diarrhea virus, a tissue culture surrogate of human hepatitis C virus (HCV). Here we show that in MDBK cells α-glucosidase inhibitors prevented the formation and secretion of infectious bovine viral diarrhea virus. Data also are presented showing that NN-DNJ, compared with NB-DNJ, exhibits a prolonged retention in liver in vivo. Because viral secretion is selectively hypersensitive to glucosidase inhibition relative to the secretion of cellular proteins, the possibility that glucosidase inhibitors could be used as broad-based antiviral hepatitis agents is discussed. A single drug against HBV, HCV, and, possibly, HDV, which together chronically infect more than 400 million people worldwide, would be of great therapeutic value. PMID:10518544

  6. Design-oriented analytic model of phase and frequency modulated optical links

    NASA Astrophysics Data System (ADS)

    Monsurrò, Pietro; Saitto, Antonio; Tommasino, Pasquale; Trifiletti, Alessandro; Vannucci, Antonello; Cimmino, Rosario F.

    2016-07-01

    An analytic design-oriented model of phase and frequency modulated microwave optical links has been developed. The models are suitable for design of broadband high dynamic range optical links for antenna remoting and optical beamforming, where noise and linearity of the subsystems are a concern Digital filter design techniques have been applied to the design of optical filters working as frequency discriminator, that are the bottleneck in terms of linearity for these systems. The models of frequency modulated, phase modulated, and coherent I/Q link have been used to compare performance of the different architectures in terms of linearity and SFDR.

  7. Theory and Practice: An Integrative Model Linking Class and Field

    ERIC Educational Resources Information Center

    Lesser, Joan Granucci; Cooper, Marlene

    2006-01-01

    Social work has evolved over the years taking on the challenges of the times. The profession now espouses a breadth of theoretical approaches and treatment modalities. We have developed a model to help graduate social work students master the skill of integrating theory and social work practice. The Integrative Model has five components: (l) The…

  8. A Model for Linking Organizational Culture and Performance. Innovative Session 6. [AHRD Conference, 2001].

    ERIC Educational Resources Information Center

    McCullough, Cathy Bolton

    An innovative session was conducted to introduce session participants to a concept and researched model for linking organizational culture and performance. The session goals were as follows: (1) give participants a working knowledge of the link between business culture and key business performance indicators; (2) give participants a hands-on…

  9. Viral surveillance and discovery

    PubMed Central

    Lipkin, Walter Ian; Firth, Cadhla

    2014-01-01

    The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health. PMID:23602435

  10. Modelling the spread of bovine viral diarrhea virus (BVDV) in a beef cattle herd and its impact on herd productivity.

    PubMed

    Damman, Alix; Viet, Anne-France; Arnoux, Sandie; Guerrier-Chatellet, Marie-Claude; Petit, Etienne; Ezanno, Pauline

    2015-02-24

    Bovine viral diarrhea virus (BVDV) is a common pathogen of cattle herds that causes economic losses due to reproductive disorders in breeding cattle and increased morbidity and mortality amongst infected calves. Our objective was to evaluate the impact of BVDV spread on the productivity of a beef cow-calf herd using a stochastic model in discrete time that accounted for (1) the difference in transmission rates when animals are housed indoors versus grazing on pasture, (2) the external risk of disease introductions through fenceline contact with neighboring herds and the purchase of infected cattle, and (3) the risk of individual pregnant cattle generating persistently infected (PI) calves based on their stage in gestation. The model predicted the highest losses from BVDV during the first 3 years after disease was introduced into a naive herd. During the endemic phase, the impact of BVDV on the yearly herd productivity was much lower due to herd immunity. However, cumulative losses over 10 years in an endemic situation greatly surpassed the losses that occurred during the acute phase. A sensitivity analysis of key model parameters revealed that herd size, the duration of breeding, grazing, and selling periods, renewal rate of breeding females, and the level of numerical productivity expected by the farmer had a significant influence on the predicted losses. This model provides a valuable framework for evaluating the impact of BVDV and the efficacy of different control strategies in beef cow-calf herds.

  11. Tools and Algorithms to Link Horizontal Hydrologic and Vertical Hydrodynamic Models and Provide a Stochastic Modeling Framework

    NASA Astrophysics Data System (ADS)

    Salah, Ahmad M.; Nelson, E. James; Williams, Gustavious P.

    2010-04-01

    We present algorithms and tools we developed to automatically link an overland flow model to a hydrodynamic water quality model with different spatial and temporal discretizations. These tools run the linked models which provide a stochastic simulation frame. We also briefly present the tools and algorithms we developed to facilitate and analyze stochastic simulations of the linked models. We demonstrate the algorithms by linking the Gridded Surface Subsurface Hydrologic Analysis (GSSHA) model for overland flow with the CE-QUAL-W2 model for water quality and reservoir hydrodynamics. GSSHA uses a two-dimensional horizontal grid while CE-QUAL-W2 uses a two-dimensional vertical grid. We implemented the algorithms and tools in the Watershed Modeling System (WMS) which allows modelers to easily create and use models. The algorithms are general and could be used for other models. Our tools create and analyze stochastic simulations to help understand uncertainty in the model application. While a number of examples of linked models exist, the ability to perform automatic, unassisted linking is a step forward and provides the framework to easily implement stochastic modeling studies.

  12. Modeling and control of a hydraulically actuated flexible-prismatic link robot

    SciTech Connect

    Love, L.; Kress, R.; Jansen, J.

    1996-12-01

    Most of the research related to flexible link manipulators to date has focused on single link, fixed length, single plane of vibration test beds. In addition, actuation has been predominantly based upon electromagnetic motors. Ironically, these elements are rarely found in the existing industrial long reach systems. This manuscript describes a new hydraulically actuated, long reach manipulator with a flexible prismatic link at Oak Ridge National Laboratory (ORNL). Focus is directed towards both modeling and control of hydraulic actuators as well as flexible links that have variable natural frequencies.

  13. Non-viral delivery of the porphobilinogen deaminase cDNA into a mouse model of acute intermittent porphyria.

    PubMed

    Johansson, Annika; Nowak, Grzegorz; Möller, Christer; Harper, Pauline

    2004-05-01

    Acute intermittent porphyria (AIP), an inborn error of metabolism, results from the deficient activity of the third enzyme in the heme biosynthetic pathway, porphobilinogen deaminase (PBGD). Clinical symptoms of this autosomal dominant hepatic porphyria include episodic acute attacks of abdominal pain, neuropathy, and psychiatric disturbances. Current therapy based on intravenous heme administration is palliative and there is no way to prevent the attacks. Thus, efforts are focused on methods to replace the deficient activity in the liver to prevent the acute attacks of this hepatic porphyria. Here we explore the efficiency of a non-viral gene delivery to obtain PBGD expression in the liver of AIP transgenic mice. Four vectors were evaluated: naked DNA and DNA complexed to liposomes, polyethylenimine (PEI), and PEI-galactose, using a luciferase construct as reporter gene. The vectors were administered intravenously or directly into the portal vein with transient blood flow blockage. After tail vein injection of the DNA complexes, the liposome vector had the highest luciferase expression in lung and less in liver. When injected into the portal vein, the naked DNA had considerably higher hepatic reporter gene expression; 100 microg of naked DNA had the highest hepatic luciferase expression 24h after portal vein injection. When these vectors were used to deliver the PBGD gene into the AIP mouse model no enhancement of the endogenous PBGD activity in liver was detectable, despite the presence of the PBGD-plasmids as verified by PCR. Thus, more efficient non-viral vectors are needed to express sufficient PBGD activity over the endogenous hepatic level (approximately 30% of normal) in this murine system.

  14. A Positive Cooperativity Binding Model between Ly49 Natural Killer Cell Receptors and the Viral Immunoevasin m157

    PubMed Central

    Romasanta, Pablo N.; Curto, Lucrecia M.; Urtasun, Nicolas; Sarratea, María B.; Chiappini, Santiago; Miranda, María V.; Delfino, José M.; Mariuzza, Roy A.; Fernández, Marisa M.; Malchiodi, Emilio L.

    2014-01-01

    Natural killer (NK) cells discriminate between healthy and virally infected or transformed cells using diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 NK receptors, which can adopt two distinct conformations (backfolded and extended), are of particular importance for detecting cells infected with mouse cytomegalovirus (CMV) via recognition of the viral immunoevasin m157. The interaction of m157 with activating (Ly49H) and inhibitory (Ly49I) receptors governs the spread of mouse CMV. We carried out kinetic and thermodynamic experiments to elucidate the Ly49/m157 binding mechanism. Combining surface plasmon resonance, fluorescence anisotropy, and circular dichroism (CD), we determined that the best model to describe both the Ly49H/m157 and Ly49I/m157 interactions is a conformational selection mechanism where only the extended conformation of Ly49 (Ly49*) is able to bind the first m157 ligand followed by binding of the Ly49*/m157 complex to the second m157. The interaction is characterized by strong positive cooperativity such that the second m157 binds the Ly49 homodimer with a 1000-fold higher sequential constant than the first m157 (∼108 versus ∼105 m−1). Using far-UV CD, we obtained evidence for a conformational change in Ly49 upon binding m157 that could explain the positive cooperativity. The rate-limiting step of the overall mechanism is a conformational transition in Ly49 from its backfolded to extended form. The global thermodynamic parameters from the initial state (backfolded Ly49 and m157) to the final state (Ly49*/(m157)2) are characterized by an unfavorable enthalpy that is compensated by a favorable entropy, making the interaction spontaneous. PMID:24379405

  15. Recombination between poliovirus and coxsackie A viruses of species C: a model of viral genetic plasticity and emergence.

    PubMed

    Combelas, Nicolas; Holmblat, Barbara; Joffret, Marie-Line; Colbère-Garapin, Florence; Delpeyroux, Francis

    2011-08-01

    Genetic recombination in RNA viruses was discovered many years ago for poliovirus (PV), an enterovirus of the Picornaviridae family, and studied using PV or other picornaviruses as models. Recently, recombination was shown to be a general phenomenon between different types of enteroviruses of the same species. In particular, the interest for this mechanism of genetic plasticity was renewed with the emergence of pathogenic recombinant circulating vaccine-derived polioviruses (cVDPVs), which were implicated in poliomyelitis outbreaks in several regions of the world with insufficient vaccination coverage. Most of these cVDPVs had mosaic genomes constituted of mutated poliovaccine capsid sequences and part or all of the non-structural sequences from other human enteroviruses of species C (HEV-C), in particular coxsackie A viruses. A study in Madagascar showed that recombinant cVDPVs had been co-circulating in a small population of children with many different HEV-C types. This viral ecosystem showed a surprising and extensive biodiversity associated to several types and recombinant genotypes, indicating that intertypic genetic recombination was not only a mechanism of evolution for HEV-C, but an usual mode of genetic plasticity shaping viral diversity. Results suggested that recombination may be, in conjunction with mutations, implicated in the phenotypic diversity of enterovirus strains and in the emergence of new pathogenic strains. Nevertheless, little is known about the rules and mechanisms which govern genetic exchanges between HEV-C types, as well as about the importance of intertypic recombination in generating phenotypic variation. This review summarizes our current knowledge of the mechanisms of evolution of PV, in particular recombination events leading to the emergence of recombinant cVDPVs.

  16. Derivation of free energy expressions for tube models from coarse-grained slip-link models.

    PubMed

    Steenbakkers, Rudi J A; Schieber, Jay D

    2012-07-21

    We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)] by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)] can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)] starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)]. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)]. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical formulation of tube models. The next step will be to formulate the dynamics of the primitive

  17. Derivation of free energy expressions for tube models from coarse-grained slip-link models

    NASA Astrophysics Data System (ADS)

    Steenbakkers, Rudi J. A.; Schieber, Jay D.

    2012-07-01

    We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)], 10.1063/1.3314727 by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)], 10.1515/JNETDY.2003.010 can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)], 10.1021/ma8009855 starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)], 10.1122/1.1595099. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)], 10.1063/1.1553764. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical

  18. Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin.

    PubMed

    Zhang, Ming; Gaschen, Brian; Blay, Wendy; Foley, Brian; Haigwood, Nancy; Kuiken, Carla; Korber, Bette

    2004-12-01

    Human and simian immunodeficiency viruses (HIV and SIV), influenza virus, and hepatitis C virus (HCV) have heavily glycosylated, highly variable surface proteins. Here we explore N-linked glycosylation site (sequon) variation at the population level in these viruses, using a new Web-based program developed to facilitate the sequon tracking and to define patterns (www.hiv.lanl.gov). This tool allowed rapid visualization of the two distinctive patterns of sequon variation found in HIV-1, HIV-2, and SIV CPZ. The first pattern (fixed) describes readily aligned sites that are either simply present or absent. These sites tend to be occupied by high-mannose glycans. The second pattern (shifting) refers to sites embedded in regions of extreme local length variation and is characterized by shifts in terms of the relative position and local density of sequons; these sites tend to be populated by complex carbohydrates. HIV, with its extreme variation in number and precise location of sequons, does not have a net increase in the number of sites over time at the population level. Primate lentiviral lineages have host species-dependent levels of sequon shifting, with HIV-1 in humans the most extreme. HCV E1 and E2 proteins, despite evolving extremely rapidly through point mutation, show limited sequon variation, although two shifting sites were identified. Human influenza A hemagglutinin H3 HA1 is accumulating sequons over time, but this trend is not evident in any other avian or human influenza A serotypes.

  19. Strengthening the weak link: Built Environment modelling for loss analysis

    NASA Astrophysics Data System (ADS)

    Millinship, I.

    2012-04-01

    Methods to analyse insured losses from a range of natural perils, including pricing by primary insurers and catastrophe modelling by reinsurers, typically lack sufficient exposure information. Understanding the hazard intensity in terms of spatial severity and frequency is only the first step towards quantifying the risk of a catastrophic event. For any given event we need to know: Are any structures affected? What type of buildings are they? How much damaged occurred? How much will the repairs cost? To achieve this, detailed exposure information is required to assess the likely damage and to effectively calculate the resultant loss. Modelling exposures in the Built Environment therefore plays as important a role in understanding re/insurance risk as characterising the physical hazard. Across both primary insurance books and aggregated reinsurance portfolios, the location of a property (a risk) and its monetary value is typically known. Exactly what that risk is in terms of detailed property descriptors including structure type and rebuild cost - and therefore its vulnerability to loss - is often omitted. This data deficiency is a primary source of variations between modelled losses and the actual claims value. Built Environment models are therefore required at a high resolution to describe building attributes that relate vulnerability to property damage. However, national-scale household-level datasets are often not computationally practical in catastrophe models and data must be aggregated. In order to provide more accurate risk analysis, we have developed and applied a methodology for Built Environment modelling for incorporation into a range of re/insurance applications, including operational models for different international regions and different perils and covering residential, commercial and industry exposures. Illustrated examples are presented, including exposure modelling suitable for aggregated reinsurance analysis for the UK and bespoke high resolution

  20. Multiple-to-dominant path collapse of linked-flux model for diffusion-limited nucleation

    NASA Astrophysics Data System (ADS)

    Lau, Y. H.; Wu, D. T.

    2013-01-01

    While capable of estimating diffusion-limited nucleation rates, Kelton's linked-flux model has no simple solution. To increase the model's usability, we simplify the model by retaining only the dominant nucleation path to obtain a series solution. The solution agrees well with the Kelton's model's predictions of the nucleation rate, and thus provides a simple estimate of diffusion-limited nucleation rates.

  1. Residual Viremia in an RT-SHIV Rhesus Macaque HAART Model Marked by the Presence of a Predominant Plasma Clone and a Lack of Viral Evolution

    PubMed Central

    Kauffman, Robert C.; Villalobos, Andradi; Bowen, Joanne H.; Adamson, Lourdes; Schinazi, Raymond F.

    2014-01-01

    Highly active antiretroviral therapy (HAART) significantly reduces HIV-1 replication and prevents progression to AIDS. However, residual low-level viremia (LLV) persists and long-lived viral reservoirs are maintained in anatomical sites. These reservoirs permit a recrudescence of viremia upon cessation of therapy and thus HAART must be maintained indefinitely. HIV-1 reservoirs include latently infected resting memory CD4+ T-cells and macrophages which may contribute to residual viremia. It has not been conclusively determined if a component of LLV may also be due to residual replication in cells with sub-therapeutic drug levels and/or long-lived chronically infected cells. In this study, RT-SHIVmac239 diversity was characterized in five rhesus macaques that received a five-drug HAART regimen [tenofovir, emtricitabine, zidovudine, amdoxovir, (A, C, T, G nucleoside analogs) and the non-nucleoside reverse transcriptase (RT) inhibitor efavirenz]. Before maximal viral load suppression, longitudinal plasma viral RNA RT diversity was analyzed using a 454 sequencer. After suppression, LLV RT diversity (amino acids 65-210) was also assessed. LLV samples had viral levels less than our standard detection limit (50 viral RNA copies/mL) and few transient blips <200 RNA copies/mL. HAART was discontinued in three macaques after 42 weeks of therapy resulting in viral rebound. The level of viral divergence and the prevalence of specific alleles in LLV was similar to pre-suppression viremia. While some LLV sequences contained mutations not observed in the pre-suppression profile, LLV was not characterized by temporal viral evolution or apparent selection of drug resistance mutations. Similarly, resistance mutations were not detected in the viral rebound population. Interestingly, one macaque maintained a putative LLV predominant plasma clone sequence. Together, these results suggest that residual replication did not markedly contribute to LLV and that this model mimics the

  2. A model integration framework for linking SWAT and MODFLOW

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hydrological response and transport phenomena are driven by atmospheric, surface and subsurface processes. These complex processes occur at different spatiotemporal scales requiring comprehensive modeling to assess the impact of anthropogenic activity on hydrology and fate and transport of chemical ...

  3. Linking Time and Space Scales in Distributed Hydrological Modelling - a case study for the VIC model

    NASA Astrophysics Data System (ADS)

    Melsen, Lieke; Teuling, Adriaan; Torfs, Paul; Zappa, Massimiliano; Mizukami, Naoki; Clark, Martyn; Uijlenhoet, Remko

    2015-04-01

    One of the famous paradoxes of the Greek philosopher Zeno of Elea (~450 BC) is the one with the arrow: If one shoots an arrow, and cuts its motion into such small time steps that at every step the arrow is standing still, the arrow is motionless, because a concatenation of non-moving parts does not create motion. Nowadays, this reasoning can be refuted easily, because we know that motion is a change in space over time, which thus by definition depends on both time and space. If one disregards time by cutting it into infinite small steps, motion is also excluded. This example shows that time and space are linked and therefore hard to evaluate separately. As hydrologists we want to understand and predict the motion of water, which means we have to look both in space and in time. In hydrological models we can account for space by using spatially explicit models. With increasing computational power and increased data availability from e.g. satellites, it has become easier to apply models at a higher spatial resolution. Increasing the resolution of hydrological models is also labelled as one of the 'Grand Challenges' in hydrology by Wood et al. (2011) and Bierkens et al. (2014), who call for global modelling at hyperresolution (~1 km and smaller). A literature survey on 242 peer-viewed articles in which the Variable Infiltration Capacity (VIC) model was used, showed that the spatial resolution at which the model is applied has decreased over the past 17 years: From 0.5 to 2 degrees when the model was just developed, to 1/8 and even 1/32 degree nowadays. On the other hand the literature survey showed that the time step at which the model is calibrated and/or validated remained the same over the last 17 years; mainly daily or monthly. Klemeš (1983) stresses the fact that space and time scales are connected, and therefore downscaling the spatial scale would also imply downscaling of the temporal scale. Is it worth the effort of downscaling your model from 1 degree to 1

  4. A Link Loss Model for the On-Body Propagation Channel for Binaural Hearing Aids

    NASA Astrophysics Data System (ADS)

    Chandra, Rohit; Johansson, Anders J.

    2013-12-01

    Binaural hearing aids communicate with each other through a wireless link for synchronization. A propagation model is needed to estimate the ear-to-ear link loss for such binaural hearing aids. The link loss is a critical parameter in a link budget to decide the sensitivity of the transceiver. In this paper, we have presented a model for the deterministic component of the ear-to-ear link loss. The model takes into account the dominant paths having most of the power of the creeping wave from the transceiver in one ear to the transceiver in other ear and the effect of the protruding part of the outer ear called pinna. Simulations are done to validate the model using in-the-ear (ITE) placement of antennas at 2.45 GHz on two heterogeneous phantoms of different age-group and body size. The model agrees with the simulations. The ear-to-ear link loss between the antennas for the binaural hearing aids in the homogeneous SAM phantom is compared with a heterogeneous phantom. It is found that the absence of the pinna and the lossless shell in the SAM phantom underestimate the link loss. This is verified by the measurements on a phantom where we have included the pinnas fabricated by 3D-printing.

  5. A simple model linking galaxy and dark matter evolution

    SciTech Connect

    Birrer, Simon; Lilly, Simon; Amara, Adam; Paranjape, Aseem; Refregier, Alexandre E-mail: simon.lilly@phys.ethz.ch

    2014-09-20

    We construct a simple phenomenological model for the evolving galaxy population by incorporating predefined baryonic prescriptions into a dark matter hierarchical merger tree. The model is based on the simple gas-regulator model introduced by Lilly et al., coupled with the empirical quenching rules of Peng et al. The simplest model already does quite well in reproducing, without re-adjusting the input parameters, many observables, including the main sequence sSFR-mass relation, the faint end slope of the galaxy mass function, and the shape of the star forming and passive mass functions. Similar to observations and/or the recent phenomenological model of Behroozi et al., which was based on epoch-dependent abundance-matching, our model also qualitatively reproduces the evolution of the main sequence sSFR(z) and SFRD(z) star formation rate density relations, the M{sub s} – M{sub h} stellar-to-halo mass relation, and the SFR – M{sub h} relation. Quantitatively the evolution of sSFR(z) and SFRD(z) is not steep enough, the M{sub s} – M{sub h} relation is not quite peaked enough, and, surprisingly, the ratio of quenched to star forming galaxies around M* is not quite high enough. We show that these deficiencies can simultaneously be solved by ad hoc allowing galaxies to re-ingest some of the gas previously expelled in winds, provided that this is done in a mass-dependent and epoch-dependent way. These allow the model galaxies to reduce an inherent tendency to saturate their star formation efficiency, which emphasizes how efficient galaxies around M* are in converting baryons into stars and highlights the fact that quenching occurs at the point when galaxies are rapidly approaching the maximum possible efficiency of converting baryons into stars.

  6. EVALUATION OF MURINE NOROVIRUS, FELINE CALICIVIRUS, POLIOVIRUS, AND MS2 AS SURROGATES FOR HUMAN NOROVIRUS IN a Model of Viral Persistence in SURFACE Water AND GROUNDWATER

    EPA Science Inventory

    Human noroviruses (NoV) are a significant cause of non bacterial gastroenteritis worldwide with contaminated drinking water a potential transmission route. The absence of a cell culture infectivity model for NoV necessitates the use of molecular methods and/or viral surrogate mod...

  7. Modeling photosynthesis of discontinuous plant canopies by linking Geometric Optical Radiative Transfer model with biochemical processes

    NASA Astrophysics Data System (ADS)

    Xin, Q.; Gong, P.; Li, W.

    2015-02-01

    Modeling vegetation photosynthesis is essential for understanding carbon exchanges between terrestrial ecosystems and the atmosphere. The radiative transfer process within plant canopies is one of the key drivers that regulate canopy photosynthesis. Most vegetation cover consists of discrete plant crowns, of which the physical observation departs from the underlying assumption of a homogenous and uniform medium in classic radiative transfer theory. Here we advance the Geometric Optical Radiative Transfer (GORT) model to simulate photosynthesis activities for discontinuous plant canopies. We separate radiation absorption into two components that are absorbed by sunlit and shaded leaves, and derive analytical solutions by integrating over the canopy layer. To model leaf-level and canopy-level photosynthesis, leaf light absorption is then linked to the biochemical process of gas diffusion through leaf stomata. The canopy gap probability derived from GORT differs from classic radiative transfer theory, especially when the leaf area index is high, due to leaf clumping effects. Tree characteristics such as tree density, crown shape, and canopy length affect leaf clumping and regulate radiation interception. Modeled gross primary production (GPP) for two deciduous forest stands could explain more than 80% of the variance of flux tower measurements at both near hourly and daily time scales. We also demonstrate that the ambient CO2 concentration influences daytime vegetation photosynthesis, which needs to be considered in state-of-the-art biogeochemical models. The proposed model is complementary to classic radiative transfer theory and shows promise in modeling the radiative transfer process and photosynthetic activities over discontinuous forest canopies.

  8. Response of the Italian agile frog (Rana latastei) to a Ranavirus, frog virus 3: a model for viral emergence in naïve populations.

    PubMed

    Pearman, Peter B; Garner, Trenton W J; Straub, Monika; Greber, Urs F

    2004-10-01

    Ranavirus (family Iridoviridae) is a genus of pathogens of poikilotherms, and some ranaviruses may play a role in widespread mortality of amphibians. Ecology of viral transmission in amphibians is poorly known but can be addressed through experimentation in the laboratory. In this study, we use the Ranavirus frog virus 3 (FV3) as an experimental model for pathogen emergence in naive populations of tadpoles. We simulated emerging disease by exposing tadpoles of the Italian agile frog (Rana latastei), to the North American Ranavirus FV3. We demonstrated that mortality occurred due to viral exposure, exposure of tadpoles to decreasing concentrations of FV3 in the laboratory produced dose-dependent survival rates, and cannibalism of virus-carrying carcasses increased mortality due to FV3. These experiments suggest the potential for ecological mechanisms to affect the level of exposure of tadpoles to Ranavirus and to impact transmission of viral pathogens in aquatic systems.

  9. Linking Models: Reasoning from Patterns to Tables and Equations

    ERIC Educational Resources Information Center

    Switzer, J. Matt

    2013-01-01

    Patterns are commonly used in middle years mathematics classrooms to teach students about functions and modelling with tables, graphs, and equations. Grade 6 students are expected to, "continue and create sequences involving whole numbers, fractions and decimals," and "describe the rule used to create the sequence." (Australian…

  10. Links between fluid mechanics and quantum mechanics: a model for information in economics?

    PubMed

    Haven, Emmanuel

    2016-05-28

    This paper tallies the links between fluid mechanics and quantum mechanics, and attempts to show whether those links can aid in beginning to build a formal template which is usable in economics models where time is (a)symmetric and memory is absent or present. An objective of this paper is to contemplate whether those formalisms can allow us to model information in economics in a novel way.

  11. Shuttle Communications and Tracking Systems Modeling and TDRSS Link Simulations Studies

    NASA Technical Reports Server (NTRS)

    Chie, C. M.; Dessouky, K.; Lindsey, W. C.; Tsang, C. S.; Su, Y. T.

    1985-01-01

    An analytical simulation package (LinCsim) which allows the analytical verification of data transmission performance through TDRSS satellites was modified. The work involved the modeling of the user transponder, TDRS, TDRS ground terminal, and link dynamics for forward and return links based on the TDRSS performance specifications (4) and the critical design reviews. The scope of this effort has recently been expanded to include the effects of radio frequency interference (RFI) on the bit error rate (BER) performance of the S-band return links. The RFI environment and the modified TDRSS satellite and ground station hardware are being modeled in accordance with their description in the applicable documents.

  12. Modeling water quality, temperature, and flow in Link River, south-central Oregon

    USGS Publications Warehouse

    Sullivan, Annett B.; Rounds, Stewart A.

    2016-09-09

    The 2.1-km (1.3-mi) Link River connects Upper Klamath Lake to the Klamath River in south-central Oregon. A CE-QUAL-W2 flow and water-quality model of Link River was developed to provide a connection between an existing model of the upper Klamath River and any existing or future models of Upper Klamath Lake. Water-quality sampling at six locations in Link River was done during 2013–15 to support model development and to provide a better understanding of instream biogeochemical processes. The short reach and high velocities in Link River resulted in fast travel times and limited water-quality transformations, except for dissolved oxygen. Reaeration through the reach, especially at the falls in Link River, was particularly important in moderating dissolved oxygen concentrations that at times entered the reach at Link River Dam with marked supersaturation or subsaturation. This reaeration resulted in concentrations closer to saturation downstream at the mouth of Link River.

  13. Nonlinear Models for the Delayed Immune Response to a Viral Infection

    NASA Astrophysics Data System (ADS)

    Gleria, Iram; Neto, Adhemar Ranciaro; Canabarro, Askery

    2015-08-01

    We analyze ordinary differential equations modeling systems of biological interest. We focus on analytical properties of delayed equations that simulate the dynamics between cells of the immune system and a target population. We present the basic features of the linear stability analysis in delayed equations. New analytical results in a four-dimensional system are presented, as well as an analysis of a two-dimensional model.

  14. Linking agent-based models and stochastic models of financial markets.

    PubMed

    Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H Eugene

    2012-05-29

    It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that "fat" tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting.

  15. Linking agent-based models and stochastic models of financial markets

    PubMed Central

    Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H. Eugene

    2012-01-01

    It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that “fat” tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting. PMID:22586086

  16. An integrative model linking feedback environment and organizational citizenship behavior.

    PubMed

    Peng, Jei-Chen; Chiu, Su-Fen

    2010-01-01

    Past empirical evidence has suggested that a positive supervisor feedback environment may enhance employees' organizational citizenship behavior (OCB). In this study, we aim to extend previous research by proposing and testing an integrative model that examines the mediating processes underlying the relationship between supervisor feedback environment and employee OCB. Data were collected from 259 subordinate-supervisor dyads across a variety of organizations in Taiwan. We used structural equation modeling to test our hypotheses. The results demonstrated that supervisor feedback environment influenced employees' OCB indirectly through (1) both positive affective-cognition and positive attitude (i.e., person-organization fit and organizational commitment), and (2) both negative affective-cognition and negative attitude (i.e., role stressors and job burnout). Theoretical and practical implications are discussed. PMID:21166326

  17. Linking model systems to cancer therapeutics: the case of Mastermind

    PubMed Central

    Yedvobnick, Barry; Moberg, Ken

    2010-01-01

    Genetics, and more recently genomics, reveal striking conservation in the fundamental signaling pathways that underlie normal and aberrant cell processes. Consequently, various genetic model organisms are now attracting the interest of biomedical scientists who are focused on therapeutic approaches to human disease. There are now several examples of studies in which Drosophila seems likely to facilitate advances in potential therapies, and a recent report has demonstrated the utility of the fly model for understanding and treating human disease. Basic developmental genetic information first obtained in Drosophila was used to design a therapeutic block to oncogenic Notch signaling that was associated with leukemia in mice. The story of Notch signaling in Drosophila demonstrates the potential for standard Drosophila molecular genetics in developing therapeutic strategies that are relevant to human disease. PMID:20663965

  18. Links between detonation wave propagation and reactive flow models.

    SciTech Connect

    Swift, D. C.; White, S. J.

    2002-01-01

    An accurate reactive flow model is necessary to be able to predict the initiation properties of explosives by complicated shock structures, but a very fine the spatial resolution is needed in reactive flow to reproduce the detailed dynamics of a detonation wave. However, it is not often necessary to use a reactive flow model to simulate the motion of a fully-developed detonation wave. In many situations the same results can be obtained with a coarse computational mesh using programmed burn techniques. In the WBL model [Lambourn89,Swift93], an eikonal detonation wave propagates through a body of explosive at a speed which depends on the curvature of the wave. The model describes the motion of the leading shock of the detonation wave. Here we use the level set method for integrating the WBL equations in time [Collyer98,Bdzil93,Osher88,Aslam98]. This method is attractive because complicated detonation wave shapes can be represented simply. It was found possible to initialize the level set field by a set of source points derived from a reactive flow simulation, by taking 'trigger states' from the reactive flow. The level set scheme was generalized further to take account of motion of the material behind the detonation wave, allowing it to be used for simulations coupled with reactive flow, where detonation may propagate through preshocked and moving material. The modified level set scheme was implemented in 1D and 2D Lagrangian hydrocodes. Trial calculations were performed of initiation and detonation in the TATB-based explosive LX-17, using the Lee - Tarver model. A CJ detonation was simulated in order to verify that the modified level set algorithm operated correctly. The detonation speed was in very good agreement with the expected value. Single-shock initiation was simulated. The position - time history of the leading shock from the coupled model was in excellent agreement with full reactive flow; the pressure profiles were similar but not identical, because of the

  19. An integrative model linking feedback environment and organizational citizenship behavior.

    PubMed

    Peng, Jei-Chen; Chiu, Su-Fen

    2010-01-01

    Past empirical evidence has suggested that a positive supervisor feedback environment may enhance employees' organizational citizenship behavior (OCB). In this study, we aim to extend previous research by proposing and testing an integrative model that examines the mediating processes underlying the relationship between supervisor feedback environment and employee OCB. Data were collected from 259 subordinate-supervisor dyads across a variety of organizations in Taiwan. We used structural equation modeling to test our hypotheses. The results demonstrated that supervisor feedback environment influenced employees' OCB indirectly through (1) both positive affective-cognition and positive attitude (i.e., person-organization fit and organizational commitment), and (2) both negative affective-cognition and negative attitude (i.e., role stressors and job burnout). Theoretical and practical implications are discussed.

  20. Cross Linking and Degradation Mechanisms in Model Sealant Candidates

    NASA Technical Reports Server (NTRS)

    Paciorek, K. L.; Kaufman, J.; Ito, T. I.; Nakahara, J. H.; Kratzer, R. H.

    1977-01-01

    Model compounds were investigated as to which type of heterocyclic ring is the most advantageous for curing sealants based on perfluoroalkylether chains. The relative thermal, thermal oxidative, hydrolytic, and fuel stability of potential crosslinks were determined. Specifically substituted materials were synthesized and evaluation of their stabilities in air, inert atmosphere, water, and Jet-A fuel at 235 and 325 C was made. Three heterocyclic ring systems were considered, namely, triazine, 1,2,4- and 1,3,4-oxadiazoles.

  1. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

    Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

    2015-04-01

    Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools

  2. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

    Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

    2014-12-01

    Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that

  3. Genetic analysis of vibriosis and viral nervous necrosis resistance in Atlantic cod (Gadus morhua L.) using a cure model.

    PubMed

    Bangera, R; Ødegård, J; Nielsen, H M; Gjøen, H M; Mortensen, A

    2013-08-01

    The aim of this study was to investigate whether observed time-until-death of Atlantic cod (Gadus morhua L.) juveniles in separate challenge tests with Vibrio anguillarum (causes vibriosis) and nodavirus [causes viral nervous necrosis (VNN)] are due to differences in susceptibility (whether at risk or not) or increased endurance (individual hazard, given that the animal is susceptible) using a cure mixture (CURE) model with Gibbs sampling. Observed time-until-death, prepared as sequential binary records, were analyzed with the CURE model and results were compared with cross-sectional threshold (SIMPLE) and an ordinary longitudinal survival score (NAÏVE) model (i.e., assuming that all animals are susceptible). Overall mortality at the end of the test was 86 and 71% for vibriosis and VNN, respectively. But the CURE model estimated 92 and 82% of the population to be susceptible to vibriosis and VNN, respectively. Hence, a substantial fraction among the survivors were considered to be susceptible but with high endurance. The underlying heritability of susceptibility was moderate for vibriosis (0.33) and extremely high for VNN (0.91), somewhat greater compared with classical SIMPLE model (0.19 and 0.76 for vibriosis and VNN, respectively), analyzing end survival as a cross-sectional binary trait. Estimates of the underlying heritability were low for single test-day scores of both endurance (0.02 and 0.15 for vibriosis and VNN, respectively) in the CURE model and for the NAÏVE model (0.02 and 0.18 for vibriosis and VNN, respectively). Based on the CURE model, the genetic correlation between susceptibility and endurance was low to moderately positive and significantly different from unity (P < 0.01) for both vibriosis (0.13) and VNN (0.47). Estimated breeding values from the SIMPLE and NAÏVE models showed moderate to high correlations (0.41 to 0.96) with EBV for susceptibility and endurance in the CURE model. The analyses indicate that susceptibility and endurance are

  4. Modeling Prairie Pothole Lakes: Linking Satellite Observation and Calibration (Invited)

    NASA Astrophysics Data System (ADS)

    Schwartz, F. W.; Liu, G.; Zhang, B.; Yu, Z.

    2009-12-01

    This paper examines the response of a complex lake wetland system to variations in climate. The focus is on the lakes and wetlands of the Missouri Coteau, which is part of the larger Prairie Pothole Region of the Central Plains of North America. Information on lake size was enumerated from satellite images, and yielded power law relationships for different hydrological conditions. More traditional lake-stage data were made available to us from the USGS Cottonwood Lake Study Site in North Dakota. A Probabilistic Hydrologic Model (PHM) was developed to simulate lake complexes comprised of tens-of-thousands or more individual closed-basin lakes and wetlands. What is new about this model is a calibration scheme that utilizes remotely-sensed data on lake area as well as stage data for individual lakes. Some ¼ million individual data points are used within a Genetic Algorithm to calibrate the model by comparing the simulated results with observed lake area-frequency power law relationships derived from Landsat images and water depths from seven individual lakes and wetlands. The simulated lake behaviors show good agreement with the observations under average, dry, and wet climatic conditions. The calibrated model is used to examine the impact of climate variability on a large lake complex in ND, in particular, the “Dust Bowl Drought” 1930s. This most famous drought of the 20th Century devastated the agricultural economy of the Great Plains with health and social impacts lingering for years afterwards. Interestingly, the drought of 1930s is unremarkable in relation to others of greater intensity and frequency before AD 1200 in the Great Plains. Major droughts and deluges have the ability to create marked variability of the power law function (e.g. up to one and a half orders of magnitude variability from the extreme Dust Bowl Drought to the extreme 1993-2001 deluge). This new probabilistic modeling approach provides a novel tool to examine the response of the

  5. Linking continuous and discrete intervertebral disc models through homogenisation.

    PubMed

    Karajan, N; Röhrle, O; Ehlers, W; Schmitt, S

    2013-06-01

    At present, there are two main numerical approaches that are frequently used to simulate the mechanical behaviour of the human spine. Researchers with a continuum-mechanical background often utilise the finite-element method (FEM), where the involved biological soft and hard tissues are modelled on a macroscopic (continuum) level. In contrast, groups associated with the science of human movement usually apply discrete multi-body systems (MBS). Herein, the bones are modelled as rigid bodies, which are connected by Hill-type muscles and non-linear rheological spring-dashpot models to represent tendons and cartilaginous connective tissue like intervertebral discs (IVD). A possibility to benefit from both numerical methods is to couple them and use each approach, where it is most appropriate. Herein, the basic idea is to utilise MBS in simulations of the overall body and apply the FEM only to selected regions of interest. In turn, the FEM is used as homogenisation tool, which delivers more accurate non-linear relationships describing the behaviour of the IVD in the multi-body dynamics model. The goal of this contribution is to present an approach to couple both numerical methods without the necessity to apply a gluing algorithm in the context of a co-simulation. Instead, several pre-computations of the intervertebral disc are performed offline to generate an approximation of the homogenised finite-element (FE) result. In particular, the discrete degrees of freedom (DOF) of the MBS, that is, three displacements and three rotations, are applied to the FE model of the IVD, and the resulting homogenised forces and moments are recorded. Moreover, a polynomial function is presented with the discrete DOF of the MBS as variables and the discrete forces an moments as function values. For the sake of a simple verification, the coupling method is applied to a simplified motion segment of the spine. Herein, two stiff cylindrical vertebrae with an interjacent homogeneous

  6. A brain slice culture model of viral encephalitis reveals an innate CNS cytokine response profile and the therapeutic potential of caspase inhibition

    PubMed Central

    Dionne, Kalen R.; Leser, J. Smith; Lorenzen, Kristi A.; Beckham, J. David; Tyler, Kenneth L.

    2011-01-01

    Viral encephalitis is a significant cause of human morbidity and mortality in large part due to suboptimal diagnosis and treatment. Murine reovirus infection serves as a classic experimental model of viral encephalitis. Infection of neonatal mice with T3 reoviruses results in lethal encephalitis associated with neuronal infection, apoptosis, and CNS tissue injury. We have developed an ex vivo brain slice culture (BSC) system that recapitulates the basic pathological features and kinetics of viral replication seen in vivo. We utilize the BSC model to identify an innate, brain-tissue specific inflammatory cytokine response to reoviral infection, which is characterized by the release of IL6, CXCL10, RANTES, and murine IL8 analog (KC). Additionally, we demonstrate the potential utility of this system as a pharmaceutical screening platform by inhibiting reovirus-induced apoptosis and CNS tissue injury with the pan-caspase inhibitor, Q-VD-OPh. Cultured brain slices not only serve to model events occurring during viral encephalitis, but can also be utilized to investigate aspects of pathogenesis and therapy that are not experimentally accessible in vivo. PMID:21241693

  7. A Dual-Process Model of the Alcohol-Behavior Link for Social Drinking

    ERIC Educational Resources Information Center

    Moss, Antony C.; Albery, Ian P.

    2009-01-01

    A dual-process model of the alcohol-behavior link is presented, synthesizing 2 of the major social-cognitive approaches: expectancy and myopia theories. Substantial evidence has accrued to support both of these models, and recent neurocognitive models of the effects of alcohol on thought and behavior have provided evidence to support both as well.…

  8. LINKING THE CMAQ AND HYSPLIT MODELING SYSTEM INTERFACE PROGRAM AND EXAMPLE APPLICATION

    EPA Science Inventory

    A new software tool has been developed to link the Eulerian-based Community Multiscale Air Quality (CMAQ) modeling system with the Lagrangian-based HYSPLIT (HYbrid Single-Particle Lagrangian Integrated Trajectory) model. Both models require many of the same hourly meteorological...

  9. Model analysis of the link between interest rates and crashes

    NASA Astrophysics Data System (ADS)

    Broga, Kristijonas M.; Viegas, Eduardo; Jensen, Henrik Jeldtoft

    2016-09-01

    We analyse the effect of distinct levels of interest rates on the stability of the financial network under our modelling framework. We demonstrate that banking failures are likely to emerge early on under sustained high interest rates, and at much later stage-with higher probability-under a sustained low interest rate scenario. Moreover, we demonstrate that those bank failures are of a different nature: high interest rates tend to result in significantly more bankruptcies associated to credit losses whereas lack of liquidity tends to be the primary cause of failures under lower rates.

  10. Linking seasonal climate forecasts with crop models in Iberian Peninsula

    NASA Astrophysics Data System (ADS)

    Capa, Mirian; Ines, Amor; Baethgen, Walter; Rodriguez-Fonseca, Belen; Han, Eunjin; Ruiz-Ramos, Margarita

    2015-04-01

    Translating seasonal climate forecasts into agricultural production forecasts could help to establish early warning systems and to design crop management adaptation strategies that take advantage of favorable conditions or reduce the effect of adverse conditions. In this study, we use seasonal rainfall forecasts and crop models to improve predictability of wheat yield in the Iberian Peninsula (IP). Additionally, we estimate economic margins and production risks associated with extreme scenarios of seasonal rainfall forecast. This study evaluates two methods for disaggregating seasonal climate forecasts into daily weather data: 1) a stochastic weather generator (CondWG), and 2) a forecast tercile resampler (FResampler). Both methods were used to generate 100 (with FResampler) and 110 (with CondWG) weather series/sequences for three scenarios of seasonal rainfall forecasts. Simulated wheat yield is computed with the crop model CERES-wheat (Ritchie and Otter, 1985), which is included in Decision Support System for Agrotechnology Transfer (DSSAT v.4.5, Hoogenboom et al., 2010). Simulations were run at two locations in northeastern Spain where the crop model was calibrated and validated with independent field data. Once simulated yields were obtained, an assessment of farmer's gross margin for different seasonal climate forecasts was accomplished to estimate production risks under different climate scenarios. This methodology allows farmers to assess the benefits and risks of a seasonal weather forecast in IP prior to the crop growing season. The results of this study may have important implications on both, public (agricultural planning) and private (decision support to farmers, insurance companies) sectors. Acknowledgements Research by M. Capa-Morocho has been partly supported by a PICATA predoctoral fellowship of the Moncloa Campus of International Excellence (UCM-UPM) and MULCLIVAR project (CGL2012-38923-C02-02) References Hoogenboom, G. et al., 2010. The Decision

  11. Modelling Optimal Control of Cholera in Communities Linked by Migration.

    PubMed

    Njagarah, J B H; Nyabadza, F

    2015-01-01

    A mathematical model for the dynamics of cholera transmission with permissible controls between two connected communities is developed and analysed. The dynamics of the disease in the adjacent communities are assumed to be similar, with the main differences only reflected in the transmission and disease related parameters. This assumption is based on the fact that adjacent communities often have different living conditions and movement is inclined toward the community with better living conditions. Community specific reproduction numbers are given assuming movement of those susceptible, infected, and recovered, between communities. We carry out sensitivity analysis of the model parameters using the Latin Hypercube Sampling scheme to ascertain the degree of effect the parameters and controls have on progression of the infection. Using principles from optimal control theory, a temporal relationship between the distribution of controls and severity of the infection is ascertained. Our results indicate that implementation of controls such as proper hygiene, sanitation, and vaccination across both affected communities is likely to annihilate the infection within half the time it would take through self-limitation. In addition, although an infection may still break out in the presence of controls, it may be up to 8 times less devastating when compared with the case when no controls are in place. PMID:26246850

  12. Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation

    SciTech Connect

    Mathur, C.; Jimsheena, V.K.; Banerjee, S.; Makinen, K.; Gowda, L.R.; Savithri, H.S.

    2012-01-20

    Regulation of NIa-Pro is crucial for polyprotein processing and hence, for successful infection of potyviruses. We have examined two novel mechanisms that could regulate NIa-Pro activity. Firstly, the influence of VPg domain on the proteolytic activity of NIa-Pro was investigated. It was shown that the turnover number of the protease increases when these two domains interact (cis: two-fold; trans: seven-fold) with each other. Secondly, the protease activity of NIa-Pro could also be modulated by phosphorylation at Ser129. A mutation of this residue either to aspartate (phosphorylation-mimic) or alanine (phosphorylation-deficient) drastically reduces the protease activity. Based on these observations and molecular modeling studies, we propose that interaction with VPg as well as phosphorylation of Ser129 could relay a signal through Trp143 present at the protein surface to the active site pocket by subtle conformational changes, thus modulating protease activity of NIa-Pro.

  13. Promoting remyelination: utilizing a viral model of demyelination to assess cell-based therapies

    PubMed Central

    Marro, Brett S; Blanc, Caroline A; Loring, Jeanne F; Cahalan, Michael D; Lane, Thomas E

    2014-01-01

    Multiple sclerosis (MS) is a chronic inflammatory disease of the CNS. While a broad range of therapeutics effectively reduce the incidence of focal white matter inflammation and plaque formation for patients with relapse-remitting forms of MS, a challenge within the field is to develop therapies that allow for axonal protection and remyelination. In the last decade, growing interest has focused on utilizing neural precursor cells (NPCs) to promote remyelination. To understand how NPCs function in chronic demyelinating environments, several excellent pre-clinical mouse models have been developed. One well accepted model is infection of susceptible mice with neurotropic variants of mouse hepatitis virus (MHV) that undergo chronic demyelination exhibiting clinical and histopathologic similarities to MS patients. Combined with the possibility that an environmental agent such as a virus could trigger MS, the MHV model of demyelination presents a relevant mouse model to assess the therapeutic potential of NPCs transplanted into an environment in which inflammatory-mediated demyelination is established. PMID:25245576

  14. Zika in the Brain: New Models Shed Light on Viral Infection.

    PubMed

    Hickman, Heather D; Pierson, Theodore C

    2016-08-01

    The current Zika virus (ZIKV) outbreak is associated with high numbers of human congenital birth defects, yet it has been unclear how ZIKV infection during pregnancy causes these abnormalities. Three new mouse models now show that ZIKV crosses the placenta and replicates in the brains of fetal mice.

  15. Zika in the Brain: New Models Shed Light on Viral Infection.

    PubMed

    Hickman, Heather D; Pierson, Theodore C

    2016-08-01

    The current Zika virus (ZIKV) outbreak is associated with high numbers of human congenital birth defects, yet it has been unclear how ZIKV infection during pregnancy causes these abnormalities. Three new mouse models now show that ZIKV crosses the placenta and replicates in the brains of fetal mice. PMID:27345865

  16. Horizontal gene transfer in eukaryotes: the weak-link model.

    PubMed

    Huang, Jinling

    2013-10-01

    The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.

  17. A simulation model to quantify the value of implementing whole-herd Bovine viral diarrhea virus testing strategies in beef cow-calf herds.

    PubMed

    Nickell, Jason S; White, Brad J; Larson, Robert L; Renter, David G; Sanderson, Mike W

    2011-03-01

    Although numerous diagnostic tests are available to identify cattle persistently infected (PI) with Bovine viral diarrhea virus (BVDV) in cow-calf herds, data are sparse when evaluating the economic viability of individual tests or diagnostic strategies. Multiple factors influence BVDV testing in determining if testing should be performed and which strategy to use. A stochastic model was constructed to estimate the value of implementing various whole-herd BVDV cow-calf testing protocols. Three common BVDV tests (immunohistochemistry, antigen-capture enzyme-linked immunosorbent assay, and polymerase chain reaction) performed on skin tissue were evaluated as single- or two-test strategies. The estimated testing value was calculated for each strategy at 3 herd sizes that reflect typical farm sizes in the United States (50, 100, and 500 cows) and 3 probabilities of BVDV-positive herd status (0.077, 0.19, 0.47) based upon the literature. The economic value of testing was the difference in estimated gross revenue between simulated cow-calf herds that either did or did not apply the specific testing strategy. Beneficial economic outcomes were more frequently observed when the probability of a herd being BVDV positive was 0.47. Although the relative value ranking of many testing strategies varied by each scenario, the two-test strategy composed of immunohistochemistry had the highest estimated value in all but one herd size-herd prevalence permutation. These data indicate that the estimated value of applying BVDV whole-herd testing strategies is influenced by the selected strategy, herd size, and the probability of herd BVDV-positive status; therefore, these factors should be considered when designing optimum testing strategies for cow-calf herds.

  18. Model for ranking freshwater fish farms according to their risk of infection and illustration for viral haemorrhagic septicaemia.

    PubMed

    Oidtmann, Birgit C; Pearce, Fiona M; Thrush, Mark A; Peeler, Edmund J; Ceolin, Chiara; Stärk, Katharina D C; Dalla Pozza, Manuela; Afonso, Ana; Diserens, Nicolas; Reese, R Allan; Cameron, Angus

    2014-08-01

    We developed a model to calculate a quantitative risk score for individual aquaculture sites. The score indicates the risk of the site being infected with a specific fish pathogen (viral haemorrhagic septicaemia virus (VHSV); infectious haematopoietic necrosis virus, Koi herpes virus), and is intended to be used for risk ranking sites to support surveillance for demonstration of zone or member state freedom from these pathogens. The inputs to the model include a range of quantitative and qualitative estimates of risk factors organised into five risk themes (1) Live fish and egg movements; (2) Exposure via water; (3) On-site processing; (4) Short-distance mechanical transmission; (5) Distance-independent mechanical transmission. The calculated risk score for an individual aquaculture site is a value between zero and one and is intended to indicate the risk of a site relative to the risk of other sites (thereby allowing ranking). The model was applied to evaluate 76 rainbow trout farms in 3 countries (42 from England, 32 from Italy and 2 from Switzerland) with the aim to establish their risk of being infected with VHSV. Risk scores for farms in England and Italy showed great variation, clearly enabling ranking. Scores ranged from 0.002 to 0.254 (mean score 0.080) in England and 0.011 to 0.778 (mean of 0.130) for Italy, reflecting the diversity of infection status of farms in these countries. Requirements for broader application of the model are discussed. Cost efficient farm data collection is important to realise the benefits from a risk-based approach.

  19. Linking Air Quality and Watershed Models for Environmental Assessments: Analysis of the Effects of Model-Specific Precipitation Estimates on Calculated Water Flux

    EPA Science Inventory

    Directly linking air quality and watershed models could provide an effective method for estimating spatially-explicit inputs of atmospheric contaminants to watershed biogeochemical models. However, to adequately link air and watershed models for wet deposition estimates, each mod...

  20. Upregulation of the cannabinoid CB2 receptor in environmental and viral inflammation-driven rat models of Parkinson's disease.

    PubMed

    Concannon, Ruth M; Okine, Bright N; Finn, David P; Dowd, Eilís

    2016-09-01

    In recent years, it has become evident that Parkinson's disease is associated with a self-sustaining cycle of neuroinflammation and neurodegeneration, with dying neurons activating microglia, which, once activated, can release several factors that kill further neurons. One emerging pharmacological target that has the potential to break this cycle is the microglial CB2 receptor which, when activated, can suppress microglial activity and reduce their neurotoxicity. However, very little is known about CB2 receptor expression in animal models of Parkinson's disease which is essential for valid preclinical assessment of the anti-Parkinsonian efficacy of drugs targeting the CB2 receptor. Therefore, the aim of this study was to investigate and compare the changes that occur in CB2 receptor expression in environmental and inflammation-driven models of Parkinson's disease. To do so, male Sprague Dawley rats were given unilateral, intra-striatal injections of the Parkinson's disease-associated agricultural pesticide, rotenone, or the viral-like inflammagen, polyinosinic:polycytidylic acid (Poly (I:C)). Animals underwent behavioural testing for motor dysfunction on days 7, 14 and 28 post-surgery, and were sacrificed on days 1, 4, 14 and 28. Changes in the endocannabinoid system and neuroinflamamtion were investigated by qRT-PCR, liquid chromatography-mass spectrometry and immunohistochemistry. After injection of rotenone or Poly (I:C) into the rat striatum, we found that expression of the CB2 receptor was significantly elevated in both models, and that this increase correlated significantly with an increase in microglial activation in the rotenone model. Interestingly, the increase in CB2 receptor expression in the inflammation-driven Poly (I:C) model was significantly more pronounced than that in the neurotoxic rotenone model. Thus, this study has shown that CB2 receptor expression is dysregulated in animal models of Parkinson's disease, and has also revealed significant

  1. Modeling and Representing National Climate Assessment Information using Linked Data

    NASA Astrophysics Data System (ADS)

    Zheng, J.; Tilmes, C.; Smith, A.; Zednik, S.; Fox, P. A.

    2012-12-01

    Every four years, earth scientists work together on a National Climate Assessment (NCA) report which integrates, evaluates, and interprets the findings of climate change and impacts on affected industries such as agriculture, natural environment, energy production and use, etc. Given the amount of information presented in each report, and the wide range of information sources and topics, it can be difficult for users to find and identify desired information. To ease the user effort of information discovery, well-structured metadata is needed that describes the report's key statements and conclusions and provide for traceable provenance of data sources used. We present an assessment ontology developed to describe terms, concepts and relations required for the NCA metadata. Wherever possible, the assessment ontology reuses terms from well-known ontologies such as Semantic Web for Earth and Environmental Terminology (SWEET) ontology, Dublin Core (DC) vocabulary. We have generated sample National Climate Assessment metadata conforming to our assessment ontology and publicly exposed via a SPARQL-endpoint and website. We have also modeled provenance information for the NCA writing activities using the W3C recommendation-candidate PROV-O ontology. Using this provenance the user will be able to trace the sources of information used in the assessment and therefore make trust decisions. In the future, we are planning to implement a faceted browser over the metadata to enhance metadata traversal and information discovery.

  2. Viral Parkinsonism

    PubMed Central

    Jang, Haeman; Boltz, David A.; Webster, Robert G.; Smeyne, Richard Jay

    2015-01-01

    Parkinson's disease is a debilitating neurological disorder characterized that affects 1-2% of the adult population over 55 years of age. For the vast majority of cases, the etiology of this disorder is unknown, although it is generally accepted that there is a genetic susceptibility to any number of environmental agents. One such agent may be viruses. It has been shown that numerous viruses can enter the nervous system, i.e. they are neurotropic, and induce a number of encephalopathies. One of the secondary consequences of these encephalopathies can be parkinsonism, that is both transient as well as permanent. One of the most highlighted and controversial cases of viral parkinsonism is that which followed the 1918 influenza outbreak and the subsequent induction of von Economo's encephalopathy. In this review, we discuss the neurological sequelae of infection by influenza virus as well as that of other viruses known to induce parkinsonism including Coxsackie, Japanese encephalitis B, St. Louis, West Nile and HIV viruses. PMID:18760350

  3. Simulating the link between ENSO and summer drought in Southern Africa using regional climate models

    NASA Astrophysics Data System (ADS)

    Meque, Arlindo; Abiodun, Babatunde J.

    2015-04-01

    This study evaluates the capability of regional climate models (RCMs) in simulating the link between El Niño Southern Oscillation (ENSO) and Southern African droughts. It uses the Standardized Precipitation-Evapotranspiration Index (SPEI, computed using rainfall and temperature data) to identify 3-month drought over Southern Africa, and compares the observed and simulated correlation between ENSO and SPEI. The observation data are from the Climate Research Unit, while the simulation data are from ten RCMs (ARPEGE, CCLM, HIRHAM, RACMO, REMO, PRECIS, RegCM3, RCA, WRF, and CRCM) that participated in the regional climate downscaling experiment (CORDEX) project. The study analysed the rainy season (December-February) data for 19 years (1989-2008). The results show a strong link between ENSO and droughts (SPEI) over Southern Africa. The link is owing to the influence of ENSO on both rainfall and temperature fields, but the correlation between ENSO and temperature is stronger than the correlation between ENSO and rainfall. Hence, using only rainfall to monitor droughts in Southern Africa may underestimate the influence of ENSO on the droughts. Only few CORDEX RCMs simulate the influence of ENSO on Southern African drought as observed. In this regard, the ARPEGE model shows the best simulation, while CRCM shows the worst. The different in the performance may be due to their lateral boundary conditions. The RCA-simulated link between ENSO and Southern African droughts is sensitive to the global dataset used as the lateral boundary conditions. In some cases, using RCA to downscale global circulation models (GCM) simulations adds value to the simulated link between ENSO and the droughts, but in other cases the downscaling adds no value to the link. The added value of RCA to the simulated link decreases as the capability of the GCM to simulate the link increases. This study suggests that downscaling GCM simulations with RCMs over Southern Africa may improve or depreciate the

  4. Porous Hyaluronic Acid Hydrogels for Localized Non-Viral DNA Delivery in a Diabetic Wound Healing Model

    PubMed Central

    Tokatlian, Talar; Cam, Cynthia; Segura, Tatiana

    2015-01-01

    The treatment of impaired wounds requires the use of biomaterials that can provide mechanical and biological queues to the surrounding environment to promote angiogenesis, granulation tissue formation, and wound closure. Porous hydrogels have previously been shown to promote angiogenesis even in the absence of pro-angiogenic factors. We hypothesized that the added delivery of non-viral DNA encoding for pro-angiogenic growth factors could further enhance this effect. Here, 100 and 60 μm porous and non-porous (n-pore) hyaluronic acid-MMP hydrogels with encapsulated reporter (pGFPluc) or pro-angiogenic (pVEGF) plasmids were used to investigate scaffold-mediated gene delivery for local gene therapy in a diabetic wound healing mouse model. Porous hydrogels allowed for significantly faster wound closure compared to n-pore hydrogels, which did not degrade and essentially provided a mechanical barrier to closure. Interestingly, the delivery of pDNA/PEI polyplexes positively promoted granulation tissue formation even when the DNA did not encode for an angiogenic protein. And although transfected cells were present throughout the granulation tissue surrounding all hydrogels at 2 weeks, pVEGF delivery did not further enhance the angiogenic response. Despite this, the presence of transfected cells shows promise for the use of polyplex-loaded porous hydrogels for local gene delivery in the treatment of diabetic wounds. PMID:25694196

  5. Adeno-Associated Viral-Mediated LARGE Gene Therapy Rescues the Muscular Dystrophic Phenotype in Mouse Models of Dystroglycanopathy

    PubMed Central

    Yu, Miao; He, Yonglin; Wang, Kejian; Zhang, Peng; Zhang, Shengle

    2013-01-01

    Abstract Dystroglycanopathies are a group of congenital muscular dystrophies (CMD) often caused by mutations in genes encoding glycosyltransferases that lead to hypoglycosylation of α-dystroglycan (α-DG) and reduce its extracellular matrix-binding activity. Overexpressing LARGE (formerly known as like-glycosyltransferase) generates an extracellular matrix-binding carbohydrate epitope in cells with CMD-causing mutations in not only LARGE but also other glycosyltransferases, including POMT1, POMGnT1, and fukutin, creating the possibilities of a one-for-all gene therapy. To determine the feasibility of LARGE gene therapy, a serotype 9 adeno-associated viral vector for overexpressing LARGE (AAV9-LARGE) was injected intracardially into newborns of two mouse models of CMD: the natural LARGE mutant Largemyd mice and protein O-mannose N-acetylglucosaminyltransferase 1 (POMGnT1) knockout mice. AAV9-LARGE virus treatment yielded partial restoration of α-DG glycosylation and ligand-binding activity. The muscular dystrophy phenotype in skeletal muscles was ameliorated as revealed by significantly reduced fibrosis, necrosis, and numbers of centrally located nuclei with improved motor function. These results indicate that LARGE overexpression in vivo by AAV9-mediated gene therapy is effective at restoring functional glycosylation of α-DG and rescuing the muscular dystrophy phenotype in deficiency of not only LARGE but also POMGnT1, providing evidence that in vivo LARGE gene therapy may be broadly useful in dystroglycanopathies. PMID:23379513

  6. A methodology for linking 2D overland flow models with the sewer network model SWMM 5.1 based on dynamic link libraries.

    PubMed

    Leandro, Jorge; Martins, Ricardo

    2016-01-01

    Pluvial flooding in urban areas is characterized by a gradually varying inundation process caused by surcharge of the sewer manholes. Therefore urban flood models need to simulate the interaction between the sewer network and the overland flow in order to accurately predict the flood inundation extents. In this work we present a methodology for linking 2D overland flow models with the storm sewer model SWMM 5. SWMM 5 is a well-known free open-source code originally developed in 1971. The latest major release saw its structure re-written in C ++ allowing it to be compiled as a command line executable or through a series of calls made to function inside a dynamic link library (DLL). The methodology developed herein is written inside the same DLL in C + +, and is able to simulate the bi-directional interaction between both models during simulation. Validation is done in a real case study with an existing urban flood coupled model. The novelty herein is that the new methodology can be added to SWMM without the need for editing SWMM's original code. Furthermore, it is directly applicable to other coupled overland flow models aiming to use SWMM 5 as the sewer network model. PMID:27332848

  7. A Drosophila XPD model links cell cycle coordination with neuro-development and suggests links to cancer

    PubMed Central

    Stettler, Karin; Li, Xiaoming; Sandrock, Björn; Braga-Lagache, Sophie; Heller, Manfred; Dümbgen, Lutz; Suter, Beat

    2015-01-01

    XPD functions in transcription, DNA repair and in cell cycle control. Mutations in human XPD (also known as ERCC2) mainly cause three clinical phenotypes: xeroderma pigmentosum (XP), Cockayne syndrome (XP/CS) and trichothiodystrophy (TTD), and only XP patients have a high predisposition to developing cancer. Hence, we developed a fly model to obtain novel insights into the defects caused by individual hypomorphic alleles identified in human XP-D patients. This model revealed that the mutations that displayed the greatest in vivo UV sensitivity in Drosophila did not correlate with those that led to tumor formation in humans. Immunoprecipitations followed by targeted quantitative MS/MS analysis showed how different xpd mutations affected the formation or stability of different transcription factor IIH (TFIIH) subcomplexes. The XP mutants most clearly linked to high cancer risk, Xpd R683W and R601L, showed a reduced interaction with the core TFIIH and also an abnormal interaction with the Cdk-activating kinase (CAK) complex. Interestingly, these two XP alleles additionally displayed high levels of chromatin loss and free centrosomes during the rapid nuclear division phase of the Drosophila embryo. Finally, the xpd mutations showing defects in the coordination of cell cycle timing during the Drosophila embryonic divisions correlated with those human mutations that cause the neurodevelopmental abnormalities and developmental growth defects observed in XP/CS and TTD patients. PMID:25431422

  8. An information-theoretic model for link prediction in complex networks

    PubMed Central

    Zhu, Boyao; Xia, Yongxiang

    2015-01-01

    Various structural features of networks have been applied to develop link prediction methods. However, because different features highlight different aspects of network structural properties, it is very difficult to benefit from all of the features that might be available. In this paper, we investigate the role of network topology in predicting missing links from the perspective of information theory. In this way, the contributions of different structural features to link prediction are measured in terms of their values of information. Then, an information-theoretic model is proposed that is applicable to multiple structural features. Furthermore, we design a novel link prediction index, called Neighbor Set Information (NSI), based on the information-theoretic model. According to our experimental results, the NSI index performs well in real-world networks, compared with other typical proximity indices. PMID:26335758

  9. Mechanism of tumor remission by cytomegalovirus in a murine lymphoma model: evidence for involvement of virally induced cellular interleukin-15.

    PubMed

    Erlach, Katja C; Reddehase, Matthias J; Podlech, Jürgen

    2015-06-01

    A murine model of B and T cell lymphomas in recipients after hematoablative conditioning for hematopoietic cell transplantation (HCT) has previously revealed a tumor-repressive, metastasis-inhibiting function of murine cytomegalovirus (mCMV). More recently, this prediction from the experimental model was put on trial in several clinical studies that indeed gave evidence for a lower incidence of tumor relapse associated with early reactivation of latent human cytomegalovirus (hCMV) after allogeneic HCT in patients treated against different types of hematopoietic malignancies, including lymphoma and acute as well as chronic leukemias. Due to the limitations inherent to clinical studies, the tumor-repressive role of hCMV remained observational with no approach to clarify mechanisms. Although the tumor-repressive mechanisms of mCMV and hCMV may differ and depend on the type of tumor, experimental approaches in the murine model might give valuable hints for concepts to follow in clinical research. We have previously shown for the liver-adapted A20-derived B cell lymphoma E12E that mCMV does not infect the lymphoma cells for causing cell death by viral cytopathogenicity but triggers tumor-selective apoptosis at a tissue site of tumor metastasis distant from a local site of infection. This finding suggested involvement of a cytokine that triggers apoptosis, directly or indirectly. Here we used a series of differential high-density microarray analyses to identify cellular genes whose expression is specifically upregulated at the site of virus entry only by viruses capable of triggering lymphoma cell apoptosis. This strategy identified interleukin-15 (IL-15) as most promising candidate, eventually confirmed by lymphoma repression with recombinant IL-15. PMID:25805565

  10. Breaking a virus: Identifying molecular level failure modes of a viral capsid by multiscale modeling

    NASA Astrophysics Data System (ADS)

    Krishnamani, V.; Globisch, C.; Peter, C.; Deserno, M.

    2016-07-01

    We use coarse-grained (CG) simulations to study the deformation of empty Cowpea Chlorotic Mottle Virus (CCMV) capsids under uniaxial compression, from the initial elastic response up to capsid breakage. Our CG model is based on the MARTINI force field and has been amended by a stabilizing elastic network, acting only within individual proteins, that was tuned to capture the fluctuation spectrum of capsid protein dimers, obtained from all atom simulations. We have previously shown that this model predicts force-compression curves that match AFM indentation experiments on empty CCMV capsids. Here we investigate details of the actual breaking events when the CCMV capsid finally fails. We present a symmetry classification of all relevant protein contacts and show that they differ significantly in terms of stability. Specifically, we show that interfaces which break readily are precisely those which are believed to form last during assembly, even though some of them might share the same contacts as other non-breaking interfaces. In particular, the interfaces that form pentamers of dimers never break, while the virtually identical interfaces within hexamers of dimers readily do. Since these units differ in the large-scale geometry and, most noticeably, the cone-angle at the center of the 5- or 6-fold vertex, we propose that the hexameric unit fails because it is pre-stressed. This not only suggests that hexamers of dimers form less frequently during the early stages of assembly; it also offers a natural explanation for the well-known β-barrel motif at the hexameric center as a post-aggregation stabilization mechanism. Finally, we identify those amino acid contacts within all key protein interfaces that are most persistent during compressive deformation of the capsid, thereby providing potential targets for mutation studies aiming to elucidate the key contacts upon which overall stability rests.

  11. Bayesian modeling for linking causally related observations in chest X-ray reports.

    PubMed Central

    Chapman, W. W.; Haug, P. J.

    1998-01-01

    Our natural language understanding system outputs a list of diseases, findings, and appliances found in a chest x-ray report. The system described in this paper links those diseases and findings that are causally related. Using Bayesian networks to model the conceptual and diagnostic information found in a chest x-ray we are able to infer more specific information about the findings that are linked to diseases. PMID:9929287

  12. Viral hepatitis*

    PubMed Central

    Deinhardt, F.; Gust, I. D.

    1982-01-01

    Three forms of viral hepatitis can be recognized: hepatitis A, hepatitis B, and hepatitis non-A, non-B. Hepatitis A is caused by a picornavirus, is transmitted by the faceal—oral route, does not become chronic, and no chronic virus carriers exist. The virus can be grown in cell cultures, and killed as well as live attenuated virus vaccines are under development. Hepatitis B is caused by an enveloped virus containing a circular, double-stranded form of DNA. The disease is transmitted parenterally through inoculation of blood or blood products containing virus or through close personal contact with a virus-positive person. Hepatitis B becomes chronic in a certain number of cases and can lead to cirrhosis and primary liver cell carcinoma. The blood and certain body secretions of individuals with a persistent or chronic infection may remain infectious for many years. The hepatitis B virus cannot be grown in cell cultures but the entire genome has been sequenced and cloned in bacterial and eukaryotic cells. An inactivated virus vaccine has been prepared from hepatitis B surface antigen present in the plasma of hepatitis B virus carriers and further vaccines are under development. The agents of hepatitis non-A, non-B have not been identified. It is possible to distinguish between a predominantly parenterally transmitted and an orally transmitted form of hepatitis non-A, non-B. The latter is reported to be caused by a picornavirus that does not, however, have any antigenic relationship with hepatitis A virus. PMID:6817933

  13. Viral gene transfer of APPsα rescues synaptic failure in an Alzheimer's disease mouse model.

    PubMed

    Fol, Romain; Braudeau, Jerome; Ludewig, Susann; Abel, Tobias; Weyer, Sascha W; Roederer, Jan-Peter; Brod, Florian; Audrain, Mickael; Bemelmans, Alexis-Pierre; Buchholz, Christian J; Korte, Martin; Cartier, Nathalie; Müller, Ulrike C

    2016-02-01

    Alzheimer's disease (AD) is characterized by synaptic failure, dendritic and axonal atrophy, neuronal death and progressive loss of cognitive functions. It is commonly assumed that these deficits arise due to β-amyloid accumulation and plaque deposition. However, increasing evidence indicates that loss of physiological APP functions mediated predominantly by neurotrophic APPsα produced in the non-amyloidogenic α-secretase pathway may contribute to AD pathogenesis. Upregulation of APPsα production via induction of α-secretase might, however, be problematic as this may also affect substrates implicated in tumorigenesis. Here, we used a gene therapy approach to directly overexpress APPsα in the brain using AAV-mediated gene transfer and explored its potential to rescue structural, electrophysiological and behavioral deficits in APP/PS1∆E9 AD model mice. Sustained APPsα overexpression in aged mice with already preexisting pathology and amyloidosis restored synaptic plasticity and partially rescued spine density deficits. Importantly, AAV-APPsα treatment also resulted in a functional rescue of spatial reference memory in the Morris water maze. Moreover, we demonstrate a significant reduction of soluble Aβ species and plaque load. In addition, APPsα induced the recruitment of microglia with a ramified morphology into the vicinity of plaques and upregulated IDE and TREM2 expression suggesting enhanced plaque clearance. Collectively, these data indicate that APPsα can mitigate synaptic and cognitive deficits, despite established pathology. Increasing APPsα may therefore be of therapeutic relevance for AD.

  14. Contrasting Roles for Axonal Degeneration in an Autoimmune versus Viral Model of Multiple Sclerosis

    PubMed Central

    Tsunoda, Ikuo; Tanaka, Tomoko; Terry, Emily Jane; Fujinami, Robert S.

    2007-01-01

    Although demyelination is a cardinal feature in multiple sclerosis, axonal injury also occurs. We tested whether a delay in axonal degeneration could affect the disease severity in two models for multiple sclerosis: experimental autoimmune encephalomyelitis (EAE) and Theiler’s murine encephalomyelitis virus (TMEV) infection. We compared wild-type C57BL/6 (B6) mice with C57BL/Wlds (Wld) mice, which carry a mutation that delays axonal degeneration. In EAE, both mouse strains were sensitized with myelin oligodendrocyte glycoprotein (MOG)35-55 peptide and showed a similar disease onset, MOG-specific lymphoproliferative responses, and inflammation during the acute stage of EAE. However, during the chronic stage, B6 mice continued to show paralysis with a greater extent of axonal damage, demyelination, and MOG-specific lymphoproliferative responses compared with Wld mice, which showed complete recovery. In TMEV infection, only Wld mice were paralyzed and had increased inflammation, virus antigen-positive cells, and TMEV-specific lymphoproliferative responses versus infected B6 mice. Because TMEV can use axons to disseminate in the brain, axonal degeneration in B6 mice might be a beneficial mechanism that limits the virus spread, whereas slow axonal degeneration in Wld mice could favor virus spread. Therefore, axonal degeneration plays contrasting roles (beneficial versus detrimental) depending on the initiator driving the disease. PMID:17200195

  15. Multiaxial deformations of end-linked poly(dimethylsiloxane) networks. 4. Further assessment of the slip-link model for chain-entanglement effect on rubber elasticity

    NASA Astrophysics Data System (ADS)

    Urayama, Kenji; Kawamura, Takanobu; Kohjiya, Shinzo

    2003-03-01

    The Edwards-Vilgis slip-link model for the chain-entanglement effect on rubber elasticity is critically assessed on the basis of quasiequilibrium biaxial stress—strain data of end-linked polydimethylsiloxane (PDMS) networks with different entanglement densities. The PDMS networks with different entanglement densities were prepared by end-linking end-reactive long precursor PDMS in solutions with different solvent contents. The slip-link model, in which trapped entanglement is modeled by fictitious mobile slip-link attaching two entangled chains, satisfactorily describes the biaxial data over the entire range of deformation for all the networks examined. The model-specific parameters, i.e., slippage of slip-link (η) and inextensibility of network (α), were employed as adjustable parameters in data-fitting. The fitted values of η and α vary reasonably with the degree of dilution at network preparation, i.e., entanglement density. With an increase in dilution, i.e., decrease in entanglement density, η increases, whereas α decreases. In addition, the fitted values of η and α are in good agreement with the estimates from another molecular approach independent of mechanical testings: η=Me/Mc, where Me and Mc are the molecular masses between neighboring entanglements and between adjacent cross-links, respectively; α=nj-1/2, where nj is the number of Kuhn segments between adjacent elastically effective junctions including cross-links and trapped entanglements. The satisfactory data-fit with the model parameters of physically reasonable magnitudes supports the validity of the slip-link model for entanglement effects on rubber elasticity.

  16. Conditions for Viral Influence Spreading through Multiplex Correlated Social Networks

    NASA Astrophysics Data System (ADS)

    Hu, Yanqing; Havlin, Shlomo; Makse, Hernán A.

    2014-04-01

    A fundamental problem in network science is to predict how certain individuals are able to initiate new networks to spring up "new ideas." Frequently, these changes in trends are triggered by a few innovators who rapidly impose their ideas through "viral" influence spreading, producing cascades of followers and fragmenting an old network to create a new one. Typical examples include the rise of scientific ideas or abrupt changes in social media, like the rise of Facebook to the detriment of Myspace. How this process arises in practice has not been conclusively demonstrated. Here, we show that a condition for sustaining a viral spreading process is the existence of a multiplex-correlated graph with hidden "influence links." Analytical solutions predict percolation-phase transitions, either abrupt or continuous, where networks are disintegrated through viral cascades of followers, as in empirical data. Our modeling predicts the strict conditions to sustain a large viral spreading via a scaling form of the local correlation function between multilayers, which we also confirm empirically. Ultimately, the theory predicts the conditions for viral cascading in a large class of multiplex networks ranging from social to financial systems and markets.

  17. An Extension of Least Squares Estimation of IRT Linking Coefficients for the Graded Response Model

    ERIC Educational Resources Information Center

    Kim, Seonghoon

    2010-01-01

    The three types (generalized, unweighted, and weighted) of least squares methods, proposed by Ogasawara, for estimating item response theory (IRT) linking coefficients under dichotomous models are extended to the graded response model. A simulation study was conducted to confirm the accuracy of the extended formulas, and a real data study was…

  18. A Simple Forecasting Model Linking Macroeconomic Policy to Industrial Employment Demand.

    ERIC Educational Resources Information Center

    Malley, James R.; Hady, Thomas F.

    A study detailed further a model linking monetary and fiscal policy to industrial employment in metropolitan and nonmetropolitan areas of four United States regions. The model was used to simulate the impacts on area and regional employment of three events in the economy: changing real gross national product (GNP) via monetary policy, holding the…

  19. Protein modification during anti-viral heat-treatment bioprocessing of factor VIII concentrates, factor IX concentrates, and model proteins in the presence of sucrose.

    PubMed

    Smales, C Mark; Pepper, Duncan S; James, David C

    2002-01-01

    To ensure the optimal safety of plasma derived and new generation recombinant proteins, heat treatment is customarily applied in the manufacturing of such biopharmaceuticals as a means of viral inactivation. In subjecting proteins to anti-viral heat-treatment it is necessary to use high concentrations of thermostabilizing excipients to prevent protein damage, and it is therefore imperative that the correct balance between bioprocessing conditions, maintenance of protein integrity and virus kill is found. In this study we have utilized model proteins (lysozyme, fetuin, and human serum albumin) and plasma-derived therapeutic proteins (factor VIII and factor IX) to investigate the protein modifications that occur during anti-viral heat treatment. Specifically, we investigated the relationship between bioprocessing conditions and the type and extent of protein modification under a variety of industrially relevant wet and lyophilized heat treatments using sucrose as a thermostabilizing agent. Heat treatment led to the formation of disulfide crosslinks and aggregates in proteins containing free cysteine residues. Terminal oligosaccharide sialic acid residues were hydrolyzed from the glycan moieties of glycoproteins during anti-viral heat treatment. Heat treatment promoted sucrose hydrolysis to yield glucose and fructose, leading, in turn, to the glycation of lysine amino groups in those proteins containing di-lysine motifs. During extended hear treatments, 1,2-dicarbonyl type advanced glycation end-products were also formed. Glycation-type modifications were more prevalent in wet heat-treated protein formulations.

  20. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.

    PubMed

    Hamacher, K; Hübsch, A; McCammon, J A

    2006-04-28

    Programmed cell death regulating protein motifs play an essential role in the development of an organism, its immune response, and disease-related cellular mechanisms. Among those motifs the BH3 domain of the BCL-2 family is found to be of crucial importance. Recent experiments showed how the isolated, otherwise unstructured BH3 peptide can be modified by a hydrocarbon linkage to regain function. We parametrized a reduced, dynamic model for the stability effects of such covalent cross-linking and confirmed that the model reproduces the reinforcement of the structural stability of the BH3 motif by cross-linking. We show that an analytically solvable model for thermostability around the native state is not capable of reproducing the stabilization effect. This points to the crucial importance of the peptide dynamics and the fluctuations neglected in the analytic model for the cross-linking system to function properly. This conclusion is supported by a thorough analysis of a simulated Go model. The resulting model is suitable for rational design of generic cross-linking systems in silicio.

  1. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking

    NASA Astrophysics Data System (ADS)

    Hamacher, K.; Hübsch, A.; McCammon, J. A.

    2006-04-01

    Programmed cell death regulating protein motifs play an essential role in the development of an organism, its immune response, and disease-related cellular mechanisms. Among those motifs the BH3 domain of the BCL-2 family is found to be of crucial importance. Recent experiments showed how the isolated, otherwise unstructured BH3 peptide can be modified by a hydrocarbon linkage to regain function. We parametrized a reduced, dynamic model for the stability effects of such covalent cross-linking and confirmed that the model reproduces the reinforcement of the structural stability of the BH3 motif by cross-linking. We show that an analytically solvable model for thermostability around the native state is not capable of reproducing the stabilization effect. This points to the crucial importance of the peptide dynamics and the fluctuations neglected in the analytic model for the cross-linking system to function properly. This conclusion is supported by a thorough analysis of a simulated Gō model. The resulting model is suitable for rational design of generic cross-linking systems in silicio.

  2. Combination of reverse transcription real-time polymerase chain reaction and antigen capture enzyme-linked immunosorbent assay for the detection of animals persistently infected with Bovine viral diarrhea virus.

    PubMed

    Yan, Lifang; Zhang, Shuping; Pace, Lanny; Wilson, Floyd; Wan, Henry; Zhang, Michael

    2011-01-01

    Bovine viral diarrhea virus (BVDV) is an economically important pathogen of cattle. A successful control program requires early detection and removal of persistently infected (PI) animals. The objective of the current study was to develop, validate, and apply a cost-effective testing scheme for the detection of BVDV PI animals in exposed herds. Pooled samples were screened by using a real-time reverse transcription polymerase chain reaction (real-time RT-PCR), and individual positives were identified with an antigen capture enzyme-linked immunosorbent assay (ACE). The detection limits of the optimized real-time RT-PCR were 10 and 100 RNA copies per reaction for BVDV-1 and BVDV-2, respectively. The semiquantitative results of real-time RT-PCR and ACE or real-time RT-PCR and immunohistochemistry were moderately correlated. The threshold cycle of real-time RT-PCR performed on pooled samples was significantly correlated with the pool size (R(2)  =  0.993). The least-cost pool sizes were 50 at a prevalence of 0.25-0.5% and 25 at a prevalence of 0.75-2.0%. By using the combined real-time RT-PCR and ACE procedure, 111 of 27,932 samples (0.4%) tested positive for BVDV. At this prevalence, cost reduction associated with the application of real-time RT-PCR and ACE ranged from 61% to 94%, compared with testing individual samples by ACE, immunohistochemistry, or real-time RT-PCR. Real-time RT-PCR screening also indicated that 92.94% of PI animals were infected with BVDV-1, 3.53% with BVDV-2, and 3.53% with both BVDV-1 and BVDV-2. Analysis of the 5'-untranslated region of 22 isolates revealed the predominance of BVDV-1b followed by BVDV-2a.

  3. Discovering link communities in complex networks by an integer programming model and a genetic algorithm.

    PubMed

    Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

    2013-01-01

    Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks.

  4. Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation.

    PubMed

    Shu, Bo; Gong, Peng

    2016-07-12

    Viral RNA-dependent RNA polymerases (RdRPs) play essential roles in viral genome replication and transcription. We previously reported several structural states of the poliovirus RdRP nucleotide addition cycle (NAC) that revealed a unique palm domain-based active site closure mechanism and proposed a six-state NAC model including a hypothetical state representing translocation intermediates. Using the RdRP from another human enterovirus, enterovirus 71, here we report seven RdRP elongation complex structures derived from a crystal lattice that allows three NAC events. These structures suggested a key order of events in initial NTP binding and NTP-induced active site closure and revealed a bona fide translocation intermediate featuring asymmetric movement of the template-product duplex. Our work provides essential missing links in understanding NTP recognition and translocation mechanisms in viral RdRPs and emphasizes the uniqueness of the viral RdRPs compared with other processive polymerases. PMID:27339134

  5. Synthesizing within-host and population-level selective pressures on viral populations: the impact of adaptive immunity on viral immune escape

    PubMed Central

    Volkov, Igor; Pepin, Kim M.; Lloyd-Smith, James O.; Banavar, Jayanth R.; Grenfell, Bryan T.

    2010-01-01

    The evolution of viruses to escape prevailing host immunity involves selection at multiple integrative scales, from within-host viral and immune kinetics to the host population level. In order to understand how viral immune escape occurs, we develop an analytical framework that links the dynamical nature of immunity and viral variation across these scales. Our epidemiological model incorporates within-host viral evolutionary dynamics for a virus that causes acute infections (e.g. influenza and norovirus) with changes in host immunity in response to genetic changes in the virus population. We use a deterministic description of the within-host replication dynamics of the virus, the pool of susceptible host cells and the host adaptive immune response. We find that viral immune escape is most effective at intermediate values of immune strength. At very low levels of immunity, selection is too weak to drive immune escape in recovered hosts, while very high levels of immunity impose such strong selection that viral subpopulations go extinct before acquiring enough genetic diversity to escape host immunity. This result echoes the predictions of simpler models, but our formulation allows us to dissect the combination of within-host and transmission-level processes that drive immune escape. PMID:20335194

  6. Summary goodness-of-fit statistics for binary generalized linear models with noncanonical link functions.

    PubMed

    Canary, Jana D; Blizzard, Leigh; Barry, Ronald P; Hosmer, David W; Quinn, Stephen J

    2016-05-01

    Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness-of-fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (TG), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer-Lemeshow (HL) and Pigeon-Heyse (J(2) ) statistics can be applied directly. In a simulation study, TG, HL, and J(2) were used to evaluate the fit of probit, log-log, complementary log-log, and log models, all calculated with a common grouping method. The TG statistic consistently maintained Type I error rates, while those of HL and J(2) were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, TG had more power than HL or J(2) . PMID:26584470

  7. Summary goodness-of-fit statistics for binary generalized linear models with noncanonical link functions.

    PubMed

    Canary, Jana D; Blizzard, Leigh; Barry, Ronald P; Hosmer, David W; Quinn, Stephen J

    2016-05-01

    Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness-of-fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (TG), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer-Lemeshow (HL) and Pigeon-Heyse (J(2) ) statistics can be applied directly. In a simulation study, TG, HL, and J(2) were used to evaluate the fit of probit, log-log, complementary log-log, and log models, all calculated with a common grouping method. The TG statistic consistently maintained Type I error rates, while those of HL and J(2) were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, TG had more power than HL or J(2) .

  8. Bovine respiratory disease model based on dual infections with infection with bovine viral diarrhea virus and bovine corona virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine respiratory disease complex (BRDC) is the leading cause of economic loss in the U.S. cattle industry. BRDC likely results from simultaneous or sequential infections with multiple pathogens including both viruses and bacteria. Bovine viral diarrhea virus (BVDV) and bovine corona virus (BoCV...

  9. [Viral superantigens].

    PubMed

    Us, Dürdal

    2016-07-01

    , expression of endogenous SAgs leads to thymic deletion of responding T cells (bearing Vβ6-9+ TCR) due to self-tolerance induction during the fetal life, and protects the host against future exogenous MMTV infections. The SAg of rabies virus is the N protein found in nucleocapsid structure and stimulates Vβ8+TCR-bearing T cells. The SAg-induced polyclonal activation of T cells leads to turn-off the specific immune response, to enhance the immunopathogenesis and facilitates viral transmission from the initial site of infection (the muscle tissue) to the nerve endings. In case of EBV-associated SAg that activates Vβ13+TCR-bearing T cells, it was detected that the SAg activity was not encoded by EBV itself, but instead was due to the transactivation of HERV-K18 by EBV latent membrane proteins, whose env gene encodes the SAg (Sutkowski, et al. 2001). It has been denoted that EBV-induced SAg expression plays a role in the long-term persistence and latency of virus in memory B cells, in the development of autoimmune diseases and in the oncogenesis mechanisms. The proteins which are identified as SAgs of HIV are Nef and gp120. It is believed that, the massive activation of CD4+ T cells (selectively with Vβ-12+, Vβ-5.3+ and Vβ-18+ TCRs) in early stages of infection and clonal deletion, anergy and apoptosis of bystander T cells in the late stages may be due to SAg property of Nef protein, as well as the other mechanisms. However there are some studies indicating that Nef does not act as a SAg (Lapatschek, et al. 2001). HIV gp120 glycoprotein is a B-cell SAg that binds to VH3-expressing B cell receptors and causes polyclonal B cell activation. In addition, binding of gp120 to IgE on the surface of basophiles and mast cells causes activation of those cells, secretion of high level proinflammatory mediators leading to allergic reactions and tissue damage. In a recent study, the depletion (anergy or deletion) of T cell populations bearing Vβ12+, Vβ13+ and Vβ17+ TCR have been

  10. Multiscale Modeling for Linking Growth, Microstructure, and Properties of Inorganic Microporous Films

    NASA Technical Reports Server (NTRS)

    Vlachos, Dion G.

    2002-01-01

    The focus of this presentation is on multiscale modeling in order to link processing, microstructure, and properties of materials. Overview of problems we study includes: Growth mechanisms in chemical and physical vapor epitaxy; thin films of zeolites for separation and sensing; thin Pd films for hydrogen separation and pattern formation by self-regulation routes.

  11. Exploring Alternative Characteristic Curve Approaches to Linking Parameter Estimates from the Generalized Partial Credit Model.

    ERIC Educational Resources Information Center

    Roberts, James S.; Bao, Han; Huang, Chun-Wei; Gagne, Phill

    Characteristic curve approaches for linking parameters from the generalized partial credit model were examined for cases in which common (anchor) items are calibrated separately in two groups. Three of these approaches are simple extensions of the test characteristic curve (TCC), item characteristic curve (ICC), and operating characteristic curve…

  12. Concerns about School-Linked Services: Institution-Based versus Community-Based Models.

    ERIC Educational Resources Information Center

    Chaskin, Robert J.; Richman, Harold A.

    1993-01-01

    Reviews concerns about school-linked services programs, exploring institutional-based versus community-based models of service delivery. It is argued that the community is the appropriate context for providing and facilitating access to services and opportunities. Too strong an institutional bias runs the risk of limiting access and community…

  13. The Gender-Linked Language Effect: An Empirical Test of a General Process Model

    ERIC Educational Resources Information Center

    Mulac, Anthony; Giles, Howard; Bradac, James J.; Palomares, Nicholas A.

    2013-01-01

    The gender-linked language effect (GLLE) is a phenomenon in which transcripts of female communicators are rated higher on Socio-Intellectual Status and Aesthetic Quality and male communicators are rated higher on Dynamism. This study proposed and tested a new general process model explanation for the GLLE, a central mediating element of which…

  14. The Chain-Link Fence Model: A Framework for Creating Security Procedures

    ERIC Educational Resources Information Center

    Houghton, Robert F.

    2013-01-01

    A long standing problem in information technology security is how to help reduce the security footprint. Many specific proposals exist to address specific problems in information technology security. Most information technology solutions need to be repeatable throughout the course of an information systems lifecycle. The Chain-Link Fence Model is…

  15. Cannabidiol provides long-lasting protection against the deleterious effects of inflammation in a viral model of multiple sclerosis: a role for A2A receptors.

    PubMed

    Mecha, M; Feliú, A; Iñigo, P M; Mestre, L; Carrillo-Salinas, F J; Guaza, C

    2013-11-01

    Inflammation in the central nervous system (CNS) is a complex process that involves a multitude of molecules and effectors, and it requires the transmigration of blood leukocytes across the blood-brain barrier (BBB) and the activation of resident immune cells. Cannabidiol (CBD), a non-psychotropic cannabinoid constituent of Cannabis sativa, has potent anti-inflammatory and immunosuppressive properties. Yet, how this compound modifies the deleterious effects of inflammation in TMEV-induced demyelinating disease (TMEV-IDD) remains unknown. Using this viral model of multiple sclerosis (MS), we demonstrate that CBD decreases the transmigration of blood leukocytes by downregulating the expression of vascular cell adhesion molecule-1 (VCAM-1), chemokines (CCL2 and CCL5) and the proinflammatory cytokine IL-1β, as well as by attenuating the activation of microglia. Moreover, CBD administration at the time of viral infection exerts long-lasting effects, ameliorating motor deficits in the chronic phase of the disease in conjunction with reduced microglial activation and pro-inflammatory cytokine production. Adenosine A2A receptors participate in some of the anti-inflammatory effects of CBD, as the A2A antagonist ZM241385 partially blocks the protective effects of CBD in the initial stages of inflammation. Together, our findings highlight the anti-inflammatory effects of CBD in this viral model of MS and demonstrate the significant therapeutic potential of this compound for the treatment of pathologies with an inflammatory component.

  16. Entangled polymer dynamics in equilibrium and flow modeled through slip links.

    PubMed

    Schieber, Jay D; Andreev, Marat

    2014-01-01

    The idea that the dynamics of concentrated, high-molecular weight polymers are largely governed by entanglements is now widely accepted and typically understood through the tube model. Here we review alternative approaches, slip-link models, that share some similarities to and offer some advantages over tube models. Although slip links were proposed at the same time as tubes, only recently have detailed, quantitative mathematical models arisen based on this picture. In this review, we focus on these models, with most discussion limited to mathematically well-defined objects that conform to state-of-the-art beyond-equilibrium thermodynamics. These models are connected to each other through successive coarse graining, using nonequilibrium thermodynamics along the way, and with a minimal parameter set. In particular, the most detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. Once the remaining parameter is determined for any system, all parameters for all members of the hierarchy are determined. We show how, using this hierarchy of slip-link models combined with atomistic simulations, we can make predictions about the nonlinear rheology of monodisperse homopolymer melts, polydisperse melts, or blends of different architectures. Mathematical details are given elsewhere, so these are limited here, and physical ideas are emphasized. We conclude with an outlook on remaining challenges that might be tackled successfully using this approach, including complex flow fields and polymer blends. PMID:24655135

  17. Computational mechanics of viral capsids.

    PubMed

    Gibbons, Melissa M; Perotti, Luigi E; Klug, William S

    2015-01-01

    Viral capsids undergo significant mechanical deformations during their assembly, maturation, and infective life-span. In order to characterize the mechanics of viral capsids, their response to applied external forces is analyzed in several experimental studies using, for instance, Atomic Force Microscope (AFM) indentation experiments. In recent years, a broader approach to study the mechanics of viral capsids has leveraged the theoretical tools proper of continuum mechanics. Even though the theory of continuum elasticity is most commonly used to study deformable bodies at larger macroscopic length scales, it has been shown that this very rich theoretical field can still offer useful insights into the mechanics of viral structures at the nanometer scale. Here we show the construction of viral capsid continuum mechanics models starting from different forms of experimental data. We will discuss the kinematics assumptions, the issue of the reference configuration, the material constitutive laws, and the numerical discretization necessary to construct a complete Finite Element capsid mechanical model. Some examples in the second part of the chapter will show the predictive capabilities of the constructed models and underline useful practical aspects related to efficiency and accuracy. We conclude each example by collecting several key findings discovered by simulating AFM indentation experiments using the constructed numerical models.

  18. Dynamical modeling of serial manipulators with flexible links and joints using the method of kinematic influence

    NASA Technical Reports Server (NTRS)

    Graves, Philip L.

    1989-01-01

    A method of formulating the dynamical equations of a flexible, serial manipulator is presented, using the Method of Kinematic Influence. The resulting equations account for rigid body motion, structural motion due to link and joint flexibilities, and the coupling between these two motions. Nonlinear inertial loads are included in the equations. A finite order mode summation method is used to model flexibilities. The structural data may be obtained from experimental, finite element, or analytical methods. Nonlinear flexibilities may be included in the model.

  19. Linking Parameters Estimated with the Generalized Graded Unfolding Model: A Comparison of the Accuracy of Characteristic Curve Methods

    ERIC Educational Resources Information Center

    Anderson Koenig, Judith; Roberts, James S.

    2007-01-01

    Methods for linking item response theory (IRT) parameters are developed for attitude questionnaire responses calibrated with the generalized graded unfolding model (GGUM). One class of IRT linking methods derives the linking coefficients by comparing characteristic curves, and three of these methods---test characteristic curve (TCC), item…

  20. Viral Skin Diseases.

    PubMed

    Ramdass, Priya; Mullick, Sahil; Farber, Harold F

    2015-12-01

    In the vast world of skin diseases, viral skin disorders account for a significant percentage. Most viral skin diseases present with an exanthem (skin rash) and, oftentimes, an accompanying enanthem (lesions involving the mucosal membrane). In this article, the various viral skin diseases are explored, including viral childhood exanthems (measles, rubella, erythema infectiosum, and roseola), herpes viruses (herpes simplex virus, varicella zoster virus, Kaposi sarcoma herpes virus, viral zoonotic infections [orf, monkeypox, ebola, smallpox]), and several other viral skin diseases, such as human papilloma virus, hand, foot, and mouth disease, molluscum contagiosum, and Gianotti-Crosti syndrome.

  1. Viral Skin Diseases.

    PubMed

    Ramdass, Priya; Mullick, Sahil; Farber, Harold F

    2015-12-01

    In the vast world of skin diseases, viral skin disorders account for a significant percentage. Most viral skin diseases present with an exanthem (skin rash) and, oftentimes, an accompanying enanthem (lesions involving the mucosal membrane). In this article, the various viral skin diseases are explored, including viral childhood exanthems (measles, rubella, erythema infectiosum, and roseola), herpes viruses (herpes simplex virus, varicella zoster virus, Kaposi sarcoma herpes virus, viral zoonotic infections [orf, monkeypox, ebola, smallpox]), and several other viral skin diseases, such as human papilloma virus, hand, foot, and mouth disease, molluscum contagiosum, and Gianotti-Crosti syndrome. PMID:26612372

  2. Rainfall retrieval in urban areas using commercial microwave links from mobile networks: A modelling feasibility study

    NASA Astrophysics Data System (ADS)

    Zohidov, Bahtiyor; Andrieu, Hervé; Servières, Myriam; Normand, Nicolas

    2014-05-01

    Rainfall is usually measured by networks of rain gauges and weather radars. Many cities worldwide are not supplied with these devices; however, they are generally equipped with mobile telecommunication networks. Mobile networks use atmospheric Hyper-Frequency (HF) links whose transmitted signal power is attenuated by rainfall. Measuring that signal attenuation along each link could allow the measurement of path-averaged rainfall [Leijnse et al 2007, Overeem et al 2013, Messer et al 2006, Guili et al 1991, Zinevich et al 2008, Cuccoli et al 2011]. As HF links are concentrated in cities, these networks could constitute a self-sufficient approach to monitoring rainfall in urban areas. We adopt a simulation approach in order to study the feasibility of mapping rainfall fields at the city scale by means of existing HF links. Our domain of study is the central part of the city of Nantes, France, where the density of cellular networks is greatest. As a basis, we use a data set consisting of hundreds of weather radar images recorded by the Météo-France C band weather radar at high spatial (250m x 250m) and temporal (5 minute) resolutions located about 10 km north of the center of Nantes. We convert these images into rainfall maps using the Z-R relation and consider them as reference rainfall fields. The simulation is performed as follows. First, we simulate the measurement of total attenuation along each HF link using a rain-attenuation model based on Mie theory and a known drop size distribution in a continental temperate climate. This procedure is applied for 256 real radio links operating at different frequencies (18, 23, 38 GHz) with lengths ranging from 0.4 to 16 km. This helps us to substitute the attenuation data for the signal power received from microwave links. Error sources affecting measurement accuracy are introduced as a zero-mean Gaussian distributed random variable with variance of 10% of total attenuation. The retrieval of the rainfield is performed by a

  3. Spectral model of optical scintillation for terrestrial free-space optical communication link design

    NASA Astrophysics Data System (ADS)

    Kim, Kyung-Hwan; Higashino, Takeshi; Tsukamoto, Katsutoshi; Komaki, Shozo; Kazaura, Kamugisha; Matsumoto, Mitsuji

    2011-03-01

    Since a deep and long-term fading in optical intensity results in considerable burst errors in the data, a terrestrial free-space optical (FSO) system has to be designed with consideration of a frequency characteristic of optical scintillation to achieve high quality wireless services over the link. In designing a terrestrial FSO link, we had better design the system considering variations caused by some slow time-varying parameters. This paper proposes a Butterworth-type spectral model of optical scintillation to design a terrestrial FSO link, which enables us to estimate the power spectral density of optical scintillation in a current optical wireless channel when time zone and weather parameters, such as temperature and rainfall intensity, are given. The spectral parameters of optical scintillation, cut-off frequency, and spectral slope are estimated from the data obtained in the experiment, and then their dependencies on time zone, temperature, and rainfall intensity are examined.

  4. Chemically linked phage idiotype vaccination in the murine B cell lymphoma 1 model

    PubMed Central

    2013-01-01

    Background B cell malignancies are characterized by clonal expansion of B cells expressing tumor-specific idiotypes on their surface. These idiotypes are ideal target antigens for an individualized immunotherapy. However, previous idiotype vaccines mostly lacked efficiency due to a low immunogenicity of the idiotype. The objective of the present study was the determination of the feasibility, safety and immunogenicity of a novel chemically linked phage idiotype vaccine. Methods In the murine B cell lymphoma 1 model, tumor idiotypes were chemically linked to phage particles used as immunological carriers. For comparison, the idiotype was genetically expressed on the major phage coat protein g8 or linked to keyhole limpet hemocynanin. After intradermal immunizations with idiotype vaccines, tolerability and humoral immune responses were assessed. Results Feasibility and tolerability of the chemically linked phage idiotype vaccine was demonstrated. Vaccination with B cell lymphoma 1 idiotype expressing phage resulted in a significant survival benefit in the murine B cell lymphoma 1 protection model (60.2 ± 23.8 days vs. 41.8 ± 1.6 days and 39.8 ± 3.8 days after vaccination with wild type phage or phosphate buffered saline, respectively). Superior immunogenicity of the chemically linked phage idiotype vaccine compared to the genetically engineered phage idiotype and keyhole limpet hemocynanin-coupled idiotype vaccine was demonstrated by significantly higher B cell lymphoma 1 idiotype-specific IgG levels after vaccination with chemically linked phage idiotype. Conclusion We present a novel, simple, time- and cost-efficient phage idiotype vaccination strategy, which represents a safe and feasible therapy and may produce a superior immune response compared to previously employed idiotype vaccination strategies. PMID:24152874

  5. Experimental scleral cross-linking increases glaucoma damage in a mouse model

    PubMed Central

    Kimball, Elizabeth C.; Nguyen, Cathy; Steinhart, Matthew R.; Nguyen, Thao D.; Pease, Mary E.; Oglesby, Ericka N.; Oveson, Brian C.; Quigley, Harry A.

    2014-01-01

    The purpose of this study was to assess the effect of a scleral cross-linking agent on susceptibility to glaucoma damage in a mouse model. CD1 mice underwent 3 subconjunctival injections of 0.5 M glyceraldehyde (GA) in 1 week, then had elevated intraocular pressure (IOP) induced by bead injection. Degree of cross-linking was measured by enzyme-linked immunosorbent assay (ELISA), scleral permeability was measured by fluorescence recovery after photobleaching (FRAP), and the mechanical effects of GA exposure were measured by inflation testing. Control mice had buffer injection or no injection in 2 separate glaucoma experiments. IOP was monitored by Tonolab and retinal ganglion cell (RGC) loss was measured by histological axon counting. To rule out undesirable effects of GA, we performed electroretinography and detailed histology of the retina. GA exposure had no detectable effects on RGC number, retinal structure or function either histologically or electrophysiologically. GA increased cross-linking of sclera by 37% in an ELISA assay, decreased scleral permeability (FRAP, p = 0.001), and produced a steeper pressure—strain behavior by in vitro inflation testing. In two experimental glaucoma experiments, GA-treated eyes had greater RGC axon loss from elevated IOP than either buffer-injected or control eyes, controlling for level of IOP exposure over time (p = 0.01, and 0.049, multivariable regression analyses). This is the first report that experimental alteration of the sclera, by cross-linking, increases susceptibility to RGC damage in mice. PMID:25285424

  6. Standardization of enzyme-linked immunosorbent assays (ELISAs) for quantitative estimation of antibodies specific for infectious bovine rhinotracheitis virus, respiratory syncytial virus, parainfluenza-3 virus, and bovine viral diarrhea virus.

    PubMed

    Graham, D A; Mawhinney, K A; McShane, J; Connor, T J; Adair, B M; Merza, M

    1997-01-01

    Commercial enzyme-linked immunosorbent assays (ELISAs) for detection of serum antibodies to bovine viral diarrhea virus (BVDV), parainfluenza-3 virus (PI3V), respiratory syncytial virus (RSV), and infectious bovine rhinotracheitis virus (IBRV) were standardized to give a quantitative result when testing was performed at a single optimum dilution. For each test, serum samples were titrated and their end point titers calculated by an algebraic method directly from a plot of each titration series and also from a regression line fitted to this plot. The corrected optical density (COD) of each sample when tested at dilutions of 1/25, 1/50, and 1/100 was expressed as a percentage of the COD of a positive reference serum included on each plate, this value was the sample/positive (S/P) ratio. For each test, the linear relationship between the S/P ratio obtained at a dilution of 1/25, 1/50, and 1/100 and the end point titer calculated by each method was determined. In each case, the best linear relationship existed when samples were tested at a dilution of 1/100 (r = 0.973 for BVDV, 0.962 for PI3V, 0.961 for RSV, 0.947 for IBRV). From the equation of these lines, an increase in the S/P ratio between acute and convalescent serum samples of 31%, 23%, 21%, and 35% would correspond to a 4-fold rise in ELISA titer to BVDV, PI3V, RSV, and IBRV, respectively. ELISA titers calculated from S/P ratios at 1/100 were significantly related to virus neutralization titers to BVDV, RSV, and IBRV and to hemagglutination inhibition titers to PI3V (P < < 0.001 in all cases). Samples with low S/P ratios had the greatest intraassay and interassay variation. Intraassay reproducibility ranged from 3.5% to 22.3% (coefficient of variation), with a median value of 9.5%. Interassay reproducibility was lower, ranging from 6.0% to 50.6%, with a median of 17.4%.

  7. Assessment of sea ice-atmosphere links in CMIP5 models

    NASA Astrophysics Data System (ADS)

    Boland, Emma J. D.; Bracegirdle, Thomas J.; Shuckburgh, Emily F.

    2016-09-01

    The Arctic is currently undergoing drastic changes in climate, largely thought to be due to so-called `Arctic amplification', whereby local feedbacks enhance global warming. Recently, a number of observational and modelling studies have questioned what the implications of this change in Arctic sea ice extent might be for weather in Northern Hemisphere midlatitudes, and in particular whether recent extremely cold winters such as 2009/10 might be consistent with an influence from observed Arctic sea ice decline. However, the proposed mechanisms for these links have not been consistently demonstrated. In a uniquely comprehensive cross-season and cross-model study, we show that the CMIP5 models provide no support for a relationship between declining Arctic sea ice and a negative NAM, or between declining Barents-Kara sea ice and cold European temperatures. The lack of evidence for the proposed links is consistent with studies that report a low signal-to-noise ratio in these relationships. These results imply that, whilst links may exist between declining sea ice and extreme cold weather events in the Northern Hemisphere, the CMIP5 model experiments do not show this to be a leading order effect in the long-term. We argue that this is likely due to a combination of the limitations of the CMIP5 models and an indication of other important long-term influences on Northern Hemisphere climate.

  8. Accessible, almost ab initio multi-scale modeling of entangled polymers via slip-links

    NASA Astrophysics Data System (ADS)

    Andreev, Marat

    It is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to entanglement modeling known as slip-links. Recently, slip-links were shown to possess important advantages over tube models, namely they have strong connections to atomistic, multichain levels of description, agree with non-equilibrium thermodynamics, are applicable to any chain architecture and can be used in linear or non-linear rheology. We present a hierarchy of slip-link models that are connected to each other through successive coarse graining. Models in the hierarchy are consistent in their overlapping domains of applicability in order to allow a straightforward mapping of parameters. In particular, the most--detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. On the other hand, the least--detailed member of the hierarchy is numerically accessible, and allows for non-equilibrium flow predictions of complex chain architectures. Using GPU implementation these predictions can be obtained in minutes of computational time on a single desktop equipped with a mainstream gaming GPU. The GPU code is available online for free download.

  9. Expression and in Silico analysis of the recombinant bovine papillomavirus E6 protein as a model for viral oncoproteins studies.

    PubMed

    Mazzuchelli-de-Souza, J; Carvalho, R F; Ruiz, R M; Melo, T C; Araldi, R P; Carvalho, E; Thompson, C E; Sircili, M P; Beçak, W; Stocco, R C

    2013-01-01

    Bovine papillomaviruses (BPVs) are recognized as the causal agents of economical relevant diseases in cattle, associated with the development of tumors in skin and mucosa. The oncogenesis process is mainly associated with different viral oncoprotein expressions, which are involved in cell transformation. The expression and characterization of recombinant viral oncoproteins represent an attractive strategy to obtain biotechnological products as antibodies and potential vaccines, Thus, the aim of this work was to clone and express the BPV-1 and BPV-2 E6 recombinant proteins and perform in silico analysis in order to develop a strategy for the systematic study of other papillomaviruses oncoproteins. The results demonstrated that BPV-1 and BPV-2 E6 recombinant proteins were expressed and purified from bacterial system as well as its in silico analysis was performed in order to explore and predict biological characteristics of these proteins.

  10. Efficient estimation and prediction for the Bayesian binary spatial model with flexible link functions.

    PubMed

    Roy, Vivekananda; Evangelou, Evangelos; Zhu, Zhengyuan

    2016-03-01

    Spatial generalized linear mixed models (SGLMMs) are popular models for spatial data with a non-Gaussian response. Binomial SGLMMs with logit or probit link functions are often used to model spatially dependent binomial random variables. It is known that for independent binomial data, the robit regression model provides a more robust (against extreme observations) alternative to the more popular logistic and probit models. In this article, we introduce a Bayesian spatial robit model for spatially dependent binomial data. Since constructing a meaningful prior on the link function parameter as well as the spatial correlation parameters in SGLMMs is difficult, we propose an empirical Bayes (EB) approach for the estimation of these parameters as well as for the prediction of the random effects. The EB methodology is implemented by efficient importance sampling methods based on Markov chain Monte Carlo (MCMC) algorithms. Our simulation study shows that the robit model is robust against model misspecification, and our EB method results in estimates with less bias than full Bayesian (FB) analysis. The methodology is applied to a Celastrus Orbiculatus data, and a Rhizoctonia root data. For the former, which is known to contain outlying observations, the robit model is shown to do better for predicting the spatial distribution of an invasive species. For the latter, our approach is doing as well as the classical models for predicting the disease severity for a root disease, as the probit link is shown to be appropriate. Though this article is written for Binomial SGLMMs for brevity, the EB methodology is more general and can be applied to other types of SGLMMs. In the accompanying R package geoBayes, implementations for other SGLMMs such as Poisson and Gamma SGLMMs are provided. PMID:26331903

  11. Efficient estimation and prediction for the Bayesian binary spatial model with flexible link functions.

    PubMed

    Roy, Vivekananda; Evangelou, Evangelos; Zhu, Zhengyuan

    2016-03-01

    Spatial generalized linear mixed models (SGLMMs) are popular models for spatial data with a non-Gaussian response. Binomial SGLMMs with logit or probit link functions are often used to model spatially dependent binomial random variables. It is known that for independent binomial data, the robit regression model provides a more robust (against extreme observations) alternative to the more popular logistic and probit models. In this article, we introduce a Bayesian spatial robit model for spatially dependent binomial data. Since constructing a meaningful prior on the link function parameter as well as the spatial correlation parameters in SGLMMs is difficult, we propose an empirical Bayes (EB) approach for the estimation of these parameters as well as for the prediction of the random effects. The EB methodology is implemented by efficient importance sampling methods based on Markov chain Monte Carlo (MCMC) algorithms. Our simulation study shows that the robit model is robust against model misspecification, and our EB method results in estimates with less bias than full Bayesian (FB) analysis. The methodology is applied to a Celastrus Orbiculatus data, and a Rhizoctonia root data. For the former, which is known to contain outlying observations, the robit model is shown to do better for predicting the spatial distribution of an invasive species. For the latter, our approach is doing as well as the classical models for predicting the disease severity for a root disease, as the probit link is shown to be appropriate. Though this article is written for Binomial SGLMMs for brevity, the EB methodology is more general and can be applied to other types of SGLMMs. In the accompanying R package geoBayes, implementations for other SGLMMs such as Poisson and Gamma SGLMMs are provided.

  12. Bacterial, viral and turbidity removal by intermittent slow sand filtration for household use in developing countries: experimental investigation and modeling.

    PubMed

    Jenkins, Marion W; Tiwari, Sangam K; Darby, Jeannie

    2011-11-15

    A two-factor three-block experimental design was developed to permit rigorous evaluation and modeling of the main effects and interactions of sand size (d(10) of 0.17 and 0.52 mm) and hydraulic head (10, 20, and 30 cm) on removal of fecal coliform (FC) bacteria, MS2 bacteriophage virus, and turbidity, under two batch operating modes ('long' and 'short') in intermittent slow sand filters (ISSFs). Long operation involved an overnight pause time between feeding of two successive 20 L batches (16 h average batch residence time (RT)). Short operation involved no pause between two 20 L batch feeds (5h average batch RT). Conditions tested were representative of those encountered in developing country field settings. Over a ten week period, the 18 experimental filters were fed river water augmented with wastewater (influent turbidity of 5.4-58.6 NTU) and maintained with the wet harrowing method. Linear mixed modeling allowed systematic estimates of the independent marginal effects of each independent variable on each performance outcome of interest while controlling for the effects of variations in a batch's actual residence time, days since maintenance, and influent turbidity. This is the first study in which simultaneous measurement of bacteria, viruses and turbidity removal at the batch level over an extended duration has been undertaken with a large number of replicate units to permit rigorous modeling of ISSF performance variability within and across a range of likely filter design configurations and operating conditions. On average, the experimental filters removed 1.40 log fecal coliform CFU (SD 0.40 log, N=249), 0.54 log MS2 PFU (SD 0.42 log, N=245) and 89.0 percent turbidity (SD 6.9 percent, N=263). Effluent turbidity averaged 1.24 NTU (SD 0.53 NTU, N=263) and always remained below 3 NTU. Under the best performing design configuration and operating mode (fine sand, 10 cm head, long operation, initial HLR of 0.01-0.03 m/h), mean 1.82 log removal of bacteria (98

  13. A spectral model of Linke's turbidity factor and its experimental implications

    SciTech Connect

    Grenier, J.C.; De La Casiniere, A.; Cabot, T. )

    1994-04-01

    A model of Linke's turbidity factor, T[sub L], is developed by means of updated spectral extraterrestrial irradiances and extinction coefficients of gaseous absorbers. It is shown that the new values of T[sub L] are clearly different from those obtained by Kasten's formula which parameterizes the optical thickness of the clean dry atmosphere. The model is used to investigate the dependence of T[sub L] on the relative optical air mass and to elucidate the relationships linking T[sub L] to Angstroem's turbidity coefficient and to the water vapor content. For any T[sub L], the corresponding value related to the air mass 2.0 can be determined. Such a standardized value is independent of solar elevation and is therefore strictly representative of the atmospheric turbidity. It can be linked to Angstroem's turbidity coefficient. Practical procedures and algorithms for computing the standard Linke's turbidity factor and determining Angstroem's turbidity coefficient are described. A relationship for converting the T[sub L] values obtained by Kasten's formula into the new values is proposed.

  14. A linked hydrodynamic and water quality model for the Salton Sea

    USGS Publications Warehouse

    Chung, E.G.; Schladow, S.G.; Perez-Losada, J.; Robertson, D.M.

    2008-01-01

    A linked hydrodynamic and water quality model was developed and applied to the Salton Sea. The hydrodynamic component is based on the one-dimensional numerical model, DLM. The water quality model is based on a new conceptual model for nutrient cycling in the Sea, and simulates temperature, total suspended sediment concentration, nutrient concentrations, including PO4-3, NO3-1 and NH4+1, DO concentration and chlorophyll a concentration as functions of depth and time. Existing water temperature data from 1997 were used to verify that the model could accurately represent the onset and breakup of thermal stratification. 1999 is the only year with a near-complete dataset for water quality variables for the Salton Sea. The linked hydrodynamic and water quality model was run for 1999, and by adjustment of rate coefficients and other water quality parameters, a good match with the data was obtained. In this article, the model is fully described and the model results for reductions in external phosphorus load on chlorophyll a distribution are presented. ?? 2008 Springer Science+Business Media B.V.

  15. Influence of atmospheric turbulence on OAM-based FSO system with use of realistic link model

    NASA Astrophysics Data System (ADS)

    Li, Ming; Yu, Zhongyuan; Cvijetic, Milorad

    2016-04-01

    We study the influence of atmospheric turbulence on OAM-based free-space optical (FSO) communication by using the Pump turbulence spectrum model which accurately characterizes the realistic FSO link. A comprehensive comparison is made between the Pump and Kolmogorov spectrum models with respect to the turbulence impact. The calculated results show that obtained turbulence-induced crosstalk is lower, which means that a higher channel capacity is projected when the realistic Pump spectrum is used instead of the Kolmogorov spectrum. We believe that our results prove that performance of practical OAM-based FSO is better than one predicted by using the original Kolmogorov turbulence model.

  16. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties.

    PubMed

    Powell, Jeff R; Welsh, Allana; Hallin, Sara

    2015-07-01

    Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems. Soil nitrate was the most important single predictor of denitrification potential (the change in Akaike's information criterion, corrected for sample size, ΔAIC(c) = 20.29); however, the inclusion of biotic variables (particularly the evenness and size of denitrifier communities [ΔAIC(c) = 12.02], and the abundance of one denitrifier genotype [ΔAIC(c) = 18.04]) had a substantial effect on model precision, comparable to the inclusion of abiotic variables (biotic R2 = 0.28, abiotic R2 = 0.50, biotic + abiotic R2 = 0.76). This approach provides a valuable tool for explicitly linking microbial communities to ecosystem functioning. By making this link, we have demonstrated that including aspects of microbial community structure and diversity in biogeochemical models can improve predictions of nutrient cycling in ecosystems and enhance our understanding of ecosystem functionality.

  17. Towards Controlling the Glycoform: A Model Framework Linking Extracellular Metabolites to Antibody Glycosylation

    PubMed Central

    Jedrzejewski, Philip M.; del Val, Ioscani Jimenez; Constantinou, Antony; Dell, Anne; Haslam, Stuart M.; Polizzi, Karen M.; Kontoravdi, Cleo

    2014-01-01

    Glycoproteins represent the largest group of the growing number of biologically-derived medicines. The associated glycan structures and their distribution are known to have a large impact on pharmacokinetics. A modelling framework was developed to provide a link from the extracellular environment and its effect on intracellular metabolites to the distribution of glycans on the constant region of an antibody product. The main focus of this work is the mechanistic in silico reconstruction of the nucleotide sugar donor (NSD) metabolic network by means of 34 species mass balances and the saturation kinetics rates of the 60 metabolic reactions involved. NSDs are the co-substrates of the glycosylation process in the Golgi apparatus and their simulated dynamic intracellular concentration profiles were linked to an existing model describing the distribution of N-linked glycan structures of the antibody constant region. The modelling framework also describes the growth dynamics of the cell population by means of modified Monod kinetics. Simulation results match well to experimental data from a murine hybridoma cell line. The result is a modelling platform which is able to describe the product glycoform based on extracellular conditions. It represents a first step towards the in silico prediction of the glycoform of a biotherapeutic and provides a platform for the optimisation of bioprocess conditions with respect to product quality. PMID:24637934

  18. Space Station communications and tracking systems modeling and RF link simulation

    NASA Astrophysics Data System (ADS)

    Tsang, Chit-Sang; Chie, Chak M.; Lindsey, William C.

    1986-07-01

    In this final report, the effort spent on Space Station Communications and Tracking System Modeling and RF Link Simulation is described in detail. The effort is mainly divided into three parts: frequency division multiple access (FDMA) system simulation modeling and software implementation; a study on design and evaluation of a functional computerized RF link simulation/analysis system for Space Station; and a study on design and evaluation of simulation system architecture. This report documents the results of these studies. In addition, a separate User's Manual on Space Communications Simulation System (SCSS) (Version 1) documents the software developed for the Space Station FDMA communications system simulation. The final report, SCSS user's manual, and the software located in the NASA JSC system analysis division's VAX 750 computer together serve as the deliverables from LinCom for this project effort.

  19. Data Reduction of Traffic Information Forecast Model Performed by Multi-link Shared Feature Space Projection

    NASA Astrophysics Data System (ADS)

    Kumagai, Masatoshi; Fushiki, Takumi; Kimita, Kazuya; Yokota, Takayoshi

    This paper discusses an extended method of “Feature Space Forecast Method" which we proposed before. When we forecast traffic information, we have to consider various factors such as days, seasons, holidays, and so on. Furthermore, for nation-wide forecast services, the number of road links handled by a forecast model reaches more than 0.1 million. Therefore, in order to provide accurate nation-wide services, a forecast method that can efficiently deal with a large amount of traffic data is required. The proposed method achieves an efficient forecast process with a small forecast model that is one-tenth as large as that of traditional methods, by performing forecasting calculation in the feature space shared by multiple road links.

  20. Space Station communications and tracking systems modeling and RF link simulation

    NASA Technical Reports Server (NTRS)

    Tsang, Chit-Sang; Chie, Chak M.; Lindsey, William C.

    1986-01-01

    In this final report, the effort spent on Space Station Communications and Tracking System Modeling and RF Link Simulation is described in detail. The effort is mainly divided into three parts: frequency division multiple access (FDMA) system simulation modeling and software implementation; a study on design and evaluation of a functional computerized RF link simulation/analysis system for Space Station; and a study on design and evaluation of simulation system architecture. This report documents the results of these studies. In addition, a separate User's Manual on Space Communications Simulation System (SCSS) (Version 1) documents the software developed for the Space Station FDMA communications system simulation. The final report, SCSS user's manual, and the software located in the NASA JSC system analysis division's VAX 750 computer together serve as the deliverables from LinCom for this project effort.

  1. Linking Physical and Numerical Modelling in Hydrogeology using Sand Tank Experiments and COMSOL Multiphysics

    NASA Astrophysics Data System (ADS)

    Singha, Kamini; Loheide, Steven P., II

    2011-03-01

    Visualising subsurface processes in hydrogeology and building intuition for how these processes are controlled by changes in forcing is hard for many undergraduate students. While numerical modelling is one way to help undergraduate students explore outcomes of multiple scenarios, many codes are not user-friendly with respect to defining domains, boundary conditions, and coupling processes, and numerical modelling exercises are also often disconnected from systems that the students understand, limiting their ability to extrapolate what they have learned for other situations. Here, we test the hypothesis that hydrogeology students will better estimate rates of groundwater flow and contaminant transport and the magnitudes of the parameters that control flow and transport by linking physical and numerical models. We present an exercise that links physical and numerical modelling of fluid flow and solute transport using 2-D 'ant farm' sand tanks with parallel models in COMSOL Multiphysics. The sand tank exercises provide students with a way to visualise subsurface flow and transport processes, while COMSOL allows them to explicitly pull apart the mathematics associated with these systems and build intuition for their solutions. Given coupled experimentation and numerical exercises, we find that students will connect processes that they see in the laboratory with the outcomes of numerical models, and the post-exercise tests indicate that they have an improved understanding of: (1) the magnitude and importance of properties and parameters that control flow and transport and (2) the simplifications made in numerical models of physical systems.

  2. Characterizing Class-Specific Exposure-Viral Load Suppression Response of HIV Antiretrovirals Using A Model-Based Meta-Analysis.

    PubMed

    Xu, Y; Li, Y F; Zhang, D; Dockendorf, M; Tetteh, E; Rizk, M L; Grobler, J A; Lai, M-T; Gobburu, J; Ankrom, W

    2016-08-01

    We applied model-based meta-analysis of viral suppression as a function of drug exposure and in vitro potency for short-term monotherapy in human immunodeficiency virus type 1 (HIV-1)-infected treatment-naïve patients to set pharmacokinetic targets for development of nonnucleoside reverse transcriptase inhibitors (NNRTIs) and integrase strand transfer inhibitors (InSTIs). We developed class-specific models relating viral load kinetics from monotherapy studies to potency normalized steady-state trough plasma concentrations. These models were integrated with a literature assessment of doses which demonstrated to have long-term efficacy in combination therapy, in order to set steady-state trough concentration targets of 6.17- and 2.15-fold above potency for NNRTIs and InSTIs, respectively. Both the models developed and the pharmacokinetic targets derived can be used to guide compound selection during preclinical development and to predict the dose-response of new antiretrovirals to inform early clinical trial design. PMID:27171172

  3. Equine herpesvirus type 1 tegument protein VP22 is not essential for pathogenicity in a hamster model, but is required for efficient viral growth in cultured cells

    PubMed Central

    OKADA, Ayaka; IZUME, Satoko; OHYA, Kenji; FUKUSHI, Hideto

    2015-01-01

    VP22 is a major tegument protein of Equine herpesvirus type 1 (EHV-1) that is a conserved protein among alphaherpesviruses. However, the roles of VP22 differ among each virus, and the roles of EHV-1 VP22 are still unclear. Here, we constructed an EHV-1 VP22 deletion mutant and a revertant virus to clarify the role of VP22. We found that EHV-1 VP22 was required for efficient viral growth in cultured cells, but not for virulence in a hamster model. PMID:25948053

  4. Neuroinvasion and Inflammation in Viral Central Nervous System Infections

    PubMed Central

    Schroten, Horst

    2016-01-01

    Neurotropic viruses can cause devastating central nervous system (CNS) infections, especially in young children and the elderly. The blood-brain barrier (BBB) and the blood-cerebrospinal fluid barrier (BCSFB) have been described as relevant sites of entry for specific viruses as well as for leukocytes, which are recruited during the proinflammatory response in the course of CNS infection. In this review, we illustrate examples of established brain barrier models, in which the specific reaction patterns of different viral families can be analyzed. Furthermore, we highlight the pathogen specific array of cytokines and chemokines involved in immunological responses in viral CNS infections. We discuss in detail the link between specific cytokines and chemokines and leukocyte migration profiles. The thorough understanding of the complex and interrelated inflammatory mechanisms as well as identifying universal mediators promoting CNS inflammation is essential for the development of new diagnostic and treatment strategies. PMID:27313404

  5. NEW GHOST-NODE METHOD FOR LINKING DIFFERENT MODELS WITH VARIED GRID REFINEMENT

    SciTech Connect

    S.C. James; J.E. Dickinson; S.W. Mehl; M.C. Hill; S.A. Leake; G.A. zyvoloski; A. Eddebbarh

    2006-02-15

    A flexible, robust method for linking grids of locally refined models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined ''child'' model that is contained within a larger and coarser ''parent'' model that is based on the iterative method of Mehl and Hill (2002, 2004). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has either matching grids (parent cells border an integer number of child cells; Figure 2a) or non-matching grids (parent cells border a non-integer number of child cells; Figure 2b). The coupled grids are simulated using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models (Mehl and Hill, 2002). When the grids are non-matching, model accuracy is slightly increased over matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to accurately couple distinct models because the overall error is less than if only the regional model was used to simulate flow in the child model's domain.

  6. New ghost-node method for linking different models with varied grid refinement

    USGS Publications Warehouse

    James, S.C.; Dickinson, J.E.; Mehl, S.W.; Hill, M.C.; Leake, S.A.; Zyvoloski, G.A.; Eddebbarh, A.-A.

    2006-01-01

    A flexible, robust method for linking grids of locally refined ground-water flow models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined "child" model that is contained within a larger and coarser "parent" model that is based on the iterative method of Steffen W. Mehl and Mary C. Hill (2002, Advances in Water Res., 25, p. 497-511; 2004, Advances in Water Res., 27, p. 899-912). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has matching grids (parent cells border an integer number of child cells) or nonmatching grids. The coupled grids are simulated by using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child-cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models. When the grids are nonmatching, model accuracy is slightly increased compared to that for matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to couple distinct models because the overall head and flow errors relative to the analytical solution are less than if only the regional coarse-grid model was used to simulate flow in the child model's domain.

  7. New Ghost-node method for linking different models with varied grid refinement.

    SciTech Connect

    Mehl, Steffen W.; Hill, Mary Catherine.; James, Scott Carlton; Leake, Stanley A.; Zyvoloski, George A.; Dickinson, Jesse E.; Eddebbarh, Al A.

    2006-01-01

    A flexible, robust method for linking grids of locally refined models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined 'child' model that is contained within a larger and coarser 'parent' model that is based on the iterative method of Mehl and Hill (2002, 2004). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has either matching grids (parent cells border an integer number of child cells; Figure 2a) or non-matching grids (parent cells border a non-integer number of child cells; Figure 2b). The coupled grids are simulated using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models (Mehl and Hill, 2002). When the grids are non-matching, model accuracy is slightly increased over matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to accurately couple distinct models because the overall error is less than if only the regional model was used to simulate flow in the child model's domain.

  8. Linking Climate Information, Remote Sensing and Crop Models for Crop Yield Forecasting and Food Security Assessment

    NASA Astrophysics Data System (ADS)

    Ines, A. M.; Hansen, J. W.; Baethgen, W.; Das, N. N.

    2011-12-01

    The need for better information on crop yield outlooks at different temporal scales requires the use of state of the art tools in climate prediction, crop simulations and remote sensing, often combining them to come up with better results. In this talk, we will present methodologies on how to link advanced climate information with crop simulation models to predict crop yields at the seasonal time scale, the assimilation of remotely sensed soil moisture and vegetation index, to reduce modeling related errors in the predicted yields, and a framework for generating plausible climate change scenarios and linking them with crop models. At the seasonal time scale, we will address the issue of scale mismatch between climate forecasts and crop model requirements, both at the spatial and temporal levels. Data assimilation with an ensemble Kalman filter is used to integrate remotely sensed bio-physical variables in crop yield simulations. At the climate change time scale, we will propose a plausible method on how to translate climate models' and observations' projections into crop model inputs to simulate crop yields and explore options to improve crop productivity in a variable and changing climate. Several case studies in Africa, South East South America (SESA), US and Australia will be presented.

  9. Modelling the multidimensional niche by linking functional traits to competitive performance.

    PubMed

    Maynard, Daniel S; Leonard, Kenneth E; Drake, John M; Hall, David W; Crowther, Thomas W; Bradford, Mark A

    2015-07-22

    Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified,and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts. PMID:26136444

  10. Modelling the multidimensional niche by linking functional traits to competitive performance

    PubMed Central

    Maynard, Daniel S.; Leonard, Kenneth E.; Drake, John M.; Hall, David W.; Crowther, Thomas W.; Bradford, Mark A.

    2015-01-01

    Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified, and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts. PMID:26136444

  11. A NEW GHOST-NODE METHOD FOR LINKING DIFFERENT MODELS WITH VARIED GRID REFINEMENT

    SciTech Connect

    J. dickinson; S.C. James; S. Mehl; M.C. Hill; S. Leake; G.A. Zyvoloski

    2005-10-18

    A flexible, robust method for linking grids of locally refined models that may be constructed using different types of numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method based on the iterative method of Mehl and Hill (2002, 2004). It is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that facilitates clear analysis of typical problems. The coupled grids are simulated using the finite-difference and finite-element models MODFLOW and FEHM. Results indicate that when the grids are matched spatially so that nodes and control volume boundaries are aligned, the new coupling technique has approximately twice the error as coupling using two MODFLOW models. When the grids are non-matching; model accuracy is slightly increased over matching grid cases. Overall, results indicate that the ghost-node technique is a viable means to accurately couple distinct models.

  12. A simple pharmacokinetic model linking plasma progesterone concentrations with the hormone released from bovine intravaginal inserts.

    PubMed

    Mariano, R N; Turino, L N; Cabrera, M I; Scándolo, D E; Maciel, M G; Grau, R J A

    2010-10-01

    On the basis of pharmacokinetic modeling, this study provides some insights into predicting in vivo plasma progesterone concentrations when using bovine intravaginal inserts for systemic progesterone delivery. More significantly, this contribution is the first attempt to build a simple pharmacokinetic model that links plasma progesterone concentrations with the hormone released from bovine intravaginal inserts. After evaluating three rival pharmacokinetic models and considering some phenomena involved in the intravaginal administration of progesterone, a primary pharmacokinetic model having a good data fitting capability with only two adjustable parameters is proposed to the above mentioned task. Kinetic parameters are given for lactating Holstein dairy cows with two levels of daily milk yields; and non-pregnant, non-lactating Holstein-Friesian cattle. Model predictions indicate the occurrence of a preferential distribution of the intravaginally administered progesterone dose through a first uterine pass effect.

  13. Linking models of land use, resources, and economy to simulate the development of mountain regions (ALPSCAPE).

    PubMed

    Lundström, Corinne; Kytzia, Susanne; Walz, Ariane; Gret-Regamey, Adrienne; Bebi, Peter

    2007-09-01

    We present a framework of a scenario-based model that simulates the development of the municipality of Davos (Swiss Alps). We illustrate our method with the calculation of the scenario for 2050 "Decrease in subsidies for mountain agriculture and liberalization of markets." The main objective was to link submodels of land-use allocation (regression-based approach), material and energy flows submodels (Material and Energy Flux Analysis), and economic submodels (Input-Output Analysis). Letting qualitative and quantitative information flow from one submodel to the next, following the storyline describing a scenario, has proven to be suitable for linking submodels. The succession of the submodels is then strongly dependent on the scenario. Qualitative information flows are simulated with microsimulations of actor choices. Links between the submodels show different degrees of robustness: although the links involving microsimulations are the weakest, the uncertainty introduced by the land-use allocation model is actually advantageous because it allows one possible change in the landscape in the future to be simulated. The modeling results for the scenario here presented show that the disappearance of agriculture only marginally affects the region's factor income, but that the consequences for the self-sufficiency rate, for various landscape-related indicators and ecosystem services, and for the economy in the long term may be considerable. These benefits compensate for agriculture's modest direct economic value. The framework presented can potentially be applied to any region and scenario. This framework provides a basis for a learning package that allows potential detrimental consequences of regional development to be anticipated at an early stage.

  14. Joint longitudinal hurdle and time-to-event models: an application related to viral load and duration of the first treatment regimen in patients with HIV initiating therapy.

    PubMed

    Brilleman, Samuel L; Crowther, Michael J; May, Margaret T; Gompels, Mark; Abrams, Keith R

    2016-09-10

    Shared parameter joint models provide a framework under which a longitudinal response and a time to event can be modelled simultaneously. A common assumption in shared parameter joint models has been to assume that the longitudinal response is normally distributed. In this paper, we instead propose a joint model that incorporates a two-part 'hurdle' model for the longitudinal response, motivated in part by longitudinal response data that is subject to a detection limit. The first part of the hurdle model estimates the probability that the longitudinal response is observed above the detection limit, whilst the second part of the hurdle model estimates the mean of the response conditional on having exceeded the detection limit. The time-to-event outcome is modelled using a parametric proportional hazards model, assuming a Weibull baseline hazard. We propose a novel association structure whereby the current hazard of the event is assumed to be associated with the current combined (expected) outcome from the two parts of the hurdle model. We estimate our joint model under a Bayesian framework and provide code for fitting the model using the Bayesian software Stan. We use our model to estimate the association between HIV RNA viral load, which is subject to a lower detection limit, and the hazard of stopping or modifying treatment in patients with HIV initiating antiretroviral therapy. Copyright © 2016 John Wiley & Sons, Ltd.

  15. A link-segment model of upright human posture for analysis of head-trunk coordination

    NASA Technical Reports Server (NTRS)

    Nicholas, S. C.; Doxey-Gasway, D. D.; Paloski, W. H.

    1998-01-01

    Sensory-motor control of upright human posture may be organized in a top-down fashion such that certain head-trunk coordination strategies are employed to optimize visual and/or vestibular sensory inputs. Previous quantitative models of the biomechanics of human posture control have examined the simple case of ankle sway strategy, in which an inverted pendulum model is used, and the somewhat more complicated case of hip sway strategy, in which multisegment, articulated models are used. While these models can be used to quantify the gross dynamics of posture control, they are not sufficiently detailed to analyze head-trunk coordination strategies that may be crucial to understanding its underlying mechanisms. In this paper, we present a biomechanical model of upright human posture that extends an existing four mass, sagittal plane, link-segment model to a five mass model including an independent head link. The new model was developed to analyze segmental body movements during dynamic posturography experiments in order to study head-trunk coordination strategies and their influence on sensory inputs to balance control. It was designed specifically to analyze data collected on the EquiTest (NeuroCom International, Clackamas, OR) computerized dynamic posturography system, where the task of maintaining postural equilibrium may be challenged under conditions in which the visual surround, support surface, or both are in motion. The performance of the model was tested by comparing its estimated ground reaction forces to those measured directly by support surface force transducers. We conclude that this model will be a valuable analytical tool in the search for mechanisms of balance control.

  16. Display of the Viral Epitopes on Lactococcus lactis: A Model for Food Grade Vaccine against EV71.

    PubMed

    Varma, Nadimpalli Ravi S; Toosa, Haryanti; Foo, Hooi Ling; Alitheen, Noorjahan Banu Mohamed; Nor Shamsudin, Mariana; Arbab, Ali S; Yusoff, Khatijah; Abdul Rahim, Raha

    2013-01-01

    In this study, we have developed a system for display of antigens of Enterovirus type 71 (EV71) on the cell surface of L. lactis. The viral capsid protein (VP1) gene from a local viral isolate was utilized as the candidate vaccine for the development of oral live vaccines against EV71 using L. lactis as a carrier. We expressed fusion proteins in E. coli and purified fusion proteins were incubated with L. lactis. We confirmed that mice orally fed with L. lactis displaying these fusion proteins on its surface were able to mount an immune response against the epitopes of EV71. This is the first example of an EV71 antigen displayed on the surface of a food grade organism and opens a new perspective for alternative vaccine strategies against the EV71. We believe that the method of protein docking utilized in this study will allow for more flexible presentations of short peptides and proteins on the surface of L. lactis to be useful as a delivery vehicle.

  17. Determination of urban groundwater pollution in alluvial aquifer using linked process models considering urban water cycle

    NASA Astrophysics Data System (ADS)

    Vizintin, Goran; Souvent, Petra; Veselič, Miran; Cencur Curk, Barbara

    2009-10-01

    SummaryThis paper presents the results of the 5th FP project AISUWRS (Assessing and Improving the Sustainability of Urban Water Resources and Systems) which aimed to assess the impact of the urban water infrastructure to underlying or nearby aquifers with the urban water balance modelling approach - a chain of different models that handle with contaminant fluxes and the movement of contaminants from the urban infrastructure into the underlying aquifer. An existing urban water management model UVQ was linked to a model for sewer infiltration and exfiltration (NEIMO), as well as unsaturated zone models (SLeakI/POSI, UL_FLOW) with existing numerical groundwater models. The linked process models offer the prospect of better quantification of urban water balance and contaminant loads, including improved estimates of total recharge and its components in urban areas. Once the model framework has been set up for a selected city, it can easily be updated in the future and it can be used for other purposes like planning of local remediation measures in the vicinity of individual contaminant spillages. This paper describes the application and results of the urban water model chain for the city of Ljubljana, which is the capital of Slovenia. The results from this study suggest that residential land-uses in urban areas with thick unsaturated zone may have significantly smaller impact on the groundwater than agriculture or industry. This can be seen as a speculative understanding of the groundwater pollutions problems. In this respect, use of sustainable urban development systems like on-site infiltration of roof runoff and improved sewer control and standards could result in better groundwater quality.

  18. Linking Local- and Aquifer-scale Groundwater Models Using Telescopic Mesh Refinement

    NASA Astrophysics Data System (ADS)

    Willson, C. S.; Rahman, A.; Milner, R.; Hanson, B.

    2001-12-01

    Groundwater modeling is a useful tool for evaluating and predicting whether a particular aquifer system is capable of supporting large volumes of groundwater withdrawals over long periods of time and what effect, if any, such activity will have on specific community water supplies, local agricultural and industrial needs, and the regional aquifer or aquifer system as a whole. High-resolution or refined models are necessary for quantification of local processes and phenomena. However, stand-alone refined models do not provide information on regional flow dynamics. Telescopic mesh refinement (TMR) is one technique that can be used to develop high-resolution groundwater models within larger-scale aquifer models. The objective of this study is to utilize TMR to develop parish-level high-resolution models within an existing U.S. Geological Survey groundwater model of the Chicot Aquifer in Southwestern Louisiana. These parish-level models will be used to identify and assess critical groundwater areas. The regional aquifer is used to identify possible long-term problems such as changes in recharge or salt-water encroachment. Issues that must be addressed when linking local and regional models include: incorporation of aquifer stratigraphy, recharge rates, incorporation of individual wells, boundary conditions, and model calibration.

  19. Full Scale Rotor Aeroacoustic Predictions and the Link to Model Scale Rotor Data

    NASA Technical Reports Server (NTRS)

    Boyd, D. Douglas, Jr.; Burley, Casey L.; Conner, David A.

    2004-01-01

    The NASA Aeroacoustic Prediction System (NAPS) is used to establish a link between model-scale and full-scale rotor predictions and is partially validated against measured wind tunnel and flight aeroacoustic data. The prediction approach of NAPS couples a comprehensive rotorcraft analysis with acoustic source noise and propagation codes. The comprehensive analysis selected for this study is CAMRAD-II, which provides the performance/trim/wake solution for a given rotor or flight condition. The post-trim capabilities of CAMRAD-II are used to compute high-resolution sectional airloads for the acoustic tone noise analysis, WOPMOD. The tone noise is propagated to observers on the ground with the propagation code, RNM (Rotor Noise Model). Aeroacoustic predictions are made with NAPS for an isolated rotor and compared to results of the second Harmonic Aeroacoustic Rotor Test (HART-II) program, which tested a 40% dynamically and Mach-scaled BO-105 main rotor at the DNW. The NAPS is validated with comparisons for three rotor conditions: a baseline condition and two Higher Harmonic Control (HHC) conditions. To establish a link between model and full-scale rotor predictions, a full-scale BO-105 main rotor input deck for NAPS is created from the 40% scale rotor input deck. The full-scale isolated rotor predictions are then compared to the model predictions. The comparisons include aerodynamic loading, acoustic levels, and acoustic pressure time histories for each of the three conditions. With this link established, full-scale predictions are made for a range of descent flight conditions and compared with measured trends from the recent Rotorcraft Operational Noise Abatement Procedures (RONAP) flight test conducted by DLR and ONERA. Additionally, the effectiveness of two HHC conditions from the HART-II program is demonstrated for the full-scale rotor in flight.

  20. Linked Hydrologic-Hydrodynamic Model Framework to Forecast Impacts of Rivers on Beach Water Quality

    NASA Astrophysics Data System (ADS)

    Anderson, E. J.; Fry, L. M.; Kramer, E.; Ritzenthaler, A.

    2014-12-01

    The goal of NOAA's beach quality forecasting program is to use a multi-faceted approach to aid in detection and prediction of bacteria in recreational waters. In particular, our focus has been on the connection between tributary loads and bacteria concentrations at nearby beaches. While there is a clear link between stormwater runoff and beach water quality, quantifying the contribution of river loadings to nearshore bacterial concentrations is complicated due to multiple processes that drive bacterial concentrations in rivers as well as those processes affecting the fate and transport of bacteria upon exiting the rivers. In order to forecast potential impacts of rivers on beach water quality, we developed a linked hydrologic-hydrodynamic water quality framework that simulates accumulation and washoff of bacteria from the landscape, and then predicts the fate and transport of washed off bacteria from the watershed to the coastal zone. The framework includes a watershed model (IHACRES) to predict fecal indicator bacteria (FIB) loadings to the coastal environment (accumulation, wash-off, die-off) as a function of effective rainfall. These loadings are input into a coastal hydrodynamic model (FVCOM), including a bacteria transport model (Lagrangian particle), to simulate 3D bacteria transport within the coastal environment. This modeling system provides predictive tools to assist local managers in decision-making to reduce human health threats.

  1. Primary hemocyte culture of Penaeus monodon as an in vitro model for white spot syndrome virus titration, viral and immune related gene expression and cytotoxicity assays.

    PubMed

    Jose, Seena; Mohandas, A; Philip, Rosamma; Bright Singh, I S

    2010-11-01

    Immortal cell lines have not yet been reported from Penaeus monodon, which delimits the prospects of investigating the associated viral pathogens especially white spot syndrome virus (WSSV). In this context, a method of developing primary hemocyte culture from this crustacean has been standardized by employing modified double strength Leibovitz-15 (L-15) growth medium supplemented with 2% glucose, MEM vitamins (1×), tryptose phosphate broth (2.95 gl⁻¹), 20% FBS, N-phenylthiourea (0.2 mM), 0.06 μg ml⁻¹ chloramphenicol, 100 μg ml⁻¹ streptomycin and 100 IU ml⁻¹ penicillin and hemolymph drawn from shrimp grown under a bio-secured recirculating aquaculture system (RAS). In this medium the hemocytes remained viable up to 8 days. 5-Bromo-2'-deoxyuridine (BrdU) labeling assay revealed its incorporation in 22 ± 7% of cells at 24h. Susceptibility of the cells to WSSV was confirmed by immunofluorescence assay using a monoclonal antibody against 28 kDa envelope protein of WSSV. A convenient method for determining virus titer as MTT(50)/ml was standardized employing the primary hemocyte culture. Expression of viral genes and cellular immune genes were also investigated. The cell culture could be demonstrated for determining toxicity of a management chemical (benzalkonium chloride) by determining its IC(50). The primary hemocyte culture could serve as a model for WSSV titration and viral and cellular immune related gene expression and also for investigations on cytotoxicity of aquaculture drugs and chemicals.

  2. Biomine: predicting links between biological entities using network models of heterogeneous databases

    PubMed Central

    2012-01-01

    Background Biological databases contain large amounts of data concerning the functions and associations of genes and proteins. Integration of data from several such databases into a single repository can aid the discovery of previously unknown connections spanning multiple types of relationships and databases. Results Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. We present Biomine and evaluate its performance in link prediction, where the goal is to predict pairs of nodes that will be connected in the future, based on current data. In particular, we formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. We consider and experiment with several such measures, and perform a parameter optimization procedure where different edge types are weighted to optimize link prediction accuracy. We also propose a novel method for disease-gene prioritization, defined as finding a subset of candidate genes that cluster together in the graph. We experimentally evaluate Biomine by predicting future annotations in the source databases and prioritizing lists of putative disease genes. Conclusions The experimental results show that Biomine has strong potential for predicting links when a set of selected candidate links is available. The predictions obtained using the entire Biomine dataset are shown to clearly outperform ones obtained using any single source of data alone, when different types of links are suitably weighted. In the gene prioritization task, an established reference set of disease-associated genes is useful, but the results show that under favorable conditions, Biomine can also perform

  3. The Repeated Insertion Model for Rankings: Missing Link between Two Subset Choice Models

    ERIC Educational Resources Information Center

    Doignon, Jean-Paul; Pekec, Aleksandar; Regenwetter, Michel

    2004-01-01

    Several probabilistic models for subset choice have been proposed in the literature, for example, to explain approval voting data. We show that Marley et al.'s latent scale model is subsumed by Falmagne and Regenwetter's size-independent model, in the sense that every choice probability distribution generated by the former can also be explained by…

  4. Application of cross-linked and hydrolyzed arabinoxylans in baking of model rye bread.

    PubMed

    Buksa, Krzysztof; Nowotna, Anna; Ziobro, Rafał

    2016-02-01

    The role of water extractable arabinoxylan with varying molar mass and structure (cross-linked vs. hydrolyzed) in the structure formation of rye bread was examined using a model bread. Instead of the normal flour, the dough contained starch, arabinoxylan and protein, which were isolated from rye wholemeal. It was observed that the applied mixes of these constituents result in a product closely resembling typical rye bread, even if arabinoxylan was modified (by cross-linking or hydrolysis). The levels of arabinoxylan required for bread preparation depended on its modification and mix composition. At 3% protein, the maximum applicable level of poorly soluble cross-linked arabinoxylan was 3%, as higher amounts of this preparation resulted in an extensively viscous dough and diminished bread volume. On the other hand highly soluble, hydrolyzed arabinoxylan could be used at a higher level (6%) together with larger amounts of rye protein (3% or 6%). Further addition of arabinoxylan leads to excessive water absorption, resulting in a decreased viscosity of the dough during baking and insufficient gas retention. PMID:26304439

  5. Synthesis, cholinesterase inhibition and molecular modelling studies of coumarin linked thiourea derivatives.

    PubMed

    Saeed, Aamer; Zaib, Sumera; Ashraf, Saba; Iftikhar, Javeria; Muddassar, Muhammad; Zhang, Kam Y J; Iqbal, Jamshed

    2015-12-01

    Alzheimer's disease is among the most widespread neurodegenerative disorder. Cholinesterases (ChEs) play an indispensable role in the control of cholinergic transmission and thus the acetylcholine level in the brain is enhanced by inhibition of ChEs. Coumarin linked thiourea derivatives were designed, synthesized and evaluated biologically in order to determine their inhibitory activity against acetylcholinesterases (AChE) and butyrylcholinesterases (BChE). The synthesized derivatives of coumarin linked thiourea compounds showed potential inhibitory activity against AChE and BChE. Among all the synthesized compounds, 1-(2-Oxo-2H-chromene-3-carbonyl)-3-(3-chlorophenyl)thiourea (2e) was the most potent inhibitor against AChE with an IC50 value of 0.04±0.01μM, while 1-(2-Oxo-2H-chromene-3-carbonyl)-3-(2-methoxyphenyl)thiourea (2b) showed the most potent inhibitory activity with an IC50 value of 0.06±0.02μM against BChE. Molecular docking simulations were performed using the homology models of both cholinesterases in order to explore the probable binding modes of inhibitors. Results showed that the novel synthesized coumarin linked thiourea derivatives are potential candidates to develop for potent and efficacious acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors.

  6. Application of cross-linked and hydrolyzed arabinoxylans in baking of model rye bread.

    PubMed

    Buksa, Krzysztof; Nowotna, Anna; Ziobro, Rafał

    2016-02-01

    The role of water extractable arabinoxylan with varying molar mass and structure (cross-linked vs. hydrolyzed) in the structure formation of rye bread was examined using a model bread. Instead of the normal flour, the dough contained starch, arabinoxylan and protein, which were isolated from rye wholemeal. It was observed that the applied mixes of these constituents result in a product closely resembling typical rye bread, even if arabinoxylan was modified (by cross-linking or hydrolysis). The levels of arabinoxylan required for bread preparation depended on its modification and mix composition. At 3% protein, the maximum applicable level of poorly soluble cross-linked arabinoxylan was 3%, as higher amounts of this preparation resulted in an extensively viscous dough and diminished bread volume. On the other hand highly soluble, hydrolyzed arabinoxylan could be used at a higher level (6%) together with larger amounts of rye protein (3% or 6%). Further addition of arabinoxylan leads to excessive water absorption, resulting in a decreased viscosity of the dough during baking and insufficient gas retention.

  7. An atomistic model for cross-linked HNBR elastomers used in seals

    NASA Astrophysics Data System (ADS)

    Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

    2015-03-01

    Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

  8. LERC-SLAM - THE NASA LEWIS RESEARCH CENTER SATELLITE LINK ATTENUATION MODEL PROGRAM (IBM PC VERSION)

    NASA Technical Reports Server (NTRS)

    Manning, R. M.

    1994-01-01

    The frequency and intensity of rain attenuation affecting the communication between a satellite and an earth terminal is an important consideration in planning satellite links. The NASA Lewis Research Center Satellite Link Attenuation Model Program (LeRC-SLAM) provides a static and dynamic statistical assessment of the impact of rain attenuation on a communications link established between an earth terminal and a geosynchronous satellite. The program is designed for use in the specification, design and assessment of satellite links for any terminal location in the continental United States. The basis for LeRC-SLAM is the ACTS Rain Attenuation Prediction Model, which uses a log-normal cumulative probability distribution to describe the random process of rain attenuation on satellite links. The derivation of the statistics for the rainrate process at the specified terminal location relies on long term rainfall records compiled by the U.S. Weather Service during time periods of up to 55 years in length. The theory of extreme value statistics is also utilized. The user provides 1) the longitudinal position of the satellite in geosynchronous orbit, 2) the geographical position of the earth terminal in terms of latitude and longitude, 3) the height above sea level of the terminal site, 4) the yearly average rainfall at the terminal site, and 5) the operating frequency of the communications link (within 1 to 1000 GHz, inclusive). Based on the yearly average rainfall at the terminal location, LeRC-SLAM calculates the relevant rain statistics for the site using an internal data base. The program then generates rain attenuation data for the satellite link. This data includes a description of the static (i.e., yearly) attenuation process, an evaluation of the cumulative probability distribution for attenuation effects, and an evaluation of the probability of fades below selected fade depths. In addition, LeRC-SLAM calculates the elevation and azimuth angles of the terminal

  9. LERC-SLAM - THE NASA LEWIS RESEARCH CENTER SATELLITE LINK ATTENUATION MODEL PROGRAM (MACINTOSH VERSION)

    NASA Technical Reports Server (NTRS)

    Manning, R. M.

    1994-01-01

    The frequency and intensity of rain attenuation affecting the communication between a satellite and an earth terminal is an important consideration in planning satellite links. The NASA Lewis Research Center Satellite Link Attenuation Model Program (LeRC-SLAM) provides a static and dynamic statistical assessment of the impact of rain attenuation on a communications link established between an earth terminal and a geosynchronous satellite. The program is designed for use in the specification, design and assessment of satellite links for any terminal location in the continental United States. The basis for LeRC-SLAM is the ACTS Rain Attenuation Prediction Model, which uses a log-normal cumulative probability distribution to describe the random process of rain attenuation on satellite links. The derivation of the statistics for the rainrate process at the specified terminal location relies on long term rainfall records compiled by the U.S. Weather Service during time periods of up to 55 years in length. The theory of extreme value statistics is also utilized. The user provides 1) the longitudinal position of the satellite in geosynchronous orbit, 2) the geographical position of the earth terminal in terms of latitude and longitude, 3) the height above sea level of the terminal site, 4) the yearly average rainfall at the terminal site, and 5) the operating frequency of the communications link (within 1 to 1000 GHz, inclusive). Based on the yearly average rainfall at the terminal location, LeRC-SLAM calculates the relevant rain statistics for the site using an internal data base. The program then generates rain attenuation data for the satellite link. This data includes a description of the static (i.e., yearly) attenuation process, an evaluation of the cumulative probability distribution for attenuation effects, and an evaluation of the probability of fades below selected fade depths. In addition, LeRC-SLAM calculates the elevation and azimuth angles of the terminal

  10. Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components

    PubMed Central

    2014-01-01

    Background The life cycle of human immunodeficiency virus type-1 (HIV-1) makes possible the realization of regulatory strategies that can lead to complex dynamical behavior of the system. We analyze the strategy which is based on two feedback mechanisms, one mediating a positive regulation of the virus replication by Tat protein via the antitermination of the genomic RNAs transcription on TAR (transactivation responsive) element of the proviral DNA and the second mechanism providing a negative regulation of the splicing of the full-length (9 kb) RNAs and incompletely spliced (4 kb) RNAs via their transport from the nucleus to the cytoplasm. Although the existence of these two regulatory feedback loops has been considered in other mathematical models, none of them examined the conditions for the emergence of complex oscillatory patterns in the intracellular dynamics of viral components. Results We developed a mechanistic mathematical model for the Tat-Rev mediated regulation of HIV-1 replication, which considers the activation of proviral DNA transcription, the Tat-specific antitermination of transcription on TAR-element, resulting in the synthesis of the full-length 9 kb RNA, the splicing of the 9 kb RNA down to the 4 kb RNA and the 4 kb RNA to 2 kb RNA, the transport of 2 kb mRNAs from the nucleus to the cytoplasm by the intracellular mechanisms, the multiple binding of the Rev protein to RRE (Rev Response Element) sites on 9 kb and 4 kb RNA resulting in their export to the cytoplasm and the synthesis of Tat and Rev proteins in the cytoplasm followed by their transport into the nucleus. The degradation of all viral proteins and RNAs both in the cytoplasm and the nucleus is described. The model parameters values were derived from the published literature data. The model was used to examine the dynamics of the synthesis of the viral proteins Tat and Rev, the mRNAs under the intracellular conditions specific for activated HIV-1 infected macrophages. In addition, we

  11. Two Allergen Model Reveals Complex Relationship Between IgE Cross-Linking and Degranulation

    PubMed Central

    Handlogten, Michael W.; Deak, Peter E.; Bilgicer, Basar

    2014-01-01

    Summary Allergy is an immune response to complex mixtures of multiple allergens yet current models use a single synthetic allergen. Multiple allergens were modeled using two well-defined tetravalent allergens each specific for a distinct IgE thus enabling a systematic approach to evaluate the effect of each allergen and percent of allergen specific IgE on mast cell degranulation. We found the overall degranulation response caused by two allergens is additive for low allergen concentrations or low percent specific IgE, does not change for moderate allergen concentrations with moderate to high percent specific IgE, and is reduced for high allergen concentrations with moderate to high percent specific IgE. These results provide further evidence that supra-optimal IgE cross-linking decreases the degranulation response and establishes the two allergen model as a relevant experimental system to elucidate mast cell degranulation mechanisms. PMID:25308278

  12. A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

    PubMed

    Ryll, A; Bucher, J; Bonin, A; Bongard, S; Gonçalves, E; Saez-Rodriguez, J; Niklas, J; Klamt, S

    2014-10-01

    Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism, signalling and gene regulation) are still scarce. Consequently, model integration methods capable of fusing different types of biological networks and various model formalisms become a key methodology to increase the scope of cellular processes covered by mathematical models. Here we propose a new integration approach to couple logical models of signalling or/and gene-regulatory networks with kinetic models of metabolic processes. The procedure ends up with an integrated dynamic model of both layers relying on differential equations. The feasibility of the approach is shown in an illustrative case study integrating a kinetic model of central metabolic pathways in hepatocytes with a Boolean logical network depicting the hormonally induced signal transduction and gene regulation events involved. In silico simulations demonstrate the integrated model to qualitatively describe the physiological switch-like behaviour of hepatocytes in response to nutritionally regulated changes in extracellular glucagon and insulin levels. A simulated failure mode scenario addressing insulin resistance furthermore illustrates the pharmacological potential of a model covering interactions between signalling, gene regulation and metabolism. PMID:25063553

  13. Estimating marginal and incremental effects on health outcomes using flexible link and variance function models.

    PubMed

    Basu, Anirban; Rathouz, Paul J

    2005-01-01

    We propose an extension to the estimating equations in generalized linear models to estimate parameters in the link function and variance structure simultaneously with regression coefficients. Rather than focusing on the regression coefficients, the purpose of these models is inference about the mean of the outcome as a function of a set of covariates, and various functionals of the mean function used to measure the effects of the covariates. A commonly used functional in econometrics, referred to as the marginal effect, is the partial derivative of the mean function with respect to any covariate, averaged over the empirical distribution of covariates in the model. We define an analogous parameter for discrete covariates. The proposed estimation method not only helps to identify an appropriate link function and to suggest an underlying distribution for a specific application but also serves as a robust estimator when no specific distribution for the outcome measure can be identified. Using Monte Carlo simulations, we show that the resulting parameter estimators are consistent. The method is illustrated with an analysis of inpatient expenditure data from a study of hospitalists.

  14. Modeling channel interference in an orbital angular momentum-multiplexed laser link

    NASA Astrophysics Data System (ADS)

    Anguita, Jaime A.; Neifeld, Mark A.; Vasic, Bane V.

    2009-08-01

    We study the effects of optical turbulence on the energy crosstalk among constituent orbital angular momentum (OAM) states in a vortex-based multi-channel laser communication link and determine channel interference in terms of turbulence strength and OAM state separation. We characterize the channel interference as a function of C2n and transmit OAM state, and propose probability models to predict the random fluctuations in the received signals for such architecture. Simulations indicate that turbulence-induced channel interference is mutually correlated across receive channels.

  15. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging.

    PubMed

    Deng, Li; Gregory, Ann; Yilmaz, Suzan; Poulos, Bonnie T; Hugenholtz, Philip; Sullivan, Matthew B

    2012-01-01

    Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. We have developed a method called viral tagging (VT), which combines mixtures of host cells and fluorescent viruses with flow cytometry. We investigated multiple viruses which infect each of two model marine bacteria that represent the slow-growing, photoautotrophic genus Synechococcus (Cyanobacteria) and the fast-growing, heterotrophic genus Pseudoalteromonas (Gammaproteobacteria). Overall, viral tagging results for viral infection were consistent with plaque and liquid infection assays for cyanobacterial myo-, podo- and siphoviruses and some (myo- and podoviruses) but not all (four siphoviruses) heterotrophic bacterial viruses. Virus-tagged Pseudoalteromonas organisms were proportional to the added viruses under varied infection conditions (virus-bacterium ratios), while no more than 50% of the Synechococcus organisms were virus tagged even at viral abundances that exceeded (5 to 10×) that of their hosts. Further, we found that host growth phase minimally impacts the fraction of virus-tagged Synechococcus organisms while greatly affecting phage adsorption to Pseudoalteromonas. Together these findings suggest that at least two contrasting viral life strategies exist in the oceans and that they likely reflect adaptation to their host microbes. Looking forward to the point at which the virus-tagging signature is well understood (e.g., for Synechococcus), application to natural communities should begin to provide population genomic data at the proper scale for predictively modeling two of the most abundant biological entities on Earth. Viral study suffers from an inability to link viruses to hosts en

  16. A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches

    PubMed Central

    Gérard, Claude; Gonze, Didier; Lemaigre, Frédéric; Novák, Béla

    2014-01-01

    Recently, a molecular pathway linking inflammation to cell transformation has been discovered. This molecular pathway rests on a positive inflammatory feedback loop between NF-κB, Lin28, Let-7 microRNA and IL6, which leads to an epigenetic switch allowing cell transformation. A transient activation of an inflammatory signal, mediated by the oncoprotein Src, activates NF-κB, which elicits the expression of Lin28. Lin28 decreases the expression of Let-7 microRNA, which results in higher level of IL6 than achieved directly by NF-κB. In turn, IL6 can promote NF-κB activation. Finally, IL6 also elicits the synthesis of STAT3, which is a crucial activator for cell transformation. Here, we propose a computational model to account for the dynamical behavior of this positive inflammatory feedback loop. By means of a deterministic model, we show that an irreversible bistable switch between a transformed and a non-transformed state of the cell is at the core of the dynamical behavior of the positive feedback loop linking inflammation to cell transformation. The model indicates that inhibitors (tumor suppressors) or activators (oncogenes) of this positive feedback loop regulate the occurrence of the epigenetic switch by modulating the threshold of inflammatory signal (Src) needed to promote cell transformation. Both stochastic simulations and deterministic simulations of a heterogeneous cell population suggest that random fluctuations (due to molecular noise or cell-to-cell variability) are able to trigger cell transformation. Moreover, the model predicts that oncogenes/tumor suppressors respectively decrease/increase the robustness of the non-transformed state of the cell towards random fluctuations. Finally, the model accounts for the potential effect of competing endogenous RNAs, ceRNAs, on the dynamics of the epigenetic switch. Depending on their microRNA targets, the model predicts that ceRNAs could act as oncogenes or tumor suppressors by regulating the occurrence of

  17. Linking nutrient loading and oxygen in the coastal ocean: A new global scale model

    NASA Astrophysics Data System (ADS)

    Reed, Daniel C.; Harrison, John A.

    2016-03-01

    Recent decades have witnessed an exponential spread of low-oxygen regions in the coastal ocean due at least in-part to enhanced terrestrial nutrient inputs. As oxygen deprivation is a major stressor on marine ecosystems, there is a great need to quantitatively link shifts in nutrient loading with changes in oxygen concentrations. To this end, we have developed and here describe, evaluate, and apply the Coastal Ocean Oxygen Linked to Benthic Exchange And Nutrient Supply (COOLBEANS) model, a first-of-its-kind, spatially explicit (with 152 coastal segments) model, global model of coastal oxygen and nutrient dynamics. In COOLBEANS, benthic oxygen demand (BOD) is calculated using empirical models for aerobic respiration, iron reduction, and sulfate reduction, while oxygen supply is represented by a simple parameterization of exchange between surface and bottom waters. A nutrient cycling component translates shifts in riverine nutrient inputs into changes in organic matter delivery to sediments and, ultimately, oxygen uptake. Modeled BOD reproduces observations reasonably well (Nash-Sutcliffe efficiency = 0.71), and estimates of exchange between surface and bottom waters correlate with stratification. The model examines sensitivity of bottom water oxygen to changes in nutrient inputs and vertical exchange between surface and bottom waters, highlighting the importance of this vertical exchange in defining the susceptibility of a system to oxygen depletion. These sensitivities along with estimated maximum hypoxic areas that are supported by present day nutrient loads are consistent with existing hypoxic regions. Sensitivities are put into context by applying historic changes in nitrogen loading observed in the Gulf of Mexico to the global coastal ocean, demonstrating that such loads would drive many systems anoxic or even sulfidic.

  18. Nonzero θ13 linking to dark matter from non-Abelian discrete flavor model in radiative seesaw model

    NASA Astrophysics Data System (ADS)

    Ahn, Y. H.; Okada, Hiroshi

    2012-04-01

    We propose a new scenario in a radiative seesaw model based on A4 flavor symmetry. In this model, we explore a possibility of linking nonzero θ13 to dark matter. And we analyze the lepton sector to predict the observed neutrinos and mixings, especially obtaining a lower bound of θ13≳3.5°. We show that the nonzero θ13 is correlated with our heavy Majorana type of dark matter. Also we predict that the mass be O(1-10)TeV, as a result of analyzing the Wilkinson-Microwave-Anisotropy-Probe and lepton flavor violation.

  19. Autistic disorder and viral infections.

    PubMed

    Libbey, Jane E; Sweeten, Thayne L; McMahon, William M; Fujinami, Robert S

    2005-02-01

    Autistic disorder (autism) is a behaviorally defined developmental disorder with a wide range of behaviors. Although the etiology of autism is unknown, data suggest that autism results from multiple etiologies with both genetic and environmental contributions, which may explain the spectrum of behaviors seen in this disorder. One proposed etiology for autism is viral infection very early in development. The mechanism, by which viral infection may lead to autism, be it through direct infection of the central nervous system (CNS), through infection elsewhere in the body acting as a trigger for disease in the CNS, through alteration of the immune response of the mother or offspring, or through a combination of these, is not yet known. Animal models in which early viral infection results in behavioral changes later in life include the influenza virus model in pregnant mice and the Borna disease virus model in newborn Lewis rats. Many studies over the years have presented evidence both for and against the association of autism with various viral infections. The best association to date has been made between congenital rubella and autism; however, members of the herpes virus family may also have a role in autism. Recently, controversy has arisen as to the involvement of measles virus and/or the measles, mumps, rubella (MMR) vaccine in the development of autism. Biological assays lend support to the association between measles virus or MMR and autism whereas epidemiologic studies show no association between MMR and autism. Further research is needed to clarify both the mechanisms whereby viral infection early in development may lead to autism and the possible involvement of the MMR vaccine in the development of autism.

  20. A Model to Provide Comprehensive Testing for HIV, Viral Hepatitis, and Sexually Transmitted Infections at a Short Term Drug Treatment Center

    PubMed Central

    Lally, Michelle A.; MacNevin, Ryan; Sergie, Ziad; Hitt, Robert; DiSpigno, Melissa; Cenedella, Carly; Stein, Michael D.

    2006-01-01

    Substance users are at high risk for blood borne infections as well as those that are transmitted sexually. Substance abuse treatment centers present an opportunity to offer comprehensive counseling and testing (CCT) for HIV, viral hepatitis, and sexually transmitted infections (STIs) to this high-risk population. We examined the feasibility and acceptability of one model of CCT among substance users. CCT was offered to 145 consecutive inpatients; study participants completed a risk factor questionnaire and selected from a menu of testing options. Thirty-six percent of those approached agreed to participate and accepted at least one biologic test. Sixty-two percent of participants accepted all tests that were offered. While beneficial to those who accept testing, the described model of CCT is feasible in a drug treatment center, but acceptable to only a minority of inpatients. PMID:15916492

  1. Combination fluconazole/paroxetine treatment is neuroprotective despite ongoing neuroinflammation and viral replication in an SIV model of HIV neurological disease

    PubMed Central

    Meulendyke, Kelly A.; Queen, Suzanne E.; Engle, Elizabeth L.; Shirk, Erin N.; Liu, Jiayang; Steiner, Joseph P.; Nath, Avindra; Tarwater, Patrick M.; Graham, David R.; Mankowski, Joseph L.; Zink, M. Christine

    2014-01-01

    Effective combined antiretroviral therapy (cART) in HIV infected patients has made HIV a treatable condition; however, debilitating HIV-associated neurocognitive disorders (HAND) can still affect up to 50% of HIV infected individuals even under cART. While cART has greatly reduced the prevalence of the most severe form of HAND, milder forms have increased in prevalence, leaving a the total proportion of HIV-infected individuals suffering from HAND relatively unchanged. In this study an in vitro drug screen identified fluconazole and paroxetine as protective compounds against HIV gp120 and Tat neurotoxicity. Using an accelerated, consistent SIV/macaque model of HIV-associated CNS disease, we tested the in vivo neuroprotective capabilities of combination fluconazole/paroxetine (FluPar) treatment. FluPar treatment protected macaques from SIV-induced neurodegeneration, as measured by neurofilament light chain in the CSF, APP accumulation in the axons, and CaMKIIα in the frontal cortex, but did not significantly reduce markers of neuroinflammation or plasma or CNS viral loads. Since HIV and SIV neurodegeneration is often attributed to accompanying neuroinflammation, this study provides proof of concept that neuroprotection can be achieved even in the face of ongoing neuroinflammation and viral replication. PMID:25227932

  2. Combination fluconazole/paroxetine treatment is neuroprotective despite ongoing neuroinflammation and viral replication in an SIV model of HIV neurological disease.

    PubMed

    Meulendyke, Kelly A; Queen, Suzanne E; Engle, Elizabeth L; Shirk, Erin N; Liu, Jiayang; Steiner, Joseph P; Nath, Avindra; Tarwater, Patrick M; Graham, David R; Mankowski, Joseph L; Zink, M Christine

    2014-12-01

    Effective combined antiretroviral therapy (cART) in HIV-infected patients has made HIV a treatable infection; however, debilitating HIV-associated neurocognitive disorders (HAND) can still affect approximately 50% of HIV-infected individuals even under cART. While cART has greatly reduced the prevalence of the most severe form of HAND, milder forms have increased in prevalence, leaving the total proportion of HIV-infected individuals suffering from HAND relatively unchanged. In this study, an in vitro drug screen identified fluconazole and paroxetine as protective compounds against HIV gp120 and Tat neurotoxicity. Using an accelerated, consistent SIV/macaque model of HIV-associated CNS disease, we tested the in vivo neuroprotective capabilities of combination fluconazole/paroxetine (FluPar) treatment. FluPar treatment protected macaques from SIV-induced neurodegeneration, as measured by neurofilament light chain in the CSF, APP accumulation in axons, and CaMKIIα in the frontal cortex, but did not significantly reduce markers of neuroinflammation or plasma or CNS viral loads. Since HIV and SIV neurodegeneration is often attributed to accompanying neuroinflammation, this study provides proof of concept that neuroprotection can be achieved even in the face of ongoing neuroinflammation and viral replication.

  3. Linking market interaction intensity of 3D Ising type financial model with market volatility

    NASA Astrophysics Data System (ADS)

    Fang, Wen; Ke, Jinchuan; Wang, Jun; Feng, Ling

    2016-11-01

    Microscopic interaction models in physics have been used to investigate the complex phenomena of economic systems. The simple interactions involved can lead to complex behaviors and help the understanding of mechanisms in the financial market at a systemic level. This article aims to develop a financial time series model through 3D (three-dimensional) Ising dynamic system which is widely used as an interacting spins model to explain the ferromagnetism in physics. Through Monte Carlo simulations of the financial model and numerical analysis for both the simulation return time series and historical return data of Hushen 300 (HS300) index in Chinese stock market, we show that despite its simplicity, this model displays stylized facts similar to that seen in real financial market. We demonstrate a possible underlying link between volatility fluctuations of real stock market and the change in interaction strengths of market participants in the financial model. In particular, our stochastic interaction strength in our model demonstrates that the real market may be consistently operating near the critical point of the system.

  4. Predictive statistical models linking antecedent meteorological conditions and waterway bacterial contamination in urban waterways.

    PubMed

    Farnham, David J; Lall, Upmanu

    2015-06-01

    Although the relationships between meteorological conditions and waterway bacterial contamination are being better understood, statistical models capable of fully leveraging these links have not been developed for highly urbanized settings. We present a hierarchical Bayesian regression model for predicting transient fecal indicator bacteria contamination episodes in urban waterways. Canals, creeks, and rivers of the New York City harbor system are used to examine the model. The model configuration facilitates the hierarchical structure of the underlying system with weekly observations nested within sampling sites, which in turn were nested inside of the harbor network. Models are compared using cross-validation and a variety of Bayesian and classical model fit statistics. The uncertainty of predicted enterococci concentration values is reflected by sampling from the posterior predictive distribution. Issuing predictions with the uncertainty reasonably reflected allows a water manager or a monitoring agency to issue warnings that better reflect the underlying risk of exposure. A model using only antecedent meteorological conditions is shown to correctly classify safe and unsafe levels of enterococci with good accuracy. The hierarchical Bayesian regression approach is most valuable where transient fecal indicator bacteria contamination is problematic and drainage network data are scarce. PMID:25813489

  5. Non-random patterns in viral diversity

    PubMed Central

    Anthony, Simon J.; Islam, Ariful; Johnson, Christine; Navarrete-Macias, Isamara; Liang, Eliza; Jain, Komal; Hitchens, Peta L.; Che, Xiaoyu; Soloyvov, Alexander; Hicks, Allison L.; Ojeda-Flores, Rafael; Zambrana-Torrelio, Carlos; Ulrich, Werner; Rostal, Melinda K.; Petrosov, Alexandra; Garcia, Joel; Haider, Najmul; Wolfe, Nathan; Goldstein, Tracey; Morse, Stephen S.; Rahman, Mahmudur; Epstein, Jonathan H.; Mazet, Jonna K.; Daszak, Peter; Lipkin, W. Ian

    2015-01-01

    It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely. PMID:26391192

  6. Individual-based modeling of fish: Linking to physical models and water quality.

    SciTech Connect

    Rose, K.A.

    1997-08-01

    The individual-based modeling approach for the simulating fish population and community dynamics is gaining popularity. Individual-based modeling has been used in many other fields, such as forest succession and astronomy. The popularity of the individual-based approach is partly a result of the lack of success of the more aggregate modeling approaches traditionally used for simulating fish population and community dynamics. Also, recent recognition that it is often the atypical individual that survives has fostered interest in the individual-based approach. Two general types of individual-based models are distribution and configuration. Distribution models follow the probability distributions of individual characteristics, such as length and age. Configuration models explicitly simulate each individual; the sum over individuals being the population. DeAngelis et al (1992) showed that, when distribution and configuration models were formulated from the same common pool of information, both approaches generated similar predictions. The distribution approach was more compact and general, while the configuration approach was more flexible. Simple biological changes, such as making growth rate dependent on previous days growth rates, were easy to implement in the configuration version but prevented simple analytical solution of the distribution version.

  7. A Linked Hydro-Economic Model to Examine the Effects of Water Policy on Rural Poverty

    NASA Astrophysics Data System (ADS)

    Maneta, M. P.; Torres, M.; Vosti, S. A.; Wallender, W. W.; Howitt, R.; Rodrigues, L. N.; Bassoi, L. H.; Pfeiffer, L.; Young, J.

    2006-12-01

    The sustainable intensification of small-scale agriculture is a necessary condition for reducing rural poverty in developing countries. Increasing the amount of irrigated cropland and the economic efficiency of irrigation are two key components of most intensification strategies. Improved access to water generally increases farm income but richer farmers use a disproportionate share of the available water, decreasing the chances of poor farmers to meet their water needs. Furthermore, water and poverty have strong spatial components that have so far been neglected in water planning. In that sense, too little is known about the short and long term hydrological effects, especially the externality effects of changes in on-farm water use and its implications to nearby farmers. To address this gap in knowledge, a spatially distributed and transient description of changes in surface and groundwater allocation under different agricultural management scenarios is needed. We propose a hydro-economic model providing a realistic spatio-temporal description of the linkages between the economic and hydrologic subsystems. This hydro-economic model is composed of a basin-level 3D spatially distributed transient hydrologic model (MOD-HMS) and a farm-level, spatially distributed agricultural production model. Both models are explicitly linked through the boundary conditions of the hydrologic model. The linkage will account for the spatial and temporal impact of different crop mixes, irrigation techniques and groundwater pumpage on water availability at farm level to assess the effects of policy action on the hydro-economic components of the system.

  8. Dynamic hysteresis modelling of entangled cross-linked fibres in shear

    NASA Astrophysics Data System (ADS)

    Piollet, Elsa; Poquillon, Dominique; Michon, Guilhem

    2016-11-01

    The objective of this paper is to characterize and model the vibration behaviour of entangled carbon fibres cross-linked with epoxy resin. The material is tested in shear, in a double lap configuration. Experimental testing is carried out for frequencies varying from 1 Hz to 80 Hz and for shear strain amplitudes ranging from 5 ·10-4 to 1 ·10-2. Measured shear stress-strain hysteresis loops show a nonlinear behaviour with a low frequency dependency. The hysteresis loops are decomposed in a linear part and three nonlinear parts: a dry friction hysteresis, a stiffening term and a stiction-like overshoot term. The Generalized Dahl Model is used in conjunction with other hysteresis models to develop an appropriate description of the measured hysteresis loops, based on the three nonlinear parts. In particular, a new one-state formulation of the Bliman-Sorine model is developed. A new identification procedure is also introduced for the Dahl model, based on the so-called backbone curve. The model is shown to capture well the complex shapes of the measured hysteresis loops at all amplitudes.

  9. From top Above to Down Under: Linking the Real World With UnderWorld Models

    NASA Astrophysics Data System (ADS)

    Mueller, D. R.; Heine, C.; May, D.; Moresi, L.

    2005-12-01

    Intraplate sedimentary basins often show a subsidence behaviour which can not be explained by the classical rift models. It appears that the basement heterogeneity is one of the major factors controlling the formation and long-term evolution of those basins. In our project we have tried to integrate the results of an observational study on global intraplate sedimentary basins with particle-in-cell finite element models. By using the UnderWorld(ex SNARK) and Ellipsis2d codes, we are building a numerical model library for different crustal extension scenarios involving a varying heterogeneous basement architecture and attempting to connect the ``pure'' numerical models with real world data as tightly as possible. The direct linking of numerical models with large scale observations offers a new powerful way to investigate the complex lithosphere dynamics and geological processes that account for the evolution of intraplate basins, and the influence of the basement architecture on basin evolution. Here we present the infrastructure and workflow of this new approach together with a first set of modelling results.

  10. Reaction-diffusion degradation model for delayed erosion of cross-linked polyanhydride biomaterials.

    PubMed

    Domanskyi, Sergii; Poetz, Katie L; Shipp, Devon A; Privman, Vladimir

    2015-05-28

    We develop a theoretical model to explain the long induction interval of water intake that precedes the onset of erosion due to degradation caused by hydrolysis in the recently synthesized and studied cross-linked polyanhydrides. Various kinetic mechanisms are incorporated in the model in an attempt to explain the experimental data for the mass loss profile. Our key finding is that the observed long induction interval is attributable to the nonlinear dependence of the degradation rate constants on the local water concentration, which essentially amounts to the breakdown of the standard rate-equation approach, potential causes for which are then discussed. Our theoretical results offer physical insights into which microscopic studies will be required to supplement the presently available macroscopic mass-loss data in order to fully understand the origin of the observed behavior.

  11. Linking remote sensing and ecosystem modeling for management of invasive plants in the Western United States

    NASA Astrophysics Data System (ADS)

    Bubenheim, David; Potter, Christopher; Carruthers, Raymond; Johnson, Lee

    A combination of remote sensing, mapping, modeling, and visualization technology is being adapted to quantify the impact of invasive species on ecosystems. Several prominent invasive species such as saltcedar (Tamarix spp.), yellow starthistle (Centaurea solstitialis), cheatgrass (Bromus tectorum) and important aquatic weeds, such as waterprimrose (Ludwigia hexapetala), are targeted due to their environmental, social and economic importance in the Western United States. Remote sensing imagery (both airborne and satellite) is being used to assess invasive species distribution and spread, as well as to determine biological control agent impact and control success. Linking the remote sensing with ecosystem simulation models such as the Soil Water Assessment Tool (SWAT) and NASA-CASA provides significant improvement in representation of important ecosystem processes. Current emphasis is placed on characterizing cover and spread of invasive plant species and predicting potential ecosystem impact, and quantifying the impact and effectiveness of conservation practices aimed at reducing ecosystem vulnerability to invasive plant species.

  12. A computer model for unconscious spread of anxiety-linked inhibition in cognitive networks.

    PubMed

    Blum, G S

    1989-01-01

    Unconscious inhibitory processes, triggered by a potential anxiety reaction, are reviewed in the context of an emerging rapprochement between psychodynamic and cognitive approaches in experimental psychology. Conditions underlying spread of inhibitory action to other cognitive networks are first explored in three tachistoscopic experiments utilizing words posthypnotically tied to a potential anxiety, pleasure, or neutral reaction. Response times of subjects, instructed to ignore those words while naming pictures or solving anagrams as quickly as possible, reveal a highly differentiated pattern of circumstances governing likelihood of inhibitory spread from anxiety-linked words to target stimuli. Next a computer model is constructed to simulate cognitive processes from onset of display to eventual response, and the model is then tested for its fit to the empirical data. Finally, an illustrative study shows that a subset of computer-generated predictions for spread of inhibitory action is verifiable experimentally. PMID:2920005

  13. Exosomes in Viral Disease.

    PubMed

    Anderson, Monique R; Kashanchi, Fatah; Jacobson, Steven

    2016-07-01

    Viruses have evolved many mechanisms by which to evade and subvert the immune system to ensure survival and persistence. However, for each method undertaken by the immune system for pathogen removal, there is a counteracting mechanism utilized by pathogens. The new and emerging role of microvesicles in immune intercellular communication and function is no different. Viruses across many different families have evolved to insert viral components in exosomes, a subtype of microvesicle, with many varying downstream effects. When assessed cumulatively, viral antigens in exosomes increase persistence through cloaking viral genomes, decoying the immune system, and even by increasing viral infection in uninfected cells. Exosomes therefore represent a source of viral antigen that can be used as a biomarker for disease and targeted for therapy in the control and eradication of these disorders. With the rise in the persistence of new and reemerging viruses like Ebola and Zika, exploring the role of exosomes become more important than ever. PMID:27324390

  14. The model of response to viral haemorrhagic fevers of the National Institute for Infectious Diseases "Lazzaro Spallanzani".

    PubMed

    Armignacco, O; Lauria, F N; Puro, V; Macrì, G; Petrecchia, A; Ippolito, G

    2001-01-01

    Viral haemorrhagic fevers (VHF) are severe and life-threatening diseases caused by a range of viruses. However, only four agents of VHF are known to be readily capable of person-to-person spread: Lassa virus, Crimean/Congo haemorrhagic fever virus, Ebola and Marburg viruses. Diseases caused by these viruses are endemic only in few areas in the world, most notably Africa and some rural parts of the Middle East and Eastern Europe. Nonetheless, the increasing volume of international travel presents a greater likelihood for the importation of these infections or of suspected cases in non endemic countries. Four conditions can lead to the importation and to the subsequent recognition of VHF within Europe: 1) patients arriving as a result of a planned medical evacuation; 2) persons who became sick on route to their destination; 3) persons discovered ill when entering a country, for example during routine clinical examination at the airport; 4) persons becoming sick after their arrival. Public health implications and the risk of secondary spread of pathogens in the above reported circumstances are very different. Similarly, preparedness and response should vary. This paper summarizes the present knowledge on the four VHF capable of person-to-person spread, describes the high isolation area constructed at the Italian National Institute for Infectious Diseases Lazzaro Spallanzani in Rome to respond to the occurrence of VHF. A brief overview of procedures and equipment adopted is provided.

  15. Actinobacteria from Termite Mounds Show Antiviral Activity against Bovine Viral Diarrhea Virus, a Surrogate Model for Hepatitis C Virus.

    PubMed

    Padilla, Marina Aiello; Rodrigues, Rodney Alexandre Ferreira; Bastos, Juliana Cristina Santiago; Martini, Matheus Cavalheiro; Barnabé, Ana Caroline de Souza; Kohn, Luciana Konecny; Uetanabaro, Ana Paula Trovatti; Bomfim, Getúlio Freitas; Afonso, Rafael Sanches; Fantinatti-Garboggini, Fabiana; Arns, Clarice Weis

    2015-01-01

    Extracts from termite-associated bacteria were evaluated for in vitro antiviral activity against bovine viral diarrhea virus (BVDV). Two bacterial strains were identified as active, with percentages of inhibition (IP) equal to 98%. Both strains were subjected to functional analysis via the addition of virus and extract at different time points in cell culture; the results showed that they were effective as posttreatments. Moreover, we performed MTT colorimetric assays to identify the CC50, IC50, and SI values of these strains, and strain CDPA27 was considered the most promising. In parallel, the isolates were identified as Streptomyces through 16S rRNA gene sequencing analysis. Specifically, CDPA27 was identified as S. chartreusis. The CDPA27 extract was fractionated on a C18-E SPE cartridge, and the fractions were reevaluated. A 100% methanol fraction was identified to contain the compound(s) responsible for antiviral activity, which had an SI of 262.41. GC-MS analysis showed that this activity was likely associated with the compound(s) that had a peak retention time of 5 min. Taken together, the results of the present study provide new information for antiviral research using natural sources, demonstrate the antiviral potential of Streptomyces chartreusis compounds isolated from termite mounds against BVDV, and lay the foundation for further studies on the treatment of HCV infection.

  16. Actinobacteria from Termite Mounds Show Antiviral Activity against Bovine Viral Diarrhea Virus, a Surrogate Model for Hepatitis C Virus

    PubMed Central

    Padilla, Marina Aiello; Rodrigues, Rodney Alexandre Ferreira; Bastos, Juliana Cristina Santiago; Martini, Matheus Cavalheiro; Barnabé, Ana Caroline de Souza; Kohn, Luciana Konecny; Uetanabaro, Ana Paula Trovatti; Bomfim, Getúlio Freitas; Afonso, Rafael Sanches; Fantinatti-Garboggini, Fabiana; Arns, Clarice Weis

    2015-01-01

    Extracts from termite-associated bacteria were evaluated for in vitro antiviral activity against bovine viral diarrhea virus (BVDV). Two bacterial strains were identified as active, with percentages of inhibition (IP) equal to 98%. Both strains were subjected to functional analysis via the addition of virus and extract at different time points in cell culture; the results showed that they were effective as posttreatments. Moreover, we performed MTT colorimetric assays to identify the CC50, IC50, and SI values of these strains, and strain CDPA27 was considered the most promising. In parallel, the isolates were identified as Streptomyces through 16S rRNA gene sequencing analysis. Specifically, CDPA27 was identified as S. chartreusis. The CDPA27 extract was fractionated on a C18-E SPE cartridge, and the fractions were reevaluated. A 100% methanol fraction was identified to contain the compound(s) responsible for antiviral activity, which had an SI of 262.41. GC-MS analysis showed that this activity was likely associated with the compound(s) that had a peak retention time of 5 min. Taken together, the results of the present study provide new information for antiviral research using natural sources, demonstrate the antiviral potential of Streptomyces chartreusis compounds isolated from termite mounds against BVDV, and lay the foundation for further studies on the treatment of HCV infection. PMID:26579205

  17. Actinobacteria from Termite Mounds Show Antiviral Activity against Bovine Viral Diarrhea Virus, a Surrogate Model for Hepatitis C Virus.

    PubMed

    Padilla, Marina Aiello; Rodrigues, Rodney Alexandre Ferreira; Bastos, Juliana Cristina Santiago; Martini, Matheus Cavalheiro; Barnabé, Ana Caroline de Souza; Kohn, Luciana Konecny; Uetanabaro, Ana Paula Trovatti; Bomfim, Getúlio Freitas; Afonso, Rafael Sanches; Fantinatti-Garboggini, Fabiana; Arns, Clarice Weis

    2015-01-01

    Extracts from termite-associated bacteria were evaluated for in vitro antiviral activity against bovine viral diarrhea virus (BVDV). Two bacterial strains were identified as active, with percentages of inhibition (IP) equal to 98%. Both strains were subjected to functional analysis via the addition of virus and extract at different time points in cell culture; the results showed that they were effective as posttreatments. Moreover, we performed MTT colorimetric assays to identify the CC50, IC50, and SI values of these strains, and strain CDPA27 was considered the most promising. In parallel, the isolates were identified as Streptomyces through 16S rRNA gene sequencing analysis. Specifically, CDPA27 was identified as S. chartreusis. The CDPA27 extract was fractionated on a C18-E SPE cartridge, and the fractions were reevaluated. A 100% methanol fraction was identified to contain the compound(s) responsible for antiviral activity, which had an SI of 262.41. GC-MS analysis showed that this activity was likely associated with the compound(s) that had a peak retention time of 5 min. Taken together, the results of the present study provide new information for antiviral research using natural sources, demonstrate the antiviral potential of Streptomyces chartreusis compounds isolated from termite mounds against BVDV, and lay the foundation for further studies on the treatment of HCV infection. PMID:26579205

  18. On linking an Earth system model to the equilibrium carbon representation of an economically optimizing land use model

    SciTech Connect

    Bond-Lamberty, Benjamin; Calvin, Katherine V.; Jones, Andrew D.; Mao, Jiafu; Patel, Pralit L.; Shi, Xiaoying; Thomson, Allison M.; Thornton, Peter E.; Zhou, Yuyu

    2014-01-01

    Human activities are significantly altering biogeochemical cycles at the global scale, posing a significant problem for earth system models (ESMs), which may incorporate static land-use change inputs but do not actively simulate policy or economic forces. One option to address this problem is a to couple an ESM with an economically oriented integrated assessment model. Here we have implemented and tested a coupling mechanism between the carbon cycles of an ESM (CLM) and an integrated assessment (GCAM) model, examining the best proxy variables to share between the models, and quantifying our ability to distinguish climate- and land-use-driven flux changes. CLM’s net primary production and heterotrophic respiration outputs were found to be the most robust proxy variables by which to manipulate GCAM’s assumptions of long-term ecosystem steady state carbon, with short-term forest production strongly correlated with long-term biomass changes in climate-change model runs. By leveraging the fact that carbon-cycle effects of anthropogenic land-use change are short-term and spatially limited relative to widely distributed climate effects, we were able to distinguish these effects successfully in the model coupling, passing only the latter to GCAM. By allowing climate effects from a full earth system model to dynamically modulate the economic and policy decisions of an integrated assessment model, this work provides a foundation for linking these models in a robust and flexible framework capable of examining two-way interactions between human and earth system processes.

  19. Emerging viral diseases in kidney transplant recipients.

    PubMed

    Moal, Valérie; Zandotti, Christine; Colson, Philippe

    2013-01-01

    Viruses are the most important cause of infections and a major source of mortality in Kidney Transplant Recipients (KTRs). These patients may acquire viral infections through exogenous routes including community exposure, donor organs, and blood products or by endogenous reactivation of latent viruses. Beside major opportunistic infections due to CMV and EBV and viral hepatitis B and C, several viral diseases have recently emerged in KTRs. New medical practices or technologies, implementation of new diagnostic tools, and improved medical information have contributed to the emergence of these viral diseases in this special population. The purpose of this review is to summarize the current knowledge on emerging viral diseases and newly discovered viruses in KTRs over the last two decades. We identified viruses in the field of KT that had shown the greatest increase in numbers of citations in the NCBI PubMed database. BKV was the most cited in the literature and linked to an emerging disease that represents a great clinical concern in KTRs. HHV-8, PVB19, WNV, JCV, H1N1 influenza virus A, HEV, and GB virus were the main other emerging viruses. Excluding HHV8, newly discovered viruses have been infrequently linked to clinical diseases in KTRs. Nonetheless, pathogenicity can emerge long after the discovery of the causative agent, as has been the case for BKV. Overall, antiviral treatments are very limited, and reducing immunosuppressive therapy remains the cornerstone of management. PMID:23132728

  20. Development of conceptual ecological models linking management of the Missouri River to pallid sturgeon population dynamics

    USGS Publications Warehouse

    Jacobson, Robert B.; Parsley, Michael J.; Annis, Mandy L.; Colvin, Michael E.; Welker, Timothy L.; James, Daniel A.

    2015-01-01

    This report documents the process of developing and refining conceptual ecological models (CEMs) for linking river management to pallid sturgeon (Scaphirhynchus albus) population dynamics in the Missouri River. The refined CEMs are being used in the Missouri River Pallid Sturgeon Effects Analysis to organize, document, and formalize an understanding of pallid sturgeon population responses to past and future management alternatives. The general form of the CEMs, represented by a population-level model and component life-stage models, was determined in workshops held in the summer of 2013. Subsequently, the Missouri River Pallid Sturgeon Effects Analysis team designed a general hierarchical structure for the component models, refined the graphical structure, and reconciled variation among the components and between models developed for the upper river (Upper Missouri & Yellowstone Rivers) and the lower river (Missouri River downstream from Gavins Point Dam). Importance scores attributed to the relations between primary biotic characteristics and survival were used to define a candidate set of working dominant hypotheses about pallid sturgeon population dynamics. These CEMs are intended to guide research and adaptive-management actions to benefit pallid sturgeon populations in the Missouri River.

  1. A dynamical systems analysis of the data assimilation linked ecosystem carbon (DALEC) models.

    PubMed

    Chuter, Anna M; Aston, Philip J; Skeldon, Anne C; Roulstone, Ian

    2015-03-01

    Changes in our climate and environment make it ever more important to understand the processes involved in Earth systems, such as the carbon cycle. There are many models that attempt to describe and predict the behaviour of carbon stocks and stores but, despite their complexity, significant uncertainties remain. We consider the qualitative behaviour of one of the simplest carbon cycle models, the Data Assimilation Linked Ecosystem Carbon (DALEC) model, which is a simple vegetation model of processes involved in the carbon cycle of forests, and consider in detail the dynamical structure of the model. Our analysis shows that the dynamics of both evergreen and deciduous forests in DALEC are dependent on a few key parameters and it is possible to find a limit point where there is stable sustainable behaviour on one side but unsustainable conditions on the other side. The fact that typical parameter values reside close to this limit point highlights the difficulty of predicting even the correct trend without sufficient data and has implications for the use of data assimilation methods.

  2. Immunogens of bovine viral diarrhea virus.

    PubMed

    Bolin, S R

    1993-11-01

    Bovine viral diarrhea virus (BVDV) is a ubiquitous pathogen of cattle that induces economically important diseases affecting multiple organ systems. In the United States, over 150 biological products are licensed for control of BVDV. These products contain live or killed BVDV, and many products contain other viruses or bacteria. Potency tests for these vaccines are based on animal inoculation and serology. For live virus vaccines, titration of viral infectivity in cell culture is an accepted alternative to animal inoculation. The immunogens in a killed virus vaccine may be measured by enzyme linked immunoabsorbent assay. Immunogens of BVDV that stimulate a protective immune response have not been conclusively identified. Epitopes on a putative viral envelope glycoprotein, gp53, are involved in viral neutralization. Other viral glycoproteins, gp48 and gp25, are immunogenic but epitopes on these proteins do not stimulate production of antibodies that efficiently neutralize virus. Progress in developing meaningful in vitro assays for quantitation of BVDV immunogens awaits identification of viral proteins that stimulate a protective immunity.

  3. Linking Formal and Informal Science Education: A Successful Model using Libraries, Volunteers and NASA Resources

    NASA Astrophysics Data System (ADS)

    Race, M. S.; Lafayette Library; Learning Center Foundation (Lllcf)

    2011-12-01

    In these times of budget cuts, tight school schedules, and limited opportunities for student field trips and teacher professional development, it is especially difficult to expose elementary and middle school students to the latest STEM information-particularly in the space sciences. Using our library as a facilitator and catalyst, we built a volunteer-based, multi-faceted, curriculum-linked program for students and teachers in local middle schools (Grade 8) and showcased new astronomical and planetary science information using mainly NASA resources and volunteer effort. The project began with the idea of bringing free NASA photo exhibits (FETTU) to the Lafayette and Antioch Libraries for public display. Subsequently, the effort expanded by adding layers of activities that brought space and science information to teachers, students and the pubic at 5 libraries and schools in the 2 cities, one of which serves a diverse, underserved community. Overall, the effort (supported by a pilot grant from the Bechtel Foundation) included school and library based teacher workshops with resource materials; travelling space museum visits with hands-on activities (Chabot-to-Go); separate powerpoint presentations for students and adults at the library; and concurrent ancillary space-related themes for young children's programs at the library. This pilot project, based largely on the use of free government resources and online materials, demonstrated that volunteer-based, standards-linked STEM efforts can enhance curriculum at the middle school, with libraries serving a special role. Using this model, we subsequently also obtained a small NASA-Space Grant award to bring star parties and hand-on science activities to three libraries this Fall, linking with numerous Grade 5 teachers and students in two additional underserved areas of our county. It's not necessary to reinvent the wheel, you just collect the pieces and build on what you already have.

  4. The Israeli strain IS-98-ST1 of West Nile virus as viral model for West Nile encephalitis in the Old World

    PubMed Central

    Lucas, Marianne; Frenkiel, Marie-Pascale; Mashimo, Tomoji; Guénet, Jean-Louis; Deubel, Vincent; Desprès, Philippe; Ceccaldi, Pierre-Emmanuel

    2004-01-01

    West Nile virus (WNV) recently became a major public health concern in North America, the Middle East, and Europe. In contrast with the investigations of the North-American isolates, the neurovirulence properties of Middle-Eastern strains of WNV have not been extensively characterized. Israeli WNV strain IS-98-ST1 that has been isolated from a white stork in 1998, was found to be highly neuroinvasive in adult C57BL/6 mice. Strain IS-98-ST1 infects primary neuronal cells from mouse cortex, causing neuronal death. These results demonstrate that Israeli strain IS-98-ST1 provides a suitable viral model for WNV-induced disease associated with recent WNV outbreaks in the Old World. PMID:15550172

  5. Underestimation of boreal soil carbon stocks by mathematical soil carbon models linked to soil nutrient status

    NASA Astrophysics Data System (ADS)

    Ťupek, Boris; Ortiz, Carina A.; Hashimoto, Shoji; Stendahl, Johan; Dahlgren, Jonas; Karltun, Erik; Lehtonen, Aleksi

    2016-08-01

    Inaccurate estimate of the largest terrestrial carbon pool, soil organic carbon (SOC) stock, is the major source of uncertainty in simulating feedback of climate warming on ecosystem-atmosphere carbon dioxide exchange by process-based ecosystem and soil carbon models. Although the models need to simplify complex environmental processes of soil carbon sequestration, in a large mosaic of environments a missing key driver could lead to a modeling bias in predictions of SOC stock change.We aimed to evaluate SOC stock estimates of process-based models (Yasso07, Q, and CENTURY soil sub-model v4) against a massive Swedish forest soil inventory data set (3230 samples) organized by a recursive partitioning method into distinct soil groups with underlying SOC stock development linked to physicochemical conditions.For two-thirds of measurements all models predicted accurate SOC stock levels regardless of the detail of input data, e.g., whether they ignored or included soil properties. However, in fertile sites with high N deposition, high cation exchange capacity, or moderately increased soil water content, Yasso07 and Q models underestimated SOC stocks. In comparison to Yasso07 and Q, accounting for the site-specific soil characteristics (e. g. clay content and topsoil mineral N) by CENTURY improved SOC stock estimates for sites with high clay content, but not for sites with high N deposition.Our analysis suggested that the soils with poorly predicted SOC stocks, as characterized by the high nutrient status and well-sorted parent material, indeed have had other predominant drivers of SOC stabilization lacking in the models, presumably the mycorrhizal organic uptake and organo-mineral stabilization processes. Our results imply that the role of soil nutrient status as regulator of organic matter mineralization has to be re-evaluated, since correct SOC stocks are decisive for predicting future SOC change and soil CO2 efflux.

  6. Linking Murine and Human Plasmodium falciparum Challenge Models in a Translational Path for Antimalarial Drug Development

    PubMed Central

    McCarthy, James S.; Marquart, Louise; Sekuloski, Silvana; Trenholme, Katharine; Elliott, Suzanne; Griffin, Paul; Rockett, Rebecca; O'Rourke, Peter; Sloots, Theo; Angulo-Barturen, Iñigo; Ferrer, Santiago; Jiménez-Díaz, María Belén; Martínez, María-Santos; Duparc, Stephan; Leroy, Didier; Wells, Timothy N. C.; Baker, Mark

    2016-01-01

    Effective progression of candidate antimalarials is dependent on optimal dosing in clinical studies, which is determined by a sound understanding of pharmacokinetics and pharmacodynamics (PK/PD). Recently, two important translational models for antimalarials have been developed: the NOD/SCID/IL2Rγ−/− (NSG) model, whereby mice are engrafted with noninfected and Plasmodium falciparum-infected human erythrocytes, and the induced blood-stage malaria (IBSM) model in human volunteers. The antimalarial mefloquine was used to directly measure the PK/PD in both models, which were compared to previously published trial data for malaria patients. The clinical part was a single-center, controlled study using a blood-stage Plasmodium falciparum challenge inoculum in volunteers to characterize the effectiveness of mefloquine against early malaria. The study was conducted in three cohorts (n = 8 each) using different doses of mefloquine. The characteristic delay in onset of action of about 24 h was seen in both NSG and IBSM systems. In vivo 50% inhibitory concentrations (IC50s) were estimated at 2.0 μg/ml and 1.8 μg/ml in the NSG and IBSM models, respectively, aligning with 1.8 μg/ml reported previously for patients. In the IBSM model, the parasite reduction ratios were 157 and 195 for the 10- and 15-mg/kg doses, within the range of previously reported clinical data for patients but significantly lower than observed in the mouse model. Linking mouse and human challenge models to clinical trial data can accelerate the accrual of critical data on antimalarial drug activity. Such data can guide large clinical trials required for development of urgently needed novel antimalarial combinations. (This trial was registered at the Australian New Zealand Clinical Trials Registry [http://anzctr.org.au] under registration number ACTRN12612000323820.) PMID:27044554

  7. Linking Murine and Human Plasmodium falciparum Challenge Models in a Translational Path for Antimalarial Drug Development.

    PubMed

    McCarthy, James S; Marquart, Louise; Sekuloski, Silvana; Trenholme, Katharine; Elliott, Suzanne; Griffin, Paul; Rockett, Rebecca; O'Rourke, Peter; Sloots, Theo; Angulo-Barturen, Iñigo; Ferrer, Santiago; Jiménez-Díaz, María Belén; Martínez, María-Santos; Hooft van Huijsduijnen, Rob; Duparc, Stephan; Leroy, Didier; Wells, Timothy N C; Baker, Mark; Möhrle, Jörg J

    2016-06-01

    Effective progression of candidate antimalarials is dependent on optimal dosing in clinical studies, which is determined by a sound understanding of pharmacokinetics and pharmacodynamics (PK/PD). Recently, two important translational models for antimalarials have been developed: the NOD/SCID/IL2Rγ(-/-) (NSG) model, whereby mice are engrafted with noninfected and Plasmodium falciparum-infected human erythrocytes, and the induced blood-stage malaria (IBSM) model in human volunteers. The antimalarial mefloquine was used to directly measure the PK/PD in both models, which were compared to previously published trial data for malaria patients. The clinical part was a single-center, controlled study using a blood-stage Plasmodium falciparum challenge inoculum in volunteers to characterize the effectiveness of mefloquine against early malaria. The study was conducted in three cohorts (n = 8 each) using different doses of mefloquine. The characteristic delay in onset of action of about 24 h was seen in both NSG and IBSM systems. In vivo 50% inhibitory concentrations (IC50s) were estimated at 2.0 μg/ml and 1.8 μg/ml in the NSG and IBSM models, respectively, aligning with 1.8 μg/ml reported previously for patients. In the IBSM model, the parasite reduction ratios were 157 and 195 for the 10- and 15-mg/kg doses, within the range of previously reported clinical data for patients but significantly lower than observed in the mouse model. Linking mouse and human challenge models to clinical trial data can accelerate the accrual of critical data on antimalarial drug activity. Such data can guide large clinical trials required for development of urgently needed novel antimalarial combinations. (This trial was registered at the Australian New Zealand Clinical Trials Registry [http://anzctr.org.au] under registration number ACTRN12612000323820.). PMID:27044554

  8. Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

    PubMed

    Strohm, S; Tyson, R C; Powell, J A

    2013-10-01

    Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

  9. LINKING AIR TOXIC CONCENTRATIONS FROM CMAQ TO THE HAPEM5 EXPOSURE MODEL AT NEIGHORHOOD SCALES FOR THE PHILADELPHIA AREA

    EPA Science Inventory

    This paper provides a preliminary demonstration of the EPA neighborhood scale modeling paradigm for air toxics by linking concentration from the Community Multi-scale Air Quality (CMAQ) modeling system to the fifth version of the Hazardous Pollutant Exposure Model (HAPEM5). For ...

  10. Modeling the Biodegradation of Bacterial Community Assembly Linked Antibiotics in River Sediment Using a Deterministic-Stochastic Combined Model.

    PubMed

    Zhang, Wenlong; Li, Yi; Wang, Chao; Wang, Peifang; Hou, Jun; Yu, Zhongbo; Niu, Lihua; Wang, Linqiong; Wang, Jing

    2016-08-16

    To understand the interaction between bacterial community assembly and the assembly linked antibiotics biodegradation, a unique model framework containing a Monod kinetic, a logistic kinetic, and a stochastic item was established to describe the biodegradation of bacterial community assembly linked sulfamethoxazole (SMX) in river sediment. According to the modeling results, both deterministic and stochastic processes driving bacterial population variations played important roles in controlling SMX biodegradation, and the relative importance depended on the in situ concentration of SMX. A threshold concentration of SMX, which was biodegraded in the experimental river sediment depending on different processes, was obtained (i.e., 20 μg/kg). The higher introduced concentration of SMX (>20 μg/kg) was found to promote the acclimation of antibiotic degradation bacteria in microbial community through niche differentiation, which resulted in the specific microbial metabolization of SMX. In contrast, the lower introduced concentration of SMX (<20 μg/kg) was not able to lead to a significant increase of deterministic processes and resulted in the biodegradation of SMX through co-metabolism by the coexisting microorganisms. The developed model can be considered a useful tool for improving the technologies of water environmental protection and remediation. PMID:27428250

  11. Remyelination Is Correlated with Regulatory T Cell Induction Following Human Embryoid Body-Derived Neural Precursor Cell Transplantation in a Viral Model of Multiple Sclerosis.

    PubMed

    Plaisted, Warren C; Zavala, Angel; Hingco, Edna; Tran, Ha; Coleman, Ronald; Lane, Thomas E; Loring, Jeanne F; Walsh, Craig M

    2016-01-01

    We have recently described sustained clinical recovery associated with dampened neuroinflammation and remyelination following transplantation of neural precursor cells (NPCs) derived from human embryonic stem cells (hESCs) in a viral model of the human demyelinating disease multiple sclerosis. The hNPCs used in that study were derived by a novel direct differentiation method (direct differentiation, DD-NPCs) that resulted in a unique gene expression pattern when compared to hNPCs derived by conventional methods. Since the therapeutic potential of human NPCs may differ greatly depending on the method of derivation and culture, we wanted to determine whether NPCs differentiated using conventional methods would be similarly effective in improving clinical outcome under neuroinflammatory demyelinating conditions. For the current study, we utilized hNPCs differentiated from a human induced pluripotent cell line via an embryoid body intermediate stage (EB-NPCs). Intraspinal transplantation of EB-NPCs into mice infected with the neurotropic JHM strain of mouse hepatitis virus (JHMV) resulted in decreased accumulation of CD4+ T cells in the central nervous system that was concomitant with reduced demyelination at the site of injection. Dampened neuroinflammation and remyelination was correlated with a transient increase in CD4+FOXP3+ regulatory T cells (Tregs) concentrated within the peripheral lymphatics. However, compared to our earlier study, pathological improvements were modest and did not result in significant clinical recovery. We conclude that the genetic signature of NPCs is critical to their effectiveness in this model of viral-induced neurologic disease. These comparisons will be useful for understanding what factors are critical for the sustained clinical improvement. PMID:27310015

  12. Remyelination Is Correlated with Regulatory T Cell Induction Following Human Embryoid Body-Derived Neural Precursor Cell Transplantation in a Viral Model of Multiple Sclerosis

    PubMed Central

    Plaisted, Warren C.; Zavala, Angel; Hingco, Edna; Tran, Ha; Coleman, Ronald; Lane, Thomas E.; Loring, Jeanne F.; Walsh, Craig M.

    2016-01-01

    We have recently described sustained clinical recovery associated with dampened neuroinflammation and remyelination following transplantation of neural precursor cells (NPCs) derived from human embryonic stem cells (hESCs) in a viral model of the human demyelinating disease multiple sclerosis. The hNPCs used in that study were derived by a novel direct differentiation method (direct differentiation, DD-NPCs) that resulted in a unique gene expression pattern when compared to hNPCs derived by conventional methods. Since the therapeutic potential of human NPCs may differ greatly depending on the method of derivation and culture, we wanted to determine whether NPCs differentiated using conventional methods would be similarly effective in improving clinical outcome under neuroinflammatory demyelinating conditions. For the current study, we utilized hNPCs differentiated from a human induced pluripotent cell line via an embryoid body intermediate stage (EB-NPCs). Intraspinal transplantation of EB-NPCs into mice infected with the neurotropic JHM strain of mouse hepatitis virus (JHMV) resulted in decreased accumulation of CD4+ T cells in the central nervous system that was concomitant with reduced demyelination at the site of injection. Dampened neuroinflammation and remyelination was correlated with a transient increase in CD4+FOXP3+ regulatory T cells (Tregs) concentrated within the peripheral lymphatics. However, compared to our earlier study, pathological improvements were modest and did not result in significant clinical recovery. We conclude that the genetic signature of NPCs is critical to their effectiveness in this model of viral-induced neurologic disease. These comparisons will be useful for understanding what factors are critical for the sustained clinical improvement. PMID:27310015

  13. Using the jackknife for estimation in log link Bernoulli regression models.

    PubMed

    Lipsitz, Stuart R; Fitzmaurice, Garrett M; Arriaga, Alex; Sinha, Debajyoti; Gawande, Atul A

    2015-02-10

    Bernoulli (or binomial) regression using a generalized linear model with a log link function, where the exponentiated regression parameters have interpretation as relative risks, is often more appropriate than logistic regression for prospective studies with common outcomes. In particular, many researchers regard relative risks to be more intuitively interpretable than odds ratios. However, for the log link, when the outcome is very prevalent, the likelihood may not have a unique maximum. To circumvent this problem, a 'COPY method' has been proposed, which is equivalent to creating for each subject an additional observation with the same covariates except the response variable has the outcome values interchanged (1's changed to 0's and 0's changed to 1's). The original response is given weight close to 1, while the new observation is given a positive weight close to 0; this approach always leads to convergence of the maximum likelihood algorithm, except for problems with convergence due to multicollinearity among covariates. Even though this method produces a unique maximum, when the outcome is very prevalent, and/or the sample size is relatively small, the COPY method can yield biased estimates. Here, we propose using the jackknife as a bias-reduction approach for the COPY method. The proposed method is motivated by a study of patients undergoing colorectal cancer surgery.

  14. A Linked Simulation-Optimization (LSO) Model for Conjunctive Irrigation Management using Clonal Selection Algorithm

    NASA Astrophysics Data System (ADS)

    Islam, Sirajul; Talukdar, Bipul

    2016-08-01

    A Linked Simulation-Optimization (LSO) model based on a Clonal Selection Algorithm (CSA) was formulated for application in conjunctive irrigation management. A series of measures were considered for reducing the computational burden associated with the LSO approach. Certain modifications were incurred to the formulated CSA, so as to decrease the number of function evaluations. In addition, a simple problem specific code for a two dimensional groundwater flow simulation model was developed. The flow model was further simplified by a novel approach of area reduction, in order to save computational time in simulation. The LSO model was applied in the irrigation command of the Pagladiya Dam Project in Assam, India. With a view to evaluate the performance of the CSA, a Genetic Algorithm (GA) was used as a comparison base. The results from the CSA compared well with those from the GA. In fact, the CSA was found to consume less computational time than the GA while converging to the optimal solution, due to the modifications incurred in it.

  15. A physiologically based pharmacokinetic model linking plasma protein binding interactions with drug disposition.

    PubMed

    Buur, J L; Baynes, R E; Smith, G W; Riviere, J E

    2009-04-01

    Combination drug therapy increases the chance for an adverse drug reactions due to drug-drug interactions. Altered disposition for sulfamethazine (SMZ) when concurrently administered with flunixin meglumine (FLU) in swine could lead to increased tissue residues. There is a need for a pharmacokinetic modeling technique that can predict the consequences of possible drug interactions. A physiologically based pharmacokinetic model was developed that links plasma protein binding interactions to drug disposition for SMZ and FLU in swine. The model predicted a sustained decrease in total drug and a temporary increase in free drug concentration. An in vivo study confirmed the presence of a drug interaction. Neither the model nor the in vivo study revealed clinically significant changes that alter tissue disposition. This novel linkage approach has use in the prediction of the clinical impact of plasma protein binding interactions. Ultimately it could be used in the design of dosing regimens and in the protection of the food supply through prediction and minimization of tissue residues. PMID:18721993

  16. A Linked Simulation-Optimization (LSO) Model for Conjunctive Irrigation Management using Clonal Selection Algorithm

    NASA Astrophysics Data System (ADS)

    Islam, Sirajul; Talukdar, Bipul

    2016-09-01

    A Linked Simulation-Optimization (LSO) model based on a Clonal Selection Algorithm (CSA) was formulated for application in conjunctive irrigation management. A series of measures were considered for reducing the computational burden associated with the LSO approach. Certain modifications were incurred to the formulated CSA, so as to decrease the number of function evaluations. In addition, a simple problem specific code for a two dimensional groundwater flow simulation model was developed. The flow model was further simplified by a novel approach of area reduction, in order to save computational time in simulation. The LSO model was applied in the irrigation command of the Pagladiya Dam Project in Assam, India. With a view to evaluate the performance of the CSA, a Genetic Algorithm (GA) was used as a comparison base. The results from the CSA compared well with those from the GA. In fact, the CSA was found to consume less computational time than the GA while converging to the optimal solution, due to the modifications incurred in it.

  17. MARKAL-MACRO: A linked model for energy-economy analysis

    SciTech Connect

    Manne, A.S. ); Wene, C.O. Chalmers Univ. of Tech., Goeteborg )

    1992-02-01

    MARKAL-MACRO is an experiment in model linkage for energy and economy analysis. This new tool is intended as an improvement over existing methods for energy strategy assessment. It is designed specifically for estimating the costs and analyzing the technologies proposed for reducing environmental risks such as global climate change or regional air pollution. The greenhouse gas debate illustrates the usefulness of linked energy-economy models. A central issue is the coupling between economic growth, the level of energy demands, and the development of an energy system to supply these demands. The debate is often connected with alternative modeling approaches. The competing philosophies may be labeled top-down macroeconomic'' and bottom-up engineering'' perspectives. MARKAL is a systems engineering (physical process) analysis built on the concept of a Reference Energy System (RES). MARKAL is solved by means of dynamic linear programming. In most applications, the end use demands are fixed, and an economically efficient solution is obtained by minimizing the present value of energy system's costs throughout the planning horizon. MACRO is a macroeconomic model with an aggregated view of long-term economic growth. The basis input factors of production are capital, labor and individual forms of energy. MACRO is solved by nonlinear optimization.

  18. MARKAL-MACRO: A linked model for energy-economy analysis

    SciTech Connect

    Manne, A.S.; Wene, C.O. |

    1992-02-01

    MARKAL-MACRO is an experiment in model linkage for energy and economy analysis. This new tool is intended as an improvement over existing methods for energy strategy assessment. It is designed specifically for estimating the costs and analyzing the technologies proposed for reducing environmental risks such as global climate change or regional air pollution. The greenhouse gas debate illustrates the usefulness of linked energy-economy models. A central issue is the coupling between economic growth, the level of energy demands, and the development of an energy system to supply these demands. The debate is often connected with alternative modeling approaches. The competing philosophies may be labeled ``top-down macroeconomic`` and ``bottom-up engineering`` perspectives. MARKAL is a systems engineering (physical process) analysis built on the concept of a Reference Energy System (RES). MARKAL is solved by means of dynamic linear programming. In most applications, the end use demands are fixed, and an economically efficient solution is obtained by minimizing the present value of energy system`s costs throughout the planning horizon. MACRO is a macroeconomic model with an aggregated view of long-term economic growth. The basis input factors of production are capital, labor and individual forms of energy. MACRO is solved by nonlinear optimization.

  19. Modeling photosynthesis of discontinuous plant canopies by linking the Geometric Optical Radiative Transfer model with biochemical processes

    NASA Astrophysics Data System (ADS)

    Xin, Q.; Gong, P.; Li, W.

    2015-06-01

    Modeling vegetation photosynthesis is essential for understanding carbon exchanges between terrestrial ecosystems and the atmosphere. The radiative transfer process within plant canopies is one of the key drivers that regulate canopy photosynthesis. Most vegetation cover consists of discrete plant crowns, of which the physical observation departs from the underlying assumption of a homogenous and uniform medium in classic radiative transfer theory. Here we advance the Geometric Optical Radiative Transfer (GORT) model to simulate photosynthesis activities for discontinuous plant canopies. We separate radiation absorption into two components that are absorbed by sunlit and shaded leaves, and derive analytical solutions by integrating over the canopy layer. To model leaf-level and canopy-level photosynthesis, leaf light absorption is then linked to the biochemical process of gas diffusion through leaf stomata. The canopy gap probability derived from GORT differs from classic radiative transfer theory, especially when the leaf area index is high, due to leaf clumping effects. Tree characteristics such as tree density, crown shape, and canopy length affect leaf clumping and regulate radiation interception. Modeled gross primary production (GPP) for two deciduous forest stands could explain more than 80% of the variance of flux tower measurements at both near hourly and daily timescales. We demonstrate that ambient CO2 concentrations influence daytime vegetation photosynthesis, which needs to be considered in biogeochemical models. The proposed model is complementary to classic radiative transfer theory and shows promise in modeling the radiative transfer process and photosynthetic activities over discontinuous forest canopies.

  20. Bone fracture toughness and strength correlate with collagen cross-link maturity in a dose-controlled lathyrism mouse model

    PubMed Central

    McNerny, Erin M. B.; Gong, Bo; Morris, Michael D.; Kohn, David H.

    2014-01-01

    Collagen cross-linking is altered in many diseases of bone, and enzymatic collagen cross-links are important to bone quality as evidenced by losses of strength following lysyl oxidase inhibition (lathyrism). We hypothesized that cross-links also contribute directly to bone fracture toughness. A mouse model of lathyrism using subcutaneous injection of up to 500mg/kg β-aminopropionitrile (BAPN) was developed and characterized (60 animals across 4 dosage groups). Three weeks of 150 or 350 mg/kg BAPN treatment in young growing mice significantly reduced cortical bone fracture toughness, strength, and pyridinoline cross-link content. Ratios reflecting relative cross-link maturity were positive regressors of fracture toughness (HP/[DHLNL+HLNL] r2=0.208, p<0.05; [HP+LP]/[DHNL+HLNL] r2=0.196, p<0.1), whereas quantities of mature pyridinoline cross-links were significant positive regressors of tissue strength (lysyl pyridinoline r2=0.159, p=0.014; hydroxylysyl pyridinoline r2=0.112, p<0.05). Immature and pyrrole cross-links, which were not significantly reduced by BAPN, did not correlate with mechanical properties. The effect of BAPN treatment on mechanical properties was dose specific, with the greatest impact found at the intermediate (350mg/kg) dose. Calcein labeling was used to define locations of new bone formation, allowing for the identification of regions of normally cross-linked (preexisting) and BAPN treated (newly formed, cross-link-deficient) bone. Raman spectroscopy revealed spatial differences due to relative tissue age and effects of cross-link inhibition. Newly deposited tissues had lower mineral/matrix, carbonate/phosphate and Amide I cross-link (matrix maturity) ratios compared to preexisting tissues. BAPN treatment did not affect mineral measures, but significantly increased the cross-link (matrix maturity) ratio compared to newly formed control tissue. Our study reveals that spatially localized effects of short term BAPN cross-link inhibition can alter

  1. Norovirus Polymerase Fidelity Contributes to Viral Transmission In Vivo

    PubMed Central

    Thorne, Lucy; Ghurburrun, Elsa

    2016-01-01

    ABSTRACT Intrahost genetic diversity and replication error rates are intricately linked to RNA virus pathogenesis, with alterations in viral polymerase fidelity typically leading to attenuation during infections in vivo. We have previously shown that norovirus intrahost genetic diversity also influences viral pathogenesis using the murine norovirus model, as increasing viral mutation frequency using a mutagenic nucleoside resulted in clearance of a persistent infection in mice. Given the role of replication fidelity and genetic diversity in pathogenesis, we have now investigated whether polymerase fidelity can also impact virus transmission between susceptible hosts. We have identified a high-fidelity norovirus RNA-dependent RNA polymerase mutant (I391L) which displays delayed replication kinetics in vivo but not in cell culture. The I391L polymerase mutant also exhibited lower transmission rates between susceptible hosts than the wild-type virus and, most notably, another replication defective mutant that has wild-type levels of polymerase fidelity. These results provide the first experimental evidence that norovirus polymerase fidelity contributes to virus transmission between hosts and that maintaining diversity is important for the establishment of infection. This work supports the hypothesis that the reduced polymerase fidelity of the pandemic GII.4 human norovirus isolates may contribute to their global dominance. IMPORTANCE Virus replication fidelity and hence the intrahost genetic diversity of viral populations are known to be intricately linked to viral pathogenesis and tropism as well as to immune and antiviral escape during infection. In this study, we investigated whether changes in replication fidelity can impact the ability of a virus to transmit between susceptible hosts by the use of a mouse model for norovirus. We show that a variant encoding a high-fidelity polymerase is transmitted less efficiently between mice than the wild-type strain. This

  2. Viruses and viral proteins

    PubMed Central

    Verdaguer, Nuria; Ferrero, Diego; Murthy, Mathur R. N.

    2014-01-01

    For more than 30 years X-ray crystallography has been by far the most powerful approach for determining the structures of viruses and viral proteins at atomic resolution. The information provided by these structures, which covers many important aspects of the viral life cycle such as cell-receptor recognition, viral entry, nucleic acid transfer and genome replication, has extensively enriched our vision of the virus world. Many of the structures available correspond to potential targets for antiviral drugs against important human pathogens. This article provides an overview of the current knowledge of different structural aspects of the above-mentioned processes. PMID:25485129

  3. a Six-Link Kinematic Chain Model of Human Body Using Kane's Method

    NASA Astrophysics Data System (ADS)

    Rambely, A. S.; Fazrolrozi

    A biomechanics model of six-link kinematic chain of human body is developed by using Kane's method. The kinematic data comprise of six segments; foot, calf, thigh, trunk, upper arm and forearm, are obtained through data collection of walking, running and jumping using the Vicon Nexus system. The motion capture system uses 12 Vicon MX-3+ cameras and 12 Vicon MX-F40 cameras, two DV (50 Hz) cameras and a force plate (100 Hz). Inverse dynamics approach is used to obtain the unknown value of torques produced by joint segments during walking, running and jumping activities. The results show that the largest value of torques produced occurs at the foot segment.

  4. Zebrafish model for the genetic basis of X-linked retinitis pigmentosa.

    PubMed

    Raghupathy, Rakesh Kotapati; McCulloch, Daphne L; Akhtar, Saeed; Al-mubrad, Turki M; Shu, Xinhua

    2013-03-01

    Retinitis pigmentosa (RP) affects 1/4000 individuals in most populations, and X-linked RP (XLRP) is one of the most severe forms of human retinal degeneration. Mutations in both the retinitis pigmentosa GTPase regulator (RPGR) gene and retinitis pigmentosa 2 (RP2) gene account for almost all cases of XLRP. The functional roles of both RPGR and RP2 in the pathogenesis of XLRP are unclear. Due to the surprisingly high degree of functional conservation between human genes and their zebrafish orthologues, the zebrafish has become an important model for human retinal disorders. In this brief review, we summarize the functional characterization of XLRP-causing genes, RPGR and RP2, in zebrafish, and highlight recent studies that provide insight into the cellular functions of both genes. This will not only shed light on disease mechanisms in XLRP but will also provide a solid platform to test RP-causing mutants before proposing XLRP gene therapy trials.

  5. Pathophysiology of white-nose syndrome in bats: a mechanistic model linking wing damage to mortality.

    PubMed

    Warnecke, Lisa; Turner, James M; Bollinger, Trent K; Misra, Vikram; Cryan, Paul M; Blehert, David S; Wibbelt, Gudrun; Willis, Craig K R

    2013-08-23

    White-nose syndrome is devastating North American bat populations but we lack basic information on disease mechanisms. Altered blood physiology owing to epidermal invasion by the fungal pathogen Geomyces destructans (Gd) has been hypothesized as a cause of disrupted torpor patterns of affected hibernating bats, leading to mortality. Here, we present data on blood electrolyte concentration, haematology and acid-base balance of hibernating little brown bats, Myotis lucifugus, following experimental inoculation with Gd. Compared with controls, infected bats showed electrolyte depletion (i.e. lower plasma sodium), changes in haematology (i.e. increased haematocrit and decreased glucose) and disrupted acid-base balance (i.e. lower CO2 partial pressure and bicarbonate). These findings indicate hypotonic dehydration, hypovolaemia and metabolic acidosis. We propose a mechanistic model linking tissue damage to altered homeostasis and morbidity/mortality. PMID:23720520

  6. Characterizing the nucleation flux of linked-flux model for core-shell composite nucleus

    NASA Astrophysics Data System (ADS)

    Iwamatsu, Masao

    2013-05-01

    The kinetics of nucleation of a core-shell composite nucleus that consists of a core of stable final phase surrounded by a wetting layer of an intermediate metastable phase is studied using the linked-flux model where the nucleation flux is considered in the two-dimensional space of stable and metastable components. The steady-state solution of the Fokker-Planck equation is considered not only in the size and composition space but also in the component space. It is shown that the kinetics of critical nucleus at the saddle point is more appropriately characterized in the size and composition space, while the kinetics of the post-critical nucleus is more appropriately described in the component space. Although both the free-energy landscape and the reaction rates play decisive role to determine the kinetics of nucleation at the saddle point, the details of the free energy landscape are irrelevant to the kinetics of the post critical nucleus.

  7. Assessing the potential of using telecommunication microwave links in urban drainage modelling.

    PubMed

    Fencl, M; Rieckermann, J; Schleiss, M; Stránský, D; Bareš, V

    2013-01-01

    The ability to predict the runoff response of an urban catchment to rainfall is crucial for managing drainage systems effectively and controlling discharges from urban areas. In this paper we assess the potential of commercial microwave links (MWL) to capture the spatio-temporal rainfall dynamics and thus improve urban rainfall-runoff modelling. Specifically, we perform numerical experiments with virtual rainfall fields and compare the results of MWL rainfall reconstructions to those of rain gauge (RG) observations. In a case study, we are able to show that MWL networks in urban areas are sufficiently dense to provide good information on spatio-temporal rainfall variability and can thus considerably improve pipe flow prediction, even in small subcatchments. In addition, the better spatial coverage also improves the control of discharges from urban areas. This is especially beneficial for heavy rainfall, which usually has a high spatial variability that cannot be accurately captured by RG point measurements.

  8. Pathophysiology of white-nose syndrome in bats: a mechanistic model linking wing damage to mortality

    USGS Publications Warehouse

    Warnecke, Lisa; Turner, James M.; Bollinger, Trent K.; Misra, Vikram; Cryan, Paul M.; Blehert, David S.; Wibbelt, Gudrun; Willis, Craig K.R.

    2013-01-01

    White-nose syndrome is devastating North American bat populations but we lack basic information on disease mechanisms. Altered blood physiology owing to epidermal invasion by the fungal pathogen Geomyces destructans (Gd) has been hypothesized as a cause of disrupted torpor patterns of affected hibernating bats, leading to mortality. Here, we present data on blood electrolyte concentration, haematology and acid–base balance of hibernating little brown bats, Myotis lucifugus, following experimental inoculation with Gd. Compared with controls, infected bats showed electrolyte depletion (i.e. lower plasma sodium), changes in haematology (i.e. increased haematocrit and decreased glucose) and disrupted acid–base balance (i.e. lower CO2 partial pressure and bicarbonate). These findings indicate hypotonic dehydration, hypovolaemia and metabolic acidosis. We propose a mechanistic model linking tissue damage to altered homeostasis and morbidity/mortality.

  9. Interactions between airway epithelial cells and dendritic cells during viral infections using an in vitro co-culture model

    EPA Science Inventory

    Rationale: Historically, single cell culture models have been limited in pathological and physiological relevance. A co-culture model of dendritic cells (DCs) and differentiated human airway epithelial cells was developed to examine potential interactions between these two cell t...

  10. Linking landscape characteristics to local grizzly bear abundance using multiple detection methods in a hierarchical model

    USGS Publications Warehouse

    Graves, T.A.; Kendall, K.C.; Royle, J. Andrew; Stetz, J.B.; Macleod, A.C.

    2011-01-01

    Few studies link habitat to grizzly bear Ursus arctos abundance and these have not accounted for the variation in detection or spatial autocorrelation. We collected and genotyped bear hair in and around Glacier National Park in northwestern Montana during the summer of 2000. We developed a hierarchical Markov chain Monte Carlo model that extends the existing occupancy and count models by accounting for (1) spatially explicit variables that we hypothesized might influence abundance; (2) separate sub-models of detection probability for two distinct sampling methods (hair traps and rub trees) targeting different segments of the population; (3) covariates to explain variation in each sub-model of detection; (4) a conditional autoregressive term to account for spatial autocorrelation; (5) weights to identify most important variables. Road density and per cent mesic habitat best explained variation in female grizzly bear abundance; spatial autocorrelation was not supported. More female bears were predicted in places with lower road density and with more mesic habitat. Detection rates of females increased with rub tree sampling effort. Road density best explained variation in male grizzly bear abundance and spatial autocorrelation was supported. More male bears were predicted in areas of low road density. Detection rates of males increased with rub tree and hair trap sampling effort and decreased over the sampling period. We provide a new method to (1) incorporate multiple detection methods into hierarchical models of abundance; (2) determine whether spatial autocorrelation should be included in final models. Our results suggest that the influence of landscape variables is consistent between habitat selection and abundance in this system. ?? 2011 The Authors. Animal Conservation ?? 2011 The Zoological Society of London.

  11. Linking state-and-transition simulation and timber supply models for forest biomass production scenarios

    USGS Publications Warehouse

    Costanza, Jennifer; Abt, Robert C.; McKerrow, Alexa; Collazo, Jaime

    2015-01-01

    We linked state-and-transition simulation models (STSMs) with an economics-based timber supply model to examine landscape dynamics in North Carolina through 2050 for three scenarios of forest biomass production. Forest biomass could be an important source of renewable energy in the future, but there is currently much uncertainty about how biomass production would impact landscapes. In the southeastern US, if forests become important sources of biomass for bioenergy, we expect increased land-use change and forest management. STSMs are ideal for simulating these landscape changes, but the amounts of change will depend on drivers such as timber prices and demand for forest land, which are best captured with forest economic models. We first developed state-and-transition model pathways in the ST-Sim software platform for 49 vegetation and land-use types that incorporated each expected type of landscape change. Next, for the three biomass production scenarios, the SubRegional Timber Supply Model (SRTS) was used to determine the annual areas of thinning and harvest in five broad forest types, as well as annual areas converted among those forest types, agricultural, and urban lands. The SRTS output was used to define area targets for STSMs in ST-Sim under two scenarios of biomass production and one baseline, business-as-usual scenario. We show that ST-Sim output matched SRTS targets in most cases. Landscape dynamics results indicate that, compared with the baseline scenario, forest biomass production leads to more forest and, specifically, more intensively managed forest on the landscape by 2050. Thus, the STSMs, informed by forest economics models, provide important information about potential landscape effects of bioenergy production.

  12. Static and dynamic properties of model elastomer with various cross-linking densities: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Liu, Jun; Cao, Dapeng; Zhang, Liqun

    2009-07-01

    The effects of the cross-linking density on the static and dynamic properties of polymer networks are examined by using a molecular dynamics simulation based on a simple elastomer model. Simulation results indicate that the introduced cross-linking junctions show almost no effect on the static structure factor. The glass transition temperature Tg increases slightly with the cross-linking density. By analyzing the mean square displacement of the monomers, the chain diffusion, and the incoherent intermediate dynamic structure factor ϕqs(t) at the chain and segmental length scales, it is found that the mobilities of the monomers and chains are retarded and the relaxation behavior is hindered by the cross linking of polymers. Furthermore, the spatial localization of the monomers is also observed at a long time period for a highly cross-linked system. For the cross-linked system, the time-temperature superposition principle is valid at the segmental length scale but breaks down at the chain length scale. The effect of the cross-linking density on the terminal relaxation is investigated by the end-to-end vector correlation, which is well fitted to the Kohlrauch-William-Watts (KWW) or modified KWW functions. The characteristic relaxation time shows an approximately linear relationship with the cross-linking density. It is demonstrated that the relaxation behavior tends to broaden, attributed to the stronger intermolecular coupling or cooperativity induced by the cross linking, suggesting that the system with a higher cross-linking degree becomes more fragile. For the dynamic properties, the bond orientation and the end-to-end distance along the deformed direction, which is an indicator of the entropic change, and the nonbonded energy are examined during the deformation and relaxation processes, respectively. The results explore the molecular mechanism accounting for the residual stress in the stress relaxation of cross-linked elastomer networks.

  13. Static and dynamic properties of model elastomer with various cross-linking densities: a molecular dynamics study.

    PubMed

    Liu, Jun; Cao, Dapeng; Zhang, Liqun

    2009-07-21

    The effects of the cross-linking density on the static and dynamic properties of polymer networks are examined by using a molecular dynamics simulation based on a simple elastomer model. Simulation results indicate that the introduced cross-linking junctions show almost no effect on the static structure factor. The glass transition temperature T(g) increases slightly with the cross-linking density. By analyzing the mean square displacement of the monomers, the chain diffusion, and the incoherent intermediate dynamic structure factor phi(q)(s)(t) at the chain and segmental length scales, it is found that the mobilities of the monomers and chains are retarded and the relaxation behavior is hindered by the cross linking of polymers. Furthermore, the spatial localization of the monomers is also observed at a long time period for a highly cross-linked system. For the cross-linked system, the time-temperature superposition principle is valid at the segmental length scale but breaks down at the chain length scale. The effect of the cross-linking density on the terminal relaxation is investigated by the end-to-end vector correlation, which is well fitted to the Kohlrauch-William-Watts (KWW) or modified KWW functions. The characteristic relaxation time shows an approximately linear relationship with the cross-linking density. It is demonstrated that the relaxation behavior tends to broaden, attributed to the stronger intermolecular coupling or cooperativity induced by the cross linking, suggesting that the system with a higher cross-linking degree becomes more fragile. For the dynamic properties, the bond orientation and the end-to-end distance along the deformed direction, which is an indicator of the entropic change, and the nonbonded energy are examined during the deformation and relaxation processes, respectively. The results explore the molecular mechanism accounting for the residual stress in the stress relaxation of cross-linked elastomer networks. PMID:19624229

  14. Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

    PubMed Central

    Weinberger, Ariel D.; Sun, Christine L.; Pluciński, Mateusz M.; Denef, Vincent J.; Thomas, Brian C.; Horvath, Philippe; Barrangou, Rodolphe; Gilmore, Michael S.; Getz, Wayne M.; Banfield, Jillian F.

    2012-01-01

    Well-studied innate immune systems exist throughout bacteria and archaea, but a more recently discovered genomic locus may offer prokaryotes surprising immunological adaptability. Mediated by a cassette-like genomic locus termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), the microbial adaptive immune system differs from its eukaryotic immune analogues by incorporating new immunities unidirectionally. CRISPR thus stores genomically recoverable timelines of virus-host coevolution in natural organisms refractory to laboratory cultivation. Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. This ‘trailer-end conservation’ occurs despite rapid viral mutation and despite rapid prokaryotic genomic deletion. The trailer-ends of many reconstructed CRISPR loci are also largely identical across a population. ‘Trailer-end clonality’ occurs despite predictions of host immunological diversity due to negative frequency dependent selection (kill the winner dynamics). Statistical clustering and model simulations explain this lack of diversity by capturing rapid selective sweeps by highly immune CRISPR lineages. Potentially explaining ‘trailer-end conservation,’ we record the first example of a viral bloom overwhelming a CRISPR system. The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. Our results thus link documented

  15. A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies.

    PubMed

    Romasanta, Pablo N; Curto, Lucrecia M; Urtasun, Nicolas; Sarratea, María B; Chiappini, Santiago; Miranda, María V; Delfino, José M; Mariuzza, Roy A; Fernández, Marisa M; Malchiodi, Emilio L

    2014-02-21

    Natural killer (NK) cells discriminate between healthy and virally infected or transformed cells using diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 NK receptors, which can adopt two distinct conformations (backfolded and extended), are of particular importance for detecting cells infected with mouse cytomegalovirus (CMV) via recognition of the viral immunoevasin m157. The interaction of m157 with activating (Ly49H) and inhibitory (Ly49I) receptors governs the spread of mouse CMV. We carried out kinetic and thermodynamic experiments to elucidate the Ly49/m157 binding mechanism. Combining surface plasmon resonance, fluorescence anisotropy, and circular dichroism (CD), we determined that the best model to describe both the Ly49H/m157 and Ly49I/m157 interactions is a conformational selection mechanism where only the extended conformation of Ly49 (Ly49*) is able to bind the first m157 ligand followed by binding of the Ly49*/m157 complex to the second m157. The interaction is characterized by strong positive cooperativity such that the second m157 binds the Ly49 homodimer with a 1000-fold higher sequential constant than the first m157 (∼10(8) versus ∼10(5) M(-1)). Using far-UV CD, we obtained evidence for a conformational change in Ly49 upon binding m157 that could explain the positive cooperativity. The rate-limiting step of the overall mechanism is a conformational transition in Ly49 from its backfolded to extended form. The global thermodynamic parameters from the initial state (backfolded Ly49 and m157) to the final state (Ly49*/(m157)2) are characterized by an unfavorable enthalpy that is compensated by a favorable entropy, making the interaction spontaneous.

  16. A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies.

    PubMed

    Romasanta, Pablo N; Curto, Lucrecia M; Urtasun, Nicolas; Sarratea, María B; Chiappini, Santiago; Miranda, María V; Delfino, José M; Mariuzza, Roy A; Fernández, Marisa M; Malchiodi, Emilio L

    2014-02-21

    Natural killer (NK) cells discriminate between healthy and virally infected or transformed cells using diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 NK receptors, which can adopt two distinct conformations (backfolded and extended), are of particular importance for detecting cells infected with mouse cytomegalovirus (CMV) via recognition of the viral immunoevasin m157. The interaction of m157 with activating (Ly49H) and inhibitory (Ly49I) receptors governs the spread of mouse CMV. We carried out kinetic and thermodynamic experiments to elucidate the Ly49/m157 binding mechanism. Combining surface plasmon resonance, fluorescence anisotropy, and circular dichroism (CD), we determined that the best model to describe both the Ly49H/m157 and Ly49I/m157 interactions is a conformational selection mechanism where only the extended conformation of Ly49 (Ly49*) is able to bind the first m157 ligand followed by binding of the Ly49*/m157 complex to the second m157. The interaction is characterized by strong positive cooperativity such that the second m157 binds the Ly49 homodimer with a 1000-fold higher sequential constant than the first m157 (∼10(8) versus ∼10(5) M(-1)). Using far-UV CD, we obtained evidence for a conformational change in Ly49 upon binding m157 that could explain the positive cooperativity. The rate-limiting step of the overall mechanism is a conformational transition in Ly49 from its backfolded to extended form. The global thermodynamic parameters from the initial state (backfolded Ly49 and m157) to the final state (Ly49*/(m157)2) are characterized by an unfavorable enthalpy that is compensated by a favorable entropy, making the interaction spontaneous. PMID:24379405

  17. Link between hopping models and percolation scaling laws for charge transport in mixtures of small molecules

    DOE PAGES

    Ha, Dong -Gwang; Kim, Jang -Joo; Baldo, Marc A.

    2016-04-29

    Mixed host compositions that combine charge transport materials with luminescent dyes offer superior control over exciton formation and charge transport in organic light emitting devices (OLEDs). Two approaches are typically used to optimize the fraction of charge transport materials in a mixed host composition: either an empirical percolative model, or a hopping transport model. We show that these two commonly-employed models are linked by an analytic expression which relates the localization length to the percolation threshold and critical exponent. The relation is confirmed both numerically and experimentally through measurements of the relative conductivity of Tris(4-carbazoyl-9-ylphenyl) amine (TCTA) :1,3-bis(3,5-dipyrid-3-yl-phenyl) benzene (BmPyPb)more » mixtures with different concentrations, where the TCTA plays a role as hole conductor and the BmPyPb as hole insulator. Furthermore, the analytic relation may allow the rational design of mixed layers of small molecules for high-performance OLEDs.« less

  18. Linking river management to species conservation using dynamic landscape scale models

    USGS Publications Warehouse

    Freeman, Mary C.; Buell, Gary R.; Hay, Lauren E.; Hughes, W. Brian; Jacobson, Robert B.; Jones, John W.; Jones, S.A.; LaFontaine, Jacob H.; Odom, Kenneth R.; Peterson, James T.; Riley, Jeffrey W.; Schindler, J. Stephen; Shea, C.; Weaver, J.D.

    2013-01-01

    Efforts to conserve stream and river biota could benefit from tools that allow managers to evaluate landscape-scale changes in species distributions in response to water management decisions. We present a framework and methods for integrating hydrology, geographic context and metapopulation processes to simulate effects of changes in streamflow on fish occupancy dynamics across a landscape of interconnected stream segments. We illustrate this approach using a 482 km2 catchment in the southeastern US supporting 50 or more stream fish species. A spatially distributed, deterministic and physically based hydrologic model is used to simulate daily streamflow for sub-basins composing the catchment. We use geographic data to characterize stream segments with respect to channel size, confinement, position and connectedness within the stream network. Simulated streamflow dynamics are then applied to model fish metapopulation dynamics in stream segments, using hypothesized effects of streamflow magnitude and variability on population processes, conditioned by channel characteristics. The resulting time series simulate spatially explicit, annual changes in species occurrences or assemblage metrics (e.g. species richness) across the catchment as outcomes of management scenarios. Sensitivity analyses using alternative, plausible links between streamflow components and metapopulation processes, or allowing for alternative modes of fish dispersal, demonstrate large effects of ecological uncertainty on model outcomes and highlight needed research and monitoring. Nonetheless, with uncertainties explicitly acknowledged, dynamic, landscape-scale simulations may prove useful for quantitatively comparing river management alternatives with respect to species conservation.

  19. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model.

    PubMed

    Miner, Brooks E; De Meester, Luc; Pfrender, Michael E; Lampert, Winfried; Hairston, Nelson G

    2012-05-22

    How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances. PMID:22298849

  20. Viral population dynamics and virulence thresholds.

    PubMed

    Lancaster, Karen Z; Pfeiffer, Julie K

    2012-08-01

    Viral factors and host barriers influence virally induced disease, and asymptomatic versus symptomatic infection is governed by a 'virulence threshold'. Understanding modulation of virulence thresholds could lend insight into disease outcome and aid in rational therapeutic and vaccine design. RNA viruses are an excellent system to study virulence thresholds in the context of quasispecies population dynamics. RNA viruses have high error frequencies and our understanding of viral population dynamics has been shaped by quasispecies evolutionary theory. In turn, research using RNA viruses as replicons with short generation times and high mutation rates has been an invaluable tool to test models of quasispecies theory. The challenge and new frontier of RNA virus population dynamics research is to combine multiple theoretical models and experimental data to describe viral population behavior as it changes, moving within and between hosts, to predict disease and pathogen emergence. Several excellent studies have begun to undertake this challenge using novel approaches.

  1. Viral infections during pregnancy.

    PubMed

    Silasi, Michelle; Cardenas, Ingrid; Kwon, Ja-Young; Racicot, Karen; Aldo, Paula; Mor, Gil

    2015-03-01

    Viral infections during pregnancy have long been considered benign conditions with a few notable exceptions, such as herpes virus. The recent Ebola outbreak and other viral epidemics and pandemics show how pregnant women suffer worse outcomes (such as preterm labor and adverse fetal outcomes) than the general population and non-pregnant women. New knowledge about the ways the maternal-fetal interface and placenta interact with the maternal immune system may explain these findings. Once thought to be 'immunosuppressed', the pregnant woman actually undergoes an immunological transformation, where the immune system is necessary to promote and support the pregnancy and growing fetus. When this protection is breached, as in a viral infection, this security is weakened and infection with other microorganisms can then propagate and lead to outcomes, such as preterm labor. In this manuscript, we review the major viral infections relevant to pregnancy and offer potential mechanisms for the associated adverse pregnancy outcomes. PMID:25582523

  2. VIRAL INFECTIONS DURING PREGNANCY

    PubMed Central

    Silasi, Michelle; Cardenas, Ingrid; Racicot, Karen; Kwon, Ja-Young; Aldo, Paula; Mor, Gil

    2015-01-01

    Viral infections during pregnancy have long been considered benign conditions with a few notable exceptions, such as herpes virus. The recent Ebola outbreak and other viral epidemics and pandemics show how pregnant women suffer worse outcomes (such as preterm labor and adverse fetal outcomes) than the general population and non-pregnant women. New knowledge about the ways the maternal-fetal interface and placenta interact with the maternal immune system may explain these findings. Once thought to be “immunosuppressed”, the pregnant woman actually undergoes an immunological transformation, where the immune system is necessary to promote and support the pregnancy and growing fetus. When this protection is breached, as in a viral infection, this security is weakened and infection with other microorganisms can then propagate and lead to outcomes, such as preterm labor. In this manuscript, we review the major viral infections relevant to pregnancy, and offer potential mechanisms for the associated adverse pregnancy outcomes. PMID:25582523

  3. HIV and Viral Hepatitis

    MedlinePlus

    ... prevalent among blacks as among whites. Viral Hepatitis Transmission People can be infected with the three most ... risk for HAV. • • New data suggest that sexual transmission of HCV among MSM with HIV occurs more ...

  4. Viral kinetics and exhaled droplet size affect indoor transmission dynamics of influenza infection.

    PubMed

    Chen, S C; Chio, C P; Jou, L J; Liao, C M

    2009-10-01

    The purpose of this paper was to investigate the effects of viral kinetics and exhaled droplet size on indoor transmission dynamics of influenza infection. The target cell-limited model with delayed virus production was adopted to strengthen the inner mechanisms of virus infection on human epithelial cell. The particle number and volume involved in the viral kinetics were linked with Wells-Riley mathematical equation to quantify the infection risk. We investigated population dynamics in a specific elementary school by using the seasonal susceptible - exposed - infected - recovery (SEIR) model. We found that exhaled pulmonary bioaerosol of sneeze (particle diameter <10 microm) have 10(2)-fold estimate higher than that of cough. Sneeze and cough caused risk probabilities range from 0.075 to 0.30 and 0.076, respectively; whereas basic reproduction numbers (R(0)) estimates range from 4 to 17 for sneeze and nearly 4 for cough, indicating sneeze-posed higher infection risk. The viral kinetics and exhaled droplet size for sneeze affect indoor transmission dynamics of influenza infection since date post-infection 1-7. This study provides direct mechanistic support that indoor influenza virus transmission can be characterized by viral kinetics in human upper respiratory tracts that are modulated by exhaled droplet size. Practical Implications This paper provides a predictive model that can integrate the influenza viral kinetics (target cell-limited model), indoor aerosol transmission potential (Wells-Riley mathematical equation), and population dynamic model [susceptible - exposed - infected - recovery (SEIR) model] in a proposed susceptible population. Viral kinetics expresses the competed results of human immunity ability with influenza virus generation. By linking the viral kinetics and different exposure parameters and environmental factors in a proposed school setting with five age groups, the influenza infection risk can be estimated. On the other hand, we implicated

  5. Viral kinetics and exhaled droplet size affect indoor transmission dynamics of influenza infection.

    PubMed

    Chen, S C; Chio, C P; Jou, L J; Liao, C M

    2009-10-01

    The purpose of this paper was to investigate the effects of viral kinetics and exhaled droplet size on indoor transmission dynamics of influenza infection. The target cell-limited model with delayed virus production was adopted to strengthen the inner mechanisms of virus infection on human epithelial cell. The particle number and volume involved in the viral kinetics were linked with Wells-Riley mathematical equation to quantify the infection risk. We investigated population dynamics in a specific elementary school by using the seasonal susceptible - exposed - infected - recovery (SEIR) model. We found that exhaled pulmonary bioaerosol of sneeze (particle diameter <10 microm) have 10(2)-fold estimate higher than that of cough. Sneeze and cough caused risk probabilities range from 0.075 to 0.30 and 0.076, respectively; whereas basic reproduction numbers (R(0)) estimates range from 4 to 17 for sneeze and nearly 4 for cough, indicating sneeze-posed higher infection risk. The viral kinetics and exhaled droplet size for sneeze affect indoor transmission dynamics of influenza infection since date post-infection 1-7. This study provides direct mechanistic support that indoor influenza virus transmission can be characterized by viral kinetics in human upper respiratory tracts that are modulated by exhaled droplet size. Practical Implications This paper provides a predictive model that can integrate the influenza viral kinetics (target cell-limited model), indoor aerosol transmission potential (Wells-Riley mathematical equation), and population dynamic model [susceptible - exposed - infected - recovery (SEIR) model] in a proposed susceptible population. Viral kinetics expresses the competed results of human immunity ability with influenza virus generation. By linking the viral kinetics and different exposure parameters and environmental factors in a proposed school setting with five age groups, the influenza infection risk can be estimated. On the other hand, we implicated

  6. Papillomaviruses: Viral evolution, cancer and evolutionary medicine.

    PubMed

    Bravo, Ignacio G; Félez-Sánchez, Marta

    2015-01-28

    Papillomaviruses (PVs) are a numerous family of small dsDNA viruses infecting virtually all mammals. PVs cause infections without triggering a strong immune response, and natural infection provides only limited protection against reinfection. Most PVs are part and parcel of the skin microbiota. In some cases, infections by certain PVs take diverse clinical presentations from highly productive self-limited warts to invasive cancers. We propose PVs as an excellent model system to study the evolutionary interactions between the immune system and pathogens causing chronic infections: genotypically, PVs are very diverse, with hundreds of different genotypes infecting skin and mucosa; phenotypically, they display extremely broad gradients and trade-offs between key phenotypic traits, namely productivity, immunogenicity, prevalence, oncogenicity and clinical presentation. Public health interventions have been launched to decrease the burden of PV-associated cancers, including massive vaccination against the most oncogenic human PVs, as well as systematic screening for PV chronic anogenital infections. Anti-PVs vaccines elicit protection against infection, induce cross-protection against closely related viruses and result in herd immunity. However, our knowledge on the ecological and intrapatient dynamics of PV infections remains fragmentary. We still need to understand how the novel anthropogenic selection pressures posed by vaccination and screening will affect viral circulation and epidemiology. We present here an overview of PV evolution and the connection between PV genotypes and the phenotypic, clinical manifestations of the diseases they cause. This differential link between viral evolution and the gradient cancer-warts-asymptomatic infections makes PVs a privileged playground for evolutionary medicine research.

  7. Linking near- and far-field hydrodynamic models for simulation of desalination plant brine discharges.

    PubMed

    Botelho, D A; Barry, M E; Collecutt, G C; Brook, J; Wiltshire, D

    2013-01-01

    A desalination plant is proposed to be the major water supply to the Olympic Dam Expansion Mining project. Located in the Upper Spencer Gulf, South Australia, the site was chosen due to the existence of strong currents and their likely advantages in terms of mixing and dilution of discharged return water. A high-resolution hydrodynamic model (Estuary, Lake and Coastal Ocean Model, ELCOM) was constructed and, through a rigorous review process, was shown to reproduce the intricate details of the Spencer Gulf dynamics, including those characterising the discharge site. Notwithstanding this, it was found that deploying typically adopted 'direct insertion' techniques to simulate the brine discharge within the hydrodynamic model was problematic. Specifically, it was found that in this study the direct insertion technique delivered highly conservative brine dilution predictions in and around the proposed site, and that these were grid and time-step dependent. To improve the predictive capability, a strategy to link validated computational fluid dynamics (CFD) predictions to hydrodynamic simulations was devised. In this strategy, environmental conditions from ELCOM were used to produce boundary conditions for execution of a suite of CFD simulations. In turn, the CFD simulations provided the brine dilutions and flow rates to be applied in ELCOM. In order to conserve mass in a system-wide sense, artificial salt sinks were introduced to the ELCOM model such that salt quantities were conserved. As a result of this process, ELCOM predictions were naturally very similar to CFD predictions near the diffuser, whilst at the same time they produced an area of influence (further afield) comparable to direct insertion methods. It was concluded that the linkage of the models, in comparison to direct insertion methods, constituted a more realistic and defensible alternative to predict the far-field dispersion of outfall discharges, particularly with regards to the estimation of brine

  8. Viral miRNAs.

    PubMed

    Plaisance-Bonstaff, Karlie; Renne, Rolf

    2011-01-01

    Since 2004, more than 200 microRNAs (miRNAs) have been discovered in double-stranded DNA viruses, mainly herpesviruses and polyomaviruses (Nucleic Acids Res 32:D109-D111, 2004). miRNAs are short 22  ±  3 nt RNA molecules that posttranscriptionally regulate gene expression by binding to 3'-untranslated regions (3'UTR) of target mRNAs, thereby inducing translational silencing and/or transcript degradation (Nature 431:350-355, 2004; Cell 116:281-297, 2004). Since miRNAs require only limited complementarity for binding, miRNA targets are difficult to determine (Mol Cell 27:91-105, 2007). To date, targets have only been experimentally verified for relatively few viral miRNAs, which either target viral or host cellular gene expression: For example, SV40 and related polyomaviruses encode miRNAs which target viral large T antigen expression (Nature 435:682-686, 2005; J Virol 79:13094-13104, 2005; Virology 383:183-187, 2009; J Virol 82:9823-9828, 2008) and miRNAs of α-, β-, and γ-herpesviruses have been implicated in regulating the transition from latent to lytic gene expression, a key step in the herpesvirus life cycle. Viral miRNAs have also been shown to target various host cellular genes. Although this field is just beginning to unravel the multiple roles of viral miRNA in biology and pathogenesis, the current data strongly suggest that virally encoded miRNAs are able to regulate fundamental biological processes such as immune recognition, promotion of cell survival, angiogenesis, proliferation, and cell differentiation. This chapter aims to summarize our current knowledge of viral miRNAs, their targets and function, and the challenges lying ahead to decipher their role in viral biology, pathogenesis, and for γ-herepsvirus-encoded miRNAs, potentially tumorigenesis. PMID:21431678

  9. Use of the Syrian Hamster as a New Model of Ebola Virus Disease and Other Viral Hemorrhagic Fevers

    PubMed Central

    Wahl-Jensen, Victoria; Bollinger, Laura; Safronetz, David; de Kok-Mercado, Fabian; Scott, Dana P.; Ebihara, Hideki

    2012-01-01

    Historically, mice and guinea pigs have been the rodent models of choice for therapeutic and prophylactic countermeasure testing against Ebola virus disease (EVD). Recently, hamsters have emerged as a novel animal model for the in vivo study of EVD. In this review, we discuss the history of the hamster as a research laboratory animal, as well as current benefits and challenges of this model. Availability of immunological reagents is addressed. Salient features of EVD in hamsters, including relevant pathology and coagulation parameters, are compared directly with the mouse, guinea pig and nonhuman primate models. PMID:23242370

  10. Immigration and viral hepatitis.

    PubMed

    Sharma, Suraj; Carballo, Manuel; Feld, Jordan J; Janssen, Harry L A

    2015-08-01

    WHO estimates reveal that the global prevalence of viral hepatitis may be as high as 500 million, with an annual mortality rate of up to 1.3 million individuals. The majority of this global burden of disease is borne by nations of the developing world with high rates of vertical and iatrogenic transmission of HBV and HCV, as well as poor access to healthcare. In 2013, 3.2% of the global population (231 million individuals) migrated into a new host nation. Migrants predominantly originate from the developing countries of the south, into the developed economies of North America and Western Europe. This mass migration of individuals from areas of high-prevalence of viral hepatitis poses a unique challenge to the healthcare systems of the host nations. Due to a lack of universal standards for screening, vaccination and treatment of viral hepatitis, the burden of chronic liver disease and hepatocellular carcinoma continues to increase among migrant populations globally. Efforts to increase case identification and treatment among migrants have largely been limited to small outreach programs in urban centers, such that the majority of migrants with viral hepatitis continue to remain unaware of their infection. This review summarizes the data on prevalence of viral hepatitis and burden of chronic liver disease among migrants, current standards for screening and treatment of immigrants and refugees, and efforts to improve the identification and treatment of viral hepatitis among migrants. PMID:25962882

  11. Immigration and viral hepatitis.

    PubMed

    Sharma, Suraj; Carballo, Manuel; Feld, Jordan J; Janssen, Harry L A

    2015-08-01

    WHO estimates reveal that the global prevalence of viral hepatitis may be as high as 500 million, with an annual mortality rate of up to 1.3 million individuals. The majority of this global burden of disease is borne by nations of the developing world with high rates of vertical and iatrogenic transmission of HBV and HCV, as well as poor access to healthcare. In 2013, 3.2% of the global population (231 million individuals) migrated into a new host nation. Migrants predominantly originate from the developing countries of the south, into the developed economies of North America and Western Europe. This mass migration of individuals from areas of high-prevalence of viral hepatitis poses a unique challenge to the healthcare systems of the host nations. Due to a lack of universal standards for screening, vaccination and treatment of viral hepatitis, the burden of chronic liver disease and hepatocellular carcinoma continues to increase among migrant populations globally. Efforts to increase case identification and treatment among migrants have largely been limited to small outreach programs in urban centers, such that the majority of migrants with viral hepatitis continue to remain unaware of their infection. This review summarizes the data on prevalence of viral hepatitis and burden of chronic liver disease among migrants, current standards for screening and treatment of immigrants and refugees, and efforts to improve the identification and treatment of viral hepatitis among migrants.

  12. Tectonic plates, difficulties for pupils to link models and scientific data.

    NASA Astrophysics Data System (ADS)

    David-Ameline, Jacques

    2014-05-01

    In a secondary school in the west of France, I teach Biology and Geology to young pupils from 12 to 15 years old. This poster deals with the difficulties that pupils have to link the scientific data concerning the plate tectonics and the models. I choose to reproduce for pupils some situations that faced some first scientific people as they discovered arguments for the plate tectonics. For example, they have to discover the thickness of the plates by studying the speed of the seismic waves regarding the deepness. That means that they have to construct a curve starting with a table and then to analyze it. The first step is linked to math lessons and is quite easy for them. But the second one needs to mix the curve with its signification. This point is particularly hard and as we correct it, it appears like one moment of « pure science » because they seem to discover something none did before, with the power of their brain ! The second work on this subject is to study the representations of the subduction at an oceanic trench and of the mid-ocean ridge. They first look for drawing explaining what happens for the plates in those places and then they look for proofs that permitted to create those drawings. They really need help to make the difference between scientific data (pictures, curves...) and other drawings similar to the one they choose. For this subject working with documents is not easy because pupils have to ask themselves « what kind of document is it ?» before going further into their thinking. Nevertheless, they often succeed in those works because the teacher helps them a little. Those subjects open their eyes on what science is for a geological theme. It's also a good method to make them having fun doing science and to make them being seduced by making science.

  13. The role of ecological models in linking ecological risk assessment to ecosystem services in agroecosystems.

    PubMed

    Galic, Nika; Schmolke, Amelie; Forbes, Valery; Baveco, Hans; van den Brink, Paul J

    2012-01-15

    Agricultural practices are essential for sustaining the human population, but at the same time they can directly disrupt ecosystem functioning. Ecological risk assessment (ERA) aims to estimate possible adverse effects of human activities on ecosystems and their parts. Current ERA practices, however, incorporate very little ecology and base the risk estimates on the results of standard tests with several standard species. The main obstacles for a more ecologically relevant ERA are the lack of clear protection goals and the inherent complexity of ecosystems that is hard to approach empirically. In this paper, we argue that the ecosystem services framework offers an opportunity to define clear and ecologically relevant protection goals. At the same time, ecological models provide the tools to address ecological complexity to the degree needed to link measurement endpoints and ecosystem services, and to quantify service provision and possible adverse effects from human activities. We focus on the ecosystem services relevant for agroecosystem functioning, including pollination, biocontrol and eutrophication effects and present modeling studies relevant for quantification of each of the services. The challenges of the ecosystem services approach are discussed as well as the limitations of ecological models in the context of ERA. A broad, multi-stakeholder dialog is necessary to aid the definition of protection goals in terms of services delivered by ecosystems and their parts. The need to capture spatio-temporal dynamics and possible interactions among service providers pose challenges for ecological models as a basis for decision making. However, we argue that both fields are advancing quickly and can prove very valuable in achieving more ecologically relevant ERA. PMID:21802704

  14. Ecological-network models link diversity, structure and function in the plankton food-web.

    PubMed

    D'Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera d'Alcalà, Maurizio

    2016-02-17

    A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named 'green' and 'blue' - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the 'adaptive' responses of plankton communities to perturbations.

  15. Linking Fine-Scale Observations and Model Output with Imagery at Multiple Scales

    NASA Astrophysics Data System (ADS)

    Sadler, J.; Walthall, C. L.

    2014-12-01

    The development and implementation of a system for seasonal worldwide agricultural yield estimates is underway with the international Group on Earth Observations GeoGLAM project. GeoGLAM includes a research component to continually improve and validate its algorithms. There is a history of field measurement campaigns going back decades to draw upon for ways of linking surface measurements and model results with satellite observations. Ground-based, in-situ measurements collected by interdisciplinary teams include yields, model inputs and factors affecting scene radiation. Data that is comparable across space and time with careful attention to calibration is essential for the development and validation of agricultural applications of remote sensing. Data management to ensure stewardship, availability and accessibility of the data are best accomplished when considered an integral part of the research. The expense and logistical challenges of field measurement campaigns can be cost-prohibitive and because of short funding cycles for research, access to consistent, stable study sites can be lost. The use of a dedicated staff for baseline data needed by multiple investigators, and conducting measurement campaigns using existing measurement networks such as the USDA Long Term Agroecosystem Research network can fulfill these needs and ensure long-term access to study sites.

  16. Combined use of point rain gauges, radar, microwave link and level measurements in urban hydrological modelling

    NASA Astrophysics Data System (ADS)

    Grum, Morten; Kraemer, Stefan; Verworn, Hans-Reinhard; Redder, Axel

    2005-09-01

    A methodology has been developed for the combined exploitation of the information content in several different types of rainfall and hydrological measurements. The methodology is based on simple rain plane and runoff models that are incorporated into a stochastic state-space model approach. State estimation is done using the extended Kalman filter in combination with a maximum likelihood estimation criterion and an off-line optimisation routine. This paper presents the preliminary results of the application of the methodology for the combined use of multiple rainfall and runoff data on a 4800 ha urban catchment within the Emscher river basin in Germany. The time series used come from 12 rain gauges, a C-band and an X-band radar covering the same area and a microwave link. The preliminary results support the methodology's potential as a technique for the combined use of different types of rainfall and runoff data. The results are discussed in terms of applicability, the methodology's limitations and future improvements.

  17. Ecological-network models link diversity, structure and function in the plankton food-web

    PubMed Central

    D’Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera d’Alcalà, Maurizio

    2016-01-01

    A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named ‘green’ and ‘blue’ - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the ‘adaptive’ responses of plankton communities to perturbations. PMID:26883643

  18. Ecological-network models link diversity, structure and function in the plankton food-web.

    PubMed

    D'Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera d'Alcalà, Maurizio

    2016-01-01

    A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named 'green' and 'blue' - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the 'adaptive' responses of plankton communities to perturbations. PMID:26883643

  19. ON THE TRANSITIONAL DISK CLASS: LINKING OBSERVATIONS OF T TAURI STARS AND PHYSICAL DISK MODELS

    SciTech Connect

    Espaillat, C.; Andrews, S.; Qi, C.; Wilner, D.; Ingleby, L.; Calvet, N.; Hernandez, J.; Furlan, E.; D'Alessio, P.; Muzerolle, J. E-mail: sandrews@cfa.harvard.edu E-mail: dwilner@cfa.harvard.edu E-mail: ncalvet@umich.edu E-mail: Elise.Furlan@jpl.nasa.gov E-mail: muzerol@stsci.edu

    2012-03-10

    Two decades ago 'transitional disks' (TDs) described spectral energy distributions (SEDs) of T Tauri stars with small near-IR excesses, but significant mid- and far-IR excesses. Many inferred this indicated dust-free holes in disks possibly cleared by planets. Recently, this term has been applied disparately to objects whose Spitzer SEDs diverge from the expectations for a typical full disk (FD). Here, we use irradiated accretion disk models to fit the SEDs of 15 such disks in NGC 2068 and IC 348. One group has a 'dip' in infrared emission while the others' continuum emission decreases steadily at all wavelengths. We find that the former have an inner disk hole or gap at intermediate radii in the disk and we call these objects 'transitional disks' and 'pre-transitional disks' (PTDs), respectively. For the latter group, we can fit these SEDs with FD models and find that millimeter data are necessary to break the degeneracy between dust settling and disk mass. We suggest that the term 'transitional' only be applied to objects that display evidence for a radical change in the disk's radial structure. Using this definition, we find that TDs and PTDs tend to have lower mass accretion rates than FDs and that TDs have lower accretion rates than PTDs. These reduced accretion rates onto the star could be linked to forming planets. Future observations of TDs and PTDs will allow us to better quantify the signatures of planet formation in young disks.

  20. A model linking sources of stress to approach and avoidance coping styles of Turkish basketball referees.

    PubMed

    Anshel, Mark Howard; Sutarso, Toto; Ekmekci, Ridvan; Saraswati, Intan W

    2014-01-01

    Purpose of this study was to externally validate and test a conceptual transient model involving six paths that linked sources of acute stress to avoidance and approach coping styles among Turkish basketball referees. The sample consisted of 125 Turkish basketball referees ranging in age from 18 to 36 years (mean = 25.58. σ = 3.69). The path analysis tested the relationships simultaneously from stressors, in consecutive order, distractions, subpar performance and verbal abuse, to coping styles, first both avoidance-cognitive and approach-cognitive, and then approach-behaviour. Results indicated that the model achieved a good fit and that all paths tested simultaneously were significant. The distractions stressor was positively related to subpar performance, which, in turn, was positively related to verbal abuse. Verbal abuse was negatively associated with an avoidance-cognitive coping style and positively related to the approach-cognitive coping style. The results also supported a crossover effect of both avoidance-cognitive and approach-cognitive on approach-behaviour. One implication of this study is that coping should be studied in naturally occurring stages, a process-oriented approach. Another implication is that approach and avoidance coping styles, each sub-divided into cognitive and behavioural categories, provide a meaningful framework which provides sports officials a coherent structure for learning and improving ways to cope with acute stress experienced during the contest.

  1. Playing the role of weak clique property in link prediction: A friend recommendation model

    NASA Astrophysics Data System (ADS)

    Ma, Chuang; Zhou, Tao; Zhang, Hai-Feng

    2016-07-01

    An important fact in studying link prediction is that the structural properties of networks have significant impacts on the performance of algorithms. Therefore, how to improve the performance of link prediction with the aid of structural properties of networks is an essential problem. By analyzing many real networks, we find a typical structural property: nodes are preferentially linked to the nodes with the weak clique structure (abbreviated as PWCS to simplify descriptions). Based on this PWCS phenomenon, we propose a local friend recommendation (FR) index to facilitate link prediction. Our experiments show that the performance of FR index is better than some famous local similarity indices, such as Common Neighbor (CN) index, Adamic-Adar (AA) index and Resource Allocation (RA) index. We then explain why PWCS can give rise to the better performance of FR index in link prediction. Finally, a mixed friend recommendation index (labelled MFR) is proposed by utilizing the PWCS phenomenon, which further improves the accuracy of link prediction.

  2. Studying the immune response to human viral infections using zebrafish.

    PubMed

    Goody, Michelle F; Sullivan, Con; Kim, Carol H

    2014-09-01

    Humans and viruses have a long co-evolutionary history. Viral illnesses have and will continue to shape human history: from smallpox, to influenza, to HIV, and beyond. Animal models of human viral illnesses are needed in order to generate safe and effective antiviral medicines, adjuvant therapies, and vaccines. These animal models must support the replication of human viruses, recapitulate aspects of human viral illnesses, and respond with conserved immune signaling cascades. The zebrafish is perhaps the simplest, most commonly used laboratory model organism in which innate and/or adaptive immunity can be studied. Herein, we will discuss the current zebrafish models of human viral illnesses and the insights they have provided. We will highlight advantages of early life stage zebrafish and the importance of innate immunity in human viral illnesses. We will also discuss viral characteristics to consider before infecting zebrafish with human viruses as well as predict other human viruses that may be able to infect zebrafish.

  3. Studying the immune response to human viral infections using zebrafish

    PubMed Central

    Goody, Michelle F.; Sullivan, Con; Kim, Carol H.

    2014-01-01

    Humans and viruses have a long co-evolutionary history. Viral illnesses have and will continue to shape human history: from smallpox, to influenza, to HIV, and beyond. Animal models of human viral illnesses are needed in order to generate safe and effective antiviral medicines, adjuvant therapies, and vaccines. These animal models must support the replication of human viruses, recapitulate aspects of human viral illnesses, and respond with conserved immune signaling cascades. The zebrafish is perhaps the simplest, most commonly used laboratory model organism in which innate and/or adaptive immunity can be studied. Herein, we will discuss the current zebrafish models of human viral illnesses and the insights they have provided. We will highlight advantages of early life stage zebrafish and the importance of innate immunity in human viral illnesses. We will also discuss viral characteristics to consider before infecting zebrafish with human viruses as well as predict other human viruses that may be able to infect zebrafish. PMID:24718256

  4. Patient-Specific Computational Modeling of Keratoconus Progression and Differential Responses to Collagen Cross-linking

    PubMed Central

    Sinha Roy, Abhijit

    2011-01-01

    Purpose. To model keratoconus (KC) progression and investigate the differential responses of central and eccentric cones to standard and alternative collagen cross-linking (CXL) patterns. Methods. Three-dimensional finite element models (FEMs) were generated with clinical tomography and IOP measurements. Graded reductions in regional corneal hyperelastic properties and thickness were imposed separately in the less affected eye of a KC patient. Topographic results, including maximum curvature and first-surface, higher-order aberrations (HOAs), were compared to those of the more affected contralateral eye. In two eyes with central and eccentric cones, a standard broad-beam CXL protocol was simulated with 200- and 300-μm treatment depths and compared to spatially graded broad-beam and cone-centered CXL simulations. Results. In a model of KC progression, maximum curvature and HOA increased as regional corneal hyperelastic properties were decreased. A topographic cone could be generated without a reduction in corneal thickness. Simulation of standard 9-mm-diameter CXL produced decreases in corneal curvature comparable to clinical reports and affected cone location. A 100-μm increase in CXL depth enhanced flattening by 24% to 34% and decreased HOA by 22% to 31%. Topographic effects were greatest with cone-centered CXL simulations. Conclusions. Progressive hyperelastic weakening of a cornea with subclinical KC produced topographic features of manifest KC. The clinical phenomenon of topographic flattening after CXL was replicated. The magnitude and higher-order optics of this response depended on IOP and the spatial distribution of stiffening relative to the cone location. Smaller diameter simulated treatments centered on the cone provided greater reductions in curvature and HOA than a standard broad-beam CXL pattern. PMID:22039252

  5. Linking GIS-based models to value ecosystem services in an Alpine region.

    PubMed

    Grêt-Regamey, Adrienne; Bebi, Peter; Bishop, Ian D; Schmid, Willy A

    2008-11-01

    Planning frequently fails to include the valuation of public goods and services. This can have long-term negative economic consequences for a region. This is especially the case in mountainous regions such as the Alps, which depend on tourism and where land-use changes can negatively impact key ecosystem services and hence the economy. In this study, we develop a semi-automatic procedure to value ecosystem goods and services. Several existing process-based models linked to economic valuation methods are integrated into a geographic information system (GIS) platform. The model requires the input of a digital elevation model, a land-cover map, and a spatially explicit temperature dataset. These datasets are available for most regions in Europe. We illustrate the approach by valuing four ecosystem services: avalanche protection, timber production, scenic beauty, and habitat, which are supplied by the "Landschaft Davos", an administrative district in the Swiss Alps. We compare the impacts of a human development scenario and a climate scenario on the value of these ecosystem services. Urban expansion and tourist infrastructure developments have a negative impact on scenic beauty and habitats. These impacts outweigh the benefits of the developments in the long-term. Forest expansion, predictable under a climate change scenario, favours natural avalanche protection and habitats. In general, such non-marketed benefits provided by the case-study region more than compensate for the costs of forest maintenance. Finally, we discuss the advantages and disadvantages of the approach. Despite its limitations, we show how this approach could well help decision-makers balance the impacts of different planning options on the economic accounting of a region, and guide them in selecting sustainable and economically feasible development strategies.

  6. Accelerating Influenza Research: Vaccines, Antivirals, Immunomodulators and Monoclonal Antibodies. The Manufacture of a New Wild-Type H3N2 Virus for the Human Viral Challenge Model

    PubMed Central

    Fullen, Daniel J.; Noulin, Nicolas; Catchpole, Andrew; Fathi, Hosnieh; Murray, Edward J.; Mann, Alex; Eze, Kingsley; Balaratnam, Ganesh; Borley, Daryl W.; Gilbert, Anthony; Lambkin-Williams, Rob

    2016-01-01

    Background Influenza and its associated diseases are a major cause of morbidity and mortality. The United States Advisory Committee on Immunization Practices recommends influenza vaccination for everyone over 6 months of age. The failure of the flu vaccine in 2014–2015 demonstrates the need for a model that allows the rapid development of novel antivirals, universal/intra-seasonal vaccines, immunomodulators, monoclonal antibodies and other novel treatments. To this end we manufactured a new H3N2 influenza virus in compliance with Good Manufacturing Practice for use in the Human Viral Challenge Model. Methods and Strain Selection We chose an H3N2 influenza subtype, rather than H1N1, given that this strain has the most substantial impact in terms of morbidity or mortality annually as described by the Centre for Disease Control. We first subjected the virus batch to rigorous adventitious agent testing, confirmed the virus to be wild-type by Sanger sequencing and determined the virus titres appropriate for human use via the established ferret model. We built on our previous experience with other H3N2 and H1N1 viruses to develop this unique model. Human Challenge and Conclusions We conducted an initial safety and characterisation study in healthy adult volunteers, utilising our unique clinical quarantine facility in London, UK. In this study we demonstrated this new influenza (H3N2) challenge virus to be both safe and pathogenic with an appropriate level of disease in volunteers. Furthermore, by inoculating volunteers with a range of different inoculum titres, we established the minimum infectious titre required to achieve reproducible disease whilst ensuring a sensitive model that can be translated to design of subsequent field based studies. Trial Registration ClinicalTrials.gov NCT02525055 PMID:26761707

  7. Viral fitness: definitions, measurement, and current insights

    USGS Publications Warehouse

    Wargo, Andrew R.; Kurath, Gael

    2012-01-01

    Viral fitness is an active area of research, with recent work involving an expanded number of human, non-human vertebrate, invertebrate, plant, and bacterial viruses. Many publications deal with RNA viruses associated with major disease emergence events, such as HIV-1, influenza virus, and Dengue virus. Study topics include drug resistance, immune escape, viral emergence, host jumps, mutation effects, quasispecies diversity, and mathematical models of viral fitness. Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. This is essential for a more integrated understanding of overall viral fitness, with implications for disease management in the future.

  8. Linking land use change to recreational fishery valuation with a spatially explicit behavior model: A case study from Tampa Bay, FL USA

    EPA Science Inventory

    Drawing a link between habitat change and production and delivery of ecosystem services is a priority in coastal estuarine ecosystems. This link is needed to fully understand how human communities can influence ecosystem sustainability. Mechanistic modeling tools are highly fun...

  9. The Role of VP1 Amino Acid Residue 145 of Enterovirus 71 in Viral Fitness and Pathogenesis in a Cynomolgus Monkey Model

    PubMed Central

    Kataoka, Chikako; Suzuki, Tadaki; Kotani, Osamu; Iwata-Yoshikawa, Naoko; Nagata, Noriyo; Ami, Yasushi; Wakita, Takaji; Nishimura, Yorihiro; Shimizu, Hiroyuki

    2015-01-01

    Enterovirus 71 (EV71), a major causative agent of hand, foot, and mouth disease, occasionally causes severe neurological symptoms. We identified P-selectin glycoprotein ligand-1 (PSGL-1) as an EV71 receptor and found that an amino acid residue 145 in the capsid protein VP1 (VP1-145) defined PSGL-1-binding (PB) and PSGL-1-nonbinding (non-PB) phenotypes of EV71. However, the role of PSGL-1-dependent EV71 replication in neuropathogenesis remains poorly understood. In this study, we investigated viral replication, genetic stability, and the pathogenicity of PB and non-PB strains of EV71 in a cynomolgus monkey model. Monkeys were intravenously inoculated with cDNA-derived PB and non-PB strains of EV71, EV71-02363-EG and EV71-02363-KE strains, respectively, with two amino acid differences at VP1-98 and VP1-145. Mild neurological symptoms, transient lymphocytopenia, and inflammatory cytokine responses, were found predominantly in the 02363-KE-inoculated monkeys. During the early stage of infection, viruses were frequently detected in clinical samples from 02363-KE-inoculated monkeys but rarely in samples from 02363-EG-inoculated monkeys. Histopathological analysis of central nervous system (CNS) tissues at 10 days postinfection revealed that 02363-KE induced neuropathogenesis more efficiently than that induced by 02363-EG. After inoculation with 02363-EG, almost all EV71 variants detected in clinical samples, CNS, and non-CNS tissues, possessed a G to E amino acid substitution at VP1-145, suggesting a strong in vivo selection of VP1-145E variants and CNS spread presumably in a PSGL-1-independent manner. EV71 variants with VP1-145G were identified only in peripheral blood mononuclear cells in two out of four 02363-EG-inoculated monkeys. Thus, VP1-145E variants are mainly responsible for the development of viremia and neuropathogenesis in a non-human primate model, further suggesting the in vivo involvement of amino acid polymorphism at VP1-145 in cell-specific viral

  10. Vibro-acoustic modelling of aircraft double-walls with structural links using Statistical Energy Analysis

    NASA Astrophysics Data System (ADS)

    Campolina, Bruno L.

    The prediction of aircraft interior noise involves the vibroacoustic modelling of the fuselage with noise control treatments. This structure is composed of a stiffened metallic or composite panel, lined with a thermal and acoustic insulation layer (glass wool), and structurally connected via vibration isolators to a commercial lining panel (trim). The goal of this work aims at tailoring the noise control treatments taking design constraints such as weight and space optimization into account. For this purpose, a representative aircraft double-wall is modelled using the Statistical Energy Analysis (SEA) method. Laboratory excitations such as diffuse acoustic field and point force are addressed and trends are derived for applications under in-flight conditions, considering turbulent boundary layer excitation. The effect of the porous layer compression is firstly addressed. In aeronautical applications, compression can result from the installation of equipment and cables. It is studied analytically and experimentally, using a single panel and a fibrous uniformly compressed over 100% of its surface. When compression increases, a degradation of the transmission loss up to 5 dB for a 50% compression of the porous thickness is observed mainly in the mid-frequency range (around 800 Hz). However, for realistic cases, the effect should be reduced since the compression rate is lower and compression occurs locally. Then the transmission through structural connections between panels is addressed using a four-pole approach that links the force-velocity pair at each side of the connection. The modelling integrates experimental dynamic stiffness of isolators, derived using an adapted test rig. The structural transmission is then experimentally validated and included in the double-wall SEA model as an equivalent coupling loss factor (CLF) between panels. The tested structures being flat, only axial transmission is addressed. Finally, the dominant sound transmission paths are

  11. Linked-cluster expansion for the Green's function of the infinite-U Hubbard model.

    PubMed

    Khatami, Ehsan; Perepelitsky, Edward; Rigol, Marcos; Shastry, B Sriram

    2014-06-01

    We implement a highly efficient strong-coupling expansion for the Green's function of the Hubbard model. In the limit of extreme correlations, where the onsite interaction is infinite, the evaluation of diagrams simplifies dramatically enabling us to carry out the expansion to the eighth order in powers of the hopping amplitude. We compute the finite-temperature Green's function analytically in the momentum and Matsubara frequency space as a function of the electron density. Employing Padé approximations, we study the equation of state, Kelvin thermopower, momentum distribution function, quasiparticle fraction, and quasiparticle lifetime of the system at temperatures lower than, or of the order of, the hopping amplitude. We also discuss several different approaches for obtaining the spectral functions through analytic continuation of the imaginary frequency Green's function, and show results for the system near half filling. We benchmark our results for the equation of state against those obtained from a numerical linked-cluster expansion carried out to the eleventh order. PMID:25019906

  12. Three-Dimensional Characterization and Modeling of Microstructural Weak Links for Spall Damage in FCC Metals

    SciTech Connect

    Krishnan, Kapil; Brown, Andrew; Wayne, Leda; Vo, Johnathan; Opie, Saul; Lim, Harn; Peralta, Pedro; Luo, Sheng-Nian; Byler, Darrin; McClellan, Kenneth J.; Koskelo, Aaron; Dickerson, Robert

    2014-11-25

    Local microstructural weak links for spall damage were investigated using three-dimensional (3-D) characterization in multicrystalline copper samples (grain size ≈ 450 µm) shocked with laser-driven plates at low pressures (2 to 4 GPa). The thickness of samples and flyer plates, approximately 1000 and 500 µm respectively, led to short pressure pulses that allowed isolating microstructure effects on local damage characteristics. Electron Backscattering Diffraction and optical microscopy were used to relate the presence, size, and shape of porosity to local microstructure. The experiments were complemented with 3-D finite element simulations of individual grain boundaries (GBs) that resulted in large damage volumes using crystal plasticity coupled with a void nucleation and growth model. Results from analysis of these damage sites show that the presence of a GB-affected zone, where strain concentration occurs next to a GB, correlates strongly with damage localization at these sites, most likely due to the inability of maintaining strain compatibility across these interfaces, with additional effects due to the inclination of the GB with respect to the shock. Results indicate that strain compatibility plays an important role on intergranular spall damage in metallic materials.

  13. Three-Dimensional Characterization and Modeling of Microstructural Weak Links for Spall Damage in FCC Metals

    DOE PAGES

    Krishnan, Kapil; Brown, Andrew; Wayne, Leda; Vo, Johnathan; Opie, Saul; Lim, Harn; Peralta, Pedro; Luo, Sheng-Nian; Byler, Darrin; McClellan, Kenneth J.; et al

    2014-11-25

    Local microstructural weak links for spall damage were investigated using three-dimensional (3-D) characterization in multicrystalline copper samples (grain size ≈ 450 µm) shocked with laser-driven plates at low pressures (2 to 4 GPa). The thickness of samples and flyer plates, approximately 1000 and 500 µm respectively, led to short pressure pulses that allowed isolating microstructure effects on local damage characteristics. Electron Backscattering Diffraction and optical microscopy were used to relate the presence, size, and shape of porosity to local microstructure. The experiments were complemented with 3-D finite element simulations of individual grain boundaries (GBs) that resulted in large damage volumesmore » using crystal plasticity coupled with a void nucleation and growth model. Results from analysis of these damage sites show that the presence of a GB-affected zone, where strain concentration occurs next to a GB, correlates strongly with damage localization at these sites, most likely due to the inability of maintaining strain compatibility across these interfaces, with additional effects due to the inclination of the GB with respect to the shock. Results indicate that strain compatibility plays an important role on intergranular spall damage in metallic materials.« less

  14. A model linking biology, behavior and psychiatric diagnoses in perpetrators of domestic violence.

    PubMed

    George, David T; Phillips, Monte J; Doty, Linda; Umhau, John C; Rawlings, Robert R

    2006-01-01

    Research indicates that perpetrators of domestic violence have abnormalities in central serotonin and testosterone metabolism, an increased sensitivity to anxiogenic stimuli, and an impaired neuro-connection between their cortex and the amygdala. Clinical evaluations show that perpetrators of domestic violence also have a distinguishing set of behaviors and diagnoses related to anxiety, depression, intermittent explosive disorder, and borderline personality disorder. In this paper we propose a model to understand how the biological abnormalities can potentially explain the behaviors and diagnoses exhibited by the perpetrators. Changes in the perpetrator's neurotransmitters lead to a heightened sensitivity to environmental stimuli, anxiety, and conditioned fear. Lack of cortical input to the amygdala impairs the perpetrator's ability to extinguish anxiety and/or conditioned fear and gives rise to either innate behaviors (e.g., fight, flight, and shut down) or learned fear avoidant behaviors designed to avoid anxiety (e.g., alcohol consumption, self-injurious acts, and obsessive behaviors). Linking conditioned fear and fear avoidance to the behaviors and psychiatric diagnoses will serve to change the way the medical community perceives and treats perpetrators of domestic violence.

  15. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology.

    PubMed

    Fleet, Tiffany; Stashi, Erin; Zhu, Bokai; Rajapakshe, Kimal; Marcelo, Kathrina L; Kettner, Nicole M; Gorman, Blythe K; Coarfa, Cristian; Fu, Loning; O'Malley, Bert W; York, Brian

    2016-10-01

    Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2 We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2(-/-) and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver.

  16. Link between reduced nephron number and hypertension: studies in a mutant mouse model.

    PubMed

    Poladia, Deepali Pitre; Kish, Kayle; Kutay, Benjamin; Bauer, John; Baum, Michel; Bates, Carlton M

    2006-04-01

    Low birth weight (LBW) infants with reduced nephron numbers have significantly increased risk for hypertension later in life, which is a devastating health problem. The risk from a reduction in nephron number alone is not clear. Recently, using conditional knock-out approach, we have developed a mutant mouse with reduced nephron number in utero and no change in birth weight, by deleting fibroblast growth factor receptor 2 (fgfr2) in the ureteric bud. Our purpose was to investigate the role of in utero reduced nephron number alone in absence of LBW as a risk for developing hypertension in adulthood. Using tail cuff blood pressure measurements we observed significant increases in systolic blood pressure in one year old mutant mice versus controls. We also detected cardiac end-organ injury from hypertension as shown by significant increases in normalized heart weights, left ventricular (LV) wall thickness, and LV tissue area. Two-dimensional echocardiography revealed no changes in cardiac output and therefore significant increases in systemic vascular resistance in mutants versus controls. We also observed increases in serum blood urea nitrogen (BUN) levels and histologic evidence of glomerular and renal tubular injury in mutant mice versus controls. Thus, these studies suggest that our mutant mice may serve as a relevant model to study the link between reduction of nephron number in utero and the risk of hypertension and chronic renal failure in adulthood.

  17. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology.

    PubMed

    Fleet, Tiffany; Stashi, Erin; Zhu, Bokai; Rajapakshe, Kimal; Marcelo, Kathrina L; Kettner, Nicole M; Gorman, Blythe K; Coarfa, Cristian; Fu, Loning; O'Malley, Bert W; York, Brian

    2016-10-01

    Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2 We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2(-/-) and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver. PMID:27432117

  18. Effects of Shenqi Fuzheng injection on Fas/FasL protein expression levels in the cardiomyocytes of a mouse model of viral myocarditis

    PubMed Central

    WU, TIANMIN; CHEN, JINSHUI; FAN, LIUFANG; XIE, WENYAN; XU, CHANGSHENG; WANG, HUAJUN

    2016-01-01

    The aim of the present study was to examine the effects of Shenqi Fuzheng injection (SFI) on Fas and FasL protein expression levels in the cardiomyocytes of mice with viral myocarditis (VMC) and to explore the underlying anti-apoptotic mechanisms. A total of 120 male BALB/c mice were randomly divided into five groups as follows: Blank control group, model group, ribavirin group, low-dose SFI group and high-dose SFI group. The VMC model was established by the injection of coxsackievirus group B type 3 and saline, ribavirin or SFI was administered 30 min later. Cardiac samples were harvested from mice in each group on days 3, 10 and 30. Apoptosis of cardiac cells was examined using terminal deoxynucleotidyl transferase dUTP nick-end labeling, and Fas and FasL protein expression levels were detected using immunohistochemistry. Myocardial apoptosis and Fas/FasL protein expression levels were significantly increased in the model group, as compared with the blank group (P<0.01), whereas the apoptotic index (AI) and Fas/FasL protein expression levels of cardiac cells in the high-dose SFI group were significantly decreased compared with those in the model group on day 10 (acute phase; P<0.01). The AI and Fas/FasL protein expression levels of cardiac cells in the low- and high-dose SFI groups were also significantly decreased on day 30 (chronic phase; P<0.01); however, no differences between the high- and low-dose groups were detected. In conclusion, SFI relieves VMC via the downregulation of Fas and FasL protein expression and the inhibition of cell apoptosis. PMID:27168814

  19. IrBurst Modeling and Performance Evaluation for Large Data Block Exchange over High-Speed IrDA Links

    NASA Astrophysics Data System (ADS)

    Alam, Mohammad Shah; Shawkat, Shamim Ara; Kitazumi, Gontaro; Matsumoto, Mitsuji

    IrBurst, recently proposed by IrDA, is a high speed information transmission protocol. In this paper, a mathematical model is developed which leads to derivation of the IrBurst throughput over the IrDA protocol stack. Based on this model, we compare the performance of IrBurst and existing OBEX protocol in order to investigate the suitability of IrBurst protocol for exchange of large data blocks over high-speed IrDA links. Furthermore, the model allows the evaluation of the impact of the link layer parameters, such as window size and frame length, and physical layer parameters, such as minimum turnaround time, on system through-put for high-speed IrDA links and in the presence of transmission errors. Consequently, an effective Automatic Repeat Request (ARQ) scheme is proposed at link layer to maximize the throughput efficiency for IrBurst protocol as well as for next generation high speed IrDA links. Simulation result indicates that employment of our proposed ARQ scheme results in significant improvement of IrBurst throughput efficiency at high bit error rates.

  20. An affine continuum mechanical model for cross-linked F-actin networks with compliant linker proteins.

    PubMed

    Holzapfel, Gerhard A; Unterberger, Michael J; Ogden, Ray W