WorldWideScience

Sample records for model replication program

  1. Characterization of the replication timing program of 6 human model cell lines

    Directory of Open Access Journals (Sweden)

    Djihad Hadjadj

    2016-09-01

    Full Text Available During the S-phase, the DNA replication process is finely orchestrated and regulated by two programs: the spatial program that determines where replication will start in the genome (Cadoret et al. (2008 Oct 14, Cayrou et al. (2011 Sep, Picard et al. (2014 May 1 [1–3], and the temporal program that determines when during the S phase different parts of the genome are replicated and when origins are activated. The temporal program is so well conserved for each cell type from independent individuals [4] that it is possible to identify a cell type from an unknown sample just by determining its replication timing program. Moreover, replicative domains are strongly correlated with the partition of the genome into topological domains (determined by the Hi-C method, Lieberman-Aiden et al. (2009 Oct 9, Pope et al. (2014 Nov 20 [5,6]. On the one hand, replicative areas are well defined and participate in shaping the spatial organization of the genome for a given cell type. On the other hand, studies on the timing program during cell differentiation showed a certain plasticity of this program according to the stage of cell differentiation Hiratani et al. (2008 Oct 7, 2010 Feb [7,8]. Domains where a replication timing change was observed went through a nuclear re-localization. Thus the temporal program of replication can be considered as an epigenetic mark Hiratani and Gilbert (2009 Feb 16 [9]. We present the genomic data of replication timing in 6 human model cell lines: U2OS (GSM2111308, RKO (GSM2111309, HEK 293T (GSM2111310, HeLa (GSM2111311, MRC5-SV (GSM2111312 and K562 (GSM2111313. A short comparative analysis was performed that allowed us to define regions common to the 6 cell lines. These replication timing data can be taken into account when performing studies that use these model cell lines.

  2. Implementing three evidence-based program models: early lessons from the Teen Pregnancy Prevention Replication Study.

    Science.gov (United States)

    Kelsey, Meredith; Layzer, Jean

    2014-03-01

    This article describes some of the early implementation challenges faced by nine grantees participating in the Teen Pregnancy Prevention Replication Study and their response to them. The article draws on information collected as part of a comprehensive implementation study. Sources include site and program documents; program officer reports; notes from site investigation, selection and negotiation; ongoing communications with grantees as part of putting the study into place; and semi-structured interviews with program staff. The issues faced by grantees in implementing evidence-based programs designed to prevent teen pregnancy varied by program model. Grantees implementing a classroom-based curriculum faced challenges in delivering the curriculum within the constraints of school schedules and calendars (program length and size of class). Grantees implementing a culturally tailored curriculum faced a series of challenges, including implementing the intervention as part of the regular school curriculum in schools with diverse populations; low attendance when delivered as an after-school program; and resistance on the part of schools to specific curriculum content. The third set of grantees, implementing a program in clinics, faced challenges in identifying and recruiting young women into the program and in retaining young women once they were in the program. The experiences of these grantees reflect some of the complexities that should be carefully considered when choosing to replicate evidence-based programs. The Teen Pregnancy Prevention replication study will provide important context for assessing the effectiveness of some of the more widely replicated evidence-based programs. Copyright © 2014 Society for Adolescent Health and Medicine. All rights reserved.

  3. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  4. Adressing Replication and Model Uncertainty

    DEFF Research Database (Denmark)

    Ebersberger, Bernd; Galia, Fabrice; Laursen, Keld

    innovation survey data for France, Germany and the UK, we conduct a ‘large-scale’ replication using the Bayesian averaging approach of classical estimators. Our method tests a wide range of determinants of innovation suggested in the prior literature, and establishes a robust set of findings on the variables...... which shape the introduction of new to the firm and new to the world innovations. We provide some implications for innovation research, and explore the potential application of our approach to other domains of research in strategic management.......Many fields of strategic management are subject to an important degree of model uncertainty. This is because the true model, and therefore the selection of appropriate explanatory variables, is essentially unknown. Drawing on the literature on the determinants of innovation, and by analyzing...

  5. Factor Copula Models for Replicated Spatial Data

    KAUST Repository

    Krupskii, Pavel

    2016-12-19

    We propose a new copula model that can be used with replicated spatial data. Unlike the multivariate normal copula, the proposed copula is based on the assumption that a common factor exists and affects the joint dependence of all measurements of the process. Moreover, the proposed copula can model tail dependence and tail asymmetry. The model is parameterized in terms of a covariance function that may be chosen from the many models proposed in the literature, such as the Matérn model. For some choice of common factors, the joint copula density is given in closed form and therefore likelihood estimation is very fast. In the general case, one-dimensional numerical integration is needed to calculate the likelihood, but estimation is still reasonably fast even with large data sets. We use simulation studies to show the wide range of dependence structures that can be generated by the proposed model with different choices of common factors. We apply the proposed model to spatial temperature data and compare its performance with some popular geostatistics models.

  6. Modelling the Replication Management in Information Systems

    Directory of Open Access Journals (Sweden)

    Cezar TOADER

    2017-01-01

    Full Text Available In the modern economy, the benefits of Web services are significant because they facilitates the activities automation in the framework of Internet distributed businesses as well as the cooperation between organizations through interconnection process running in the computer systems. This paper presents the development stages of a model for a reliable information system. This paper describes the communication between the processes within the distributed system, based on the message exchange, and also presents the problem of distributed agreement among processes. A list of objectives for the fault-tolerant systems is defined and a framework model for distributed systems is proposed. This framework makes distinction between management operations and execution operations. The proposed model promotes the use of a central process especially designed for the coordination and control of other application processes. The execution phases and the protocols for the management and the execution components are presented. This model of a reliable system could be a foundation for an entire class of distributed systems models based on the management of replication process.

  7. Modeling HIV-1 intracellular replication: two simulation approaches

    NARCIS (Netherlands)

    Zarrabi, N.; Mancini, E.; Tay, J.; Shahand, S.; Sloot, P.M.A.

    2010-01-01

    Many mathematical and computational models have been developed to investigate the complexity of HIV dynamics, immune response and drug therapy. However, there are not many models which consider the dynamics of virus intracellular replication at a single level. We propose a model of HIV intracellular

  8. Sabin-to-Mahoney Transition Model of Quasispecies Replication

    Energy Technology Data Exchange (ETDEWEB)

    2009-05-31

    Qspp is an agent-based stochastic simulation model of the Poliovirus Sabin-to-Mahoney transition. This code simulates a cell-to-cell model of Poliovirus replication. The model tracks genotypes (virus genomes) as they are replicated in cells, and as the cells burst and release particles into the medium of a culture dish. An inoculum is then taken from the pool of virions and is used to inoculate cells on a new dish. This process repeats. The Sabin genotype comprises the initial inoculum. Nucleotide positions that match the Sabin1 (vaccine strain) and Mahoney (wild type) genotypes, as well as the neurovirulent phenotype (from the literature) are enumerated as constants.

  9. Mathematical models of HIV replication and pathogenesis.

    Science.gov (United States)

    Wodarz, Dominik

    2014-01-01

    This review outlines how mathematical models have been helpful, and continue to be so, for obtaining insights into the in vivo dynamics of HIV infection. The review starts with a discussion of a basic mathematical model that has been frequently used to study HIV dynamics. Some crucial results are described, including the estimation of key parameters that characterize the infection, and the generation of influential theories which argued that in vivo virus evolution is a key player in HIV pathogenesis. Subsequently, more recent concepts are reviewed that have relevance for disease progression, including the multiple infection of cells and the direct cell-to-cell transmission of the virus through the formation of virological synapses. These are important mechanisms that can influence the rate at which HIV spreads through its target cell population, which is tightly linked to the rate at which the disease progresses towards AIDS.

  10. Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.

    Science.gov (United States)

    Foti, Rossana; Gnan, Stefano; Cornacchia, Daniela; Dileep, Vishnu; Bulut-Karslioglu, Aydan; Diehl, Sarah; Buness, Andreas; Klein, Felix A; Huber, Wolfgang; Johnstone, Ewan; Loos, Remco; Bertone, Paul; Gilbert, David M; Manke, Thomas; Jenuwein, Thomas; Buonomo, Sara C B

    2016-01-21

    DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control and biological function of the replication-timing program are unclear. Rif1 is required for normal genome-wide regulation of replication timing, but its molecular function is poorly understood. Here we show that in mouse embryonic stem cells, Rif1 coats late-replicating domains and, with Lamin B1, identifies most of the late-replicating genome. Rif1 is an essential determinant of replication timing of non-Lamin B1-bound late domains. We further demonstrate that Rif1 defines and restricts the interactions between replication-timing domains during the G1 phase, thereby revealing a function of Rif1 as organizer of nuclear architecture. Rif1 loss affects both number and replication-timing specificity of the interactions between replication-timing domains. In addition, during the S phase, Rif1 ensures that replication of interacting domains is temporally coordinated. In summary, our study identifies Rif1 as the molecular link between nuclear architecture and replication-timing establishment in mammals. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Replicability and models of priming: What a resource computation framework can tell us about expectations of replicability

    NARCIS (Netherlands)

    Cesario, J.; Jonas, K.J.

    2014-01-01

    In this article, we argue that whether or not a replication attempt is informative is dependent on the accuracy of one's underlying model to explain the effect, as it is the explanatory model that enumerates the contingencies necessary for producing the effect. If the model is incorrect, then a

  12. Evaluating the SOS suicide prevention program: a replication and extension

    Directory of Open Access Journals (Sweden)

    Glanovsky Jaime

    2007-07-01

    Full Text Available Abstract Background Suicide is a leading cause of death for children and youth in the United States. Although school based programs have been the principal vehicle for youth suicide prevention efforts for over two decades, few have been systematically evaluated. This study examined the effectiveness of the Signs of Suicide (SOS prevention program in reducing suicidal behavior. Methods 4133 students in 9 high schools in Columbus, Georgia, western Massachusetts, and Hartford, Connecticut were randomly assigned to intervention and control groups during the 2001–02 and 2002–03 school years. Self-administered questionnaires were completed by students in both groups approximately 3 months after program implementation. Results Significantly lower rates of suicide attempts and greater knowledge and more adaptive attitudes about depression and suicide were observed among students in the intervention group. Students' race/ethnicity, grade, and gender did not alter the impact of the intervention on any of the outcomes assessed in this analysis. Conclusion This study has confirmed preliminary analysis of Year 1 data with a larger and more racially and socio-economically diverse sample. SOS continues to be the only universal school-based suicide prevention program to demonstrate significant effects of self-reported suicide attempts in a study utilizing a randomized experimental design. Moreover, the beneficial effects of SOS were observed among high school-aged youth from diverse racial/ethnic backgrounds, highlighting the program's utility as a universal prevention program. Trial registration clinicaltrials.gov NCT000387855.

  13. Replicating the MamaToto Program in Rural Tanzania (IMCHA ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    The project team will engage district leaders, strengthen facility services, and develop the role of community health workers. They will demonstrate if and how community-based interventions can reduce maternal and child mortality by effectively bringing low-cost program efforts to scale under government leadership.

  14. Preon Model and Family Replicated E_6 Unification

    Directory of Open Access Journals (Sweden)

    Larisa V. Laperashvili

    2008-02-01

    Full Text Available Previously we suggested a new preon model of composite quark-leptons and bosons with the 'flipped' $E_6imes widetilde{E_6}$ gauge symmetry group. We assumed that preons are dyons having both hyper-electric $g$ and hyper-magnetic $ilde g$ charges, and these preons-dyons are confined by hyper-magnetic strings which are an ${f N}=1$ supersymmetric non-Abelian flux tubes created by the condensation of spreons near the Planck scale. In the present paper we show that the existence of the three types of strings with tensions $T_k=k T_0$ $(k = 1,2,3$ producing three (and only three generations of composite quark-leptons, also provides three generations of composite gauge bosons ('hyper-gluons' and, as a consequence, predicts the family replicated $[E_6]^3$ unification at the scale $sim 10^{17}$ GeV. This group of unification has the possibility of breaking to the group of symmetry: $ [SU(3_C]^3imes [SU(2_L]^3imes [U(1_Y]^3 imes [U(1_{(B-L}]^3$ which undergoes the breakdown to the Standard Model at lower energies. Some predictive advantages of the family replicated gauge groups of symmetry are briefly discussed.

  15. A joint model for multivariate hierarchical semicontinuous data with replications.

    Science.gov (United States)

    Kassahun-Yimer, Wondwosen; Albert, Paul S; Lipsky, Leah M; Nansel, Tonja R; Liu, Aiyi

    2017-01-01

    Longitudinal data are often collected in biomedical applications in such a way that measurements on more than one response are taken from a given subject repeatedly overtime. For some problems, these multiple profiles need to be modeled jointly to get insight on the joint evolution and/or association of these responses over time. In practice, such longitudinal outcomes may have many zeros that need to be accounted for in the analysis. For example, in dietary intake studies, as we focus on in this paper, some food components are eaten daily by almost all subjects, while others are consumed episodically, where individuals have time periods where they do not eat these components followed by periods where they do. These episodically consumed foods need to be adequately modeled to account for the many zeros that are encountered. In this paper, we propose a joint model to analyze multivariate hierarchical semicontinuous data characterized by many zeros and more than one replicate observations at each measurement occasion. This approach allows for different probability mechanisms for describing the zero behavior as compared with the mean intake given that the individual consumes the food. To deal with the potentially large number of multivariate profiles, we use a pairwise model fitting approach that was developed in the context of multivariate Gaussian random effects models with large number of multivariate components. The novelty of the proposed approach is that it incorporates: (1) multivariate, possibly correlated, response variables; (2) within subject correlation resulting from repeated measurements taken from each subject; (3) many zero observations; (4) overdispersion; and (5) replicate measurements at each visit time.

  16. Supplementary Material for: Factor Copula Models for Replicated Spatial Data

    KAUST Repository

    Krupskii, Pavel

    2016-01-01

    We propose a new copula model that can be used with replicated spatial data. Unlike the multivariate normal copula, the proposed copula is based on the assumption that a common factor exists and affects the joint dependence of all measurements of the process. Moreover, the proposed copula can model tail dependence and tail asymmetry. The model is parameterized in terms of a covariance function that may be chosen from the many models proposed in the literature, such as the Matérn model. For some choice of common factors, the joint copula density is given in closed form and therefore likelihood estimation is very fast. In the general case, one-dimensional numerical integration is needed to calculate the likelihood, but estimation is still reasonably fast even with large data sets. We use simulation studies to show the wide range of dependence structures that can be generated by the proposed model with different choices of common factors. We apply the proposed model to spatial temperature data and compare its performance with some popular geostatistics models.

  17. A Culturally Responsive Approach to Improving Replication of a Youth Sexual Health Program.

    Science.gov (United States)

    Mwaria, Mercy; Chen, ChiaChing; Coppola, Nanci; Maurice, Ingrid; Phifer, Mary

    2016-11-01

    Youth-serving agencies continually turn to evidence-based interventions that have been empirically assessed for effectiveness in influencing young people's lives, particularly those living in communities with considerable health inequities. Replicating promising evidence-based interventions requires thoughtful adaptation and modification to better fit participants' sociocultural context and to enhance their learning experiences. Due to the restrictive nature of a replication model, adaptations to the intervention curriculum must be minimized during full implementation. Implementers must find innovative ways to ensure content is relevant and engaging to participants without altering core elements of the curriculum. This article describes practical best practice strategies used in implementing a sexual health education program among socioculturally diverse youth in a northeastern city in the United States. The implementing agency applied Richard, Brown and Forde's framework for culturally responsive pedagogy as a heuristic approach to describe the application of implementation practices across three dimensions: institutional, personal, and instructional. The results not only highlight successful culturally responsive practices that enhanced the implementation process but also acknowledge areas in which such practices proved daunting to implement. © 2016 Society for Public Health Education.

  18. Replication of surface features from a master model to an amorphous metallic article

    Science.gov (United States)

    Johnson, William L.; Bakke, Eric; Peker, Atakan

    1999-01-01

    The surface features of an article are replicated by preparing a master model having a preselected surface feature thereon which is to be replicated, and replicating the preselected surface feature of the master model. The replication is accomplished by providing a piece of a bulk-solidifying amorphous metallic alloy, contacting the piece of the bulk-solidifying amorphous metallic alloy to the surface of the master model at an elevated replication temperature to transfer a negative copy of the preselected surface feature of the master model to the piece, and separating the piece having the negative copy of the preselected surface feature from the master model.

  19. Business Model and Replication Study of BIG HIT

    DEFF Research Database (Denmark)

    Zhao, Guangling; Ravn Nielsen, Eva

    . The BIG HIT project is creating a replicable hydrogen territory in Orkney (An island archipelago six miles offshore from North of Mainland Scotland.) by implementing a fully integrated model of hydrogen production, storage, distribution of the hydrogen across Orkney and utilised for mobility, heat...... and power. The BIG HIT project will use otherwise curtailed electricity from one wind turbine on Shapinsay and one wind turbine and a tidal test sites on Eday, and use 1.5 MW of Polymer Electrolyte Membrane (PEM) electrolyser to convert it into ~50 t pa of hydrogen. This will be used to provide heat...... and infrastructure investment and operation cost of electricity and water consumption. The functional unit is 1 kg hydrogen produced and consumed. The data collected from the project patterns and suppliers. The current analysis is based on the estimation of hydrogen production and consumption on both Shapinsay...

  20. Replication of urban innovations - prioritization of strategies for the replication of Dhaka's community-based decentralized composting model.

    Science.gov (United States)

    Yedla, Sudhakar

    2012-01-01

    Dhaka's community-based decentralized composting (DCDC) is a successful demonstration of solid waste management by adopting low-cost technology, local resources community participation and partnerships among the various actors involved. This paper attempts to understand the model, necessary conditions, strategies and their priorities to replicate DCDC in the other developing cities of Asia. Thirteen strategies required for its replication are identified and assessed based on various criteria, namely transferability, longevity, economic viability, adaptation and also overall replication. Priority setting by multi-criteria analysis by applying analytic hierarchy process revealed that immediate transferability without long-term and economic viability consideration is not advisable as this would result in unsustainable replication of DCDC. Based on the analysis, measures to ensure the product quality control; partnership among stakeholders (public-private-community); strategies to achieve better involvement of the private sector in solid waste management (entrepreneurship in approach); simple and low-cost technology; and strategies to provide an effective interface among the complementing sectors are identified as important strategies for its replication.

  1. PASHA: facilitating the replication and use of effective adolescent pregnancy and STI/HIV prevention programs.

    Science.gov (United States)

    Card, Josefina J; Lessard, Laura; Benner, Tabitha

    2007-03-01

    It is important that interventions that have been shown effective in changing risky behavior be disseminated, so that they can be replicated (implemented in a new site) and so that their effectiveness in a new setting can be investigated. This article provides an update on an innovative resource for promoting the replication of effective teen pregnancy and STI/HIV prevention programs. The resource is called the Program Archive on Sexuality, Health & Adolescence (PASHA). A Scientist Expert Panel rates candidate adolescent pregnancy and STI/HIV prevention programs based on the strength of the evidence of their effectiveness in changing risky sexual behavior among youth ages 10-19 (10-21 for STI/HIV prevention programs). Developers of selected programs are invited to make their program and evaluation materials publicly available through PASHA. PASHA publishes and disseminates replication kits for programs it successfully acquires. Fifty-six programs have been selected by PASHA's Scientist Expert Panel as "effective" in changing one or more risky behaviors associated with adolescent pregnancy or STI/HIV. Complete program and evaluation materials from 35 of these programs are now currently available through PASHA, five are pending, 12 are publicly available from other sources, and only four are not publicly available. PASHA programs are aimed at a diverse target population and cover diverse content on many abstinence and contraception/condom-related topics. Many pedagogical techniques are used to effect behavior change, noticeably role play and group discussion. PASHA illustrates well the productive research-to-practice feedback loop that is the backbone of "translation research." The resource can be used by adolescent pregnancy and STI/HIV prevention practitioners to put what works to work to continue the lowering of the nation's adolescent pregnancy and STI/HIV rates.

  2. The tripartite influence model of body image and eating disturbance: A replication with adolescent girls.

    Science.gov (United States)

    Shroff, Hemal; Thompson, J Kevin

    2006-03-01

    The tripartite influence model of body image and eating disturbance is a recent theoretical approach that includes a test of direct (peer, parental, and media factors) and mediational links (internalization of societal appearance standards, appearance comparison processes) as factors potentially leading to body dissatisfaction and eating disturbance. The theory was evaluated in the current study in a sample of 391 adolescent females. A structural equation model that evaluated the tripartite model replicated previous findings reported by Keery, van den Berg and Thompson (2004) [Keery, H., van den Berg, & Thompson, J. K. (2004). A test of the tripartite influence model of body image and eating disturbance in adolescent girls. Body Image: An International Journal of Research, 1, 237-251.]. Additionally, a second model extended these findings, suggesting that peer and media influences are more important than parental influences. The results are discussed in light of the need for prevention programs to incorporate formative influences and mediational processes in the construction of intervention strategies.

  3. Effects of Baltimore's Safe Streets Program on gun violence: a replication of Chicago's CeaseFire Program.

    Science.gov (United States)

    Webster, Daniel W; Whitehill, Jennifer Mendel; Vernick, Jon S; Curriero, Frank C

    2013-02-01

    Chicago's CeaseFire program is an evidence-based public health approach to preventing gun violence. Baltimore is one of many US cities attempting to replicate the program. We compared changes in the number of homicide and nonfatal shooting incidents per month in four intervention neighborhoods with changes in high-crime comparison areas (police posts) without the intervention, while controlling for several measures of police activity and baseline levels of homicide and nonfatal shootings. In South Baltimore there were large program-related reductions in homicide and nonfatal shooting incidents. Among three East Baltimore program sites, the program was associated with a reduction of homicides in one area, a reduction in nonfatal shootings in another area, and a simultaneous increase in homicides and decrease in nonfatal shootings in another area. In some instances, program effects extended to neighborhoods bordering the intervention areas. Program-related reductions in homicides appear to be linked with conflict mediations conducted by program outreach workers.

  4. [Replication of a computer model of auditory hallucinations in schizophrenia].

    Science.gov (United States)

    de la Fuente-Sandoval, C; Portillo, V; Fresán, A; Apiquian, R

    2005-01-01

    Abnormal synaptic pruning has been proposed by some authors as a theory to explain schizophrenia. It has been studied in different ways, some of which are computerized models. A PC computer with MATLAB version 5.3 and Neural Networks Toolbox programs were used. To reproduce the model we used Elman's network for neuronal unit and McGlashan and Hoffman's network. The corrected percentage of detection improved as synapses were prunned. It increased from 68% to 91 %, reaching the highest detection level when 60% of the synapses were eliminated. Detection capacity was reduced when synaptic elimination continued and the program started detecting words in the absence of input. This was considered as a hallucination. When pruning reached from 80% to 95%, hallucinations occurred more frequently. The computer simulation model provides a symptom formation model, and also a way of understanding pruning's adaptative utility. When the neuronal units were eliminated (instead of connections), there was only progressive worsening in word perception. This confirms the hypothesis proposed that schizophrenia pathophysiology underlies neuronal connections, not the neurons.

  5. Mediate evaluation of replicating a Training Program in Nonverbal Communication in Gerontology

    Directory of Open Access Journals (Sweden)

    Teresa Cristina Gioia Schimidt

    2015-04-01

    Full Text Available OBJECTIVE Replicating the training program in non-verbal communication based on the theoretical framework of interpersonal communication; non-verbal coding, valuing the aging aspects in the perspective of active aging, checking its current relevance through the content assimilation index after 90 days (mediate of its application. METHOD A descriptive and exploratory field study was conducted in three hospitals under direct administration of the state of São Paulo that caters exclusively to Unified Health System (SUS patients. The training lasted 12 hours divided in three meetings, applied to 102 health professionals. RESULTS Revealed very satisfactory and satisfactory mediate content assimilation index in 82.9%. CONCLUSION The program replication proved to be relevant and updated the setting of hospital services, while remaining efficient for healthcare professionals.

  6. The tripartite influence model of body image and eating disturbance: a replication with a Japanese sample.

    Science.gov (United States)

    Yamamiya, Yuko; Shroff, Hemal; Thompson, J Kevin

    2008-01-01

    To examine the tripartite influence model of body image and eating disturbance as a viable sociocultural explanation for the development of eating and body image problems with young Japanese females. A sample of 289 Japanese female undergraduates completed a variety of measures designed to index family, peer, and media influences, as well as levels of body dissatisfaction, eating disturbances, and self-esteem. The data were evaluated with structural equation modeling to test the tripartite model. Fit indices indicated a moderate fit to the overall tripartite model, replicating previous findings. This study suggests that the sociocultural variables found to influence body image and eating disturbances in Japan are similar to those observed with US samples. The implications for prevention and intervention programs are discussed.

  7. Programming Models in HPC

    Energy Technology Data Exchange (ETDEWEB)

    Shipman, Galen M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-06-13

    These are the slides for a presentation on programming models in HPC, at the Los Alamos National Laboratory's Parallel Computing Summer School. The following topics are covered: Flynn's Taxonomy of computer architectures; single instruction single data; single instruction multiple data; multiple instruction multiple data; address space organization; definition of Trinity (Intel Xeon-Phi is a MIMD architecture); single program multiple data; multiple program multiple data; ExMatEx workflow overview; definition of a programming model, programming languages, runtime systems; programming model and environments; MPI (Message Passing Interface); OpenMP; Kokkos (Performance Portable Thread-Parallel Programming Model); Kokkos abstractions, patterns, policies, and spaces; RAJA, a systematic approach to node-level portability and tuning; overview of the Legion Programming Model; mapping tasks and data to hardware resources; interoperability: supporting task-level models; Legion S3D execution and performance details; workflow, integration of external resources into the programming model.

  8. Modeling EERE deployment programs

    Energy Technology Data Exchange (ETDEWEB)

    Cort, K. A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hostick, D. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Belzer, D. B. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Livingston, O. V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2007-11-01

    The purpose of the project was to identify and characterize the modeling of deployment programs within the EERE Technology Development (TD) programs, address possible improvements to the modeling process, and note gaps in knowledge for future research.

  9. A dynamic replicator model of the players' bids in an oligopolistic electricity market

    International Nuclear Information System (INIS)

    Sahraei-Ardakani, Mostafa; Rahimi-Kian, Ashkan

    2009-01-01

    In this paper, the replicator dynamics of the power suppliers' bids in an oligopolistic electricity market are derived for both the fixed and variable demand cases. The replicator dynamics stability analysis is also performed. The dynamics of the electricity markets are the results of players' decisions. The physical parameters of the power systems (such as the lines capacities, voltage limitations, etc.) also affect the market dynamics indirectly, through the changes in players' behaviors. Assuming rational players, an optimal bidding strategy for constructing the supply function (SF) of a generating firm is presented and based on that, the dynamics of the bid replicators are studied. Both fixed demands and price sensitive demands are taken into account. The replicator model is presented in the well-known state space structure. A case study is presented to show the applicability of the developed dynamic replicator bid model, and also to show how the Nash-SFE equilibrium evolves over time. (author)

  10. Modeling EERE Deployment Programs

    Energy Technology Data Exchange (ETDEWEB)

    Cort, K. A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hostick, D. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Belzer, D. B. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Livingston, O. V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2007-11-01

    This report compiles information and conclusions gathered as part of the “Modeling EERE Deployment Programs” project. The purpose of the project was to identify and characterize the modeling of deployment programs within the EERE Technology Development (TD) programs, address possible improvements to the modeling process, and note gaps in knowledge in which future research is needed.

  11. Los Alamos Programming Models

    Energy Technology Data Exchange (ETDEWEB)

    Bergen, Benjamin Karl [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-07-07

    This is the PDF of a powerpoint presentation from a teleconference on Los Alamos programming models. It starts by listing their assumptions for the programming models and then details a hierarchical programming model at the System Level and Node Level. Then it details how to map this to their internal nomenclature. Finally, a list is given of what they are currently doing in this regard.

  12. Dynamical role of the degree of intraspecific cooperation: A simple model for prebiotic replicators and ecosystems

    Science.gov (United States)

    Fontich, Ernest; Sardanyés, Josep

    2009-05-01

    We present a simple mean field model to analyze the dynamics of competition between two populations of replicators in terms of the degree of intraspecific cooperation (i.e., autocatalysis) in one of these populations. The first population can only replicate with Malthusian kinetics while the second one can reproduce with Malthusian or autocatalytic replication or with a combination of both reproducing strategies. The model consists of two coupled, nonlinear, autonomous ordinary differential equations. We investigate analytically and numerically the phase plane dynamics and the bifurcation scenarios of this ecologically coupled system, focusing on the outcome of competition for several degrees of intraspecific cooperation, σ, in the second population of replicators. We demonstrate that the dynamics of both populations can not be governed by a limit cycle, and also that once cooperation is considered, the topology of phase space does not allow for coexistence. Even for low values of the degree of intraspecific cooperation, for large enough autocatalytic replication rates, the second population of replicators is able to outcompete the first one, having a wide basin of attraction in state space. We characterize the same power law dependence between the outcompetition extinction times, τ, and the degree of intraspecific cooperation for both populations, given by τ˜ciσ-1. Our results suggest that, under some kinetic conditions, the appearance of autocatalysis might be favorable in a population of replicators growing with Malthusian kinetics competing with another population also reproducing exponentially.

  13. 75 FR 39220 - Charter Schools Program (CSP) Grants for Replication and Expansion of High-Quality Charter Schools

    Science.gov (United States)

    2010-07-08

    ... DEPARTMENT OF EDUCATION Charter Schools Program (CSP) Grants for Replication and Expansion of High-Quality Charter Schools AGENCY: Office of Innovation and Improvement, Department of Education. ACTION... notice inviting applications for new awards for FY 2010 for the Charter Schools Program Grants for...

  14. Replication/Implementation Model Field Test: Project SHAL.

    Science.gov (United States)

    Achilles, C. M.; Young, Rufus, Jr.

    This document reports findings of a study that evaluated the implementation model developed for Project SHAL, an "effective schools" reform model. Implemented in 1980 in Area I of the St. Louis Public School District (Missouri), Project SHAL is an acronym for the four original participating schools--Stowe, Hempstead, Arlington, and…

  15. Modelling protocells the emergent synchronization of reproduction and molecular replication

    CERN Document Server

    Serra, Roberto

    2017-01-01

    The monograph discusses models of synthetic protocells, which are cell-like structures obtained from non-living matter endowed with some rudimentary kind of metabolism and genetics, but much simpler than biological cells. They should grow and proliferate, generating offsprings that resemble in some way the parent protocells with some variation, so that selection may take place. Sustainable protocell populations have not yet been obtained experimentally and mathematical models are therefore extremely important to address key questions concerning their synthesis and behavior. Different protocell “architectures” have been proposed and high-level abstract models like those that are presented in this book are particularly relevant to gain a better understanding of the different properites. These models are able to treat all the major dynamical phenomena in a unified framework, so they can be seen as “virtual laboratories” for protocell research. Particular attention is paid to the problem of synchronizatio...

  16. Modeling EERE Deployment Programs

    Energy Technology Data Exchange (ETDEWEB)

    Cort, Katherine A.; Hostick, Donna J.; Belzer, David B.; Livingston, Olga V.

    2007-11-08

    The purpose of this report is to compile information and conclusions gathered as part of three separate tasks undertaken as part of the overall project, “Modeling EERE Deployment Programs,” sponsored by the Planning, Analysis, and Evaluation office within the Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE). The purpose of the project was to identify and characterize the modeling of deployment programs within the EERE Technology Development (TD) programs, address improvements to modeling in the near term, and note gaps in knowledge where future research is needed.

  17. 3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle

    KAUST Repository

    Knodel, Markus

    2017-10-02

    Mathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors. The NSPs are responsible for the replication of the vRNA and their movement is restricted to the ER surface. Therefore, in this study we developed fully spatio-temporal resolved models of the vRNA replication cycle of HCV. Our simulations are performed upon realistic reconstructed cell structures-namely the ER surface and the membranous webs-based on data derived from immunostained cells replicating HCV vRNA. We visualized 3D simulations that reproduced dynamics resulting from interplay of the different components of our models (vRNA, NSPs, and a host factor), and we present an evaluation of the concentrations for the components within different regions of the cell. Thus far, our model is restricted to an internal portion of a hepatocyte and is qualitative more than quantitative. For a quantitative adaption to complete cells, various additional parameters will have to be determined through further in vitro cell biology experiments, which can be stimulated by the results deccribed in the present study.

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

    Science.gov (United States)

    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…

  19. North Dakota's Experience with the Academy Model: A Successful Replication

    Science.gov (United States)

    Hall, Tom; Clapper, Ann

    2016-01-01

    In this article, professors share how the district/university partnership model thriving at Kansas State University was successfully replicated in North Dakota, and was adapted to match their own department goals. While teacher leadership has become a theme among Kansas State academies, their model was created out of principal preparation efforts.…

  20. Testing the family replication-model through Bsup(O)-Bsup(-O) mixing

    International Nuclear Information System (INIS)

    Datta, A.; Pati, J.C.

    1985-07-01

    It is observed that the family-replication idea, proposed in the context of a minimal preon-model, necessarily implies a maximal mixing (i.e. ΔM>>GAMMA) either in the Bsub(s)sup(O)-B-barsub(s)sup(O) or the Bsub(d)sup(O)-B-barsub(d)sup(O) system, in contrast to the standard model. (author)

  1. Replicates in high dimensions, with applications to latent variable graphical models.

    Science.gov (United States)

    Tan, Kean Ming; Ning, Yang; Witten, Daniela M; Liu, Han

    2016-12-01

    In classical statistics, much thought has been put into experimental design and data collection. In the high-dimensional setting, however, experimental design has been less of a focus. In this paper, we stress the importance of collecting multiple replicates for each subject in this setting. We consider learning the structure of a graphical model with latent variables, under the assumption that these variables take a constant value across replicates within each subject. By collecting multiple replicates for each subject, we are able to estimate the conditional dependence relationships among the observed variables given the latent variables. To test the null hypothesis of conditional independence between two observed variables, we propose a pairwise decorrelated score test. Theoretical guarantees are established for parameter estimation and for this test. We show that our proposal is able to estimate latent variable graphical models more accurately than some existing proposals, and apply the proposed method to a brain imaging dataset.

  2. Modeling HIV-1 Latency in Primary T Cells Using a Replication-Competent Virus.

    Science.gov (United States)

    Martins, Laura J; Bonczkowski, Pawel; Spivak, Adam M; De Spiegelaere, Ward; Novis, Camille L; DePaula-Silva, Ana Beatriz; Malatinkova, Eva; Trypsteen, Wim; Bosque, Alberto; Vanderkerckhove, Linos; Planelles, Vicente

    2016-02-01

    HIV-1 latently infected cells in vivo can be found in extremely low frequencies. Therefore, in vitro cell culture models have been used extensively for the study of HIV-1 latency. Often, these in vitro systems utilize defective viruses. Defective viruses allow for synchronized infections and circumvent the use of antiretrovirals. In addition, replication-defective viruses cause minimal cytopathicity because they fail to spread and usually do not encode env or accessory genes. On the other hand, replication-competent viruses encode all or most viral genes and better recapitulate the nuances of the viral replication cycle. The study of latency with replication-competent viruses requires the use of antiretroviral drugs in culture, and this mirrors the use of antiretroviral treatment (ART) in vivo. We describe a model that utilizes cultured central memory CD4(+) T cells and replication-competent HIV-1. This method generates latently infected cells that can be reactivated using latency reversing agents in the presence of antiretroviral drugs. We also describe a method for the removal of productively infected cells prior to viral reactivation, which takes advantage of the downregulation of CD4 by HIV-1, and the use of a GFP-encoding virus for increased throughput.

  3. Introducing Program Evaluation Models

    Directory of Open Access Journals (Sweden)

    Raluca GÂRBOAN

    2008-02-01

    Full Text Available Programs and project evaluation models can be extremely useful in project planning and management. The aim is to set the right questions as soon as possible in order to see in time and deal with the unwanted program effects, as well as to encourage the positive elements of the project impact. In short, different evaluation models are used in order to minimize losses and maximize the benefits of the interventions upon small or large social groups. This article introduces some of the most recently used evaluation models.

  4. Replicating the EnhanceFitness physical activity program in Hawai`i's multicultural population, 2007-2010.

    Science.gov (United States)

    Tomioka, Michiyo; Sugihara, Naomi; Braun, Kathryn L

    2012-01-01

    Despite evidence of the benefits of regular physical activity, many older adults are not physically active. Health professionals are challenged to replicate evidence-based programs to address low levels of physical activity among members of their communities. EnhanceFitness is an evidence-based group exercise program developed in Seattle to increase the strength, flexibility, and balance of older adults. Hawai`i's Healthy Aging Partnership supported the rural island of Kaua`i to select, adapt, implement, and evaluate EnhanceFitness to increase physical activity among older adult residents (75% Asian/Pacific Islander [API]). Evaluation measures of the replication of EnhanceFitness included fidelity of EnhanceFitness delivery and participants' attendance, satisfaction with the program, confidence to exercise regularly, and pre-post fitness check measures of physical performance (chair stands, arm curls, and the up-and-go test). Between July 2007 and December 2010, 223 Kaua`i residents enrolled in EnhanceFitness; 178 (80%) participated at least 4 months and completed the 4-month fitness checks. EnhanceFitness classes were offered with a high degree of fidelity, and both API and white participants significantly improved their physical performance (chair stands, t = -11.06, P program and instructors and high confidence to continue to exercise regularly. EnhanceFitness is replicable in Hawai`i and increased physical performance among API and white older adults. This case study outlines a replication process that other communities can follow.

  5. 76 FR 16754 - Charter Schools Program (CSP) Grants for Replication and Expansion of High-Quality Charter Schools

    Science.gov (United States)

    2011-03-25

    ... DEPARTMENT OF EDUCATION Charter Schools Program (CSP) Grants for Replication and Expansion of High-Quality Charter Schools AGENCY: Office of Innovation and Improvement, Department of Education. ACTION... and Expansion of High-Quality Charter Schools grant competition. The Assistant Deputy Secretary may...

  6. The replication timing program of the Chinese hamster ?-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase

    OpenAIRE

    Li, Feng; Chen, Jianhua; Izumi, Masako; Butler, Mark C.; Keezer, Susan M.; Gilbert, David M.

    2001-01-01

    We have examined the dynamics of nuclear repositioning and the establishment of a replication timing program for the actively transcribed dihydrofolate reductase (DHFR) locus and the silent ?-globin gene locus in Chinese hamster ovary cells. The DHFR locus was internally localized and replicated early, whereas the ?-globin locus was localized adjacent to the nuclear periphery and replicated during the middle of S phase, coincident with replication of peripheral heterochromatin. Nuclei were pr...

  7. Establishing a coherent and replicable measurement model of the Edinburgh Postnatal Depression Scale.

    Science.gov (United States)

    Martin, Colin R; Redshaw, Maggie

    2018-03-23

    The 10-item Edinburgh Postnatal Depression Scale (EPDS) is an established screening tool for postnatal depression. Inconsistent findings in factor structure and replication difficulties have limited the scope of development of the measure as a multi-dimensional tool. The current investigation sought to robustly determine the underlying factor structure of the EPDS and the replicability and stability of the most plausible model identified. A between-subjects design was used. EPDS data were collected postpartum from two independent cohorts using identical data capture methods. Datasets were examined with confirmatory factor analysis, model invariance testing and systematic evaluation of relational and internal aspects of the measure. Participants were two samples of postpartum women in England assessed at three months (n = 245) and six months (n = 217). The findings showed a three-factor seven-item model of the EPDS offered an excellent fit to the data, and was observed to be replicable in both datasets and invariant as a function of time point of assessment. Some EPDS sub-scale scores were significantly higher at six months. The EPDS is multi-dimensional and a robust measurement model comprises three factors that are replicable. The potential utility of the sub-scale components identified requires further research to identify a role in contemporary screening practice. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  8. The difference between LSMC and replicating portfolio in insurance liability modeling.

    Science.gov (United States)

    Pelsser, Antoon; Schweizer, Janina

    2016-01-01

    Solvency II requires insurers to calculate the 1-year value at risk of their balance sheet. This involves the valuation of the balance sheet in 1 year's time. As for insurance liabilities, closed-form solutions to their value are generally not available, insurers turn to estimation procedures. While pure Monte Carlo simulation set-ups are theoretically sound, they are often infeasible in practice. Therefore, approximation methods are exploited. Among these, least squares Monte Carlo (LSMC) and portfolio replication are prominent and widely applied in practice. In this paper, we show that, while both are variants of regression-based Monte Carlo methods, they differ in one significant aspect. While the replicating portfolio approach only contains an approximation error, which converges to zero in the limit, in LSMC a projection error is additionally present, which cannot be eliminated. It is revealed that the replicating portfolio technique enjoys numerous advantages and is therefore an attractive model choice.

  9. A stochastic step model of replicative senescence explains ROS production rate in ageing cell populations.

    Directory of Open Access Journals (Sweden)

    Conor Lawless

    Full Text Available Increases in cellular Reactive Oxygen Species (ROS concentration with age have been observed repeatedly in mammalian tissues. Concomitant increases in the proportion of replicatively senescent cells in ageing mammalian tissues have also been observed. Populations of mitotic human fibroblasts cultured in vitro, undergoing transition from proliferation competence to replicative senescence are useful models of ageing human tissues. Similar exponential increases in ROS with age have been observed in this model system. Tracking individual cells in dividing populations is difficult, and so the vast majority of observations have been cross-sectional, at the population level, rather than longitudinal observations of individual cells.One possible explanation for these observations is an exponential increase in ROS in individual fibroblasts with time (e.g. resulting from a vicious cycle between cellular ROS and damage. However, we demonstrate an alternative, simple hypothesis, equally consistent with these observations which does not depend on any gradual increase in ROS concentration: the Stochastic Step Model of Replicative Senescence (SSMRS. We also demonstrate that, consistent with the SSMRS, neither proliferation-competent human fibroblasts of any age, nor populations of hTERT overexpressing human fibroblasts passaged beyond the Hayflick limit, display high ROS concentrations. We conclude that longitudinal studies of single cells and their lineages are now required for testing hypotheses about roles and mechanisms of ROS increase during replicative senescence.

  10. Shadow Replication: An Energy-Aware, Fault-Tolerant Computational Model for Green Cloud Computing

    Directory of Open Access Journals (Sweden)

    Xiaolong Cui

    2014-08-01

    Full Text Available As the demand for cloud computing continues to increase, cloud service providers face the daunting challenge to meet the negotiated SLA agreement, in terms of reliability and timely performance, while achieving cost-effectiveness. This challenge is increasingly compounded by the increasing likelihood of failure in large-scale clouds and the rising impact of energy consumption and CO2 emission on the environment. This paper proposes Shadow Replication, a novel fault-tolerance model for cloud computing, which seamlessly addresses failure at scale, while minimizing energy consumption and reducing its impact on the environment. The basic tenet of the model is to associate a suite of shadow processes to execute concurrently with the main process, but initially at a much reduced execution speed, to overcome failures as they occur. Two computationally-feasible schemes are proposed to achieve Shadow Replication. A performance evaluation framework is developed to analyze these schemes and compare their performance to traditional replication-based fault tolerance methods, focusing on the inherent tradeoff between fault tolerance, the specified SLA and profit maximization. The results show that Shadow Replication leads to significant energy reduction, and is better suited for compute-intensive execution models, where up to 30% more profit increase can be achieved due to reduced energy consumption.

  11. The DNA replication program is altered at the FMR1 locus in fragile X embryonic stem cells.

    Science.gov (United States)

    Gerhardt, Jeannine; Tomishima, Mark J; Zaninovic, Nikica; Colak, Dilek; Yan, Zi; Zhan, Qiansheng; Rosenwaks, Zev; Jaffrey, Samie R; Schildkraut, Carl L

    2014-01-09

    Fragile X syndrome (FXS) is caused by a CGG repeat expansion in the FMR1 gene that appears to occur during oogenesis and during early embryogenesis. One model proposes that repeat instability depends on the replication fork direction through the repeats such that (CNG)n hairpin-like structures form, causing DNA polymerase to stall and slip. Examining DNA replication fork progression on single DNA molecules at the endogenous FMR1 locus revealed that replication forks stall at CGG repeats in human cells. Furthermore, replication profiles of FXS human embryonic stem cells (hESCs) compared to nonaffected hESCs showed that fork direction through the repeats is altered at the FMR1 locus in FXS hESCs, such that predominantly the CCG strand serves as the lagging-strand template. This is due to the absence of replication initiation that would typically occur upstream of FMR1, suggesting that altered replication origin usage combined with fork stalling promotes repeat instability during early embryonic development. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. PDDP, A Data Parallel Programming Model

    Directory of Open Access Journals (Sweden)

    Karen H. Warren

    1996-01-01

    Full Text Available PDDP, the parallel data distribution preprocessor, is a data parallel programming model for distributed memory parallel computers. PDDP implements high-performance Fortran-compatible data distribution directives and parallelism expressed by the use of Fortran 90 array syntax, the FORALL statement, and the WHERE construct. Distributed data objects belong to a global name space; other data objects are treated as local and replicated on each processor. PDDP allows the user to program in a shared memory style and generates codes that are portable to a variety of parallel machines. For interprocessor communication, PDDP uses the fastest communication primitives on each platform.

  13. Canard explosion of limit cycles in templator models of self-replication mechanisms

    DEFF Research Database (Denmark)

    Brøns, Morten

    2011-01-01

    Templators are differential equation models for self-replicating chemical systems. Beutel and Peacock-López [J. Chem. Phys. 126, 125104 (2007)]10.1063/1.2716396 have numerically analyzed a model for a cross-catalytic self-replicating system and found two cases of canard explosion, that is......, a substantial change of amplitude of a limit cycle over a very short parameter interval. We show how the model can be reduced to a two-dimensional system and how canard theory for slow-fast equations can be applied to yield analytic information about the canard explosion. In particular, simple expressions...... for the parameter value where the canard explosion occurs are obtained. The connection to mixed-mode oscillations also observed in the model is briefly discussed. © 2011 American Institute of Physics....

  14. Canard explosion of limit cycles in templator models of self-replication mechanisms

    Science.gov (United States)

    Brøns, Morten

    2011-04-01

    Templators are differential equation models for self-replicating chemical systems. Beutel and Peacock-López [J. Chem. Phys. 126, 125104 (2007)], 10.1063/1.2716396 have numerically analyzed a model for a cross-catalytic self-replicating system and found two cases of canard explosion, that is, a substantial change of amplitude of a limit cycle over a very short parameter interval. We show how the model can be reduced to a two-dimensional system and how canard theory for slow-fast equations can be applied to yield analytic information about the canard explosion. In particular, simple expressions for the parameter value where the canard explosion occurs are obtained. The connection to mixed-mode oscillations also observed in the model is briefly discussed.

  15. Barriers and facilitators to replicating an evidence-based palliative care model.

    Science.gov (United States)

    Davis, E Maxwell; Jamison, Paula; Brumley, Richard; Enguídanos, Susan

    2006-01-01

    Recognition of the difficulties involved in replicating evidence- based interventions is well documented in the literature within the medical field. Promising research findings are often not translated into practice, and if they are, there is a significant time gap between study conclusion and practice adoption. The purpose of this article is to describe the barriers and facilitators encountered by two managed care organizations while replicating an evidence-based end of life in-home palliative care model. Using Diffusion of Innovation Theory as a theoretical framework, results from focus groups and interviews with the project's clinical, administrative and research teams are presented and recommendations made for improving translational efforts. The process of replicating the end of life in-home palliative care model clearly illustrated the key elements required for successfully diffusing innovation. These key elements include marketing and communication, leadership, organizational support and training and mentorship. This qualitative process study provides clear, real world perspectives of the myriad of challenges encountered in replicating an evidence-based project.

  16. 3D Printing of Intracranial Aneurysms Using Fused Deposition Modeling Offers Highly Accurate Replications.

    Science.gov (United States)

    Frölich, A M J; Spallek, J; Brehmer, L; Buhk, J-H; Krause, D; Fiehler, J; Kemmling, A

    2016-01-01

    As part of a multicenter cooperation (Aneurysm-Like Synthetic bodies for Testing Endovascular devices in 3D Reality) with focus on implementation of additive manufacturing in neuroradiologic practice, we systematically assessed the technical feasibility and accuracy of several additive manufacturing techniques. We evaluated the method of fused deposition modeling for the production of aneurysm models replicating patient-specific anatomy. 3D rotational angiographic data from 10 aneurysms were processed to obtain volumetric models suitable for fused deposition modeling. A hollow aneurysm model with connectors for silicone tubes was fabricated by using acrylonitrile butadiene styrene. Support material was dissolved, and surfaces were finished by using NanoSeal. The resulting models were filled with iodinated contrast media. 3D rotational angiography of the models was acquired, and aneurysm geometry was compared with the original patient data. Reproduction of hollow aneurysm models was technically feasible in 8 of 10 cases, with aneurysm sizes ranging from 41 to 2928 mm(3) (aneurysm diameter, 3-19 mm). A high level of anatomic accuracy was observed, with a mean Dice index of 93.6% ± 2.4%. Obstructions were encountered in vessel segments of modeling is a promising technique, which allows rapid and precise replication of cerebral aneurysms. The porosity of the models can be overcome by surface finishing. Models produced with fused deposition modeling may serve as educational and research tools and could be used to individualize treatment planning. © 2016 by American Journal of Neuroradiology.

  17. Fractional Response Models - A Replication Exercise of Papke and Wooldridge (1996

    Directory of Open Access Journals (Sweden)

    Harald Oberhofer

    2012-09-01

    Full Text Available This paper replicates the estimates of a fractional response model for share data reported in the seminal paper of Leslie E. Papke and Jeffrey M. Wooldridge published in the Journal of Applied Econometrics 11(6, 1996, pp.619-632. We have been able to replicate all of the reported estimation results concerning the determinants of employee participation rates in 401(k pension plans using the standard routines provided in Stata. As an alternative, we estimate a two-part model that is capable of coping with the excessive number of boundary values equalling one in the data. The estimated marginal effects are similar to those derived in the paper. A small-scale Monte Carlo simulation exercise suggests that the RESET tests proposed by Papke and Wooldridge in their robust form are useful for detecting neglected non-linearities in small samples.

  18. Investigating the conformational stability of prion strains through a kinetic replication model.

    Directory of Open Access Journals (Sweden)

    Mattia Zampieri

    2009-07-01

    Full Text Available Prion proteins are known to misfold into a range of different aggregated forms, showing different phenotypic and pathological states. Understanding strain specificities is an important problem in the field of prion disease. Little is known about which PrP(Sc structural properties and molecular mechanisms determine prion replication, disease progression and strain phenotype. The aim of this work is to investigate, through a mathematical model, how the structural stability of different aggregated forms can influence the kinetics of prion replication. The model-based results suggest that prion strains with different conformational stability undergoing in vivo replication are characterizable in primis by means of different rates of breakage. A further role seems to be played by the aggregation rate (i.e. the rate at which a prion fibril grows. The kinetic variability introduced in the model by these two parameters allows us to reproduce the different characteristic features of the various strains (e.g., fibrils' mean length and is coherent with all experimental observations concerning strain-specific behavior.

  19. A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

    DEFF Research Database (Denmark)

    Klochendler, Agnes; Weinberg-Corem, Noa; Moran, Maya

    2012-01-01

    Most adult mammalian tissues are quiescent, with rare cell divisions serving to maintain homeostasis. At present, the isolation and study of replicating cells from their in vivo niche typically involves immunostaining for intracellular markers of proliferation, causing the loss of sensitive biolo...

  20. Replicating Patient-Specific Severe Aortic Valve Stenosis With Functional 3D Modeling.

    Science.gov (United States)

    Maragiannis, Dimitrios; Jackson, Matthew S; Igo, Stephen R; Schutt, Robert C; Connell, Patrick; Grande-Allen, Jane; Barker, Colin M; Chang, Su Min; Reardon, Michael J; Zoghbi, William A; Little, Stephen H

    2015-10-01

    3D stereolithographic printing can be used to convert high-resolution computed tomography images into life-size physical models. We sought to apply 3D printing technologies to develop patient-specific models of the anatomic and functional characteristics of severe aortic valve stenosis. Eight patient-specific models of severe aortic stenosis (6 tricuspid and 2 bicuspid) were created using dual-material fused 3D printing. Tissue types were identified and segmented from clinical computed tomography image data. A rigid material was used for printing calcific regions, and a rubber-like material was used for soft tissue structures of the outflow tract, aortic root, and noncalcified valve cusps. Each model was evaluated for its geometric valve orifice area, echocardiographic image quality, and aortic stenosis severity by Doppler and Gorlin methods under 7 different in vitro stroke volume conditions. Fused multimaterial 3D printed models replicated the focal calcific structures of aortic stenosis. Doppler-derived measures of peak and mean transvalvular gradient correlated well with reference standard pressure catheters across a range of flow conditions (r=0.988 and r=0.978 respectively, P3D printing, we demonstrate that patient-specific models can replicate both the anatomic and functional properties of severe degenerative aortic valve stenosis. © 2015 American Heart Association, Inc.

  1. Model Program Evaluations. Fact Sheet

    Science.gov (United States)

    Arkansas Safe Schools Initiative Division, 2002

    2002-01-01

    There are probably thousands of programs and courses intended to prevent or reduce violence in this nation's schools. Evaluating these many programs has become a problem or goal in itself. There are now many evaluation programs, with many levels of designations, such as model, promising, best practice, exemplary and noteworthy. "Model program" is…

  2. The rolling-circle melting-pot model for porcine circovirus DNA replication

    Science.gov (United States)

    A stem-loop structure, formed by a pair of inverted repeats during DNA replication, is a conserved feature at the origin of DNA replication (Ori) among plant and animal viruses, bacteriophages and plasmids that replicate their genomes via the rolling-circle replication (RCR) mechanism. Porcine circo...

  3. A model for family replication and a mechanism for mass hierarchy

    International Nuclear Information System (INIS)

    Pati, J.C.

    1984-01-01

    We suggest a flavon-chromon preon model possessing two preonic scales - Λsub(M)>>1 TeV and Λsub(H)approx.=1 TeV - associated with metacolor and hypercolor gauge forces respectively. The model exhibits two desirable features: (a) a mechanism for family replication, and (b) a new mechanism for interfamily mass hierarchy. With a minimal choice of the preonic fields, the model predicts four families (e, μ, tau and tau') tau being a replication of e and tau' of μ. Barring mixing, the e- and μ-families are bound by the metacolor force and have a small size approx.=Λsub(M) -1 , while the tau and the tau', which are composites of composites, are bound by the hypercolor force and have a relatively large size approx.=Λsub(H) -1 . The model predicts that the next-generation accelerators should discover (a) compositeness of quarks and leptons, primarily through family non-diagonal processes like (e - e + or qsub(e)anti qsub(e))->tau - tau + , qsub(b)anti qsub(b) or psub(t)anti qsub(t), and (b) a breakdown of e-μ-tau universality. It also predicts observable rare decays like tau->eγ and Ksub(L)->anti μe. (orig.)

  4. Replicating and extending a model of effects of universal preventive intervention during early adolescence on young adult substance misuse.

    Science.gov (United States)

    Spoth, Richard; Trudeau, Linda; Redmond, Cleve; Shin, Chungyeol

    2016-10-01

    This brief report summarizes a replication and extension of a developmental outcome modeling study, by examining whether delayed substance initiation during adolescence, resulting from universal middle school preventive interventions, reduces problematic use in young adults Ages 25 and 27, up to 14.5 years after baseline. Participants were middle school students from 36 Iowa schools randomly assigned to the Strengthening Families Program plus Life Skills Training (SFP 10-14 + LST), LST-only, or a control condition. Self-report questionnaires originally were collected at 11 time points, through Age 22. A subsequent grant allowed for assessments at Ages 25 and 27, including measures of drunkenness, alcohol-related problems, cigarette use, illicit drug use (lifetime and frequency), marijuana use and prescription drug misuse. These outcomes were modeled as variables influenced by growth factors describing substance initiation during adolescence. Models included the effects of baseline risk, intervention condition assignment, and their interaction; risk-related moderation effects were examined and relative reduction rates were calculated for dichotomous variables. Model fits were good. Analyses showed significant or marginally significant indirect intervention effects on all outcomes, through effects on adolescent substance initiation growth factors. Intervention × Risk interaction effects favored the higher risk subsample, replicating earlier findings. Additional direct effects on young adult use were observed only for cigarette frequency. Relative reduction rates were larger for the higher risk subsamples, ranging from 3.9% to 36.2%. Universal preventive interventions implemented during early adolescence have the potential to decrease the rates of substance misuse and associated problems into young adulthood. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  5. COS-7-based model: methodological approach to study John Cunningham virus replication cycle.

    Science.gov (United States)

    Prezioso, C; Scribano, D; Rodio, D M; Ambrosi, C; Trancassini, M; Palamara, A T; Pietropaolo, V

    2018-02-05

    John Cunningham virus (JCV) is a human neurotropic polyomavirus whose replication in the Central Nervous System (SNC) induces the fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML). JCV propagation and PML investigation have been severely hampered by the lack of an animal model and cell culture systems to propagate JCV have been very limited in their availability and robustness. We previously confirmed that JCV CY strain efficiently replicated in COS-7 cells as demonstrated by the progressive increase of viral load by quantitative PCR (Q-PCR) during the time of transfection and that archetypal regulatory structure was maintained, although two characteristic point mutations were detected during the viral cycle. This short report is an important extension of our previous efforts in defining our reliable model culture system able to support a productive JCV infection.Supernatants collected from transfected cells have been used to infect freshly seeded COS-7 cell line. An infectious viral progeny was obtained as confirmed by Western blot and immunofluorescence assay. During infection, the archetype regulatory region was conserved.Importantly, in this study we developed an improved culture system to obtain a large scale production of JC virus in order to study the genetic features, the biology and the pathogenic mechanisms of JC virus that induce PML.

  6. Replication Catastrophe

    DEFF Research Database (Denmark)

    Toledo, Luis; Neelsen, Kai John; Lukas, Jiri

    2017-01-01

    Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA...... increased DNA replication stress....

  7. The replication timing program of the Chinese hamster β-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase

    Science.gov (United States)

    Li, Feng; Chen, Jianhua; Izumi, Masako; Butler, Mark C.; Keezer, Susan M.; Gilbert, David M.

    2001-01-01

    We have examined the dynamics of nuclear repositioning and the establishment of a replication timing program for the actively transcribed dihydrofolate reductase (DHFR) locus and the silent β-globin gene locus in Chinese hamster ovary cells. The DHFR locus was internally localized and replicated early, whereas the β-globin locus was localized adjacent to the nuclear periphery and replicated during the middle of S phase, coincident with replication of peripheral heterochromatin. Nuclei were prepared from cells synchronized at various times during early G1 phase and stimulated to enter S phase by introduction into Xenopus egg extracts, and the timing of DHFR and β-globin replication was evaluated in vitro. With nuclei isolated 1 h after mitosis, neither locus was preferentially replicated before the other. However, with nuclei isolated 2 or 3 h after mitosis, there was a strong preference for replication of DHFR before β-globin. Measurements of the distance of DHFR and β-globin to the nuclear periphery revealed that the repositioning of the β-globin locus adjacent to peripheral heterochromatin also took place between 1 and 2 h after mitosis. These results suggest that the CHO β-globin locus acquires the replication timing program of peripheral heterochromatin upon association with the peripheral subnuclear compartment during early G1 phase. PMID:11470818

  8. A heteroscedastic measurement error model for method comparison data with replicate measurements.

    Science.gov (United States)

    Nawarathna, Lakshika S; Choudhary, Pankaj K

    2015-03-30

    Measurement error models offer a flexible framework for modeling data collected in studies comparing methods of quantitative measurement. These models generally make two simplifying assumptions: (i) the measurements are homoscedastic, and (ii) the unobservable true values of the methods are linearly related. One or both of these assumptions may be violated in practice. In particular, error variabilities of the methods may depend on the magnitude of measurement, or the true values may be nonlinearly related. Data with these features call for a heteroscedastic measurement error model that allows nonlinear relationships in the true values. We present such a model for the case when the measurements are replicated, discuss its fitting, and explain how to evaluate similarity of measurement methods and agreement between them, which are two common goals of data analysis, under this model. Model fitting involves dealing with lack of a closed form for the likelihood function. We consider estimation methods that approximate either the likelihood or the model to yield approximate maximum likelihood estimates. The fitting methods are evaluated in a simulation study. The proposed methodology is used to analyze a cholesterol dataset. Copyright © 2015 John Wiley & Sons, Ltd.

  9. Replicating MISTERS: an epidemiological criminology framework analysis of a program for criminal justice-involved minority males in the community.

    Science.gov (United States)

    Potter, Roberto Hugh; Akers, Timothy A; Bowman, Daniel Richard

    2013-01-01

    The Men in STD Training and Empowerment Research Study (MISTERS) program and epidemiological criminology began their development in Atlanta at about the same time. MISTERS focuses on men recently released from jail to reduce both HIV/STD and crime-related risk factors through a brief educational intervention. This article examines ways in which MISTERS and epidemiological criminology have been used to inform one another in the replication of the MISTERS program in Orange County, Florida. Data from 110 MISTERS participants during the first 10 months of operation are analyzed to examine the overlapping occurrence of health and criminal risk behaviors in the men's lives. This provides a test of core hypotheses from the epidemiological criminology framework. This article also examines application of the epidemiological criminology framework to develop interventions to address health and crime risk factors simultaneously in Criminal Justice-Involved populations in the community.

  10. Linear mixed models for replication data to efficiently allow for covariate measurement error.

    Science.gov (United States)

    Bartlett, Jonathan W; De Stavola, Bianca L; Frost, Chris

    2009-11-10

    It is well known that measurement error in the covariates of regression models generally causes bias in parameter estimates. Correction for such biases requires information concerning the measurement error, which is often in the form of internal validation or replication data. Regression calibration (RC) is a popular approach to correct for covariate measurement error, which involves predicting the true covariate using error-prone measurements. Likelihood methods have previously been proposed as an alternative approach to estimate the parameters in models affected by measurement error, but have been relatively infrequently employed in medical statistics and epidemiology, partly because of computational complexity and concerns regarding robustness to distributional assumptions. We show how a standard random-intercepts model can be used to obtain maximum likelihood (ML) estimates when the outcome model is linear or logistic regression under certain normality assumptions, when internal error-prone replicate measurements are available. Through simulations we show that for linear regression, ML gives more efficient estimates than RC, although the gain is typically small. Furthermore, we show that RC and ML estimates remain consistent even when the normality assumptions are violated. For logistic regression, our implementation of ML is consistent if the true covariate is conditionally normal given the outcome, in contrast to RC. In simulations, this ML estimator showed less bias in situations where RC gives non-negligible biases. Our proposal makes the ML approach to dealing with covariate measurement error more accessible to researchers, which we hope will improve its viability as a useful alternative to methods such as RC.

  11. The Song Remains the Same: A Replication and Extension of the MUSIC Model

    Science.gov (United States)

    Rentfrow, Peter J.; Goldberg, Lewis R.; Stillwell, David J.; Kosinski, Michal; Gosling, Samuel D.; Levitin, Daniel J.

    2012-01-01

    There is overwhelming anecdotal and empirical evidence for individual differences in musical preferences. However, little is known about what drives those preferences. Are people drawn to particular musical genres (e.g., rap, jazz) or to certain musical properties (e.g., lively, loud)? Recent findings suggest that musical preferences can be conceptualized in terms of five orthogonal dimensions: Mellow, Unpretentious, Sophisticated, Intense, and Contemporary (conveniently, MUSIC). The aim of the present research is to replicate and extend that work by empirically examining the hypothesis that musical preferences are based on preferences for particular musical properties and psychological attributes as opposed to musical genres. Findings from Study 1 replicated the five-factor MUSIC structure using musical excerpts from a variety of genres and subgenres and revealed musical attributes that differentiate each factor. Results from Studies 2 and 3 show that the MUSIC structure is recoverable using musical pieces from only the jazz and rock genres, respectively. Taken together, the current work provides strong evidence that preferences for music are determined by specific musical attributes and that the MUSIC model is a robust framework for conceptualizing and measuring such preferences. PMID:24825945

  12. The Song Remains the Same: A Replication and Extension of the MUSIC Model.

    Science.gov (United States)

    Rentfrow, Peter J; Goldberg, Lewis R; Stillwell, David J; Kosinski, Michal; Gosling, Samuel D; Levitin, Daniel J

    2012-12-01

    There is overwhelming anecdotal and empirical evidence for individual differences in musical preferences. However, little is known about what drives those preferences. Are people drawn to particular musical genres (e.g., rap, jazz) or to certain musical properties (e.g., lively, loud)? Recent findings suggest that musical preferences can be conceptualized in terms of five orthogonal dimensions: Mellow, Unpretentious, Sophisticated, Intense, and Contemporary (conveniently, MUSIC). The aim of the present research is to replicate and extend that work by empirically examining the hypothesis that musical preferences are based on preferences for particular musical properties and psychological attributes as opposed to musical genres. Findings from Study 1 replicated the five-factor MUSIC structure using musical excerpts from a variety of genres and subgenres and revealed musical attributes that differentiate each factor. Results from Studies 2 and 3 show that the MUSIC structure is recoverable using musical pieces from only the jazz and rock genres, respectively. Taken together, the current work provides strong evidence that preferences for music are determined by specific musical attributes and that the MUSIC model is a robust framework for conceptualizing and measuring such preferences.

  13. Animal models for the study of hepatitis C virus infection and replication.

    Science.gov (United States)

    MacArthur, Kristin L; Wu, Catherine H; Wu, George Y

    2012-06-21

    Hepatitis C virus (HCV) hepatitis, initially termed non-A, non-B hepatitis, has become one of the leading causes of cirrhosis and hepatocellular carcinoma worldwide. With the help of animal models, our understanding of the virus has grown substantially from the time of initial discovery. There is a paucity of available animal models for the study of HCV, mainly because of the selective susceptibility limited to humans and primates. Recent work has focused modification of animals to permit HCV entry, replication and transmission. In this review, we highlight the currently available models for the study of HCV including chimpanzees, tupaia, mouse and rat models. Discussion will include methods of model design as well as the advantages and disadvantages of each model. Particular focus is dedicated to knowledge of pathophysiologic mechanisms of HCV infection that have been elucidated through animal studies. Research within animal models is critically important to establish a complete understanding of HCV infection, which will ultimately form the basis for future treatments and prevention of disease.

  14. Assessing Religious Orientations: Replication and Validation of the Commitment-Reflectivity Circumplex (CRC Model

    Directory of Open Access Journals (Sweden)

    Steven L. Isaak

    2017-09-01

    Full Text Available The Commitment-Reflectivity Circumplex (CRC model is a structural model of religious orientation that was designed to help organize and clarify measurement of foundational aspect of religiousness. The current study successfully replicated the CRC model using multidimensional scaling, and further evaluated the reliability, structure, and validity of their measures in both a university student sample (Study 1 and a nationally representative sample (Study 2. All 10 subscales of the Circumplex Religious Orientation Inventory (CROI demonstrated good reliability across both samples. A two-week test-retest of the CROI showed that the subscales are stable over time. A confirmatory factor analysis of the CROI in the representative adult sample demonstrated good model fit. Finally, the CROI’s validity was examined in relation to the Intrinsic, Extrinsic and Quest measures. Overall, the CROI appears to clarify much of the ambiguity inherent in the established scales by breaking down what were very broad orientations into very specific suborientations. The results suggest that the CRC model is applicable for diverse populations of adults. In addition, the CROI appears to be construct valid with good structural and psychometric properties across all 10 subscales.

  15. Conditionally replicating adenovirus expressing TIMP2 increases survival in a mouse model of disseminated ovarian cancer.

    Directory of Open Access Journals (Sweden)

    Sherry W Yang

    Full Text Available Ovarian cancer remains difficult to treat mainly due to presentation of the disease at an advanced stage. Conditionally-replicating adenoviruses (CRAds are promising anti-cancer agents that selectively kill the tumor cells. The present study evaluated the efficacy of a novel CRAd (Ad5/3-CXCR4-TIMP2 containing the CXCR4 promoter for selective viral replication in cancer cells together with TIMP2 as a therapeutic transgene, targeting the matrix metalloproteases (MMPs in a murine orthotopic model of disseminated ovarian cancer. An orthotopic model of ovarian cancer was established in athymic nude mice by intraperitonal injection of the human ovarian cancer cell line, SKOV3-Luc, expressing luciferase. Upon confirmation of peritoneal dissemination of the cells by non-invasive imaging, mice were randomly divided into four treatment groups: PBS, Ad-ΔE1-TIMP2, Ad5/3-CXCR4, and Ad5/3-CXCR4-TIMP2. All mice were imaged weekly to monitor tumor growth and were sacrificed upon reaching any of the predefined endpoints, including high tumor burden and significant weight loss along with clinical evidence of pain and distress. Survival analysis was performed using the Log-rank test. The median survival for the PBS cohort was 33 days; for Ad-ΔE1-TIMP2, 39 days; for Ad5/3-CXCR4, 52.5 days; and for Ad5/3-CXCR4-TIMP2, 63 days. The TIMP2-armed CRAd delayed tumor growth and significantly increased survival when compared to the unarmed CRAd. This therapeutic effect was confirmed to be mediated through inhibition of MMP9. Results of the in vivo study support the translational potential of Ad5/3-CXCR4-TIMP2 for treatment of human patients with advanced ovarian cancer.

  16. Heart Rate Variability Biofeedback Stress Relief Program for Depression A Replicated Single-Subject Design

    NARCIS (Netherlands)

    Hartogs, Bregje M. A.; Bartels-Velthuis, Agna A.; Van der Ploeg, Karen; Bos, Elske H.

    2017-01-01

    Background: Depressive disorders often have a chronic course and the efficacy of evidence-based treatments may be overestimated. Objective: To examine the effectiveness of the Heart Rate Variability Stress Reduction Program (SRP) as a supplement to standard treatment in patients with depressive

  17. Optimal therapies of a virus replication model with pharmacological delays based on reverse transcriptase inhibitors and protease inhibitors

    International Nuclear Information System (INIS)

    Pei, Yongzhen; Li, Changguo; Liang, Xiyin

    2017-01-01

    A short delay in the pharmacological effect on account of the time required for drug absorption, distribution, and penetration into target cells after application of any anti-viral drug, is defined by the pharmacological delay (Herz et al 1996 Proc. Natl Acad. Sci. USA 93 7247–51). In this paper, a virus replication model with Beddington–DeAngelis incidence rate and the pharmacological and intracellular delays is presented to describe the treatment to cure the virus infection. The optimal controls represent the efficiency of reverse transcriptase inhibitors and protease inhibitors in suppressing viral production and prohibiting new infections. Due to the fact that both the control and state variables contain delays, we derive a necessary conditions for our optimal problem. Based on these results, numerical simulations are implemented not only to show the optimal therapeutic schedules for different infection and release rates, but also to compare the effective of three treatment programs. Furthermore, comparison of therapeutic effects under different maximum tolerable dosages is shown. Our research indicates that (1) the proper and specific treatment program should be determined according to the infection rates of different virus particles; (2) the optimal combined drug treatment is the most efficient; (3) the appropriate proportion of medicament must be formulated during the therapy due to the non-monotonic relationship between maximum tolerable dosages and therapeutic effects; (4) the therapeutic effect is advantageous when the pharmacological delay is considered. (paper)

  18. Optimal therapies of a virus replication model with pharmacological delays based on reverse transcriptase inhibitors and protease inhibitors

    Science.gov (United States)

    Pei, Yongzhen; Li, Changguo; Liang, Xiyin

    2017-11-01

    A short delay in the pharmacological effect on account of the time required for drug absorption, distribution, and penetration into target cells after application of any anti-viral drug, is defined by the pharmacological delay (Herz et al 1996 Proc. Natl Acad. Sci. USA 93 7247-51). In this paper, a virus replication model with Beddington-DeAngelis incidence rate and the pharmacological and intracellular delays is presented to describe the treatment to cure the virus infection. The optimal controls represent the efficiency of reverse transcriptase inhibitors and protease inhibitors in suppressing viral production and prohibiting new infections. Due to the fact that both the control and state variables contain delays, we derive a necessary conditions for our optimal problem. Based on these results, numerical simulations are implemented not only to show the optimal therapeutic schedules for different infection and release rates, but also to compare the effective of three treatment programs. Furthermore, comparison of therapeutic effects under different maximum tolerable dosages is shown. Our research indicates that (1) the proper and specific treatment program should be determined according to the infection rates of different virus particles; (2) the optimal combined drug treatment is the most efficient; (3) the appropriate proportion of medicament must be formulated during the therapy due to the non-monotonic relationship between maximum tolerable dosages and therapeutic effects; (4) the therapeutic effect is advantageous when the pharmacological delay is considered.

  19. Program Analysis as Model Checking

    DEFF Research Database (Denmark)

    Olesen, Mads Chr.

    and abstract interpretation. Model checking views the program as a finite automaton and tries to prove logical properties over the automaton model, or present a counter-example if not possible — with a focus on precision. Abstract interpretation translates the program semantics into abstract semantics...... are considered, among others numerical analysis of c programs, and worst-case execution time analysis of ARM programs. It is shown how lattice automata allow automatic and manual tuning of the precision and efficiency of the verification procedure. In the case of worst-case execution time analysis a sound......Software programs are proliferating throughout modern life, to a point where even the simplest appliances such as lightbulbs contain software, in addition to the software embedded in cars and airplanes. The correct functioning of these programs is therefore of the utmost importance, for the quality...

  20. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

    Science.gov (United States)

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

    2016-12-13

    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  1. Cutthroat trout virus as a surrogate in vitro infection model for testing inhibitors of hepatitis E virus replication

    Science.gov (United States)

    Debing, Yannick; Winton, James; Neyts, Johan; Dallmeier, Kai

    2013-01-01

    Hepatitis E virus (HEV) is one of the most important causes of acute hepatitis worldwide. Although most infections are self-limiting, mortality is particularly high in pregnant women. Chronic infections can occur in transplant and other immune-compromised patients. Successful treatment of chronic hepatitis E has been reported with ribavirin and pegylated interferon-alpha, however severe side effects were observed. We employed the cutthroat trout virus (CTV), a non-pathogenic fish virus with remarkable similarities to HEV, as a potential surrogate for HEV and established an antiviral assay against this virus using the Chinook salmon embryo (CHSE-214) cell line. Ribavirin and the respective trout interferon were found to efficiently inhibit CTV replication. Other known broad-spectrum inhibitors of RNA virus replication such as the nucleoside analog 2′-C-methylcytidine resulted only in a moderate antiviral activity. In its natural fish host, CTV levels largely fluctuate during the reproductive cycle with the virus detected mainly during spawning. We wondered whether this aspect of CTV infection may serve as a surrogate model for the peculiar pathogenesis of HEV in pregnant women. To that end the effect of three sex steroids on in vitro CTV replication was evaluated. Whereas progesterone resulted in marked inhibition of virus replication, testosterone and 17β-estradiol stimulated viral growth. Our data thus indicate that CTV may serve as a surrogate model for HEV, both for antiviral experiments and studies on the replication biology of the Hepeviridae.

  2. Dynamic programming models and applications

    CERN Document Server

    Denardo, Eric V

    2003-01-01

    Introduction to sequential decision processes covers use of dynamic programming in studying models of resource allocation, methods for approximating solutions of control problems in continuous time, production control, more. 1982 edition.

  3. Energy efficiency in nonprofit agencies: Creating effective program models

    Energy Technology Data Exchange (ETDEWEB)

    Brown, M.A.; Prindle, B.; Scherr, M.I.; White, D.L.

    1990-08-01

    Nonprofit agencies are a critical component of the health and human services system in the US. It has been clearly demonstrated by programs that offer energy efficiency services to nonprofits that, with minimal investment, they can educe their energy consumption by ten to thirty percent. This energy conservation potential motivated the Department of Energy and Oak Ridge National Laboratory to conceive a project to help states develop energy efficiency programs for nonprofits. The purpose of the project was two-fold: (1) to analyze existing programs to determine which design and delivery mechanisms are particularly effective, and (2) to create model programs for states to follow in tailoring their own plans for helping nonprofits with energy efficiency programs. Twelve existing programs were reviewed, and three model programs were devised and put into operation. The model programs provide various forms of financial assistance to nonprofits and serve as a source of information on energy efficiency as well. After examining the results from the model programs (which are still on-going) and from the existing programs, several replicability factors'' were developed for use in the implementation of programs by other states. These factors -- some concrete and practical, others more generalized -- serve as guidelines for states devising program based on their own particular needs and resources.

  4. Chemical oscillations and Turing patterns in a generalized two-variable model of chemical self-replication

    Science.gov (United States)

    Beutel, Kathleen M.; Peacock-López, Enrique

    2006-07-01

    Chemical self-replication of oligonucleotides and helical peptides show the so-called square root rate law. Based on this rate we extend our previous work on ideal replicators to include the square root rate and other possible nonlinearities, which we couple with an enzimatic sink. Although the nonlinearity is necessary for complex dynamics, the nature of the sink is the essential feature in the mechanism that allows temporal and spatial patterns. We obtain exact general relations for the Poincare-Adronov-Hopf and Turing bifurcations, and our generalized results include the Higgins, autocatalator, and templator models as specific cases.

  5. A microhomology-mediated break-induced replication model for the origin of human copy number variation.

    Directory of Open Access Journals (Sweden)

    P J Hastings

    2009-01-01

    Full Text Available Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV. A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2-5 base pairs (bp. Third, endpoints occur near pre-existing low copy repeats (LCRs. Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR. Under these circumstances, single-strand 3' tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.

  6. A ''model'' geophysics program

    International Nuclear Information System (INIS)

    Nyquist, J.E.

    1994-01-01

    In 1993, I tested a radio-controlled airplane designed by Jim Walker of Brigham Young University for low-elevation aerial photography. Model-air photography retains most of the advantages of standard aerial photography --- the photographs can be used to detect lineaments, to map roads and buildings, and to construct stereo pairs to measure topography --- and it is far less expensive. Proven applications on the Oak Ridge Reservation include: updating older aerial records to document new construction; using repeated overflights of the same area to capture seasonal changes in vegetation and the effects of major storms; and detecting waste trench boundaries from the color and character of the overlying grass. Aerial photography is only one of many possible applications of radio-controlled aircraft. Currently, I am funded by the Department of Energy's Office of Technology Development to review the state of the art in microavionics, both military and civilian, to determine ways this emerging technology can be used for environmental site characterization. Being particularly interested in geophysical applications, I am also collaborating with electrical engineers at Oak Ridge National Laboratory to design a model plane that will carry a 3-component flux-gate magnetometer and a global positioning system, which I hope to test in the spring of 1994

  7. Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1

    Directory of Open Access Journals (Sweden)

    DasSarma Shiladitya

    2007-06-01

    Full Text Available Abstract Background Information transfer systems in Archaea, including many components of the DNA replication machinery, are similar to those found in eukaryotes. Functional assignments of archaeal DNA replication genes have been primarily based upon sequence homology and biochemical studies of replisome components, but few genetic studies have been conducted thus far. We have developed a tractable genetic system for knockout analysis of genes in the model halophilic archaeon, Halobacterium sp. NRC-1, and used it to determine which DNA replication genes are essential. Results Using a directed in-frame gene knockout method in Halobacterium sp. NRC-1, we examined nineteen genes predicted to be involved in DNA replication. Preliminary bioinformatic analysis of the large haloarchaeal Orc/Cdc6 family, related to eukaryotic Orc1 and Cdc6, showed five distinct clades of Orc/Cdc6 proteins conserved in all sequenced haloarchaea. Of ten orc/cdc6 genes in Halobacterium sp. NRC-1, only two were found to be essential, orc10, on the large chromosome, and orc2, on the minichromosome, pNRC200. Of the three replicative-type DNA polymerase genes, two were essential: the chromosomally encoded B family, polB1, and the chromosomally encoded euryarchaeal-specific D family, polD1/D2 (formerly called polA1/polA2 in the Halobacterium sp. NRC-1 genome sequence. The pNRC200-encoded B family polymerase, polB2, was non-essential. Accessory genes for DNA replication initiation and elongation factors, including the putative replicative helicase, mcm, the eukaryotic-type DNA primase, pri1/pri2, the DNA polymerase sliding clamp, pcn, and the flap endonuclease, rad2, were all essential. Targeted genes were classified as non-essential if knockouts were obtained and essential based on statistical analysis and/or by demonstrating the inability to isolate chromosomal knockouts except in the presence of a complementing plasmid copy of the gene. Conclusion The results showed that ten

  8. The uptake of apoptotic cells drives Coxiella burnetii replication and macrophage polarization: a model for Q fever endocarditis.

    Directory of Open Access Journals (Sweden)

    Marie Benoit

    2008-05-01

    Full Text Available Patients with valvulopathy have the highest risk to develop infective endocarditis (IE, although the relationship between valvulopathy and IE is not clearly understood. Q fever endocarditis, an IE due to Coxiella burnetii, is accompanied by immune impairment. Patients with valvulopathy exhibited increased levels of circulating apoptotic leukocytes, as determined by the measurement of active caspases and nucleosome determination. The binding of apoptotic cells to monocytes and macrophages, the hosts of C. burnetii, may be responsible for the immune impairment observed in Q fever endocarditis. Apoptotic lymphocytes (AL increased C. burnetii replication in monocytes and monocyte-derived macrophages in a cell-contact dependent manner, as determined by quantitative PCR and immunofluorescence. AL binding induced a M2 program in monocytes and macrophages stimulated with C. burnetii as determined by a cDNA chip containing 440 arrayed sequences and functional tests, but this program was in part different in monocytes and macrophages. While monocytes that had bound AL released high levels of IL-10 and IL-6, low levels of TNF and increased CD14 expression, macrophages that had bound AL released high levels of TGF-beta1 and expressed mannose receptor. The neutralization of IL-10 and TGF-beta1 prevented the replication of C. burnetii due to the binding of AL, suggesting that they were critically involved in bacterial replication. In contrast, the binding of necrotic cells to monocytes and macrophages led to C. burnetii killing and typical M1 polarization. Finally, interferon-gamma corrected the immune deactivation induced by apoptotic cells: it prevented the replication of C. burnetii and re-directed monocytes and macrophages toward a M1 program, which was deleterious for C. burnetii. We suggest that leukocyte apoptosis associated with valvulopathy may be critical for the pathogenesis of Q fever endocarditis by deactivating immune cells and creating a

  9. In vivo study on the replicative model validity of sister chromatid exchanges production

    International Nuclear Information System (INIS)

    Cruz V, V.L.

    1996-01-01

    The sister chromatid exchanges (SCE) frequency determination has been used as index of damage to DNA, however the biological meaning of this event is still ignored. Different models in order to explain the mechanism of their formation have been proposed and they could be contained in two categories: a) those that consider that the SCE is produced by means of discreet lesions to the DNA and that they occur in the place of the lesion, and b) those that propose that the SCE is caused by a group of lesions and that therefore the place in which they occur could not be associated with a lesion in particular. The model of Painter (1980) belongs to this last group. It suggests that the region of the DNA where the clusters are united, is the only place in which the exchange of double chain could happen during the synthesis of the DNA and makes the prediction that since the x rays retard the beginning of the duplication, the pretreatment with ionizing radiation would reduce the frequency of SCE induced by agents capable to block the lengthening of the chain of DNA, that are the most efficient SCE inducers. The objective of the present work was to establish the validity of this replicative model for the SCE formation, based in its prediction. The effect of the unilateral preexposition of mouse to gamma radiation was determined on the SCE induction by Mitomycin C (MMC), in cells of the femoral bone marrow In vivo. This strategy allows to determine the effect of the pretreatment in the same organism, minimizing the variability of the response between individuals. There was not a significant variability between the frequencies of SCE, basal and induced by gamma radiation or MMC in the same organism. The animals that received the gamma radiation pretreatment, showed a reduction of approximately the 30 % in the frequency of SCE, assuming an additive effect of the radiation with the MMC. These results coincide with the prediction of the model of Painter, however it is not

  10. Commercial Building Partnerships Replication and Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

    2013-09-16

    This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.

  11. Model Checker for Java Programs

    Science.gov (United States)

    Visser, Willem

    2007-01-01

    Java Pathfinder (JPF) is a verification and testing environment for Java that integrates model checking, program analysis, and testing. JPF consists of a custom-made Java Virtual Machine (JVM) that interprets bytecode, combined with a search interface to allow the complete behavior of a Java program to be analyzed, including interleavings of concurrent programs. JPF is implemented in Java, and its architecture is highly modular to support rapid prototyping of new features. JPF is an explicit-state model checker, because it enumerates all visited states and, therefore, suffers from the state-explosion problem inherent in analyzing large programs. It is suited to analyzing programs less than 10kLOC, but has been successfully applied to finding errors in concurrent programs up to 100kLOC. When an error is found, a trace from the initial state to the error is produced to guide the debugging. JPF works at the bytecode level, meaning that all of Java can be model-checked. By default, the software checks for all runtime errors (uncaught exceptions), assertions violations (supports Java s assert), and deadlocks. JPF uses garbage collection and symmetry reductions of the heap during model checking to reduce state-explosion, as well as dynamic partial order reductions to lower the number of interleavings analyzed. JPF is capable of symbolic execution of Java programs, including symbolic execution of complex data such as linked lists and trees. JPF is extensible as it allows for the creation of listeners that can subscribe to events during searches. The creation of dedicated code to be executed in place of regular classes is supported and allows users to easily handle native calls and to improve the efficiency of the analysis.

  12. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  13. Replication of Major Profile Patterns in Structural Equation Modeling: Effect of Bootstrapping in a Small Sample.

    Science.gov (United States)

    Kim, Se-Kang

    The effect of bootstrapping was studied by examining whether major profile patterns were replicated when sample sizes were reduced. Profile patterns estimated from the original sample (n=645) of the Wechsler Preschool and Primary Scale of IntelligenceThird Edition (WPPSI-III) Standardization Data were considered major profiles. For bootstrapping,…

  14. Interactive differential equations modeling program

    International Nuclear Information System (INIS)

    Rust, B.W.; Mankin, J.B.

    1976-01-01

    Due to the recent emphasis on mathematical modeling, many ecologists are using mathematics and computers more than ever, and engineers, mathematicians and physical scientists are now included in ecological projects. However, the individual ecologist, with intuitive knowledge of the system, still requires the means to critically examine and adjust system models. An interactive program was developed with the primary goal of allowing an ecologist with minimal experience in either mathematics or computers to develop a system model. It has also been used successfully by systems ecologists, engineers, and mathematicians. This program was written in FORTRAN for the DEC PDP-10, a remote terminal system at Oak Ridge National Laboratory. However, with relatively minor modifications, it can be implemented on any remote terminal system with a FORTRAN IV compiler, or equivalent. This program may be used to simulate any phenomenon which can be described as a system of ordinary differential equations. The program allows the user to interactively change system parameters and/or initial conditions, to interactively select a set of variables to be plotted, and to model discontinuities in the state variables and/or their derivatives. One of the most useful features to the non-computer specialist is the ability to interactively address the system parameters by name and to interactively adjust their values between simulations. These and other features are described in greater detail

  15. Database Replication

    Directory of Open Access Journals (Sweden)

    Marius Cristian MAZILU

    2010-12-01

    Full Text Available For someone who has worked in an environment in which the same database is used for data entry and reporting, or perhaps managed a single database server that was utilized by too many users, the advantages brought by data replication are clear. The main purpose of this paper is to emphasize those advantages as well as presenting the different types of Database Replication and the cases in which their use is recommended.

  16. Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization.

    Science.gov (United States)

    Smith, Owen K; Aladjem, Mirit I

    2014-10-09

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review, we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome's three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. Published by Elsevier Ltd.

  17. A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication

    Science.gov (United States)

    Ghosh, Soumendu; Mishra, Bhavya; Patra, Shubhadeep; Schadschneider, Andreas; Chowdhury, Debashish

    2018-04-01

    We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles (P) represents RNAP motors while the other (R) represents the replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of two R particles only are allowed to enter the lattice from two opposite ends whereas the unrestricted number of P particles constitutes a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. The model captures three distinct pathways for resolving the co-directional as well as head-on collision between the P and R particles. Using Monte Carlo simulations and heuristic analytical arguments that combine exact results for the TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors (P particles engaged in transcription) and the replication forks (R particles). In principle, the model can be adapted to experimental conditions to account for the data quantitatively.

  18. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  19. A new model to produce infectious hepatitis C virus without the replication requirement.

    Directory of Open Access Journals (Sweden)

    Miriam Triyatni

    2011-04-01

    Full Text Available Numerous constraints significantly hamper the experimental study of hepatitis C virus (HCV. Robust replication in cell culture occurs with only a few strains, and is invariably accompanied by adaptive mutations that impair in vivo infectivity/replication. This problem complicates the production and study of authentic HCV, including the most prevalent and clinically important genotype 1 (subtypes 1a and 1b. Here we describe a novel cell culture approach to generate infectious HCV virions without the HCV replication requirement and the associated cell-adaptive mutations. The system is based on our finding that the intracellular environment generated by a West-Nile virus (WNV subgenomic replicon rendered a mammalian cell line permissive for assembly and release of infectious HCV particles, wherein the HCV RNA with correct 5' and 3' termini was produced in the cytoplasm by a plasmid-driven dual bacteriophage RNA polymerase-based transcription/amplification system. The released particles preferentially contained the HCV-based RNA compared to the WNV subgenomic RNA. Several variations of this system are described with different HCV-based RNAs: (i HCV bicistronic particles (HCVbp containing RNA encoding the HCV structural genes upstream of a cell-adapted subgenomic replicon, (ii HCV reporter particles (HCVrp containing RNA encoding the bacteriophage SP6 RNA polymerase in place of HCV nonstructural genes, and (iii HCV wild-type particles (HCVwt containing unmodified RNA genomes of diverse genotypes (1a, strain H77; 1b, strain Con1; 2a, strain JFH-1. Infectivity was assessed based on the signals generated by the HCV RNA molecules introduced into the cytoplasm of target cells upon virus entry, i.e. HCV RNA replication and protein production for HCVbp in Huh-7.5 cells as well as for HCVwt in HepG2-CD81 cells and human liver slices, and SP6 RNA polymerase-driven firefly luciferase for HCVrp in target cells displaying candidate HCV surface receptors. HCV

  20. A new model to produce infectious hepatitis C virus without the replication requirement.

    Science.gov (United States)

    Triyatni, Miriam; Berger, Edward A; Saunier, Bertrand

    2011-04-01

    Numerous constraints significantly hamper the experimental study of hepatitis C virus (HCV). Robust replication in cell culture occurs with only a few strains, and is invariably accompanied by adaptive mutations that impair in vivo infectivity/replication. This problem complicates the production and study of authentic HCV, including the most prevalent and clinically important genotype 1 (subtypes 1a and 1b). Here we describe a novel cell culture approach to generate infectious HCV virions without the HCV replication requirement and the associated cell-adaptive mutations. The system is based on our finding that the intracellular environment generated by a West-Nile virus (WNV) subgenomic replicon rendered a mammalian cell line permissive for assembly and release of infectious HCV particles, wherein the HCV RNA with correct 5' and 3' termini was produced in the cytoplasm by a plasmid-driven dual bacteriophage RNA polymerase-based transcription/amplification system. The released particles preferentially contained the HCV-based RNA compared to the WNV subgenomic RNA. Several variations of this system are described with different HCV-based RNAs: (i) HCV bicistronic particles (HCVbp) containing RNA encoding the HCV structural genes upstream of a cell-adapted subgenomic replicon, (ii) HCV reporter particles (HCVrp) containing RNA encoding the bacteriophage SP6 RNA polymerase in place of HCV nonstructural genes, and (iii) HCV wild-type particles (HCVwt) containing unmodified RNA genomes of diverse genotypes (1a, strain H77; 1b, strain Con1; 2a, strain JFH-1). Infectivity was assessed based on the signals generated by the HCV RNA molecules introduced into the cytoplasm of target cells upon virus entry, i.e. HCV RNA replication and protein production for HCVbp in Huh-7.5 cells as well as for HCVwt in HepG2-CD81 cells and human liver slices, and SP6 RNA polymerase-driven firefly luciferase for HCVrp in target cells displaying candidate HCV surface receptors. HCV infectivity

  1. Modelling of the isothermal replication of surface microstructures in polymer melts

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Koblitz; Eriksson, Torbjörn Gerhard

    2005-01-01

    ) melt. A round PC or PS plate with a thickness of 3 mm and a diameter of 59 mm was placed between and at the centre of two squared steel plate. The bottom plate is equipped with a microstructured nickel insert, positioned 46 mm from the middle of the steel plate. The insert contained 10 parallel...... to the incoming molten plastic flow. Just before the flow-front of the melt reached the end of the inserts the polymer was frozen. The replicated PC and PS micro-structures were examined using a confocal laser scanning microscope. Uniaxial elongational viscosity and linear viscoelasticity were used...

  2. PA-X protein decreases replication and pathogenicity of swine influenza virus in cultured cells and mouse models.

    Science.gov (United States)

    Gong, Xiao-Qian; Sun, Ying-Feng; Ruan, Bao-Yang; Liu, Xiao-Min; Wang, Qi; Yang, Hai-Ming; Wang, Shuai-Yong; Zhang, Peng; Wang, Xiu-Hui; Shan, Tong-Ling; Tong, Wu; Zhou, Yan-Jun; Li, Guo-Xin; Zheng, Hao; Tong, Guang-Zhi; Yu, Hai

    2017-06-01

    Swine influenza viruses have been circulating in pigs throughout world and might be potential threats to human health. PA-X protein is a newly discovered protein produced from the PA gene by ribosomal frameshifting and the effects of PA-X on the 1918 H1N1, the pandemic 2009 H1N1, the highly pathogenic avian H5N1 and the avian H9N2 influenza viruses have been reported. However, the role of PA-X in the pathogenesis of swine influenza virus is still unknown. In this study, we rescued the H1N1 wild-type (WT) classical swine influenza virus (A/Swine/Guangdong/1/2011 (H1N1)) and H1N1 PA-X deficient virus containing mutations at the frameshift motif, and compared their replication properties and pathogenicity of swine influenza virus in vitro and in vivo. Our results show that the expression of PA-X inhibits virus replication and polymerase activity in cultured cells and decreases virulence in mouse models. Therefore, our study demonstrates that PA-X protein acts as a negative virulence regulator for classical H1N1 swine influenza virus and decreases virulence by inhibiting viral replication and polymerase activity, deepening our understanding of the pathogenesis of swine influenza virus. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A Comparative Study of Replication-Incompetent and -Competent Adenoviral Therapy-Mediated Immune Response in a Murine Glioma Model.

    Science.gov (United States)

    Kim, Julius W; Miska, Jason; Young, Jacob S; Rashidi, Aida; Kane, J Robert; Panek, Wojciech K; Kanojia, Deepak; Han, Yu; Balyasnikova, Irina V; Lesniak, Maciej S

    2017-06-16

    Oncolytic virotherapy is a treatment approach with increasing clinical relevance, as indicated by the marked survival benefit seen in animal models and its current exploration in human patients with cancer. The use of an adenovirus vector for this therapeutic modality is common, has significant clinical benefit in animals, and its efficacy has recently been linked to an anti-tumor immune response that occurs following tumor antigen presentation. Here, we analyzed the adaptive immune system's response following viral infection by comparing replication-incompetent and replication-competent adenoviral vectors. Our findings suggest that cell death caused by replication-competent adenoviral vectors is required to induce a significant anti-tumor immune response and survival benefits in immunocompetent mice bearing intracranial glioma. We observed significant changes in the repertoire of immune cells in the brain and draining lymph nodes and significant recruitment of CD103+ dendritic cells (DCs) in response to oncolytic adenoviral therapy, suggesting the active role of the immune system in anti-tumor response. Our data suggest that the response to oncolytic virotherapy is accompanied by local and systemic immune responses and should be taken in consideration in the future design of the clinical studies evaluating oncolytic virotherapy in patients with glioblastoma multiforme (GBM).

  4. A Comparative Study of Replication-Incompetent and -Competent Adenoviral Therapy-Mediated Immune Response in a Murine Glioma Model

    Directory of Open Access Journals (Sweden)

    Julius W. Kim

    2017-06-01

    Full Text Available Oncolytic virotherapy is a treatment approach with increasing clinical relevance, as indicated by the marked survival benefit seen in animal models and its current exploration in human patients with cancer. The use of an adenovirus vector for this therapeutic modality is common, has significant clinical benefit in animals, and its efficacy has recently been linked to an anti-tumor immune response that occurs following tumor antigen presentation. Here, we analyzed the adaptive immune system’s response following viral infection by comparing replication-incompetent and replication-competent adenoviral vectors. Our findings suggest that cell death caused by replication-competent adenoviral vectors is required to induce a significant anti-tumor immune response and survival benefits in immunocompetent mice bearing intracranial glioma. We observed significant changes in the repertoire of immune cells in the brain and draining lymph nodes and significant recruitment of CD103+ dendritic cells (DCs in response to oncolytic adenoviral therapy, suggesting the active role of the immune system in anti-tumor response. Our data suggest that the response to oncolytic virotherapy is accompanied by local and systemic immune responses and should be taken in consideration in the future design of the clinical studies evaluating oncolytic virotherapy in patients with glioblastoma multiforme (GBM.

  5. Conceptual Modeling via Logic Programming

    Science.gov (United States)

    1990-01-01

    CONCEPTUAL MODELING VIA LOGIC PROGRAMaNG 12. PERSONAL AUTHOR(S) John Burge, Bill Noah, Las Smith 13a. TYPE OF REPORT 13b. TIME COVERED 14. DATE OF...interpreter and named it Prolog for middle. He found that his program got into an "Programmation en logique ." It provided the infinite loop unless he used... lA N C I WA v Cruse Mle Submartine 44 0 0 0 0 0835 I 9 33 ICC 33 High F.e cruise Misaile 640 0 8S S44 0 0 High Post cruise missile 840 2 7S 440 too

  6. Replicable in vivo physiological and behavioral phenotypes of the Shank3B null mutant mouse model of autism.

    Science.gov (United States)

    Dhamne, Sameer C; Silverman, Jill L; Super, Chloe E; Lammers, Stephen H T; Hameed, Mustafa Q; Modi, Meera E; Copping, Nycole A; Pride, Michael C; Smith, Daniel G; Rotenberg, Alexander; Crawley, Jacqueline N; Sahin, Mustafa

    2017-01-01

    Autism spectrum disorder (ASD) is a clinically and biologically heterogeneous condition characterized by social, repetitive, and sensory behavioral abnormalities. No treatments are approved for the core diagnostic symptoms of ASD. To enable the earliest stages of therapeutic discovery and development for ASD, robust and reproducible behavioral phenotypes and biological markers are essential to establish in preclinical animal models. The goal of this study was to identify electroencephalographic (EEG) and behavioral phenotypes that are replicable between independent cohorts in a mouse model of ASD. The larger goal of our strategy is to empower the preclinical biomedical ASD research field by generating robust and reproducible behavioral and physiological phenotypes in animal models of ASD, for the characterization of mechanistic underpinnings of ASD-relevant phenotypes, and to ensure reliability for the discovery of novel therapeutics. Genetic disruption of the SHANK3 gene, a scaffolding protein involved in the stability of the postsynaptic density in excitatory synapses, is thought to be responsible for a relatively large number of cases of ASD. Therefore, we have thoroughly characterized the robustness of ASD-relevant behavioral phenotypes in two cohorts, and for the first time quantified translational EEG activity in Shank3B null mutant mice. In vivo physiology and behavioral assays were conducted in two independently bred and tested full cohorts of Shank3B null mutant ( Shank3B KO) and wildtype littermate control (WT) mice. EEG was recorded via wireless implanted telemeters for 7 days of baseline followed by 20 min of recording following pentylenetetrazol (PTZ) challenge. Behaviors relevant to the diagnostic and associated symptoms of ASD were tested on a battery of established behavioral tests. Assays were designed to reproduce and expand on the original behavioral characterization of Shank3B KO mice. Two or more corroborative tests were conducted within each

  7. Myc and Ras oncogenes engage different energy metabolism programs and evoke distinct patterns of oxidative and DNA replication stress

    Czech Academy of Sciences Publication Activity Database

    Maya-Mendoza, A.; Ostrakova, J.; Košař, Martin; Hall, A.; Duskova, P.; Mistrik, M.; Merchut-Maya, J.M.; Hodný, Zdeněk; Bartkova, J.; Christensen, C.; Bartek, Jiří

    2015-01-01

    Roč. 9, č. 3 (2015), s. 601-616 ISSN 1574-7891 R&D Projects: GA ČR GA13-17555S; GA MŠk(CZ) LO1304 Grant - others:Danish Council for Independent Research(DK) DFF- 1331-00262; Lundbeck Foundation(DK) R93-A8990 Institutional support: RVO:68378050 Keywords : Myc * Ras * Replication stress * DNA fork progression * Energy metabolism * DNA damage response Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.367, year: 2015

  8. Leading from the Middle: Replication of a Re-Engagement Program for Veterans with Mental Disorders Lost to Follow-Up Care

    Directory of Open Access Journals (Sweden)

    David E. Goodrich

    2012-01-01

    Full Text Available Objectives. Persons with mental disorders experience functional impairments and premature mortality. Limited continuity of care may contribute to disparities in this group. We describe the replication of an evidence-based outreach program (Re-Engage to reconnect Veterans with mental disorders into care who have dropped out of services. Methods. Using the Enhanced Replicating Effective Programs framework, population-based registries were used to identify Veterans lost-to-care, and providers used this information to determine Veteran disposition and need for care. Providers recorded Veteran preferences, health status, and care utilization, and formative process data was collected to document implementation efforts. Results. Among Veterans who dropped out of care (n=126, the mean age was 49 years, 10% were women, and 29% were African-American. Providers determined that 39% of Veterans identified for re-engagement were deceased, hospitalized, or ineligible for care. Of the remaining 68 Veterans, outreach efforts resulted in contact with 20, with 7 returning to care. Providers averaged 14.2 hours over 4 months conducting re-engagement services and reported that gaining facility leadership support and having service agreements for referrals were essential for program implementation. Conclusions. Population-level, panel management strategies to re-engage Veterans with mental disorders are potentially feasible if practices are identified to facilitate national rollout.

  9. Replication, refinement & reachability

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas T.; Slaats, Tijs

    2018-01-01

    We explore the complexity of reachability and run-time refinement under safety and liveness constraints in event-based process models. Our study is framed in the DCR? process language, which supports modular specification through a compositional operational semantics. DCR? encompasses the “Dynamic...... Condition Response (DCR) graphs” declarative process model for analysis, execution and safe run-time refinement of process-aware information systems; including replication of sub-processes. We prove that event-reachability and refinement are np-hard for DCR? processes without replication...

  10. McCoy cell line as a possible model containing CD4+ receptors for the study of HIV-1 replication

    Directory of Open Access Journals (Sweden)

    Nogueira Yeda L.

    2003-01-01

    Full Text Available Several studies have recently shown the use of recombinant rabies virus as potential vector-viral vaccine for HIV-1. The sequence homology between gp 120 and rabies virus glycoprotein has been reported. The McCoy cell line has therefore been used to show CD4+ or CD4+ like receptors. Samples of HIV-1 were isolated, when plasma of HIV-1 positive patients was inoculated in the McCoy cell line. The virus infection was then studied during successive virus passages. The proteins released in the extra cellular medium were checked for protein activity, by exposure to SDS Electrophoresis and blotting to nitro-cellulose filter, then reacting with sera of HIV positive and negative patients. Successive passages were performed, and showed viral replication, membrane permeabilization, the syncytium formation, and the cellular lysis (cytopathic effect. Flow cytometry analysis shows clear evidence that CD4+ receptors are present in this cell line, which enhances the likelihood of easy isolation and replication of HIV. The results observed allow the use of this cell line as a possible model for isolating HIV, as well as for carrying out studies of the dynamics of viral infection in several situations, including exposure to drugs in pharmacological studies, and possibly studies and analyses of the immune response in vaccine therapies.

  11. Replication of type 5 adenovirus promotes middle ear infection by Streptococcus pneumoniae in the chinchilla model of otitis media.

    Science.gov (United States)

    Murrah, Kyle A; Turner, Roberta L; Pang, Bing; Perez, Antonia C; Reimche, Jennifer L; King, Lauren B; Wren, John; Gandhi, Uma; Swords, W Edward; Ornelles, David A

    2015-03-01

    Adenoviral infection is a major risk factor for otitis media. We hypothesized that adenovirus promotes bacterial ascension into the middle ear through the disruption of normal function in the Eustachian tubes due to inflammation-induced changes. An intranasal infection model of the chinchilla was used to test the ability of type 5 adenovirus to promote middle ear infection by Streptococcus pneumoniae. The hyperinflammatory adenovirus mutant dl327 and the nonreplicating adenovirus mutant H5wt300ΔpTP were used to test the role of inflammation and viral replication, respectively, in promotion of pneumococcal middle ear infection. Precedent infection with adenovirus resulted in a significantly greater incidence of middle ear disease by S. pneumoniae as compared to nonadenovirus infected animals. Infection with the adenovirus mutant dl327 induced a comparable degree of bacterial ascension into the middle ear as did infection with the wild-type virus. By contrast, infection with the nonreplicating adenovirus mutant H5wt300ΔpTP resulted in less extensive middle ear infection compared to the wild-type adenovirus. We conclude that viral replication is necessary for adenoviral-induced pneumococcal middle ear disease. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Replication of type 5 adenovirus promotes middle ear infection by Streptococcus pneumoniae in the chinchilla model of otitis media

    Science.gov (United States)

    Murrah, Kyle A.; Turner, Roberta L.; Pang, Bing; Perez, Antonia C.; Reimche, Jennifer L.; King, Lauren B.; Wren, John; Gandhi, Uma; Swords, W. Edward; Ornelles, David A.

    2015-01-01

    Adenoviral infection is a major risk factor for otitis media. We hypothesized that adenovirus promotes bacterial ascension into the middle ear through the disruption of normal function in the Eustachian tubes due to inflammation-induced changes. An intranasal infection model of the chinchilla was used to test the ability of type 5 adenovirus to promote middle ear infection by Streptococcus pneumoniae. The hyperinflammatory adenovirus mutant dl327 and the nonreplicating adenovirus mutant H5wt300ΔpTP were used to test the role of inflammation and viral replication, respectively, in promotion of pneumococcal middle ear infection. Precedent infection with adenovirus resulted in a significantly greater incidence of middle ear disease by S. pneumoniae as compared to nonadenovirus infected animals. Infection with the adenovirus mutant dl327 induced a comparable degree of bacterial ascension into the middle ear as did infection with the wild-type virus. By contrast, infection with the nonreplicating adenovirus mutant H5wt300ΔpTP resulted in less extensive middle ear infection compared to the wild-type adenovirus. We conclude that viral replication is necessary for adenoviral-induced pneumococcal middle ear disease. PMID:25251686

  13. A Unified Approach to Modeling and Programming

    DEFF Research Database (Denmark)

    Madsen, Ole Lehrmann; Møller-Pedersen, Birger

    2010-01-01

    of this paper is to go back to the future and get inspiration from SIMULA and propose a unied approach. In addition to reintroducing the contributions of SIMULA and the Scandinavian approach to object-oriented programming, we do this by discussing a number of issues in modeling and programming and argue3 why we......SIMULA was a language for modeling and programming and provided a unied approach to modeling and programming in contrast to methodologies based on structured analysis and design. The current development seems to be going in the direction of separation of modeling and programming. The goal...

  14. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

    Directory of Open Access Journals (Sweden)

    Guillaume Guilbaud

    2011-12-01

    Full Text Available Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and

  15. The dual pathway model of overeating. Replication and extension with actual food consumption

    NARCIS (Netherlands)

    Ouwens, M.A.; Strien, T. van; Leeuwe, J.F.J. van; Staak, C.P.F. van der

    2009-01-01

    van Strien et al. [van Strien, T., Engels, R. C. M. E., van Leeuwe, J., Snoek, H. M. (2005). The Stice model of overeating: tests in clinical and non-clinical samples. Appetite, 45, 205–213] extended the negative affect pathway of Stice's dual pathway model of overeating Stice [Stice, E. (1994).

  16. The dual pathway model of overeating. Replication and extension with actual food consumption

    NARCIS (Netherlands)

    Ouwens, Machteld A; van Strien, T; Leeuwe, J.F.J.; van der Staak, C P F

    van Strien et al. [van Strien, T., Engels, R. C. M. E., van Leeuwe, J., Snoek, H. M. (2005). The Stice model of overeating: tests in clinical and non-clinical samples. Appetite, 45, 205-213] extended the negative affect pathway of Stice's dual pathway model of overeating Stice [Stice, E. (1994).

  17. Constraints on a preonic model for family replication from the anomalous magnetic moment of leptons

    International Nuclear Information System (INIS)

    Godbole, R.M.

    1986-07-01

    The additional contributions to the anomalous magnetic moment of the muon and the electron ((g-2) l ) in a recently suggested preonic model are considered. It is shown that the parameters in this model are severely restricted when the constraints coming from this analysis are combined with those obtained from the considerations of the quark-lepton mass matrices and mixing angles. (author)

  18. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

    Directory of Open Access Journals (Sweden)

    Sara Imari Walker

    Full Text Available Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for

  19. Inference Based on the Best-Fitting Model can Contribute to the Replication Crisis: Assessing Model Selection Uncertainty Using a Bootstrap Approach

    Science.gov (United States)

    Lubke, Gitta H.; Campbell, Ian

    2016-01-01

    Inference and conclusions drawn from model fitting analyses are commonly based on a single “best-fitting” model. If model selection and inference are carried out using the same data model selection uncertainty is ignored. We illustrate the Type I error inflation that can result from using the same data for model selection and inference, and we then propose a simple bootstrap based approach to quantify model selection uncertainty in terms of model selection rates. A selection rate can be interpreted as an estimate of the replication probability of a fitted model. The benefits of bootstrapping model selection uncertainty is demonstrated in a growth mixture analyses of data from the National Longitudinal Study of Youth, and a 2-group measurement invariance analysis of the Holzinger-Swineford data. PMID:28663687

  20. DNA replication origins in archaea

    Directory of Open Access Journals (Sweden)

    Zhenfang eWu

    2014-04-01

    Full Text Available DNA replication initiation, which starts at specific chromosomal site (known as replication origins, is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator-initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.

  1. An evaluation of the Bayesian approach to fitting the N-mixture model for use with pseudo-replicated count data

    Science.gov (United States)

    Toribo, S.G.; Gray, B.R.; Liang, S.

    2011-01-01

    The N-mixture model proposed by Royle in 2004 may be used to approximate the abundance and detection probability of animal species in a given region. In 2006, Royle and Dorazio discussed the advantages of using a Bayesian approach in modelling animal abundance and occurrence using a hierarchical N-mixture model. N-mixture models assume replication on sampling sites, an assumption that may be violated when the site is not closed to changes in abundance during the survey period or when nominal replicates are defined spatially. In this paper, we studied the robustness of a Bayesian approach to fitting the N-mixture model for pseudo-replicated count data. Our simulation results showed that the Bayesian estimates for abundance and detection probability are slightly biased when the actual detection probability is small and are sensitive to the presence of extra variability within local sites.

  2. Identifying the Minimum Model Features to Replicate Historic Morphodynamics of a Juvenile Delta

    Science.gov (United States)

    Czapiga, M. J.; Parker, G.

    2017-12-01

    We introduce a quasi-2D morphodynamic delta model that improves on past models that require many simplifying assumptions, e.g. a single channel representative of a channel network, fixed channel width, and spatially uniform deposition. Our model is useful for studying long-term progradation rates of any generic micro-tidal delta system with specification of: characteristic grain size, input water and sediment discharges and basin morphology. In particular, we relax the assumption of a single, implicit channel sweeping across the delta topset in favor of an implicit channel network. This network, coupled with recent research on channel-forming Shields number, quantitative assessments of the lateral depositional length of sand (corresponding loosely to levees) and length between bifurcations create a spatial web of deposition within the receiving basin. The depositional web includes spatial boundaries for areas infilling with sands carried as bed material load, as well as those filling via passive deposition of washload mud. Our main goal is to identify the minimum features necessary to accurately model the morphodynamics of channel number, width, depth, and overall delta progradation rate in a juvenile delta. We use the Wax Lake Delta in Louisiana as a test site due to its rapid growth in the last 40 years. Field data including topset/island bathymetry, channel bathymetry, topset/island width, channel width, number of channels, and radial topset length are compiled from US Army Corps of Engineers data for 1989, 1998, and 2006. Additional data is extracted from a DEM from 2015. These data are used as benchmarks for the hindcast model runs. The morphology of Wax Lake Delta is also strongly affected by a pre-delta substrate that acts as a lower "bedrock" boundary. Therefore, we also include closures for a bedrock-alluvial transition and an excess shear rate-law incision model to estimate bedrock incision. The model's framework is generic, but inclusion of individual

  3. Matching allele dynamics and coevolution in a minimal predator-prey replicator model

    Energy Technology Data Exchange (ETDEWEB)

    Sardanyes, Josep [Complex Systems Lab (ICREA-UPF), Barcelona Biomedical Research Park (PRBB-GRIB), Dr. Aiguader 88, 08003 Barcelona (Spain)], E-mail: josep.sardanes@upf.edu; Sole, Ricard V. [Complex Systems Lab (ICREA-UPF), Barcelona Biomedical Research Park (PRBB-GRIB), Dr. Aiguader 88, 08003 Barcelona (Spain); Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501 (United States)

    2008-01-21

    A minimal Lotka-Volterra type predator-prey model describing coevolutionary traits among entities with a strength of interaction influenced by a pair of haploid diallelic loci is studied with a deterministic time continuous model. We show a Hopf bifurcation governing the transition from evolutionary stasis to periodic Red Queen dynamics. If predator genotypes differ in their predation efficiency the more efficient genotype asymptotically achieves lower stationary concentrations.

  4. A Type Graph Model for Java Programs

    NARCIS (Netherlands)

    Rensink, Arend; Zambon, Eduardo

    2009-01-01

    In this report we present a type graph that models all executable constructs of the Java programming language. Such a model is useful for any graph-based technique that relies on a representation of Java programs as graphs. The model can be regarded as a common representation to which all Java

  5. A Type Graph Model for Java Programs

    NARCIS (Netherlands)

    Rensink, Arend; Zambon, Eduardo; Lee, D.; Lopes, A.; Poetzsch-Heffter, A.

    2009-01-01

    In this work we present a type graph that models all executable constructs of the Java programming language. Such a model is useful for any graph-based technique that relies on a representation of Java programs as graphs. The model can be regarded as a common representation to which all Java syntax

  6. Demonstrating Impact through Replicable Analysis: Implications of an Evaluation of Arkansas's Expanded Food and Nutrition Education Program

    Science.gov (United States)

    Phelps, Josh; Brite-Lane, Allison; Crook, Tina; Hakkak, Reza; Fuller, Serena

    2017-01-01

    The evaluation described in this article focused on the effectiveness of Arkansas's Extension-based Expanded Food and Nutrition Education Program (EFNEP) but demonstrates an analytic approach that may be useful across Extension programs. We analyzed data from 1,810 Arkansas EFNEP participants' entry and exit Behavior Checklists to assess…

  7. Educational Program Evaluation Using CIPP Model

    OpenAIRE

    Warju, Warju

    2016-01-01

    There are many models of evaluation that can be used to evaluate a program. However, the most commonly used is the context, input, process, output (CIPP) evaluation models. CIPP evaluation model developed by Stufflebeam and Shinkfield in 1985. The evaluation context is used to give a rational reason a selected program or curriculum to be implemented. A wide scale, context can be evaluated on: the program's objectives, policies that support the vision and mission of the institution, the releva...

  8. Building Program Models Incrementally from Informal Descriptions.

    Science.gov (United States)

    1979-10-01

    AD-AOB6 50 STANFORD UNIV CA DEPT OF COMPUTER SCIENCE F/G 9/2 BUILDING PROGRAM MODELS INCREMENTALLY FROM INFORMAL DESCRIPTION--ETC(U) OCT 79 B P...port SCI.ICS.U.79.2 t Building Program Models Incrementally from Informal Descriptions by Brian P. McCune Research sponsored by Defense Advanced...TYPE OF REPORT & PERIOD COVERED Building Program Models Incrementally from Informal Descriptions. , technical, October 1979 6. PERFORMING ORG

  9. Robust option replication for a Black-Scholes model extended with nondeterministic trends

    NARCIS (Netherlands)

    Schoenmakers, J.G.M.; Kloeden, P.E.

    1999-01-01

    Statistical analysis on various stocks reveals long range dependence behavior of the stock prices that is not consistent with the classical Black and Scholes model. This memory or nondeterministic trend behavior is often seen as a reflection of market sentiments and causes that the historical

  10. CENTRIOLE REPLICATION

    Science.gov (United States)

    Mizukami, Ikuko; Gall, Joseph

    1966-01-01

    Sperm formation was studied in the fern, Marsilea, and the cycad, Zamia, with particular emphasis on the centrioles. In Marsilea, the mature sperm possesses over 100 flagella, the basal bodies of which have the typical cylindrical structure of centrioles. Earlier observations by light microscopy suggested that these centrioles arise by fragmentation of a body known as the blepharoplast. In the youngest spermatids the blepharoplast is a hollow sphere approximately 0.8 µ in diameter. Its wall consists of closely packed immature centrioles, or procentrioles. The procentrioles are short cylinders which progressively lengthen during differentiation of the spermatid. At the same time they migrate to the surface of the cell, where each of them puts out a flagellum. A blepharoplast is found at each pole of the spindle during the last antheridial mitosis, and two blepharoplasts are found in the cytoplasm before this mitosis. Blepharoplasts are also found in the preceding cell generation, but their ultimate origin is obscure. Before the last mitosis the blepharoplasts are solid, consisting of a cluster of radially arranged tubules which bear some structural similarity to centrioles. In Zamia, similar stages are found during sperm formation, although here the number of flagella on each sperm is close to 20,000 and the blepharoplast measures about 10 µ in diameter. These observations are discussed in relation to theories of centriole replication. PMID:5950730

  11. Petrogenetic Modeling with a Spreadsheet Program.

    Science.gov (United States)

    Holm, Paul Eric

    1988-01-01

    Describes how interactive programs for scientific modeling may be created by using spreadsheet software such as LOTUS 1-2-3. Lists the advantages of using this method. Discusses fractional distillation, batch partial melting, and combination models as examples. (CW)

  12. Productively infected murine Kaposi's sarcoma-like tumors define new animal models for studying and targeting KSHV oncogenesis and replication.

    Directory of Open Access Journals (Sweden)

    Brittany M Ashlock

    Full Text Available Kaposi's sarcoma (KS is an AIDS-defining cancer caused by the KS-associated herpesvirus (KSHV. KS tumors are composed of KSHV-infected spindle cells of vascular origin with aberrant neovascularization and erythrocyte extravasation. KSHV genes expressed during both latent and lytic replicative cycles play important roles in viral oncogenesis. Animal models able to recapitulate both viral and host biological characteristics of KS are needed to elucidate oncogenic mechanisms, for developing targeted therapies, and to trace cellular components of KS ontogeny. Herein, we describe two new murine models of Kaposi's sarcoma. We found that murine bone marrow-derived cells, whether established in culture or isolated from fresh murine bone marrow, were infectable with rKSHV.219, formed KS-like tumors in immunocompromised mice and produced mature herpesvirus-like virions in vivo. Further, we show in vivo that the histone deacetylase (HDAC inhibitor suberoylanilide hydroxamic acid (SAHA/Vorinostat enhanced viral lytic reactivation. We propose that these novel models are ideal for studying both viral and host contributions to KSHV-induced oncogenesis as well as for testing virally-targeted antitumor strategies for the treatment of Kaposi's sarcoma. Furthermore, our isolation of bone marrow-derived cell populations containing a cell type that, when infected with KSHV, renders a tumorigenic KS-like spindle cell, should facilitate systematic identification of KS progenitor cells.

  13. VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.

    Science.gov (United States)

    Delmar, Paul; Robin, Stéphane; Daudin, Jean Jacques

    2005-02-15

    Identifying differentially regulated genes in experiments comparing two experimental conditions is often a key step in the microarray data analysis process. Many different approaches and methodological developments have been put forward, yet the question remains open. Varmixt is a powerful and efficient novel methodology for this task. It is based on a flexible and realistic variance modelling strategy. It compares favourably with other popular techniques (standard t-test, SAM and Cyber-T). The relevance of the approach is demonstrated with real-world and simulated datasets. The analysis strategy was successfully applied to both a 'two-colour' cDNA microarray and an Affymetrix Genechip. Strong control of false positive and false negative rates is proven in large simulation studies. The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html delmar@inapg.inra.fr http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html.

  14. Applied Integer Programming Modeling and Solution

    CERN Document Server

    Chen, Der-San; Dang, Yu

    2011-01-01

    An accessible treatment of the modeling and solution of integer programming problems, featuring modern applications and software In order to fully comprehend the algorithms associated with integer programming, it is important to understand not only how algorithms work, but also why they work. Applied Integer Programming features a unique emphasis on this point, focusing on problem modeling and solution using commercial software. Taking an application-oriented approach, this book addresses the art and science of mathematical modeling related to the mixed integer programming (MIP) framework and

  15. Doctoral training in statistics, measurement, and methodology in psychology: replication and extension of Aiken, West, Sechrest, and Reno's (1990) survey of PhD programs in North America.

    Science.gov (United States)

    Aiken, Leona S; West, Stephen G; Millsap, Roger E

    2008-01-01

    In a survey of all PhD programs in psychology in the United States and Canada, the authors documented the quantitative methodology curriculum (statistics, measurement, and research design) to examine the extent to which innovations in quantitative methodology have diffused into the training of PhDs in psychology. In all, 201 psychology PhD programs (86%) participated. This survey replicated and extended a previous survey (L. S. Aiken, S. G. West, L. B. Sechrest, & R. R. Reno, 1990), permitting examination of curriculum development. Most training supported laboratory and not field research. The median of 1.6 years of training in statistics and measurement was mainly devoted to the modally 1-year introductory statistics course, leaving little room for advanced study. Curricular enhancements were noted in statistics and to a minor degree in measurement. Additional coverage of both fundamental and innovative quantitative methodology is needed. The research design curriculum has largely stagnated, a cause for great concern. Elite programs showed no overall advantage in quantitative training. Forces that support curricular innovation are characterized. Human capital challenges to quantitative training, including recruiting and supporting young quantitative faculty, are discussed. Steps must be taken to bring innovations in quantitative methodology into the curriculum of PhD programs in psychology. PsycINFO Database Record (c) 2008 APA, all rights reserved.

  16. Olive baboons: a non-human primate model for testing dengue virus type 2 replication.

    Science.gov (United States)

    Valdés, Iris; Gil, Lázaro; Castro, Jorge; Odoyo, Damián; Hitler, Rikoi; Munene, Elephas; Romero, Yaremis; Ochola, Lucy; Cosme, Karelia; Kariuki, Thomas; Guillén, Gerardo; Hermida, Lisset

    2013-12-01

    This study evaluated the use of a non-human primate, the olive baboon (Papio anubis), as a model of dengue infection. Olive baboons closely resemble humans genetically and physiologically and have been used extensively for assessing novel vaccine formulations. Two doses of dengue virus type 2 (DENV-2) were tested in baboons: 10(3) and 10(4) pfu. Similarly, African green monkeys received the same quantity of virus and acted as positive controls. Following exposure, high levels of viremia were detected in both animal species. There was a trend to detect more days of viremia and more homogeneous viral titers in animals receiving the low viral dose. In addition, baboons infected with the virus generally exhibited positive virus isolation 1 day later than African green monkeys. Humoral responses consisting of antiviral and neutralizing antibodies were detected in all animals after infection. We conclude that baboons provide an alternative non-human primate species for experimental DENV-2 infection and we recommend their use for further tests of vaccines, administering the lowest dose assayed: 10(3) pfu. Copyright © 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  17. Replication of Effects of the "Positive Action" Program in Randomized Trials in Hawai'i and Chicago Schools

    Science.gov (United States)

    Flay, Brian R.

    2014-01-01

    Several social-emotional learning (SEL) or social-emotional and character development (SECD) programs have been shown to be effective at improving SEL/SECD skills, and some have also provided evidence of effectiveness in improving student behavior and academic achievement (Durlak, Weissberg, Dymnicki, Taylor, & Schellinger, 2011). Very few SEL…

  18. Model Checking JAVA Programs Using Java Pathfinder

    Science.gov (United States)

    Havelund, Klaus; Pressburger, Thomas

    2000-01-01

    This paper describes a translator called JAVA PATHFINDER from JAVA to PROMELA, the "programming language" of the SPIN model checker. The purpose is to establish a framework for verification and debugging of JAVA programs based on model checking. This work should be seen in a broader attempt to make formal methods applicable "in the loop" of programming within NASA's areas such as space, aviation, and robotics. Our main goal is to create automated formal methods such that programmers themselves can apply these in their daily work (in the loop) without the need for specialists to manually reformulate a program into a different notation in order to analyze the program. This work is a continuation of an effort to formally verify, using SPIN, a multi-threaded operating system programmed in Lisp for the Deep-Space 1 spacecraft, and of previous work in applying existing model checkers and theorem provers to real applications.

  19. Mindfulness-Based Stress Release Program for University Employees: A Pilot, Waitlist-Controlled Trial and Implementation Replication.

    Science.gov (United States)

    Koncz, Rebecca; Wolfenden, Fiona; Hassed, Craig; Chambers, Richard; Cohen, Julia; Glozier, Nicholas

    2016-10-01

    The aim of this study was to evaluate the effectiveness of a 6-week mindfulness-based stress release program (SRP) on stress and work engagement in fulltime university employees. Perceived stress, workplace wellbeing, and engagement were measured at baseline and within 1 week of the SRP completion, and contemporaneously 6 weeks apart for a waitlist control group. A second program was implemented to examine reproducibility of results. Fifty participants undertook the SRPs, and 29 participants were waitlisted. A significant improvement in distress, workplace wellbeing, and vigor was observed within the first SRP group, when compared with the control group. The improvement in distress and wellbeing was reproduced in the second SRP group. This study adds to the growing body of research that mindfulness may be an effective method for reducing workplace stress, improving employee wellbeing, and enhancing work engagement.

  20. Mental Models and Programming Aptitude

    DEFF Research Database (Denmark)

    Caspersen, Michael Edelgaard; Bennedsen, Jens; Larsen, Kasper Dalgaard

    2007-01-01

    Predicting the success of students participating in introductory programming courses has been an active research area for more than 25 years. Until recently, no variables or tests have had any significant predictive power. However, Dehnadi and Bornat claim to have found a simple test for programm...

  1. Language Teaching Models in Teacher Training Programs

    OpenAIRE

    Aslan, Alper

    2016-01-01

    Any language teacher who has gone through some kind of training program for the teaching of English should be familiar with various specific language teaching models that constitute the core of the training process. A language teaching model is a guide that helps the trainee to sequence the activities designed for the expectations and needs of learners in a lesson. This paper reviews the common language teaching models in teacher training programs (PPP, OHE, III, TTT, TBLT, ESA, ARC) and disc...

  2. LHCb experience with LFC replication

    CERN Document Server

    Bonifazi, F; Perez, E D; D'Apice, A; dell'Agnello, L; Düllmann, D; Girone, M; Re, G L; Martelli, B; Peco, G; Ricci, P P; Sapunenko, V; Vagnoni, V; Vitlacil, D

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  3. Human Mitochondrial DNA Replication

    Science.gov (United States)

    Holt, Ian J.; Reyes, Aurelio

    2012-01-01

    Elucidation of the process of DNA replication in mitochondria is in its infancy. For many years, maintenance of the mitochondrial genome was regarded as greatly simplified compared to the nucleus. Mammalian mitochondria were reported to lack all DNA repair systems, to eschew DNA recombination, and to possess but a single DNA polymerase, polymerase γ. Polγ was said to replicate mitochondrial DNA exclusively via one mechanism, involving only two priming events and a handful of proteins. In this “strand-displacement model,” leading strand DNA synthesis begins at a specific site and advances approximately two-thirds of the way around the molecule before DNA synthesis is initiated on the “lagging” strand. Although the displaced strand was long-held to be coated with protein, RNA has more recently been proposed in its place. Furthermore, mitochondrial DNA molecules with all the features of products of conventional bidirectional replication have been documented, suggesting that the process and regulation of replication in mitochondria is complex, as befits a genome that is a core factor in human health and longevity. PMID:23143808

  4. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    2009-03-01

    Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.

  5. Dialectic Antidotes to Critics of the Technology Acceptance Model: Conceptual, Methodological, and Replication Treatments for Behavioural Modelling in Technology-Mediated Environments

    Directory of Open Access Journals (Sweden)

    Weng Marc Lim

    2018-01-01

    Full Text Available The technology acceptance model (TAM is a prominent and parsimonious conceptual lens that is often applied for behavioural modelling in technology-mediated environments. However, TAM has received a great deal of criticism in recent years. This article aims to address some of the most pertinent issues confronting TAM through a rejoinder that offers dialectic antidotes—in the form of conceptual, methodological, and replication treatments—to support the continued use of TAM to understand the peculiarities of user interactions with technology in technology-mediated environments. In doing so, this article offers a useful response to a common but often inadequately answered question about how TAM can continue to be relevant for behavioural modelling in contemporary technology-mediated environments.

  6. Measurement control program at model facility

    International Nuclear Information System (INIS)

    Schneider, R.A.

    1984-01-01

    A measurement control program for the model plant is described. The discussion includes the technical basis for such a program, the application of measurement control principles to each measurement, and the use of special experiments to estimate measurement error parameters for difficult-to-measure materials. The discussion also describes the statistical aspects of the program, and the documentation procedures used to record, maintain, and process the basic data

  7. Integer Programming Models for Sales Resource Allocation

    OpenAIRE

    Andris A. Zoltners; Prabhakant Sinha

    1980-01-01

    A practical conceptual framework for sales resource allocation modeling is presented in this paper. A literature review of sales resource allocation models is described in terms of this framework. The conceptual framework also lends itself to several integer programming models which may be used to address the variety of sales resource allocation decisions faced by every sales organization. A general model for sales resource allocation is developed which incorporates multiple sales resources, ...

  8. Recombination-dependent concatemeric viral DNA replication.

    Science.gov (United States)

    Lo Piano, Ambra; Martínez-Jiménez, María I; Zecchi, Lisa; Ayora, Silvia

    2011-09-01

    The initiation of viral double stranded (ds) DNA replication involves proteins that recruit and load the replisome at the replication origin (ori). Any block in replication fork progression or a programmed barrier may act as a factor for ori-independent remodelling and assembly of a new replisome at the stalled fork. Then replication initiation becomes dependent on recombination proteins, a process called recombination-dependent replication (RDR). RDR, which is recognized as being important for replication restart and stability in all living organisms, plays an essential role in the replication cycle of many dsDNA viruses. The SPP1 virus, which infects Bacillus subtilis cells, serves as a paradigm to understand the links between replication and recombination in circular dsDNA viruses. SPP1-encoded initiator and replisome assembly proteins control the onset of viral replication and direct the recruitment of host-encoded replisomal components at viral oriL. SPP1 uses replication fork reactivation to switch from ori-dependent θ-type (circle-to-circle) replication to σ-type RDR. Replication fork arrest leads to a double strand break that is processed by viral-encoded factors to generate a D-loop into which a new replisome is assembled, leading to σ-type viral replication. SPP1 RDR proteins are compared with similar proteins encoded by other viruses and their possible in vivo roles are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Potential for Low-Pathogenic Avian H7 Influenza A Viruses To Replicate and Cause Disease in a Mammalian Model.

    Science.gov (United States)

    Zanin, Mark; Koçer, Zeynep A; Poulson, Rebecca L; Gabbard, Jon D; Howerth, Elizabeth W; Jones, Cheryl A; Friedman, Kimberly; Seiler, Jon; Danner, Angela; Kercher, Lisa; McBride, Ryan; Paulson, James C; Wentworth, David E; Krauss, Scott; Tompkins, Stephen M; Stallknecht, David E; Webster, Robert G

    2017-02-01

    H7 subtype influenza A viruses are widely distributed and have been responsible for human infections and numerous outbreaks in poultry with significant impact. Despite this, the disease-causing potential of the precursor low-pathogenic (LP) H7 viruses from the wild bird reservoir has not been investigated. Our objective was to assess the disease-causing potential of 30 LP H7 viruses isolated from wild avian species in the United States and Canada using the DBA/2J mouse model. Without prior mammalian adaptation, the majority of viruses, 27 (90%), caused mortality in mice. Of these, 17 (56.7%) caused 100% mortality and 24 were of pathogenicity similar to that of A/Anhui/1/2013 (H7N9), which is highly pathogenic in mice. Viruses of duck origin were more pathogenic than those of shorebird origin, as 13 of 18 (72.2%) duck origin viruses caused 100% mortality while 4 of 12 (33.3%) shorebird origin viruses caused 100% mortality, despite there being no difference in mean lung viral titers between the groups. Replication beyond the respiratory tract was also evident, particularly in the heart and brain. Of the 16 viruses studied for fecal shedding, 11 were detected in fecal samples. These viruses exhibited a strong preference for avian-type α2,3-linked sialic acids; however, binding to mammalian-type α2,6-linked sialic acids was also detected. These findings indicate that LP avian H7 influenza A viruses are able to infect and cause disease in mammals without prior adaptation and therefore pose a potential public health risk. Low-pathogenic (LP) avian H7 influenza A viruses are widely distributed in the avian reservoir and are the precursors of numerous outbreaks of highly pathogenic avian influenza viruses in commercial poultry farms. However, unlike highly pathogenic H7 viruses, the disease-causing potential of LP H7 viruses from the wild bird reservoir has not been investigated. To address this, we studied 30 LP avian H7 viruses isolated from wild avian species in the

  10. Establishment of a mouse melanoma model system for the efficient infection and replication of human adenovirus type 5-based oncolytic virus.

    Science.gov (United States)

    Kang, Sujin; Kim, Joo-Hang; Kim, So Young; Kang, Dongxu; Je, Suyeon; Song, Jae J

    2014-10-24

    Due to poor adenoviral infectivity and replication in mouse tumor cell types compared with human tumor cell types, use of human-type adenoviral vectors in mouse animal model systems was limited. Here, we demonstrate enhanced infectivity and productive replication of adenovirus in mouse melanoma cells following introduction of both the Coxsackievirus and adenovirus receptor (CAR) and E1B-55K genes. Introduction of CAR into B16BL6 or B16F10 cells increased the infectivity of GFP-expressing adenovirus; however, viral replication was unaffected. We demonstrated a dramatic increase of adenoviral replication (up to 100-fold) in mouse cells via E1B-55K expression and subsequent viral spreading in mouse tissue. These results reveal for the first time that human adenovirus type 5 (Ad5)-based oncolytic virus can be applied to immunocompetent mouse with the introduction of CAR and E1B-55K to syngenic mouse cell line. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Academic program models for undergraduate biomedical engineering.

    Science.gov (United States)

    Krishnan, Shankar M

    2014-01-01

    There is a proliferation of medical devices across the globe for the diagnosis and therapy of diseases. Biomedical engineering (BME) plays a significant role in healthcare and advancing medical technologies thus creating a substantial demand for biomedical engineers at undergraduate and graduate levels. There has been a surge in undergraduate programs due to increasing demands from the biomedical industries to cover many of their segments from bench to bedside. With the requirement of multidisciplinary training within allottable duration, it is indeed a challenge to design a comprehensive standardized undergraduate BME program to suit the needs of educators across the globe. This paper's objective is to describe three major models of undergraduate BME programs and their curricular requirements, with relevant recommendations to be applicable in institutions of higher education located in varied resource settings. Model 1 is based on programs to be offered in large research-intensive universities with multiple focus areas. The focus areas depend on the institution's research expertise and training mission. Model 2 has basic segments similar to those of Model 1, but the focus areas are limited due to resource constraints. In this model, co-op/internship in hospitals or medical companies is included which prepares the graduates for the work place. In Model 3, students are trained to earn an Associate Degree in the initial two years and they are trained for two more years to be BME's or BME Technologists. This model is well suited for the resource-poor countries. All three models must be designed to meet applicable accreditation requirements. The challenges in designing undergraduate BME programs include manpower, facility and funding resource requirements and time constraints. Each academic institution has to carefully analyze its short term and long term requirements. In conclusion, three models for BME programs are described based on large universities, colleges, and

  12. Logic integer programming models for signaling networks.

    Science.gov (United States)

    Haus, Utz-Uwe; Niermann, Kathrin; Truemper, Klaus; Weismantel, Robert

    2009-05-01

    We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this, we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in molecular biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included.

  13. Description of mathematical models and computer programs

    International Nuclear Information System (INIS)

    1977-01-01

    The paper gives a description of mathematical models and computer programs for analysing possible strategies for spent fuel management, with emphasis on economic analysis. The computer programs developed, describe the material flows, facility construction schedules, capital investment schedules and operating costs for the facilities used in managing the spent fuel. The computer programs use a combination of simulation and optimization procedures for the economic analyses. Many of the fuel cycle steps (such as spent fuel discharges, storage at the reactor, and transport to the RFCC) are described in physical and economic terms through simulation modeling, while others (such as reprocessing plant size and commissioning schedules, interim storage facility commissioning schedules etc.) are subjected to economic optimization procedures to determine the approximate lowest-cost plans from among the available feasible alternatives

  14. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  15. Equivalence Problem Solvability in Biparametric Gateway Program Models

    Directory of Open Access Journals (Sweden)

    A. E. Molchanov

    2014-01-01

    Full Text Available Algebraic program models with procedures are designed to analyze program semantic properties on their models called program schemes. Procedural liberisation problem and equivalence problem are stated for program models with procedures in which both defining parameters are chosen independently. Program models with procedures built over a given program model without procedures are investigated. Algorithms for both stated tasks are proposed for models where an additional restriction is applied: the intersection emptiness problem is solvable in the program model without procedures. Polynomial estimates for the complexity of the algorithms are shown. Some topics for further investigation are proposed.

  16. ZATPAC: a model consortium evaluates teen programs.

    Science.gov (United States)

    Owen, Kathryn; Murphy, Dana; Parsons, Chris

    2009-09-01

    How do we advance the environmental literacy of young people, support the next generation of environmental stewards and increase the diversity of the leadership of zoos and aquariums? We believe it is through ongoing evaluation of zoo and aquarium teen programming and have founded a consortium to pursue those goals. The Zoo and Aquarium Teen Program Assessment Consortium (ZATPAC) is an initiative by six of the nation's leading zoos and aquariums to strengthen institutional evaluation capacity, model a collaborative approach toward assessing the impact of youth programs, and bring additional rigor to evaluation efforts within the field of informal science education. Since its beginning in 2004, ZATPAC has researched, developed, pilot-tested and implemented a pre-post program survey instrument designed to assess teens' knowledge of environmental issues, skills and abilities to take conservation actions, self-efficacy in environmental actions, and engagement in environmentally responsible behaviors. Findings from this survey indicate that teens who join zoo/aquarium programs are already actively engaged in many conservation behaviors. After participating in the programs, teens showed a statistically significant increase in their reported knowledge of conservation and environmental issues and their abilities to research, explain, and find resources to take action on conservation issues of personal concern. Teens also showed statistically significant increases pre-program to post-program for various conservation behaviors, including "I talk with my family and/or friends about things they can do to help the animals or the environment," "I save water...," "I save energy...," "When I am shopping I look for recycled products," and "I help with projects that restore wildlife habitat."

  17. Database structure for plasma modeling programs

    International Nuclear Information System (INIS)

    Dufresne, M.; Silvester, P.P.

    1993-01-01

    Continuum plasma models often use a finite element (FE) formulation. Another approach is simulation models based on particle-in-cell (PIC) formulation. The model equations generally include four nonlinear differential equations specifying the plasma parameters. In simulation a large number of equations must be integrated iteratively to determine the plasma evolution from an initial state. The complexity of the resulting programs is a combination of the physics involved and the numerical method used. The data structure requirements of plasma programs are stated by defining suitable abstract data types. These abstractions are then reduced to data structures and a group of associated algorithms. These are implemented in an object oriented language (C++) as object classes. Base classes encapsulate data management into a group of common functions such as input-output management, instance variable updating and selection of objects by Boolean operations on their instance variables. Operations are thereby isolated from specific element types and uniformity of treatment is guaranteed. Creation of the data structures and associated functions for a particular plasma model is reduced merely to defining the finite element matrices for each equation, or the equations of motion for PIC models. Changes in numerical method or equation alterations are readily accommodated through the mechanism of inheritance, without modification of the data management software. The central data type is an n-relation implemented as a tuple of variable internal structure. Any finite element program may be described in terms of five relational tables: nodes, boundary conditions, sources, material/particle descriptions, and elements. Equivalently, plasma simulation programs may be described using four relational tables: cells, boundary conditions, sources, and particle descriptions

  18. Transnational nursing programs: models, advantages and challenges.

    Science.gov (United States)

    Wilson, Michael

    2002-07-01

    Conducting transnational programs can be a very rewarding activity for a School, Faculty or University. Apart from increasing the profile of the university, the conduct of transnational programs can also provide the university with openings for business opportunities, consultative activities, and collaborative research. It can also be a costly exercise placing an enormous strain on limited resources with little reward for the provider. Transnational ventures can become nonviable entities in a very short period of time due to unanticipated global economic trends. Transnational courses offered by Faculties of Business and Computing are commonplace, however, there is a growing number of health science programs, particularly nursing that are being offered transnational. This paper plans an overview of several models employed for the delivery of transnational nursing courses and discusses several key issues pertaining to conducting courses outside the host university's country.

  19. The NIAID Radiation Countermeasures Program business model.

    Science.gov (United States)

    Hafer, Nathaniel; Maidment, Bert W; Hatchett, Richard J

    2010-12-01

    The National Institute of Allergy and Infectious Diseases (NIAID) Radiation/Nuclear Medical Countermeasures Development Program has developed an integrated approach to providing the resources and expertise required for the research, discovery, and development of radiation/nuclear medical countermeasures (MCMs). These resources and services lower the opportunity costs and reduce the barriers to entry for companies interested in working in this area and accelerate translational progress by providing goal-oriented stewardship of promising projects. In many ways, the radiation countermeasures program functions as a "virtual pharmaceutical firm," coordinating the early and mid-stage development of a wide array of radiation/nuclear MCMs. This commentary describes the radiation countermeasures program and discusses a novel business model that has facilitated product development partnerships between the federal government and academic investigators and biopharmaceutical companies.

  20. Stellar Atmospheric Modelling for the ACCESS Program

    Science.gov (United States)

    Morris, Matthew; Kaiser, Mary Elizabeth; Bohlin, Ralph; Kurucz, Robert; ACCESS Team

    2018-01-01

    A goal of the ACCESS program (Absolute Color Calibration Experiment for Standard Stars) is to enable greater discrimination between theoretical astrophysical models and observations, where the comparison is limited by systematic errors associated with the relative flux calibration of the targets. To achieve these goals, ACCESS has been designed as a sub-orbital rocket borne payload and ground calibration program, to establish absolute flux calibration of stellar targets at high resolution spectra in addition to the HST/CALSPEC data, we have generated stellar atmosphere models for ACCESS flight candidates, as well as a selection of A and G stars from the CALSPEC database. Stellar atmosphere models were generated using Atlas 9 and Atlas 12 Kurucz stellar atmosphere software. The effective temperature, log(g), metallicity, and redenning were varied and the chi-squared statistic was minimized to obtain a best-fit model. A comparison of these models and the results from interpolation between grids of existing models will be presented. The impact of the flexibility of the Atlas 12 input parameters (e.g. solar metallicity fraction, abundances, microturbulent velocity) is being explored.

  1. Prophylactic use of Ganoderma lucidum extract may inhibit Mycobacterium tuberculosis replication in a new mouse model of spontaneous latent tuberculosis infection

    Directory of Open Access Journals (Sweden)

    Chuan eQin

    2016-01-01

    Full Text Available A mouse model of spontaneous latent tuberculosis infection (LTBIthat mimics latent tuberculosis infection in humans is valuable for drug/vaccine development and the study of tuberculosis. However, most LTBI mouse models require interventions, and a spontaneous LTBI mouse model with a low bacterial load is difficult to establish. In this study, mice were IV-inoculated with 100 CFU Mycobacterium tuberculosis H37Rv, and a persistent LTBI was established with low bacterial loads (0.5~1.5log10 CFU in the lung; <4log10 CFU in the spleen. Histopathological changes in the lung, spleen, and liver were mild during the first 20 weeks post-inoculation. The model was used to demonstrate the comparative effects of prophylactic and therapeutic administration of Ganoderma lucidum extract (spores and spores lipid in preventing H37Rv replication in both lung and spleen. H37Rv was inhibited with prophylactic use of G. lucidum extract relative to that of the untreated control and therapy groups, and observed in the spleen as early as post-inoculation week 3. H37Rv infection in the therapy group was comparable to that of the untreated control mice. No significant mitigation of pathological changes was observed in either the prophylactic or therapeutic groups. Our results suggest that this LTBI model is an efficient means of testing anti-tuberculosis vaccines and drugs. The use of G. lucidum extract prior to M. tuberculosis infection may protect the host against bacterial replication to some extent.

  2. Use of two-part regression calibration model to correct for measurement error in episodically consumed foods in a single-replicate study design: EPIC case study.

    Science.gov (United States)

    Agogo, George O; van der Voet, Hilko; van't Veer, Pieter; Ferrari, Pietro; Leenders, Max; Muller, David C; Sánchez-Cantalejo, Emilio; Bamia, Christina; Braaten, Tonje; Knüppel, Sven; Johansson, Ingegerd; van Eeuwijk, Fred A; Boshuizen, Hendriek

    2014-01-01

    In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model.

  3. Use of two-part regression calibration model to correct for measurement error in episodically consumed foods in a single-replicate study design: EPIC case study.

    Directory of Open Access Journals (Sweden)

    George O Agogo

    Full Text Available In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model.

  4. Use of Two-Part Regression Calibration Model to Correct for Measurement Error in Episodically Consumed Foods in a Single-Replicate Study Design: EPIC Case Study

    Science.gov (United States)

    Agogo, George O.; van der Voet, Hilko; Veer, Pieter van’t; Ferrari, Pietro; Leenders, Max; Muller, David C.; Sánchez-Cantalejo, Emilio; Bamia, Christina; Braaten, Tonje; Knüppel, Sven; Johansson, Ingegerd; van Eeuwijk, Fred A.; Boshuizen, Hendriek

    2014-01-01

    In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model. PMID:25402487

  5. Model for behavior observation training programs

    International Nuclear Information System (INIS)

    Berghausen, P.E. Jr.

    1987-01-01

    Continued behavior observation is mandated by ANSI/ANS 3.3. This paper presents a model for behavior observation training that is in accordance with this standard and the recommendations contained in US NRC publications. The model includes seventeen major topics or activities. Ten of these are discussed: Pretesting of supervisor's knowledge of behavior observation requirements, explanation of the goals of behavior observation programs, why behavior observation training programs are needed (legal and psychological issues), early indicators of emotional instability, use of videotaped interviews to demonstrate significant psychopathology, practice recording behaviors, what to do when unusual behaviors are observed, supervisor rationalizations for noncompliance, when to be especially vigilant, and prevention of emotional instability

  6. Keys to the House: Unlocking Residential Savings With Program Models for Home Energy Upgrades

    Energy Technology Data Exchange (ETDEWEB)

    Grevatt, Jim [Energy Futures Group (United States); Hoffman, Ian [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hoffmeyer, Dale [US Department of Energy, Washington, DC (United States)

    2017-07-05

    After more than 40 years of effort, energy efficiency program administrators and associated contractors still find it challenging to penetrate the home retrofit market, especially at levels commensurate with state and federal goals for energy savings and emissions reductions. Residential retrofit programs further have not coalesced around a reliably successful model. They still vary in design, implementation and performance, and they remain among the more difficult and costly options for acquiring savings in the residential sector. If programs are to contribute fully to meeting resource and policy objectives, administrators need to understand what program elements are key to acquiring residential savings as cost effectively as possible. To that end, the U.S. Department of Energy (DOE) sponsored a comprehensive review and analysis of home energy upgrade programs with proven track records, focusing on those with robustly verified savings and constituting good examples for replication. The study team reviewed evaluations for the period 2010 to 2014 for 134 programs that are funded by customers of investor-owned utilities. All are programs that promote multi-measure retrofits or major system upgrades. We paid particular attention to useful design and implementation features, costs, and savings for nearly 30 programs with rigorous evaluations of performance. This meta-analysis describes program models and implementation strategies for (1) direct install retrofits; (2) heating, ventilating and air-conditioning (HVAC) replacement and early retirement; and (3) comprehensive, whole-home retrofits. We analyze costs and impacts of these program models, in terms of both energy savings and emissions avoided. These program models can be useful guides as states consider expanding their strategies for acquiring energy savings as a resource and for emissions reductions. We also discuss the challenges of using evaluations to create program models that can be confidently applied in

  7. Generalized data stacking programming model with applications

    OpenAIRE

    Hala Samir Elhadidy; Rawya Yehia Rizk; Hassen Taher Dorrah

    2016-01-01

    Recent researches have shown that, everywhere in various sciences the systems are following stacked-based stored change behavior when subjected to events or varying environments “on and above” their normal situations. This paper presents a generalized data stack programming (GDSP) model which is developed to describe the system changes under varying environment. These changes which are captured with different ways such as sensor reading are stored in matrices. Extraction algorithm and identif...

  8. Can Household Benefit from Stochastic Programming Models?

    DEFF Research Database (Denmark)

    Rasmussen, Kourosh Marjani; Madsen, Claus A.; Poulsen, Rolf

    2014-01-01

    The Danish mortgage market is large and sophisticated. However, most Danish mortgage banks advise private home-owners based on simple, if sensible, rules of thumb. In recent years a number of papers (from Nielsen and Poulsen in J Econ Dyn Control 28:1267–1289, 2004 over Rasmussen and Zenios in J...... Risk 10:1–18, 2007 to Pedersen et al. in Ann Oper Res, 2013) have suggested a model-based, stochastic programming approach to mortgage choice. This paper gives an empirical comparison of performance over the period 2000–2010 of the rules of thumb to the model-based strategies. While the rules of thumb...

  9. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

    Beta cell mass, at any given time, is governed by cell differentiation, neogenesis, increased or decreased cell size (cell hypertrophy or atrophy), cell death (apoptosis), and beta cell proliferation. Nutrients, hormones and growth factors coupled with their signalling intermediates have been...... suggested to play a role in beta cell mass regulation. In addition, genetic mouse model studies have indicated that cyclins and cyclin-dependent kinases that determine cell cycle progression are involved in beta cell replication, and more recently, menin in association with cyclin-dependent kinase...... inhibitors has been demonstrated to be important in beta cell growth. In this review, we consider and highlight some aspects of cell cycle regulation in relation to beta cell replication. The role of cell cycle regulation in beta cell replication is mostly from studies in rodent models, but whether...

  10. Characterizing the Final Steps of Chromosomal Replication at the Single-molecule Level in the Model System Escherichia coli

    KAUST Repository

    Elshenawy, Mohamed M.

    2015-12-01

    In the circular Escherichia coli chromosome, two replisomes are assembled at the unique origin of replication and drive DNA synthesis in opposite directions until they meet in the terminus region across from the origin. Despite the difference in rates of the two replisomes, their arrival at the terminus is synchronized through a highly specialized system consisting of the terminator protein (Tus) bound to the termination sites (Ter). This synchronicity is mediated by the polarity of the Tus−Ter complex that stops replisomes from one direction (non-permissive face) but not the other (permissive face). Two oppositely oriented clusters of five Tus–Ters that each block one of the two replisomes create a “replication fork trap” for the first arriving replisome while waiting for the late arriving one. Despite extensive biochemical and structural studies, the molecular mechanism behind Tus−Ter polar arrest activity remained controversial. Moreover, none of the previous work provided answers for the long-standing discrepancy between the ability of Tus−Ter to permanently stop replisomes in vitro and its low efficiency in vivo. Here, I spearheaded a collaborative project that combined single-molecule DNA replication assays, X-ray crystallography and binding studies to provide a true molecular-level understanding of the underlying mechanism of Tus−Ter polar arrest activity. We showed that efficiency of Tus−Ter is determined by a head-to-head kinetic competition between rate of strand separation by the replisome and rate of rearrangement of Tus−Ter interactions during the melting of the first 6 base pairs of Ter. This rearrangement maintains Tus’s strong grip on the DNA and stops the advancing replisome from breaking into Tus−Ter central interactions, but only transiently. We further showed how this kinetic competition functions within the context of two mechanisms to impose permanent fork stoppage. The rate-dependent fork arrest activity of Tus

  11. Genetic Programming for Automatic Hydrological Modelling

    Science.gov (United States)

    Chadalawada, Jayashree; Babovic, Vladan

    2017-04-01

    One of the recent challenges for the hydrologic research community is the need for the development of coupled systems that involves the integration of hydrologic, atmospheric and socio-economic relationships. This poses a requirement for novel modelling frameworks that can accurately represent complex systems, given, the limited understanding of underlying processes, increasing volume of data and high levels of uncertainity. Each of the existing hydrological models vary in terms of conceptualization and process representation and is the best suited to capture the environmental dynamics of a particular hydrological system. Data driven approaches can be used in the integration of alternative process hypotheses in order to achieve a unified theory at catchment scale. The key steps in the implementation of integrated modelling framework that is influenced by prior understanding and data, include, choice of the technique for the induction of knowledge from data, identification of alternative structural hypotheses, definition of rules, constraints for meaningful, intelligent combination of model component hypotheses and definition of evaluation metrics. This study aims at defining a Genetic Programming based modelling framework that test different conceptual model constructs based on wide range of objective functions and evolves accurate and parsimonious models that capture dominant hydrological processes at catchment scale. In this paper, GP initializes the evolutionary process using the modelling decisions inspired from the Superflex framework [Fenicia et al., 2011] and automatically combines them into model structures that are scrutinized against observed data using statistical, hydrological and flow duration curve based performance metrics. The collaboration between data driven and physical, conceptual modelling paradigms improves the ability to model and manage hydrologic systems. Fenicia, F., D. Kavetski, and H. H. Savenije (2011), Elements of a flexible approach

  12. Efficacy and toxicity of replication-competent adenovirus-mediated double suicide gene therapy in combination with radiation therapy in an orthotopic mouse prostate cancer model

    International Nuclear Information System (INIS)

    Freytag, Svend O.; Paielli, Dell; Wing, Mark; Rogulski, Ken; Brown, Steve; Kolozsvary, Andy; Seely, John; Barton, Ken; Dragovic, Alek; Kim, Jae Ho

    2002-01-01

    Purpose: The purpose of this study was to evaluate the efficacy and toxicity of replication-competent adenovirus-mediated double suicide gene therapy in an adjuvant setting with external beam radiation therapy (EBRT) in an experimental prostate cancer model in preparation for a Phase I clinical study in humans. Methods: For efficacy studies, i.m. DU145 and intraprostatic LNCaP C4-2 tumors were established in immune-deficient mice. Tumors were injected with the lytic, replication-competent Ad5-CD/TKrep adenovirus containing a cytosine deaminase (CD)/herpes simplex virus thymidine kinase (HSV-1 TK) fusion gene. Two days later, mice were administered 1 week of 5-fluorocytosine + ganciclovir (GCV) prodrug therapy and fractionated doses of EBRT (trimodal therapy). Tumor control rate of trimodal therapy was compared to that of EBRT alone. For toxicology studies, immune-competent male mice received a single intraprostatic injection (10 10 vp) of the replication-competent Ad5-CD/TKrep adenovirus. Two days later, mice were administered 4 weeks of 5-fluorocytosine + GCV prodrug therapy and 56 Gy EBRT to the pelvic region. The toxicity of trimodal therapy was assessed by histopathologic analysis of major organs and clinical chemistries. Results: In both the i.m. DU145 and intraprostatic LNCaP C4-2 tumor models, trimodal therapy significantly improved primary tumor control beyond that of EBRT alone. In the DU145 model, trimodal therapy resulted in a tumor growth delay (70 days) that was more than twice that (32 days) of EBRT alone. Whereas EBRT failed to eradicate DU145 tumors, trimodal therapy resulted in 25% tumor cure. In the LNCaP C4-2 tumor model, EBRT slowed the growth of intraprostatic tumors, but resulted in no tumor cures, and 57% of the mice developed retroperitoneal lymph node metastases at 3 months. By contrast, trimodal therapy resulted in 44% tumor cure and reduced significantly the percentage (13%) of lymph node metastases relative to EBRT alone. Overall

  13. Inhibition of severe acute respiratory syndrome coronavirus replication in a lethal SARS-CoV BALB/c mouse model by stinging nettle lectin, Urtica dioica agglutinin

    Science.gov (United States)

    Kumaki, Yohichi; Wandersee, Miles K.; Smith, Aaron J.; Zhou, Yanchen; Simmons, Graham; Nelson, Nathan M.; Bailey, Kevin W.; Vest, Zachary G.; Li, Joseph K.-K.; Chan, Paul Kay-Sheung; Smee, Donald F.; Barnard, Dale L.

    2011-01-01

    Urtica dioica agglutinin (UDA) is a small plant monomeric lectin, 8.7 kDa in size, with an N-acetylglucosamine specificity that inhibits viruses from Nidovirales in vitro. In the current study, we first examined the efficacy of UDA on the replication of different SARS-CoV strains in Vero 76 cells. UDA inhibited virus replication in a dose-dependent manner and reduced virus yields of the Urbani strain by 90% at 1.1 ± 0.4 µg/ml in Vero 76 cells. Then, UDA was tested for efficacy in a lethal SARS-CoV-infected BALB/c mouse model. BALB/c mice were infected with two LD50 (575 PFU) of virus for 4 hours before the mice were treated intraperitoneally with UDA at 20, 10, 5 or 0 mg/kg/day for 4 days. Treatment with UDA at 5 mg/kg significantly protected the mice against a lethal infection with mouse-adapted SARS-CoV (p<0.001), but did not significantly reduce virus lung titers. All virus-infected mice receiving UDA treatments were also significantly protected against weight loss (p<0.001). UDA also effectively reduced lung pathology scores. At day 6 after virus exposure, all groups of mice receiving UDA had much lower lung weights than did the placebo-treated mice. Thus, our data suggest that UDA treatment of SARS infection in mice leads to a substantial therapeutic effect that protects mice against death and weight loss. Furthermore, the mode of action of UDA in vitro was further investigated using live SARS-CoV Urbani strain virus and retroviral particles pseudotyped with SARS-CoV spike (S). UDA specifically inhibited the replication of live SARS-CoV or SARS-CoV pseudotyped virus when added just before, but not after, adsorption. These data suggested that UDA likely inhibits SARS-CoV infection by targeting early stages of the replication cycle, namely, adsorption or penetration. In addition, we demonstrated that UDA neutralizes the virus infectivity, presumably by binding to the SARS-CoV spike (S) glycoprotein. Finally, the target molecule for inhibition of virus

  14. ATM and ATR Activities Maintain Replication Fork Integrity during SV40 Chromatin Replication

    Science.gov (United States)

    Sowd, Gregory A.; Li, Nancy Yan; Fanning, Ellen

    2013-01-01

    Mutation of DNA damage checkpoint signaling kinases ataxia telangiectasia-mutated (ATM) or ATM- and Rad3-related (ATR) results in genomic instability disorders. However, it is not well understood how the instability observed in these syndromes relates to DNA replication/repair defects and failed checkpoint control of cell cycling. As a simple model to address this question, we have studied SV40 chromatin replication in infected cells in the presence of inhibitors of ATM and ATR activities. Two-dimensional gel electrophoresis and southern blotting of SV40 chromatin replication products reveal that ATM activity prevents accumulation of unidirectional replication products, implying that ATM promotes repair of replication-associated double strand breaks. ATR activity alleviates breakage of a functional fork as it converges with a stalled fork. The results suggest that during SV40 chromatin replication, endogenous replication stress activates ATM and ATR signaling, orchestrating the assembly of genome maintenance machinery on viral replication intermediates. PMID:23592994

  15. Python Program to Select HII Region Models

    Science.gov (United States)

    Miller, Clare; Lamarche, Cody; Vishwas, Amit; Stacey, Gordon J.

    2016-01-01

    HII regions are areas of singly ionized Hydrogen formed by the ionizing radiaiton of upper main sequence stars. The infrared fine-structure line emissions, particularly Oxygen, Nitrogen, and Neon, can give important information about HII regions including gas temperature and density, elemental abundances, and the effective temperature of the stars that form them. The processes involved in calculating this information from observational data are complex. Models, such as those provided in Rubin 1984 and those produced by Cloudy (Ferland et al, 2013) enable one to extract physical parameters from observational data. However, the multitude of search parameters can make sifting through models tedious. I digitized Rubin's models and wrote a Python program that is able to take observed line ratios and their uncertainties and find the Rubin or Cloudy model that best matches the observational data. By creating a Python script that is user friendly and able to quickly sort through models with a high level of accuracy, this work increases efficiency and reduces human error in matching HII region models to observational data.

  16. Unified Program Design: Organizing Existing Programming Models, Delivery Options, and Curriculum

    Science.gov (United States)

    Rubenstein, Lisa DaVia; Ridgley, Lisa M.

    2017-01-01

    A persistent problem in the field of gifted education has been the lack of categorization and delineation of gifted programming options. To address this issue, we propose Unified Program Design as a structural framework for gifted program models. This framework defines gifted programs as the combination of delivery methods and curriculum models.…

  17. Program Partitioning using Dynamic Trust Models

    DEFF Research Database (Denmark)

    Søndergaard, Dan; Probst, Christian W.; Jensen, Christian D.

    2006-01-01

    Developing distributed applications is a difficult task. It is further complicated if system-wide security policies shall be specified and enforced, or if both data and hosts are owned by principals that do not fully trust each other, as is typically the case in service-oriented or grid-based sce......Developing distributed applications is a difficult task. It is further complicated if system-wide security policies shall be specified and enforced, or if both data and hosts are owned by principals that do not fully trust each other, as is typically the case in service-oriented or grid......-based scenarios. Language-based technologies have been suggested to support developers of those applications---the \\$\\backslash\\$emph{Decentralized Label Model} and \\$\\backslash\\$emph{Secure Program Partitioning} allow to annotate programs with security specifications, and to partition the annotated program...... across a set of hosts, obeying both the annotations and the trust relation between the principals. The resulting applications guarantee \\$\\backslash\\$emph{by construction} that safety and confidentiality of both data and computations are ensured. In this work, we develop a generalised version...

  18. Stochastic linear programming models, theory, and computation

    CERN Document Server

    Kall, Peter

    2011-01-01

    This new edition of Stochastic Linear Programming: Models, Theory and Computation has been brought completely up to date, either dealing with or at least referring to new material on models and methods, including DEA with stochastic outputs modeled via constraints on special risk functions (generalizing chance constraints, ICC’s and CVaR constraints), material on Sharpe-ratio, and Asset Liability Management models involving CVaR in a multi-stage setup. To facilitate use as a text, exercises are included throughout the book, and web access is provided to a student version of the authors’ SLP-IOR software. Additionally, the authors have updated the Guide to Available Software, and they have included newer algorithms and modeling systems for SLP. The book is thus suitable as a text for advanced courses in stochastic optimization, and as a reference to the field. From Reviews of the First Edition: "The book presents a comprehensive study of stochastic linear optimization problems and their applications. … T...

  19. DNA Virus Replication Compartments

    Science.gov (United States)

    Schmid, Melanie; Speiseder, Thomas; Dobner, Thomas

    2014-01-01

    Viruses employ a variety of strategies to usurp and control cellular activities through the orchestrated recruitment of macromolecules to specific cytoplasmic or nuclear compartments. Formation of such specialized virus-induced cellular microenvironments, which have been termed viroplasms, virus factories, or virus replication centers, complexes, or compartments, depends on molecular interactions between viral and cellular factors that participate in viral genome expression and replication and are in some cases associated with sites of virion assembly. These virus-induced compartments function not only to recruit and concentrate factors required for essential steps of the viral replication cycle but also to control the cellular mechanisms of antiviral defense. In this review, we summarize characteristic features of viral replication compartments from different virus families and discuss similarities in the viral and cellular activities that are associated with their assembly and the functions they facilitate for viral replication. PMID:24257611

  20. Toward Continuous Program Improvement: Using a Logic Model for Professional Development School Program Evaluation

    Science.gov (United States)

    He, Ye; Rohr, Jean; Miller, Samuel D.; Levin, Barbara B.; Mercier, Susan

    2010-01-01

    The purpose of this study was to develop a model for evaluating a professional development school program to enact an evidence-based model for a continuous cycle of program improvement. Guided by the logic model for program evaluation, we developed three survey instruments based on the professional development school standards of the National…

  1. Human factors engineering program review model

    International Nuclear Information System (INIS)

    1994-07-01

    The staff of the Nuclear Regulatory Commission is performing nuclear power plant design certification reviews based on a design process plan that describes the human factors engineering (HFE) program elements that are necessary and sufficient to develop an acceptable detailed design specification and an acceptable implemented design. There are two principal reasons for this approach. First, the initial design certification applications submitted for staff review did not include detailed design information. Second, since human performance literature and industry experiences have shown that many significant human factors issues arise early in the design process, review of the design process activities and results is important to the evaluation of an overall design. However, current regulations and guidance documents do not address the criteria for design process review. Therefore, the HFE Program Review Model (HFE PRM) was developed as a basis for performing design certification reviews that include design process evaluations as well as review of the final design. A central tenet of the HFE PRM is that the HFE aspects of the plant should be developed, designed, and evaluated on the basis of a structured top-down system analysis using accepted HFE principles. The HFE PRM consists of ten component elements. Each element in divided into four sections: Background, Objective, Applicant Submittals, and Review Criteria. This report describes the development of the HFE PRM and gives a detailed description of each HFE review element

  2. Human factors engineering program review model

    Energy Technology Data Exchange (ETDEWEB)

    1994-07-01

    The staff of the Nuclear Regulatory Commission is performing nuclear power plant design certification reviews based on a design process plan that describes the human factors engineering (HFE) program elements that are necessary and sufficient to develop an acceptable detailed design specification and an acceptable implemented design. There are two principal reasons for this approach. First, the initial design certification applications submitted for staff review did not include detailed design information. Second, since human performance literature and industry experiences have shown that many significant human factors issues arise early in the design process, review of the design process activities and results is important to the evaluation of an overall design. However, current regulations and guidance documents do not address the criteria for design process review. Therefore, the HFE Program Review Model (HFE PRM) was developed as a basis for performing design certification reviews that include design process evaluations as well as review of the final design. A central tenet of the HFE PRM is that the HFE aspects of the plant should be developed, designed, and evaluated on the basis of a structured top-down system analysis using accepted HFE principles. The HFE PRM consists of ten component elements. Each element in divided into four sections: Background, Objective, Applicant Submittals, and Review Criteria. This report describes the development of the HFE PRM and gives a detailed description of each HFE review element.

  3. Neural Network Program Package for Prosody Modeling

    Directory of Open Access Journals (Sweden)

    J. Santarius

    2004-04-01

    Full Text Available This contribution describes the programme for one part of theautomatic Text-to-Speech (TTS synthesis. Some experiments (for example[14] documented the considerable improvement of the naturalness ofsynthetic speech, but this approach requires completing the inputfeature values by hand. This completing takes a lot of time for bigfiles. We need to improve the prosody by other approaches which useonly automatically classified features (input parameters. Theartificial neural network (ANN approach is used for the modeling ofprosody parameters. The program package contains all modules necessaryfor the text and speech signal pre-processing, neural network training,sensitivity analysis, result processing and a module for the creationof the input data protocol for Czech speech synthesizer ARTIC [1].

  4. Teaching model of problem solving Programming Fundamentals

    Directory of Open Access Journals (Sweden)

    Iván Darwin Tutillo-Arcentales

    2016-10-01

    Full Text Available The formation process has been studied by several authors in those last years, although not always focusing in the technology careers which requires of a pedagogical and didactic point of view, which promotes behaviouring changes in the teachers with impact in the quality of graduates. The purposes of this paper is: to value the pedagogical fundamentals of the formation in the career Analysis of systems,in order to promote qualitative and quantitative improvements  in the students learning. The questioner applied to students and teachers proved the difficulties in the contents related to the algorithmic procedures, which constitutes a necessary content in their formation and to them contributes other syllabus of the first level. So it is necessary to model a theoretical construction which express the new relationships established from the psychological and didactic point of view in order to solving those situations from the programing.

  5. Generalized data stacking programming model with applications

    Directory of Open Access Journals (Sweden)

    Hala Samir Elhadidy

    2016-09-01

    Full Text Available Recent researches have shown that, everywhere in various sciences the systems are following stacked-based stored change behavior when subjected to events or varying environments “on and above” their normal situations. This paper presents a generalized data stack programming (GDSP model which is developed to describe the system changes under varying environment. These changes which are captured with different ways such as sensor reading are stored in matrices. Extraction algorithm and identification technique are proposed to extract the different layers between images and identify the stack class the object follows; respectively. The general multi-stacking network is presented including the interaction between various stack-based layering of some applications. The experiments prove that the concept of stack matrix gives average accuracy of 99.45%.

  6. Modeling Weather Impact on Ground Delay Programs

    Science.gov (United States)

    Wang, Yao; Kulkarni, Deepak

    2011-01-01

    Scheduled arriving aircraft demand may exceed airport arrival capacity when there is abnormal weather at an airport. In such situations, Federal Aviation Administration (FAA) institutes ground-delay programs (GDP) to delay flights before they depart from their originating airports. Efficient GDP planning depends on the accuracy of prediction of airport capacity and demand in the presence of uncertainties in weather forecast. This paper presents a study of the impact of dynamic airport surface weather on GDPs. Using the National Traffic Management Log, effect of weather conditions on the characteristics of GDP events at selected busy airports is investigated. Two machine learning methods are used to generate models that map the airport operational conditions and weather information to issued GDP parameters and results of validation tests are described.

  7. Adenovirus DNA Replication

    Science.gov (United States)

    Hoeben, Rob C.; Uil, Taco G.

    2013-01-01

    Adenoviruses have attracted much attention as probes to study biological processes such as DNA replication, transcription, splicing, and cellular transformation. More recently these viruses have been used as gene-transfer vectors and oncolytic agents. On the other hand, adenoviruses are notorious pathogens in people with compromised immune functions. This article will briefly summarize the basic replication strategy of adenoviruses and the key proteins involved and will deal with the new developments since 2006. In addition, we will cover the development of antivirals that interfere with human adenovirus (HAdV) replication and the impact of HAdV on human disease. PMID:23388625

  8. The Use of Molecular Modeling Programs in Medicinal Chemistry Instruction.

    Science.gov (United States)

    Harrold, Marc W.

    1992-01-01

    This paper describes and evaluates the use of a molecular modeling computer program (Alchemy II) in a pharmaceutical education program. Provided are the hardware requirements and basic program features as well as several examples of how this program and its features have been applied in the classroom. (GLR)

  9. Hyperthermia stimulates HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Ferdinand Roesch

    Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

  10. Replication and extension of a hierarchical model of social anxiety and depression: fear of positive evaluation as a key unique factor in social anxiety.

    Science.gov (United States)

    Weeks, Justin W

    2015-01-01

    Wang, Hsu, Chiu, and Liang (2012, Journal of Anxiety Disorders, 26, 215-224) recently proposed a hierarchical model of social interaction anxiety and depression to account for both the commonalities and distinctions between these conditions. In the present paper, this model was extended to more broadly encompass the symptoms of social anxiety disorder, and replicated in a large unselected, undergraduate sample (n = 585). Structural equation modeling (SEM) and hierarchical regression analyses were employed. Negative affect and positive affect were conceptualized as general factors shared by social anxiety and depression; fear of negative evaluation (FNE) and disqualification of positive social outcomes were operationalized as specific factors, and fear of positive evaluation (FPE) was operationalized as a factor unique to social anxiety. This extended hierarchical model explicates structural relationships among these factors, in which the higher-level, general factors (i.e., high negative affect and low positive affect) represent vulnerability markers of both social anxiety and depression, and the lower-level factors (i.e., FNE, disqualification of positive social outcomes, and FPE) are the dimensions of specific cognitive features. Results from SEM and hierarchical regression analyses converged in support of the extended model. FPE is further supported as a key symptom that differentiates social anxiety from depression.

  11. Replicator dynamics in value chains

    DEFF Research Database (Denmark)

    Cantner, Uwe; Savin, Ivan; Vannuccini, Simone

    2016-01-01

    The pure model of replicator dynamics though providing important insights in the evolution of markets has not found much of empirical support. This paper extends the model to the case of firms vertically integrated in value chains. We show that i) by taking value chains into account, the replicator...... dynamics may revert its effect. In these regressive developments of market selection, firms with low fitness expand because of being integrated with highly fit partners, and the other way around; ii) allowing partner's switching within a value chain illustrates that periods of instability in the early...... stage of industry life-cycle may be the result of an 'optimization' of partners within a value chain providing a novel and simple explanation to the evidence discussed by Mazzucato (1998); iii) there are distinct differences in the contribution to market selection between the layers of a value chain...

  12. A Component-based Programming Model for Composite, Distributed Applications

    Science.gov (United States)

    Eidson, Thomas M.; Bushnell, Dennis M. (Technical Monitor)

    2001-01-01

    The nature of scientific programming is evolving to larger, composite applications that are composed of smaller element applications. These composite applications are more frequently being targeted for distributed, heterogeneous networks of computers. They are most likely programmed by a group of developers. Software component technology and computational frameworks are being proposed and developed to meet the programming requirements of these new applications. Historically, programming systems have had a hard time being accepted by the scientific programming community. In this paper, a programming model is outlined that attempts to organize the software component concepts and fundamental programming entities into programming abstractions that will be better understood by the application developers. The programming model is designed to support computational frameworks that manage many of the tedious programming details, but also that allow sufficient programmer control to design an accurate, high-performance application.

  13. A validation test for Adagio through replication of Big Hill and Bayou Choctaw JAS3D models.

    Energy Technology Data Exchange (ETDEWEB)

    Park, Byoung Yoon

    2013-06-01

    JAS3D, a three dimensional iterative solid mechanics code, has been used for structural analyses for the Strategic Petroleum Reserve system since the 1990s. JAS3D is no longer supported by Sandia National Laboratories, and has been replaced by Adagio. To validate the transition from JAS3D to Adagio, the existing JAS3D input decks and user subroutines for Bayou Choctaw and Big Hill models were converted for use with Adagio. The calculation results from the Adagio runs are compared to the JAS3D. Since the Adagio results are very similar to the JAS3D results, Adagio is judged to be performing satisfactorily.

  14. Software for Replicating Data Between X.500 and LDAP Directories

    Science.gov (United States)

    Wolfe, Thomas

    2003-01-01

    X500/LDAP Directory Replication Utility is a computer program for replicating information between X.500 and LDAP directories. [X.500 is an international standard for on-line directory services. LDAP (Lightweight Directory Access Protocol) is a simple directory access protocol.] The utility can be used to replicate an object of any type from X.500 to LDAP or from LDAP to X.500. The program uses the LDAP version 2 protocol, which is capable of working with both X.500 and LDAP directories. The program can provide any or all of the following services: (1) replicate only modified objects; (2) force replication of all objects; (3) replicate individual objects, one level of objects, or a subtree of objects; (4) filter sets of objects to select ones to be replicated; (5) remove and/or modify object classes from objects that are replicated; and (6) select and/or limit attributes that are replicated. The program includes a separate program that is used to remove objects that are no longer required to be replicated.

  15. Differential replicative ability of clinical dengue virus isolates in an immunocompetent C57BL/6 mouse model.

    Science.gov (United States)

    Barros, Veridiana Ester; dos Santos-Junior, Nilton Nascimento; Amarilla, Alberto Anastacio; Soares, Adriana Moreira; Lourencini, Rafael; Trabuco, Amanda Cristina; Aquino, Victor Hugo

    2015-09-29

    Several experimental animal models have been used to study the pathogenesis of dengue disease; however, most of the studies used laboratory-adapted viruses, which lack the virulence of viruses circulating in humans. The aim of this study was to analyze the ability of clinical Dengue virus (DENV) isolates (D2/BR/RP/RMB/09 and D3/BR/SL3/02) to infect immunocompetent C57BL/6 mice. Two strategies of intraperitoneal infection, which were based on the concept of the antibody dependent enhancement phenomenon, were used. In one strategy, the animals were inoculated with macrophages infected in vitro with dengue viruses, which were incubated with enhancing antibodies, and in the other strategy, the animals were inoculated with a complex of enhancing antibodies and dengue viruses. The D3/BR/SL3/08 isolate showed a higher ability of infection (virus RNA was more frequently detected in the serum and in several organs) in the experimental model compared to both the D2/BR/RP/RMB/2009 isolate and a laboratory adapted DENV-1 strain (Mochizuki strain), regardless of the infection strategy used. The main features of the D3/BR/SL3/08 isolate were its neuroinvasiveness and the induction of an extended period of viremia. Enhancing antibodies did not influence on the infection of animals when macrophages were used, but the level of viremia was increased when they were used as a complex with a D3/BR/SL3/02 isolate. We showed that DENV isolates could infect immunocompetent C57BL/6 mice, which have has been previously used to study some aspect of dengue disease when infected with laboratory adapted strains. DENV genome was detected in the same organs found in humans when autopsy and biopsy samples were analyzed, showing that C57BL/6 mice reproduce some aspects of the DENV tropism observed in humans. The main difference observed between the D3/BR/SL3/02 and D2/BR/RP/RMB/2009 clinical isolates was the neuroinvasive ability of the first one. Neuroinvasiveness has been described in some DENV

  16. Animal Mitochondrial DNA Replication

    Science.gov (United States)

    Ciesielski, Grzegorz L.; Oliveira, Marcos T.; Kaguni, Laurie S.

    2016-01-01

    Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein- the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although a substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research. PMID:27241933

  17. Automation of program model developing for complex structure control objects

    International Nuclear Information System (INIS)

    Ivanov, A.P.; Sizova, T.B.; Mikhejkina, N.D.; Sankovskij, G.A.; Tyufyagin, A.N.

    1991-01-01

    A brief description of software for automated developing the models of integrating modular programming system, program module generator and program module library providing thermal-hydraulic calcualtion of process dynamics in power unit equipment components and on-line control system operation simulation is given. Technical recommendations for model development are based on experience in creation of concrete models of NPP power units. 8 refs., 1 tab., 4 figs

  18. Programming models for energy-aware systems

    Science.gov (United States)

    Zhu, Haitao

    Energy efficiency is an important goal of modern computing, with direct impact on system operational cost, reliability, usability and environmental sustainability. This dissertation describes the design and implementation of two innovative programming languages for constructing energy-aware systems. First, it introduces ET, a strongly typed programming language to promote and facilitate energy-aware programming, with a novel type system design called Energy Types. Energy Types is built upon a key insight into today's energy-efficient systems and applications: despite the popular perception that energy and power can only be described in joules and watts, real-world energy management is often based on discrete phases and modes, which in turn can be reasoned about by type systems very effectively. A phase characterizes a distinct pattern of program workload, and a mode represents an energy state the program is expected to execute in. Energy Types is designed to reason about energy phases and energy modes, bringing programmers into the optimization of energy management. Second, the dissertation develops Eco, an energy-aware programming language centering around sustainability. A sustainable program built from Eco is able to adaptively adjusts its own behaviors to stay on a given energy budget, avoiding both deficit that would lead to battery drain or CPU overheating, and surplus that could have been used to improve the quality of the program output. Sustainability is viewed as a form of supply and demand matching, and a sustainable program consistently maintains the equilibrium between supply and demand. ET is implemented as a prototyped compiler for smartphone programming on Android, and Eco is implemented as a minimal extension to Java. Programming practices and benchmarking experiments in these two new languages showed that ET can lead to significant energy savings for Android Apps and Eco can efficiently promote battery awareness and temperature awareness in real

  19. Psychology, replication & beyond.

    Science.gov (United States)

    Laws, Keith R

    2016-06-01

    Modern psychology is apparently in crisis and the prevailing view is that this partly reflects an inability to replicate past findings. If a crisis does exists, then it is some kind of 'chronic' crisis, as psychologists have been censuring themselves over replicability for decades. While the debate in psychology is not new, the lack of progress across the decades is disappointing. Recently though, we have seen a veritable surfeit of debate alongside multiple orchestrated and well-publicised replication initiatives. The spotlight is being shone on certain areas and although not everyone agrees on how we should interpret the outcomes, the debate is happening and impassioned. The issue of reproducibility occupies a central place in our whig history of psychology.

  20. Registered Replication Report

    DEFF Research Database (Denmark)

    Bouwmeester, S.; Verkoeijen, P. P.J.L.; Aczel, B.

    2017-01-01

    In an anonymous 4-person economic game, participants contributed more money to a common project (i.e., cooperated) when required to decide quickly than when forced to delay their decision (Rand, Greene & Nowak, 2012), a pattern consistent with the social heuristics hypothesis proposed by Rand...... and colleagues. The results of studies using time pressure have been mixed, with some replication attempts observing similar patterns (e.g., Rand et al., 2014) and others observing null effects (e.g., Tinghög et al., 2013; Verkoeijen & Bouwmeester, 2014). This Registered Replication Report (RRR) assessed...... the size and variability of the effect of time pressure on cooperative decisions by combining 21 separate, preregistered replications of the critical conditions from Study 7 of the original article (Rand et al., 2012). The primary planned analysis used data from all participants who were randomly assigned...

  1. Outdoor Program Models: Placing Cooperative Adventure and Adventure Education Models on the Continuum.

    Science.gov (United States)

    Guthrie, Steven P.

    In two articles on outdoor programming models, Watters distinguished four models on a continuum ranging from the common adventure model, with minimal organizational structure and leadership control, to the guide service model, in which leaders are autocratic and trips are highly structured. Club programs and instructional programs were in between,…

  2. Model Teacher - School Dental Hygiene Program.

    Science.gov (United States)

    Smith, Lowell W.

    The purpose of this study, which was carried out during the 1972-73 school year at three parochial schools in the Houston area, was to determine the effectiveness of the Toothkeeper Program, a multimedia program of oral hygiene training carefully developed and packaged to establish effective long-term dental hygiene practice. The study population…

  3. Visual Teaching Model for Introducing Programming Languages

    Science.gov (United States)

    Shehane, Ronald; Sherman, Steven

    2014-01-01

    This study examines detailed usage of online training videos that were designed to address specific course problems that were encountered in an online computer programming course. The study presents the specifics of a programming course where training videos were used to provide students with a quick start path to learning a new programming…

  4. A Model Program for International Commerce Education.

    Science.gov (United States)

    Funston, Richard

    To address the economy's growing reliance on international business, San Diego State University has recently introduced a program in international commerce. The program was developed by packaging coursework in three existing areas: business administration, language training, and area studies. Although still in its infancy, the international…

  5. The 1995 Ratings of Doctoral Programs: A Hedonic Model.

    Science.gov (United States)

    Ehrenberg, Ronald G.; Hurst, Peter J.

    1998-01-01

    Describes how to employ multivariate regression models and National Research Council data (used to rank doctoral programs) to analyze how measures of program size, faculty seniority, and faculty research and doctoral-degree productivity influence subjective ratings of doctoral programs in 35 academic fields. Illustrates how to compute the effects…

  6. Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

    OpenAIRE

    Donley, Nathan; Stoffregen, Eric P.; Smith, Leslie; Montagna, Christina; Thayer, Mathew J.

    2013-01-01

    Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encod...

  7. The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Sass, Ehud; Suski, Catherine

    2014-01-01

    Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tu...

  8. Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase.

    Directory of Open Access Journals (Sweden)

    Amnon Koren

    2010-08-01

    Full Text Available Eukaryotic centromeres are maintained at specific chromosomal sites over many generations. In the budding yeast Saccharomyces cerevisiae, centromeres are genetic elements defined by a DNA sequence that is both necessary and sufficient for function; whereas, in most other eukaryotes, centromeres are maintained by poorly characterized epigenetic mechanisms in which DNA has a less definitive role. Here we use the pathogenic yeast Candida albicans as a model organism to study the DNA replication properties of centromeric DNA. By determining the genome-wide replication timing program of the C. albicans genome, we discovered that each centromere is associated with a replication origin that is the first to fire on its respective chromosome. Importantly, epigenetic formation of new ectopic centromeres (neocentromeres was accompanied by shifts in replication timing, such that a neocentromere became the first to replicate and became associated with origin recognition complex (ORC components. Furthermore, changing the level of the centromere-specific histone H3 isoform led to a concomitant change in levels of ORC association with centromere regions, further supporting the idea that centromere proteins determine origin activity. Finally, analysis of centromere-associated DNA revealed a replication-dependent sequence pattern characteristic of constitutively active replication origins. This strand-biased pattern is conserved, together with centromere position, among related strains and species, in a manner independent of primary DNA sequence. Thus, inheritance of centromere position is correlated with a constitutively active origin of replication that fires at a distinct early time. We suggest a model in which the distinct timing of DNA replication serves as an epigenetic mechanism for the inheritance of centromere position.

  9. Modeling, Specification and Construction of PLC-programs

    Directory of Open Access Journals (Sweden)

    E. V. Kuzmin

    2013-01-01

    Full Text Available A new approach to construction of reliable discrete PLC-programs with timers — programming based on specification and verification — is proposed. Timers are modelled in a discrete way. For the specification of a program behavior we use the linear-time temporal logic LTL. Programming is carried out in the ST-language according to a LTLspecification. A new approach to programming of PLC is shown by an example. The proposed programming approach provides an ability of a correctness analysis of PLC-programs using the model checking method. The programming requires fulfillment of the following two conditions: 1 a value of each variable should be changed not more than once per one full PLC-program implementation (per one full working cycle of PLC; 2 a value of each variable should only be changed in one place of a PLC-program. Under the proposed approach the change of the value of each program variable is described by a pair of LTL-formulas. The first LTL-formula describes situations that increase the value of the corresponding variable, the second LTL-formula specifies conditions leading to a decrease of the variable value. The LTL-formulas (used for specification of the corresponding variable behavior are constructive in the sense that they construct the PLC-program, which satisfies temporal properties expressed by these formulas. Thus, the programming of PLC is reduced to the construction of LTL-specification of the behavior of each program variable.

  10. Evolution of Replication Machines

    Science.gov (United States)

    Yao, Nina Y.; O'Donnell, Mike E.

    2016-01-01

    The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some “gears” of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the “replisome” machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus. PMID:27160337

  11. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T

    2001-01-01

    In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20...

  12. Developing robotic behavior using a genetic programming model

    International Nuclear Information System (INIS)

    Pryor, R.J.

    1998-01-01

    This report describes the methodology for using a genetic programming model to develop tracking behaviors for autonomous, microscale robotic vehicles. The use of such vehicles for surveillance and detection operations has become increasingly important in defense and humanitarian applications. Through an evolutionary process similar to that found in nature, the genetic programming model generates a computer program that when downloaded onto a robotic vehicle's on-board computer will guide the robot to successfully accomplish its task. Simulations of multiple robots engaged in problem-solving tasks have demonstrated cooperative behaviors. This report also discusses the behavior model produced by genetic programming and presents some results achieved during the study

  13. Mathematical programming model for the optimization of nutritional ...

    African Journals Online (AJOL)

    The use of a mathematical programming model for determining optimal nutritional strategy for a dairy cow is described. Mixed Integer Programming (MIP) may be used to fit curvilinear functions, such as the changes in the nutrient requirements of the cow, into a standard mathematical programme. The model determines the.

  14. Modeling the effects of study abroad programs on college students

    Science.gov (United States)

    Alvin H. Yu; Garry E. Chick; Duarte B. Morais; Chung-Hsien Lin

    2009-01-01

    This study explored the possibility of modeling the effects of a study abroad program on students from a university in the northeastern United States. A program effect model was proposed after conducting an extensive literature review and empirically examining a sample of 265 participants in 2005. Exploratory factor analysis (EFA), confirmatory factor analysis (CFA),...

  15. Process of a cyclotron modeling with SNOP program

    International Nuclear Information System (INIS)

    Smirnov, V.L.

    2015-01-01

    The description of the SNOP program developed in JINR and intended for numerical modeling of a beam dynamics in accelerating setups of cyclotron type is presented. The main methods of work with program components, and also stages of numerical modeling of a cyclotron, the analysis of the main characteristics of the accelerated bunch by means of the SNOP are given. The explanation of some algorithms and procedures used in the program is given. [ru

  16. LHCb Data Replication During SC3

    CERN Multimedia

    Smith, A

    2006-01-01

    LHCb's participation in LCG's Service Challenge 3 involves testing the bulk data transfer infrastructure developed to allow high bandwidth distribution of data across the grid in accordance with the computing model. To enable reliable bulk replication of data, LHCb's DIRAC system has been integrated with gLite's File Transfer Service middleware component to make use of dedicated network links between LHCb computing centres. DIRAC's Data Management tools previously allowed the replication, registration and deletion of files on the grid. For SC3 supplementary functionality has been added to allow bulk replication of data (using FTS) and efficient mass registration to the LFC replica catalog.Provisional performance results have shown that the system developed can meet the expected data replication rate required by the computing model in 2007. This paper details the experience and results of integration and utilisation of DIRAC with the SC3 transfer machinery.

  17. Designing Academic Leadership Minor Programs: Emerging Models

    Science.gov (United States)

    Diallo, Lamine; Gerhardt, Kris

    2017-01-01

    With a growing number of leadership programs in universities and colleges in North America, leadership educators and researchers are engaged in a wide ranging dialogue to propose clear processes, content, and designs for providing academic leadership education. This research analyzes the curriculum design of 52 institutions offering a "Minor…

  18. Stochastic dynamic programming model for optimal resource ...

    Indian Academy of Sciences (India)

    M Bhuvaneswari

    2018-04-11

    Apr 11, 2018 ... containers, doctors, nurses, cash and stocks. Similarly, the uncertainty may have different characterizations in these applications. An approximate stochastic dynamic programming (SDP) [3] allows nodes with a number of possible actions with clear strategies for devising an effective decision on optimal ...

  19. A simulation model for wind energy storage systems. Volume 3: Program descriptions

    Science.gov (United States)

    Warren, A. W.; Edsinger, R. W.; Burroughs, J. D.

    1977-01-01

    Program descriptions, flow charts, and program listings for the SIMWEST model generation program, the simulation program, the file maintenance program, and the printer plotter program are given. For Vol 2, see .

  20. Symbolic Game Semantics for Model Checking Program Families

    DEFF Research Database (Denmark)

    Dimovski, Aleksandar

    2016-01-01

    . In this paper, we propose an efficient game semantics based approach for verifying open program families, i.e. program families with free (undefined) identifiers. We use symbolic representation of algorithmic game semantics, where concrete values are replaced with symbolic ones. In this way, we can compactly...... represent program families with infinite integers as so-called (finite-state) featured symbolic automata. Specifically designed model checking algorithms are then employed to verify safety of all programs from a family at once and pinpoint those programs that are unsafe (respectively, safe). We present...

  1. Development and Implementation of a Program Management Maturity Model

    Energy Technology Data Exchange (ETDEWEB)

    Hartwig, Laura; Smith, Matt

    2008-12-15

    In 2006, Honeywell Federal Manufacturing & Technologies (FM&T) announced an updatedvision statement for the organization. The vision is “To be the most admired team within the NNSA [National Nuclear Security Administration] for our relentless drive to convert ideas into the highest quality products and services for National Security by applying the right technology, outstanding program management and best commercial practices.” The challenge to provide outstanding program management was taken up by the Program Management division and the Program Integration Office (PIO) of the company. This article describes how Honeywell developed and deployed a program management maturity model to drive toward excellence.

  2. Service systems concepts, modeling, and programming

    CERN Document Server

    Cardoso, Jorge; Poels, Geert

    2014-01-01

    This SpringerBrief explores the internal workings of service systems. The authors propose a lightweight semantic model for an effective representation to capture the essence of service systems. Key topics include modeling frameworks, service descriptions and linked data, creating service instances, tool support, and applications in enterprises.Previous books on service system modeling and various streams of scientific developments used an external perspective to describe how systems can be integrated. This brief introduces the concept of white-box service system modeling as an approach to mo

  3. Molecular Mechanisms of DNA Replication Checkpoint Activation

    Directory of Open Access Journals (Sweden)

    Bénédicte Recolin

    2014-03-01

    Full Text Available The major challenge of the cell cycle is to deliver an intact, and fully duplicated, genetic material to the daughter cells. To this end, progression of DNA synthesis is monitored by a feedback mechanism known as replication checkpoint that is untimely linked to DNA replication. This signaling pathway ensures coordination of DNA synthesis with cell cycle progression. Failure to activate this checkpoint in response to perturbation of DNA synthesis (replication stress results in forced cell division leading to chromosome fragmentation, aneuploidy, and genomic instability. In this review, we will describe current knowledge of the molecular determinants of the DNA replication checkpoint in eukaryotic cells and discuss a model of activation of this signaling pathway crucial for maintenance of genomic stability.

  4. Replication-Competent Controlled Herpes Simplex Virus.

    Science.gov (United States)

    Bloom, David C; Feller, Joyce; McAnany, Peterjon; Vilaboa, Nuria; Voellmy, Richard

    2015-10-01

    We present the development and characterization of a replication-competent controlled herpes simplex virus 1 (HSV-1). Replication-essential ICP4 and ICP8 genes of HSV-1 wild-type strain 17syn+ were brought under the control of a dually responsive gene switch. The gene switch comprises (i) a transactivator that is activated by a narrow class of antiprogestins, including mifepristone and ulipristal, and whose expression is mediated by a promoter cassette that comprises an HSP70B promoter and a transactivator-responsive promoter and (ii) transactivator-responsive promoters that drive the ICP4 and ICP8 genes. Single-step growth experiments in different cell lines demonstrated that replication of the recombinant virus, HSV-GS3, is strictly dependent on an activating treatment consisting of administration of a supraphysiological heat dose in the presence of an antiprogestin. The replication-competent controlled virus replicates with an efficiency approaching that of the wild-type virus from which it was derived. Essentially no replication occurs in the absence of activating treatment or if HSV-GS3-infected cells are exposed only to heat or antiprogestin. These findings were corroborated by measurements of amounts of viral DNA and transcripts of the regulated ICP4 gene and the glycoprotein C (gC) late gene, which was not regulated. Similar findings were made in experiments with a mouse footpad infection model. The alphaherpesviruses have long been considered vectors for recombinant vaccines and oncolytic therapies. The traditional approach uses vector backbones containing attenuating mutations that restrict replication to ensure safety. The shortcoming of this approach is that the attenuating mutations tend to limit both the immune presentation and oncolytic properties of these vectors. HSV-GS3 represents a novel type of vector that, when activated, replicates with the efficiency of a nonattenuated virus and whose safety is derived from deliberate, stringent regulation of

  5. Consideration of an applied model of public health program infrastructure.

    Science.gov (United States)

    Lavinghouze, René; Snyder, Kimberly; Rieker, Patricia; Ottoson, Judith

    2013-01-01

    Systemic infrastructure is key to public health achievements. Individual public health program infrastructure feeds into this larger system. Although program infrastructure is rarely defined, it needs to be operationalized for effective implementation and evaluation. The Ecological Model of Infrastructure (EMI) is one approach to defining program infrastructure. The EMI consists of 5 core (Leadership, Partnerships, State Plans, Engaged Data, and Managed Resources) and 2 supporting (Strategic Understanding and Tactical Action) elements that are enveloped in a program's context. We conducted a literature search across public health programs to determine support for the EMI. Four of the core elements were consistently addressed, and the other EMI elements were intermittently addressed. The EMI provides an initial and partial model for understanding program infrastructure, but additional work is needed to identify evidence-based indicators of infrastructure elements that can be used to measure success and link infrastructure to public health outcomes, capacity, and sustainability.

  6. Research on teacher education programs: logic model approach.

    Science.gov (United States)

    Newton, Xiaoxia A; Poon, Rebecca C; Nunes, Nicole L; Stone, Elisa M

    2013-02-01

    Teacher education programs in the United States face increasing pressure to demonstrate their effectiveness through pupils' learning gains in classrooms where program graduates teach. The link between teacher candidates' learning in teacher education programs and pupils' learning in K-12 classrooms implicit in the policy discourse suggests a one-to-one correspondence. However, the logical steps leading from what teacher candidates have learned in their programs to what they are doing in classrooms that may contribute to their pupils' learning are anything but straightforward. In this paper, we argue that the logic model approach from scholarship on evaluation can enhance research on teacher education by making explicit the logical links between program processes and intended outcomes. We demonstrate the usefulness of the logic model approach through our own work on designing a longitudinal study that focuses on examining the process and impact of an undergraduate mathematics and science teacher education program. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. A stochastic dynamic programming model for stream water quality ...

    Indian Academy of Sciences (India)

    This paper deals with development of a seasonal fraction-removal policy model for waste load allocation in streams addressing uncertainties due to randomness and fuzziness. A stochastic dynamic programming (SDP) model is developed to arrive at the steady-state seasonal fraction-removal policy. A fuzzy decision model ...

  8. Optimum workforce-size model using dynamic programming approach

    African Journals Online (AJOL)

    This paper presents an optimum workforce-size model which determines the minimum number of excess workers (overstaffing) as well as the minimum total recruitment cost during a specified planning horizon. The model is an extension of other existing dynamic programming models for manpower planning in the sense ...

  9. optimum workforce-size model using dynamic programming approach

    African Journals Online (AJOL)

    DJFLEX

    This paper presents an optimum workforce-size model which determines the minimum number of excess workers (overstaffing) as well as the minimum total recruitment cost during a specified planning horizon. The model is an extension of other existing dynamic programming models for manpower planning in the sense ...

  10. Credibilistic programming an introduction to models and applications

    CERN Document Server

    2014-01-01

    It provides fuzzy programming approach to solve real-life decision problems in fuzzy environment. Within the framework of credibility theory, it provides a self-contained, comprehensive and up-to-date presentation of fuzzy programming models, algorithms and applications in portfolio analysis.

  11. Application of the simplex method of linear programming model to ...

    African Journals Online (AJOL)

    This work discussed how the simplex method of linear programming could be used to maximize the profit of any business firm using Saclux Paint Company as a case study. It equally elucidated the effect variation in the optimal result obtained from linear programming model, will have on any given firm. It was demonstrated ...

  12. Time Aquatic Resources Modeling and Analysis Program (STARMAP)

    Data.gov (United States)

    Federal Laboratory Consortium — Colorado State University has received funding from the U.S. Environmental Protection Agency (EPA) for its Space-Time Aquatic Resources Modeling and Analysis Program...

  13. State of the Short Dipole Model Program for the LHC

    CERN Document Server

    Andreyev, N I; Kurtyka, T; Oberli, L R; Perini, D; Russenschuck, Stephan; Siegel, N; Siemko, A; Tommasini, D; Vanenkov, I; Walckiers, L

    1998-01-01

    Superconducting single and twin aperture 1-m long dipole magnets are currently being fabricated at CERN at a rate of about one per month in the framework of the short dipole model program for the LHC. The program allows to study performance improvements coming from refinements in design, components and assembly options and to accumulate statistics based on a small-scale production. The experience thus gained provides in turn feedback into the long magnet program in industry. In recent models initial quenching fields above 9 T have been obtained and after a short training the conductor limit at 2 K is reached, resulting in a central bore field exceeding 10 T. The paper describes the features of recent single aperture models, the results obtained during cold tests and the plans to ensure the continuation of a vigorous model program providing input for the fabrication of the main LHC dipoles.

  14. Applying Model Checking to Industrial-Sized PLC Programs

    CERN Document Server

    AUTHOR|(CDS)2079190; Darvas, Daniel; Blanco Vinuela, Enrique; Tournier, Jean-Charles; Bliudze, Simon; Blech, Jan Olaf; Gonzalez Suarez, Victor M

    2015-01-01

    Programmable logic controllers (PLCs) are embedded computers widely used in industrial control systems. Ensuring that a PLC software complies with its specification is a challenging task. Formal verification has become a recommended practice to ensure the correctness of safety-critical software but is still underused in industry due to the complexity of building and managing formal models of real applications. In this paper, we propose a general methodology to perform automated model checking of complex properties expressed in temporal logics (\\eg CTL, LTL) on PLC programs. This methodology is based on an intermediate model (IM), meant to transform PLC programs written in various standard languages (ST, SFC, etc.) to different modeling languages of verification tools. We present the syntax and semantics of the IM and the transformation rules of the ST and SFC languages to the nuXmv model checker passing through the intermediate model. Finally, two real cases studies of \\CERN PLC programs, written mainly in th...

  15. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  16. Photovoltaic subsystem marketing and distribution model: programming manual. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1982-07-01

    Complete documentation of the marketing and distribution (M and D) computer model is provided. The purpose is to estimate the costs of selling and transporting photovoltaic solar energy products from the manufacturer to the final customer. The model adjusts for the inflation and regional differences in marketing and distribution costs. The model consists of three major components: the marketing submodel, the distribution submodel, and the financial submodel. The computer program is explained including the input requirements, output reports, subprograms and operating environment. The program specifications discuss maintaining the validity of the data and potential improvements. An example for a photovoltaic concentrator collector demonstrates the application of the model.

  17. Extremal dynamics in random replicator ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Kärenlampi, Petri P., E-mail: petri.karenlampi@uef.fi

    2015-10-02

    The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation–extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation–extinction dynamics in the replicator system. No criticality is found from the speciation–extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon. - Highlights: • Extremal Dynamics organizes random replicator ecosystems to two phases in fitness space. • Replicator systems show power-law scaling of activity. • Species extinction interferes with Bak–Sneppen type mutation activity. • Speciation–extinction dynamics does not show any critical phase transition. • Biological macroevolution probably is not a self-organized critical phenomenon.

  18. Methadone enhances human influenza A virus replication.

    Science.gov (United States)

    Chen, Yun-Hsiang; Wu, Kuang-Lun; Tsai, Ming-Ta; Chien, Wei-Hsien; Chen, Mao-Liang; Wang, Yun

    2017-01-01

    Growing evidence has indicated that opioids enhance replication of human immunodeficiency virus and hepatitis C virus in target cells. However, it is unknown whether opioids can enhance replication of other clinically important viral pathogens. In this study, the interaction of opioid agonists and human influenza A/WSN/33 (H1N1) virus was examined in human lung epithelial A549 cells. Cells were exposed to morphine, methadone or buprenorphine followed by human H1N1 viral infection. Exposure to methadone differentially enhanced viral propagation, consistent with an increase in virus adsorption, susceptibility to virus infection and viral protein synthesis. In contrast, morphine or buprenorphine did not alter H1N1 replication. Because A549 cells do not express opioid receptors, methadone-enhanced H1N1 replication in human lung cells may not be mediated through these receptors. The interaction of methadone and H1N1 virus was also examined in adult mice. Treatment with methadone significantly increased H1N1 viral replication in lungs. Our data suggest that use of methadone facilitates influenza A viral infection in lungs and might raise concerns regarding the possible consequence of an increased risk of serious influenza A virus infection in people who receive treatment in methadone maintenance programs. © 2015 Society for the Study of Addiction.

  19. Programming models used on Many-Core architectures

    Science.gov (United States)

    Novotný, Jan

    2014-12-01

    The time in which we live is characterized by an ever-increasing amount of data that we are able to explore and acquire. In all fields of science we could find some examples. Processing large volumes of information thus brings the requirement for engaging computational science. With increasing demands on data processing is advantageous to use new technology and start using parallel computation. Effective use of current technology requires from programmers new knowledge and skills. They meet with the countless new programming models and tools. In this article, we summarize the most commonly used programming models and points which good programming model should meet. The article also try to highlight the reasons why one should use a structured parallel programming.

  20. A Decision Model for Evaluating Potential Change in Instructional Programs.

    Science.gov (United States)

    Amor, J. P.; Dyer, J. S.

    A statistical model designed to assist elementary school principals in the process of selection educational areas which should receive additional emphasis is presented. For each educational area, the model produces an index number which represents the expected "value" per dollar spent on an instructional program appropriate for strengthening that…

  1. Currency Arbitrage Detection Using a Binary Integer Programming Model

    Science.gov (United States)

    Soon, Wanmei; Ye, Heng-Qing

    2011-01-01

    In this article, we examine the use of a new binary integer programming (BIP) model to detect arbitrage opportunities in currency exchanges. This model showcases an excellent application of mathematics to the real world. The concepts involved are easily accessible to undergraduate students with basic knowledge in Operations Research. Through this…

  2. Model-Checking Real-Time Control Programs

    DEFF Research Database (Denmark)

    Iversen, T. K.; Kristoffersen, K. J.; Larsen, Kim Guldstrand

    2000-01-01

    In this paper, we present a method for automatic verification of real-time control programs running on LEGO(R) RCX(TM) bricks using the verification tool UPPALL. The control programs, consisting of a number of tasks running concurrently, are automatically translated into the mixed automata model...... of UPPAAL. The fixed scheduling algorithm used by the LEGO(R) RCX(TM) processor is modeled in UPPALL, and supply of similar (sufficient) timed automata models for the environment allows analysis of the overall real-time system using the tools of UPPALL. To illustrate our technique for sorting LEGO(R) bricks...

  3. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  4. SPSS and SAS programming for the testing of mediation models.

    Science.gov (United States)

    Dudley, William N; Benuzillo, Jose G; Carrico, Mineh S

    2004-01-01

    Mediation modeling can explain the nature of the relation among three or more variables. In addition, it can be used to show how a variable mediates the relation between levels of intervention and outcome. The Sobel test, developed in 1990, provides a statistical method for determining the influence of a mediator on an intervention or outcome. Although interactive Web-based and stand-alone methods exist for computing the Sobel test, SPSS and SAS programs that automatically run the required regression analyses and computations increase the accessibility of mediation modeling to nursing researchers. To illustrate the utility of the Sobel test and to make this programming available to the Nursing Research audience in both SAS and SPSS. The history, logic, and technical aspects of mediation testing are introduced. The syntax files sobel.sps and sobel.sas, created to automate the computation of the regression analysis and test statistic, are available from the corresponding author. The reported programming allows the user to complete mediation testing with the user's own data in a single-step fashion. A technical manual included with the programming provides instruction on program use and interpretation of the output. Mediation modeling is a useful tool for describing the relation between three or more variables. Programming and manuals for using this model are made available.

  5. Submicron Composite Mirror Replication (PDRT08-027), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR program will identify and address the primary technical issues that limit the current precision of replicated CFRP optics. These issues must be resolved to...

  6. Report of the 2014 Programming Models and Environments Summit

    Energy Technology Data Exchange (ETDEWEB)

    Heroux, Michael [US Dept. of Energy, Washington, DC (United States); Lethin, Richard [US Dept. of Energy, Washington, DC (United States)

    2016-09-19

    Programming models and environments play the essential roles in high performance computing of enabling the conception, design, implementation and execution of science and engineering application codes. Programmer productivity is strongly influenced by the effectiveness of our programming models and environments, as is software sustainability since our codes have lifespans measured in decades, so the advent of new computing architectures, increased concurrency, concerns for resilience, and the increasing demands for high-fidelity, multi-physics, multi-scale and data-intensive computations mean that we have new challenges to address as part of our fundamental R&D requirements. Fortunately, we also have new tools and environments that make design, prototyping and delivery of new programming models easier than ever. The combination of new and challenging requirements and new, powerful toolsets enables significant synergies for the next generation of programming models and environments R&D. This report presents the topics discussed and results from the 2014 DOE Office of Science Advanced Scientific Computing Research (ASCR) Programming Models & Environments Summit, and subsequent discussions among the summit participants and contributors to topics in this report.

  7. Modelling the work flow of a nuclear waste management program

    International Nuclear Information System (INIS)

    Hoeyer Mortensen, K.; Pinci, V.

    1997-03-01

    In this paper we describe a modelling project to improve a nuclear waste management program in charge of the creation of a new system for the permanent disposal of nuclear waste. SADT (Structural Analysis and Design Technique) is used in order to provide a work-flow description of the functions to be performed by the waste management program. This description is then translated into a number of Coloured Petri Nets (CPN or CP-nets) corresponding to different program functions where additional behavioural inscriptions provide basis for simulation. Each of these CP-nets is simulated to produce timed event charts that are useful for understanding the behaviour of the program functions under different scenarios. Then all the CPN models are linked together to form a single stand-alone application that is useful for validating the interaction and cooperation between the different program functions. A technique for linking executable CPN models is developed for supporting large modelling projects and parallel development of independent CPN models. (au) 11 refs

  8. Modeling and prioritizing demand response programs in power markets

    International Nuclear Information System (INIS)

    Aalami, H.A.; Moghaddam, M. Parsa; Yousefi, G.R.

    2010-01-01

    One of the responsibilities of power market regulator is setting rules for selecting and prioritizing demand response (DR) programs. There are many different alternatives of DR programs for improving load profile characteristics and achieving customers' satisfaction. Regulator should find the optimal solution which reflects the perspectives of each DR stakeholder. Multi Attribute Decision Making (MADM) is a proper method for handling such optimization problems. In this paper, an extended responsive load economic model is developed. The model is based on price elasticity and customer benefit function. Prioritizing of DR programs can be realized by means of Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) method. Considerations of ISO/utility/customer regarding the weighting of attributes are encountered by entropy method. An Analytical Hierarchy Process (AHP) is used for selecting the most effective DR program. Numerical studies are conducted on the load curve of the Iranian power grid in 2007. (author)

  9. Center for Programming Models for Scalable Parallel Computing

    Energy Technology Data Exchange (ETDEWEB)

    John Mellor-Crummey

    2008-02-29

    Rice University's achievements as part of the Center for Programming Models for Scalable Parallel Computing include: (1) design and implemention of cafc, the first multi-platform CAF compiler for distributed and shared-memory machines, (2) performance studies of the efficiency of programs written using the CAF and UPC programming models, (3) a novel technique to analyze explicitly-parallel SPMD programs that facilitates optimization, (4) design, implementation, and evaluation of new language features for CAF, including communication topologies, multi-version variables, and distributed multithreading to simplify development of high-performance codes in CAF, and (5) a synchronization strength reduction transformation for automatically replacing barrier-based synchronization with more efficient point-to-point synchronization. The prototype Co-array Fortran compiler cafc developed in this project is available as open source software from http://www.hipersoft.rice.edu/caf.

  10. Solving seismological problems using sgraph program: II-waveform modeling

    International Nuclear Information System (INIS)

    Abdelwahed, Mohamed F.

    2012-01-01

    One of the seismological programs to manipulate seismic data is SGRAPH program. It consists of integrated tools to perform advanced seismological techniques. SGRAPH is considered a new system for maintaining and analyze seismic waveform data in a stand-alone Windows-based application that manipulate a wide range of data formats. SGRAPH was described in detail in the first part of this paper. In this part, I discuss the advanced techniques including in the program and its applications in seismology. Because of the numerous tools included in the program, only SGRAPH is sufficient to perform the basic waveform analysis and to solve advanced seismological problems. In the first part of this paper, the application of the source parameters estimation and hypocentral location was given. Here, I discuss SGRAPH waveform modeling tools. This paper exhibits examples of how to apply the SGRAPH tools to perform waveform modeling for estimating the focal mechanism and crustal structure of local earthquakes.

  11. Programming biological models in Python using PySB.

    Science.gov (United States)

    Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

    2013-01-01

    Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.

  12. Automatic generation of Fortran programs for algebraic simulation models

    International Nuclear Information System (INIS)

    Schopf, W.; Rexer, G.; Ruehle, R.

    1978-04-01

    This report documents a generator program by which econometric simulation models formulated in an application-orientated language can be transformed automatically in a Fortran program. Thus the model designer is able to build up, test and modify models without the need of a Fortran programmer. The development of a computer model is therefore simplified and shortened appreciably; in chapter 1-3 of this report all rules are presented for the application of the generator to the model design. Algebraic models including exogeneous and endogeneous time series variables, lead and lag function can be generated. In addition, to these language elements, Fortran sequences can be applied to the formulation of models in the case of complex model interrelations. Automatically the generated model is a module of the program system RSYST III and is therefore able to exchange input and output data with the central data bank of the system and in connection with the method library modules can be used to handle planning problems. (orig.) [de

  13. A model for training medical student innovators: the Harvard Medical School Center for Primary Care Abundance Agents of Change program

    Directory of Open Access Journals (Sweden)

    David B. Duong

    2016-06-01

    Full Text Available Background: In 2013, the Harvard Medical School Center for Primary Care established the Abundance Agents of Change (AoC program to promote interprofessional learning and innovation, increase partnership between 15 academic and community health centers (CHCs in Boston's most under-served communities, and increase medical student interest in primary care careers. Methods: The AoC is modeled in the form of a ‘grants challenge’, offering $20,000 to interprofessional student teams to develop an innovative solution that addresses a healthcare delivery need identified by CHCs. The program's initial two years were characterized by a four-stage process which included working with CHCs and crafting a request for proposals, forming interprofessional 20 student teams comprising students from across and outside of Harvard University, training students using a systems-based innovation curriculum, and performing program evaluation. Results: Our evaluation data from cohorts 1 and 2 of the AoC program demonstrate that we succeeded in training students as innovators and members of interprofessional teams. We also learned valuable lessons regarding creating better alignment with CHC priorities, extending the program cycle from 12 to 18 months, and changing the way funding is disbursed to 25 students, which will be incorporated in later versions of the program. Conclusions: Based on our experience and evaluation data, we believe that this program is a replicable way to train students as innovators and members of interprofessional teams to address the current complex healthcare environment.

  14. Utility of Small Animal Models of Developmental Programming.

    Science.gov (United States)

    Reynolds, Clare M; Vickers, Mark H

    2018-01-01

    Any effective strategy to tackle the global obesity and rising noncommunicable disease epidemic requires an in-depth understanding of the mechanisms that underlie these conditions that manifest as a consequence of complex gene-environment interactions. In this context, it is now well established that alterations in the early life environment, including suboptimal nutrition, can result in an increased risk for a range of metabolic, cardiovascular, and behavioral disorders in later life, a process preferentially termed developmental programming. To date, most of the mechanistic knowledge around the processes underpinning development programming has been derived from preclinical research performed mostly, but not exclusively, in laboratory mouse and rat strains. This review will cover the utility of small animal models in developmental programming, the limitations of such models, and potential future directions that are required to fully maximize information derived from preclinical models in order to effectively translate to clinical use.

  15. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    OpenAIRE

    Hendro Nindito; Evaristus Didik Madyatmadja; Albert Verasius Dian Sano

    2014-01-01

    The application of diverse database technologies in enterprises today is increasingly a common practice. To provide high availability and survavibality of real-time information, a database replication technology that has capability to replicate databases under heterogenous platforms is required. The purpose of this research is to find the technology with such capability. In this research, the data source is stored in MSSQL database server running on Windows. The data will be replicated to MyS...

  16. Temporal organization of cellular self-replication

    Science.gov (United States)

    Alexandrov, Victor; Pugatch, Rami

    Recent experiments demonstrate that single cells grow exponentially in time. A coarse grained model of cellular self-replication is presented based on a novel concept - the cell is viewed as a self-replicating queue. This allows to have a more fundamental look into various temporal organizations and, importantly, the inherent non-Markovianity of noise distributions. As an example, the distribution of doubling times can be inferred and compared to single cell experiments in bacteria. We observe data collapse upon scaling by the average doubling time for different environments and present an inherent task allocation trade-off. Support from the Simons Center for Systems Biology, IAS, Princeon.

  17. A model technology transfer program for independent operators

    Energy Technology Data Exchange (ETDEWEB)

    Schoeling, L.G.

    1996-08-01

    In August 1992, the Energy Research Center (ERC) at the University of Kansas was awarded a contract by the US Department of Energy (DOE) to develop a technology transfer regional model. This report describes the development and testing of the Kansas Technology Transfer Model (KTTM) which is to be utilized as a regional model for the development of other technology transfer programs for independent operators throughout oil-producing regions in the US. It describes the linkage of the regional model with a proposed national technology transfer plan, an evaluation technique for improving and assessing the model, and the methodology which makes it adaptable on a regional basis. The report also describes management concepts helpful in managing a technology transfer program.

  18. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...... synthesis is perturbed, cells can suffer loss of both genome and epigenome integrity with severe consequences for the organism....

  19. Non-determinism in Byzantine Fault-Tolerant Replication

    OpenAIRE

    Cachin, Christian; Vukolic, Marko; Schubert, Simon

    2016-01-01

    Service replication distributes an application over many processes for tolerating faults, attacks, and misbehavior among a subset of the processes. With the recent interest in blockchain technologies, distributed execution of one logical application has become a prominent topic. The established state-machine replication paradigm inherently requires the application to be deterministic. This paper distinguishes three models for dealing with non-determinism in replicated services, where some pro...

  20. High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

    Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

  1. Transforming PLC Programs into Formal Models for Verification Purposes

    CERN Document Server

    Darvas, D; Blanco, E

    2013-01-01

    Most of CERN’s industrial installations rely on PLC-based (Programmable Logic Controller) control systems developed using the UNICOS framework. This framework contains common, reusable program modules and their correctness is a high priority. Testing is already applied to find errors, but this method has limitations. In this work an approach is proposed to transform automatically PLC programs into formal models, with the goal of applying formal verification to ensure their correctness. We target model checking which is a precise, mathematical-based method to check formalized requirements automatically against the system.

  2. Model-based automated testing of critical PLC programs.

    CERN Document Server

    Fernández Adiego, B; Tournier, J-C; González Suárez, V M; Bliudze, S

    2014-01-01

    Testing of critical PLC (Programmable Logic Controller) programs remains a challenging task for control system engineers as it can rarely be automated. This paper proposes a model based approach which uses the BIP (Behavior, Interactions and Priorities) framework to perform automated testing of PLC programs developed with the UNICOS (UNified Industrial COntrol System) framework. This paper defines the translation procedure and rules from UNICOS to BIP which can be fully automated in order to hide the complexity of the underlying model from the control engineers. The approach is illustrated and validated through the study of a water treatment process.

  3. On the Feasibility of a Unified Modelling and Programming Paradigm

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth; Peleska, Jan

    2016-01-01

    In this article, the feasibility of a unified modelling and programming paradigm is discussed from the perspective of large scale system development and verification in collaborative development environments. We motivate the necessity to utilise multiple formalisms for development and verification......, in particular for complex cyber-physical systems or systems of systems. Though modelling, programming, and verification will certainly become more closely integrated in the future, we do not expect a single formalism to become universally applicable and accepted by the development and verification communities...

  4. A constraint programming model for mixed model type 2 assembly line balancing problem

    Directory of Open Access Journals (Sweden)

    Hacı Mehmet Alağaş

    2016-08-01

    Full Text Available This paper presents a new constraint programming model for mixed-model assembly line balancing problem. The proposed model minimizes the cycle time for a given number of stations. The proposed model is tested with literature problems and its performance is evaluated by comparing to mathematical model. Best obtained solution and elapsed CPU time are used as performance criteria. The experimental results show that the proposed constraint programming model performs well and can be used as an alternative modeling technique to solve the problem.

  5. Effectiveness of a free exercise program in a neighborhood park

    Directory of Open Access Journals (Sweden)

    Bing Han

    2015-01-01

    Conclusions: Active programming can increase park-based moderate-to-vigorous physical activity, but without programming, people may lack the motivation to exercise on their own. Creating a partnership between parks and kinesiology programs is a promising health promotion model. Replicating this type of program could yield important health dividends.

  6. Integration of a Multizone Airflow Model into a Thermalsimulation Program

    DEFF Research Database (Denmark)

    Jensen, Rasmus Lund; Sørensen, Karl Grau; Heiselberg, Per

    2007-01-01

    An existing computer model for dynamic hygrothermal analysis of buildings has been extended with a multizone airflow model based on loop equations to account for the coupled thermal and airflow in natural and hybrid ventilated buildings. In water distribution network and related fields loop...... a methodology adopted from water distribution network that automatically sets up the independent loops and is easy to implement into a computer program. Finally an example of verification of the model is given which demonstrates the ability of the models to accurately predict the airflow of a simple multizone...

  7. Community Based Educational Model on Water Conservation Program

    Science.gov (United States)

    Sudiajeng, L.; Parwita, I. G. L.; Wiraga, I. W.; Mudhina, M.

    2018-01-01

    The previous research showed that there were indicators of water crisis in the northern and eastern part of Denpasar city and most of coastal area experienced on seawater intrusion. The recommended water conservation programs were rainwater harvesting and educate the community to develop a water saving and environmentally conscious culture. This research was conducted to built the community based educational model on water conservation program through ergonomics SHIP approach which placed the human aspect as the first consideration, besides the economic and technically aspects. The stakeholders involved in the program started from the problem analyses to the implementation and the maintenance as well. The model was built through three main steps, included determination of accepted design; building the recharge wells by involving local communities; guidance and assistance in developing a water saving and environmentally conscious culture for early childhood, elementary and junior high school students, community and industry. The program was implemented based on the “TRIHITA KARANA” concept, which means the relationship between human to God, human-to-human, and human to environment. Through the development of the model, it is expected to grow a sense of belonging and awareness from the community to maintain the sustainability of the program.

  8. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

  9. Model of Communication Program Corporate Social Responsibility for Empowerment Community

    Directory of Open Access Journals (Sweden)

    David Rizar Nugroho

    2016-12-01

    Full Text Available Community empowerment is one of the keys to success in running development of a region. The empowerment program carried out with models, shapes and different strategies. The purpose of this study was to analyze (1 Determine the perception of the implementation of communication channels and approaches to communications made in the program CSR companies. (2 Analyze the influence of the characteristics of the beneficiaries, and the communication channel communication approach CSR program the company towards community empowerment. The samples used in this study were 410 respondents. This study is designed as a quantitative research boosted by the approach of a qualitative study using descriptive analysis and structural equation modeling (SEM. The results of this study include: (1 Perception of beneficiaries for variables communication channels, communication approach and community empowerment approach is generally considered good. (2 The variables that affect the community empowerment are approach communication and communication channels, while the characteristics of the beneficiaries had no significant effect.

  10. Menu variations for diabetes mellitus patients using Goal Programming model

    Science.gov (United States)

    Dhoruri, Atmini; Lestari, Dwi; Ratnasari, Eminugroho

    2017-08-01

    Diabetes mellitus (DM) was a chronic metabolic disease characterized by higher than normal blood glucose level (normal blood glucose level = = 80 -120 mg/dl). In this study, type 2 DM which mostly caused by unhealthy eating habits would be investigated. Related to eating habit, DM patients needed dietary menu planning with an extracare regarding their nutrients intake (energy, protein, fat and carbohydrate). Therefore, the measures taken were by organizing nutritious dietary menu for diabetes mellitus patients. Dietary menu with appropriate amount of nutrients was organized by considering the amount of calories, proteins, fats and carbohydrates. In this study, Goal Programming model was employed to determine optimal dietary menu variations for diabetes mellitus patients by paying attention to optimal expenses. According to the data obtained from hospitals in Yogyakarta, optimal menu variations would be analyzed by using Goal Programming model and would be completed by using LINGO computer program.

  11. Replication of bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    Tsurimoto, T.; Matsubara, K.

    1983-01-01

    In this paper results of studies on the mechanism of bacteriophage lambda replication using molecular biological and biochemical approaches are reported. The purification of the initiator proteins, O and P, and the role of the O and P proteins in the initiation of lambda DNA replication through interactions with specific DNA sequences are described. 47 references, 15 figures

  12. Application of Logic Models in a Large Scientific Research Program

    Science.gov (United States)

    O'Keefe, Christine M.; Head, Richard J.

    2011-01-01

    It is the purpose of this article to discuss the development and application of a logic model in the context of a large scientific research program within the Commonwealth Scientific and Industrial Research Organisation (CSIRO). CSIRO is Australia's national science agency and is a publicly funded part of Australia's innovation system. It conducts…

  13. PROGRAM COMPLEX FOR MODELING OF THE DETAILS HARDENING PROCESS

    Directory of Open Access Journals (Sweden)

    S. P. Kundas

    2004-01-01

    Full Text Available In the article there is presented the program complex ThermoSim, consisting of preprocessor, processor and postprocessor and intended for modeling (analysis of thermalphysic processes and characteristics of details of instrument-making and machine-building, diagnostics and optimization of technological processes of heat treatment and details constructions without using the destructive control methods.

  14. A quadratic programming model for crop combinations in intercropping

    African Journals Online (AJOL)

    One particularly known problem that confronts the farmer is that of determining optimal crop combinations for an intercropping scheme. This work therefore sets out to develop a model which determines optimally a crop combination that will yield maximum profit when interactive effects are present. A quadratic programming ...

  15. Universal Instructional Design as a Model for Educational Programs

    Science.gov (United States)

    Higbee, Jeanne L.

    2007-01-01

    This article describes Universal Instructional Design as an inclusive pedagogical model for use in educational programs, whether provided by traditional educational institutions, community-based initiatives, or workplace literacy projects. For the benefit of public relations specialists and classroom educators alike, the article begins with a…

  16. Fuzzy Goal Programming Approach in Selective Maintenance Reliability Model

    Directory of Open Access Journals (Sweden)

    Neha Gupta

    2013-12-01

    Full Text Available 800x600 In the present paper, we have considered the allocation problem of repairable components for a parallel-series system as a multi-objective optimization problem and have discussed two different models. In first model the reliability of subsystems are considered as different objectives. In second model the cost and time spent on repairing the components are considered as two different objectives. These two models is formulated as multi-objective Nonlinear Programming Problem (MONLPP and a Fuzzy goal programming method is used to work out the compromise allocation in multi-objective selective maintenance reliability model in which we define the membership functions of each objective function and then transform membership functions into equivalent linear membership functions by first order Taylor series and finally by forming a fuzzy goal programming model obtain a desired compromise allocation of maintenance components. A numerical example is also worked out to illustrate the computational details of the method.  Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4

  17. The architecture and function of the chromatin replication machinery.

    Science.gov (United States)

    Miller, Thomas Cr; Costa, Alessandro

    2017-12-01

    Genomic DNA in eukaryotic cells is packaged into nucleosome arrays. During replication, nucleosomes need to be dismantled ahead of the advancing replication fork and reassembled on duplicated DNA. The architecture and function of the core replisome machinery is now beginning to be elucidated, with recent insights shaping our view on DNA replication processes. Simultaneously, breakthroughs in our mechanistic understanding of epigenetic inheritance allow us to build new models of how histone chaperones integrate with the replisome to reshuffle nucleosomes. The emerging picture indicates that the core eukaryotic DNA replication machinery has evolved elements that handle nucleosomes to facilitate chromatin duplication. Copyright © 2017. Published by Elsevier Ltd.

  18. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia

    2016-01-01

    to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7...... is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads...

  19. Tomato bushy stunt virus and DI RNAs as a model for studying mechanisms of RNA virus replication, pathogenicity and recombination. Final technical report for 1994--1997

    Energy Technology Data Exchange (ETDEWEB)

    Morris, T.J. [Univ. of Nebraska, Lincoln, NE (United States). School of Biological Sciences; Jackson, A.O. [Univ. of California, Berkeley, CA (United States). Dept. of Plant Biology

    1997-12-31

    Tomato bushy stunt virus (TBSV) is a small icosahedral virus with a very broad host-range. The symptoms of systemic infection range from mild mosaic to severe necrosis that often results in death. The genome of TBSV is composed of a single plus stranded RNA molecule with five genes. Two 5 inch genes are translated from the viral RNA, and the remaining three are translated from two subgenomic RNAs. Prior to the DOE supported studies, TBSV gene function had been assigned solely on the basis of sequence similarity with other virus genes of known function. The two 5 inch proximal genes (p33 and p92) were thought to be involved in viral replication, the middle gene encoded the capsid protein (p41), but no clear function was assigned to two nested 3 inch genes (p19 and p22), although it was suggested that at least one could be involved in movement. This research has determined the roles of each of the viral genes in the infection process, and the authors have obtained considerable genetic information pertinent to the contributions of the coat protein and the nested genes to the disease phenotypes observed in several host plants. They have also identified another genetic element with a short open reading frame in the 3 inch-noncoding region of the genome that provides a host-dependent replication function.

  20. Cytosine methylation inhibits replication of African cassava mosaic virus by two distinct mechanisms.

    OpenAIRE

    Ermak, G; Paszkowski, U; Wohlmuth, M; Scheid, O M; Paszkowski, J

    1993-01-01

    Extrachromosomally replicating viral DNA is usually free of cytosine methylation and viral templates methylated in vitro are poor substrates when used in replication assays. We have investigated the mechanism of inhibition of viral replication by DNA methylation using as a model the DNA A of African cassava mosaic virus. We have constructed two component helper systems which allow for separation of the transcriptional inhibition of viral genes necessary for replication from replication inhibi...

  1. The causes of replication stress and their consequences on genome stability and cell fate.

    Science.gov (United States)

    Magdalou, Indiana; Lopez, Bernard S; Pasero, Philippe; Lambert, Sarah A E

    2014-06-01

    Alterations of the dynamics of DNA replication cause genome instability. These alterations known as "replication stress" have emerged as a major source of genomic instability in pre-neoplasic lesions, contributing to cancer development. The concept of replication stress covers a wide variety of events that distort the temporal and spatial DNA replication program. These events have endogenous or exogenous origins and impact globally or locally on the dynamics of DNA replication. They may arise within a short window of time (acute stress) or during each S phase (chronic stress). Here, we review the known situations in which the dynamics of DNA replication is distorted. We have united them in four main categories: (i) inadequate firing of replication origins (deficiency or excess), (ii) obstacles to fork progression, (iii) conflicts between replication and transcription and (iv) DNA replication under inappropriate metabolic conditions (unbalanced DNA replication). Because the DNA replication program is a process tightly regulated by many factors, replication stress often appears as a cascade of events. A local stress may prevent the completion of DNA replication at a single locus and subsequently compromise chromosome segregation in mitosis and therefore have a global effect on genome integrity. Finally, we discuss how replication stress drives genome instability and to what extent it is relevant to cancer biology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Supporting universal prevention programs: a two-phased coaching model.

    Science.gov (United States)

    Becker, Kimberly D; Darney, Dana; Domitrovich, Celene; Keperling, Jennifer Pitchford; Ialongo, Nicholas S

    2013-06-01

    Schools are adopting evidence-based programs designed to enhance students' emotional and behavioral competencies at increasing rates (Hemmeter et al. in Early Child Res Q 26:96-109, 2011). At the same time, teachers express the need for increased support surrounding implementation of these evidence-based programs (Carter and Van Norman in Early Child Educ 38:279-288, 2010). Ongoing professional development in the form of coaching may enhance teacher skills and implementation (Noell et al. in School Psychol Rev 34:87-106, 2005; Stormont et al. 2012). There exists a need for a coaching model that can be applied to a variety of teacher skill levels and one that guides coach decision-making about how best to support teachers. This article provides a detailed account of a two-phased coaching model with empirical support developed and tested with coaches and teachers in urban schools (Becker et al. 2013). In the initial universal coaching phase, all teachers receive the same coaching elements regardless of their skill level. Then, in the tailored coaching phase, coaching varies according to the strengths and needs of each teacher. Specifically, more intensive coaching strategies are used only with teachers who need additional coaching supports, whereas other teachers receive just enough support to consolidate and maintain their strong implementation. Examples of how coaches used the two-phased coaching model when working with teachers who were implementing two universal prevention programs (i.e., the PATHS curriculum and PAX Good Behavior Game [PAX GBG]) provide illustrations of the application of this model. The potential reach of this coaching model extends to other school-based programs as well as other settings in which coaches partner with interventionists to implement evidence-based programs.

  3. DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins.

    Science.gov (United States)

    Milbredt, Sarah; Farmani, Neda; Sobetzko, Patrick; Waldminghaus, Torsten

    2016-10-21

    The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.

  4. Use of linear programming models in experimentation with plant nutrients

    Directory of Open Access Journals (Sweden)

    Mauro Brino Garcia

    2013-06-01

    Full Text Available Nutrition is an important issue of plant cultivation and experimentation with plant nutrients is a supporting tool for agriculture. However, use of high purity grade reagents as nutrient sources can be expensive and increases the cost of an experiment. The objective of this study was to minimize the acquisition cost of high purity grade reagents in experiments on plant nutrient deficiency by using the missing element technique through linear programming models, and to generate recommendation tables for preparation of culture solutions, as well as to quantify gains through a simulated experiment. Two linear programming models were formulated containing concentration constraints for each nutrient in the culture solution. Model A was based on 16 reagents for preparation of the culture solution, while model B was based on 27 reagents, looking to increase choice options. Results showed that both models minimized the acquisition cost of reagents, allowing a 9.03% reduction in model A and a 25.98% reduction in model B. The missing sulfur treatment proved the most costly for reagent acquisition while the missing nitrogen treatment proved the least costly. It was concluded that the formulated models were capable of reducing acquisition costs of reagents, yet the recommendations generated by them should be tested and checked for practical viability.

  5. Programming Models for Concurrency and Real-Time

    Science.gov (United States)

    Vitek, Jan

    Modern real-time applications are increasingly large, complex and concurrent systems which must meet stringent performance and predictability requirements. Programming those systems require fundamental advances in programming languages and runtime systems. This talk presents our work on Flexotasks, a programming model for concurrent, real-time systems inspired by stream-processing and concurrent active objects. Some of the key innovations in Flexotasks are that it support both real-time garbage collection and region-based memory with an ownership type system for static safety. Communication between tasks is performed by channels with a linear type discipline to avoid copying messages, and by a non-blocking transactional memory facility. We have evaluated our model empirically within two distinct implementations, one based on Purdue’s Ovm research virtual machine framework and the other on Websphere, IBM’s production real-time virtual machine. We have written a number of small programs, as well as a 30 KLOC avionics collision detector application. We show that Flexotasks are capable of executing periodic threads at 10 KHz with a standard deviation of 1.2us and have performance competitive with hand coded C programs.

  6. A Programming Model for Massive Data Parallelism with Data Dependencies

    International Nuclear Information System (INIS)

    Cui, Xiaohui; Mueller, Frank; Potok, Thomas E.; Zhang, Yongpeng

    2009-01-01

    Accelerating processors can often be more cost and energy effective for a wide range of data-parallel computing problems than general-purpose processors. For graphics processor units (GPUs), this is particularly the case when program development is aided by environments such as NVIDIA s Compute Unified Device Architecture (CUDA), which dramatically reduces the gap between domain-specific architectures and general purpose programming. Nonetheless, general-purpose GPU (GPGPU) programming remains subject to several restrictions. Most significantly, the separation of host (CPU) and accelerator (GPU) address spaces requires explicit management of GPU memory resources, especially for massive data parallelism that well exceeds the memory capacity of GPUs. One solution to this problem is to transfer data between the GPU and host memories frequently. In this work, we investigate another approach. We run massively data-parallel applications on GPU clusters. We further propose a programming model for massive data parallelism with data dependencies for this scenario. Experience from micro benchmarks and real-world applications shows that our model provides not only ease of programming but also significant performance gains

  7. Trajectory of Externalizing Child Behaviors in a KEEP Replication

    Science.gov (United States)

    Uretsky, Mathew C.; Lee, Bethany R.; Greeno, Elizabeth J.; Barth, Richard P.

    2017-01-01

    Objective: The purpose of this study is to examine the correlates of child behavior change over time in a replication of the KEEP intervention. Method: The study sample was drawn from the treatment group of the Maryland replication of KEEP (n=65). Change over time was analyzed using multilevel linear mixed modeling. Results: Parents' use of…

  8. Modeling and prototyping of biometric systems using dataflow programming

    Science.gov (United States)

    Minakova, N.; Petrov, I.

    2018-01-01

    The development of biometric systems is one of the labor-intensive processes. Therefore, the creation and analysis of approaches and techniques is an urgent task at present. This article presents a technique of modeling and prototyping biometric systems based on dataflow programming. The technique includes three main stages: the development of functional blocks, the creation of a dataflow graph and the generation of a prototype. A specially developed software modeling environment that implements this technique is described. As an example of the use of this technique, an example of the implementation of the iris localization subsystem is demonstrated. A variant of modification of dataflow programming is suggested to solve the problem related to the undefined order of block activation. The main advantage of the presented technique is the ability to visually display and design the model of the biometric system, the rapid creation of a working prototype and the reuse of the previously developed functional blocks.

  9. Hybrid programming model for implicit PDE simulations on multicore architectures

    KAUST Repository

    Kaushik, Dinesh

    2011-01-01

    The complexity of programming modern multicore processor based clusters is rapidly rising, with GPUs adding further demand for fine-grained parallelism. This paper analyzes the performance of the hybrid (MPI+OpenMP) programming model in the context of an implicit unstructured mesh CFD code. At the implementation level, the effects of cache locality, update management, work division, and synchronization frequency are studied. The hybrid model presents interesting algorithmic opportunities as well: the convergence of linear system solver is quicker than the pure MPI case since the parallel preconditioner stays stronger when hybrid model is used. This implies significant savings in the cost of communication and synchronization (explicit and implicit). Even though OpenMP based parallelism is easier to implement (with in a subdomain assigned to one MPI process for simplicity), getting good performance needs attention to data partitioning issues similar to those in the message-passing case. © 2011 Springer-Verlag.

  10. Flexible building stock modelling with array-programming

    DEFF Research Database (Denmark)

    Brøgger, Morten; Wittchen, Kim Bjarne

    2017-01-01

    Many building stock models employ archetype-buildings in order to capture the essential characteristics of a diverse building stock. However, these models often require multiple archetypes, which make them inflexible. This paper proposes an array-programming based model, which calculates the heat...... demand of each building separately. This approach makes it possible to study any subset of the building stock without loss of information. Moreover, the calculated heat demand can readily be compared to a registered consumption in individual buildings to account for discrepancies. Results show, that we...

  11. Modelling of windmill induction generators in dynamic simulation programs

    DEFF Research Database (Denmark)

    Akhmatov, Vladislav; Knudsen, Hans

    1999-01-01

    For AC networks with large amounts of induction generators-in case of e.g. windmills-the paper demonstrates a significant discrepancy in the simulated voltage recovery after faults in weak networks, when comparing result obtained with dynamic stability programs and transient programs, respectively...... with and without a model of the mechanical shaft. The reason for the discrepancies are explained, and it is shown that the phenomenon is due partly to the presence of DC offset currents in the induction machine stator, and partly to the mechanical shaft system of the wind turbine and the generator rotor...

  12. Replication-uncoupled histone deposition during adenovirus DNA replication.

    Science.gov (United States)

    Komatsu, Tetsuro; Nagata, Kyosuke

    2012-06-01

    In infected cells, the chromatin structure of the adenovirus genome DNA plays critical roles in its genome functions. Previously, we reported that in early phases of infection, incoming viral DNA is associated with both viral core protein VII and cellular histones. Here we show that in late phases of infection, newly synthesized viral DNA is also associated with histones. We also found that the knockdown of CAF-1, a histone chaperone that functions in the replication-coupled deposition of histones, does not affect the level of histone H3 bound on viral chromatin, although CAF-1 is accumulated at viral DNA replication foci together with PCNA. Chromatin immunoprecipitation assays using epitope-tagged histone H3 demonstrated that histone variant H3.3, which is deposited onto the cellular genome in a replication-independent manner, is selectively associated with both incoming and newly synthesized viral DNAs. Microscopic analyses indicated that histones but not USF1, a transcription factor that regulates viral late gene expression, are excluded from viral DNA replication foci and that this is achieved by the oligomerization of the DNA binding protein (DBP). Taken together, these results suggest that histone deposition onto newly synthesized viral DNA is most likely uncoupled with viral DNA replication, and a possible role of DBP oligomerization in this replication-uncoupled histone deposition is discussed.

  13. An occupational medical program for a 'model' uranium mill

    International Nuclear Information System (INIS)

    Miller, H.T.

    1979-01-01

    The basic purpose of occupational health programs in uranium milling are to insure that no employee receives an exposure to carcinogenic, mutagenic, teratogenic, highly toxic, pneumoconiosis-producing, or dangerous physical agents that could result in chronic or acute injury and to assure that significant concentrations or levels of the above are not present in either the plant or general environment. This paper defines a model mill as consisting of crushing, sizing, acid leach, separation, solvent extraction, drying and packaging operations and describes the employee health hazards associated with each. It also describes a type program consisting of a balanced combination of exposure monitoring and survey, air samples, personnel dosimetry, bioassay, training, medical surveillance, and emergency planning based on the employee exposure situation. Experience with such a program is also discussed, and some techniques of practically meeting the regulatory requirements and protecting the worker are outlined. (Auth.)

  14. Efficient mixed integer programming models for family scheduling problems

    Directory of Open Access Journals (Sweden)

    Meng-Ye Lin

    Full Text Available This paper proposes several mixed integer programming models which incorporate optimal sequence properties into the models, to solve single machine family scheduling problems. The objectives are total weighted completion time and maximum lateness, respectively. Experiment results indicate that there are remarkable improvements in computational efficiency when optimal sequence properties are included in the models. For the total weighted completion time problems, the best model solves all of the problems up to 30-jobs within 5 s, all 50-job problems within 4 min and about 1/3 of the 75-job to 100-job problems within 1 h. For maximum lateness problems, the best model solves almost all the problems up to 30-jobs within 11 min and around half of the 50-job to 100-job problems within 1 h. Keywords: Family scheduling, Sequence independent setup, Total weighted completion time, Maximum lateness

  15. Development of CANDU 6 Primary Heat Transport System Modeling Program

    International Nuclear Information System (INIS)

    Seo, Hyung-beom; Kim, Sung-min; Park, Joong-woo; Kim, Kwang-su; Ko, Dae-hack; Han, Bong-seob

    2007-01-01

    NUCIRC is a steady-state thermal-hydraulic code used for design and performance analyses of CANDU Heat Transport System. The code is used to build PHT model in Wolsong NPP and to calculate channel flow distribution. Wolsong NPP has to calculate channel flow distribution and quality of coolant at the ROH header after every outage by OPP (Operating Policy and Principal). PHT modeling work is time consuming which need a lot of operation experience and specialty. It is very difficult to build PHT model as plant operator in two weeks which is obligate for plant operation after every outage. That is why Wolsong NPP develop NUMODEL (NUcirc MODELing) with many-years experience and a know-how of using NUCIRC code. NUMODEL is computer program which is used to create PHT model based on utilizing NUCIRC code

  16. The FITS model office ergonomics program: a model for best practice.

    Science.gov (United States)

    Chim, Justine M Y

    2014-01-01

    An effective office ergonomics program can predict positive results in reducing musculoskeletal injury rates, enhancing productivity, and improving staff well-being and job satisfaction. Its objective is to provide a systematic solution to manage the potential risk of musculoskeletal disorders among computer users in an office setting. A FITS Model office ergonomics program is developed. The FITS Model Office Ergonomics Program has been developed which draws on the legislative requirements for promoting the health and safety of workers using computers for extended periods as well as previous research findings. The Model is developed according to the practical industrial knowledge in ergonomics, occupational health and safety management, and human resources management in Hong Kong and overseas. This paper proposes a comprehensive office ergonomics program, the FITS Model, which considers (1) Furniture Evaluation and Selection; (2) Individual Workstation Assessment; (3) Training and Education; (4) Stretching Exercises and Rest Break as elements of an effective program. An experienced ergonomics practitioner should be included in the program design and implementation. Through the FITS Model Office Ergonomics Program, the risk of musculoskeletal disorders among computer users can be eliminated or minimized, and workplace health and safety and employees' wellness enhanced.

  17. Original article Rehabilitation model program for seriously ill patients

    Directory of Open Access Journals (Sweden)

    Adrienne Kegye

    2014-10-01

    Full Text Available Background Patients receiving cancer treatment start lifestyle changes mostly at the end of the treatment during the rehabilitation period. Most often, the first step is a dietary change and physical exercises built into the daily routine. Patients who do this in groups led by qualified therapists and based on professional counseling can build more effective and more permanent changes into their life. To develop a complex rehabilitation program which, in the short term, aims to familiarize patients with a lifestyle which harmonizes the physical, mental, spiritual and social spheres of life and, in the long term, to build it into their everyday life in order to ameliorate the physical and mental state and reduce the psychological symptoms and the isolation of patients. The physical component focuses on diet and exercise. The psycho-social-spiritual support focuses on discovering inner sources of strength, developing active coping mechanisms and helping to achieve more open communication. Participants and procedure In February and March 2011, 8 patients treated for malignant tumors participated in the model program. The components of the model program were psychotherapy, physiotherapy, cancer consultation, nutrition counseling, creative activities and walking. Results During the period of the model program the isolation of the patients decreased and their social support and ability of coping with the illness ameliorated. They reported an ease in anxiety and depression in their everyday activities. According to feedback, their communication with each other, with the staff and with their relatives became more open. Altogether this had advantageous effects on the functioning of the ward and the mood of the staff. Conclusions The rehabilitation program confirmed that beside individual psycho-social support, beneficial and economic psycho-social support can be provided for the patients in group form along with the most effective assignment of the

  18. Programming

    International Nuclear Information System (INIS)

    Jackson, M.A.

    1982-01-01

    The programmer's task is often taken to be the construction of algorithms, expressed in hierarchical structures of procedures: this view underlies the majority of traditional programming languages, such as Fortran. A different view is appropriate to a wide class of problem, perhaps including some problems in High Energy Physics. The programmer's task is regarded as having three main stages: first, an explicit model is constructed of the reality with which the program is concerned; second, this model is elaborated to produce the required program outputs; third, the resulting program is transformed to run efficiently in the execution environment. The first two stages deal in network structures of sequential processes; only the third is concerned with procedure hierarchies. (orig.)

  19. Programming

    CERN Document Server

    Jackson, M A

    1982-01-01

    The programmer's task is often taken to be the construction of algorithms, expressed in hierarchical structures of procedures: this view underlies the majority of traditional programming languages, such as Fortran. A different view is appropriate to a wide class of problem, perhaps including some problems in High Energy Physics. The programmer's task is regarded as having three main stages: first, an explicit model is constructed of the reality with which the program is concerned; second, this model is elaborated to produce the required program outputs; third, the resulting program is transformed to run efficiently in the execution environment. The first two stages deal in network structures of sequential processes; only the third is concerned with procedure hierarchies.

  20. Summary of multi-core hardware and programming model investigations

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, Suzanne Marie; Pedretti, Kevin Thomas Tauke; Levenhagen, Michael J.

    2008-05-01

    This report summarizes our investigations into multi-core processors and programming models for parallel scientific applications. The motivation for this study was to better understand the landscape of multi-core hardware, future trends, and the implications on system software for capability supercomputers. The results of this study are being used as input into the design of a new open-source light-weight kernel operating system being targeted at future capability supercomputers made up of multi-core processors. A goal of this effort is to create an agile system that is able to adapt to and efficiently support whatever multi-core hardware and programming models gain acceptance by the community.

  1. Final Report: Center for Programming Models for Scalable Parallel Computing

    Energy Technology Data Exchange (ETDEWEB)

    Mellor-Crummey, John [William Marsh Rice University

    2011-09-13

    As part of the Center for Programming Models for Scalable Parallel Computing, Rice University collaborated with project partners in the design, development and deployment of language, compiler, and runtime support for parallel programming models to support application development for the “leadership-class” computer systems at DOE national laboratories. Work over the course of this project has focused on the design, implementation, and evaluation of a second-generation version of Coarray Fortran. Research and development efforts of the project have focused on the CAF 2.0 language, compiler, runtime system, and supporting infrastructure. This has involved working with the teams that provide infrastructure for CAF that we rely on, implementing new language and runtime features, producing an open source compiler that enabled us to evaluate our ideas, and evaluating our design and implementation through the use of benchmarks. The report details the research, development, findings, and conclusions from this work.

  2. EVALUASI PROGRAM PEMBELAJARAN IPA SMP MENGGUNAKAN MODEL COUNTENANCE STAKE

    Directory of Open Access Journals (Sweden)

    Astin Lukum

    2015-06-01

    THE EVALUATION OF SCIENCE TEACHING ON JUNIOR HIGH SCHOOL USING STAKE’S COUNTENANCE MODEL Abstract The purpose of the study was to describe the science learning program on junior high school in Bone Bolanga district based on the Regulation of Minister of Education and Culture of the Republic of Indonesia, Number 65 of 2013 about Processing Standard of Primary and Secondary Education. This study used Stake’s Countanance evaluation model. The data were collected using observation, interview and documentation techniques. The conclusion was: (1 the planning of science learning was categorized fair (68%, it was found that lesson plan was not in accordance with the learning processing standard. (2 The implementation of science learning was categorized fair (57%, that unconformitted with learning processing implementation standard. (3 Student learning outcomes have not met the completeness of minimum criteria (KKM that categorized enough (65% and (4 There were the contingency of planing learning proces and outcome. Keywords: Program Evaluation, Stake's Countenance, Science Learning

  3. Using Runtime Analysis to Guide Model Checking of Java Programs

    Science.gov (United States)

    Havelund, Klaus; Norvig, Peter (Technical Monitor)

    2001-01-01

    This paper describes how two runtime analysis algorithms, an existing data race detection algorithm and a new deadlock detection algorithm, have been implemented to analyze Java programs. Runtime analysis is based on the idea of executing the program once. and observing the generated run to extract various kinds of information. This information can then be used to predict whether other different runs may violate some properties of interest, in addition of course to demonstrate whether the generated run itself violates such properties. These runtime analyses can be performed stand-alone to generate a set of warnings. It is furthermore demonstrated how these warnings can be used to guide a model checker, thereby reducing the search space. The described techniques have been implemented in the b e grown Java model checker called PathFinder.

  4. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  5. Comparison of Building Energy Modeling Programs: Building Loads

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Dandan [Tsinghua Univ., Beijing (China); Hong, Tianzhen [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Yan, Da [Tsinghua Univ., Beijing (China); Wang, Chuang [Tsinghua Univ., Beijing (China)

    2012-06-01

    This technical report presented the methodologies, processes, and results of comparing three Building Energy Modeling Programs (BEMPs) for load calculations: EnergyPlus, DeST and DOE-2.1E. This joint effort, between Lawrence Berkeley National Laboratory, USA and Tsinghua University, China, was part of research projects under the US-China Clean Energy Research Center on Building Energy Efficiency (CERC-BEE). Energy Foundation, an industrial partner of CERC-BEE, was the co-sponsor of this study work. It is widely known that large discrepancies in simulation results can exist between different BEMPs. The result is a lack of confidence in building simulation amongst many users and stakeholders. In the fields of building energy code development and energy labeling programs where building simulation plays a key role, there are also confusing and misleading claims that some BEMPs are better than others. In order to address these problems, it is essential to identify and understand differences between widely-used BEMPs, and the impact of these differences on load simulation results, by detailed comparisons of these BEMPs from source code to results. The primary goal of this work was to research methods and processes that would allow a thorough scientific comparison of the BEMPs. The secondary goal was to provide a list of strengths and weaknesses for each BEMP, based on in-depth understandings of their modeling capabilities, mathematical algorithms, advantages and limitations. This is to guide the use of BEMPs in the design and retrofit of buildings, especially to support China’s building energy standard development and energy labeling program. The research findings could also serve as a good reference to improve the modeling capabilities and applications of the three BEMPs. The methodologies, processes, and analyses employed in the comparison work could also be used to compare other programs. The load calculation method of each program was analyzed and compared to

  6. Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

    Science.gov (United States)

    Farkash-Amar, Shlomit; David, Yaara; Polten, Andreas; Hezroni, Hadas; Eldar, Yonina C; Meshorer, Eran; Yakhini, Zohar; Simon, Itamar

    2012-01-01

    DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR). Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs) in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs) in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR). Our algorithm, ARTO (Analysis of Replication Timing and Organization), uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are associated with

  7. Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

    Directory of Open Access Journals (Sweden)

    Shlomit Farkash-Amar

    Full Text Available DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR. Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR. Our algorithm, ARTO (Analysis of Replication Timing and Organization, uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are

  8. Coupling R and PHREEQC: Efficient Programming of Geochemical Models

    OpenAIRE

    De Lucia, Marco; Kühn, Michael

    2013-01-01

    We present a new interface between the geochemical simulator PHREEQC and the open source language R. It represents a tool to flexibly and efficiently program and automate every aspect of geochemical modelling. The interface helps particularly to setup and run large numbers of simulations and visualise the results. Also profiting of numberless high-quality R extension packages, performing sensitivity analysis or Monte Carlo simulations becomes straightforward. Further, an algorithm to speedup ...

  9. Model-Based Programming of Fault-Aware Systems

    OpenAIRE

    Williams, Brian C.; Ingham, Michel D.; Chung, Seung; Elliott, Paul; Hofbaur, Michael; Sullivan, Gregory T.

    2003-01-01

    A wide range of sensor-rich, networked embedded systems are being created that must operate robustly for years in the face of novel failures by managing complex autonomic processes. These systems are being composed, for example, into vast networks of space, air, ground, and underwater vehicles. Our objective is to revolutionize the way in which we control these new artifacts by creating reactive model-based programming languages that enable everyday systems to reason intelligently and enable ...

  10. Synchronous replication of remote storage

    OpenAIRE

    Mirzoev, Dr. Timur

    2014-01-01

    Storage replication is one of the essential requirements for network environments. While many forms of Network Attached Storage (NAS), Storage Area Networks (SAN) and other forms of network storage exist, there is a need for a reliable synchronous storage replication technique between distant sites (less than 1 mile). Such technology allows setting new standards for network failover and failback systems for virtual servers; specifically, addressing the growing need for effective disaster reco...

  11. The Athletic Prevention Programming and Leadership Education (APPLE) Model: Developing Substance Abuse Prevention Programs

    OpenAIRE

    Grossman, Susan J.; Gieck, Joe; Fang, Wei Li; Freedman, Alan

    1993-01-01

    Alcohol and other drug (AOD) abuse affects every sector of society, and student-athletes are no exception. Because many factors affecting athletes do not affect other students, athletic departments commonly approach prevention through AOD education. Different educational approaches are described in this article, particularly the Athletic Prevention Programming and Leadership Education (APPLE) model. Project APPLE is designed to enable an athletic department to systematically analyze its AOD p...

  12. Tecnomatix Plant Simulation modeling and programming by means of examples

    CERN Document Server

    Bangsow, Steffen

    2015-01-01

    This book systematically introduces the development of simulation models as well as the implementation and evaluation of simulation experiments with Tecnomatix Plant Simulation. It deals with all users of Plant Simulation, who have more complex tasks to handle. It also looks for an easy entry into the program. Particular attention has been paid to introduce the simulation flow language SimTalk and its use in various areas of the simulation. The author demonstrates with over 200 examples how to combine the blocks for simulation models and how to deal with SimTalk for complex control and analys

  13. An integer programming model for distal humerus fracture fixation planning.

    Science.gov (United States)

    Maratt, Joseph D; Peaks, Ya-Sin A; Doro, Lisa Case; Karunakar, Madhav A; Hughes, Richard E

    2008-05-01

    To demonstrate the feasibility of an integer programming model to assist in pre-operative planning for open reduction and internal fixation of a distal humerus fracture. We describe an integer programming model based on the objective of maximizing the reward for screws placed while satisfying the requirements for sound internal fixation. The model maximizes the number of bicortical screws placed while avoiding screw collision and favoring screws of greater length that cross multiple fracture planes. The model was tested on three types of total articular fractures of the distal humerus. Solutions were generated using 5, 9, 21 and 33 possible screw orientations per hole. Solutions generated using 33 possible screw orientations per hole and five screw lengths resulted in the most clinically relevant fixation plan and required the calculation of 1,191,975 pairs of screws that resulted in collision. At this level of complexity, the pre-processor took 104 seconds to generate the constraints for the solver, and a solution was generated in under one minute in all three cases. Despite the large size of this problem, it can be solved in a reasonable amount of time, making use of the model practical in pre-surgical planning.

  14. A Game-Theoretic Model for Distributed Programming by Contract

    DEFF Research Database (Denmark)

    Henriksen, Anders Starcke; Hvitved, Tom; Filinski, Andrzej

    2009-01-01

    We present an extension of the programming-by-contract (PBC) paradigm to a concurrent and distributed environment.  Classical PBC is characterized by absolute conformance of code to its specification, assigning blame in case of failures, and a hierarchical, cooperative decomposition model – none...... of which extend naturally to a distributed environment with multiple administrative peers. We therefore propose a more nuanced contract model based on quantifiable performance of implementations; assuming responsibility for success; and a fundamentally adversarial model of system integration, where each...... component provider is optimizing its behavior locally, with respect to potentially conflicting demands.  This model gives rise to a game-theoretic formulation of contract-governed process interactions that supports compositional reasoning about contract conformance....

  15. Model - Model Pembelajaran pada Program Studi Pendidikan Guru Madrasah Ibtidaiyah (PGMI STAIN Samarinda

    Directory of Open Access Journals (Sweden)

    Syeh Hawib Hamzah

    2014-06-01

    Full Text Available The model of learning is a vital thing in education. A good appropriate model of learning could reach the goal of learning efficently and effectively. The lecturers of education and teacher training program of STAIN Samarinda implement a various teaching and learning models when they perform their teaching, such as: model of contectual teaching, social interaction, informational proces, personal-based learning, behaviorism, cooperative learning, and problem-based learning.

  16. A model for a national low level waste program

    International Nuclear Information System (INIS)

    Blankenhorn, James A.

    2009-01-01

    A national program for the management of low level waste is essential to the success of environmental clean-up, decontamination and decommissioning, current operations and future missions. The value of a national program is recognized through procedural consistency and a shared set of resources. A national program requires a clear waste definition and an understanding of waste characteristics matched against available and proposed disposal options. A national program requires the development and implementation of standards and procedures for implementing the waste hierarchy, with a specitic emphasis on waste avoidance, minimization and recycling. It requires a common set of objectives for waste characterization based on the disposal facility's waste acceptance criteria, regulatory and license requirements and performance assessments. Finally, a national waste certification program is required to ensure compliance. To facilitate and enhance the national program, a centralized generator services organization, tasked with providing technical services to the generators on behalf of the national program, is necessary. These subject matter experts are the interface between the generating sites and the disposal facility(s). They provide an invaluable service to the generating organizations through their involvement in waste planning prior to waste generation and through championing implementation of the waste hierarchy. Through their interface, national treatment and transportation services are optimized and new business opportunities are identified. This national model is based on extensive experience in the development and on-going management of a national transuranic waste program and management of the national repository, the Waste Isolation Pilot Plant. The Low Level Program at the Savannah River Site also successfully developed and implemented the waste hierarchy, waste certification and waste generator services concepts presented below. The Savannah River Site

  17. Optical Neural Network Models Applied To Logic Program Execution

    Science.gov (United States)

    Stormon, Charles D.

    1988-05-01

    Logic programming is being used extensively by Artificial Intelligence researchers to solve problems including natural language processing and expert systems. These languages, of which Prolog is the most widely used, promise to revolutionize software engineering, but much greater performance is needed. Researchers have demonstrated the applicability of neural network models to the solution of certain NP-complete problems, but these methods are not obviously applicable to the execution of logic programs. This paper outlines the use of neural networks in four aspects of the logic program execution cycle, and discusses results of a simulation of three of these. Four neural network functional units are described, called the substitution agent, the clause filter, the structure processor, and the heuristics generator, respectively. Simulation results suggest that the system described may provide several orders of magnitude improvement in execution speed for large logic programs. However, practical implementation of the proposed architecture will require the application of optical computing techniques due to the large number of neurons required, and the need for massive, adaptive connectivity.

  18. Evaluation of Medical Education virtual Program: P3 model.

    Science.gov (United States)

    Rezaee, Rita; Shokrpour, Nasrin; Boroumand, Maryam

    2016-10-01

    In e-learning, people get involved in a process and create the content (product) and make it available for virtual learners. The present study was carried out in order to evaluate the first virtual master program in medical education at Shiraz University of Medical Sciences according to P3 Model. This is an evaluation research study with post single group design used to determine how effective this program was. All students 60 who participated more than one year in this virtual program and 21 experts including teachers and directors participated in this evaluation project. Based on the P3 e-learning model, an evaluation tool with 5-point Likert rating scale was designed and applied to collect the descriptive data. Students reported storyboard and course design as the most desirable element of learning environment (2.30±0.76), but they declared technical support as the less desirable part (1.17±1.23). Presence of such framework in this regard and using it within the format of appropriate tools for evaluation of e-learning in universities and higher education institutes, which present e-learning curricula in the country, may contribute to implementation of the present and future e-learning curricula efficiently and guarantee its implementation in an appropriate way.

  19. Genetic Programming and Standardization in Water Temperature Modelling

    Directory of Open Access Journals (Sweden)

    Maritza Arganis

    2009-01-01

    Full Text Available An application of Genetic Programming (an evolutionary computational tool without and with standardization data is presented with the aim of modeling the behavior of the water temperature in a river in terms of meteorological variables that are easily measured, to explore their explanatory power and to emphasize the utility of the standardization of variables in order to reduce the effect of those with large variance. Recorded data corresponding to the water temperature behavior at the Ebro River, Spain, are used as analysis case, showing a performance improvement on the developed model when data are standardized. This improvement is reflected in a reduction of the mean square error. Finally, the models obtained in this document were applied to estimate the water temperature in 2004, in order to provide evidence about their applicability to forecasting purposes.

  20. Mathematical model for HIV spreads control program with ART treatment

    Science.gov (United States)

    Maimunah; Aldila, Dipo

    2018-03-01

    In this article, using a deterministic approach in a seven-dimensional nonlinear ordinary differential equation, we establish a mathematical model for the spread of HIV with an ART treatment intervention. In a simplified model, when no ART treatment is implemented, disease-free and the endemic equilibrium points were established analytically along with the basic reproduction number. The local stability criteria of disease-free equilibrium and the existing criteria of endemic equilibrium were analyzed. We find that endemic equilibrium exists when the basic reproduction number is larger than one. From the sensitivity analysis of the basic reproduction number of the complete model (with ART treatment), we find that the increased number of infected humans who follow the ART treatment program will reduce the basic reproduction number. We simulate this result also in the numerical experiment of the autonomous system to show how treatment intervention impacts the reduction of the infected population during the intervention time period.

  1. Stochastic programming framework for Lithuanian pension payout modelling

    Directory of Open Access Journals (Sweden)

    Audrius Kabašinskas

    2014-12-01

    Full Text Available The paper provides a scientific approach to the problem of selecting a pension fund by taking into account some specific characteristics of the Lithuanian Republic (LR pension accumulation system. The decision making model, which can be used to plan a long-term pension accrual of the Lithuanian Republic (LR citizens, in an optimal way is presented. This model focuses on factors that influence the sustainability of the pension system selection under macroeconomic, social and demographic uncertainty. The model is formalized as a single stage stochastic optimization problem where the long-term optimal strategy can be obtained based on the possible scenarios generated for a particular participant. Stochastic programming methods allow including the pension fund rebalancing moment and direction of investment, and taking into account possible changes of personal income, changes of society and the global financial market. The collection of methods used to generate scenario trees was found useful to solve strategic planning problems.

  2. Mathematical Modeling of Intestinal Iron Absorption Using Genetic Programming.

    Science.gov (United States)

    Colins, Andrea; Gerdtzen, Ziomara P; Nuñez, Marco T; Salgado, J Cristian

    2017-01-01

    Iron is a trace metal, key for the development of living organisms. Its absorption process is complex and highly regulated at the transcriptional, translational and systemic levels. Recently, the internalization of the DMT1 transporter has been proposed as an additional regulatory mechanism at the intestinal level, associated to the mucosal block phenomenon. The short-term effect of iron exposure in apical uptake and initial absorption rates was studied in Caco-2 cells at different apical iron concentrations, using both an experimental approach and a mathematical modeling framework. This is the first report of short-term studies for this system. A non-linear behavior in the apical uptake dynamics was observed, which does not follow the classic saturation dynamics of traditional biochemical models. We propose a method for developing mathematical models for complex systems, based on a genetic programming algorithm. The algorithm is aimed at obtaining models with a high predictive capacity, and considers an additional parameter fitting stage and an additional Jackknife stage for estimating the generalization error. We developed a model for the iron uptake system with a higher predictive capacity than classic biochemical models. This was observed both with the apical uptake dataset used for generating the model and with an independent initial rates dataset used to test the predictive capacity of the model. The model obtained is a function of time and the initial apical iron concentration, with a linear component that captures the global tendency of the system, and a non-linear component that can be associated to the movement of DMT1 transporters. The model presented in this paper allows the detailed analysis, interpretation of experimental data, and identification of key relevant components for this complex biological process. This general method holds great potential for application to the elucidation of biological mechanisms and their key components in other complex

  3. Recovery Act. Development of a Model Energy Conservation Training Program

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2012-07-05

    The overall objective of this project was to develop an updated model Energy Conservation training program for stationary engineers. This revision to the IUOE National Training Fund’s existing Energy Conservation training curriculum is designed to enable stationary engineers to incorporate essential energy management into routine building operation and maintenance tasks. The curriculum uses a blended learning approach that includes classroom, hands-on, computer simulation and web-based training in addition to a portfolio requirement for a workplace-based learning application. The Energy Conservation training program goal is development of a workforce that can maintain new and existing commercial buildings at optimum energy performance levels. The grant start date was July 6, 2010 and the project continued through September 30, 2012, including a three month non-funded extension.

  4. C++, objected-oriented programming, and astronomical data models

    Science.gov (United States)

    Farris, A.

    1992-01-01

    Contemporary astronomy is characterized by increasingly complex instruments and observational techniques, higher data collection rates, and large data archives, placing severe stress on software analysis systems. The object-oriented paradigm represents a significant new approach to software design and implementation that holds great promise for dealing with this increased complexity. The basic concepts of this approach will be characterized in contrast to more traditional procedure-oriented approaches. The fundamental features of objected-oriented programming will be discussed from a C++ programming language perspective, using examples familiar to astronomers. This discussion will focus on objects, classes and their relevance to the data type system; the principle of information hiding; and the use of inheritance to implement generalization/specialization relationships. Drawing on the object-oriented approach, features of a new database model to support astronomical data analysis will be presented.

  5. Implementing a citizen's DWI reporting program using the Extra Eyes model

    Science.gov (United States)

    2008-09-01

    This manual is a guide for law enforcement agencies and community organizations in creating and implementing a citizens DWI reporting program in their communities modeling the Operation Extra Eyes program. Extra Eyes is a program that engages volu...

  6. Optimal timing of joint replacement using mathematical programming and stochastic programming models.

    Science.gov (United States)

    Keren, Baruch; Pliskin, Joseph S

    2011-12-01

    The optimal timing for performing radical medical procedures as joint (e.g., hip) replacement must be seriously considered. In this paper we show that under deterministic assumptions the optimal timing for joint replacement is a solution of a mathematical programming problem, and under stochastic assumptions the optimal timing can be formulated as a stochastic programming problem. We formulate deterministic and stochastic models that can serve as decision support tools. The results show that the benefit from joint replacement surgery is heavily dependent on timing. Moreover, for a special case where the patient's remaining life is normally distributed along with a normally distributed survival of the new joint, the expected benefit function from surgery is completely solved. This enables practitioners to draw the expected benefit graph, to find the optimal timing, to evaluate the benefit for each patient, to set priorities among patients and to decide if joint replacement should be performed and when.

  7. Architecture and Programming Models for High Performance Intensive Computation

    Science.gov (United States)

    2016-06-29

    written in funJava, a functional programming language. • Implement selected test programs in funJava for demonstrating performance and en- ergy efficiency... Programming language The funJava programming language is a version of standard Java , restricted to a functional subset. This simple functional programming ... programs written in funJava, a functional programming language. • Implement selected test programs in funJava for demonstrating performance and energy

  8. A Stochastic Programming Model for Fuel Treatment Management

    Directory of Open Access Journals (Sweden)

    Mohannad Kabli

    2015-06-01

    Full Text Available This work considers a two-stage stochastic integer programming (SIP approach for optimizing fuel treatment planning under uncertainty in weather and fire occurrence for rural forests. Given a set of areas for potentially performing fuel treatment, the problem is to decide the best treatment option for each area under uncertainty in future weather and fire occurrence. A two-stage SIP model is devised whose objective is to minimize the here-and-now cost of fuel treatment in the first-stage, plus the expected future costs due to uncertain impact from potential fires in the second-stage calculated as ecosystem services losses. The model considers four fuel treatment options: no treatment, mechanical thinning, prescribed fire, and grazing. Several constraints such as budgetary and labor constraints are included in the model and a standard fire behavior model is used to estimate some of the parameters of the model such as fuel levels at the beginning of the fire season. The SIP model was applied to data for a study area in East Texas with 15 treatment areas under different weather scenarios. The results of the study show, for example, that unless the expected ecosystem services values for an area outweigh fuel treatment costs, no treatment is the best choice for the area. Thus the valuation of the area together with the probability of fire occurrence and behavior strongly drive fuel treatment choices.

  9. Defects of mitochondrial DNA replication.

    Science.gov (United States)

    Copeland, William C

    2014-09-01

    Mitochondrial DNA is replicated by DNA polymerase γ in concert with accessory proteins such as the mitochondrial DNA helicase, single-stranded DNA binding protein, topoisomerase, and initiating factors. Defects in mitochondrial DNA replication or nucleotide metabolism can cause mitochondrial genetic diseases due to mitochondrial DNA deletions, point mutations, or depletion, which ultimately cause loss of oxidative phosphorylation. These genetic diseases include mitochondrial DNA depletion syndromes such as Alpers or early infantile hepatocerebral syndromes, and mitochondrial DNA deletion disorders, such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. This review focuses on our current knowledge of genetic defects of mitochondrial DNA replication (POLG, POLG2, C10orf2, and MGME1) that cause instability of mitochondrial DNA and mitochondrial disease. © The Author(s) 2014.

  10. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

    Biomarkers of replicative senescence can be defined as those ultrastructural and physiological variations as well as molecules whose changes in expression, activity or function correlate with aging, as a result of the gradual exhaustion of replicative potential and a state of permanent cell cycle...... arrest. The biomarkers that characterize the path to an irreversible state of cell cycle arrest due to proliferative exhaustion may also be shared by other forms of senescence-inducing mechanisms. Validation of senescence markers is crucial in circumstances where quiescence or temporary growth arrest may...... be triggered or is thought to be induced. Pre-senescence biomarkers are also important to consider as their presence indicate that induction of aging processes is taking place. The bona fide pathway leading to replicative senescence that has been extensively characterized is a consequence of gradual reduction...

  11. THE PROGRAMED CELL DEATH REGULATORS OF ISOLATED MODEL SYSTEMS

    Directory of Open Access Journals (Sweden)

    D. V. Vatlitsov

    2016-06-01

    Full Text Available The technology evolution creates the prerequisites for the emergence of new informational concept and approaches to the formation of a fundamentally new principles of biological objects understanding. The aim was to study the activators of the programmed cell death in an isolated system model. Cell culture aging parameters were performed on flow cytometer. It had formed the theory that the changes in the concentrations of metal ions and increase their extracellular concentration had formed a negative gradient into the cells.regulation of cell death. It was shown that the metals ions concentrations.

  12. Managing problem employees: a model program and practical guide.

    Science.gov (United States)

    Miller, Laurence

    2010-01-01

    This article presents a model program for managing problem employees that includes a description ofthe basic types of problem employees and employee problems, as well as practical recommendations for. (1) selection and screening, (2) education and training, (3) coaching and counseling, (4) discipline, (5) psychological fitness-for-duty evaluations, (6) mental health services, (7) termination, and (8) leadership and administrative strategies. Throughout, the emphasis on balancing the need for order and productivity in the workplace with fairness and concern for employee health and well-being.

  13. Personality and Academic Motivation: Replication, Extension, and Replication

    Science.gov (United States)

    Jones, Martin H.; McMichael, Stephanie N.

    2015-01-01

    Previous work examines the relationships between personality traits and intrinsic/extrinsic motivation. We replicate and extend previous work to examine how personality may relate to achievement goals, efficacious beliefs, and mindset about intelligence. Approximately 200 undergraduates responded to the survey with a 150 participants replicating…

  14. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    to local environments and under the impact of new learning. To illuminate these issues, we draw on a longitudinal in-depth study of Swedish home furnishing giant IKEA, involving more than 70 interviews. We find that IKEA has developed organizational mechanisms that support an ongoing learning process aimed...... at frequent modification of the format for replication. Another finding is that IKEA treats replication as hierarchical: lower-level features (marketing efforts, pricing, etc.) are allowed to vary across IKEA stores in response to market-based learning, while higher-level features (fundamental values, vision...

  15. Groundwater modelling of Aespoe using the ECLIPSE program

    Energy Technology Data Exchange (ETDEWEB)

    Wokil, H.

    1995-06-01

    The pre-investigations indicated that the dominant rocks ranged in composition from true granite to dioritic or gabbroic rocks. In conjunction with these investigations at the area, a number of indications were obtained of high transmissive fracture zones. To be able to understand the fracture zone NE-1 as well as possible, a number of hydraulic tests were performed, for example a tracer test. The program ECLIPSE 100 is one of the standard programs in the oil industry which is used to simulate oil fields. ECLIPSE 100 is a multi-facility simulator and it can be used to simulate 1, 2 and 3 phase systems, one option is oil, two phase options are oil/gas, oil/water or gas/water, and the third option is oil/gas/water. Good results were obtained from the simulator match of the tracer concentration versus time to the measured values from the tracer test of the fracture zone NE-1. The simulation was less successful in modelling the draw-down of water in the wells. We were also unable to reach a balance situation for the water pressure prior to injecting the tracer in order to accommodate several weeks of leakage into the tunnel prior to the tracer test. As a main conclusion, we found the results of the simulation to be satisfactory and we believe that further work should be done to adapt the program completely for groundwater simulation. 19 refs, 10 tabs, 13 figs.

  16. Cooperative Fish and Wildlife Research Units - A model partnership program

    Science.gov (United States)

    Dennerline, Donald E.; Childs, Dawn E.

    2017-04-20

    The U.S. Geological Survey (USGS) Cooperative Fish and Wildlife Research Units (CRU) program is a unique model of cooperative partnership among the USGS, other U.S. Department of the Interior and Federal agencies, universities, State fish and wildlife agencies, and the Wildlife Management Institute. These partnerships are maintained as one of the USGS’s strongest links to Federal and State land and natural resource management agencies.Established in 1935 to meet the need for trained professionals in the growing field of wildlife management, the program currently consists of 40 Cooperative Fish and Wildlife Research Units located on university campuses in 38 States and supports 119 research scientist positions when fully funded. The threefold mission of the CRU program is to (1) conduct scientific research for the management of fish, wildlife, and other natural resources; (2) provide technical assistance to natural resource managers in the application of scientific information to natural resource policy and management; and (3) train future natural resource professionals.

  17. Replication, Communication, and the Population Dynamics of Scientific Discovery.

    Science.gov (United States)

    McElreath, Richard; Smaldino, Paul E

    2015-01-01

    Many published research results are false (Ioannidis, 2005), and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework that jointly represents hypothesis formation, replication, publication bias, and variation in research quality. We develop a mathematical model of scientific discovery that combines all of these elements. This model provides both a dynamic model of research as well as a formal framework for reasoning about the normative structure of science. We show that replication may serve as a ratchet that gradually separates true hypotheses from false, but the same factors that make initial findings unreliable also make replications unreliable. The most important factors in improving the reliability of research are the rate of false positives and the base rate of true hypotheses, and we offer suggestions for addressing each. Our results also bring clarity to verbal debates about the communication of research. Surprisingly, publication bias is not always an obstacle, but instead may have positive impacts-suppression of negative novel findings is often beneficial. We also find that communication of negative replications may aid true discovery even when attempts to replicate have diminished power. The model speaks constructively to ongoing debates about the design and conduct of science, focusing analysis and discussion on precise, internally consistent models, as well as highlighting the importance of population dynamics.

  18. Faculty development program models to advance teaching and learning within health science programs.

    Science.gov (United States)

    Lancaster, Jason W; Stein, Susan M; MacLean, Linda Garrelts; Van Amburgh, Jenny; Persky, Adam M

    2014-06-17

    Within health science programs there has been a call for more faculty development, particularly for teaching and learning. The primary objectives of this review were to describe the current landscape for faculty development programs for teaching and learning and make recommendations for the implementation of new faculty development programs. A thorough search of the pertinent health science databases was conducted, including the Education Resource Information Center (ERIC), MEDLINE, and EMBASE, and faculty development books and relevant information found were reviewed in order to provide recommendations for best practices. Faculty development for teaching and learning comes in a variety of forms, from individuals charged to initiate activities to committees and centers. Faculty development has been effective in improving faculty perceptions on the value of teaching, increasing motivation and enthusiasm for teaching, increasing knowledge and behaviors, and disseminating skills. Several models exist that can be implemented to support faculty teaching development. Institutions need to make informed decisions about which plan could be most successfully implemented in their college or school.

  19. Integer programming model for optimizing bus timetable using genetic algorithm

    Science.gov (United States)

    Wihartiko, F. D.; Buono, A.; Silalahi, B. P.

    2017-01-01

    Bus timetable gave an information for passengers to ensure the availability of bus services. Timetable optimal condition happened when bus trips frequency could adapt and suit with passenger demand. In the peak time, the number of bus trips would be larger than the off-peak time. If the number of bus trips were more frequent than the optimal condition, it would make a high operating cost for bus operator. Conversely, if the number of trip was less than optimal condition, it would make a bad quality service for passengers. In this paper, the bus timetabling problem would be solved by integer programming model with modified genetic algorithm. Modification was placed in the chromosomes design, initial population recovery technique, chromosomes reconstruction and chromosomes extermination on specific generation. The result of this model gave the optimal solution with accuracy 99.1%.

  20. ModelArchiver—A program for facilitating the creation of groundwater model archives

    Science.gov (United States)

    Winston, Richard B.

    2018-03-01

    ModelArchiver is a program designed to facilitate the creation of groundwater model archives that meet the requirements of the U.S. Geological Survey (USGS) policy (Office of Groundwater Technical Memorandum 2016.02, https://water.usgs.gov/admin/memo/GW/gw2016.02.pdf, https://water.usgs.gov/ogw/policy/gw-model/). ModelArchiver version 1.0 leads the user step-by-step through the process of creating a USGS groundwater model archive. The user specifies the contents of each of the subdirectories within the archive and provides descriptions of the archive contents. Descriptions of some files can be specified automatically using file extensions. Descriptions also can be specified individually. Those descriptions are added to a readme.txt file provided by the user. ModelArchiver moves the content of the archive to the archive folder and compresses some folders into .zip files.As part of the archive, the modeler must create a metadata file describing the archive. The program has a built-in metadata editor and provides links to websites that can aid in creation of the metadata. The built-in metadata editor is also available as a stand-alone program named FgdcMetaEditor version 1.0, which also is described in this report. ModelArchiver updates the metadata file provided by the user with descriptions of the files in the archive. An optional archive list file generated automatically by ModelMuse can streamline the creation of archives by identifying input files, output files, model programs, and ancillary files for inclusion in the archive.

  1. Template role of double-stranded RNA in tombusvirus replication.

    Science.gov (United States)

    Kovalev, Nikolay; Pogany, Judit; Nagy, Peter D

    2014-05-01

    replication. During the production of new plus strands, the viral replicase displaces the old plus strand in the dsRNA template, leading to asymmetrical RNA synthesis. The presented data are in agreement with the model that the dsRNA is present in nuclease-resistant membranous VRCs. This strategy likely allows TBSV to protect the replicating viral RNA from degradation as well as to evade the early detection of viral dsRNAs by the host surveillance system.

  2. Optimizing Crawler4j using MapReduce Programming Model

    Science.gov (United States)

    Siddesh, G. M.; Suresh, Kavya; Madhuri, K. Y.; Nijagal, Madhushree; Rakshitha, B. R.; Srinivasa, K. G.

    2017-06-01

    World wide web is a decentralized system that consists of a repository of information on the basis of web pages. These web pages act as a source of information or data in the present analytics world. Web crawlers are used for extracting useful information from web pages for different purposes. Firstly, it is used in web search engines where the web pages are indexed to form a corpus of information and allows the users to query on the web pages. Secondly, it is used for web archiving where the web pages are stored for later analysis phases. Thirdly, it can be used for web mining where the web pages are monitored for copyright purposes. The amount of information processed by the web crawler needs to be improved by using the capabilities of modern parallel processing technologies. In order to solve the problem of parallelism and the throughput of crawling this work proposes to optimize the Crawler4j using the Hadoop MapReduce programming model by parallelizing the processing of large input data. Crawler4j is a web crawler that retrieves useful information about the pages that it visits. The crawler Crawler4j coupled with data and computational parallelism of Hadoop MapReduce programming model improves the throughput and accuracy of web crawling. The experimental results demonstrate that the proposed solution achieves significant improvements with respect to performance and throughput. Hence the proposed approach intends to carve out a new methodology towards optimizing web crawling by achieving significant performance gain.

  3. Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations

    DEFF Research Database (Denmark)

    Goldar, A.; Arneodo, A.; Audit, B.

    2016-01-01

    , and by taking into account the chromatin's fractal dimension, we derive an analytical expression for the rate of replication initiation. This model predicts with no free parameter the temporal profiles of initiation rate, replication fork density and fraction of replicated DNA, in quantitative agreement...

  4. Chameleon Chasing II: A Replication.

    Science.gov (United States)

    Newsom, Doug A.; And Others

    1993-01-01

    Replicates a 1972 survey of students, educators, and Public Relations Society of America members regarding who the public relations counselor really serves. Finds that, in 1992, most respondents thought primary responsibility was to the client, then to the client's relevant publics, then to self, then to society, and finally to media. Compares…

  5. Manual of Cupule Replication Technology

    Directory of Open Access Journals (Sweden)

    Giriraj Kumar

    2015-09-01

    Full Text Available Throughout the world, iconic rock art is preceded by non-iconic rock art. Cupules (manmade, roughly semi-hemispherical depressions on rocks form the major bulk of the early non-iconic rock art globally. The antiquity of cupules extends back to the Lower Paleolithic in Asia and Africa, hundreds of thousand years ago. When one observes these cupules, the inquisitive mind poses so many questions with regard to understanding their technology, reasons for selecting the site, which rocks were used to make the hammer stones used, the skill and cognitive abilities employed to create the different types of cupules, the objective of their creation, their age, and so on. Replication of the cupules can provide satisfactory answers to some of these questions. Comparison of the hammer stones and cupules produced by the replication process with those obtained from excavation can provide support to observations. This paper presents a manual of cupule replication technology based on our experience of cupule replication on hard quartzite rock near Daraki-Chattan in the Chambal Basin, India.

  6. Localization of adenovirus morphogenesis players, together with visualization of assembly intermediates and failed products, favor a model where assembly and packaging occur concurrently at the periphery of the replication center.

    Directory of Open Access Journals (Sweden)

    Gabriela N Condezo

    2017-04-01

    Full Text Available Adenovirus (AdV morphogenesis is a complex process, many aspects of which remain unclear. In particular, it is not settled where in the nucleus assembly and packaging occur, and whether these processes occur in a sequential or a concerted manner. Here we use immunofluorescence and immunoelectron microscopy (immunoEM to trace packaging factors and structural proteins at late times post infection by either wildtype virus or a delayed packaging mutant. We show that representatives of all assembly factors are present in the previously recognized peripheral replicative zone, which therefore is the AdV assembly factory. Assembly intermediates and abortive products observed in this region favor a concurrent assembly and packaging model comprising two pathways, one for capsid proteins and another one for core components. Only when both pathways are coupled by correct interaction between packaging proteins and the genome is the viral particle produced. Decoupling generates accumulation of empty capsids and unpackaged cores.

  7. Localization of adenovirus morphogenesis players, together with visualization of assembly intermediates and failed products, favor a model where assembly and packaging occur concurrently at the periphery of the replication center.

    Science.gov (United States)

    Condezo, Gabriela N; San Martín, Carmen

    2017-04-01

    Adenovirus (AdV) morphogenesis is a complex process, many aspects of which remain unclear. In particular, it is not settled where in the nucleus assembly and packaging occur, and whether these processes occur in a sequential or a concerted manner. Here we use immunofluorescence and immunoelectron microscopy (immunoEM) to trace packaging factors and structural proteins at late times post infection by either wildtype virus or a delayed packaging mutant. We show that representatives of all assembly factors are present in the previously recognized peripheral replicative zone, which therefore is the AdV assembly factory. Assembly intermediates and abortive products observed in this region favor a concurrent assembly and packaging model comprising two pathways, one for capsid proteins and another one for core components. Only when both pathways are coupled by correct interaction between packaging proteins and the genome is the viral particle produced. Decoupling generates accumulation of empty capsids and unpackaged cores.

  8. Improving public health training and research capacity in Africa: a replicable model for linking training to health and socio-demographic surveillance data.

    Science.gov (United States)

    Williams, Jill R; Schatz, Enid J; Clark, Benjamin D; Collinson, Mark A; Clark, Samuel J; Menken, Jane; Kahn, Kathleen; Tollman, Stephen M

    2010-08-31

    Research training for public health professionals is key to the future of public health and policy in Africa. A growing number of schools of public health are connected to health and socio-demographic surveillance system field sites in developing countries, in Africa and Asia in particular. Linking training programs with these sites provides important opportunities to improve training, build local research capacity, foreground local health priorities, and increase the relevance of research to local health policy. To increase research training capacity in public health programs by providing targeted training to students and increasing the accessibility of existing data. This report is a case study of an approach to linking public health research and training at the University of the Witwatersrand. We discuss the development of a sample training database from the Agincourt Health and Socio-demographic Surveillance System in South Africa and outline a concordant transnational intensive short course on longitudinal data analysis offered by the University of the Witwatersrand and the University of Colorado-Boulder. This case study highlights ways common barriers to linking research and training can be overcome. This collaborative effort demonstrates that linking training to ongoing data collection can improve student research, accelerate student training, and connect students to an international network of scholars. Importantly, the approach can be adapted to other partnerships between schools of public health and longitudinal research sites.

  9. Improving public health training and research capacity in Africa: a replicable model for linking training to health and socio-demographic surveillance data

    Directory of Open Access Journals (Sweden)

    Jill R. Williams

    2010-08-01

    Full Text Available Background: Research training for public health professionals is key to the future of public health and policy in Africa. A growing number of schools of public health are connected to health and socio-demographic surveillance system field sites in developing countries, in Africa and Asia in particular. Linking training programs with these sites provides important opportunities to improve training, build local research capacity, foreground local health priorities, and increase the relevance of research to local health policy. Objective: To increase research training capacity in public health programs by providing targeted training to students and increasing the accessibility of existing data. Design: This report is a case study of an approach to linking public health research and training at the University of the Witwatersrand. We discuss the development of a sample training database from the Agincourt Health and Socio-demographic Surveillance System in South Africa and outline a concordant transnational intensive short course on longitudinal data analysis offered by the University of the Witwatersrand and the University of Colorado-Boulder. This case study highlights ways common barriers to linking research and training can be overcome. Results and Conclusions: This collaborative effort demonstrates that linking training to ongoing data collection can improve student research, accelerate student training, and connect students to an international network of scholars. Importantly, the approach can be adapted to other partnerships between schools of public health and longitudinal research sites.

  10. Replacement model of city bus: A dynamic programming approach

    Science.gov (United States)

    Arifin, Dadang; Yusuf, Edhi

    2017-06-01

    This paper aims to develop a replacement model of city bus vehicles operated in Bandung City. This study is driven from real cases encountered by the Damri Company in the efforts to improve services to the public. The replacement model propounds two policy alternatives: First, to maintain or keep the vehicles, and second is to replace them with new ones taking into account operating costs, revenue, salvage value, and acquisition cost of a new vehicle. A deterministic dynamic programming approach is used to solve the model. The optimization process was heuristically executed using empirical data of Perum Damri. The output of the model is to determine the replacement schedule and the best policy if the vehicle has passed the economic life. Based on the results, the technical life of the bus is approximately 20 years old, while the economic life is an average of 9 (nine) years. It means that after the bus is operated for 9 (nine) years, managers should consider the policy of rejuvenation.

  11. The role of dimerization in prion replication.

    Science.gov (United States)

    Tompa, Peter; Tusnády, Gábor E; Friedrich, Peter; Simon, István

    2002-04-01

    The central theme in prion diseases is the conformational transition of a cellular protein from a physiologic to a pathologic (so-called scrapie) state. Currently, two alternative models exist for the mechanism of this autocatalytic process; in the template assistance model the prion is assumed to be a monomer of the scrapie conformer, whereas in the nucleated polymerization model it is thought to be an amyloid rod. A recent variation on the latter assumes disulfide reshuffling as the mechanism of polymerization. The existence of stable dimers, let alone their mechanistic role, is not taken into account in either of these models. In this paper we review evidence supporting that the dimerization of either the normal or the scrapie state, or both, has a decisive role in prion replication. The contribution of redox changes, i.e., the temporary opening and possible rearrangement of the intramolecular disulfide bridge is also considered. We present a model including these features largely ignored so far and show that it adheres satisfactorily to the observed phenomenology of prion replication.

  12. Parallel phase model : a programming model for high-end parallel machines with manycores.

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Junfeng (Syracuse University, Syracuse, NY); Wen, Zhaofang; Heroux, Michael Allen; Brightwell, Ronald Brian

    2009-04-01

    This paper presents a parallel programming model, Parallel Phase Model (PPM), for next-generation high-end parallel machines based on a distributed memory architecture consisting of a networked cluster of nodes with a large number of cores on each node. PPM has a unified high-level programming abstraction that facilitates the design and implementation of parallel algorithms to exploit both the parallelism of the many cores and the parallelism at the cluster level. The programming abstraction will be suitable for expressing both fine-grained and coarse-grained parallelism. It includes a few high-level parallel programming language constructs that can be added as an extension to an existing (sequential or parallel) programming language such as C; and the implementation of PPM also includes a light-weight runtime library that runs on top of an existing network communication software layer (e.g. MPI). Design philosophy of PPM and details of the programming abstraction are also presented. Several unstructured applications that inherently require high-volume random fine-grained data accesses have been implemented in PPM with very promising results.

  13. Changing community health behaviors: a model for program development and management.

    Science.gov (United States)

    Hargreaves, M R; Laitakari, J K; Huff, F; Rautaharju, P M

    1986-01-01

    A model has been proposed to improve program development and management of behavior change programs with large-scale community impact. It can be applied to epidemiologic problems of which lifestyle is an important component, such as heart disease, adolescent pregnancy, hypertension, weight control, and cancer control and prevention programs. The model combines two previously existing models: one indicating that program development is an ongoing cyclical process which starts with uncertainty yet can progress to institutionalization with suitable testing; and the second model indicating that program management within each developmental cycle progresses through specific phases which can be hampered by plateaus and setbacks. Nine systems are essential for program development and operations: education (philosophy, objectives, and content), communications, reward, intervention, program process, program development, and program evaluation. These systems can be used as a guide to facilitate selection from the many guidelines recommended in the literature, and to ensure coordination of innovative program elements.

  14. CuATSM efficacy is independently replicated in a SOD1 mouse model of ALS while unmetallated ATSM therapy fails to reveal benefits

    Directory of Open Access Journals (Sweden)

    Fernando G. Vieira

    2017-06-01

    Full Text Available A copper chelator known as diacetylbis(N(4-methylthiosemicarbazonato copper II (CuATSM, has been reported to be efficacious in multiple transgenic SOD1 models of amyotrophic lateral sclerosis (ALS, a fatal neurodegenerative disorder affecting motor neurons. Here we report that we also observed CuATSM efficacy on disease onset and progression in a standardized litter-matched and gender-balanced efficacy study using B6SJL-SOD1G93A/1Gur mice. We also report improved survival trends with CuATSM treatment. In addition, we report a lack of efficacy by unmetallated ATSM in the same model using the same standardized study design. These results add to existing evidence supporting an efficacious role for copper delivery using chaperone molecules in mouse models of ALS.

  15. Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6.

    Science.gov (United States)

    Donley, Nathan; Stoffregen, Eric P; Smith, Leslie; Montagna, Christina; Thayer, Mathew J

    2013-04-01

    Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes.

  16. Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6.

    Directory of Open Access Journals (Sweden)

    Nathan Donley

    2013-04-01

    Full Text Available Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes.

  17. UTeach Replication: Impacting Teacher Preparation at a University Near You

    Science.gov (United States)

    Marshall, Jill

    2008-03-01

    In 2007 the National Mathematics and Science Initiative, with a grant from Exxon-Mobil, launched two major programs to improve science and mathematics education in the US: an Advanced Placement initiative and replication of the UTeach program. Twelve colleges and universities, from Florida to California, have been selected to receive grants of up to 2.4 million to start UTeach-type programs. I will report on the requirements for these grants, what it really means to have a ``UTeach-type'' program and the evidence that such programs can affect the quantity and quality of physics teachers in the US.

  18. A sample theory-based logic model to improve program development, implementation, and sustainability of Farm to School programs.

    Science.gov (United States)

    Ratcliffe, Michelle M

    2012-08-01

    Farm to School programs hold promise to address childhood obesity. These programs may increase students’ access to healthier foods, increase students’ knowledge of and desire to eat these foods, and increase their consumption of them. Implementing Farm to School programs requires the involvement of multiple people, including nutrition services, educators, and food producers. Because these groups have not traditionally worked together and each has different goals, it is important to demonstrate how Farm to School programs that are designed to decrease childhood obesity may also address others’ objectives, such as academic achievement and economic development. A logic model is an effective tool to help articulate a shared vision for how Farm to School programs may work to accomplish multiple goals. Furthermore, there is evidence that programs based on theory are more likely to be effective at changing individuals’ behaviors. Logic models based on theory may help to explain how a program works, aid in efficient and sustained implementation, and support the development of a coherent evaluation plan. This article presents a sample theory-based logic model for Farm to School programs. The presented logic model is informed by the polytheoretical model for food and garden-based education in school settings (PMFGBE). The logic model has been applied to multiple settings, including Farm to School program development and evaluation in urban and rural school districts. This article also includes a brief discussion on the development of the PMFGBE, a detailed explanation of how Farm to School programs may enhance the curricular, physical, and social learning environments of schools, and suggestions for the applicability of the logic model for practitioners, researchers, and policy makers.

  19. On the Growth Rate of Non-Enzymatic Molecular Replicators

    Directory of Open Access Journals (Sweden)

    Harold Fellermann

    2011-10-01

    Full Text Available It is well known that non-enzymatic template directed molecular replicators X + nO -> 2X exhibit parabolic growth d[X]/dt -> k[X]1/2. Here, we analyze the dependence of the effective replication rate constant k on hybridization energies, temperature, strand length, and sequence composition. First we derive analytical criteria for the replication rate k based on simple thermodynamic arguments. Second we present a Brownian dynamics model for oligonucleotides that allows us to simulate their diffusion and hybridization behavior. The simulation is used to generate and analyze the effect of strand length, temperature, and to some extent sequence composition, on the hybridization rates and the resulting optimal overall rate constant k. Combining the two approaches allows us to semi-analytically depict a replication rate landscape for template directed replicators. The results indicate a clear replication advantage for longer strands at lower temperatures in the regime where the ligation rate is rate limiting. Further the results indicate the existence of an optimal replication rate at the boundary between the two regimes where the ligation rate and the dehybridization rates are rate limiting.

  20. Tools for Economic Analysis of Patient Management Interventions in Heart Failure Cost-Effectiveness Model: A Web-based program designed to evaluate the cost-effectiveness of disease management programs in heart failure.

    Science.gov (United States)

    Reed, Shelby D; Neilson, Matthew P; Gardner, Matthew; Li, Yanhong; Briggs, Andrew H; Polsky, Daniel E; Graham, Felicia L; Bowers, Margaret T; Paul, Sara C; Granger, Bradi B; Schulman, Kevin A; Whellan, David J; Riegel, Barbara; Levy, Wayne C

    2015-11-01

    Heart failure disease management programs can influence medical resource use and quality-adjusted survival. Because projecting long-term costs and survival is challenging, a consistent and valid approach to extrapolating short-term outcomes would be valuable. We developed the Tools for Economic Analysis of Patient Management Interventions in Heart Failure Cost-Effectiveness Model, a Web-based simulation tool designed to integrate data on demographic, clinical, and laboratory characteristics; use of evidence-based medications; and costs to generate predicted outcomes. Survival projections are based on a modified Seattle Heart Failure Model. Projections of resource use and quality of life are modeled using relationships with time-varying Seattle Heart Failure Model scores. The model can be used to evaluate parallel-group and single-cohort study designs and hypothetical programs. Simulations consist of 10,000 pairs of virtual cohorts used to generate estimates of resource use, costs, survival, and incremental cost-effectiveness ratios from user inputs. The model demonstrated acceptable internal and external validity in replicating resource use, costs, and survival estimates from 3 clinical trials. Simulations to evaluate the cost-effectiveness of heart failure disease management programs across 3 scenarios demonstrate how the model can be used to design a program in which short-term improvements in functioning and use of evidence-based treatments are sufficient to demonstrate good long-term value to the health care system. The Tools for Economic Analysis of Patient Management Interventions in Heart Failure Cost-Effectiveness Model provides researchers and providers with a tool for conducting long-term cost-effectiveness analyses of disease management programs in heart failure. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Optimizing Biorefinery Design and Operations via Linear Programming Models

    Energy Technology Data Exchange (ETDEWEB)

    Talmadge, Michael; Batan, Liaw; Lamers, Patrick; Hartley, Damon; Biddy, Mary; Tao, Ling; Tan, Eric

    2017-03-28

    The ability to assess and optimize economics of biomass resource utilization for the production of fuels, chemicals and power is essential for the ultimate success of a bioenergy industry. The team of authors, consisting of members from the National Renewable Energy Laboratory (NREL) and the Idaho National Laboratory (INL), has developed simple biorefinery linear programming (LP) models to enable the optimization of theoretical or existing biorefineries. The goal of this analysis is to demonstrate how such models can benefit the developing biorefining industry. It focuses on a theoretical multi-pathway, thermochemical biorefinery configuration and demonstrates how the biorefinery can use LP models for operations planning and optimization in comparable ways to the petroleum refining industry. Using LP modeling tools developed under U.S. Department of Energy's Bioenergy Technologies Office (DOE-BETO) funded efforts, the authors investigate optimization challenges for the theoretical biorefineries such as (1) optimal feedstock slate based on available biomass and prices, (2) breakeven price analysis for available feedstocks, (3) impact analysis for changes in feedstock costs and product prices, (4) optimal biorefinery operations during unit shutdowns / turnarounds, and (5) incentives for increased processing capacity. These biorefinery examples are comparable to crude oil purchasing and operational optimization studies that petroleum refiners perform routinely using LPs and other optimization models. It is important to note that the analyses presented in this article are strictly theoretical and they are not based on current energy market prices. The pricing structure assigned for this demonstrative analysis is consistent with $4 per gallon gasoline, which clearly assumes an economic environment that would favor the construction and operation of biorefineries. The analysis approach and examples provide valuable insights into the usefulness of analysis tools for

  2. A Model Intervention Program for Secondary School Education

    Directory of Open Access Journals (Sweden)

    Brian Gerber

    2012-01-01

    Full Text Available Valdosta State University and the Valdosta City Schools (Valdosta, GA partnered in 2008 to form the Valdosta Early College Academy (VECA. VECA epitomizes the early college concept of (a admitting underperforming students with multiple risk factors for dropping out of school (e.g., low socioeconomic status, minority, and first-generation high school or college and (b providing college level dual enrollment courses. VECA is very different than nearly every other early college school in the nation. Most (85% of the 200 early colleges currently operating in the United States begin with students in the 9th grade. Nearly all of the remaining early colleges begin with 7th grade; only a few are 6–12-grade schools. VECA targets two primary priorities, (a innovations that complement the implementation of higher standards and high-quality assessments and (b innovations that support college access and success. The primary purpose of this paper is to chronicle the genesis and development of VECA. This program is very successful, replete with research opportunities, and represents a model early college program. We plan to continue to grow VECA to ultimately include grades six through twelve and to research that growth and development.

  3. Minnesota 4-H Youth Program Quality Improvement Model

    Science.gov (United States)

    Herman, Margo; Grant, Samantha

    2015-01-01

    The University of Minnesota Extension Center for Youth Development made an organizational decision in 2011 to invest in a system-wide approach to implement youth program quality into the 4-H program using the Youth Program Quality Assessment (YPQA) tool. This article describes the four key components to the Minnesota Youth Program Quality…

  4. A Tool for Performance Modeling of Parallel Programs

    Directory of Open Access Journals (Sweden)

    J.A. González

    2003-01-01

    Full Text Available Current performance prediction analytical models try to characterize the performance behavior of actual machines through a small set of parameters. In practice, substantial deviations are observed. These differences are due to factors as memory hierarchies or network latency. A natural approach is to associate a different proportionality constant with each basic block, and analogously, to associate different latencies and bandwidths with each "communication block". Unfortunately, to use this approach implies that the evaluation of parameters must be done for each algorithm. This is a heavy task, implying experiment design, timing, statistics, pattern recognition and multi-parameter fitting algorithms. Software support is required. We present a compiler that takes as source a C program annotated with complexity formulas and produces as output an instrumented code. The trace files obtained from the execution of the resulting code are analyzed with an interactive interpreter, giving us, among other information, the values of those parameters.

  5. A Model Program for Translational Medicine in Epilepsy Genetics

    Science.gov (United States)

    Smith, Lacey A.; Ullmann, Jeremy F. P.; Olson, Heather E.; El Achkar, Christelle M.; Truglio, Gessica; Kelly, McKenna; Rosen-Sheidley, Beth; Poduri, Annapurna

    2017-01-01

    Recent technological advances in gene sequencing have led to a rapid increase in gene discovery in epilepsy. However, the ability to assess pathogenicity of variants, provide functional analysis, and develop targeted therapies has not kept pace with rapid advances in sequencing technology. Thus, although clinical genetic testing may lead to a specific molecular diagnosis for some patients, test results often lead to more questions than answers. As the field begins to focus on therapeutic applications of genetic diagnoses using precision medicine, developing processes that offer more than equivocal test results is essential. The success of precision medicine in epilepsy relies on establishing a correct genetic diagnosis, analyzing functional consequences of genetic variants, screening potential therapeutics in the preclinical laboratory setting, and initiating targeted therapy trials for patients. We describe the structure of a comprehensive, pediatric Epilepsy Genetics Program that can serve as a model for translational medicine in epilepsy. PMID:28056630

  6. A Model Program for Translational Medicine in Epilepsy Genetics.

    Science.gov (United States)

    Smith, Lacey A; Ullmann, Jeremy F P; Olson, Heather E; Achkar, Christelle M El; Truglio, Gessica; Kelly, McKenna; Rosen-Sheidley, Beth; Poduri, Annapurna

    2017-03-01

    Recent technological advances in gene sequencing have led to a rapid increase in gene discovery in epilepsy. However, the ability to assess pathogenicity of variants, provide functional analysis, and develop targeted therapies has not kept pace with rapid advances in sequencing technology. Thus, although clinical genetic testing may lead to a specific molecular diagnosis for some patients, test results often lead to more questions than answers. As the field begins to focus on therapeutic applications of genetic diagnoses using precision medicine, developing processes that offer more than equivocal test results is essential. The success of precision medicine in epilepsy relies on establishing a correct genetic diagnosis, analyzing functional consequences of genetic variants, screening potential therapeutics in the preclinical laboratory setting, and initiating targeted therapy trials for patients. The authors describe the structure of a comprehensive, pediatric Epilepsy Genetics Program that can serve as a model for translational medicine in epilepsy.

  7. DNA replication, development and cancer: a homeotic connection?

    Science.gov (United States)

    Falaschi, Arturo; Abdurashidova, Gulnara; Biamonti, Giuseppe

    2010-02-01

    The homeotic proteins are transcription factors, highly conserved in metazoan organisms, exerting a pivotal role in development and differentiation. They individually display a loose specificity for the DNA sequence they can bind, but operate mainly in multi-molecular associations that assure their target and function specificity. Homeotic proteins are known to play a role in the positive or negative regulation of cell proliferation. Furthermore, many homeotic proteins are actually proto-oncogenes, since different translocations involving their genes cause tumors, particularly in the hematopoietic system. A one-hybrid screen to detect proteins with affinity for the lamin B2 replication origin identified three homeotic proteins, namely HoxA13, HoxC10 and HoxC13. Recent data demonstrate that the HoxC13 oncoprotein specifically associates with replication foci and binds in vitro and in vivo to several human DNA replication origins. Moreover, Hox proteins interact with geminin, a regulator of cell cycle progression, and control the interaction of this protein with the DNA replication licensing factor Ctd1. Thus, the homeotic proteins, by participating directly in the function of DNA replication origins, may provide a direct link between the accurate regulation of DNA replication required by the morphogenetic program and the deregulation of this process typical of cancer.

  8. Lattice gas simulations of replicating domains

    International Nuclear Information System (INIS)

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-01-01

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting

  9. Lattice gas simulations of replicating domains

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-12-31

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting.

  10. Replication Clamps and Clamp Loaders

    Science.gov (United States)

    Hedglin, Mark; Kumar, Ravindra; Benkovic, Stephen J.

    2013-01-01

    To achieve the high degree of processivity required for DNA replication, DNA polymerases associate with ring-shaped sliding clamps that encircle the template DNA and slide freely along it. The closed circular structure of sliding clamps necessitates an enzyme-catalyzed mechanism, which not only opens them for assembly and closes them around DNA, but specifically targets them to sites where DNA synthesis is initiated and orients them correctly for replication. Such a feat is performed by multisubunit complexes known as clamp loaders, which use ATP to open sliding clamp rings and place them around the 3′ end of primer–template (PT) junctions. Here we discuss the structure and composition of sliding clamps and clamp loaders from the three domains of life as well as T4 bacteriophage, and provide our current understanding of the clamp-loading process. PMID:23545418

  11. Remote programming of cochlear implants: a telecommunications model.

    Science.gov (United States)

    McElveen, John T; Blackburn, Erin L; Green, J Douglas; McLear, Patrick W; Thimsen, Donald J; Wilson, Blake S

    2010-09-01

    Evaluate the effectiveness of remote programming for cochlear implants. Retrospective review of the cochlear implant performance for patients who had undergone mapping and programming of their cochlear implant via remote connection through the Internet. Postoperative Hearing in Noise Test and Consonant/Nucleus/Consonant word scores for 7 patients who had undergone remote mapping and programming of their cochlear implant were compared with the mean scores of 7 patients who had been programmed by the same audiologist over a 12-month period. Times required for remote and direct programming were also compared. The quality of the Internet connection was assessed using standardized measures. Remote programming was performed via a virtual private network with a separate software program used for video and audio linkage. All 7 patients were programmed successfully via remote connectivity. No untoward patient experiences were encountered. No statistically significant differences could be found in comparing postoperative Hearing in Noise Test and Consonant/Nucleus/Consonant word scores for patients who had undergone remote programming versus a similar group of patients who had their cochlear implant programmed directly. Remote programming did not require a significantly longer programming time for the audiologist with these 7 patients. Remote programming of a cochlear implant can be performed safely without any deterioration in the quality of the programming. This ability to remotely program cochlear implant patients gives the potential to extend cochlear implantation to underserved areas in the United States and elsewhere.

  12. Simulation model for wind energy storage systems. Volume III. Program descriptions. [SIMWEST CODE

    Energy Technology Data Exchange (ETDEWEB)

    Warren, A.W.; Edsinger, R.W.; Burroughs, J.D.

    1977-08-01

    The effort developed a comprehensive computer program for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel and pneumatic). An acronym for the program is SIMWEST (Simulation Model for Wind Energy Storage). The level of detail of SIMWEST is consistent with a role of evaluating the economic feasibility as well as the general performance of wind energy systems. The software package consists of two basic programs and a library of system, environmental, and load components. Volume III, the SIMWEST program description contains program descriptions, flow charts and program listings for the SIMWEST Model Generation Program, the Simulation program, the File Maintenance program and the Printer Plotter program. Volume III generally would not be required by SIMWEST user.

  13. Challenge pools of hepatitis C virus genotypes 1-6 prototype strains: replication fitness and pathogenicity in chimpanzees and human liver-chimeric mouse models

    DEFF Research Database (Denmark)

    Bukh, Jens; Meuleman, Philip; Tellier, Raymond

    2010-01-01

    Chimpanzees represent the only animal model for studies of the natural history of hepatitis C virus (HCV). To generate virus stocks of important HCV variants, we infected chimpanzees with HCV strains of genotypes 1-6 and determined the infectivity titer of acute-phase plasma pools in additional...... animals. The courses of first- and second-passage infections were similar, with early appearance of viremia, HCV RNA titers of >10(4.7) IU/mL, and development of acute hepatitis; the chronicity rate was 56%. The challenge pools had titers of 10(3)-10(5) chimpanzee infectious doses/mL. Human liver...

  14. A Program Evaluation Model: Using Bloom's Taxonomy to Identify Outcome Indicators in Outcomes-Based Program Evaluations

    Science.gov (United States)

    McNeil, Rita C.

    2011-01-01

    Outcomes-based program evaluation is a systematic approach to identifying outcome indicators and measuring results against those indicators. One dimension of program evaluation is assessing the level of learner acquisition to determine if learning objectives were achieved as intended. The purpose of the proposed model is to use Bloom's Taxonomy to…

  15. Replicating Data for Better Performances in X10

    DEFF Research Database (Denmark)

    Andrić, Marina; De Nicola, Rocco; Lluch Lafuente, Alberto

    2015-01-01

    used to experiment with X10, a parallel programming language primarily targeting clusters of multi-core processors linked in a large-scale system via high-performance networks. Our approach aims at allowing the programmer to specify and coordinate the replication of shared data items by taking...

  16. Linear programming model can explain respiration of fermentation products.

    Directory of Open Access Journals (Sweden)

    Philip Möller

    Full Text Available Many differentiated cells rely primarily on mitochondrial oxidative phosphorylation for generating energy in the form of ATP needed for cellular metabolism. In contrast most tumor cells instead rely on aerobic glycolysis leading to lactate to about the same extent as on respiration. Warburg found that cancer cells to support oxidative phosphorylation, tend to ferment glucose or other energy source into lactate even in the presence of sufficient oxygen, which is an inefficient way to generate ATP. This effect also occurs in striated muscle cells, activated lymphocytes and microglia, endothelial cells and several mammalian cell types, a phenomenon termed the "Warburg effect". The effect is paradoxical at first glance because the ATP production rate of aerobic glycolysis is much slower than that of respiration and the energy demands are better to be met by pure oxidative phosphorylation. We tackle this question by building a minimal model including three combined reactions. The new aspect in extension to earlier models is that we take into account the possible uptake and oxidation of the fermentation products. We examine the case where the cell can allocate protein on several enzymes in a varying distribution and model this by a linear programming problem in which the objective is to maximize the ATP production rate under different combinations of constraints on enzymes. Depending on the cost of reactions and limitation of the substrates, this leads to pure respiration, pure fermentation, and a mixture of respiration and fermentation. The model predicts that fermentation products are only oxidized when glucose is scarce or its uptake is severely limited.

  17. A replication of the Uruguayan model in the province of Buenos Aires, Argentina, as a public policy for reducing abortion-related maternal mortality.

    Science.gov (United States)

    Matía, Marisa G; Trumper, Eugenia C; Fures, Nery Orlando; Orchuela, Jimena

    2016-08-01

    To describe the application of the risk and harm reduction model at primary care level to decrease the mortality due to unsafe abortion in the Province of Buenos Aires, Argentina, and evaluate the results. The services offered at primary health units to women undergoing abortion are described-first, only risk reduction and later, legal termination of the pregnancy-including their evolution between 2010 and 2015. The changes in abortion-related maternal mortality are also evaluated. The χ(2) test was used to evaluate the differences in the percentage of abortion-related deaths out of the total number of maternal deaths. Primary care services increased progressively, both for risk reduction and for legal termination of pregnancy, which was carried out successfully, including manual vacuum aspiration, by general physicians and midwives. The proportion of abortion-related maternal deaths with respect to total maternal deaths fell by two-thirds between 2010 and 2014 (P<0.001). The Uruguayan risk reduction model was successfully applied in primary care in the Province of Buenos Aires. Copyright © 2016 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

  18. The New York State Bird Conservation Area (BCA) Program: A Model for the United States

    Science.gov (United States)

    M. F. Burger; D. J. Adams; T. Post; L. Sommers; B. Swift

    2005-01-01

    The New York State Bird Conservation Area (BCA) Program, modeled after the National Audubon Society?s Important Bird Areas Program, is based on legislation signed by Governor Pataki in 1997. New York is the first state in the nation to enact such a program. The BCA Program seeks to provide a comprehensive, ecosystem approach to conserving birds and their habitats on...

  19. Exploiting replicative stress to treat cancer

    DEFF Research Database (Denmark)

    Dobbelstein, Matthias; Sørensen, Claus Storgaard

    2015-01-01

    DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms...... that govern replicative stress, thus providing ample opportunities to enhance replicative stress for therapeutic purposes. Rather than trying to halt cell cycle progression, cancer therapeutics could aim to increase replicative stress by further loosening the checkpoints that remain available to cancer cells...

  20. Field replication of classwide peer tutoring.

    Science.gov (United States)

    Greenwood, C R; Dinwiddie, G; Bailey, V; Carta, J J; Dorsey, D; Kohler, F W; Nelson, C; Rotholz, D; Schulte, D

    1987-01-01

    We conducted a large-scale field replication study of classwide peer tutoring applied to spelling instruction (Greenwood, Delquadri, & Hall, 1984). Two hundred and eleven inner-city students in four schools participated during their first- and second-grade school years. The effects of classwide peer tutoring were compared to teacher instructional procedures and pretest probes using a group replication design (Barlow, Hayes, & Nelson, 1984). Analysis of group and individual results indicated that (a) both teacher instructional procedures and classwide peer tutoring were effective in increasing spelling performance above pretest levels, (b) peer tutoring produced statistically greater gains relative to the teachers' procedures for both low and high student groups formed on pretest levels, (c) these outcomes were representative of groups, classes, individuals, and years during the project, and (d) participant satisfaction with the program was generally high. A separate analysis of the social importance of treatment outcome revealed differential findings for low and high groups related to pretest levels. Implications of these findings are discussed.

  1. Field replication of classwide peer tutoring.

    Science.gov (United States)

    Greenwood, C R; Dinwiddie, G; Bailey, V; Carta, J J; Dorsey, D; Kohler, F W; Nelson, C; Rotholz, D; Schulte, D

    1987-01-01

    We conducted a large-scale field replication study of classwide peer tutoring applied to spelling instruction (Greenwood, Delquadri, & Hall, 1984). Two hundred and eleven inner-city students in four schools participated during their first- and second-grade school years. The effects of classwide peer tutoring were compared to teacher instructional procedures and pretest probes using a group replication design (Barlow, Hayes, & Nelson, 1984). Analysis of group and individual results indicated that (a) both teacher instructional procedures and classwide peer tutoring were effective in increasing spelling performance above pretest levels, (b) peer tutoring produced statistically greater gains relative to the teachers' procedures for both low and high student groups formed on pretest levels, (c) these outcomes were representative of groups, classes, individuals, and years during the project, and (d) participant satisfaction with the program was generally high. A separate analysis of the social importance of treatment outcome revealed differential findings for low and high groups related to pretest levels. Implications of these findings are discussed. PMID:3610894

  2. Fish Processed Production Planning Using Integer Stochastic Programming Model

    Science.gov (United States)

    Firmansyah, Mawengkang, Herman

    2011-06-01

    Fish and its processed products are the most affordable source of animal protein in the diet of most people in Indonesia. The goal in production planning is to meet customer demand over a fixed time horizon divided into planning periods by optimizing the trade-off between economic objectives such as production cost and customer satisfaction level. The major decisions are production and inventory levels for each product and the number of workforce in each planning period. In this paper we consider the management of small scale traditional business at North Sumatera Province which performs processing fish into several local seafood products. The inherent uncertainty of data (e.g. demand, fish availability), together with the sequential evolution of data over time leads the production planning problem to a nonlinear mixed-integer stochastic programming model. We use scenario generation based approach and feasible neighborhood search for solving the model. The results which show the amount of each fish processed product and the number of workforce needed in each horizon planning are presented.

  3. Marketing for a Web-Based Master's Degree Program in Light of Marketing Mix Model

    Science.gov (United States)

    Pan, Cheng-Chang

    2012-01-01

    The marketing mix model was applied with a focus on Web media to re-strategize a Web-based Master's program in a southern state university in U.S. The program's existing marketing strategy was examined using the four components of the model: product, price, place, and promotion, in hopes to repackage the program (product) to prospective students…

  4. The Component Model of Infrastructure: A Practical Approach to Understanding Public Health Program Infrastructure

    Science.gov (United States)

    Snyder, Kimberly; Rieker, Patricia P.

    2014-01-01

    Functioning program infrastructure is necessary for achieving public health outcomes. It is what supports program capacity, implementation, and sustainability. The public health program infrastructure model presented in this article is grounded in data from a broader evaluation of 18 state tobacco control programs and previous work. The newly developed Component Model of Infrastructure (CMI) addresses the limitations of a previous model and contains 5 core components (multilevel leadership, managed resources, engaged data, responsive plans and planning, networked partnerships) and 3 supporting components (strategic understanding, operations, contextual influences). The CMI is a practical, implementation-focused model applicable across public health programs, enabling linkages to capacity, sustainability, and outcome measurement. PMID:24922125

  5. Specification of an Exception Handling System for a Replicated Agent Environment

    OpenAIRE

    Dony, Christophe; Tibermacine, Chouki; Urtado, Christelle; Vauttier, Sylvain

    2008-01-01

    International audience; Exception handling and replication are two mechanisms that increase the reliability of applications. Exception handling helps programmers to control situations in which the normal flow of a program execution cannot continue. Replication handles system failures. Exceptions handling and replication do not apply to the same situations and are two complementary mechanisms to increase the reliability of applications. Moreover, each technique can benefit from the other: exce...

  6. Visual Environment for Rich Data Interpretation (VERDI) program for environmental modeling systems

    Science.gov (United States)

    VERDI is a flexible, modular, Java-based program used for visualizing multivariate gridded meteorology, emissions and air quality modeling data created by environmental modeling systems such as the CMAQ model and WRF.

  7. An abort-aware model of transactional programming

    OpenAIRE

    Etessami, Kousha; Godefroid, Patrice

    2011-01-01

    There has been a lot of recent research on transaction-based concurrent programming, aimed at offering an easier concurrent programming paradigm that enables programmers to better exploit the parallelism of modern multi-processor machines, such as multi-core microprocessors. We introduce Transactional State Machines (TSMs) as an abstract finite-datamodel of transactional shared-memory concurrent programs. TSMs are a variant of concurrent boolean programs (or concurrent extended recursive stat...

  8. The Father Friendly Initiative within Families: Using a logic model to develop program theory for a father support program.

    Science.gov (United States)

    Gervais, Christine; de Montigny, Francine; Lacharité, Carl; Dubeau, Diane

    2015-10-01

    The transition to fatherhood, with its numerous challenges, has been well documented. Likewise, fathers' relationships with health and social services have also begun to be explored. Yet despite the problems fathers experience in interactions with healthcare services, few programs have been developed for them. To explain this, some authors point to the difficulty practitioners encounter in developing and structuring the theory of programs they are trying to create to promote and support father involvement (Savaya, R., & Waysman, M. (2005). Administration in Social Work, 29(2), 85), even when such theory is key to a program's effectiveness (Chen, H.-T. (2005). Practical program evaluation. Thousand Oaks, CA: Sage Publications). The objective of the present paper is to present a tool, the logic model, to bridge this gap and to equip practitioners for structuring program theory. This paper addresses two questions: (1) What would be a useful instrument for structuring the development of program theory in interventions for fathers? (2) How would the concepts of a father involvement program best be organized? The case of the Father Friendly Initiative within Families (FFIF) program is used to present and illustrate six simple steps for developing a logic model that are based on program theory and demonstrate its relevance. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  9. Development of a Program Logic Model and Evaluation Plan for a Participatory Ergonomics Intervention in Construction

    Science.gov (United States)

    Jaegers, Lisa; Dale, Ann Marie; Weaver, Nancy; Buchholz, Bryan; Welch, Laura; Evanoff, Bradley

    2013-01-01

    Background Intervention studies in participatory ergonomics (PE) are often difficult to interpret due to limited descriptions of program planning and evaluation. Methods In an ongoing PE program with floor layers, we developed a logic model to describe our program plan, and process and summative evaluations designed to describe the efficacy of the program. Results The logic model was a useful tool for describing the program elements and subsequent modifications. The process evaluation measured how well the program was delivered as intended, and revealed the need for program modifications. The summative evaluation provided early measures of the efficacy of the program as delivered. Conclusions Inadequate information on program delivery may lead to erroneous conclusions about intervention efficacy due to Type III error. A logic model guided the delivery and evaluation of our intervention and provides useful information to aid interpretation of results. PMID:24006097

  10. A Model for Evaluating Mental Health Programs: The Functional Baseline System.

    Science.gov (United States)

    Krowinski, William J.; Fitt, David X.

    1978-01-01

    This paper presents an evaluation model for a partial hospitalization program. The evaluation instrument, the Functional Baseline System (FBS), is presented with its use in assessing program effectiveness and efficiency. (Author)

  11. Reliable self-replicating machines in asynchronous cellular automata.

    Science.gov (United States)

    Lee, Jia; Adachi, Susumu; Peper, Ferdinand

    2007-01-01

    We propose a self-replicating machine that is embedded in a two-dimensional asynchronous cellular automaton with von Neumann neighborhood. The machine dynamically encodes its shape into description signals, and despite the randomness of cell updating, it is able to successfully construct copies of itself according to the description signals. Self-replication on asynchronously updated cellular automata may find application in nanocomputers, where reconfigurability is an essential property, since it allows avoidance of defective parts and simplifies programming of such computers.

  12. Education Model Program on Water-Energy Research: A New STEM Graduate Program from Development through Evaluation

    Science.gov (United States)

    McCay, D.; Fiorenza, P.; Lautz, L.

    2017-12-01

    More than half of Ph.D. scientists and engineers find employment in non-academic sectors. Recognizing the range of career options for graduate degree holders and the need to align graduate education with the expectations of prospective employers, the National Science Foundation (NSF) created the NSF Research Traineeship (NRT) program. To date, over 100 NRT programs have been funded. As these programs are implemented, it is important to assess their progress, successes, and challenges. This presentation describes the ongoing evaluation of one NRT program, "Education Model Program on Water-Energy Research" (or EMPOWER) at Syracuse University. Through seminars, mini-grants, professional development activities, field courses, internship opportunities, and coursework, EMPOWER's goal is to equip students with the skills needed for the range of career options in water and energy. In collaboration with an external evaluator, EMPOWER is examining the fidelity of the program to proposed goals, providing feedback to inform project improvement (formative assessment) and assessing the effectiveness of achieving program goals (summative assessment). Using a convergent parallel mixed method design, qualitative and quantitative data were collected to develop a full assessment of the first year of the program. Evaluation findings have resulted in several positive changes to the program. For example, EMPOWER students perceive themselves to have high technical skills, but the data show that the students do not believe that they have a strong professional network. Based on those findings, EMPOWER offered several professional development events focused on building one's professional network. Preliminary findings have enabled the EMPOWER leadership team to make informed decisions about the ways the program elements can be redesigned to better meet student needs, about how to the make the program more effective, and determine the program elements that may be sustained beyond the funding

  13. Replication of micro and nano surface geometries

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Hocken, R.J.; Tosello, Guido

    2011-01-01

    The paper describes the state-of-the-art in replication of surface texture and topography at micro and nano scale. The description includes replication of surfaces in polymers, metals and glass. Three different main technological areas enabled by surface replication processes are presented......: manufacture of net-shape micro/nano surfaces, tooling (i.e. master making), and surface quality control (metrology, inspection). Replication processes and methods as well as the metrology of surfaces to determine the degree of replication are presented and classified. Examples from various application areas...... are given including replication for surface texture measurements, surface roughness standards, manufacture of micro and nano structured functional surfaces, replicated surfaces for optical applications (e.g. optical gratings), and process chains based on combinations of repeated surface replication steps....

  14. Evaluating replicability of laboratory experiments in economics.

    Science.gov (United States)

    Camerer, Colin F; Dreber, Anna; Forsell, Eskil; Ho, Teck-Hua; Huber, Jürgen; Johannesson, Magnus; Kirchler, Michael; Almenberg, Johan; Altmejd, Adam; Chan, Taizan; Heikensten, Emma; Holzmeister, Felix; Imai, Taisuke; Isaksson, Siri; Nave, Gideon; Pfeiffer, Thomas; Razen, Michael; Wu, Hang

    2016-03-25

    The replicability of some scientific findings has recently been called into question. To contribute data about replicability in economics, we replicated 18 studies published in the American Economic Review and the Quarterly Journal of Economics between 2011 and 2014. All of these replications followed predefined analysis plans that were made publicly available beforehand, and they all have a statistical power of at least 90% to detect the original effect size at the 5% significance level. We found a significant effect in the same direction as in the original study for 11 replications (61%); on average, the replicated effect size is 66% of the original. The replicability rate varies between 67% and 78% for four additional replicability indicators, including a prediction market measure of peer beliefs. Copyright © 2016, American Association for the Advancement of Science.

  15. From Safety Critical Java Programs to Timed Process Models

    DEFF Research Database (Denmark)

    Thomsen, Bent; Luckow, Kasper Søe; Thomsen, Lone Leth

    2015-01-01

    The idea of analysing real programs by process algebraic methods probably goes back to the Occam language using the CSP process algebra [43]. In [16,24] Degano et al. followed in that tradition by analysing Mobile Agent Programs written in the Higher Order Functional, Concurrent and Distributed......, programming language Facile [47], by equipping Facile with a process algebraic semantics based on true concurrency. This semantics facilitated analysis of programs revealing subtle bugs that would otherwise be very hard to find. Inspired by the idea of translating real programs into process algebraic...

  16. Reliability in the Power System Modeled in a Multi- Stage Stochastic Mixed Integer Programming Model

    DEFF Research Database (Denmark)

    Simonsen Nielsen, Michael Pascal

    Contributions from this article are that it takes the characteristics of the power system into account at different stages, which gives a more realistic presentation of the welfare aspects to be gained by an optimal operation/ dispatch of the power system. This article is utilizing a Multi......-Stage Stochastic Mixed Integer Programming Model that handles uncertainty in a flexible and practical way. The method applied relies on state-of-the-art modeling within this field, but the method applied in this article is extended by using decomposition....

  17. EvoBuild: A Quickstart Toolkit for Programming Agent-Based Models of Evolutionary Processes

    Science.gov (United States)

    Wagh, Aditi; Wilensky, Uri

    2017-10-01

    Extensive research has shown that one of the benefits of programming to learn about scientific phenomena is that it facilitates learning about mechanisms underlying the phenomenon. However, using programming activities in classrooms is associated with costs such as requiring additional time to learn to program or students needing prior experience with programming. This paper presents a class of programming environments that we call quickstart: Environments with a negligible threshold for entry into programming and a modest ceiling. We posit that such environments can provide benefits of programming for learning without incurring associated costs for novice programmers. To make this claim, we present a design-based research study conducted to compare programming models of evolutionary processes with a quickstart toolkit with exploring pre-built models of the same processes. The study was conducted in six seventh grade science classes in two schools. Students in the programming condition used EvoBuild, a quickstart toolkit for programming agent-based models of evolutionary processes, to build their NetLogo models. Students in the exploration condition used pre-built NetLogo models. We demonstrate that although students came from a range of academic backgrounds without prior programming experience, and all students spent the same number of class periods on the activities including the time students took to learn programming in this environment, EvoBuild students showed greater learning about evolutionary mechanisms. We discuss the implications of this work for design research on programming environments in K-12 science education.

  18. EvoBuild: A Quickstart Toolkit for Programming Agent-Based Models of Evolutionary Processes

    Science.gov (United States)

    Wagh, Aditi; Wilensky, Uri

    2018-04-01

    Extensive research has shown that one of the benefits of programming to learn about scientific phenomena is that it facilitates learning about mechanisms underlying the phenomenon. However, using programming activities in classrooms is associated with costs such as requiring additional time to learn to program or students needing prior experience with programming. This paper presents a class of programming environments that we call quickstart: Environments with a negligible threshold for entry into programming and a modest ceiling. We posit that such environments can provide benefits of programming for learning without incurring associated costs for novice programmers. To make this claim, we present a design-based research study conducted to compare programming models of evolutionary processes with a quickstart toolkit with exploring pre-built models of the same processes. The study was conducted in six seventh grade science classes in two schools. Students in the programming condition used EvoBuild, a quickstart toolkit for programming agent-based models of evolutionary processes, to build their NetLogo models. Students in the exploration condition used pre-built NetLogo models. We demonstrate that although students came from a range of academic backgrounds without prior programming experience, and all students spent the same number of class periods on the activities including the time students took to learn programming in this environment, EvoBuild students showed greater learning about evolutionary mechanisms. We discuss the implications of this work for design research on programming environments in K-12 science education.

  19. Variance Swap Replication: Discrete or Continuous?

    Directory of Open Access Journals (Sweden)

    Fabien Le Floc’h

    2018-02-01

    Full Text Available The popular replication formula to price variance swaps assumes continuity of traded option strikes. In practice, however, there is only a discrete set of option strikes traded on the market. We present here different discrete replication strategies and explain why the continuous replication price is more relevant.

  20. Risk assessment to an integrated planning model for UST programs

    International Nuclear Information System (INIS)

    Ferguson, K.W.

    1993-01-01

    The US Postal Service maintains the largest civilian fleet in the United States totaling approximately 180,000 vehicles. To support the fleets daily energy requirements, the Postal Service also operates one of the largest networks of underground storage tanks nearly 7,500 nationwide. A program to apply risk assessment to planning, budget development and other management actions was implemented during September, 1989. Working closely with a consultant, the postal service developed regulatory and environmental risk criteria and weighting factors for a ranking model. The primary objective was to identify relative risks for each underground tank at individual facilities. Relative risks at each facility were determined central to prioritizing scheduled improvements to the tank network. The survey was conducted on 302 underground tanks in the Northeast Region of the US. An environmental and regulatory risk score was computed for each UST. By ranking the tanks according to their risk score, tanks were classified into management action categories including, but the limited to, underground tank testing, retrofit, repair, replacement and closure

  1. A program for verification of phylogenetic network models.

    Science.gov (United States)

    Gunawan, Andreas D M; Lu, Bingxin; Zhang, Louxin

    2016-09-01

    Genetic material is transferred in a non-reproductive manner across species more frequently than commonly thought, particularly in the bacteria kingdom. On one hand, extant genomes are thus more properly considered as a fusion product of both reproductive and non-reproductive genetic transfers. This has motivated researchers to adopt phylogenetic networks to study genome evolution. On the other hand, a gene's evolution is usually tree-like and has been studied for over half a century. Accordingly, the relationships between phylogenetic trees and networks are the basis for the reconstruction and verification of phylogenetic networks. One important problem in verifying a network model is determining whether or not certain existing phylogenetic trees are displayed in a phylogenetic network. This problem is formally called the tree containment problem. It is NP-complete even for binary phylogenetic networks. We design an exponential time but efficient method for determining whether or not a phylogenetic tree is displayed in an arbitrary phylogenetic network. It is developed on the basis of the so-called reticulation-visible property of phylogenetic networks. A C-program is available for download on http://www.math.nus.edu.sg/∼matzlx/tcp_package matzlx@nus.edu.sg Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Modelling and Analysis of Real Time Systems with Logic Programming and Constraints

    DEFF Research Database (Denmark)

    Banda, Gourinath

    to verify the reactive behaviour of concur- rent systems. Computation Tree Logic (CTL) is a temporal property specification language. Logic programming is a general purpose programming language based on predicate logic. In this dissertation, the LHA models are verified by encoding them as con- straint logic...... programs. The constraint logic program (CLP) encoding an LHA model is first specialised and then a concrete minimal model (or possibly an ab- stract minimal model) for the residual program is computed. The abstract minimal model is computed by applying the theory of abstract interpretation. The com- puted...... by a compiler. To facilitate forward and backward reasoning, two different ways to model an LHA are defined. A framework consist- ing of general purpose constraint logic program tools is presented to accomplish the reachability analysis to verify a class of safety and liveness properties. A tool to compute...

  3. Devil is in the details: Using logic models to investigate program process.

    Science.gov (United States)

    Peyton, David J; Scicchitano, Michael

    2017-12-01

    Theory-based logic models are commonly developed as part of requirements for grant funding. As a tool to communicate complex social programs, theory based logic models are an effective visual communication. However, after initial development, theory based logic models are often abandoned and remain in their initial form despite changes in the program process. This paper examines the potential benefits of committing time and resources to revising the initial theory driven logic model and developing detailed logic models that describe key activities to accurately reflect the program and assist in effective program management. The authors use a funded special education teacher preparation program to exemplify the utility of drill down logic models. The paper concludes with lessons learned from the iterative revision process and suggests how the process can lead to more flexible and calibrated program management. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Integration of the Hydrologic Simulation Program--FORTRAN (HSPF) Watershed Water Quality Model into the Watershed Modeling System (WMS)

    National Research Council Canada - National Science Library

    Deliman, Patrick

    1999-01-01

    ...) into the Watershed Modeling System (WMS) was initiated as part of an overall goal of the Water Quality Research Program to provide water quality capabilities within the framework of a comprehensive graphical modeling environment...

  5. Thermal models of buildings. Determination of temperatures, heating and cooling loads. Theories, models and computer programs

    Energy Technology Data Exchange (ETDEWEB)

    Kaellblad, K.

    1998-05-01

    The need to estimate indoor temperatures, heating or cooling load and energy requirements for buildings arises in many stages of a buildings life cycle, e.g. at the early layout stage, during the design of a building and for energy retrofitting planning. Other purposes are to meet the authorities requirements given in building codes. All these situations require good calculation methods. The main purpose of this report is to present the authors work with problems related to thermal models and calculation methods for determination of temperatures and heating or cooling loads in buildings. Thus the major part of the report deals with treatment of solar radiation in glazing systems, shading of solar and sky radiation and the computer program JULOTTA used to simulate the thermal behavior of rooms and buildings. Other parts of thermal models of buildings are more briefly discussed and included in order to give an overview of existing problems and available solutions. A brief presentation of how thermal models can be built up is also given and it is a hope that the report can be useful as an introduction to this part of building physics as well as during development of calculation methods and computer programs. The report may also serve as a help for the users of energy related programs. Independent of which method or program a user choose to work with it is his or her own responsibility to understand the limits of the tool, else wrong conclusions may be drawn from the results 52 refs, 22 figs, 4 tabs

  6. A generalized threading model using integer programming that allows for secondary structure element deletion.

    Science.gov (United States)

    Ellrott, Kyle; Guo, Jun-tao; Olman, Victor; Xu, Ying

    2006-01-01

    Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization.

  7. CISLUNAR program manual: A low-thrust trajectory determination model

    Science.gov (United States)

    1988-09-01

    CISLUNAR is a stand-alone computer program designed to generate the trajectory of a low-thrust spacecraft travelling in Earth-Moon space. The program allows the creation of functional trajectories dependent on the supplied spacecraft characteristics. The trajectory generation is a user interactive process. The original intent was for the program user to modify the necessary control values until a staisfactory trajectory has been created.

  8. Physically Embedded Minimal Self-Replicating Systems

    DEFF Research Database (Denmark)

    Fellermann, Harold

    Self-replication is a fundamental property of all living organisms, yet has only been accomplished to limited extend in manmade systems. This thesis is part of the ongoing research endeavor to bridge the two sides of this gap. In particular, we present simulation results of a minimal life...... for any model above the atomistic scale. This is achieved by deriving an alternative scaling procedure for interaction parameters in the model. We perform system-level simulations of the design which attempt to account for theoretical, and experimental knowledge, as well as results from other...... other life-like features can be achieved in systems of formerly unanticipated simplicity – if these systems exploit physicochemical principles that are immanent to their physical scale....

  9. Programming While Construction of Engineering 3D Models of Complex Geometry

    Science.gov (United States)

    Kheyfets, A. L.

    2017-11-01

    The capabilities of geometrically accurate computational 3D models construction with the use of programming are presented. The construction of models of an architectural arch and a glo-boid worm gear is considered as an example. The models are designed in the AutoCAD pack-age. Three programs of construction are given. The first program is for designing a multi-section architectural arch. The control of the arch’s geometry by impacting its main parameters is shown. The second program is for designing and studying the working surface of a globoid gear’s worm. The article shows how to make the animation for this surface’s formation. The third program is for formation of a worm gear cavity surface. The cavity formation dynamics is studied. The programs are written in the AutoLisp programming language. The program texts are provided.

  10. Prenatal programming of sexual partner preference: the ram model.

    Science.gov (United States)

    Roselli, C E; Stormshak, F

    2009-03-01

    In our laboratory, the domestic ram is used as an experimental model to study the early programming of neural mechanisms underlying same-sex partner preference. This interest developed from the observation that approximately 8% of domestic rams are sexually attracted to other rams (male-oriented) in contrast to the majority of rams that are attracted to oestrous ewes (female-oriented). One prominent feature of sexual differentiation in many species is the presence of a sexually dimorphic nucleus (SDN) in the preoptic/anterior hypothalamus that is larger in males than in females. Lesion studies in rats and ferrets implicate the SDN in the expression of sexual preferences. We discovered an ovine SDN (oSDN) in the preoptic/anterior hypothalamus that is smaller in male- than in female-oriented rams and similar in size to the oSDN of ewes. Neurones of the oSDN show abundant aromatase expression that is also reduced in male-oriented compared to female-oriented rams. This observation suggests that sexual partner preferences are neurologically hard-wired and could be influenced by hormones. Aromatase-containing neurones constitute a nascent oSDN as early as day 60 of gestation, which becomes sexually dimorphic by day 135 of gestation when it is two-fold larger in males than in females. Exposure of fetal female lambs to exogenous testosterone from days 30-90 of gestation resulted in a masculinised oSDN. These data demonstrate that the oSDN develops prenatally and may influence adult sexual preferences. Surprisingly, inhibition of aromatase activity in the brain of ram foetuses during the critical period did not interfere with defeminisation of adult sexual partner preference or oSDN volume. These results fail to support an essential role for neural aromatase in the sexual differentiation of sheep brain and behaviour. Thus, we propose that oSDN morphology and male-typical partner preferences may instead be programmed through an androgen receptor mechanism not involving

  11. Replication of genetic associations as pseudoreplication due to shared genealogy.

    Science.gov (United States)

    Rosenberg, Noah A; Vanliere, Jenna M

    2009-09-01

    The genotypes of individuals in replicate genetic association studies have some level of correlation due to shared descent in the complete pedigree of all living humans. As a result of this genealogical sharing, replicate studies that search for genotype-phenotype associations using linkage disequilibrium between marker loci and disease-susceptibility loci can be considered as "pseudoreplicates" rather than true replicates. We examine the size of the pseudoreplication effect in association studies simulated from evolutionary models of the history of a population, evaluating the excess probability that both of a pair of studies detect a disease association compared to the probability expected under the assumption that the two studies are independent. Each of nine combinations of a demographic model and a penetrance model leads to a detectable pseudoreplication effect, suggesting that the degree of support that can be attributed to a replicated genetic association result is less than that which can be attributed to a replicated result in a context of true independence.

  12. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

    Directory of Open Access Journals (Sweden)

    Victor M. Bii

    2016-10-01

    Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

  13. The Development Study of a Medical Ethics Education Program by Using Simple ISD Model.

    Science.gov (United States)

    Kim, Young Jon; Yoo, Hyoo Hyun; Joo, Chan Uhng

    2011-09-01

    Simple instructional systems design (ISD) model is based on a fast development, usability test, and continuos feedback, which are necessary for educational program development in medical school. This study aims to figure out the usability of Simple ISD model for a medical ethics education program by describing a developmental details of each phase and its evaluation results. Research has been conducted in two steps. First, while researchers participated in the program development by using Simple ISD model, we collected empirical data of each development activities. Second, the developed program was evaluated by students' web-based usability test, a 8-students' focus group interview and 5 faculty members' individual interviews in 4 domains; learning contents, instructional methods and strategies, achievement evaluation, and self-evaluation. Following the circular process of analysis, design, development, and usability test of Simple ISD model, a 10-week medical ethics program covering 9 instructional topics was developed. The average points of response on the developed medical ethics program in 2008 and 2009 are increased from 3.96 to 4.59 and 4.41, respectively. The prospects and limitations of the program are discussed. From a development study of the medical ethics program by using Simple ISD model, we could implement a more usable medical ethics program, and found 4 different usability of the Simple ISD model; the rapid development of educational program, program improvement by continuous feedback, faculty members' engagement in instructional design, and professional development of the faculty members.

  14. Replicative DNA polymerase mutations in cancer☆

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-01-01

    Three DNA polymerases — Pol α, Pol δ and Pol ɛ — are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson–Crick base pairing and 3′exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to ‘polymerase proofreading associated polyposis’ (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an ‘ultramutator’ phenotype, with a dramatic increase in base substitutions. PMID:24583393

  15. Replicative DNA polymerase mutations in cancer.

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-02-01

    Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Repair replication in replicating and nonreplicating DNA after irradiation with uv light

    Energy Technology Data Exchange (ETDEWEB)

    Slor, H.; Cleaver, J.E.

    1978-06-01

    Ultraviolet light induces more pyrimidine dimers and more repair replication in DNA that replicates within 2 to 3 h of irradiation than in DNA that does not replicate during this period. This difference may be due to special conformational changes in DNA and chromatin that might be associated with semiconservative DNA replication.

  17. Dance Educator Enrichment Program (DEEP): A Model for Professional Development

    Science.gov (United States)

    Sofras, Pamela Anderson; Emory-Maier, Ambre

    2005-01-01

    In 2001, North Carolina Dance Theatre, The University of North Carolina at Charlotte, and the Charlotte-Mecklenburg School system joined forces to create a multidimensional, professional development program for dance professionals (teachers and artists) in the public schools called, The Dance Educator Enrichment Program (DEEP). DEEP was designed…

  18. Building Psychosocial Programming in Geriatrics Fellowships: A Consortium Model

    Science.gov (United States)

    Adelman, Ronald D.; Ansell, Pamela; Breckman, Risa; Snow, Caitlin E.; Ehrlich, Amy R.; Greene, Michele G.; Greenberg, Debra F.; Raik, Barrie L.; Raymond, Joshua J.; Clabby, John F.; Fields, Suzanne D.; Breznay, Jennifer B.

    2011-01-01

    Geriatric psychosocial problems are prevalent and significantly affect the physical health and overall well-being of older adults. Geriatrics fellows require psychosocial education, and yet to date, geriatrics fellowship programs have not developed a comprehensive geriatric psychosocial curriculum. Fellowship programs in the New York tristate area…

  19. The 1995 NRC Ratings of Doctoral Programs: A Hedonic Model.

    Science.gov (United States)

    Ehrenberg, Ronald G.; Hurst, Peter J.

    1996-01-01

    Using the 1995 National Research Council ratings of doctoral programs in 41 fields, a statistical methodology is offered for assessing how measures of program size, faculty seniority, faculty research productivity, and faculty productivity in producing doctoral degrees influenced raters' decisions. Then using data for one field, economics,…

  20. Program MAMLAC : a mathematical model for impacts against crash barriers.

    NARCIS (Netherlands)

    Giavotto, V.

    1972-01-01

    The digital simulation system that has been developed for impact test against safety barriers has proved to be a valuable tool; it may reduce the cost of a program, or better increase largely the extent of a program without increasing the cost. In fact it may permit to reduce considerably the number

  1. Model Programs for Infants and Toddlers with Handicaps.

    Science.gov (United States)

    Karnes, Merle B.; Stayton, Vicki D.

    Part of a volume which explores current issues in service delivery to infants and toddlers (ages birth to 3) with handicapping conditions, this chapter describes the history of the Handicapped Children's Early Education Program (HCEEP) and provides information on exemplary program components based on written responses to a survey of 67 HCEEP…

  2. Identifying Inter-task Communication in Shared Memory Programming Models

    DEFF Research Database (Denmark)

    Larsen, Per; Karlsson, Sven; Madsen, Jan

    2009-01-01

    Modern computers often use multi-core architectures, cov- ering clusters of homogeneous cores for high performance computing,to heterogeneous architectures typically found in embedded systems. To efficiently program such architectures, it is important to be able to par- tition and map programs onto...... the cores of the architecture. We believe that communication patterns need to become explicit in the source code to make it easier to analyze and partition parallel programs. Extraction of these patterns are difficult to automate due to limitations in compiler techniques when determining the effects...... of pointers. In this paper, we propose an OpenMP extension which allows programmers to explicitly declare the pointer based data-sharing between coarse-grain program parts. We present a dependency directive, expressing the input and output relation between program parts and pointers to shared data, as well...

  3. Updating Linear Schedules with Lowest Cost: a Linear Programming Model

    Science.gov (United States)

    Biruk, Sławomir; Jaśkowski, Piotr; Czarnigowska, Agata

    2017-10-01

    Many civil engineering projects involve sets of tasks repeated in a predefined sequence in a number of work areas along a particular route. A useful graphical representation of schedules of such projects is time-distance diagrams that clearly show what process is conducted at a particular point of time and in particular location. With repetitive tasks, the quality of project performance is conditioned by the ability of the planner to optimize workflow by synchronizing the works and resources, which usually means that resources are planned to be continuously utilized. However, construction processes are prone to risks, and a fully synchronized schedule may expire if a disturbance (bad weather, machine failure etc.) affects even one task. In such cases, works need to be rescheduled, and another optimal schedule should be built for the changed circumstances. This typically means that, to meet the fixed completion date, durations of operations have to be reduced. A number of measures are possible to achieve such reduction: working overtime, employing more resources or relocating resources from less to more critical tasks, but they all come at a considerable cost and affect the whole project. The paper investigates the problem of selecting the measures that reduce durations of tasks of a linear project so that the cost of these measures is kept to the minimum and proposes an algorithm that could be applied to find optimal solutions as the need to reschedule arises. Considering that civil engineering projects, such as road building, usually involve less process types than construction projects, the complexity of scheduling problems is lower, and precise optimization algorithms can be applied. Therefore, the authors put forward a linear programming model of the problem and illustrate its principle of operation with an example.

  4. Using Program Theory Models in Evaluation of Industrial Modernization Programs: Three Case Studies.

    Science.gov (United States)

    Torvatn, Hans

    1999-01-01

    Uses three case studies from Norwegian industrial modernization programs (a formative evaluation, a summative evaluation, and an additionality analysis) to demonstrate the strengths and weaknesses of an evaluation tool called "chains of reasoning." Chains of reasoning uses text and a graphic image to present program activities and goals.…

  5. Effect of replication on epigenetic memory and consequences on gene transcription

    Science.gov (United States)

    Zerihun, Mehari B.; Vaillant, Cédric; Jost, Daniel

    2015-04-01

    Gene activity in eukaryotes is in part regulated at the level of chromatin through the assembly of local chromatin states that are more or less permissive to transcription. How do these chromatin states achieve their functions and whether or not they contribute to the epigenetic inheritance of the transcriptional program remain to be elucidated. In cycling cells, stability is indeed strongly challenged by the periodic occurrence of replication and cell division. To address this question, we perform simulations of the stochastic dynamics of chromatin states when driven out-of-equilibrium by periodic perturbations. We show how epigenetic memory is significantly affected by the cell cycle length. In addition, we develop a simple model to connect the epigenetic state to the transcriptional state and gene activity. In particular, it suggests that replication may induce transcriptional bursting at repressive loci. Finally, we discuss how our findings—effect of replication and link to gene transcription—have original and deep implications to various biological contexts of epigenetic memory.

  6. Promoting peer acceptance of females with higher-functioning autism in a mainstream education setting: a replication and extension of the effects of an autism anti-stigma program.

    Science.gov (United States)

    Ranson, Natalia J; Byrne, Mitchell K

    2014-11-01

    This study evaluated the effects of an eight-session female higher-functioning autism anti-stigma program on the knowledge, attitudes and behavioural intentions of adolescent girls. Participants were seventh-, eighth- and ninth-grade students (N = 273) in a mainstream school. Two-eighth-grade classes were randomly allocated to the intervention condition. The remaining students were either allocated to the no-intervention peer or no-intervention non-peer condition. The anti-stigma program positively influenced knowledge, attitudes and to a lesser extent behavioural intentions towards peers with higher-functioning autism within the intervention condition. Some degree of attitudinal improvement occurred across all conditions following the program suggesting some spill over effects. Overall, findings provide preliminary evidence supporting the efficacy of an anti-stigma program tailored to support females with higher-functioning autism.

  7. Replication and reconfiguration in a distributed mail repository

    Science.gov (United States)

    Day, Mark S.

    1987-04-01

    Conventional approaches to programming produce centralized programs that run on a single computer. However, an unconventional approach can take advantage of low-cost communication and small, inexpensive computers. A distributed program provides service through programs executing at several nodes of a distributed system. Distributed programs can offer two important advantages over centralized programs: high availability and scalability. In a highly-available system, it is very likely that a randomly-chosen transaction will complete successfully. A scalable system's capacity can be increased or decreased to match changes in the demands placed on the system. When a node is unavailable because of maintenance or a crash, transactions may fail unless copies of the node's information are stored at other nodes. Thus, high availability requires replication of data. This thesis considers the problem of building scalable and highly-available distributed programs without using special processors with redundant hardware and software. It describes a design and implementation of an example distributed program, an electronic mail repository. The thesis focuses on how to design and implement replication and reconfiguration for the distributed mail repository.

  8. Coordination between chromosome replication, segregation, and cell division in Caulobacter crescentus

    DEFF Research Database (Denmark)

    Jensen, Rasmus Bugge

    2006-01-01

    , and the completely replicated terminus regions stay associated with each other after chromosome replication is completed, disassociating very late in the cell cycle shortly before the final cell division event. Invagination of the cytoplasmic membrane occurs earlier than separation of the replicated terminus regions......Progression through the Caulobacter crescentus cell cycle is coupled to a cellular differentiation program. The swarmer cell is replicationally quiescent, and DNA replication initiates at the swarmer-to-stalked cell transition. There is a very short delay between initiation of DNA replication...... and formation of separate nucleoids, which results in trapping of a chromosome on either side of the cell division septum, indicating that there is not a nucleoid exclusion phenotype....

  9. Higher Education Program Curricula Models in Tourism and Hospitality Education: A Review of the Literature

    Science.gov (United States)

    Scotland, Miriam

    2006-01-01

    The relevancy of program curricula in tourism and hospitality education has been called into question by key stakeholders in light of ongoing changes in the multifaceted tourism and hospitality industry. Various program models have been identified. Program content and quality of student preparedness have been debated. Balance and areas of emphasis…

  10. Using the Improvement-Focused Model to Evaluate an Online Teacher Education Program

    Science.gov (United States)

    Snyder, Lisa M.

    2010-01-01

    The purpose of this evaluation was to determine the effectiveness of an online reading teacher and literacy instructor training program. A mixed-method research design was used in conjunction with the improvement-focused model of program evaluation to help the researcher identify strengths and weaknesses of the program. Overall, data showed the…

  11. A model technology transfer program for independent operators: Kansas Technology Transfer Model (KTTM)

    Energy Technology Data Exchange (ETDEWEB)

    Schoeling, L.G.

    1993-09-01

    This report describes the development and testing of the Kansas Technology Transfer Model (KTTM) which is to be utilized as a regional model for the development of other technology transfer programs for independent operators throughout oil-producing regions in the US. It describes the linkage of the regional model with a proposed national technology transfer plan, an evaluation technique for improving and assessing the model, and the methodology which makes it adaptable on a regional basis. The report also describes management concepts helpful in managing a technology transfer program. The original Tertiary Oil Recovery Project (TORP) activities, upon which the KTTM is based, were developed and tested for Kansas and have proved to be effective in assisting independent operators in utilizing technology. Through joint activities of TORP and the Kansas Geological Survey (KGS), the KTTM was developed and documented for application in other oil-producing regions. During the course of developing this model, twelve documents describing the implementation of the KTTM were developed as deliverables to DOE. These include: (1) a problem identification (PI) manual describing the format and results of six PI workshops conducted in different areas of Kansas, (2) three technology workshop participant manuals on advanced waterflooding, reservoir description, and personal computer applications, (3) three technology workshop instructor manuals which provides instructor material for all three workshops, (4) three technologies were documented as demonstration projects which included reservoir management, permeability modification, and utilization of a liquid-level acoustic measuring device, (5) a bibliography of all literature utilized in the documents, and (6) a document which describes the KTTM.

  12. FMCSA safety program effectiveness measurement : Intervention Model in fiscal year 2007

    Science.gov (United States)

    2011-04-01

    This report presents results from FMCSAs Roadside Intervention Model for fiscal year 2007. The model estimates the number of crashes avoided, as well as injuries avoided and lives saved, as a result of the Agencys roadside inspection program. T...

  13. A generic model for evaluation of the Federal Aviation Administration air traffic control specialist training programs.

    Science.gov (United States)

    1982-03-01

    The Systems Analysis Research Unit at the Civil Aeromedical Institute (CAMI) has developed a generic model for Federal Aviation Administration (FAA) Academy training program evaluation. The model will serve as a basis for integrating the total data b...

  14. LDA-Based Unified Topic Modeling for Similar TV User Grouping and TV Program Recommendation.

    Science.gov (United States)

    Pyo, Shinjee; Kim, Eunhui; Kim, Munchurl

    2015-08-01

    Social TV is a social media service via TV and social networks through which TV users exchange their experiences about TV programs that they are viewing. For social TV service, two technical aspects are envisioned: grouping of similar TV users to create social TV communities and recommending TV programs based on group and personal interests for personalizing TV. In this paper, we propose a unified topic model based on grouping of similar TV users and recommending TV programs as a social TV service. The proposed unified topic model employs two latent Dirichlet allocation (LDA) models. One is a topic model of TV users, and the other is a topic model of the description words for viewed TV programs. The two LDA models are then integrated via a topic proportion parameter for TV programs, which enforces the grouping of similar TV users and associated description words for watched TV programs at the same time in a unified topic modeling framework. The unified model identifies the semantic relation between TV user groups and TV program description word groups so that more meaningful TV program recommendations can be made. The unified topic model also overcomes an item ramp-up problem such that new TV programs can be reliably recommended to TV users. Furthermore, from the topic model of TV users, TV users with similar tastes can be grouped as topics, which can then be recommended as social TV communities. To verify our proposed method of unified topic-modeling-based TV user grouping and TV program recommendation for social TV services, in our experiments, we used real TV viewing history data and electronic program guide data from a seven-month period collected by a TV poll agency. The experimental results show that the proposed unified topic model yields an average 81.4% precision for 50 topics in TV program recommendation and its performance is an average of 6.5% higher than that of the topic model of TV users only. For TV user prediction with new TV programs, the average

  15. An OpenACC-Based Unified Programming Model for Multi-accelerator Systems

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jungwon [ORNL; Lee, Seyong [ORNL; Vetter, Jeffrey S [ORNL

    2015-01-01

    This paper proposes a novel SPMD programming model of OpenACC. Our model integrates the different granularities of parallelism from vector-level parallelism to node-level parallelism into a single, unified model based on OpenACC. It allows programmers to write programs for multiple accelerators using a uniform programming model whether they are in shared or distributed memory systems. We implement a prototype of our model and evaluate its performance with a GPU-based supercomputer using three benchmark applications.

  16. Overcoming natural replication barriers: differential helicase requirements.

    Science.gov (United States)

    Anand, Ranjith P; Shah, Kartik A; Niu, Hengyao; Sung, Patrick; Mirkin, Sergei M; Freudenreich, Catherine H

    2012-02-01

    DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.

  17. Satin: A high-level and efficient grid programming model

    NARCIS (Netherlands)

    van Nieuwpoort, R.V.; Wrzesinska, G.; Jacobs, C.J.H.; Bal, H.E.

    2010-01-01

    Computational grids have an enormous potential to provide compute power. However, this power remains largely unexploited today for most applications, except trivially parallel programs. Developing parallel grid applications simply is too difficult. Grids introduce several problems not encountered

  18. Non-linear nuclear engineering models as genetic programming application

    International Nuclear Information System (INIS)

    Domingos, Roberto P.; Schirru, Roberto; Martinez, Aquilino S.

    1997-01-01

    This work presents a Genetic Programming paradigm and a nuclear application. A field of Artificial Intelligence, based on the concepts of Species Evolution and Natural Selection, can be understood as a self-programming process where the computer is the main agent responsible for the discovery of a program able to solve a given problem. In the present case, the problem was to find a mathematical expression in symbolic form, able to express the existent relation between equivalent ratio of a fuel cell, the enrichment of fuel elements and the multiplication factor. Such expression would avoid repeatedly reactor physics codes execution for core optimization. The results were compared with those obtained by different techniques such as Neural Networks and Linear Multiple Regression. Genetic Programming has shown to present a performance as good as, and under some features superior to Neural Network and Linear Multiple Regression. (author). 10 refs., 8 figs., 1 tabs

  19. Advanced communication system time domain modeling techniques ASYSTD software description. Volume 2: Program support documentation

    Science.gov (United States)

    1972-01-01

    The theoretical basis for the ASYSTD program is discussed in detail. In addition, the extensive bibliography given in this document illustrates some of the extensive work accomplished in the area of time domain simulation. Additions have been in the areas of modeling and language program enhancements, orthogonal transform modeling, error analysis, general filter models, BER measurements, etc. Several models have been developed which utilize the COMSAT generated orthogonal transform algorithms.

  20. Mathematical programming models for classification problems with applications to credit scoring

    OpenAIRE

    Falangis, Konstantinos

    2013-01-01

    Mathematical programming (MP) can be used for developing classification models for the two–group classification problem. An MP model can be used to generate a discriminant function that separates the observations in a training sample of known group membership into the specified groups optimally in terms of a group separation criterion. The simplest models for MP discriminant analysis are linear programming models in which the group separation measure is generally based on th...

  1. Assessing the relationship between computational speed and precision: a case study comparing an interpreted versus compiled programming language using a stochastic simulation model in diabetes care.

    Science.gov (United States)

    McEwan, Phil; Bergenheim, Klas; Yuan, Yong; Tetlow, Anthony P; Gordon, Jason P

    2010-01-01

    Simulation techniques are well suited to modelling diseases yet can be computationally intensive. This study explores the relationship between modelled effect size, statistical precision, and efficiency gains achieved using variance reduction and an executable programming language. A published simulation model designed to model a population with type 2 diabetes mellitus based on the UKPDS 68 outcomes equations was coded in both Visual Basic for Applications (VBA) and C++. Efficiency gains due to the programming language were evaluated, as was the impact of antithetic variates to reduce variance, using predicted QALYs over a 40-year time horizon. The use of C++ provided a 75- and 90-fold reduction in simulation run time when using mean and sampled input values, respectively. For a series of 50 one-way sensitivity analyses, this would yield a total run time of 2 minutes when using C++, compared with 155 minutes for VBA when using mean input values. The use of antithetic variates typically resulted in a 53% reduction in the number of simulation replications and run time required. When drawing all input values to the model from distributions, the use of C++ and variance reduction resulted in a 246-fold improvement in computation time compared with VBA - for which the evaluation of 50 scenarios would correspondingly require 3.8 hours (C++) and approximately 14.5 days (VBA). The choice of programming language used in an economic model, as well as the methods for improving precision of model output can have profound effects on computation time. When constructing complex models, more computationally efficient approaches such as C++ and variance reduction should be considered; concerns regarding model transparency using compiled languages are best addressed via thorough documentation and model validation.

  2. More scalability, less pain: A simple programming model and its implementation for extreme computing

    International Nuclear Information System (INIS)

    Lusk, E.L.; Pieper, S.C.; Butler, R.M.

    2010-01-01

    This is the story of a simple programming model, its implementation for extreme computing, and a breakthrough in nuclear physics. A critical issue for the future of high-performance computing is the programming model to use on next-generation architectures. Described here is a promising approach: program very large machines by combining a simplified programming model with a scalable library implementation. The presentation takes the form of a case study in nuclear physics. The chosen application addresses fundamental issues in the origins of our Universe, while the library developed to enable this application on the largest computers may have applications beyond this one.

  3. The Displacement Effect of Labour-Market Programs: Estimates from the MONASH Model

    OpenAIRE

    Peter B. Dixon; Maureen T. Rimmer

    2005-01-01

    A key question concerning labour-market programs is the extent to which they generate jobs for their target group at the expense of others. This effect is measured by displacement percentages. We describe a version of the MONASH model designed to quantify the effects of labour-market programs. Our simulation results suggests that: (1) labour-market programs can generate significant long-run increases in employment; (2) displacement percentages depend on how a labour-market program affects the...

  4. Policy Subsystem Portfolio Management: A Neural Network Model of the Gulf of Mexico Program

    OpenAIRE

    Larkin, George Richard

    1999-01-01

    This study provides insights into the behavior of an environmental policy subsystem. The study uses neural network theory to model the Gulf of Mexico Program's allocation of implementation funds. The Gulf of Mexico Program is a prototype effort to institutionalize a policy subsystem. A project implementation fund is at the core of the Gulf of Mexico Program. The United States Environmental Protection Agency provides the implementation fund and the Mexico Program Office (GMPO) administers it. ...

  5. PROGRAMS FOR MODELLING RANDOM EVENTS FOR THE SAKE OF LEARNING BOTH PROGRAMMING AND MATHEMATICS

    Directory of Open Access Journals (Sweden)

    Y. Gayev

    2015-04-01

    Full Text Available MATLAB-programs of some discrete random event has been developed and intended (1 as an exercise at the study of Algorithmization and Programming Course, and (2 for carrying out some "experiments" by lecturing the Course of Probability and Statistics Theory, or at its self-study by students. The programs allows to do several probabilistic experiments in a necessary amount M, using the random number generator, to count up frequency of "favorable events" appearance and compare it to theoretical probability. This displays the Law of large numbers, i.e. approaching experimental results to theory with unlimited increase of М. The work, however, lies not only in this pragmatic result. It should encourage students to study problems of Probability Theory by means of creation appropriate computer codes. The most easy and quick way to this leads to MATLAB-environment. That is why the paper suggests principles of programming in it along with creation of graphical user interface (GUI.

  6. A model for the design and programming of multi-cores

    NARCIS (Netherlands)

    Jesshope, C.; Grandinetti, L.

    2008-01-01

    This paper describes a machine/programming model for the era of multi-core chips. It is derived from the sequential model but replaces sequential composition with concurrent composition at all levels in the program except at the level where the compiler is able to make deterministic decisions on

  7. Evaluation for Community-Based Programs: The Integration of Logic Models and Factor Analysis

    Science.gov (United States)

    Helitzer, Deborah; Hollis, Christine; de Hernandez, Brisa Urquieta; Sanders, Margaret; Roybal, Suzanne; Van Deusen, Ian

    2010-01-01

    Purpose: To discuss the utility of and value of the use of logic models for program evaluation of community-based programs and more specifically, the integration of logic models and factor analysis to develop and revise a survey as part of an effective evaluation plan. Principal results: Diverse stakeholders with varying outlooks used a logic…

  8. MBA in Education Leadership: A Model for Developing an Interdisciplinary Principal Preparation Program

    Science.gov (United States)

    Smith, Rachel A.; Somers, John

    2016-01-01

    This paper presents a model for developing an interdisciplinary principal preparation program, an MBA in Education Leadership, which integrates best practices in both education and business within an educational context. The paper addresses gaps that exist in many traditional principal preparation programs and provides an alternative model, which…

  9. Quorum-based Data Replication in Grid Environment

    Directory of Open Access Journals (Sweden)

    Rohaya Latip

    2009-12-01

    Full Text Available Replication is a useful technique for distributed database systems and can be implemented in a grid computation environment to provide a high availability, fault tolerant, and enhance the performance of the system. This paper discusses a new protocol named Diagonal Data Replication in 2D Mesh structure (DR2M protocol where the performance addressed are data availability which is compared with the previous replication protocols, Read-One Write-All (ROWA, Voting (VT, Tree Quorum (TQ, Grid Configuration (GC, and Neighbor Replication on Grid (NRG. DR2M protocol is organized in a logical two dimensional mesh structure and by using quorums and voting techniques to improve the performance and availability of the replication protocol where it reduce the number of copies of data replication for read or write operations. The data file is copied at the selected node of the diagonal site in a quorum. The selection of a replica depends on the diagonal location of the structured two dimensional mesh quorum where the middle node is selected because it is the best location to get a copy of the data if every node has the equal number of request and data accessing in the network. The algorithm in this paper also calculates the best number of nodes in each quorum and how many quorums are needed for N number of nodes in a network. DR2M protocol also ensures that the data for read and write operations is consistency, by proofing the quorum must not have a nonempty intersection quorum. To evaluate DR2M protocol, we developed a simulation model in Java. Our results prove that DR2M protocol improves the performance of the data availability compare to the previous data replication protocol, ROWA, VT, TQ, GC and NRG.

  10. Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.

    Science.gov (United States)

    Ishikawa-Sasaki, Kumiko; Nagashima, Shigeo; Taniguchi, Koki; Sasaki, Jun

    2018-04-15

    Positive-strand RNA viruses, including picornaviruses, utilize cellular machinery for genome replication. Previously, we reported that each of the 2B, 2BC, 2C, 3A, and 3AB proteins of Aichi virus (AiV), a picornavirus, forms a complex with the Golgi apparatus protein ACBD3 and phosphatidylinositol 4-kinase IIIβ (PI4KB) at viral RNA replication sites (replication organelles [ROs]), enhancing PI4KB-dependent phosphatidylinositol 4-phosphate (PI4P) production. Here, we demonstrate AiV hijacking of the cellular cholesterol transport system involving oxysterol-binding protein (OSBP), a PI4P-binding cholesterol transfer protein. AiV RNA replication was inhibited by silencing cellular proteins known to be components of this pathway, OSBP, the ER membrane proteins VAPA and VAPB (VAP-A/B), the PI4P-phosphatase SAC1, and PI-transfer protein β. OSBP, VAP-A/B, and SAC1 were present at RNA replication sites. We also found various previously unknown interactions among the AiV proteins (2B, 2BC, 2C, 3A, and 3AB), ACBD3, OSBP, VAP-A/B, and SAC1, and the interactions were suggested to be involved in recruiting the component proteins to AiV ROs. Importantly, the OSBP-2B interaction enabled PI4P-independent recruitment of OSBP to AiV ROs, indicating preferential recruitment of OSBP among PI4P-binding proteins. Protein-protein interaction-based OSBP recruitment has not been reported for other picornaviruses. Cholesterol was accumulated at AiV ROs, and inhibition of OSBP-mediated cholesterol transfer impaired cholesterol accumulation and AiV RNA replication. Electron microscopy showed that AiV-induced vesicle-like structures were close to ER membranes. Altogether, we conclude that AiV directly recruits the cholesterol transport machinery through protein-protein interactions, resulting in formation of membrane contact sites between the ER and AiV ROs and cholesterol supply to the ROs. IMPORTANCE Positive-strand RNA viruses utilize host pathways to modulate the lipid composition of

  11. Programs as Polypeptides.

    Science.gov (United States)

    Williams, Lance R

    2016-01-01

    Object-oriented combinator chemistry (OOCC) is an artificial chemistry with composition devices borrowed from object-oriented and functional programming languages. Actors in OOCC are embedded in space and subject to diffusion; since they are neither created nor destroyed, their mass is conserved. Actors use programs constructed from combinators to asynchronously update their own states and the states of other actors in their neighborhoods. The fact that programs and combinators are themselves reified as actors makes it possible to build programs that build programs from combinators of a few primitive types using asynchronous spatial processes that resemble chemistry as much as computation. To demonstrate this, OOCC is used to define a parallel, asynchronous, spatially distributed self-replicating system modeled in part on the living cell. Since interactions among its parts result in the construction of more of these same parts, the system is strongly constructive. The system's high normalized complexity is contrasted with that of a simple composome.

  12. Replication Vesicles are Load- and Choke-Points in the Hepatitis C Virus Lifecycle

    Science.gov (United States)

    Clausznitzer, Diana; Schulze, Manuel; Hüber, Christian M.; Lenz, Simon M.; Schlöder, Johannes P.; Trippler, Martin; Bartenschlager, Ralf; Lohmann, Volker; Kaderali, Lars

    2013-01-01

    Hepatitis C virus (HCV) infection develops into chronicity in 80% of all patients, characterized by persistent low-level replication. To understand how the virus establishes its tightly controlled intracellular RNA replication cycle, we developed the first detailed mathematical model of the initial dynamic phase of the intracellular HCV RNA replication. We therefore quantitatively measured viral RNA and protein translation upon synchronous delivery of viral genomes to host cells, and thoroughly validated the model using additional, independent experiments. Model analysis was used to predict the efficacy of different classes of inhibitors and identified sensitive substeps of replication that could be targeted by current and future therapeutics. A protective replication compartment proved to be essential for sustained RNA replication, balancing translation versus replication and thus effectively limiting RNA amplification. The model predicts that host factors involved in the formation of this compartment determine cellular permissiveness to HCV replication. In gene expression profiling, we identified several key processes potentially determining cellular HCV replication efficiency. PMID:23990783

  13. Replication vesicles are load- and choke-points in the hepatitis C virus lifecycle.

    Directory of Open Access Journals (Sweden)

    Marco Binder

    Full Text Available Hepatitis C virus (HCV infection develops into chronicity in 80% of all patients, characterized by persistent low-level replication. To understand how the virus establishes its tightly controlled intracellular RNA replication cycle, we developed the first detailed mathematical model of the initial dynamic phase of the intracellular HCV RNA replication. We therefore quantitatively measured viral RNA and protein translation upon synchronous delivery of viral genomes to host cells, and thoroughly validated the model using additional, independent experiments. Model analysis was used to predict the efficacy of different classes of inhibitors and identified sensitive substeps of replication that could be targeted by current and future therapeutics. A protective replication compartment proved to be essential for sustained RNA replication, balancing translation versus replication and thus effectively limiting RNA amplification. The model predicts that host factors involved in the formation of this compartment determine cellular permissiveness to HCV replication. In gene expression profiling, we identified several key processes potentially determining cellular HCV replication efficiency.

  14. Replicated x-ray optics for space applications

    Science.gov (United States)

    Hudec, René; Pína, Ladislav; Inneman, Adolf

    2017-11-01

    We report on the program of design and development of X-ray optics for space applications in the Czech Republic. Having more than 30 years background in X-ray optics development for space applications (for use in astronomical X-ray telescopes onboard spacecrafts, before 1989 mostly for Soviet and East European INTERKOSMOS program), we focus nowadays on novel technologies and approaches, thin shell replicated mirrors, as well as studies of light-weight mirrors based on innovative materials such as ceramics. The collaboration includes teams from the Academy of Sciences, Universities, and industry. We will describe and discuss both the history of the development of Xray optics in the Czech Republic and the developed technologies and approaches (with focus on replication technology) as well as recent activities and developments including our participation on the ESA XEUS mirror technology development based on the Agreement between ESA and Czech Government.

  15. Global profiling of DNA replication timing and efficiency reveals that efficient replication/firing occurs late during S-phase in S. pombe.

    Directory of Open Access Journals (Sweden)

    Majid Eshaghi

    Full Text Available BACKGROUND: During S. pombe S-phase, initiation of DNA replication occurs at multiple sites (origins that are enriched with AT-rich sequences, at various times. Current studies of genome-wide DNA replication profiles have focused on the DNA replication timing and origin location. However, the replication and/or firing efficiency of the individual origins on the genomic scale remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: Using the genome-wide ORF-specific DNA microarray analysis, we show that in S. pombe, individual origins fire with varying efficiencies and at different times during S-phase. The increase in DNA copy number plotted as a function of time is approximated to the near-sigmoidal model, when considering the replication start and end timings at individual loci in cells released from HU-arrest. Replication efficiencies differ from origin to origin, depending on the origin's firing efficiency. We have found that DNA replication is inefficient early in S-phase, due to inefficient firing at origins. Efficient replication occurs later, attributed to efficient but late-firing origins. Furthermore, profiles of replication timing in cds1Delta cells are abnormal, due to the failure in resuming replication at the collapsed forks. The majority of the inefficient origins, but not the efficient ones, are found to fire in cds1Delta cells after HU removal, owing to the firing at the remaining unused (inefficient origins during HU treatment. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that efficient DNA replication/firing occurs late in S-phase progression in cells after HU removal, due to efficient late-firing origins. Additionally, checkpoint kinase Cds1p is required for maintaining the efficient replication/firing late in S-phase. We further propose that efficient late-firing origins are essential for ensuring completion of DNA duplication by the end of S-phase.

  16. Promoting Peer Acceptance of Females with Higher-Functioning Autism in a Mainstream Education Setting: A Replication and Extension of the Effects of an Autism Anti-Stigma Program

    Science.gov (United States)

    Ranson, Natalia J.; Byrne, Mitchell K.

    2014-01-01

    This study evaluated the effects of an eight-session female higher-functioning autism anti-stigma program on the knowledge, attitudes and behavioural intentions of adolescent girls. Participants were seventh-, eighth- and ninth-grade students (N = 273) in a mainstream school. Two-eighth-grade classes were randomly allocated to the intervention…

  17. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms....

  18. Modeling Mathematical Programs with Equilibrium Constraints in Pyomo

    Energy Technology Data Exchange (ETDEWEB)

    Hart, William E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Siirola, John Daniel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-07-01

    We describe new capabilities for modeling MPEC problems within the Pyomo modeling software. These capabilities include new modeling components that represent complementar- ity conditions, modeling transformations for re-expressing models with complementarity con- ditions in other forms, and meta-solvers that apply transformations and numeric optimization solvers to optimize MPEC problems. We illustrate the breadth of Pyomo's modeling capabil- ities for MPEC problems, and we describe how Pyomo's meta-solvers can perform local and global optimization of MPEC problems.

  19. INTERLINE, a railroad routing model: program description and user's manual

    International Nuclear Information System (INIS)

    Peterson, B.E.

    1985-11-01

    INTERLINE is an interactive computer program that finds likely routes for shipments over the US railroad system. It is based on a shortest path algorithm modified both to reflect the nature of railroad company operations and to accommodate computer resource limitations in dealing with a large transportation network. The first section of the report discusses the nature of railroad operations and routing practices in the United States, including the tendency to concentrate traffic on a limited number of mainlines, the competition for traffic by different companies operating in the same corridors, and the tendency of originating carriers to retain traffic on their systems before transferring it to terminating carriers. The theoretical foundation and operation of shortest path algorithms are described, as well as the techniques used to simulate actual operating practices within this framework. The second section is a user's guide that describes the program operation and data structures, program features, and user access. 11 refs., 11 figs

  20. Stochastic Fractional Programming Approach to a Mean and Variance Model of a Transportation Problem

    Directory of Open Access Journals (Sweden)

    V. Charles

    2011-01-01

    Full Text Available In this paper, we propose a stochastic programming model, which considers a ratio of two nonlinear functions and probabilistic constraints. In the former, only expected model has been proposed without caring variability in the model. On the other hand, in the variance model, the variability played a vital role without concerning its counterpart, namely, the expected model. Further, the expected model optimizes the ratio of two linear cost functions where as variance model optimize the ratio of two non-linear functions, that is, the stochastic nature in the denominator and numerator and considering expectation and variability as well leads to a non-linear fractional program. In this paper, a transportation model with stochastic fractional programming (SFP problem approach is proposed, which strikes the balance between previous models available in the literature.

  1. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity

    Directory of Open Access Journals (Sweden)

    Mitali Das

    2014-01-01

    Full Text Available As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM 2–7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the “MCM paradox.” Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  2. DATABASE OF MIGRATION AND REPLICATION WITH ORACLE GOLDEN GATE

    Directory of Open Access Journals (Sweden)

    Suharjito Suharjito

    2014-10-01

    Full Text Available The main goal of this research is to analyze and design a database configuration of migration and replication in PT Metro Batavia. Research methodologies used in this research are data collecting, analysis and design model. Data collecting method is conducted with library research and direct survey in the company. Analysis method is conducted by analyzing hangar system, migration and reflection process and the available problems. Design method is conducted by designing a prototype for migration process with the implementation of Oracle SQL Developer and replication process with implementation of Oracle Golden Gate. The result of this research is a prototype for configuration of migration and replication process by using Oracle Golden Gate, which can produce two sets of identical data for the purpose of backup and recovery, and also design a simple tool that is expected to help active-active or active-passive replication process. The conclusion of this research is migration process of MySQL database to Oracle database by using Oracle Golden Gate hasn’t been conducted, because Oracle Golden Gate still has bug related to binary log, so database of migration is conducted by using Oracle Golden Gate. However, replication of bi-directional in between database of Oracle by using Oracle SQL Developer can guarantee data availability and reduce work burden from primary database.

  3. Enzymatic recognition of DNA replication origins

    International Nuclear Information System (INIS)

    Stayton, M.M.; Bertsch, L.; Biswas, S.

    1983-01-01

    In this paper we discuss the process of recognition of the complementary-strand origin with emphasis on RNA polymerase action in priming M13 DNA replication, the role of primase in G4 DNA replication, and the function of protein n, a priming protein, during primosome assembly. These phage systems do not require several of the bacterial DNA replication enzymes, particularly those involved in the regulation of chromosome copy number of the initiatiion of replication of duplex DNA. 51 references, 13 figures, 1 table

  4. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells.

    OpenAIRE

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-01-01

    Udgivelsesdato: 2008-Feb DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells by using the model organisms Escherichia coli and Schizosaccharomyces pombe as examples. Although the underlying molecular details are different, the logic behind the con...

  5. Beyond 1-Safety and 2-Safety for replicated databases: Group-Safety

    OpenAIRE

    Wiesmann, M.; Schiper, A.

    2004-01-01

    In this paper, we study the safety guarantees of group communication-based database replication techniques. We show that there is a model mismatch between group communication and database, and because of this, classical group communication systems cannot be used to build 2-safe database replication. We propose a new group communication primitive called \\emph{end-to-end atomic broadcast} that solves the problem, i.e., can be used to implement 2-safe database replication. We also introduce...

  6. Model Kepemimpinan Modern di Program Pascasarjana Universitas Ahmad Dahlan

    Directory of Open Access Journals (Sweden)

    Dwi Sulisworo

    2012-01-01

    Full Text Available In the management of higher education, demand a change can be done effectively when the leadership and management are well developed. In general, internal conflicts in the education management occurred due to poor leadership. This study is a qualitative study with a phenomenological approach. The subject of the study is Graduate Program of University Ahmad Dahlan which manages five master programs. Determination of each of people which considers his/her competence, knowledge, experience and personal attributes will affect to performance and operational leadership roles, organizational, and public. Cross-departmental activities and external parties become a focus for leadership in achieving the vision and mission of the organization.

  7. Developing a model lifeline protection program for DOE facilities

    International Nuclear Information System (INIS)

    Lowing, A.N.

    1996-01-01

    A National Lifeline Standard Development Program is currently being conducted by FEMA and NIST. The Department of Energy is following these developments and supplementing them to meet Life-Safety and mission requirements for all DOE facilities as part of the Natural Phenomena Hazards Mitigation Plan. The task will be overseen by a DOE management team with technical guidance provided by a Steering Group of management and operating contractor representatives. The DOE will participate in the federal program by conducting a workshop on lifeline protection issues, developing an overall plan, organizing a Steering Group, and conducting a pilot study at a DOE facility

  8. A spatial stochastic programming model for timber and core area management under risk of fires

    Science.gov (United States)

    Yu Wei; Michael Bevers; Dung Nguyen; Erin Belval

    2014-01-01

    Previous stochastic models in harvest scheduling seldom address explicit spatial management concerns under the influence of natural disturbances. We employ multistage stochastic programming models to explore the challenges and advantages of building spatial optimization models that account for the influences of random stand-replacing fires. Our exploratory test models...

  9. Minority games, evolving capitals and replicator dynamics

    Science.gov (United States)

    Galla, Tobias; Zhang, Yi-Cheng

    2009-11-01

    We discuss a simple version of the minority game (MG) in which agents hold only one strategy each, but in which their capitals evolve dynamically according to their success and in which the total trading volume varies in time accordingly. This feature is known to be crucial for MGs to reproduce stylized facts of real market data. The stationary states and phase diagram of the model can be computed, and we show that the ergodicity breaking phase transition common for MGs, and marked by a divergence of the integrated response, is present also in this simplified model. An analogous majority game turns out to be relatively void of interesting features, and the total capital is found to diverge in time. Introducing a restraining force leads to a model akin to the replicator dynamics of evolutionary game theory, and we demonstrate that here a different type of phase transition is observed. Finally we briefly discuss the relation of this model with one strategy per player to more sophisticated minority games with dynamical capitals and several trading strategies per agent.

  10. A Cost Model for Storage and Weeding Programs.

    Science.gov (United States)

    Lawrence, Gary S.

    1981-01-01

    Presents a simple cost model to analyze trade-offs involved in considering storage and weeding as alternatives to new construction for academic libraries. References are provided, and the Palmour cost model is presented as an appendix. (RAA)

  11. Uncertain and multi-objective programming models for crop planting structure optimization

    Directory of Open Access Journals (Sweden)

    Mo LI,Ping GUO,Liudong ZHANG,Chenglong ZHANG

    2016-03-01

    Full Text Available Crop planting structure optimization is a significant way to increase agricultural economic benefits and improve agricultural water management. The complexities of fluctuating stream conditions, varying economic profits, and uncertainties and errors in estimated modeling parameters, as well as the complexities among economic, social, natural resources and environmental aspects, have led to the necessity of developing optimization models for crop planting structure which consider uncertainty and multi-objectives elements. In this study, three single-objective programming models under uncertainty for crop planting structure optimization were developed, including an interval linear programming model, an inexact fuzzy chance-constrained programming (IFCCP model and an inexact fuzzy linear programming (IFLP model. Each of the three models takes grayness into account. Moreover, the IFCCP model considers fuzzy uncertainty of parameters/variables and stochastic characteristics of constraints, while the IFLP model takes into account the fuzzy uncertainty of both constraints and objective functions. To satisfy the sustainable development of crop planting structure planning, a fuzzy-optimization-theory-based fuzzy linear multi-objective programming model was developed, which is capable of reflecting both uncertainties and multi-objective. In addition, a multi-objective fractional programming model for crop structure optimization was also developed to quantitatively express the multi-objective in one optimization model with the numerator representing maximum economic benefits and the denominator representing minimum crop planting area allocation. These models better reflect actual situations, considering the uncertainties and multi-objectives of crop planting structure optimization systems. The five models developed were then applied to a real case study in Minqin County, north-west China. The advantages, the applicable conditions and the solution methods

  12. Modeling Activities in the Department of Energy’s Atmospheric Sciences Program

    Energy Technology Data Exchange (ETDEWEB)

    Fast, Jerome D.; Ghan, Steven J.; Schwartz, Stephen E.

    2009-03-01

    The Department of Energy's Atmospheric Science Program (ASP) conducts research pertinent to radiative forcing of climate change by atmospheric aerosols. The program consists of approximately 40 highly interactive peer-reviewed research projects that examine aerosol properties and processes and the evolution of aerosols in the atmosphere. Principal components of the program are instrument development, laboratory experiments, field studies, theoretical investigations, and modeling. The objectives of the Program are to 1) improve the understanding of aerosol processes associated with light scattering and absorption properties and interactions with clouds that affect Earth's radiative balance and to 2) develop model-based representations of these processes that enable the effects of aerosols on Earth's climate system to be properly represented in global-scale numerical climate models. Although only a few of the research projects within ASP are explicitly identified as primarily modeling activities, modeling actually comprises a substantial component of a large fraction of ASP research projects. This document describes the modeling activities within the Program as a whole, the objectives and intended outcomes of these activities, and the linkages among the several modeling components and with global-scale modeling activities conducted under the support of the Department of Energy's Climate Sciences Program and other aerosol and climate research programs.

  13. Modelling and Formal Verification of Timing Aspects in Large PLC Programs

    CERN Document Server

    Fernandez Adiego, B; Blanco Vinuela, E; Tournier, J-C; Gonzalez Suarez, V M; Blech, J O

    2014-01-01

    One of the main obstacle that prevents model checking from being widely used in industrial control systems is the complexity of building formal models out of PLC programs, especially when timing aspects need to be integrated. This paper brings an answer to this obstacle by proposing a methodology to model and verify timing aspects of PLC programs. Two approaches are proposed to allow the users to balance the trade-off between the complexity of the model, i.e. its number of states, and the set of specifications possible to be verified. A tool supporting the methodology which allows to produce models for different model checkers directly from PLC programs has been developed. Verification of timing aspects for real-life PLC programs are presented in this paper using NuSMV.

  14. Geometric Modeling Applications Interface Program (GMAP). Volume 1. Executive Overview

    Science.gov (United States)

    1989-09-01

    Z . Code) 10. SOURCE OF FUNDING NOS. PROGRAM PROJECT TASK WORK UNIT ELEMENT NO. NO. NO. NO. 11. TITLE (Include Security Classification) GEOMETRIC...342f CI FTR560240OOlU September 1989 SECTION 2 SCOPE OF GMAP GMAP focused on the generacion , control, and exchange of computer information to replace

  15. Access, Equity, and Opportunity. Women in Machining: A Model Program.

    Science.gov (United States)

    Warner, Heather

    The Women in Machining (WIM) program is a Machine Action Project (MAP) initiative that was developed in response to a local skilled metalworking labor shortage, despite a virtual absence of women and people of color from area shops. The project identified post-war stereotypes and other barriers that must be addressed if women are to have an equal…

  16. 76 FR 68011 - Medicare Program; Advanced Payment Model

    Science.gov (United States)

    2011-11-02

    ... Vol. 76 Wednesday, No. 212 November 2, 2011 Part IV Department of Health and Human Services... HEALTH AND HUMAN SERVICES Centers for Medicare & Medicaid Services [CMS-5505-N] Medicare Program... at the start of the first performance year and end at the settlement scheduled at the end of that...

  17. Toward external coupling of building energy and airflow modeling programs

    NARCIS (Netherlands)

    Djunaedy, E.; Hensen, J.L.M.; Loomans, M.G.L.C.

    2003-01-01

    This paper presents the objectives and results of the initial stage of an ongoing research project on coupling of building energy simulation (BES), airflow network (AFN), and compu-tational Huid dynamics (CFD) programs. The objective of the research underlying this paper is to develop and verifi, a

  18. Projected 2050 Model Simulations for the Chesapeake Bay Program

    Science.gov (United States)

    The Chesapeake Bay Program as has been tasked with assessing how changes in climate systems are expected to alter key variables and processes within the Watershed in concurrence with land use changes. EPA’s Office of Research and Development will be conducting historic and...

  19. Alcohol and Other Drug Prevention on College Campuses: Model Programs

    Science.gov (United States)

    US Department of Education, 2008

    2008-01-01

    In response to recent alcohol-related tragedies and to ongoing concern about unacceptable levels of alcohol and other drug use on college campuses, Congress authorized the U.S. Department of Education to identify and promote effective campus-based prevention programs. Since 1999, the U.S. Department of Education has awarded approximately $3.5…

  20. A goal programming model for planning management of Miombo ...

    African Journals Online (AJOL)

    This study used a Goal Programming approach to investigate the effects of changes in agricultural policies and labour supply due to deaths in farming households, on use of woodlands under two regimes; namely one where utilization of forest resources was restricted to within sustainable levels and under another where ...

  1. Game Theory and its Relationship with Linear Programming Models ...

    African Journals Online (AJOL)

    Game theory, a branch of operations research, has been successfully applied to solve various categories of problems arising from human decisions making characterized by the complexity of situations and the limits of individual processing abilities. This paper shows that game theory and linear programming problem are ...

  2. Developing Supply Chain Management Program: A Competency Model

    Science.gov (United States)

    Sauber, Matthew H.; McSurely, Hugh B.; Tummala, V. M. Rao

    2008-01-01

    Purpose: This paper aims to show the process of designing and measuring learning competencies in program development. Design/methodology/approach: The paper includes cross-sectoral comparisons to draw on programmatic and pedagogical strategies, more commonly utilized in vocational education, and transfer the application of these strategies into…

  3. PEMILIHAN PROGRAM PENGENTASAN KEMISKINAN MELALUI PENGEMBANGAN MODEL PEMBERDAYAAN MASYARAKAT DENGAN PENDEKATAN SISTEM

    Directory of Open Access Journals (Sweden)

    Sutikno Sutikno

    2015-06-01

    Full Text Available This research aims to compile the programs for poverty alleviation by community empowerment model and review the determination program as effectiveness evaluation poverty alleviation program which still can’t be worked properly. Stages the compiling program of poverty alleviation is mapping the socioeconomic conditions of the poor, basic infrastructure conditions, socio-cultural issues, and potential issues; identifying the hopes and predicting the economic development opportunities; creating the poverty alleviation program by SWOT analysis and planning implementation program with KPD. Based on the result of SWOT and scoring analysis, the selected programs are training and assistance, the establishment of cooperative saving and loans, clean water for poor households, rural development with the utilization of clean water, household waste management, and package education program A, B, and C.

  4. Service and business model for technology enabled and home-based cardiac rehabilitation programs.

    Science.gov (United States)

    Sarela, Antti; Whittaker, Frank; Korhonen, Ilkka

    2009-01-01

    Cardiac rehabilitation programs are comprehensive life-style programs aimed at preventing recurrence of a cardiac event. However, the current programs have globally significantly low levels of uptake. Home-based model can be a viable alternative to hospital-based programs. We developed and analysed a service and business model for home based cardiac rehabilitation based on personal mentoring using mobile phones and web services. We analysed the different organizational and economical aspects of setting up and running the home based program and propose a potential business model for a sustainable and viable service. The model can be extended to management of other chronic conditions to enable transition from hospital and care centre based treatments to sustainable home-based care.

  5. A process model of voluntary travel behavior modification and effects of Travel Feedback Programs (TFPs)

    OpenAIRE

    Taniguchi, Ayako

    2007-01-01

    This study tested an integrated process model of travel behavior modification. We used a model that combined the theory of planned behavior (TPB), norm activation theory (NAT), a theory of implementation intention, and theories of habit. To test the integrated model, we used panel data (n = 208) obtained before and after travel feedback programs (TFPs); the TFP is a communication program aimed at voluntary travel behavior modification, from automobile use to non-auto means of travel such as p...

  6. Human Genome Replication Proceeds through Four Chromatin States

    Science.gov (United States)

    Julienne, Hanna; Zoufir, Azedine; Audit, Benjamin; Arneodo, Alain

    2013-01-01

    Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a

  7. Proficient Replication of the Yeast Genome by a Viral DNA Polymerase.

    Science.gov (United States)

    Stodola, Joseph L; Stith, Carrie M; Burgers, Peter M

    2016-05-27

    DNA replication in eukaryotic cells requires minimally three B-family DNA polymerases: Pol α, Pol δ, and Pol ϵ. Pol δ replicates and matures Okazaki fragments on the lagging strand of the replication fork. Saccharomyces cerevisiae Pol δ is a three-subunit enzyme (Pol3-Pol31-Pol32). A small C-terminal domain of the catalytic subunit Pol3 carries both iron-sulfur cluster and zinc-binding motifs, which mediate interactions with Pol31, and processive replication with the replication clamp proliferating cell nuclear antigen (PCNA), respectively. We show that the entire N-terminal domain of Pol3, containing polymerase and proofreading activities, could be effectively replaced by those from bacteriophage RB69, and could carry out chromosomal DNA replication in yeast with remarkable high fidelity, provided that adaptive mutations in the replication clamp PCNA were introduced. This result is consistent with the model that all essential interactions for DNA replication in yeast are mediated through the small C-terminal domain of Pol3. The chimeric polymerase carries out processive replication with PCNA in vitro; however, in yeast, it requires an increased involvement of the mutagenic translesion DNA polymerase ζ during DNA replication. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. On Node Replication Attack in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Mumtaz Qabulio

    2016-04-01

    Full Text Available WSNs (Wireless Sensor Networks comprise a large number of small, inexpensive, low power and memory constrained sensing devices (called sensor nodes that are densely deployed to measure a given physical phenomenon. Since WSNs are commonly deployed in a hostile and unattended environment, it is easy for an adversary to physically capture one or more legitimate sensor nodes, re-program and redeploy them in the network. As a result, the adversary becomes able to deploy several identical copies of physically captured nodes in the network in order to perform illegitimate activities. This type of attack is referred to as Node Replication Attack or Clone Node Attack. By launching node replication attack, an adversary can easily get control on the network which consequently is the biggest threat to confidentiality, integrity and availability of data and services. Thus, detection and prevention of node replication attack in WSNs has become an active area of research and to date more than two dozen schemes have been proposed, which address this issue. In this paper, we present a comprehensive review, classification and comparative analysis of twenty five of these schemes which help to detect and/or prevent node replication attack in WSNs

  9. Mathematical Analysis of Replication by Cash Flow Matching

    Directory of Open Access Journals (Sweden)

    Jan Natolski

    2017-02-01

    Full Text Available The replicating portfolio approach is a well-established approach carried out by many life insurance companies within their Solvency II framework for the computation of risk capital. In this note,weelaborateononespecificformulationofareplicatingportfolioproblem. Incontrasttothetwo most popular replication approaches, it does not yield an analytic solution (if, at all, a solution exists andisunique. Further,althoughconvex,theobjectivefunctionseemstobenon-smooth,andhencea numericalsolutionmightthusbemuchmoredemandingthanforthetwomostpopularformulations. Especially for the second reason, this formulation did not (yet receive much attention in practical applications, in contrast to the other two formulations. In the following, we will demonstrate that the (potential non-smoothness can be avoided due to an equivalent reformulation as a linear second order cone program (SOCP. This allows for a numerical solution by efficient second order methods like interior point methods or similar. We also show that—under weak assumptions—existence and uniqueness of the optimal solution can be guaranteed. We additionally prove that—under a further similarly weak condition—the fair value of the replicating portfolio equals the fair value of liabilities. Based on these insights, we argue that this unloved stepmother child within the replication problem family indeed represents an equally good formulation for practical purposes.

  10. Structural Equation Modeling with Mplus Basic Concepts, Applications, and Programming

    CERN Document Server

    Byrne, Barbara M

    2011-01-01

    Modeled after Barbara Byrne's other best-selling structural equation modeling (SEM) books, this practical guide reviews the basic concepts and applications of SEM using Mplus Versions 5 & 6. The author reviews SEM applications based on actual data taken from her own research. Using non-mathematical language, it is written for the novice SEM user. With each application chapter, the author "walks" the reader through all steps involved in testing the SEM model including: an explanation of the issues addressed illustrated and annotated testing of the hypothesized and post hoc models expl

  11. Parallel programming practical aspects, models and current limitations

    CERN Document Server

    Tarkov, Mikhail S

    2014-01-01

    Parallel programming is designed for the use of parallel computer systems for solving time-consuming problems that cannot be solved on a sequential computer in a reasonable time. These problems can be divided into two classes: 1. Processing large data arrays (including processing images and signals in real time)2. Simulation of complex physical processes and chemical reactions For each of these classes, prospective methods are designed for solving problems. For data processing, one of the most promising technologies is the use of artificial neural networks. Particles-in-cell method and cellular automata are very useful for simulation. Problems of scalability of parallel algorithms and the transfer of existing parallel programs to future parallel computers are very acute now. An important task is to optimize the use of the equipment (including the CPU cache) of parallel computers. Along with parallelizing information processing, it is essential to ensure the processing reliability by the relevant organization ...

  12. Approximate Dynamic Programming Based on High Dimensional Model Representation

    Czech Academy of Sciences Publication Activity Database

    Pištěk, Miroslav

    2013-01-01

    Roč. 49, č. 5 (2013), s. 720-737 ISSN 0023-5954 R&D Projects: GA ČR(CZ) GAP102/11/0437 Institutional support: RVO:67985556 Keywords : approximate dynamic programming * Bellman equation * approximate HDMR minimization * trust region problem Subject RIV: BC - Control Systems Theory Impact factor: 0.563, year: 2013 http:// library .utia.cas.cz/separaty/2013/AS/pistek-0399560.pdf

  13. A simulation model of IT risk on program trading

    Science.gov (United States)

    Xia, Bingying; Jiang, Wenbao; Luo, Guangxuan

    2015-12-01

    The biggest difficulty for Program trading IT risk measures lies in the loss of data, in view of this situation, the current scholars approach is collecting court, network and other public media such as all kinds of accident of IT both at home and abroad for data collection, and the loss of IT risk quantitative analysis based on this database. However, the IT risk loss database established by this method can only fuzzy reflect the real situation and not for real to make fundamental explanation. In this paper, based on the study of the concept and steps of the MC simulation, we use computer simulation method, by using the MC simulation method in the "Program trading simulation system" developed by team to simulate the real programming trading and get the IT risk loss of data through its IT failure experiment, at the end of the article, on the effectiveness of the experimental data is verified. In this way, better overcome the deficiency of the traditional research method and solves the problem of lack of IT risk data in quantitative research. More empirically provides researchers with a set of simulation method are used to study the ideas and the process template.

  14. Host factors involved in chikungunya virus replication

    NARCIS (Netherlands)

    Scholte, Florine Elisabeth Maria

    2015-01-01

    In this thesis the interplay of CHIKV with cellular (host) factors involved in its replication is addressed. An in-depth understanding of the interactions between the viral proteins and those of their host is required for the elucidation of molecular mechanisms underlying viral replication. A

  15. Using Replication Projects in Teaching Research Methods

    Science.gov (United States)

    Standing, Lionel G.; Grenier, Manuel; Lane, Erica A.; Roberts, Meigan S.; Sykes, Sarah J.

    2014-01-01

    It is suggested that replication projects may be valuable in teaching research methods, and also address the current need in psychology for more independent verification of published studies. Their use in an undergraduate methods course is described, involving student teams who performed direct replications of four well-known experiments, yielding…

  16. Replication and Robustness in Developmental Research

    Science.gov (United States)

    Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

    2014-01-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

  17. Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

    OpenAIRE

    Klein, Richard A.; Ratliff, Kate A; Vianello, Michelangelo; Adams Jr., Reginald B; Bahník, Stĕpán; Bernstein, Michael J; Bocian, Konrad; Brandt, Mark J; Brooks, Beach; Brumbaugh, Claudia Chloe; Cemalcilar, Zeynep; Chandler, Jesse; Cheong, Winnee; Davis, William E; Devos, Thierry

    2014-01-01

    This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These da...

  18. The Norwegian Healthier Goats program--modeling lactation curves using a multilevel cubic spline regression model.

    Science.gov (United States)

    Nagel-Alne, G E; Krontveit, R; Bohlin, J; Valle, P S; Skjerve, E; Sølverød, L S

    2014-07-01

    In 2001, the Norwegian Goat Health Service initiated the Healthier Goats program (HG), with the aim of eradicating caprine arthritis encephalitis, caseous lymphadenitis, and Johne's disease (caprine paratuberculosis) in Norwegian goat herds. The aim of the present study was to explore how control and eradication of the above-mentioned diseases by enrolling in HG affected milk yield by comparison with herds not enrolled in HG. Lactation curves were modeled using a multilevel cubic spline regression model where farm, goat, and lactation were included as random effect parameters. The data material contained 135,446 registrations of daily milk yield from 28,829 lactations in 43 herds. The multilevel cubic spline regression model was applied to 4 categories of data: enrolled early, control early, enrolled late, and control late. For enrolled herds, the early and late notations refer to the situation before and after enrolling in HG; for nonenrolled herds (controls), they refer to development over time, independent of HG. Total milk yield increased in the enrolled herds after eradication: the total milk yields in the fourth lactation were 634.2 and 873.3 kg in enrolled early and enrolled late herds, respectively, and 613.2 and 701.4 kg in the control early and control late herds, respectively. Day of peak yield differed between enrolled and control herds. The day of peak yield came on d 6 of lactation for the control early category for parities 2, 3, and 4, indicating an inability of the goats to further increase their milk yield from the initial level. For enrolled herds, on the other hand, peak yield came between d 49 and 56, indicating a gradual increase in milk yield after kidding. Our results indicate that enrollment in the HG disease eradication program improved the milk yield of dairy goats considerably, and that the multilevel cubic spline regression was a suitable model for exploring effects of disease control and eradication on milk yield. Copyright © 2014

  19. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells.

    Science.gov (United States)

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-02-01

    DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells by using the model organisms Escherichia coli and Schizosaccharomyces pombe as examples. Although the underlying molecular details are different, the logic behind the control mechanisms is similar. For example, after initiation, crucial molecules required for the loading of replicative helicases in both prokaryotes and eukaryotes are inactivated until the next cell cycle. Furthermore, in both systems the beta-clamp of the replicative polymerase associates with enzymatic activities that contribute to the inactivation of the helicase loaders. Finally, recent studies suggest that the control mechanism that prevents re-replication in both systems also increases the synthesis of DNA building blocks.

  20. Pile group program for full material modeling and progressive failure.

    Science.gov (United States)

    2008-12-01

    Strain wedge (SW) model formulation has been used, in previous work, to evaluate the response of a single pile or a group of piles (including its : pile cap) in layered soils to lateral loading. The SW model approach provides appropriate prediction f...