WorldWideScience

Sample records for model replication program

  1. 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.

  2. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  3. Navajo-ABLE: Replication Model Navajo Assistive Technology Loan Program. Final Program Evaluation.

    Science.gov (United States)

    Norton, Katie Jebb

    This final report discusses the activities and outcomes of the Navajo Assistive Bank of Loanable Equipment (Navajo-ABLE), a federally funded program designed to provide assistive technology (AT) devices, services, technical information, funding information, and training for Navajo children and youth with disabilities. The program was operated and…

  4. Replication of a Crisis Shelter Model of Care in Staff Secure Detention Programs.

    Science.gov (United States)

    Teare, John F.; Castrianno, Lynn M.; Novicoff, Carolyn D.; Peterson, Roger; Authier, Karen; Daly, Daniel

    This paper presents preliminary evidence for the effectiveness of a model of care designed to provide safe and effective services in both short-term shelter and short-term staff secure detention programs. Boys Town short-term crisis shelter programs were designed to provide a safe and therapeutic environment for homeless and runaway youth in need…

  5. Semiconservative replication in the quasispecies model

    Science.gov (United States)

    Tannenbaum, Emmanuel; Deeds, Eric J.; Shakhnovich, Eugene I.

    2004-06-01

    This paper extends Eigen’s quasispecies equations to account for the semiconservative nature of DNA replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness landscape. We show that the error catastrophe occurs when μ , the product of sequence length and per base pair mismatch probability, exceeds 2 ln [2/ ( 1+1/k ) ] , where k>1 is the first-order growth rate constant of the viable “master” sequence (with all other sequences having a first-order growth rate constant of 1 ). This is in contrast to the result of ln k for conservative replication. In particular, as k→∞ , the error catastrophe is never reached for conservative replication, while for semiconservative replication the critical μ approaches 2 ln 2 . Semiconservative replication is therefore considerably less robust than conservative replication to the effect of replication errors. We also show that the mean equilibrium fitness of a semiconservatively replicating system is given by k ( 2 e-μ/2 -1 ) below the error catastrophe, in contrast to the standard result of k e-μ for conservative replication (derived by Kimura and Maruyama in 1966). From this result it is readily shown that semiconservative replication is necessary to account for the observation that, at sufficiently high mutagen concentrations, faster replicating cells will die more quickly than more slowly replicating cells. Thus, in contrast to Eigen’s original model, the semiconservative quasispecies equations are able to provide a mathematical basis for explaining the efficacy of mutagens as chemotherapeutic agents.

  6. Genome-wide alterations of the DNA replication program during tumor progression

    Science.gov (United States)

    Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

    2016-08-01

    Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

  7. Adressing Replication and Model Uncertainty

    DEFF Research Database (Denmark)

    Ebersberger, Bernd; Galia, Fabrice; Laursen, Keld

    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 inno...

  8. Adressing Replication and Model Uncertainty

    DEFF Research Database (Denmark)

    Ebersberger, Bernd; Galia, Fabrice; Laursen, Keld

    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 inno...

  9. Multiseason occupancy models for correlated replicate surveys

    Science.gov (United States)

    Hines, James; Nichols, James; Collazo, Jaime

    2014-01-01

    Occupancy surveys collecting data from adjacent (sometimes correlated) spatial replicates have become relatively popular for logistical reasons. Hines et al. (2010) presented one approach to modelling such data for single-season occupancy surveys. Here, we present a multiseason analogue of this model (with corresponding software) for inferences about occupancy dynamics. We include a new parameter to deal with the uncertainty associated with the first spatial replicate for both single-season and multiseason models. We use a case study, based on the brown-headed nuthatch, to assess the need for these models when analysing data from the North American Breeding Bird Survey (BBS), and we test various hypotheses about occupancy dynamics for this species in the south-eastern United States. The new model permits inference about local probabilities of extinction, colonization and occupancy for sampling conducted over multiple seasons. The model performs adequately, based on a small simulation study and on results of the case study analysis. The new model incorporating correlated replicates was strongly favoured by model selection for the BBS data for brown-headed nuthatch (Sitta pusilla). Latitude was found to be an important source of variation in local colonization and occupancy probabilities for brown-headed nuthatch, with both probabilities being higher near the centre of the species range, as opposed to more northern and southern areas. We recommend this new occupancy model for detection–nondetection studies that use potentially correlated replicates.

  10. Multiscale modeling of virus replication and spread.

    Science.gov (United States)

    Kumberger, Peter; Frey, Felix; Schwarz, Ulrich S; Graw, Frederik

    2016-07-01

    Replication and spread of human viruses is based on the simultaneous exploitation of many different host functions, bridging multiple scales in space and time. Mathematical modeling is essential to obtain a systems-level understanding of how human viruses manage to proceed through their life cycles. Here, we review corresponding advances for viral systems of large medical relevance, such as human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV). We will outline how the combination of mathematical models and experimental data has advanced our quantitative knowledge about various processes of these pathogens, and how novel quantitative approaches promise to fill remaining gaps.

  11. Replicator-dynamics models of sexual conflict.

    Science.gov (United States)

    Kimura, Mariko; Ihara, Yasuo

    2009-09-07

    Evolutionary conflict between the sexes has been studied in various taxa and in various contexts. When the sexes are in conflict over mating rates, natural selection favors both males that induce higher mating rates and females that are more successful at resisting mating attempts. Such sexual conflict may result in an escalating coevolutionary arms race between males and females. In this article, we develop simple replicator-dynamics models of sexual conflict in order to investigate its evolutionary dynamics. Two specific models of the dependence of a female's fitness on her number of matings are considered: in model 1, female fitness decreases linearly with increasing number of matings and in model 2, there is an optimal number of matings that maximizes female fitness. For each of these models, we obtain the conditions for a coevolutionary process to establish costly male and female traits and examine under what circumstances polymorphism is maintained at equilibrium. Then we discuss how assumptions in previous models of sexual conflict are translated to fit to our model framework and compare our results with those of the previous studies. The simplicity of our models allows us to consider sexual conflict in various contexts within a single framework. In addition, we find that our model 2 shows more complicated evolutionary dynamics than model 1. In particular, the population exhibits bistability, where the evolutionary outcome depends on the initial state, only in model 2.

  12. 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.

  13. Entanglement Swapping Model of DNA Replication

    CERN Document Server

    Pusuluk, Onur

    2011-01-01

    Molecular biology explains function of molecules by their geometric and electronic structures which are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any significant role in the essential processes of life. On the contrary, consideration of quantum circuits/protocols and organic molecules as software and hardware of living systems that are co-optimized during evolution, may be useful to pass over the difficulties raised by biochemical complexity and to understand the physics of life. In this sense, we model DNA replication with a reliable qubit representation of the nucleotides: 1) molecular recognition of a nucleotide is assumed to trigger an intrabase entanglement corresponding to a superposition of different tautomer forms and 2) pairing of complementary nucleotides is described by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits/protocols to be used to obtain intr...

  14. Replication of the training program in nonverbal communication in gerontology.

    Science.gov (United States)

    Schimidt, Teresa Cristina Gioia; Duarte, Yeda Aparecida de Oliveira

    2015-01-01

    to measure the rate of assimilation of applied content at immediate and subsequent moments after a nonverbal communication in gerontology training program. descriptive and exploratory fi eld study developed in three state administered hospitals, which attend Brazilian National Health Service (SUS) clients. The duration of the training was twelve hours, applied with 102 healthcare professionals. the results revealed that the rate of assimilation of the content immediately after the program was satisfactory, as well as being satisfactory in the aspects concept of aging; strategies to foster the independence and autonomy of the elderly person; communication interferences linked to the elderly and the professional; recognition of non-verbal functions and dimensions. The exception was the professional perception faced with aspects that influence the success of communication. it was concluded that the replication of this program was relevant and current for the hospital context, remaining effi cient for healthcare professionals.

  15. Application of hepatitis B virus replication mouse model

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    AIM:To evaluate the value of the hepatitis B virus(HBV) replication mouse model with regard to several aspects of the study of HBV biology.METHODS:To evaluate the HBV replication mouse model in detecting the efficacy of anti-HBV agents,the interferon inducer polyinosinic-polytidylin acid(polyIC) and nucleotide analogues adefovir and entecavir were administered to mice injected with wild type pHBV4.1,and the inhibiting effect of these agents on HBV DNA replication was evaluated.To identify the model's value ...

  16. The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture.

    Science.gov (United States)

    Pope, Benjamin D; Gilbert, David M

    2013-11-29

    The "Replicon Theory" of Jacob, Brenner, and Cuzin has reliably served as the paradigm for regulating the sites where individual replicons initiate replication. Concurrent with the replicon model was Taylor's demonstration that plant and animal chromosomes replicate segmentally in a defined temporal sequence, via cytologically defined units too large to be accounted for by a single replicon. Instead, there seemed to be a program to choreograph when chromosome units replicate during S phase, executed by initiation at clusters of individual replicons within each segment. Here, we summarize recent molecular evidence for the existence of such units, now known as "replication domains", and discuss how the organization of large chromosomes into structural units has added additional layers of regulation to the original replicon model.

  17. 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.

  18. A Paper Model of DNA Structure and Replication.

    Science.gov (United States)

    Sigismondi, Linda A.

    1989-01-01

    A paper model which is designed to give students a hands-on experience during lecture and blackboard instruction on DNA structure is provided. A list of materials, paper patterns, and procedures for using the models to teach DNA structure and replication are given. (CW)

  19. Experiments in Model-Checking Optimistic Replication Algorithms

    CERN Document Server

    Boucheneb, Hanifa

    2008-01-01

    This paper describes a series of model-checking experiments to verify optimistic replication algorithms based on Operational Transformation (OT) approach used for supporting collaborative edition. We formally define, using tool UPPAAL, the behavior and the main consistency requirement (i.e. convergence property) of the collaborative editing systems, as well as the abstract behavior of the environment where these systems are supposed to operate. Due to data replication and the unpredictable nature of user interactions, such systems have infinitely many states. So, we show how to exploit some features of the UPPAAL specification language to attenuate the severe state explosion problem. Two models are proposed. The first one, called concrete model, is very close to the system implementation but runs up against a severe explosion of states. The second model, called symbolic model, aims to overcome the limitation of the concrete model by delaying the effective selection and execution of editing operations until th...

  20. Replicating hedge fund returns: A factor model approach

    OpenAIRE

    Naser, Omar

    2007-01-01

    Growth in the Hedge Fund industry mirrors the growth in the Mutual Fund industry. This raises the possibility of creating a passive strategy that replicates Hedge Fund returns at lower cost using liquid, exchange-traded instruments. Using monthly returns for the period 1991-2005 on thirteen Hedge Fund strategies, I build a linear factor models (“clones”) that replicate Hedge Fund returns. I use six common factors to determine the amount of expected return and variation in returns that can be ...

  1. Theoretical models for the regulation of DNA replication in fast-growing bacteria

    Science.gov (United States)

    Creutziger, Martin; Schmidt, Mischa; Lenz, Peter

    2012-09-01

    Growing in always changing environments, Escherichia coli cells are challenged by the task to coordinate growth and division. In particular, adaption of their growth program to the surrounding medium has to guarantee that the daughter cells obtain fully replicated chromosomes. Replication is therefore to be initiated at the right time, which is particularly challenging in media that support fast growth. Here, the mother cell initiates replication not only for the daughter but also for the granddaughter cells. This is possible only if replication occurs from several replication forks that all need to be correctly initiated. Despite considerable efforts during the last 40 years, regulation of this process is still unknown. Part of the difficulty arises from the fact that many details of the relevant molecular processes are not known. Here, we develop a novel theoretical strategy for dealing with this general problem: instead of analyzing a single model, we introduce a wide variety of 128 different models that make different assumptions about the unknown processes. By comparing the predictions of these models we are able to identify the key quantities that allow the experimental discrimination of the different models. Analysis of these quantities yields that out of the 128 models 94 are not consistent with available experimental data. From the remaining 34 models we are able to conclude that mass growth and DNA replication need either to be truly coupled, by coupling DNA replication initiation to the event of cell division, or to the amount of accumulated mass. Finally, we make suggestions for experiments to further reduce the number of possible regulation scenarios.

  2. A quantitative model of DNA replication in Xenopus embryos: reliable replication despite stochasticity

    Science.gov (United States)

    Cheng-Hsin Yang, Scott; Bechhoefer, John

    2008-03-01

    DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the replication time and may lead to cell death if replication takes longer than the cell cycle time (˜ 25 min.). Surprisingly, although the typical replication time is about 20 min., in vivo experiments show that replication fails to complete only about 1 in 250 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two mechanisms: the first uses a regular spatial distribution of origins, while the second uses randomly located origins but increases their probability of initiation as the cell cycle proceeds. Here, we show that both mechanisms yield similar end-time distributions, implying that regular origin spacing is not needed for control of replication time. Moreover, we show that the experimentally inferred time-dependent initiation rate satisfies the observed low failure probability and nearly optimizes the use of replicative proteins.

  3. Widening Disparity and its Suppression in a Stochastic Replicator Model

    CERN Document Server

    Sakaguchi, Hidetsugu

    2016-01-01

    Winner-take-all phenomena are observed in various competitive systems. We find similar phenomena in replicator models with randomly fluctuating growth rates. The disparity between winners and losers increases indefinitely, even if all elements are statistically equivalent. A lognormal distribution describes well the nonstationary time evolution. If a nonlinear load corresponding to progressive taxation is introduced, a stationary distribution is obtained and disparity widening is suppressed.

  4. 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.

  5. Using Model Replication to Improve the Reliability of Agent-Based Models

    Science.gov (United States)

    Zhong, Wei; Kim, Yushim

    The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

  6. AcMNPV As A Model for Baculovirus DNA Replication

    Institute of Scientific and Technical Information of China (English)

    Eric B. Carstens

    2009-01-01

    Baculoviruses were first identified as insect-specific pathogens, and it was this specificity that lead to their use as safe, target specific biological pesticides. For the past 30 years, AcMNPV has served as the subject of intense basic molecular research into the baculovirus infectious cycle including the interaction of the virus with a continuous insect cell line derived from Spodoptera frugiperda. The studies on baculoviruese have led to an in-depth understanding of the physical organization of the viral genomes including many complete genomic sequences, the time course of gene expression, and the application of this basic research to the use of baculoviruses not only as insecticides, but also as a universal eukaryotic protein expression system, and a potential vector in gene therapy. A great deal has also been discovered about the viral genes required for the replication of the baculovirus genome, while much remains to be learned about the mechanism of viral DNA replication. This report outlines the current knowledge of the factors involved in baculovirus DNA replication, using data on AcMNPV as a model for most members of the Baculoviridae.

  7. Replicating vesicles as models of primitive cell growth and division.

    Science.gov (United States)

    Hanczyc, Martin M; Szostak, Jack W

    2004-12-01

    Primitive cells, lacking the complex bio-machinery present in modern cells, would have had to rely on the self-organizing properties of their components and on interactions with their environment to achieve basic cellular functions such as growth and division. Many bilayer-membrane vesicles, depending on their composition and environment, can exhibit complex morphological changes such as growth, fusion, fission, budding, internal vesicle assembly and vesicle-surface interactions. The rich dynamic properties of these vesicles provide interesting models of how primitive cellular replication might have occurred in response to purely physical and chemical forces.

  8. Preon Model and Family Replicated E_6 Unification

    Science.gov (United States)

    Das, Chitta Ranjan; Laperashvili, Larisa V.

    2008-02-01

    Previously we suggested a new preon model of composite quark-leptons and bosons with the 'flipped' E6 × ˜E6 gauge symmetry group. We assumed that preons are dyons having both hyper-electric g and hyper-magnetic ˜g charges, and these preons-dyons are confined by hyper-magnetic strings which are an 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 Tk = kT0 (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 [E6]3 unification at the scale ~1017 GeV. This group of unification ha! s the possibility of breaking to the group of symmetry: [SU(3)C]3 × [SU(2)L]3 × [U(1)Y]3 × [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.

  9. 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.

  10. 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.

  11. 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.

  12. Mobile and replicated alignment of arrays in data-parallel programs

    Science.gov (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

  13. 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.

  14. 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.

  15. [Mediate evaluation of replicating a Training Program in Nonverbal Communication in Gerontology].

    Science.gov (United States)

    Schimidt, Teresa Cristina Gioia; Duarte, Yeda Aparecida de Oliveira; Silva, Maria Julia Paes da

    2015-04-01

    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. 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. Revealed very satisfactory and satisfactory mediate content assimilation index in 82.9%. The program replication proved to be relevant and updated the setting of hospital services, while remaining efficient for healthcare professionals.

  16. 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.

  17. Preon model and family replicated E_6 unification

    CERN Document Server

    Das, C R

    2007-01-01

    Previously we suggested a new preon model of composite quark-leptons and bosons with the 'flipped' E_6\\times \\tilde{E_6} gauge symmetry group. We assumed that preons are dyons having both hyper-electric g and hyper-magnetic \\tilde g charges, and these preons-dyons are confined by hyper-magnetic strings which are an N=1 supersymmetric non-Abelian flux tubes created by the condensation of spreons near the Planck scale. In the present talk 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 near the Planck scale. This group of unification has the possibility of breaking to the group of symmetry: [SU(3)_C]^3\\times [SU(2)_L]^3\\times [U(1)_Y]^3 \\times [U(1)_{(B-L)}]^3 which undergoes the breakdown to the Standard Model at lower energies. The AntiGUT scenario ...

  18. Experimental Models in Syrian Golden Hamster Replicate Human Acute Pancreatitis.

    Science.gov (United States)

    Wang, Yunan; Kayoumu, Abudurexiti; Lu, Guotao; Xu, Pengfei; Qiu, Xu; Chen, Liye; Qi, Rong; Huang, Shouxiong; Li, Weiqin; Wang, Yuhui; Liu, George

    2016-06-15

    The hamster has been shown to share a variety of metabolic similarities with humans. To replicate human acute pancreatitis with hamsters, we comparatively studied the efficacy of common methods, such as the peritoneal injections of caerulein, L-arginine, the retrograde infusion of sodium taurocholate, and another novel model with concomitant administration of ethanol and fatty acid. The severity of pancreatitis was evaluated by serum amylase activity, pathological scores, myeloperoxidase activity, and the expression of inflammation factors in pancreas. The results support that the severity of pathological injury is consistent with the pancreatitis induced in mice and rat using the same methods. Specifically, caerulein induced mild edematous pancreatitis accompanied by minimal lung injury, while L-arginine induced extremely severe pancreatic injury including necrosis and neutrophil infiltration. Infusion of Na-taurocholate into the pancreatic duct induced necrotizing pancreatitis in the head of pancreas and lighter inflammation in the distal region. The severity of acute pancreatitis induced by combination of ethanol and fatty acids was between the extent of caerulein and L-arginine induction, with obvious inflammatory cells infiltration. In view of the advantages in lipid metabolism features, hamster models are ideally suited for the studies of pancreatitis associated with altered metabolism in humans.

  19. Dissemination and benefits of a replicable Tai Chi and Qigong program for older adults.

    Science.gov (United States)

    Jahnke, Roger A; Larkey, Linda K; Rogers, Carol

    2010-01-01

    Tai Chi and Qigong (TCQG) show promise for improving many health outcomes and are recommended for dissemination to older adults. A simplified, easy-to-replicate version of TCQG, "Tai Chi Easy," was tested using a train-the-trainer method to demonstrate feasibility of dissemination to a widespread population of older adults through community sites and achievement of perceived outcomes. Nonexpert facilitators known as "practice leaders" were trained to implement Tai Chi Easy sessions at 18 sites across the United States. Outstanding facilitator (100%) and participant (94%) adherence was achieved. With 330 completers, mean age 73 years, significant improvements were found for participants' perceived stress levels (P = .003). Sleep quality and energy/vitality were markedly improved. Eighty-nine percent enjoyed the program, 91% were committed to continue, and 67% stated that they had increased their weekly levels of physical activity. A train-the-facilitator model for Tai Chi Easy is easily disseminated to older adults and may promote a sustainable alternative exercise, yielding favorable quality of life benefits. Copyright 2010 Mosby, Inc. All rights reserved.

  20. Replication of a Career Academy Model: The Georgia Central Educational Center and Four Replication Sites. Summary. Issues & Answers. REL 2011-No. 101

    Science.gov (United States)

    Detgen, Amy; Alfeld, Corinne

    2011-01-01

    The study surveyed four career academies in Georgia that replicated the model of the Georgia Central Educational Center, which integrates technical instruction and academics at the high school level. The four replication sites adhered to the major tenets of the model. The model's flexibility helped the new sites meet community needs. [For the main…

  1. 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.

  2. 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.

  3. Aggregate and Individual Replication Probability within an Explicit Model of the Research Process

    Science.gov (United States)

    Miller, Jeff; Schwarz, Wolf

    2011-01-01

    We study a model of the research process in which the true effect size, the replication jitter due to changes in experimental procedure, and the statistical error of effect size measurement are all normally distributed random variables. Within this model, we analyze the probability of successfully replicating an initial experimental result by…

  4. Aggregate and Individual Replication Probability within an Explicit Model of the Research Process

    Science.gov (United States)

    Miller, Jeff; Schwarz, Wolf

    2011-01-01

    We study a model of the research process in which the true effect size, the replication jitter due to changes in experimental procedure, and the statistical error of effect size measurement are all normally distributed random variables. Within this model, we analyze the probability of successfully replicating an initial experimental result by…

  5. The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

    Directory of Open Access Journals (Sweden)

    Franck Picard

    2014-05-01

    Full Text Available The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins. The molecular mechanisms coordinating the activation of about [Formula: see text] predicted origins remain poorly understood, partly due to the intrinsic rarity of replication bubbles, making it difficult to purify short nascent strands (SNS. The precise identification of origins based on the high-throughput sequencing of SNS constitutes a new methodological challenge. We propose a new statistical method with a controlled resolution, adapted to the detection of replication origins from SNS data. We detected an average of 80,000 replication origins in different cell lines. To evaluate the consistency between different protocols, we compared SNS detections with bubble trapping detections. This comparison demonstrated a good agreement between genome-wide methods, with 65% of SNS-detected origins validated by bubble trapping, and 44% of bubble trapping origins validated by SNS origins, when compared at the same resolution. We investigated the interplay between the spatial and the temporal programs of replication at fine scales. We show that most of the origins detected in regions replicated in early S phase are shared by all the cell lines investigated whereas cell-type-specific origins tend to be replicated in late S phase. We shed a new light on the key role of CpG islands, by showing that 80% of the origins associated with CGIs are constitutive. Our results further show that at least 76% of CGIs are origins of replication. The analysis of associations with chromatin marks at different timing of cell division revealed new potential epigenetic regulators driving the spatiotemporal activity of replication origins. We highlight the potential role of H4K20me1 and H3K27me3, the coupling of which is correlated with increased efficiency of replication origins, clearly identifying those

  6. Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.

    Directory of Open Access Journals (Sweden)

    Josep Sardanyés

    Full Text Available Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses replicate and infect cells that are rarely in suspension but spatially organized. Surprisingly, most quasispecies models of virus replication have ignored these two phenomena. In order to study these two viral characteristics, we have developed stochastic cellular automata models that simulate two different modes of replication (geometric vs stamping machine for quasispecies replicating and spreading on a two-dimensional space. Furthermore, we explored these two replication models considering epistatic fitness landscapes (antagonistic vs synergistic and different scenarios for cell-to-cell spread, one with free superinfection and another with superinfection inhibition. We found that the master sequences for populations replicating geometrically and with antagonistic fitness effects vanished at low critical mutation rates. By contrast, the highest critical mutation rate was observed for populations replicating geometrically but with a synergistic fitness landscape. Our simulations also showed that for stamping machine replication and antagonistic epistasis, a combination that appears to be common among plant viruses, populations further increased their robustness by inhibiting superinfection. We have also shown that the mode of replication strongly influenced the linkage between viral loci, which rapidly reached linkage equilibrium at increasing mutations for geometric replication. We also found that the strategy that minimized the time required to spread over the whole space was the stamping machine with antagonistic epistasis among mutations. Finally, our simulations revealed that the multiplicity of infection fluctuated but generically increased along

  7. Alpha interferon induces distinct translational control programs to suppress hepatitis C virus RNA replication.

    Science.gov (United States)

    Wang, Chunfu; Pflugheber, Jill; Sumpter, Rhea; Sodora, Donald L; Hui, Daniel; Sen, Ganes C; Gale, Michael

    2003-04-01

    Hepatitis C virus (HCV) infection is treated with interferon (IFN)-based therapy. The mechanisms by which IFN suppresses HCV replication are not known, and only limited efficacy is achieved with therapy because the virus directs mechanisms to resist the host IFN response. In the present study we characterized the effects of IFN action upon the replication of two distinct quasispecies of an HCV replicon whose encoded NS5A protein exhibited differential abilities to bind and inhibit protein kinase R (PKR). Metabolic labeling experiments revealed that IFN had little overall effect upon HCV protein stability or polyprotein processing but specifically blocked translation of the HCV RNA, such that the replication of both viral quasispecies was suppressed by IFN treatment of the Huh7 host cells. However, within cells expressing an NS5A variant that inhibited PKR, we observed a reduced level of eukaryotic initiation factor 2 alpha subunit (eIF2alpha) phosphorylation and a concomitant increase in HCV protein synthetic rates, enhancement of viral RNA replication, and a partial rescue of viral internal ribosome entry site (IRES) function from IFN suppression. Assessment of the ribosome distribution of the HCV replicon RNA demonstrated that the NS5A-mediated block in eIF2alpha phosphorylation resulted in enhanced recruitment of the HCV RNA into polyribosome complexes in vivo but only partially rescued the RNA from polyribosome dissociation induced by IFN treatment. Examination of cellular proteins associated with HCV-translation complexes in IFN-treated cells identified the P56 protein as an eIF3-associated factor that fractionated with the initiator ribosome-HCV RNA complex. Importantly, we found that P56 could independently suppress HCV IRES function both in vitro and in vivo, but a mutant P56 that was unable to bind eIF3 had no suppressive action. We conclude that IFN blocks HCV replication through translational control programs involving PKR and P56 to, respectively

  8. 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.

  9. NACSA Charter School Replication Guide: The Spectrum of Replication Options. Authorizing Matters. Replication Brief 1

    Science.gov (United States)

    O'Neill, Paul

    2010-01-01

    One of the most important and high-profile issues in public education reform today is the replication of successful public charter school programs. With more than 5,000 failing public schools in the United States, there is a tremendous need for strong alternatives for parents and students. Replicating successful charter school models is an…

  10. ASYMPTOTIC NORMALITY OF PARAMETERS ESTIMATION IN EV MODEL WITH REPLICATED OBSERVATIONS

    Institute of Scientific and Technical Information of China (English)

    张三国; 陈希孺

    2002-01-01

    This paper based on the essay [1], studies in case that replicated observations are available in some experimental points, the parameters estimation of one dimensional linear errors-in-variables (EV) models. Asymptotic normality is established.

  11. 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.

  12. Establishment and primary application of a mouse model with hepatitis B virus replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    AIM: To establish a rapid and convenient animal model with hepatitis B virus (HBV) replication. METHODS: A naked DNA solution of HBV-replicationcompetent plasmid was transferred to BALB/C mice via the tail vein, using a hydrodynamic in vivo transfection procedure. After injection, these mice were sacrificed on d 1, 3, 4, 5, 7 and 10. HBV DNA replication intermediates in the liver were analyzed by Southern blot hybridization. The expression of hepatitis B core antigen (HBcAg) and hepatitis B surface antigen (HBsAg) in the liver was checked by immunohistochemistry. Serum HBsAg and hepatitis B e antigen (HBeAg) was detected by enzymelinked immunosorbent assay (ELISA). Inhibition of HBV replication was compared in HBV replication model mice treated intraperitoneally with polyinosinic-polytidylin acid (polyIC) or phosphate-buffered saline (PBS). RESULTS: After hydrodynamicin vivo transfection, HBV DNA replication intermediates in the mouse liver were detectable on d 1 and abundant on d 3 and 4, the levels were slightly decreased and remained relatively stable between d 5 and 7, and were almost undetectable on d 10. The expression patterns of HBcAg and HBsAg were similar to that of HBV replication intermediate DNA, except that they reached a peak on d 1 after injection. No obvious differences in HBV DNA replication intermediates were observed in the left, right and middle lobes of the liver. After treatment with polyIC, the level of HBV intermediate DNA in the liver was lower than that in the control mice injected with PBS. CONCLUSION: A rapid and convenient mouse model with a high level of HBV replication was developed and used to investigate the inhibitory effect of polyIC on HBV replication, which provides a useful tool for future functional studies of the HBV genome.

  13. A dynamic stochastic model for DNA replication initiation in early embryos.

    Directory of Open Access Journals (Sweden)

    Arach Goldar

    Full Text Available BACKGROUND: Eukaryotic cells seem unable to monitor replication completion during normal S phase, yet must ensure a reliable replication completion time. This is an acute problem in early Xenopus embryos since DNA replication origins are located and activated stochastically, leading to the random completion problem. DNA combing, kinetic modelling and other studies using Xenopus egg extracts have suggested that potential origins are much more abundant than actual initiation events and that the time-dependent rate of initiation, I(t, markedly increases through S phase to ensure the rapid completion of unreplicated gaps and a narrow distribution of completion times. However, the molecular mechanism that underlies this increase has remained obscure. METHODOLOGY/PRINCIPAL FINDINGS: Using both previous and novel DNA combing data we have confirmed that I(t increases through S phase but have also established that it progressively decreases before the end of S phase. To explore plausible biochemical scenarios that might explain these features, we have performed comparisons between numerical simulations and DNA combing data. Several simple models were tested: i recycling of a limiting replication fork component from completed replicons; ii time-dependent increase in origin efficiency; iii time-dependent increase in availability of an initially limiting factor, e.g. by nuclear import. None of these potential mechanisms could on its own account for the data. We propose a model that combines time-dependent changes in availability of a replication factor and a fork-density dependent affinity of this factor for potential origins. This novel model quantitatively and robustly accounted for the observed changes in initiation rate and fork density. CONCLUSIONS/SIGNIFICANCE: This work provides a refined temporal profile of replication initiation rates and a robust, dynamic model that quantitatively explains replication origin usage during early embryonic S phase

  14. 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.

  15. Estimation in partial linear EV models with replicated observations

    Institute of Scientific and Technical Information of China (English)

    CUI; Hengjian

    2004-01-01

    The aim of this work is to construct the parameter estimators in the partial linear errors-in-variables (EV) models and explore their asymptotic properties. Unlike other related References, the assumption of known error covariance matrix is removed when the sample can be repeatedly drawn at each designed point from the model. The estimators of interested regression parameters, and the model error variance, as well as the nonparametric function, are constructed. Under some regular conditions, all of the estimators prove strongly consistent. Meanwhile, the asymptotic normality for the estimator of regression parameter is also presented. A simulation study is reported to illustrate our asymptotic results.

  16. 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...

  17. Cellular replication limits in the Luria-Delbrück mutation model

    Science.gov (United States)

    Rodriguez-Brenes, Ignacio A.; Wodarz, Dominik; Komarova, Natalia L.

    2016-08-01

    Originally developed to elucidate the mechanisms of natural selection in bacteria, the Luria-Delbrück model assumed that cells are intrinsically capable of dividing an unlimited number of times. This assumption however, is not true for human somatic cells which undergo replicative senescence. Replicative senescence is thought to act as a mechanism to protect against cancer and the escape from it is a rate-limiting step in cancer progression. Here we introduce a Luria-Delbrück model that explicitly takes into account cellular replication limits in the wild type cell population and models the emergence of mutants that escape replicative senescence. We present results on the mean, variance, distribution, and asymptotic behavior of the mutant population in terms of three classical formulations of the problem. More broadly the paper introduces the concept of incorporating replicative limits as part of the Luria-Delbrück mutational framework. Guidelines to extend the theory to include other types of mutations and possible applications to the modeling of telomere crisis and fluctuation analysis are also discussed.

  18. 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.

  19. Replication program of active and inactive multigene families in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Hatton, K.S.; Dhar, V.; Brown, E.H.; Iqbal, M.A.; Stuart, S.; Didamo, V.T.; Schildkraut, C.L.

    1988-05-01

    In a comprehensive study, the temporal replication of tissue-specific genes and flanking sequences was compared in nine cells lines exhibiting different tissue-specific functions. Some of the rules the authors determined for the replication of these tissue specific genes include the following. (i) Actively transcribed genes usually replicate during the first quarter of the S phase. (ii) Some immunoglobulin genes replicate during the first half of S phase even when no transcriptional activity is detected but appear to replicate even earlier in cell lines where they are transcribed. (iii) Nontranscribed genes can replicate during any interval of S phase. (iv) Multigene families arranged in clusters of 250 kilobases or less define a temporal compartment comprising approximately one-quarter of S phase. While these rules, and others that are discussed, apply to the tissue-specific genes studied here, all tissue-specific genes may not follow this pattern. In addition, housekeeping genes did not follow some of these rules. These results provide the first molecular evidence that the coordinate timing of replication of contiguous sequences within a multigene family is a general property of the mammalian genome. The relationship between replication very early during S phase and the transcriptional activity within a chromosomal domain is discussed.

  20. Determining host metabolic limitations on viral replication via integrated modeling and experimental perturbation.

    Directory of Open Access Journals (Sweden)

    Elsa W Birch

    Full Text Available Viral replication relies on host metabolic machinery and precursors to produce large numbers of progeny - often very rapidly. A fundamental example is the infection of Escherichia coli by bacteriophage T7. The resource draw imposed by viral replication represents a significant and complex perturbation to the extensive and interconnected network of host metabolic pathways. To better understand this system, we have integrated a set of structured ordinary differential equations quantifying T7 replication and an E. coli flux balance analysis metabolic model. Further, we present here an integrated simulation algorithm enforcing mutual constraint by the models across the entire duration of phage replication. This method enables quantitative dynamic prediction of virion production given only specification of host nutritional environment, and predictions compare favorably to experimental measurements of phage replication in multiple environments. The level of detail of our computational predictions facilitates exploration of the dynamic changes in host metabolic fluxes that result from viral resource consumption, as well as analysis of the limiting processes dictating maximum viral progeny production. For example, although it is commonly assumed that viral infection dynamics are predominantly limited by the amount of protein synthesis machinery in the host, our results suggest that in many cases metabolic limitation is at least as strict. Taken together, these results emphasize the importance of considering viral infections in the context of host metabolism.

  1. 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.

  2. Consistency of modified MLE in EV model with replicated observations

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Sanguo

    2001-01-01

    [1]Kendall, M., Stuart, A., The Advanced Theory of Statistics, Vol. 2, New York: Charles Griffin, 1979.[2]Anderson, T. W., Estimating linear statistical relationships, Ann. Statist., 1984, 12: 1.[3]Cui Hengjian, Asymptotic normality of M-estimates in the EV model, Sys. Sci. and Math. Sci., 1997, 10(3): 225.[4]Madansky, A., The fitting of straight lines when both variables are subject to error, JASA, 1959, 54: 173.[5]Villegas, C., Maximum likelihood estimations of a linear functional relationship, Ann. Math. Statist., 1961, 32(4): 1048.[6]Stout, W. F., Almost Sure Convergence, New York: Academic Press, 1974.[7]Petrov, V. V., Sums of Independent Random Variables, New York: Springer-Verlag, 1975.[8]Lai, T. L., Robbins, H., Wei, C. Z., Strong consistency of least squares estimates in multiple regression, J. Multivariate Anal., 1979, 9: 343.[9]Chen Xiru, On limiting properties of U-statistics and von-Mises statistics, Scientia Sinica (in Chinese), 1980, (6): 522.

  3. Tumor promoters alter the temporal program of adenovirus replication in human cells.

    Science.gov (United States)

    Fisher, P B; Young, C S; Weinstein, I B; Carter, T H

    1981-04-01

    In this study we evaluated the effect of phorbol ester tumor promoters on the kinetics of adenovirus type 5 (Ad5) replication in human cells. When added at the time of infection, 12-O-tetradecanoyl-phorbol-13-acetate (TPA) accelerated the appearance of an early virus antigen (72,000-molecular-weight [72K] deoxyribonucleic acid-binding protein), the onset of viral deoxyribonucleic acid synthesis, and the production of infectious virus. The appearance of an Ad5-specific cytopathic effect (CPE) was also accelerated in infected cultures exposed to TPA, whereas phorbol, 4 alpha-phorbol-12,13-didecanoate and 4-OmeTPA, which are inactive as tumor promoters, were ineffective in inducing this morphological change. The acceleration of the CPE seen in TPA-treated Ad5-infected cells was not caused by TPA induction of the protease plasminogen activator, since the protease inhibitors leupeptin and antipain do not inhibit the earlier onset of this CPE and, in contrast, epidermal growth factor, which induces plasminogen activator in HeLa cells, does not induce an earlier CPE. Evidence for a direct effect of TPA on viral gene expression was obtained by analyzing viral messenger ribonucleic acid (mRNA) synthesis. TPA accelerated the appearance of mRNA from all major early regions of Ad5, transiently stimulated the accumulation of region III mRNA, and accelerated the appearance of late Ad5 mRNA. Thus, TPA altered the temporal program of Ad5 mRNA production and accelerated the appearance of at least some Ad5-specific polypeptides during lytic infection of human cells. These effects presumably explain the earlier onset of the Ad5-specific CPE in TPA-treated cells and may have relevance to the effects of TPA on viral gene expression in nonpermissive cells carrying integrated viral deoxyribonucleic acid sequences.

  4. A two-substrate Michaelis-Menten model for the growth of self-replicating polymers.

    Science.gov (United States)

    Ferreira, R

    1987-10-07

    A two-substrate Michaelis-Menten model is proposed for the growth of autocatalytic self-replicating polymers. Selective growth depends on the existence of two complementary pairs of monomers. Discrimination among sequences results from different products of binding constants, KCGnKAUm. The results support an earlier renormalization group treatment (Ferreira & Tsallis, 1985).

  5. Modeling a Dynamic Data Replication Strategy to Increase System Availability in Cloud Computing Environments

    Institute of Scientific and Technical Information of China (English)

    Da-Wei Sun; Gui-Ran Chang; Shang Gao; Li-Zhong Jin; Xing-Wei Wang

    2012-01-01

    Failures are normal rather than exceptional in the cloud computing environmcnts.To improve system availability,replicating the popular data to multiple suitable locations is an advisable choice,as users can access the data from a nearby site.This is,however,not the case for replicas which must have a fixed number of copies on several locations.How to decide a reasonable number and right locations for replicas has become a challenge in the cloud computing.In this paper,a dynamic data replication strategy is put forward with a brief survey of replication strategy suitable for distributed computing environments.It includes:1) analyzing and modeling the relationship between system availability and the number of replicas; 2) evaluating and identifying the popular data and triggering a replication operation when the popularity data passes a dynamic threshold; 3) calculating a suitable number of copies to meet a reasonable system byte effective rate requirement and placing replicas among data nodes in a balanced way; 4) designing the dynamic data replication algorithm in a cloud.Experimental results demonstrate the efficiency and effectiveness of the improved system brought by the proposed strategy in a cloud.

  6. 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.

  7. 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....

  8. 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.

  9. Deterministic slope failure hazard assessment in a model catchment and its replication in neighbourhood terrain

    Directory of Open Access Journals (Sweden)

    Kiran Prasad Acharya

    2016-01-01

    Full Text Available In this work, we prepare and replicate a deterministic slope failure hazard model in small-scale catchments of tertiary sedimentary terrain of Niihama city in western Japan. It is generally difficult to replicate a deterministic model from one catchment to another due to lack of exactly similar geo-mechanical and hydrological parameters. To overcome this problem, discriminant function modelling was done with the deterministic slope failure hazard model and the DEM-based causal factors of slope failure, which yielded an empirical parametric relationship or a discriminant function equation. This parametric relationship was used to predict the slope failure hazard index in a total of 40 target catchments in the study area. From ROC plots, the prediction rate between 0.719–0.814 and 0.704–0.805 was obtained with inventories of September and October slope failures, respectively. This means September slope failures were better predicted than October slope failures by approximately 1%. The results show that the prediction of the slope failure hazard index is possible, even in a small catchment scale, in similar geophysical settings. Moreover, the replication of the deterministic model through discriminant function modelling was found to be successful in predicting typhoon rainfall-induced slope failures with moderate to good accuracy without any use of geo-mechanical and hydrological parameters.

  10. 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...

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

    Science.gov (United States)

    Maya-Mendoza, Apolinar; Ostrakova, Jitka; Kosar, Martin; Hall, Arnaldur; Duskova, Pavlina; Mistrik, Martin; Merchut-Maya, Joanna Maria; Hodny, Zdenek; Bartkova, Jirina; Christensen, Claus; Bartek, Jiri

    2015-03-01

    Both Myc and Ras oncogenes impact cellular metabolism, deregulate redox homeostasis and trigger DNA replication stress (RS) that compromises genomic integrity. However, how are such oncogene-induced effects evoked and temporally related, to what extent are these kinetic parameters shared by Myc and Ras, and how are these cellular changes linked with oncogene-induced cellular senescence in different cell context(s) remain poorly understood. Here, we addressed the above-mentioned open questions by multifaceted comparative analyses of human cellular models with inducible expression of c-Myc and H-RasV12 (Ras), two commonly deregulated oncoproteins operating in a functionally connected signaling network. Our study of DNA replication parameters using the DNA fiber approach and time-course assessment of perturbations in glycolytic flux, oxygen consumption and production of reactive oxygen species (ROS) revealed the following results. First, overabundance of nuclear Myc triggered RS promptly, already after one day of Myc induction, causing slow replication fork progression and fork asymmetry, even before any metabolic changes occurred. In contrast, Ras overexpression initially induced a burst of cell proliferation and increased the speed of replication fork progression. However, after several days of induction Ras caused bioenergetic metabolic changes that correlated with slower DNA replication fork progression and the ensuing cell cycle arrest, gradually leading to senescence. Second, the observed oncogene-induced RS and metabolic alterations were cell-type/context dependent, as shown by comparative analyses of normal human BJ fibroblasts versus U2-OS sarcoma cells. Third, the energy metabolic reprogramming triggered by Ras was more robust compared to impact of Myc. Fourth, the detected oncogene-induced oxidative stress was due to ROS (superoxide) of non-mitochondrial origin and mitochondrial OXPHOS was reduced (Crabtree effect). Overall, our study provides novel

  12. Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations

    CERN Document Server

    Yu, Jin

    2015-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We keep away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while address only statistical physics modeling approach and all-atom molecular dynamics simulation approach. We organize this review around our own modeling and simulation practices on a single-subunit T7 RNA poly...

  13. 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.

  14. Statistical modeling of program performance

    Directory of Open Access Journals (Sweden)

    A. P. Karpenko

    2014-01-01

    Full Text Available A task of evaluation of program performance often occurs in the process of design of computer systems or during iterative compilation. A traditional way to solve this problem is emulation of program execution on the target system. A modern alternative approach to evaluation of program performance is based on statistical modeling of program performance on a computer under investigation. This statistical method of modeling program performance called Velocitas was introduced in this work. The method and its implementation in the Adaptor framework were presented. Investigation of the method's effectiveness showed high adequacy of program performance prediction.

  15. 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.

  16. A Self-Replication Model for Long Channelized Lava Flows on the Mars Plains

    Science.gov (United States)

    Baloga, S. M.; Glaze, L. S.

    2008-01-01

    A model is presented for channelized lava flows emplaced by a self-replicating, levee-building process over long distances on the plains of Mars. Such flows may exhibit morphologic evidence of stagnation, overspills, and upstream breakouts. However, these processes do not inhibit the formation and persistence of a prominent central channel that can often be traced for more than 100 km. The two central assumptions of the self-replication model are (1) the flow advances at the average upstream velocity of the molten core and (2) the fraction of the lava that travels faster than the average upstream velocity forms stationary margins in the advancing distal zone to preserve the self-replication process. For an exemplary 300 km long flow north of Pavonis Mons, the model indicates that 8 m of crust must have formed during emplacement, as determined from the channel and levee dimensions. When combined with independent thermal dynamic estimates for the crustal growth rate, relatively narrow constraints are obtained for the flow rate (2250 m3 s 1), emplacement duration (600 d), and the lava viscosity of the molten interior (106 Pa s). Minor, transient overspills and breakouts increase the emplacement time by only a factor of 2. The primary difference between the prodigious channelized Martian flows and their smaller terrestrial counterparts is that high volumetric flow rates must have persisted for many hundreds of days on Mars, in contrast to a few hours or days on Earth.

  17. Small rodent models of hepatitis B and C virus replication and pathogenesis

    Institute of Scientific and Technical Information of China (English)

    Mark A.Feitelson; Alla Arzumanyan; Marcia M.Clayton

    2012-01-01

    The narrow host range of infection supporting the long-term propagation of hepatitis B and C viruses is a major limitation that has prevented a more thorough understanding of persistent infection and the pathogenesis of chronic liver disease (CLD).With hepatitis B virus (HBV),this has been partially overcome by the discovery and characterization of HBV-like viruses in wild animals.With hepatitis C virus (HCV),related Fiaviviruses have been used as surrogate systems for such studies.Independent work has developed various mouse strains for the transplantation of human hepatocytes,which are then susceptible to infection with HBV and HCV.Other laboratories have developed transgenic mice that express virus gene products and/or support virus replication.Some HBV transgenic mouse models develop fulminant hepatitis,acute hepatitis,or CLD following adoptive transfer,while others spontaneously develop hepatocellular carcinoma (HCC),as in human infections.Among HCV transgenic mice,most develop no disease,but acute hepatitis has been observed in one model,while HCC appears in another.Other mouse models include the introduction of xenographs that replicate HBV or HCV.Although mice are not susceptible to these viruses,their ability to support virus replication and to develop liver disease characteristic of human infections,provides new opportunities to study pathogenesis and develop novel therapeutics.

  18. A new stochastic model for subgenomic hepatitis C virus replication considers drug resistant mutants.

    Directory of Open Access Journals (Sweden)

    Nikita V Ivanisenko

    Full Text Available As an RNA virus, hepatitis C virus (HCV is able to rapidly acquire drug resistance, and for this reason the design of effective anti-HCV drugs is a real challenge. The HCV subgenomic replicon-containing cells are widely used for experimental studies of the HCV genome replication mechanisms, for drug testing in vitro and in studies of HCV drug resistance. The NS3/4A protease is essential for virus replication and, therefore, it is one of the most attractive targets for developing specific antiviral agents against HCV. We have developed a stochastic model of subgenomic HCV replicon replication, in which the emergence and selection of drug resistant mutant viral RNAs in replicon cells is taken into account. Incorporation into the model of key NS3 protease mutations leading to resistance to BILN-2061 (A156T, D168V, R155Q, VX-950 (A156S, A156T, T54A and SCH 503034 (A156T, A156S, T54A inhibitors allows us to describe the long term dynamics of the viral RNA suppression for various inhibitor concentrations. We theoretically showed that the observable difference between the viral RNA kinetics for different inhibitor concentrations can be explained by differences in the replication rate and inhibitor sensitivity of the mutant RNAs. The pre-existing mutants of the NS3 protease contribute more significantly to appearance of new resistant mutants during treatment with inhibitors than wild-type replicon. The model can be used to interpret the results of anti-HCV drug testing on replicon systems, as well as to estimate the efficacy of potential drugs and predict optimal schemes of their usage.

  19. Model-Driven Constraint Programming

    CERN Document Server

    Chenouard, Raphael; Soto, Ricardo; 10.1145/1389449.1389479

    2010-01-01

    Constraint programming can definitely be seen as a model-driven paradigm. The users write programs for modeling problems. These programs are mapped to executable models to calculate the solutions. This paper focuses on efficient model management (definition and transformation). From this point of view, we propose to revisit the design of constraint-programming systems. A model-driven architecture is introduced to map solving-independent constraint models to solving-dependent decision models. Several important questions are examined, such as the need for a visual highlevel modeling language, and the quality of metamodeling techniques to implement the transformations. A main result is the s-COMMA platform that efficiently implements the chain from modeling to solving constraint problems

  20. Positive youth development programs targeting students with greater psychosocial needs: a replication.

    Science.gov (United States)

    Lee, Tak Lan; Shek, Daniel T L

    2010-02-12

    The Tier 2 Program of the Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programmes) targets adolescents with greater psychosocial needs, and the related programs were designed and implemented by school social workers. After completion of the Tier 2 Program (Secondary 1 Level), 9,931 participants in 212 schools responded to the Subjective Outcome Evaluation Form (Form C) in order to assess their views of the program, workers, and perceived effectiveness of the program. Based on the consolidated reports submitted by the agencies to the funding body, the research team aggregated the consolidated data to form a "reconstructed" overall profile on the perceptions of the program participants. Four major types of program were identified, including programs based on the adventure-based counseling approach (n = 58), programs concentrating on volunteer training and services (n = 31), programs offering both adventure-based counseling and volunteer training activities (n = 91), and other programs with different foci (n = 32). Results showed that high proportions of the respondents had positive perceptions of the programs and the workers, and over four-fifths of the respondents regarded the program as helpful to them. The present study provides support for the effectiveness of the Tier 2 Program of the Project P.A.T.H.S. in Hong Kong for the Full Implementation Phase.

  1. Positive Youth Development Programs Targeting Students with Greater Psychosocial Needs: A Replication

    Directory of Open Access Journals (Sweden)

    Tak Yan Lee

    2010-01-01

    Full Text Available The Tier 2 Program of the Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programmes targets adolescents with greater psychosocial needs, and the related programs were designed and implemented by school social workers. After completion of the Tier 2 Program (Secondary 1 Level, 9,931 participants in 212 schools responded to the Subjective Outcome Evaluation Form (Form C in order to assess their views of the program, workers, and perceived effectiveness of the program. Based on the consolidated reports submitted by the agencies to the funding body, the research team aggregated the consolidated data to form a “reconstructed” overall profile on the perceptions of the program participants. Four major types of program were identified, including programs based on the adventure-based counseling approach (n = 58, programs concentrating on volunteer training and services (n = 31, programs offering both adventure-based counseling and volunteer training activities (n = 91, and other programs with different foci (n = 32. Results showed that high proportions of the respondents had positive perceptions of the programs and the workers, and over four-fifths of the respondents regarded the program as helpful to them. The present study provides support for the effectiveness of the Tier 2 Program of the Project P.A.T.H.S. in Hong Kong for the Full Implementation Phase.

  2. Manual for Replication of the Mother-Child Home Program. (Preliminary Version, for Field-Testing).

    Science.gov (United States)

    Levenstein, Phyllis; And Others

    Information to assist local institutions in operating Mother-Child Programs i s provided in this manual as part of the Verbal Interaction Project. Following an introduction, the manual discusses the following topics: (1) Ingredients and Procedures of a Mother-Child Program, (2) Major Program Components, (3) Administrative and Other Practical…

  3. 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...

  4. Immunosuppressive drugs modulate the replication of hepatitis B virus (HBV in a hydrodynamic injection mouse model.

    Directory of Open Access Journals (Sweden)

    Junzhong Wang

    Full Text Available Hepatitis B virus (HBV reactivation and recurrence are common in patients under immunosuppression and can be controlled by hepatitis B immunoglobulin, antivirals, and hepatitis B vaccine. However, the detailed analysis of HBV infection under immunosuppression is essential for the prophylaxis and therapy for HBV reactivation and recurrence. In this study, HBV replication and T cell responses were analyzed in a HBV-transfected mouse model under immunosuppressive therapy. During the treatment, HBV replication was at a high level in mice treated with dexamethasone, cyclosporine, and cyclophosphamide, whereas was terminated in mice treated with mycophenolate mofetil. After the withdrawal, HBV replication was at low or high levels in the dexamethasone-treated mice or in both cyclosporine- and cyclophosphamide-treated mice. The early withdrawal of cyclosporine allowed the recovery of suppressed T cell responses and led to subsequent HBV clearance, while the adoptive immune transfer to the mice with HBV persistence led to HBV suppression. Taken together, long-term HBV persistence under immunosuppression depends on the immunosuppressive drugs used and on the treatment duration and is mediated by the suppressed intrahepatic CD8 T cell response. These data may be helpful for individualized immunosuppressive therapy in patients with high risk of HBV reactivation and recurrence, and the mouse system is suitable for studying HBV reactivation and recurrence under immunosuppression.

  5. A replication study of priorities and attitudes of two nursing programs' communities of interest: an appreciative inquiry.

    Science.gov (United States)

    Farrell, Marie; Wallis, Nancy C; Evans, Marci Tyler

    2007-01-01

    American universities and nursing faculties, caught between the imperatives of community demand and university financial constraints, need to analyze their communities of interests' shared priorities for nursing education. This replication study's objective was to compare the priorities and attitudes of two nursing programs' communities of interest using appreciative inquiry (AI). The researchers used AI to conduct a qualitative, comparative analysis of data from two nursing programs. They used one-on-one and focus group interviews to examine stakeholders' views of the best of the nursing program's past, their vision and approaches to realizing the vision, and their roles in contributing to the vision they created. The researchers analyzed the qualitative data using a standardized codebook and content analysis. Respondents' priorities for both academic programs were similar, with the western respondents emphasizing nursing's contribution to quality care and the southern respondents emphasizing its leadership and commitment to diversity. Both identified the role of legislators and the community in partnering with nursing to secure funds for expansion. Both programs' respondents viewed nursing as a major part of the university and considered their role as supporters of the university's academic and financial goals. The two nursing programs appeared to harness external and internal support in their respective communities. While some priorities differed between the two nursing programs, respondents were aware of the ripple effect of decreased funding for nursing education on the delivery of nursing services to the community. Differences among the undergraduate and graduate students, which reflect a nursing program's student mix, underscore the priorities that nursing programs must emphasize.

  6. 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.

  7. Quality of life among people with multiple sclerosis: Replication of a three-factor prediction model.

    Science.gov (United States)

    Bishop, Malachy; Rumrill, Phillip D; Roessler, Richard T

    2015-01-01

    This article presents a replication of Rumrill, Roessler, and Fitzgerald's 2004 analysis of a three-factor model of the impact of multiple sclerosis (MS) on quality of life (QOL). The three factors in the original model included illness-related, employment-related, and psychosocial adjustment factors. To test hypothesized relationships between QOL and illness-related, employment-related, and psychosocial variables using data from a survey of the employment concerns of Americans with MS (N = 1,839). An ex post facto, multiple correlational design was employed incorporating correlational and multiple regression analyses. QOL was positively related to educational level, employment status, job satisfaction, and job-match, and negatively related to number of symptoms, severity of symptoms, and perceived stress level. The three-factor model explained approximately 37 percent of the variance in QOL scores. The results of this replication confirm the continuing value of the three-factor model for predicting the QOL of adults with MS, and demonstrate the importance of medical, mental health, and vocational rehabilitation interventions and services in promoting QOL.

  8. Identification of replication-competent HSV-1 Cgal+ strain targets in a mouse model of human hepatocarcinoma xenograft

    OpenAIRE

    Santamaria, E. (Enrique); Mora, M.I.; Carro-Roldan, E. (Elvira); M Molina; Fernandez-Irigoyen, J. (Joaquín); Marconi, P; Manservigi, R; Greco, A.; Epstein, A L; Prieto, J.; Hernandez-Alcoceba, R. (Rubén); Corrales, F. J.

    2009-01-01

    Recent studies based on animal models have shown the advantages and potential of oncolytic viral therapy using HSV-1 -based replication-competent vectors in the treatment of liver tumors, but little is known about the cellular targets that are modulated during viral infection. In the present work, we have studied the effects of intratumoral injections of HSV-1 Cgal(+) strain in a murine model of human hepatoma xenografts. Viral replication was assessed for more than 1month, leading to a signi...

  9. Immunosuppression enhances oncolytic adenovirus replication and antitumor efficacy in the Syrian hamster model.

    Science.gov (United States)

    Thomas, Maria A; Spencer, Jacqueline F; Toth, Karoly; Sagartz, John E; Phillips, Nancy J; Wold, William S M

    2008-10-01

    We recently described an immunocompetent Syrian hamster model for oncolytic adenoviruses (Ads) that permits virus replication in tumor cells as well as some normal tissues. This model allows exploration of interactions between the virus, tumor, normal organs, and host immune system that could not be examined in the immunodeficient or nonpermissive animal models previously used in the oncolytic Ad field. Here we asked whether the immune response to oncolytic Ad enhances or limits antitumor efficacy. We first determined that cyclophosphamide (CP) is a potent immunosuppressive agent in the Syrian hamster and that CP alone had no effect on tumor growth. Importantly, we found that the antitumor efficacy of oncolytic Ads was significantly enhanced in immunosuppressed animals. In animals that received virus therapy plus immunosuppression, significant differences were observed in tumor histology, and in many cases little viable tumor remained. Notably, we also determined that immunosuppression allowed intratumoral virus levels to remain elevated for prolonged periods. Although favorable tumor responses can be achieved in immunocompetent animals, the rate of virus clearance from the tumor may lead to varied antitumor efficacy. Immunosuppression, therefore, allows sustained Ad replication and oncolysis, which leads to substantially improved suppression of tumor growth.

  10. 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.

  11. From discrete to continuous evolution models: a unifying approach to drift-diffusion and replicator dynamics

    CERN Document Server

    Chalub, Fabio A C C

    2008-01-01

    We study the large population limit of the Moran process, assuming weak-selection, and for different scalings. Depending on the particular choice of scalings, we obtain a continuous model that may highlight the genetic-drift (neutral evolution) or natural selection; for one precise scaling, both effects are present. For the scalings that take the genetic-drift into account, the continuous model is given by a singular diffusion equation, together with two conservation laws that are already present at the discrete level. For scalings that take into account only natural selection, we obtain a hyperbolic singular equation that embeds the Replicator Dynamics and satisfies only one conservation law. The derivation is made in two steps: a formal one, where the candidate limit model is obtained, and a rigorous one, where convergence of the probability density is proved. Additional results on the fixation probabilities are also presented.

  12. 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.

  13. Scalable spheroid model of human hepatocytes for hepatitis C infection and replication.

    Science.gov (United States)

    Ananthanarayanan, Abhishek; Nugraha, Bramasta; Triyatni, Miriam; Hart, Stefan; Sankuratri, Suryanarayana; Yu, Hanry

    2014-07-07

    Developing effective new drugs against hepatitis C (HCV) virus has been challenging due to the lack of appropriate small animal and in vitro models recapitulating the entire life cycle of the virus. Current in vitro models fail to recapitulate the complexity of human liver physiology. Here we present a method to study HCV infection and replication on spheroid cultures of Huh 7.5 cells and primary human hepatocytes. Spheroid cultures are constructed using a galactosylated cellulosic sponge with homogeneous macroporosity, enabling the formation and maintenance of uniformly sized spheroids. This facilitates easy handling of the tissue-engineered constructs and overcomes limitations inherent of traditional spheroid cultures. Spheroids formed in the galactosylated cellulosic sponge show enhanced hepatic functions in Huh 7.5 cells and maintain liver-specific functions of primary human hepatocytes for 2 weeks in culture. Establishment of apical and basolateral polarity along with the expression and localization of all HCV specific entry proteins allow for a 9-fold increase in viral entry in spheroid cultures over conventional monolayer cultures. Huh 7.5 cells cultured in the galactosylated cellulosic sponge also support replication of the HCV clone, JFH (Japanese fulminant hepatitis)-1 at higher levels than in monolayer cultures. The advantages of our system in maintaining liver-specific functions and allowing HCV infection together with its ease of handling make it suitable for the study of HCV biology in basic research and pharmaceutical R&D.

  14. Solving Two Deadlock Cycles through Neighbor Replication on Grid Deadlock Detection Model

    Directory of Open Access Journals (Sweden)

    Ahmed N. Abdalla

    2012-01-01

    Full Text Available A data grid is compose of hundreds of geographically distributed computers and storage resources usually locate under different places and enables users to share data and other resources. Problem statement: Data replication is one of the mechanisms in managing data grid architecture that receive particular attention since it can provide efficient access to data, fault tolerance, reduce access latency and also can enhance the performance of the system. However, during transaction deadlock may occur that can reduce the throughput by minimizing the available resources, so it becomes an important resource management problem in distributed systems. Approach: The Neighbor Replication on Grid Deadlock Detection (NRGDD transaction model has been developed to handle two deadlock cycle problems on grid. By deploying this method, the transactions communicate with each other by passing the probe messages. The victim message has been used to detect the deadlock when the number of waiting resource by other transaction is highest and become as the cause of deadlock occurs. In addition, this transaction must be aborted to solve the problem. Results: NRGDD transaction model are able to detect and solve more than one cycle of deadlocks. Conclusion: NRGDD has resolve the deadlock problem by sending the minimum number of probes message to detect the deadlock and it can resolve the deadlock to ensure the transaction can be done smoothly.

  15. Replication of the Wellcome Trust genome-wide association study of essential hypertension: the Family Blood Pressure Program.

    Science.gov (United States)

    Ehret, Georg B; Morrison, Alanna C; O'Connor, Ashley A; Grove, Megan L; Baird, Lisa; Schwander, Karen; Weder, Alan; Cooper, Richard S; Rao, D C; Hunt, Steven C; Boerwinkle, Eric; Chakravarti, Aravinda

    2008-12-01

    Essential hypertension is a principal cardiovascular risk factor whose origin remains unknown. Classical genetic studies have shown that blood pressure is at least partially heritable, opening a window to understanding the pathophysiology of essential hypertension in the human using modern genetic tools. The Wellcome Trust Case Control Consortium has recently published the results of screening the genomes of 2000 essential hypertension cases and 3000 controls using 500 000 genome-wide single nucleotide polymorphisms (SNPs). None of the variants proved to be genome-wide significant after correction for multiple tests but the most significantly associated SNPs (PFamily Blood Pressure Program comprising 11 433 individuals recruited by hypertensive families. The results suggest that only one of the six SNPs might be associated with essential hypertension in Americans of European origin. This SNP shows a significant but opposite effect in Americans of Hispanic origin and no association in African Americans. The significance of the opposing effect estimates is unclear. No replication could be shown for hypertension status, but there are differences in study design. This attempted replication highlights that essential hypertension studies will require more comprehensive and larger genetic screens.

  16. Mathematical modelling of DNA replication reveals a trade-off between coherence of origin activation and robustness against rereplication.

    Directory of Open Access Journals (Sweden)

    Anneke Brümmer

    2010-05-01

    Full Text Available Eukaryotic genomes are duplicated from multiple replication origins exactly once per cell cycle. In Saccharomyces cerevisiae, a complex molecular network has been identified that governs the assembly of the replication machinery. Here we develop a mathematical model that links the dynamics of this network to its performance in terms of rate and coherence of origin activation events, number of activated origins, the resulting distribution of replicon sizes and robustness against DNA rereplication. To parameterize the model, we use measured protein expression data and systematically generate kinetic parameter sets by optimizing the coherence of origin firing. While randomly parameterized networks yield unrealistically slow kinetics of replication initiation, networks with optimized parameters account for the experimentally observed distribution of origin firing times. Efficient inhibition of DNA rereplication emerges as a constraint that limits the rate at which replication can be initiated. In addition to the separation between origin licensing and firing, a time delay between the activation of S phase cyclin-dependent kinase (S-Cdk and the initiation of DNA replication is required for preventing rereplication. Our analysis suggests that distributive multisite phosphorylation of the S-Cdk targets Sld2 and Sld3 can generate both a robust time delay and contribute to switch-like, coherent activation of replication origins. The proposed catalytic function of the complex formed by Dpb11, Sld3 and Sld2 strongly enhances coherence and robustness of origin firing. The model rationalizes how experimentally observed inefficient replication from fewer origins is caused by premature activation of S-Cdk, while premature activity of the S-Cdk targets Sld2 and Sld3 results in DNA rereplication. Thus the model demonstrates how kinetic deregulation of the molecular network governing DNA replication may result in genomic instability.

  17. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

    Science.gov (United States)

    Jin, Yu

    2016-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale. Project supported by the National Natural Science Foundation (Grant No. 11275022).

  18. 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.

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

    Institute of Scientific and Technical Information of China (English)

    Kristin L MacArthur; Catherine H Wu; George Y Wu

    2012-01-01

    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.

  20. Sudden infant death syndrome prevention: a model program for NICUs.

    Science.gov (United States)

    McMullen, Sherri L; Lipke, Bethann; LeMura, Catherine

    2009-01-01

    Health care providers' opinions can influence how parents place their infant to sleep. Neonatal nurses can improve how they teach and model safe infant sleep practices to parents. To increase neonatal nurses' knowledge, a sudden infant death syndrome (SIDS) prevention program was implemented. Program components included a computerized teaching tool, a crib card, sleep sacks, and discharge instructions. Initial program evaluation showed that 98 percent of infants slept supine and 93 percent slept in sleep sacks in open cribs. However, nurses continued to swaddle some infants with blankets to improve thermoregulation. To increase nursing compliance in modeling safe infant sleep practices, Halo SleepSack Swaddles were provided for nurses to use in place of a blanket to regulate infant temperature. Recent data show that 100 percent of infants in open cribs are now sleeping supine wearing a Halo Swaddle or a traditional Halo SleepSack. This model program can easily be replicated to enhance neonatal nurses' knowledge about SIDS prevention.

  1. 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.

  2. Approximating uncertainty of annual runoff and reservoir yield using stochastic replicates of global climate model data

    Science.gov (United States)

    Peel, M. C.; Srikanthan, R.; McMahon, T. A.; Karoly, D. J.

    2015-04-01

    Two key sources of uncertainty in projections of future runoff for climate change impact assessments are uncertainty between global climate models (GCMs) and within a GCM. Within-GCM uncertainty is the variability in GCM output that occurs when running a scenario multiple times but each run has slightly different, but equally plausible, initial conditions. The limited number of runs available for each GCM and scenario combination within the Coupled Model Intercomparison Project phase 3 (CMIP3) and phase 5 (CMIP5) data sets, limits the assessment of within-GCM uncertainty. In this second of two companion papers, the primary aim is to present a proof-of-concept approximation of within-GCM uncertainty for monthly precipitation and temperature projections and to assess the impact of within-GCM uncertainty on modelled runoff for climate change impact assessments. A secondary aim is to assess the impact of between-GCM uncertainty on modelled runoff. Here we approximate within-GCM uncertainty by developing non-stationary stochastic replicates of GCM monthly precipitation and temperature data. These replicates are input to an off-line hydrologic model to assess the impact of within-GCM uncertainty on projected annual runoff and reservoir yield. We adopt stochastic replicates of available GCM runs to approximate within-GCM uncertainty because large ensembles, hundreds of runs, for a given GCM and scenario are unavailable, other than the Climateprediction.net data set for the Hadley Centre GCM. To date within-GCM uncertainty has received little attention in the hydrologic climate change impact literature and this analysis provides an approximation of the uncertainty in projected runoff, and reservoir yield, due to within- and between-GCM uncertainty of precipitation and temperature projections. In the companion paper, McMahon et al. (2015) sought to reduce between-GCM uncertainty by removing poorly performing GCMs, resulting in a selection of five better performing GCMs from

  3. Replication of the Association of BDNF and MC4R Variants With Dietary Intake in the Diabetes Prevention Program.

    Science.gov (United States)

    McCaffery, Jeanne M; Jablonski, Kathleen A; Franks, Paul W; Delahanty, Linda M; Aroda, Vanita; Marrero, David; Hamman, Richard F; Horton, Edward S; Dagogo-Jack, Samuel; Wylie-Rosett, Judith; Barrett-Connor, Elizabeth; Kitabchi, Abbas; Knowler, William C; Wing, Rena R; Florez, Jose C

    Genomewide association studies (GWAS) have identified consistent associations with obesity, with a number of studies implicating eating behavior as a primary mechanism. Few studies have replicated genetic associations with dietary intake. This study evaluates the association between obesity susceptibility loci and dietary intake. Data were obtained as part of the Diabetes Prevention Program (DPP), a clinical trial of diabetes prevention in persons at high risk of diabetes. The association of 31 genomewide association studies identified obesity risk alleles with dietary intake, measured through a food frequency questionnaire, was investigated in 3,180 participants from DPP at baseline. The minor allele at BDNF, identified as protective against obesity, was associated with lower total caloric intake (β = -106.06, SE = 33.13; p = .0014) at experimentwide statistical significance (p = .0016), whereas association of MC4R rs571312 with higher caloric intake reached nominal significance (β = 61.32, SE = 26.24; p = .0194). Among non-Hispanic white participants, the association of BDNF rs2030323 with total caloric intake was stronger (β = -151.99, SE = 30.09; p < .0001), and association of FTO rs1421085 with higher caloric intake (β = 56.72, SE = 20.69; p = .0061) and percentage fat intake (β = 0.37, SE = 0.08; p = .0418) was also observed. These results demonstrate with the strength of independent replication that BDNF rs2030323 is associated with 100 to 150 greater total caloric intake per allele, with additional contributions of MC4R and, in non-Hispanic white individuals, FTO. As it has been argued that an additional 100 kcal/d could account for the trends in weight gain, prevention focusing on genetic profiles with high dietary intake may help to quell adverse obesity trends. Clinicaltrials.gov,NCT00004992.

  4. PDDP: A data parallel programming model. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    Warren, K.H.

    1995-06-01

    PDDP, the Parallel Data Distribution Preprocessor, is a data parallel programming model for distributed memory parallel computers. PDDP impelments High Performance Fortran compatible data distribution directives and parallelism expressed by the use of Fortran 90 array syntax, the FORALL statement, and the (WRERE?) construct. Distribued 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.

  5. Factor Analytic Replication and Model Comparison of the BASC-2 Behavioral and Emotional Screening System.

    Science.gov (United States)

    Splett, Joni Williams; Raborn, Anthony; Lane, Kathleen Lynne; Binney, Alexandra J; Chafouleas, Sandra M

    2017-03-06

    We conducted this study to add to literature of previous conflicting factorial examinations of the BASC-2 Behavioral and Emotional Screening System (BESS), Teacher Form-Child/Adolescent. Data were collected by an urban school district in the southeastern United States including 2,228 students rated by 120 teachers in Fall 2014 and 1,955 students rated by 104 teachers in Spring 2015. In both samples, we replicated and then conceptually and statistically compared factor models to examine the (a) 4-factor structure from which the BESS Teacher Form was developed, and (b) existence of a general factor currently being used. Previous studies examined the 4-factor and bifactor structure of the BESS Teacher Form on separate samples. Our model comparison results support a multidimensional interpretation. We recovered similar fit statistics and standardized factor loadings as previous factor analyses. However, measures of variance accounted for by the general factor were below recommended thresholds of a unidimensional construct. We recommend advancing a factorial model that represents a weighted combination of general and specific factors, but do not support continued use of a unidimensional total T score. Limitations and implications of the study are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  6. A bridging model for persistence of a polycomb group protein complex through DNA replication in vitro.

    Science.gov (United States)

    Lo, Stanley M; Follmer, Nicole E; Lengsfeld, Bettina M; Madamba, Egbert V; Seong, Samuel; Grau, Daniel J; Francis, Nicole J

    2012-06-29

    Epigenetic regulation may involve heritable chromatin states, but how chromatin features can be inherited through DNA replication is incompletely understood. We address this question using cell-free replication of chromatin. Previously, we showed that a Polycomb group complex, PRC1, remains continuously associated with chromatin through DNA replication. Here we investigate the mechanism of persistence. We find that a single PRC1 subunit, Posterior sex combs (PSC), can reconstitute persistence through DNA replication. PSC binds nucleosomes and self-interacts, bridging nucleosomes into a stable, oligomeric structure. Within these structures, individual PSC-chromatin contacts are dynamic. Stable association of PSC with chromatin, including through DNA replication, depends on PSC-PSC interactions. Our data suggest that labile individual PSC-chromatin contacts allow passage of the DNA replication machinery while PSC-PSC interactions prevent PSC from dissociating, allowing it to rebind to replicated chromatin. This mechanism may allow inheritance of chromatin proteins including PRC1 through DNA replication to maintain chromatin states.

  7. 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.

  8. 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...... problems as the other by a reformulation. This thesis argues that there is even a convergence on the practical level, and that a generalisation of the formalism of timed automata into lattice automata captures key aspects of both methods; indeed model checking timed automata can be formulated in terms...... of an abstract interpretation. For the generalisation to lattice automata to have benefit it is important that efficient tools exist. This thesis presents multi-core tools for efficient and scalable reachability and Büchi emptiness checking of timed/lattice automata. Finally, a number of case studies...

  9. Metabolically Coupled Replicator Systems: Overview of an RNA-world model concept of prebiotic evolution on mineral surfaces.

    Science.gov (United States)

    Czárán, Tamás; Könnyű, Balázs; Szathmáry, Eörs

    2015-09-21

    Metabolically Coupled Replicator Systems (MCRS) are a family of models implementing a simple, physico-chemically and ecologically feasible scenario for the first steps of chemical evolution towards life. Evolution in an abiotically produced RNA-population sets in as soon as any one of the RNA molecules become autocatalytic by engaging in template directed self-replication from activated monomers, and starts increasing exponentially. Competition for the finite external supply of monomers ignites selection favouring RNA molecules with catalytic activity helping self-replication by any possible means. One way of providing such autocatalytic help is to become a replicase ribozyme. An additional way is through increasing monomer supply by contributing to monomer synthesis from external resources, i.e., by evolving metabolic enzyme activity. Retroevolution may build up an increasingly autotrophic, cooperating community of metabolic ribozymes running an increasingly complicated and ever more efficient metabolism. Maintaining such a cooperating community of metabolic replicators raises two serious ecological problems: one is keeping the system coexistent in spite of the different replicabilities of the cooperating replicators; the other is constraining parasitism, i.e., keeping "cheaters" in check. Surface-bound MCRS provide an automatic solution to both problems: coexistence and parasite resistance are the consequences of assuming the local nature of metabolic interactions. In this review we present an overview of results published in previous articles, showing that these effects are, indeed, robust in different MCRS implementations, by considering different environmental setups and realistic chemical details in a few different models. We argue that the MCRS model framework naturally offers a suitable starting point for the future modelling of membrane evolution and extending the theory to cover the emergence of the first protocell in a self-consistent manner. The

  10. 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.

  11. 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.

  12. Information management in DNA replication modeled by directional, stochastic chains with memory

    Science.gov (United States)

    Arias-Gonzalez, J. Ricardo

    2016-11-01

    Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Stochastic chains are of special significance to molecular biology, where genes are conveyed by linear polymers made up of molecular subunits and transferred from DNA to proteins by specialized molecular motors in the presence of errors. Here, we demonstrate that when memory is introduced, the statistics of the chain depends on the mechanism by which objects or symbols are assembled, even in the slow dynamics limit wherein friction can be neglected. To analyze these systems, we introduce a sequence-dependent partition function, investigate its properties, and compare it to the standard normalization defined by the statistical physics of ensembles. We then apply this theory to characterize the enzyme-mediated information transfer involved in DNA replication under the real, non-equilibrium conditions, reproducing measured error rates and explaining the typical 100-fold increase in fidelity that is experimentally found when proofreading and edition take place. Our model further predicts that approximately 1 kT has to be consumed to elevate fidelity in one order of magnitude. We anticipate that our results are necessary to interpret configurational order and information management in many molecular systems within biophysics, materials science, communication, and engineering.

  13. Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations

    OpenAIRE

    Yu, Jin

    2015-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molec...

  14. 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

  15. Immunotherapeutics to prevent the replication of Brucella in a treatment failure mouse model.

    Science.gov (United States)

    Jain-Gupta, N; Contreras-Rodriguez, A; Smith, G P; Garg, V K; Witonsky, S G; Isloor, S; Vemulapalli, R; Boyle, S M; Sriranganathan, N

    2014-02-12

    Outer membrane vesicles (OMVs) from Brucella melitensis and irradiated Brucella neotomae have been shown to be effective vaccines against a B. melitensis challenge in a mouse model. The present study evaluates the efficacy of these two vaccines as immuno-therapeutics in combination with conventional antibiotics against a B. melitensis infection. BALB/c mice chronically infected with B. melitensis were treated for 4 weeks with doxycycline and gentamicin and vaccinated twice during the course of therapy. Antibiotics in sub-therapeutic concentrations were chosen in such a way that the treatment would result in a therapeutic failure in mice. Although no additive effect of vaccines and antibiotics was seen on the clearance of B. melitensis, mice receiving vaccines along with antibiotics exhibited no Brucella replication post-treatment compared to mice treated only with antibiotics. Administration of irradiated B. neotomae along with antibiotics led to higher production of IFN-γ ex vivo by splenocytes upon stimulation with heat inactivated B. melitensis while no such effect was seen by splenocytes from mice vaccinated with OMVs. OMV vaccinated mice developed significantly higher anti-Brucella IgG antibody titers at the end of the treatment compared to the mice that received only antibiotics. The mice that received only vaccines did not show any significant clearance of Brucella from spleens and livers compared to non-treated control mice. This study suggests that incorporating OMVs or irradiated B. neotomae along with conventional antibiotics might be able to improve therapeutic efficacy and control the progression of disease in treatment failure cases.

  16. In vitro model for lytic replication, latency, and transformation of an oncogenic alphaherpesvirus.

    Science.gov (United States)

    Schermuly, Julia; Greco, Annachiara; Härtle, Sonja; Osterrieder, Nikolaus; Kaufer, Benedikt B; Kaspers, Bernd

    2015-06-09

    Marek's disease virus (MDV) is an alphaherpesvirus that causes deadly T-cell lymphomas in chickens and serves as a natural small animal model for virus-induced tumor formation. In vivo, MDV lytically replicates in B cells that transfer the virus to T cells in which the virus establishes latency. MDV also malignantly transforms CD4+ T cells with a T(reg) signature, ultimately resulting in deadly lymphomas. No in vitro infection system for primary target cells of MDV has been available due to the short-lived nature of these cells in culture. Recently, we characterized cytokines and monoclonal antibodies that promote survival of cultured chicken B and T cells. We used these survival stimuli to establish a culture system that allows efficient infection of B and T cells with MDV. We were able to productively infect with MDV B cells isolated from spleen, bursa or blood cultured in the presence of soluble CD40L. Virus was readily transferred from infected B to T cells stimulated with an anti-TCRαVβ1 antibody, thus recapitulating the in vivo situation in the culture dish. Infected T cells could then be maintained in culture for at least 90 d in the absence of TCR stimulation, which allowed the establishment of MDV-transformed lymphoblastoid cell lines (LCL). The immortalized cells had a signature comparable to MDV-transformed CD4+ α/β T cells present in tumors. In summary, we have developed a novel in vitro system that precisely reflects the life cycle of an oncogenic herpesivrus in vivo and will allow us to investigate the interaction between virus and target cells in an easily accessible system.

  17. Informatics and Physics Models of Recognitions of DNA Replication and Their Biological Applications

    Directory of Open Access Journals (Sweden)

    Kang Cheng

    2006-01-01

    Full Text Available We initially propose concepts of Informative Intensity, Informative Response Intensity and Informative Flux, with different expressions. In a special expression of electrostatics, we describe Informative Intensity, Informative Response Intensity and Informative Flux in terms of electric field intensity, electric field force and electric field flux respectively. In a special expression of quantum mechanics, we originally propose a concept of Probability Flux. Then we present Informative Intensity in terms of a wave function of Schrödinger equation and Informative Response Intensity in terms of an interactive force between or among objects, Informative Flux in terms of a probability flux. Based on these concepts, we develop our Informatics and physics models of recognitions between a DNA polymerase and an initiation site and of pairing deoxyribonucleotides, for a natural DNA replication, beyond lengths of chemical bounds and half quantitatively explain a probability of the wrong paring. We originally hypothesize the information is, stored in structured charges or masses, transmitted with Informative Intensity in a media and recognized with an Informative Response Intensity by other structured charges or masses. We further generalize, Informative Intensity as multiple layers of fields, potentials or waves, Informative Response Intensity as multiple layers of forces and Informative Flux as an integration of Informative Intensity. We also initially define Transverse Information: Informative Intensity is perpendicular to the direction of information propagation, e.g. electromagnetic wave or magnetic field; and Longitudinal Information: Informative Intensity is parallel or antiparalell to the direction of information propagation, e.g. electric field or gravitational field.

  18. 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

  19. 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.

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

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Koblitz; Eriksson, Torbjörn Gerhard

    2005-01-01

    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...

  1. A primary care Web-based Intervention Modeling Experiment replicated behavior changes seen in earlier paper-based experiment

    OpenAIRE

    Treweek, S.; Francis, JJ; Bonetti, D; Barnett, K; Eccles, MP; Hudson, J.; Jones, C.; Pitts, NB; Ricketts, IW; Sullivan, F; Weal, M; MacLennan, G.

    2016-01-01

    OBJECTIVES: Intervention Modeling Experiments (IMEs) are a way of developing and testing behavior change interventions before a trial. We aimed to test this methodology in a Web-based IME that replicated the trial component of an earlier, paper-based IME. STUDY DESIGN AND SETTING: Three-arm, Web-based randomized evaluation of two interventions (persuasive communication and action plan) and a "no intervention" comparator. The interventions were designed to reduce the number of antibiotic p...

  2. Validation, replication, and sensitivity testing of Heckman-type selection models to adjust estimates of HIV prevalence.

    Directory of Open Access Journals (Sweden)

    Samuel J Clark

    Full Text Available A recent study using Heckman-type selection models to adjust for non-response in the Zambia 2007 Demographic and Health Survey (DHS found a large correction in HIV prevalence for males. We aim to validate this finding, replicate the adjustment approach in other DHSs, apply the adjustment approach in an external empirical context, and assess the robustness of the technique to different adjustment approaches. We used 6 DHSs, and an HIV prevalence study from rural South Africa to validate and replicate the adjustment approach. We also developed an alternative, systematic model of selection processes and applied it to all surveys. We decomposed corrections from both approaches into rate change and age-structure change components. We are able to reproduce the adjustment approach for the 2007 Zambia DHS and derive results comparable with the original findings. We are able to replicate applying the approach in several other DHSs. The approach also yields reasonable adjustments for a survey in rural South Africa. The technique is relatively robust to how the adjustment approach is specified. The Heckman selection model is a useful tool for assessing the possibility and extent of selection bias in HIV prevalence estimates from sample surveys.

  3. Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.

    Directory of Open Access Journals (Sweden)

    István Zachar

    Full Text Available The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.

  4. Wave equation modelling using Julia programming language

    Science.gov (United States)

    Kim, Ahreum; Ryu, Donghyun; Ha, Wansoo

    2016-04-01

    Julia is a young high-performance dynamic programming language for scientific computations. It provides an extensive mathematical function library, a clean syntax and its own parallel execution model. We developed 2d wave equation modeling programs using Julia and C programming languages and compared their performance. We used the same modeling algorithm for the two modeling programs. We used Julia version 0.3.9 in this comparison. We declared data type of function arguments and used inbounds macro in the Julia program. Numerical results showed that the C programs compiled with Intel and GNU compilers were faster than Julia program, about 18% and 7%, respectively. Taking the simplicity of dynamic programming language into consideration, Julia can be a novel alternative of existing statically typed programming languages.

  5. High School Graduation Effects of a Verbal Interaction Program for At-Risk Toddlers: A Study of Long-Term Outcomes in a Replication of the Mother-Child Home Program.

    Science.gov (United States)

    Levenstein, Phyllis

    High school outcomes were assessed for 123 young adults, originally toddlers in the home-based, low-intensity Mother-Child Home Program (MCHP) and at risk for dropping out of high school because of their parents' low income and education. Participants were recruited for the Pittsfield, MA, replication of the MCHP and randomly selected into program…

  6. Synthetic models of distributed memory parallel programs

    Energy Technology Data Exchange (ETDEWEB)

    Poplawski, D.A. (Michigan Technological Univ., Houghton, MI (USA). Dept. of Computer Science)

    1990-09-01

    This paper deals with the construction and use of simple synthetic programs that model the behavior of more complex, real parallel programs. Synthetic programs can be used in many ways: to construct an easily ported suite of benchmark programs, to experiment with alternate parallel implementations of a program without actually writing them, and to predict the behavior and performance of an algorithm on a new or hypothetical machine. Synthetic programs are constructed easily from scratch, from existing programs, and can even be constructed using nothing but information obtained from traces of the real program's execution.

  7. 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...

  8. Cluster-cluster aggregation with particle replication and chemotaxy: a simple model for the growth of animal cells in culture

    Science.gov (United States)

    Alves, S. G.; Martins, M. L.

    2010-09-01

    Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and in vitro drug testing. In the present paper, a cluster-cluster aggregation model with stochastic particle replication and chemotactically driven motility is investigated as a model for the growth of animal cells in culture. The focus is on the scaling laws governing the aggregation kinetics. Our simulations reveal that in the absence of chemotaxy the mean cluster size and the total number of clusters scale in time as stretched exponentials dependent on the particle replication rate. Also, the dynamical cluster size distribution functions are represented by a scaling relation in which the scaling function involves a stretched exponential of the time. The introduction of chemoattraction among the particles leads to distribution functions decaying as power laws with exponents that decrease in time. The fractal dimensions and size distributions of the simulated clusters are qualitatively discussed in terms of those determined experimentally for several normal and tumoral cell lines growing in culture. It is shown that particle replication and chemotaxy account for the simplest cluster size distributions of cellular aggregates observed in culture.

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

    Science.gov (United States)

    Goldar, A.; Arneodo, A.; Audit, B.; Argoul, F.; Rappailles, A.; Guilbaud, G.; Petryk, N.; Kahli, M.; Hyrien, O.

    2016-03-01

    We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in eukaryote cell populations. By picturing replication initiation as a two-state system and considering all possible transition configurations, 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 with corresponding experimental data from both S. cerevisiae and human cells and provides a quantitative estimate of initiation site redundancy. This study shows that, to a large extent, the program that regulates the dynamics of eukaryotic DNA replication is a collective phenomenon that emerges from the stochastic nature of replication origins initiation.

  10. [Replication of the subgenomic hepatitis C virus replicon in the presence of the NS3 protease inhibitors: a stochastic model].

    Science.gov (United States)

    Ivanisenko, N V; Mishchenko, E L; Akberdin, I R; Demenkov, P S; Likhoshvai, V A; Kozlov, K N; Todorov, D I; Samsonova, M G; Samsonov, A M; Kolchanov, N A; Ivanisenko, V A

    2013-01-01

    The hepatitis C virus (HCV) belongs to Flaviviridae family and causes hazardous liver diseases leading frequently to cirrhosis and hepatocellular carcinoma. HCV is able to rapidly acquire drug resistance and for this reason there is currently no effective anti-HCV therapy in spite of appearance of new potential drugs. Mathematical models are relevant to predict the efficacy of potential drugs against virus or host targets. One of the promising targets for development of new drugs is the viral NS3 protease. Here we developed a stochastic model of the subgenomic HCV replicon replication in Huh-7 cells and in the presence of the NS3 protease inhibitors. Along with consideration of the stochastic nature of the subgenomic HCV replicon replication the model takes into account the existence and generation of main NS3 protease drug resistant mutants, namely BILN-2061 (A156T, D168V, R155Q), VX-950 (A156S, A156T, T54A) and SCH-503034 (A156T, A156S, T54A). The model reproduces well the viral RNA kinetics in the cell from the moment of the subgenomic HCV replicon transfection to steady state, as well as the viral RNA suppression kinetics in the presence of NS3 protease inhibitors BILN-2061, VX-950 and SCH-503034. We showed that the resistant mutants should be taken into account for the correct description of biphasic kinetics of the viral RNA suppression. The mutants selected in the presence of different inhibitor concentrations have maximal replication capacity in the given inhibitor concentration range. Our model can be used to interpret the results of the new anti-HCV drug testing in replicon systems, as well as to predict the efficacy of new potential drugs and optimize the regimen of their use.

  11. 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

  12. 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

  13. 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

  14. 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 synta

  15. 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 programming aptitude to cleanly separate programming sheep from non-programming goats. We briefly present their theory and test instrument. We have repeated their test in our local context in order to verify and perhaps generalise their findings, but we could not show that the test predicts students' success...... in our introductory program-ming course. Based on this failure of the test instrument, we discuss various explanations for our differing results and suggest a research method from which it may be possible to generalise local results in this area. Furthermore, we discuss and criticize Dehnadi and Bornat...

  16. Differential program evaluation model in child protection.

    Science.gov (United States)

    Lalayants, Marina

    2012-01-01

    Increasingly attention has been focused to the degree to which social programs have effectively and efficiently delivered services. Using the differential program evaluation model by Tripodi, Fellin, and Epstein (1978) and by Bielawski and Epstein (1984), this paper described the application of this model to evaluating a multidisciplinary clinical consultation practice in child protection. This paper discussed the uses of the model by demonstrating them through the four stages of program initiation, contact, implementation, and stabilization. This organizational case study made a contribution to the model by introducing essential and interrelated elements of a "practical evaluation" methodology in evaluating social programs, such as a participatory evaluation approach; learning, empowerment and sustainability; and a flexible individualized approach to evaluation. The study results demonstrated that by applying the program development model, child-protective administrators and practitioners were able to evaluate the existing practices and recognize areas for program improvement.

  17. 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.

  18. Mathematical Programming Models in Educational Planning.

    Science.gov (United States)

    McNamara, James F.

    This document begins by defining and discussing educational planning. A brief overview of mathematical programing with an explanation of the general linear programing model is then provided. Some recent applications of mathematical programing techniques to educational planning problems are reviewed, and their implications for educational research…

  19. A Parallel Programming Model With Sequential Semantics

    Science.gov (United States)

    1996-01-01

    Parallel programming is more difficult than sequential programming in part because of the complexity of reasoning, testing, and debugging in the...context of concurrency. In the thesis, we present and investigate a parallel programming model that provides direct control of parallelism in a notation

  20. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  1. 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

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

    Science.gov (United States)

    Guilbaud, Guillaume; Rappailles, Aurélien; Baker, Antoine; Chen, Chun-Long; Arneodo, Alain; Goldar, Arach; d'Aubenton-Carafa, Yves; Thermes, Claude; Audit, Benjamin; Hyrien, Olivier

    2011-12-01

    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 provide a general

  3. 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.

  4. A Model for Slicing JAVA Programs Hierarchically

    Institute of Scientific and Technical Information of China (English)

    Bi-Xin Li; Xiao-Cong Fan; Jun Pang; Jian-Jun Zhao

    2004-01-01

    Program slicing can be effectively used to debug, test, analyze, understand and maintain objectoriented software. In this paper, a new slicing model is proposed to slice Java programs based on their inherent hierarchical feature. The main idea of hierarchical slicing is to slice programs in a stepwise way, from package level, to class level, method level, and finally up to statement level. The stepwise slicing algorithm and the related graph reachability algorithms are presented, the architecture of the Java program Analyzing Tool (JATO) based on hierarchical slicing model is provided, the applications and a small case study are also discussed.

  5. 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

    We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in eukaryote cell populations. By picturing replication initiation as a two-state system and considering all possible transition configurations......, 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...... with corresponding experimental data from both S. cerevisiae and human cells and provides a quantitative estimate of initiation site redundancy. This study shows that, to a large extent, the program that regulates the dynamics of eukaryotic DNA replication is a collective phenomenon that emerges from the stochastic...

  6. Geometric Modeling Application Interface Program

    Science.gov (United States)

    1990-11-01

    Manual IDEF-Extended ( IDEFIX ) Integrated Information Support System (IISS), ICAM Project 6201, Contract F33615-80-C-5155, December 1985. Interim...Differential Geometry of Curves and Surfaces, M. P. de Carmo, Prentice-Hall, Inc., 1976. IDEFIX Readers Reference, D. Appleton Company, December 1985...Modeling. IDEFI -- IDEF Information Modeling. IDEFIX -- IDEF Extended Information Modeling. IDEF2 -- IDEF Dynamics Modeling. IDSS -- Integrated Decision

  7. 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

  8. A primary care Web-based Intervention Modeling Experiment replicated behavior changes seen in earlier paper-based experiment.

    Science.gov (United States)

    Treweek, Shaun; Francis, Jill J; Bonetti, Debbie; Barnett, Karen; Eccles, Martin P; Hudson, Jemma; Jones, Claire; Pitts, Nigel B; Ricketts, Ian W; Sullivan, Frank; Weal, Mark; MacLennan, Graeme

    2016-12-01

    Intervention Modeling Experiments (IMEs) are a way of developing and testing behavior change interventions before a trial. We aimed to test this methodology in a Web-based IME that replicated the trial component of an earlier, paper-based IME. Three-arm, Web-based randomized evaluation of two interventions (persuasive communication and action plan) and a "no intervention" comparator. The interventions were designed to reduce the number of antibiotic prescriptions in the management of uncomplicated upper respiratory tract infection. General practitioners (GPs) were invited to complete an online questionnaire and eight clinical scenarios where an antibiotic might be considered. One hundred twenty-nine GPs completed the questionnaire. GPs receiving the persuasive communication did not prescribe an antibiotic in 0.70 more scenarios (95% confidence interval [CI] = 0.17-1.24) than those in the control arm. For the action plan, GPs did not prescribe an antibiotic in 0.63 (95% CI = 0.11-1.15) more scenarios than those in the control arm. Unlike the earlier IME, behavioral intention was unaffected by the interventions; this may be due to a smaller sample size than intended. A Web-based IME largely replicated the findings of an earlier paper-based study, providing some grounds for confidence in the IME methodology. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Proposal of Enhanced Extreme Programming Model

    Directory of Open Access Journals (Sweden)

    M. Rizwan Jameel Qureshi

    2015-01-01

    Full Text Available Extreme programming is one of the commonly used agile methodologies in software development. It is very responsive to changing requirements even in the late phases of the project. However, quality activities in extreme programming phases are implemented sequentially along with the activities that work on the functional requirements. This reduces the agility to deliver increments continuously and makes an inverse relationship between quality and agility. Due to this relationship, extreme programming does not consume enough time on making extensive documentation and robust design. To overcome these issues, an enhanced extreme programming model is proposed. Enhanced extreme programming introduces parallelism in the activities' execution through putting quality activities into a separate execution line. In this way, the focus on delivering increments quickly is achieved without affecting the quality of the final output. In enhanced extreme programming, the quality concept is extended to include refinement of all phases of classical extreme programming and creating architectural design based on the refined design documents.

  10. Integer Programming Models for Computational Biology Problems

    Institute of Scientific and Technical Information of China (English)

    Giuseppe Lancia

    2004-01-01

    The recent years have seen an impressive increase in the use of Integer Programming models for the solution of optimization problems originating in Molecular Biology. In this survey, some of the most successful Integer Programming approaches are described, while a broad overview of application areas being is given in modern Computational Molecular Biology.

  11. 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

  12. Universal Sequence Replication, Reversible Polymerization and Early Functional Biopolymers: A Model for the Initiation of Prebiotic Sequence Evolution

    Science.gov (United States)

    Walker, Sara Imari; Grover, Martha A.; Hud, Nicholas V.

    2012-01-01

    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 regularly varying monomer

  13. 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.

  14. Data-Generating Program for ASKA Modeling

    Science.gov (United States)

    Karimi-Dechesh, A.; Cheng, T. K.

    1985-01-01

    Carrier plate assemblies of NASA Space Shuttle thermal protection system provided for easy access to protected vital parts of Shuttle. Each assembly mounted on substructure with fasteners through holes in protective tiles. Automatic System of Kinematic Analysis (ASKA) finite-element program evaluates these assemblies. PLATEFORT computer program developed as data generator for ASKA modeling. PLATEFORT greatly reduces amount of time and data required for building ASKA model of these assemblies.

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

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Koblitz; Eriksson, Torbjörn Gerhard

    2005-01-01

    The forming of micro surface structures on polymer materials is well established in polymer-processing operations. Numerical flow calculations were performed using the Lagrangian Integral Method where the fluid was described by a MSF constitutive model. The numerical modelling of the flow was per...

  16. Comparison of Data-Collection Methods in a Behavioral Intervention Program for Children with Pervasive Developmental Disorders: A Replication

    Science.gov (United States)

    Najdowski, Adel C.; Chilingaryan, Vardui; Bergstrom, Ryan; Granpeesheh, Doreen; Balasanyan, Susie; Aguilar, Barbara; Tarbox, Jonathan

    2009-01-01

    Cummings and Carr (2009) compared two methods of data collection in a behavioral intervention program for children with pervasive developmental disorders: collecting data on all trials versus only the first trial in a session. Results showed that basing a child's progress on first-trial data resulted in identifying mastery-level responding…

  17. Replication-Independent Histone Variant H3.3 Controls Animal Lifespan through the Regulation of Pro-longevity Transcriptional Programs

    Directory of Open Access Journals (Sweden)

    Antonia Piazzesi

    2016-10-01

    Full Text Available Chromatin structure orchestrates the accessibility to the genetic material. Replication-independent histone variants control transcriptional plasticity in postmitotic cells. The life-long accumulation of these histones has been described, yet the implications on organismal aging remain elusive. Here, we study the importance of the histone variant H3.3 in Caenorhabditis elegans longevity pathways. We show that H3.3-deficient nematodes have negligible lifespan differences compared to wild-type animals. However, H3.3 is essential for the lifespan extension of C. elegans mutants in which pronounced transcriptional changes control longevity programs. Notably, H3.3 loss critically affects the expression of a very large number of genes in long-lived nematodes, resulting in transcriptional profiles similar to wild-type animals. We conclude that H3.3 positively contributes to diverse lifespan-extending signaling pathways, with potential implications on age-related processes in multicellular organisms.

  18. Parser for Sabin-to-Mahoney Transition Model of Quasispecies Replication

    Energy Technology Data Exchange (ETDEWEB)

    2016-01-03

    This code is a data parse for preparing output from the Qspp agent-based stochastic simulation model for plotting in Excel. This code is specific to a set of simulations that were run for the purpose of preparing data for a publication. It is necessary to make this code open-source in order to publish the model code (Qspp), which has already been released. There is a necessity of assuring that results from using Qspp for a publication

  19. 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.

  20. Anthropometric dependence of the response of a thorax FE model under high speed loading: validation and real world accident replication.

    Science.gov (United States)

    Roth, Sébastien; Torres, Fabien; Feuerstein, Philippe; Thoral-Pierre, Karine

    2013-05-01

    Finite element analysis is frequently used in several fields such as automotive simulations or biomechanics. It helps researchers and engineers to understand the mechanical behaviour of complex structures. The development of computer science brought the possibility to develop realistic computational models which can behave like physical ones, avoiding the difficulties and costs of experimental tests. In the framework of biomechanics, lots of FE models have been developed in the last few decades, enabling the investigation of the behaviour of the human body submitted to heavy damage such as in road traffic accidents or in ballistic impact. In both cases, the thorax/abdomen/pelvis system is frequently injured. The understanding of the behaviour of this complex system is of extreme importance. In order to explore the dynamic response of this system to impact loading, a finite element model of the human thorax/abdomen/pelvis system has, therefore, been developed including the main organs: heart, lungs, kidneys, liver, spleen, the skeleton (with vertebrae, intervertebral discs, ribs), stomach, intestines, muscles, and skin. The FE model is based on a 3D reconstruction, which has been made from medical records of anonymous patients, who have had medical scans with no relation to the present study. Several scans have been analyzed, and specific attention has been paid to the anthropometry of the reconstructed model, which can be considered as a 50th percentile male model. The biometric parameters and laws have been implemented in the dynamic FE code (Radioss, Altair Hyperworks 11©) used for dynamic simulations. Then the 50th percentile model was validated against experimental data available in the literature, in terms of deflection, force, whose curve must be in experimental corridors. However, for other anthropometries (small male or large male models) question about the validation and results of numerical accident replications can be raised.

  1. Learning from Television and Books: A Dutch Replication Study Based on Salomon's Model.

    Science.gov (United States)

    Beentjes, Johannes W. J.

    1989-01-01

    Discussion of the amount of mental effort children invest in television viewing versus book reading focuses on a Dutch study based on Salomon's model and his studies with children in Israel and the United States. The depth of information processed is discussed, and differences in results are examined. (18 references) (LRW)

  2. Economic Pressure in African American Families: A Replication and Extension of the Family Stress Model.

    Science.gov (United States)

    Conger, Rand D.; Wallace, Lora Ebert; Sun, Yumei; Simons, Ronald L.; McLoyd, Vonnie C.; Brody, Gene H.

    2002-01-01

    Evaluated applicability of family stress model of economic hardship for understanding economic influences on child development among African American families with a 10- or 11-year-old child. Found that economic hardship positively related to economic pressure in families, and to emotional distress of caregivers, which in turn damaged the…

  3. A multilingual programming model for coupled systems.

    Energy Technology Data Exchange (ETDEWEB)

    Ong, E. T.; Larson, J. W.; Norris, B.; Tobis, M.; Steder, M.; Jacob, R. L.; Mathematics and Computer Science; Univ. of Wisconsin; Univ. of Chicago; The Australian National Univ.

    2008-01-01

    Multiphysics and multiscale simulation systems share a common software requirement-infrastructure to implement data exchanges between their constituent parts-often called the coupling problem. On distributed-memory parallel platforms, the coupling problem is complicated by the need to describe, transfer, and transform distributed data, known as the parallel coupling problem. Parallel coupling is emerging as a new grand challenge in computational science as scientists attempt to build multiscale and multiphysics systems on parallel platforms. An additional coupling problem in these systems is language interoperability between their constituent codes. We have created a multilingual parallel coupling programming model based on a successful open-source parallel coupling library, the Model Coupling Toolkit (MCT). This programming model's capabilities reach beyond MCT's native Fortran implementation to include bindings for the C++ and Python programming languages. We describe the method used to generate the interlanguage bindings. This approach enables an object-based programming model for implementing parallel couplings in non-Fortran coupled systems and in systems with language heterogeneity. We describe the C++ and Python versions of the MCT programming model and provide short examples. We report preliminary performance results for the MCT interpolation benchmark. We describe a major Python application that uses the MCT Python bindings, a Python implementation of the control and coupling infrastructure for the community climate system model. We conclude with a discussion of the significance of this work to productivity computing in multidisciplinary computational science.

  4. Replicating the Ice-Volume Signal of the Early Pleistocene with a Complex Earth System Model

    Science.gov (United States)

    Tabor, C. R.; Poulsen, C. J.; Pollard, D.

    2013-12-01

    Milankovitch theory proposes high-latitude summer insolation intensity paces the ice ages by controlling perennial snow cover amounts (Milankovitch, 1941). According to theory, the ~21 kyr cycle of precession should dominate the ice-volume records since it has the greatest influence on high-latitude summer insolation. Modeling experiments frequently support Milankovitch theory by attributing the majority of Northern Hemisphere high-latitude summer snowmelt to changes in the cycle of precession (e.g. Jackson and Broccoli, 2003). However, ice-volume proxy records, especially those of the Early Pleistocene (2.6-0.8 Ma), display variability with a period of ~41 kyr (Raymo and Lisiecki, 2005), indicative of insolation forcing from obliquity, which has a much smaller influence on summer insolation intensity than precession. Several hypotheses attempt to explain the discrepancies between Milkankovitch theory and the proxy records by invoking phenomena such as insolation gradients (Raymo and Nisancioglu, 2003), hemispheric offset (Raymo et al., 2006; Lee and Poulsen, 2009), and integrated summer energy (Huybers, 2006); however, all of these hypotheses contain caveats (Ruddiman, 2006) and have yet to be supported by modeling studies that use a complex GCM. To explore potential solutions to this '41 kyr problem,' we use an Earth system model composed of the GENESIS GCM and Land Surface model, the BIOME4 vegetation model, and the Pennsylvania State ice-sheet model. Using an asynchronous coupling technique, we run four idealized transient combinations of obliquity and precession, representing the orbital extremes of the Pleistocene (Berger and Loutre, 1991). Each experiment is run through several complete orbital cycles with a dynamic ice domain spanning North America and Greenland, and fixed preindustrial greenhouse-gas concentrations. For all orbital configurations, model results produce greater ice-volume spectral power at the frequency of obliquity despite significantly

  5. Econometric Model Evaluation: Implications for Program Evaluation.

    Science.gov (United States)

    Ridge, Richard S.; And Others

    1990-01-01

    The problem associated with evaluating an econometric model using values outside those used in the model estimation is illustrated in the evaluations of a residential load management program during each of two successive years. Analysis reveals that attention must be paid to this problem. (Author/TJH)

  6. Programming Models for Heterogeneous Multicore Systems

    Science.gov (United States)

    2011-08-08

    Badia, F.D. Igual, J. Labarta, R. Mayo and E.S. Quintana- Orti . “An extension of the StarSs Programming Model for Platforms with Multiple GPUs...R. Mayo, J.M. Perez, J. Planas, E.S. Quintana- Orti . “A Proposal to Extend the OpenMP Tasking Model for Heterogeneous Architectures ” LNCS Vol. 5568

  7. Validation of the Cyberchondria Severity Scale (CSS): replication and extension with bifactor modeling.

    Science.gov (United States)

    Norr, Aaron M; Allan, Nicholas P; Boffa, Joseph W; Raines, Amanda M; Schmidt, Norman B

    2015-04-01

    Internet help seeking behaviors are increasingly common. Despite the positives associated with technology, cyberchondria, or the process of increased anxiety in response to internet medical information seeking, is on the rise. The Cyberchondria Severity Scale (CSS) was recently developed to provide a valid measure of cyberchondria across multiple dimensions. The current study sought to extend previous work on the CSS factor structure by examining a bifactor model. Participants (N=526) from a community sample completed the CSS via online crowd sourcing. Results revealed that the bifactor model of the CSS provided superior fit to the data, suggesting that it is useful to conceptualize the CSS as containing a General Cyberchondria factor that is orthogonal to its subfactors. Similar to previous work, the CSS Mistrust factor does not appear to be necessary to this construct. Finally, results revealed unique relations between General and Specific Cyberchondria factors with lower-order health anxiety dimensions. Copyright © 2015. Published by Elsevier Ltd.

  8. Investigations for modelling hardness of biomedical implant during replication of FDM-based patterns by vacuum moulding

    Indian Academy of Sciences (India)

    RUPINDER SINGH; GURINDER SINGH

    2017-03-01

    In the present work, effort has been made for modelling the microhardness of biomedical implant prepared by combining fused deposition modelling, vacuum moulding and stir casting (SC) process. A dynamic condylar screw (DCS) plate was selected as a real ‘3D’ biomedical implant for this case study. The DCS plate,made of acrylonitrile butadiene styrene material, was fabricated as a master pattern by fused deposition modelling. After preparation of the master pattern, the mould cavity was fabricated by the vacuum moulding process.Finally a metal–matrix composite of Al and Al2O3 prepared by SC process has been poured in the vacuum mould for fabrication of DCS plate. This study outlines the replication procedure of DCS plate in detail from the master pattern to final product. The contribution of the paper is towards finding out the effect and optimumvalues of three different process parameters (namely: percentage composition of Al and Al2O3, vacuum pressure and grain size of silica) towards microhardness of the DCS plate manufactured by the combined process.

  9. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

    "Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

  10. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Science.gov (United States)

    Raj, Anil; Shim, Heejung; Gilad, Yoav; Pritchard, Jonathan K; Stephens, Matthew

    2015-01-01

    Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  11. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Directory of Open Access Journals (Sweden)

    Anil Raj

    Full Text Available Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  12. Program Partitioning using Dynamic Trust Models

    DEFF Research Database (Denmark)

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

    2006-01-01

    -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...

  13. Retention models for programmed gas chromatography.

    Science.gov (United States)

    Castello, G; Moretti, P; Vezzani, S

    2009-03-06

    The models proposed by many authors for the prediction of retention times and temperatures, peak widths, retention indices and separation numbers in programmed temperature and pressure gas chromatography by starting from preliminary measurements of the retention in isothermal and isobaric conditions are reviewed. Several articles showing the correlation between retention data and thermodynamic parameters and the determination of the optimum programming rate are reported. The columns of different polarity used for the experimental measurement and the main equations, mathematical models and calculation procedures are listed. An empirical approach was used in the early models, followed by the application of thermodynamic considerations, iterative calculation procedures and statistical methods, based on increased computing power now available. Multiple column arrangements, simultaneous temperature and pressure programming, applications of two-dimensional and fast chromatography are summarised.

  14. Model Checking with Probabilistic Tabled Logic Programming

    CERN Document Server

    Gorlin, Andrey; Smolka, Scott A

    2012-01-01

    We present a formulation of the problem of probabilistic model checking as one of query evaluation over probabilistic logic programs. To the best of our knowledge, our formulation is the first of its kind, and it covers a rich class of probabilistic models and probabilistic temporal logics. The inference algorithms of existing probabilistic logic-programming systems are well defined only for queries with a finite number of explanations. This restriction prohibits the encoding of probabilistic model checkers, where explanations correspond to executions of the system being model checked. To overcome this restriction, we propose a more general inference algorithm that uses finite generative structures (similar to automata) to represent families of explanations. The inference algorithm computes the probability of a possibly infinite set of explanations directly from the finite generative structure. We have implemented our inference algorithm in XSB Prolog, and use this implementation to encode probabilistic model...

  15. 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.

  16. LHCb experience with LFC replication

    CERN Document Server

    Carbone, Angelo; Dafonte Perez, Eva; D'Apice, Antimo; dell'Agnello, Luca; Duellmann, Dirk; Girone, Maria; Lo Re, Giuseppe; Martelli, Barbara; Peco, Gianluca; Ricci, Pier Paolo; Sapunenko, Vladimir; Vagnoni, Vincenzo; Vitlacil, Dejan

    2007-01-01

    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. 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 Informations (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.

  17. Chlamydia pneumoniae replicates in Kupffer cells in mouse model of liver infection

    Institute of Scientific and Technical Information of China (English)

    Antonella Marangoni; Manuela Donati; Francesca Cavrini; Rita Aldini; Silvia Accardo; Vittorio Sambri; Marco Montagnani; Roberto Cevenini

    2006-01-01

    AIM: To develop an animal model of liver infection with Chlamydia pneumoniae (C.pneumoniae) in intraperitoneally infected mice for studying the presence of chlamydiae in Kupffer cells and hepatocytes.METHODS: A total of 80 BALB/c mice were inoculated intraperitoneally with C. pneumoniae and sacrificed at various time points after infection. Chlamydiae were looked for in liver homogenates as well as in Kupffer cells and hepatocytes separated by liver perfusion with collagenase. C. pneumoniae was detected by both isolation in LLC-MK2 cells and fluorescence in situ hybridization (FISH). The releasing of TNFA-α by C. pneumoniae in vitro stimulated Kupffer cells was studied by enzymelinked immunosorbent assay.RESULTS: C. pneumoniae isolation from liver homogenates reached a plateau on d 7 after infection when 6 of 10 animals were positive, then decreased, and became negative by d 20. C. pneumoniae isolation from separated Kupffer cells reached a plateau on d 7 when 5 of 10 animals were positive, and became negative by d 20.The detection of C. pneumoniae in separated Kupffer cells by FISH, confirmed the results obtained by culture.Isolated hepatocytes were always negative. Stimulation of Kupffer cells by alive C. pneumoniae elicited high TNF-α levels.CONCLUSION: A productive infection by C. pneumoniae may take place in Kupffer cells and C. pneumoniae induces a local pro-inflammatory activity. C. pneumoniae is therefore, able to act as antigenic stimulus when localized in the liver. One could speculate that C. pneumoniae infection, involving cells of the innate immunity such as Kupffer cells, could also trigger pathological immune reactions involving the liver, as observed in human patients with primary biliary cirrhosis.

  18. 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

  19. Sex differences in developmental programming models.

    Science.gov (United States)

    Aiken, Catherine E; Ozanne, Susan E

    2013-01-01

    The theory of developmental programming suggests that diseases such as the metabolic syndrome may be 'programmed' by exposure to adverse stimuli during early development. The developmental programming literature encompasses the study of a wide range of suboptimal intrauterine environments in a variety of species and correlates these with diverse phenotypic outcomes in the offspring. At a molecular level, a large number of variables have been measured and suggested as the basis of the programmed phenotype. The range of both dependent and independent variables studied often makes the developmental programming literature complex to interpret and the drawing of definitive conclusions difficult. A common, though under-explored, theme of many developmental programming models is a sex difference in offspring outcomes. This holds true across a range of interventions, including dietary, hypoxic, and surgical models. The molecular and phenotypic outcomes of adverse in utero conditions are often more prominent in male than female offspring, although there is little consideration given to the basis for this observation in most studies. We review the evidence that maternal energy investment in male and female conceptuses may not be equal and may be environment dependent. It is suggested that male and female development could be viewed as separate processes from the time of conception, with differences in both timing and outcomes.

  20. STEW A Nonlinear Data Modeling Computer Program

    CERN Document Server

    Chen, H

    2000-01-01

    A nonlinear data modeling computer program, STEW, employing the Levenberg-Marquardt algorithm, has been developed to model the experimental sup 2 sup 3 sup 9 Pu(n,f) and sup 2 sup 3 sup 5 U(n,f) cross sections. This report presents results of the modeling of the sup 2 sup 3 sup 9 Pu(n,f) and sup 2 sup 3 sup 5 U(n,f) cross-section data. The calculation of the fission transmission coefficient is based on the double-humped-fission-barrier model of Bjornholm and Lynn. Incident neutron energies of up to 5 MeV are considered.

  1. STEW: A Nonlinear Data Modeling Computer Program

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H.

    2000-03-04

    A nonlinear data modeling computer program, STEW, employing the Levenberg-Marquardt algorithm, has been developed to model the experimental {sup 239}Pu(n,f) and {sup 235}U(n,f) cross sections. This report presents results of the modeling of the {sup 239}Pu(n,f) and {sup 235}U(n,f) cross-section data. The calculation of the fission transmission coefficient is based on the double-humped-fission-barrier model of Bjornholm and Lynn. Incident neutron energies of up to 5 MeV are considered.

  2. 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.

  3. Novel inhibitors of neurotropic alphavirus replication that improve host survival in a mouse model of acute viral encephalitis.

    Science.gov (United States)

    Sindac, Janice A; Yestrepsky, Bryan D; Barraza, Scott J; Bolduc, Kyle L; Blakely, Pennelope K; Keep, Richard F; Irani, David N; Miller, David J; Larsen, Scott D

    2012-04-12

    Arboviral encephalitis is a potentially devastating human disease with no approved therapies that target virus replication. We previously discovered a novel class of thieno[3,2-b]pyrrole-based inhibitors active against neurotropic alphaviruses such as western equine encephalitis virus (WEEV) in cultured cells. In this report, we describe initial development of these novel antiviral compounds, including bioisosteric replacement of the 4H-thieno[3,2-b]pyrrole core with indole to improve metabolic stability and the introduction of chirality to assess target enantioselectivity. Selected modifications enhanced antiviral activity while maintaining low cytotoxicity, increased stability to microsomal metabolism, and also revealed striking enantiospecific activity in cultured cells. Furthermore, we demonstrate improved outcomes (both symptoms and survival) following treatment with indole analogue 9h (CCG-203926) in an in vivo mouse model of alphaviral encephalitis that closely correlate with the enantiospecific in vitro antiviral activity. These results represent a substantial advancement in the early preclinical development of a promising class of novel antiviral drugs against virulent neurotropic alphaviruses.

  4. The viral polymerase inhibitor 2'-C-methylcytidine inhibits Norwalk virus replication and protects against norovirus-induced diarrhea and mortality in a mouse model.

    Science.gov (United States)

    Rocha-Pereira, Joana; Jochmans, Dirk; Debing, Yannick; Verbeken, Erik; Nascimento, Maria S J; Neyts, Johan

    2013-11-01

    Human noroviruses are a major cause of food-borne illness, accountable for 50% of all-etiologies outbreaks of acute gastroenteritis (in both developing and developed countries). There is no vaccine or antiviral drug for the prophylaxis or treatment of norovirus-induced gastroenteritis. We recently reported the inhibitory effect of 2'-C-methylcytidine (2CMC), a hepatitis C virus polymerase inhibitor, on the in vitro replication of murine norovirus (MNV). Here we evaluated the inhibitory effect of 2CMC on in vitro human norovirus replication through a Norwalk virus replicon model and in a mouse model by using AG129 mice orally infected with MNV. Survival, weight, and fecal consistency were monitored, and viral loads in stool samples and organs were quantified. Intestines were examined histologically. 2CMC reduced Norwalk virus replicon replication in a dose-dependent manner and was able to clear cells of the replicon. Treatment of MNV-infected AG129 mice with 2CMC (i) prevented norovirus-induced diarrhea; (ii) markedly delayed the appearance of viral RNA and reduced viral RNA titers in the intestine, mesenteric lymph nodes, spleen, lungs, and stool; (iii) completely prevented virus-induced mortality; and (iv) resulted in protective immunity against a rechallenge. We demonstrate for the first time that a small-molecule inhibitor of norovirus replication protects from virus-induced disease and mortality in a relevant animal model. These findings pave the way for the development of potent and safe antivirals as prophylaxis and therapy of norovirus infection.

  5. 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."

  6. A Linguistic Model in Component Oriented Programming

    Science.gov (United States)

    Crăciunean, Daniel Cristian; Crăciunean, Vasile

    2016-12-01

    It is a fact that the component-oriented programming, well organized, can bring a large increase in efficiency in the development of large software systems. This paper proposes a model for building software systems by assembling components that can operate independently of each other. The model is based on a computing environment that runs parallel and distributed applications. This paper introduces concepts as: abstract aggregation scheme and aggregation application. Basically, an aggregation application is an application that is obtained by combining corresponding components. In our model an aggregation application is a word in a language.

  7. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

  8. Keratinocytes derived from chicken embryonic stem cells support Marek's disease virus infection: a highly differentiated cell model to study viral replication and morphogenesis.

    Science.gov (United States)

    Couteaudier, Mathilde; Courvoisier, Katia; Trapp-Fragnet, Laetitia; Denesvre, Caroline; Vautherot, Jean-François

    2016-01-07

    Marek's disease is a virus disease with worldwide distribution that causes major losses to poultry production. Vaccines against Marek's disease virus, an oncogenic alphaherpesvirus, reduce tumour formation but have no effect on virus shedding. Successful horizontal virus transmission is linked to the active viral replication in feather follicle epithelial cells of infected chickens, from which infectious viral particles are shed into the environment. The feather follicle epithelium is the sole tissue in which those infectious particles are produced and no in vitro cell-systems can support this highly efficient morphogenesis. We previously characterized embryonic stem-cell-derived keratinocytes, showing they display a marker-gene profile similar to skin keratinocytes, and therefore we tested their susceptibility to Marek's disease virus infection. We show herein that keratinocytes derived from chicken embryonic stem-cells are fully permissive to the replication of either non-pathogenic or pathogenic Marek's disease viruses. All viruses replicated on all three keratinocyte lines and kinetics of viral production as well as viral loads were similar to those obtained on primary cells. Morphogenesis studies were conducted on infected keratinocytes and on corneocytes, showing that all types of capsids/virions were present inside the cells, but extracellular viruses were absent. The keratinocyte lines are the first epithelial cell-line showing ectodermal specific markers supporting Marek's disease virus replication. In this in vitro model the replication lead to the production of cell-associated viral progeny. Further work will be devoted to the study of relationship between 3D differentiation of keratinocytes and Marek's disease virus replication.

  9. 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.

  10. 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

  11. New Experimental Models of Diabetic Nephropathy in Mice Models of Type 2 Diabetes: Efforts to Replicate Human Nephropathy

    Directory of Open Access Journals (Sweden)

    María José Soler

    2012-01-01

    Full Text Available Diabetic nephropathy (DN is the leading cause of end-stage renal disease. The use of experimental models of DN has provided valuable information regarding many aspects of DN, including pathophysiology, progression, implicated genes, and new therapeutic strategies. A large number of mouse models of diabetes have been identified and their kidney disease was characterized to various degrees. Most experimental models of type 2 DN are helpful in studying early stages of DN, but these models have not been able to reproduce the characteristic features of more advanced DN in humans such as nodules in the glomerular tuft or glomerulosclerosis. The generation of new experimental models of DN created by crossing, knockdown, or knockin of genes continues to provide improved tools for studying DN. These models provide an opportunity to search for new mechanisms involving the development of DN, but their shortcomings should be recognized as well. Moreover, it is important to recognize that the genetic background has a substantial effect on the susceptibility to diabetes and kidney disease development in the various models of diabetes.

  12. Human Factors Engineering Program Review Model

    Science.gov (United States)

    2004-02-01

    AA NUREG -0711,Rev. 2 Human Factors Engineering Program Review Model 20081009191 I i m To] Bi U.S. Nuclear Regulatory Commission Office of...Material As of November 1999, you may electronically access NUREG -series publications and other NRC records at NRC’s Public Electronic Reading Room at...http://www.nrc.qov/readinq-rm.html. Publicly released records include, to name a few, NUREG -series publications; Federal Register notices; applicant

  13. 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

  14. Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model.

    Science.gov (United States)

    de Wilde, Adriaan H; Falzarano, Darryl; Zevenhoven-Dobbe, Jessika C; Beugeling, Corrine; Fett, Craig; Martellaro, Cynthia; Posthuma, Clara C; Feldmann, Heinz; Perlman, Stanley; Snijder, Eric J

    2017-01-15

    Currently, there is no registered treatment for infections with emerging zoonotic coronaviruses like SARS- and MERS-coronavirus. We here report that in cultured cells low-micromolar concentrations of alisporivir, a non-immunosuppressive cyclosporin A-analog, inhibit the replication of four different coronaviruses, including MERS- and SARS-coronavirus. Ribavirin was found to further potentiate the antiviral effect of alisporivir in these cell culture-based infection models, but this combination treatment was unable to improve the outcome of SARS-CoV infection in a mouse model. Nevertheless, our data provide a basis to further explore the potential of Cyp inhibitors as host-directed, broad-spectrum inhibitors of coronavirus replication.

  15. Jnk2 effects on tumor development, genetic instability and replicative stress in an oncogene-driven mouse mammary tumor model.

    Directory of Open Access Journals (Sweden)

    Peila Chen

    Full Text Available Oncogenes induce cell proliferation leading to replicative stress, DNA damage and genomic instability. A wide variety of cellular stresses activate c-Jun N-terminal kinase (JNK proteins, but few studies have directly addressed the roles of JNK isoforms in tumor development. Herein, we show that jnk2 knockout mice expressing the Polyoma Middle T Antigen transgene developed mammary tumors earlier and experienced higher tumor multiplicity compared to jnk2 wildtype mice. Lack of jnk2 expression was associated with higher tumor aneuploidy and reduced DNA damage response, as marked by fewer pH2AX and 53BP1 nuclear foci. Comparative genomic hybridization further confirmed increased genomic instability in PyV MT/jnk2-/- tumors. In vitro, PyV MT/jnk2-/- cells underwent replicative stress and cell death as evidenced by lower BrdU incorporation, and sustained chromatin licensing and DNA replication factor 1 (CDT1 and p21(Waf1 protein expression, and phosphorylation of Chk1 after serum stimulation, but this response was not associated with phosphorylation of p53 Ser15. Adenoviral overexpression of CDT1 led to similar differences between jnk2 wildtype and knockout cells. In normal mammary cells undergoing UV induced single stranded DNA breaks, JNK2 localized to RPA (Replication Protein A coated strands indicating that JNK2 responds early to single stranded DNA damage and is critical for subsequent recruitment of DNA repair proteins. Together, these data support that JNK2 prevents replicative stress by coordinating cell cycle progression and DNA damage repair mechanisms.

  16. Program evaluation of a model to integrate internationally educated health professionals into clinical practice.

    Science.gov (United States)

    Greig, Alison; Dawes, Diana; Murphy, Susan; Parker, Gillian; Loveridge, Brenda

    2013-10-11

    The demand for health professionals continues to increase, partially due to the aging population and the high proportion of practitioners nearing retirement. The University of British Columbia (UBC) has developed a program to address this demand, by providing support for internationally trained Physiotherapists in their preparation for taking the National Physiotherapy competency examinations.The aim was to create a program comprised of the educational tools and infrastructure to support internationally educated physiotherapists (IEPs) in their preparation for entry to practice in Canada and, to improve their pass rate on the national competency examination. The program was developed using a logic model and evaluated using program evaluation methodology. Program tools and resources included educational modules and curricular packages which were developed and refined based on feedback from clinical experts, IEPs and clinical physical therapy mentors. An examination bank was created and used to include test-enhanced education. Clinical mentors were recruited and trained to provide clinical and cultural support for participants. The IEP program has recruited 124 IEPs, with 69 now integrated into the Canadian physiotherapy workforce, and more IEPs continuing to apply to the program. International graduates who participated in the program had an improved pass rate on the national Physiotherapy Competency Examination (PCE); participation in the program resulted in them having a 28% (95% CI, 2% to 59%) greater possibility of passing the written section than their counterparts who did not take the program. In 2010, 81% of all IEP candidates who completed the UBC program passed the written component, and 82% passed the clinical component. The program has proven to be successful and sustainable. This program model could be replicated to support the successful integration of other international health professionals into the workforce.

  17. 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.

  18. Wellness: A Developmental Programming Model for Residence Halls.

    Science.gov (United States)

    Warner, Mark J.

    1985-01-01

    Demonstrates how a Wellness model can be an effective vehicle for promoting developmental programs in residence halls. The Wellness model is examined in terms of marketing, student development theory, and balanced programming. (BL)

  19. A Linear Programming Model to Optimize Various Objective Functions of a Foundation Type State Support Program.

    Science.gov (United States)

    Matzke, Orville R.

    The purpose of this study was to formulate a linear programming model to simulate a foundation type support program and to apply this model to a state support program for the public elementary and secondary school districts in the State of Iowa. The model was successful in producing optimal solutions to five objective functions proposed for…

  20. The organotypic multicellular spheroid is a relevant three-dimensional model to study adenovirus replication and penetration in human tumors in vitro.

    Science.gov (United States)

    Grill, Jacques; Lamfers, Martine L M; van Beusechem, Victor W; Dirven, Clemens M; Pherai, D Shareen; Kater, Mathijs; Van der Valk, Paul; Vogels, Ronald; Vandertop, W Peter; Pinedo, Herbert M; Curiel, David T; Gerritsen, Winald R

    2002-11-01

    The use of adenoviruses for gene transfer and as oncolytic agents is currently receiving widespread attention. As specific constraints to adenovirus distribution and spread cannot be studied in cell cultures, there is a need for an in vitro three-dimensional (3D) model mimicking the in vivo biology of tumors. We studied the interactions between tumor and adenoviruses using multicellular spheroids grown from primary brain tumor material. Using beta-galactosidase and luciferase reporter genes expressed by replication-defective adenoviruses, we showed that infection was restricted to the first layer of cells. Using a replication-competent adenovirus expressing the luciferase gene, we showed that transgene expression in the spheroid was considerably enhanced and that viral spreading deep into the 3D structure took place. In addition, a tetrazolium salt-based metabolic assay could be used to compare the oncolytic activity of different concentrations of replication-competent adenoviruses. We can conclude that organotypic spheroids offer a versatile in vitro system for studying distribution, spread, and oncolysis by adenoviruses in a clinically relevant model.

  1. 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...

  2. Identification and replication of prediction models for ovulation, pregnancy and live birth in infertile women with polycystic ovary syndrome.

    Science.gov (United States)

    Kuang, Hongying; Jin, Susan; Hansen, Karl R; Diamond, Michael P; Coutifaris, Christos; Casson, Peter; Christman, Gregory; Alvero, Ruben; Huang, Hao; Bates, G Wright; Usadi, Rebecca; Lucidi, Scott; Baker, Valerie; Santoro, Nanette; Eisenberg, Esther; Legro, Richard S; Zhang, Heping

    2015-09-01

    Can we build and validate predictive models for ovulation and pregnancy outcomes in infertile women with polycystic ovary syndrome (PCOS)? We were able to develop and validate a predictive model for pregnancy outcomes in women with PCOS using simple clinical and biochemical criteria particularly duration of attempting conception, which was the most consistent predictor among all considered factors for pregnancy outcomes. Predictive models for ovulation and pregnancy outcomes in infertile women with polycystic ovary syndrome have been reported, but such models require validation. This is a secondary analysis of the data from the Pregnancy in Polycystic Ovary Syndrome I and II (PPCOS-I and -II) trials. Both trials were double-blind, randomized clinical trials that included 626 and 750 infertile women with PCOS, respectively. PPCOS-I participants were randomized to either clomiphene citrate (CC), metformin, or their combination, and PPCOS-II participants to either letrozole or CC for up to five treatment cycles. Linear logistic regression models were fitted using treatment, BMI, and other published variables as predictors of ovulation, conception, clinical pregnancy, and live birth as the outcome one at a time. We first evaluated previously reported significant predictors, and then constructed new prediction models. Receiver operating characteristic (ROC) curves were constructed and the area under the curves (AUCs) was calculated to compare performance using different models and data. Chi-square tests were used to examine the goodness-of-fit and prediction power of logistic regression model. Predictive factors were similar between PPCOS-I and II, but the two participant samples differed statistically significantly but the differences were clinically minor on key baseline characteristics and hormone levels. Women in PPCOS-II had an overall more severe PCOS phenotype than women in PPCOS-I. The clinically minor but statistically significant differences may be due to the

  3. Shell Separation for Mirror Replication

    Science.gov (United States)

    1999-01-01

    NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery, and materials to replicate electro-formed nickel mirrors. Optics replication uses reusable forms, called mandrels, to make telescope mirrors ready for final finishing. MSFC optical physicist Bill Jones monitors a device used to chill a mandrel, causing it to shrink and separate from the telescope mirror without deforming the mirror's precisely curved surface.

  4. Comparison of three replication strategies in complex multicellular organisms: Asexual replication, sexual replication with identical gametes, and sexual replication with distinct sperm and egg gametes

    Science.gov (United States)

    Tannenbaum, Emmanuel

    2008-01-01

    This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually replicating population that produces identical gametes. The third model considers a sexually replicating population that produces distinct sperm and egg gametes. All models assume diploid organisms whose genomes consist of two chromosomes, each of which is taken to be functional if equal to some master sequence, and defective otherwise. In the asexual population, the asexual diploid spores develop directly into adult organisms. In the sexual populations, the haploid gametes enter a haploid pool, where they may fuse with other haploids. The resulting immature diploid organisms then proceed to develop into mature organisms. Based on an analysis of all three models, we find that, as organism size increases, a sexually replicating population can only outcompete an asexually replicating population if the adult organisms produce distinct sperm and egg gametes. A sexual replication strategy that is based on the production of large numbers of sperm cells to fertilize a small number of eggs is found to be necessary in order to maintain a sufficiently low cost for sex for the strategy to be selected for over a purely asexual strategy. We discuss the usefulness of this model in understanding the evolution and maintenance of sexual replication as the preferred replication strategy in complex, multicellular organisms.

  5. Nucleotide Metabolism and DNA Replication.

    Science.gov (United States)

    Warner, Digby F; Evans, Joanna C; Mizrahi, Valerie

    2014-10-01

    The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.

  6. Suggestion Program and Model Installation Program - Duplication of Effort.

    Science.gov (United States)

    1988-04-01

    REPORTNUMBER88-26- TITL SUGESIONPROGAM ND ODE INSALLTIO PRGRAM -DULICTIO OF EFFORT AUTHR(S)MAJR DOALD . TOWBRDGEUSA FACUTY DVISRMAOR SEVE L.HANSN, CSC/824STU...NIP Evaluation Process............................ 13 FIGURE 3--USAF MIP Growth................................... 17 0. p.r vip I -.# EXECUTIVE SUMMARY...the study centers on program processes for submitting and evaluating proposals. The Suggestion Program and MIP processes are similar in that they both

  7. Replication Restart in Bacteria.

    Science.gov (United States)

    Michel, Bénédicte; Sandler, Steven J

    2017-07-01

    In bacteria, replication forks assembled at a replication origin travel to the terminus, often a few megabases away. They may encounter obstacles that trigger replisome disassembly, rendering replication restart from abandoned forks crucial for cell viability. During the past 25 years, the genes that encode replication restart proteins have been identified and genetically characterized. In parallel, the enzymes were purified and analyzed in vitro, where they can catalyze replication initiation in a sequence-independent manner from fork-like DNA structures. This work also revealed a close link between replication and homologous recombination, as replication restart from recombination intermediates is an essential step of DNA double-strand break repair in bacteria and, conversely, arrested replication forks can be acted upon by recombination proteins and converted into various recombination substrates. In this review, we summarize this intense period of research that led to the characterization of the ubiquitous replication restart protein PriA and its partners, to the definition of several replication restart pathways in vivo, and to the description of tight links between replication and homologous recombination, responsible for the importance of replication restart in the maintenance of genome stability. Copyright © 2017 American Society for Microbiology.

  8. Delay Scheduling Based Replication Scheme for Hadoop Distributed File System

    Directory of Open Access Journals (Sweden)

    S. Suresh

    2015-03-01

    Full Text Available The data generated and processed by modern computing systems burgeon rapidly. MapReduce is an important programming model for large scale data intensive applications. Hadoop is a popular open source implementation of MapReduce and Google File System (GFS. The scalability and fault-tolerance feature of Hadoop makes it as a standard for BigData processing. Hadoop uses Hadoop Distributed File System (HDFS for storing data. Data reliability and faulttolerance is achieved through replication in HDFS. In this paper, a new technique called Delay Scheduling Based Replication Algorithm (DSBRA is proposed to identify and replicate (dereplicate the popular (unpopular files/blocks in HDFS based on the information collected from the scheduler. Experimental results show that, the proposed method achieves 13% and 7% improvements in response time and locality over existing algorithms respectively.

  9. 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.

  10. 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.

  11. 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.

  12. 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)

  13. A mouse model based on replication-competent Tiantan vaccinia expressing luciferase/HIV-1 Gag fusion protein for the evaluation of protective efficacy of HIV vaccine

    Institute of Scientific and Technical Information of China (English)

    HUANG Yang; QIU Chao; LIU Lian-xing; FENG Yan-meng; ZHU Ting; XU Jian-qing

    2009-01-01

    Background Developing an effective vaccine against human immunodeficiency virus type 1 (HIV-1) remains a grand challenge after more than two decades of intensive effort. It is partially due to the lack of suitable animal models for screening and prioritizing vaccine candidates. In this study, we aim to develop a mice model to test HIV-1 vaccine efficacy. Methods We constructed a recombinant vaccinia expressing firefly luciferase and HIV-1 Gag fusion protein based on Tiantan strain, an attenuated but replication-competent poxvirus (rTTV-lucgag). By quantifying the luciferase activity as its read out, we defined the biodistribution of Tiantan strain poxvirus in mice inoculated intraperitoneally and attempted to apply this model to evaluate the HIV-1 vaccine efficacy. Results Our data demonstrated that the rTTV-lucgag was able to express high level of luciferase (≤106 relative luciferase units (RLU)/mg protein) and HIV-1 Gag (>3 folds increase comparing to the control). After intraperitoneal inoculation, this virus had dominant replication in the ovary, uterus, and cervix of mice and the luciferase activities in those organs are significantly correlated with viral titers (r2=0.71, P <0.01). Pre-immunization with an HIV gag DNA vaccine reduced the luciferase activity in ovary from (6006+3141) RLU/mg protein in control group to (1538±463) RLU/mg protein in vaccine group (P=0.1969). Conclusions The luciferase activity in ovary could represent viral replication in vivo;, this rTTV-lucgag/mice model may be suitable to assess the protective efficacy of cytotoxic T-cell responses to HIV Gag with less tedious work and high through-put.

  14. 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].

  15. 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...

  16. 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

  17. 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 (pSARS 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 replication was partially characterized. When UDA was exposed to N-acetylglucosamine and then UDA was added to cells just prior to adsorption, UDA did not inhibit the virus infection. These data support the conclusion that UDA might bind to N-acetylglucosamine-like residues present on the glycosylated envelope glycoproteins, thereby preventing virus attachment to cells. PMID:21338626

  18. Program MAMO: Models for avian management optimization-user guide

    Science.gov (United States)

    Guillaumet, Alban; Paxton, Eben

    2017-01-01

    The following chapters describe the structure and code of MAMO, and walk the reader through running the different components of the program with sample data. This manual should be used alongside a computer running R, so that the reader can copy and paste code into R, observe the output, and follow along interactively. Taken together, chapters 2–4 will allow the user to replicate a simulation study investigating the consequences of climate change and two potential management actions on the population dynamics of a vulnerable and iconic Hawaiian forest bird, the ‘I‘iwi (Drepanis coccinea; hereafter IIWI).

  19. Support for career development in youth: program models and evaluations.

    Science.gov (United States)

    Mekinda, Megan A

    2012-01-01

    This article examines four influential programs-Citizen Schools, After School Matters, career academies, and Job Corps-to demonstrate the diversity of approaches to career programming for youth. It compares the specific program models and draws from the evaluation literature to discuss strengths and weaknesses of each. The article highlights three key lessons derived from the models that have implications for career development initiatives more generally: (1) career programming can and should be designed for youth across a broad age range, (2) career programming does not have to come at the expense of academic training or preparation for college, and (3) program effectiveness depends on intentional design and high-quality implementation.

  20. BUILDING MATHEMATICAL MODELS IN DYNAMIC PROGRAMMING

    Directory of Open Access Journals (Sweden)

    LIANA RODICA PATER

    2012-05-01

    Full Text Available In short, we can say that dynamic programming is a method of optimization of systems, using their mathematical representation in phases or sequences or as we say, periods. Such systems are common in economic studies at the implementation of programs on the most advanced techniques, such as for example that involving cosmic navigation. Another concept that is involved in the study of dynamic programs is the economic horizon (number of periods or phases that a dynamic program needs. This concept often leads to the examination of the convergence of certain variables on infinite horizon. In many cases from the real economy by introducing updating, dynamic programs can be made convergent.

  1. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    OpenAIRE

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    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 ...

  2. 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...... 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....

  3. 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

  4. A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle

    Science.gov (United States)

    He, Christine; Gállego, Isaac; Laughlin, Brandon; Grover, Martha A.; Hud, Nicholas V.

    2017-04-01

    Many hypotheses concerning the nature of early life assume that genetic information was once transferred through the template-directed synthesis of RNA, before the emergence of coded enzymes. However, attempts to demonstrate enzyme-free, template-directed synthesis of nucleic acids have been limited by 'strand inhibition', whereby transferring information from a template strand in the presence of its complementary strand is inhibited by the stability of the template duplex. Here, we use solvent viscosity to circumvent strand inhibition, demonstrating information transfer from a gene-length template (>300 nt) within a longer (545 bp or 3 kb) duplex. These results suggest that viscous environments on the prebiotic Earth, generated periodically by water evaporation, could have facilitated nucleic acid replication—particularly of long, structured sequences such as ribozymes. Our approach works with DNA and RNA, suggesting that viscosity-mediated replication is possible for a range of genetic polymers, perhaps even for informational polymers that may have preceded RNA.

  5. An epigenome-wide association meta-analysis of prenatal maternal stress in neonates: A model approach for replication.

    Science.gov (United States)

    Rijlaarsdam, Jolien; Pappa, Irene; Walton, Esther; Bakermans-Kranenburg, Marian J; Mileva-Seitz, Viara R; Rippe, Ralph C A; Roza, Sabine J; Jaddoe, Vincent W V; Verhulst, Frank C; Felix, Janine F; Cecil, Charlotte A M; Relton, Caroline L; Gaunt, Tom R; McArdle, Wendy; Mill, Jonathan; Barker, Edward D; Tiemeier, Henning; van IJzendoorn, Marinus H

    2016-01-01

    Prenatal maternal stress exposure has been associated with neonatal differential DNA methylation. However, the available evidence in humans is largely based on candidate gene methylation studies, where only a few CpG sites were evaluated. The aim of this study was to examine the association between prenatal exposure to maternal stress and offspring genome-wide cord blood methylation using different methods. First, we conducted a meta-analysis and follow-up pathway analyses. Second, we used novel region discovery methods [i.e., differentially methylated regions (DMRs) analyses]. To this end, we used data from two independent population-based studies, the Generation R Study (n = 912) and the Avon Longitudinal Study of Parents and Children (ALSPAC, n = 828), to (i) measure genome-wide DNA methylation in cord blood and (ii) extract a prenatal maternal stress composite. The meta-analysis (ntotal = 1,740) revealed no epigenome-wide (meta P meta-analysis (meta P meta-analysis, the current study indicates that there are no large effects of prenatal maternal stress exposure on neonatal DNA methylation. Such replication efforts are essential in the search for robust associations, whether derived from candidate gene methylation or epigenome-wide studies.

  6. A Model Program for Dental Assisting Education in California.

    Science.gov (United States)

    California State Dept. of Education, Sacramento. Bureau of Industrial Education.

    Intended to provide assistance for developing new programs and improving existing ones, the guide was constructed by dental assisting instructors and other professional participants in a 196 5 workshop conference. Elements of the model program were derived from a statistical analysis of California junior colleg e programs in dental assisting and…

  7. Support for Career Development in Youth: Program Models and Evaluations

    Science.gov (United States)

    Mekinda, Megan A.

    2012-01-01

    This article examines four influential programs--Citizen Schools, After School Matters, career academies, and Job Corps--to demonstrate the diversity of approaches to career programming for youth. It compares the specific program models and draws from the evaluation literature to discuss strengths and weaknesses of each. The article highlights…

  8. Evaluating Vocational Programs: A Three Dimensional Model.

    Science.gov (United States)

    Rehman, Sharaf N.; Nejad, Mahmoud

    The traditional methods of assessing the academic programs in the liberal arts are inappropriate for evaluating vocational and technical programs. In traditional academic disciplines, assessment of instruction is conducted in two fashions: student evaluation at the end of a course and institutional assessment of its goals and mission. Because of…

  9. 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…

  10. Building an advanced climate model: Program plan for the CHAMMP (Computer Hardware, Advanced Mathematics, and Model Physics) Climate Modeling Program

    Energy Technology Data Exchange (ETDEWEB)

    1990-12-01

    The issue of global warming and related climatic changes from increasing concentrations of greenhouse gases in the atmosphere has received prominent attention during the past few years. The Computer Hardware, Advanced Mathematics, and Model Physics (CHAMMP) Climate Modeling Program is designed to contribute directly to this rapid improvement. The goal of the CHAMMP Climate Modeling Program is to develop, verify, and apply a new generation of climate models within a coordinated framework that incorporates the best available scientific and numerical approaches to represent physical, biogeochemical, and ecological processes, that fully utilizes the hardware and software capabilities of new computer architectures, that probes the limits of climate predictability, and finally that can be used to address the challenging problem of understanding the greenhouse climate issue through the ability of the models to simulate time-dependent climatic changes over extended times and with regional resolution.

  11. Mantis: Predicting System Performance through Program Analysis and Modeling

    CERN Document Server

    Chun, Byung-Gon; Lee, Sangmin; Maniatis, Petros; Naik, Mayur

    2010-01-01

    We present Mantis, a new framework that automatically predicts program performance with high accuracy. Mantis integrates techniques from programming language and machine learning for performance modeling, and is a radical departure from traditional approaches. Mantis extracts program features, which are information about program execution runs, through program instrumentation. It uses machine learning techniques to select features relevant to performance and creates prediction models as a function of the selected features. Through program analysis, it then generates compact code slices that compute these feature values for prediction. Our evaluation shows that Mantis can achieve more than 93% accuracy with less than 10% training data set, which is a significant improvement over models that are oblivious to program features. The system generates code slices that are cheap to compute feature values.

  12. Evolutionary Model to Traditional Culture and Program Organization

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jing-xiao; JIN Wei-xing; YANG De-qin

    2006-01-01

    To study the relationship between the evolutions of Chinese Traditional Culture (CTC) and program organization, an outline of the CTC is generalized by reviewing literature, and which is also compartmentalized into two aspects according to economic philosophy views: traditional philosophy aspect and value judgment. Based on three dimensions, which are the philosophy aspect (P), program organization model (P), and value judgment from economic philosophy views (V), and this evolution sequence, the CTC's influence on the program organization model in the evolution is discussed; then the cultural spatial evolution model for program organization based on the three dimensions (PPV) is constructed. From analyzing the plane matrix of P-P and empirical investigating on the organizational model of construction enterprises, it is found that the ancient Chinese government organizational model still has prevailing influence on the modern program organizational model in China.

  13. Deadlock Detection in Basic Models of MPI Synchronization Communication Programs

    CERN Document Server

    Liao, Ming-xue

    2007-01-01

    A model of MPI synchronization communication programs is presented and its three basic simplified models are also defined. A series of theorems and methods for deciding whether deadlocks will occur among the three models are given and proved strictly. These theories and methods for simple models' deadlock detection are the necessary base for real MPI program deadlock detection. The methods are based on a static analysis through programs and with runtime detection in necessary cases and they are able to determine before compiling whether it will be deadlocked for two of the three basic models. For another model, some deadlock cases can be found before compiling and others at runtime. Our theorems can be used to prove the correctness of currently popular MPI program deadlock detection algorithms. Our methods may decrease codes that those algorithms need to change to MPI source or profiling interface and may detects deadlocks ahead of program execution, thus the overheads can be reduced greatly.

  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. Integer Programming Model for Maximum Clique in Graph

    Institute of Scientific and Technical Information of China (English)

    YUAN Xi-bo; YANG You; ZENG Xin-hai

    2005-01-01

    The maximum clique or maximum independent set of graph is a classical problem in graph theory. Combined with Boolean algebra and integer programming, two integer programming models for maximum clique problem,which improve the old results were designed in this paper. Then, the programming model for maximum independent set is a corollary of the main results. These two models can be easily applied to computer algorithm and software, and suitable for graphs of any scale. Finally the models are presented as Lingo algorithms, verified and compared by several examples.

  16. Constructive Replication of the Visual-Perceptual-Image Rotation Model in Thurstone's (1941) Battery of 60 Tests of Mental Ability

    Science.gov (United States)

    Johnson, W.; Bouchard, T.J.

    2005-01-01

    We recently evaluated the relative statistical performance of the Cattell-Horn fluid-crystallized model and the Vernon verbal-perceptual model of the structure of human intelligence in a sample of 436 adults heterogeneous for age, place of origin, and educational background who completed 42 separate tests of mental ability from three test…

  17. 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.

  18. Hyperthermia stimulates HIV-1 replication.

    Science.gov (United States)

    Roesch, Ferdinand; Meziane, Oussama; Kula, Anna; Nisole, Sébastien; Porrot, Françoise; Anderson, Ian; Mammano, Fabrizio; Fassati, Ariberto; Marcello, Alessandro; Benkirane, Monsef; Schwartz, Olivier

    2012-01-01

    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.

  19. A Microswitch-Cluster Program to Foster Adaptive Responses and Head Control in Students with Multiple Disabilities: Replication and Validation Assessment

    Science.gov (United States)

    Lancioni, Giulio E.; Singh, Nirbhay N.; O'Reilly, Mark F.; Sigafoos, Jeff; Oliva, Doretta; Gatti, Michela; Manfredi, Francesco; Megna, Gianfranco; La Martire, Maria L.; Tota, Alessia; Smaldone, Angela; Groeneweg, Jop

    2008-01-01

    A program relying on microswitch clusters (i.e., combinations of microswitches) and preferred stimuli was recently developed to foster adaptive responses and head control in persons with multiple disabilities. In the last version of this program, preferred stimuli (a) are scheduled for adaptive responses occurring in combination with head control…

  20. Efficient Global Programming Model for Discriminant Analysis

    Directory of Open Access Journals (Sweden)

    M.ANGULAKSHMI

    2011-03-01

    Full Text Available Conventional statistical analysis includes the capacity to systematically assign individuals to groups. We suggest alternative assignment procedures, utilizing a set of interrelated goal programming formulations. This paper represents an effort to suggest ways by which the discriminant problem might reasonably be addressed via straightforward linear goal programming formulations. Simple and direct, such formulations may ultimately compete with conventional approaches - free of the classical assumptions and possessing a stronger intuitive appeal. We further demonstrate via simple illustration the potential of these procedures to play a significant part in addressing the discriminant problem, and indicate fundamental ideas that lay the foundation for other more sophisticated approaches.

  1. The Replication Recipe: What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, A.J.; Farach, F.J.; Geller, J.; Giner-Sorolla, R.; Grange, J.A.; Perugini, M.; Spies, J.R.; Veer, A. van 't

    2014-01-01

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  2. 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.

  3. How frog embryos replicate their DNA reliably

    Science.gov (United States)

    Bechhoefer, John; Marshall, Brandon

    2007-03-01

    Frog embryos contain three billion base pairs of DNA. In early embryos (cycles 2-12), DNA replication is extremely rapid, about 20 min., and the entire cell cycle lasts only 25 min., meaning that mitosis (cell division) takes place in about 5 min. In this stripped-down cell cycle, there are no efficient checkpoints to prevent the cell from dividing before its DNA has finished replication - a disastrous scenario. Even worse, the many origins of replication are laid down stochastically and are also initiated stochastically throughout the replication process. Despite the very tight time constraints and despite the randomness introduced by origin stochasticity, replication is extremely reliable, with cell division failing no more than once in 10,000 tries. We discuss a recent model of DNA replication that is drawn from condensed-matter theories of 1d nucleation and growth. Using our model, we discuss different strategies of replication: should one initiate all origins as early as possible, or is it better to hold back and initiate some later on? Using concepts from extreme-value statistics, we derive the distribution of replication times given a particular scenario for the initiation of origins. We show that the experimentally observed initiation strategy for frog embryos meets the reliability constraint and is close to the one that requires the fewest resources of a cell.

  4. 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.

  5. Organizational analysis of three community support program models.

    Science.gov (United States)

    Reinke, B; Greenley, J R

    1986-06-01

    Little attention has been paid to the organizational and administrative characteristics of effective community support programs for the chronic mentally ill. The authors analyzed three successful support programs in Wisconsin that employ three different models of service delivery: one provides services through caseworkers who carry specialized caseloads, another through local nonprofessionals who work with a centrally located program coordinator, and the third through a team of various mental health workers. Each program has tailored its organizational process to suit the types of clients it sees, the size of its catchment area, and the availability of other professional resources. The interrelated strengths and weaknesses of each model are discussed.

  6. 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…

  7. Model checking abstract state machines with answer set programming

    OpenAIRE

    2006-01-01

    Answer Set Programming (ASP) is a logic programming paradigm that has been shown as a useful tool in various application areas due to its expressive modelling language. These application areas include Bourided Model Checking (BMC). BMC is a verification technique that is recognized for its strong ability of finding errors in computer systems. To apply BMC, a system needs to be modelled in a formal specification language, such as the widely used formalism of Abstract State Machines (ASMs). In ...

  8. 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...

  9. ALREST High Fidelity Modeling Program Approach

    Science.gov (United States)

    2011-05-18

    Gases and Mixtures of Redlich - Kwong and Peng- Robinson Fluids Assumed pdf Model based on k- ε-g Model in NASA/LaRc Vulcan code Level Set model...Potential Attractiveness Of Liquid Hydrocarbon Engines For Boost Applications • Propensity Of Hydrocarbon Engines For Combustion Instability • Air

  10. Abiotic self-replication.

    Science.gov (United States)

    Meyer, Adam J; Ellefson, Jared W; Ellington, Andrew D

    2012-12-18

    The key to the origins of life is the replication of information. Linear polymers such as nucleic acids that both carry information and can be replicated are currently what we consider to be the basis of living systems. However, these two properties are not necessarily coupled. The ability to mutate in a discrete or quantized way, without frequent reversion, may be an additional requirement for Darwinian evolution, in which case the notion that Darwinian evolution defines life may be less of a tautology than previously thought. In this Account, we examine a variety of in vitro systems of increasing complexity, from simple chemical replicators up to complex systems based on in vitro transcription and translation. Comparing and contrasting these systems provides an interesting window onto the molecular origins of life. For nucleic acids, the story likely begins with simple chemical replication, perhaps of the form A + B → T, in which T serves as a template for the joining of A and B. Molecular variants capable of faster replication would come to dominate a population, and the development of cycles in which templates could foster one another's replication would have led to increasingly complex replicators and from thence to the initial genomes. The initial genomes may have been propagated by RNA replicases, ribozymes capable of joining oligonucleotides and eventually polymerizing mononucleotide substrates. As ribozymes were added to the genome to fill gaps in the chemistry necessary for replication, the backbone of a putative RNA world would have emerged. It is likely that such replicators would have been plagued by molecular parasites, which would have been passively replicated by the RNA world machinery without contributing to it. These molecular parasites would have been a major driver for the development of compartmentalization/cellularization, as more robust compartments could have outcompeted parasite-ridden compartments. The eventual outsourcing of metabolic

  11. Adenovirus DNA Replication

    OpenAIRE

    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 deve...

  12. 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.

  13. 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.

  14. Escalation of error catastrophe for enzymatic self-replicators

    Science.gov (United States)

    Obermayer, B.; Frey, E.

    2009-11-01

    It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication, we analyze highly specific enzymatic self-replication mediated through an otherwise neutral recognition region, which leads to frequency-dependent replication rates. We find a significant reduction of the maximally tolerable error rate, because the replication rate of the fittest molecules decreases with the fraction of functional enzymes. Our analysis is extended to hypercyclic couplings as an example for catalytic networks.

  15. Mental Effort and Perceptions of TV and Books: A Dutch Replication Study Based on Salomon's Model of Learning.

    Science.gov (United States)

    Beentjes, Hans W. J.

    This comparison of students' learning from reading books and from watching television uses Gavriel Salomon's model of learning effects, which is based on the amount of mental effort invested (AIME) in a medium as determining how deeply the information from that medium is processed. Mental effort, in turn, is predicted to depend on two perceptions…

  16. Community-based senior health promotion program using a collaborative practice model: the Escalante Health Partnerships.

    Science.gov (United States)

    Nuñez, Diane E; Armbruster, Charlotte; Phillips, Wayne T; Gale, Betty J

    2003-01-01

    Recent research demonstrates that, although the risk of disease and disability clearly increases with age, poor health need not be an inevitable consequence of aging. A healthy lifestyle is more influential than genetic factors in assisting older adults avoid the decline and deterioration traditionally associated with aging. Many effective strategies for reducing disease and disability are widely underused. The Escalante Health Partnerships is a community-based, nurse-managed health promotion and chronic disease care management program for community-residing older adults. The program base supports a multidisciplinary, collaborative practice model, which has responded to the health needs of members of a community at high risk of having or developing chronic conditions. Preliminary comparisons of the health status of program participants with national norms demonstrate that these seniors report better general health, performance of roles, and social functioning, with the strongest correlations occurring between general health and vitality and between general health and role-physical. In addition, these participants have 4.2 doctor visits per year, in comparison with 7.1 office visits for a national comparison group and 1.6 hospital days per year, in comparison with 2.1 hospital days in the same referenced population. This collaborative partnership is a model that can be replicated cost-effectively in other communities.

  17. 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.

  18. 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

  19. 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...

  20. 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.

  1. The Gold Medal Fitness Program: A Model for Teacher Change

    Science.gov (United States)

    Wright, Jan; Konza, Deslea; Hearne, Doug; Okely, Tony

    2008-01-01

    Background: Following the 2000 Sydney Olympics, the NSW Premier, Mr Bob Carr, launched a school-based initiative in NSW government primary schools called the "Gold Medal Fitness Program" to encourage children to be fitter and more active. The Program was introduced into schools through a model of professional development, "Quality…

  2. Minichromosome replication in vitro: inhibition of re-replication by replicatively assembled nucleosomes.

    Science.gov (United States)

    Krude, T; Knippers, R

    1994-08-19

    Single-stranded circular DNA, containing the SV40 origin sequence, was used as a template for complementary DNA strand synthesis in cytosolic extracts from HeLa cells. In the presence of the replication-dependent chromatin assembly factor CAF-1, defined numbers of nucleosomes were assembled during complementary DNA strand synthesis. These minichromosomes were then induced to semiconservatively replicate by the addition of the SV40 initiator protein T antigen (re-replication). The results indicate that re-replication of minichromosomes appears to be inhibited by two independent mechanisms. One acts at the initiation of minichromosome re-replication, and the other affects replicative chain elongation. To directly demonstrate the inhibitory effect of replicatively assembled nucleosomes, two types of minichromosomes were prepared: (i) post-replicative minichromosomes were assembled in a reaction coupled to replication as above; (ii) pre-replicative minichromosomes were assembled independently of replication on double-stranded DNA. Both types of minichromosomes were used as templates for DNA replication under identical conditions. Replicative fork movement was found to be impeded only on post-replicative minichromosome templates. In contrast, pre-replicative minichromosomes allowed one unconstrained replication cycle, but re-replication was inhibited due to a block in fork movement. Thus, replicatively assembled chromatin may have a profound influence on the re-replication of DNA.

  3. The MAP program: building the digital terrain model.

    Science.gov (United States)

    R.H. Twito; R.W. Mifflin; R.J. McGaughey

    1987-01-01

    PLANS, a software package for integrated timber-harvest planning, uses digital terrain models to provide the topographic data needed to fit harvest and transportation designs to specific terrain. MAP, an integral program in the PLANS package, is used to construct the digital terrain models required by PLANS. MAP establishes digital terrain models using digitizer-traced...

  4. Program Models for Mental Health Treatment of Refugees.

    Science.gov (United States)

    Jaranson, James M.; Bamford, Pauline

    This paper presents the approach used by the Technical Assistance Center (TAC) of the University of Minnesota's Refugee Assistance Program in Mental Health for identifying successful and culturally sensitive mental health service delivery models. It divides these into four categories: the psychiatric model; the community mental health model; the…

  5. Genetic programming-based chaotic time series modeling

    Institute of Scientific and Technical Information of China (English)

    张伟; 吴智铭; 杨根科

    2004-01-01

    This paper proposes a Genetic Programming-Based Modeling (GPM) algorithm on chaotic time series. GP is used here to search for appropriate model structures in function space, and the Particle Swarm Optimization (PSO) algorithm is used for Nonlinear Parameter Estimation (NPE) of dynamic model structures. In addition, GPM integrates the results of Nonlinear Time Series Analysis (NTSA) to adjust the parameters and takes them as the criteria of established models. Experiments showed the effectiveness of such improvements on chaotic time series modeling.

  6. Down-regulation of BLIMP1α by the EBV oncogene, LMP-1, disrupts the plasma cell differentiation program and prevents viral replication in B cells: implications for the pathogenesis of EBV-associated B-cell lymphomas.

    Science.gov (United States)

    Vrzalikova, Katerina; Vockerodt, Martina; Leonard, Sarah; Bell, Andrew; Wei, Wenbin; Schrader, Alexandra; Wright, Kenneth L; Kube, Dieter; Rowe, Martin; Woodman, Ciaran B; Murray, Paul G

    2011-06-02

    An important pathogenic event in Epstein-Barr virus (EBV)-associated lymphomas is the suppression of virus replication, which would otherwise lead to cell death. Because virus replication in B cells is intimately linked to their differentiation toward plasma cells, we asked whether the physiologic signals that drive normal B-cell differentiation are absent in EBV-transformed cells. We focused on BLIMP1α, a transcription factor that is required for plasma cell differentiation and that is inactivated in diffuse large B-cell lymphomas. We show that BLIMP1α expression is down-regulated after EBV infection of primary germinal center B cells and that the EBV oncogene, latent membrane protein-1 (LMP-1), is alone capable of inducing this down-regulation in these cells. Furthermore, the down-regulation of BLIMP1α by LMP-1 was accompanied by a partial disruption of the BLIMP1α transcriptional program, including the aberrant induction of MYC, the repression of which is required for terminal differentiation. Finally, we show that the ectopic expression of BLIMP1α in EBV-transformed cells can induce the viral lytic cycle. Our results suggest that LMP-1 expression in progenitor germinal center B cells could contribute to the pathogenesis of EBV-associated lymphomas by down-regulating BLIMP1α, in turn preventing plasma cell differentiation and induction of the viral lytic cycle.

  7. Evaluation of a school-based program designed to improve body image satisfaction, global self-esteem, and eating attitudes and behaviors: a replication study.

    Science.gov (United States)

    McVey, Gail L; Davis, Ron; Tweed, Stacey; Shaw, Brian F

    2004-07-01

    The purpose of the current study was to evaluate the effectiveness of a life-skills promotion program designed to improve body image satisfaction and global self-esteem, while reducing negative eating attitudes and behaviors and feelings of perfectionism, all of which have been identified as predisposing factors to disordered eating. A total of 258 girls with a mean age of 11.8 years (intervention group = 182 and control group = 76) completed questionnaires before, and 1 week after, the six-session school-based program, and again 6 and 12 months later. The intervention was successful in improving body image satisfaction and global self-esteem and in reducing dieting attitude scores at post intervention only. The gains were not maintained at the 12-month follow-up. The need to assess the influence of health promotion programs on predisposing risk factors, compared with problem-based outcome measures, is discussed. Copyright 2004 by Wiley Periodicals, Inc.

  8. Modelling of windmill induction generators in dynamic simulation programs

    DEFF Research Database (Denmark)

    Akhmatov, Vladislav; Knudsen, Hans

    1999-01-01

    . It is shown that it is possible to include a transient model in dynamic stability programs and thus obtain correct results also in dynamic stability programs. A mechanical model of the shaft system has also been included in the generator model...... 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......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...

  9. 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...

  10. 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.

  11. 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...

  12. Investigating variation in replicability: A "Many Labs" replication project

    NARCIS (Netherlands)

    Klein, R.A.; Ratliff, K.A.; Vianello, M.; Adams, R.B.; Bahnik, S.; Bernstein, M.J.; Bocian, K.; Brandt, M.J.; Brooks, B.; Brumbaugh, C.C.; Cemalcilar, Z.; Chandler, J.; Cheong, W.; Davis, W.E.; Devos, T.; Eisner, M.; Frankowska, N.; Furrow, D.; Galliani, E.M.; Hasselman, F.W.; Hicks, J.A.; Hovermale, J.F.; Hunt, S.J.; Huntsinger, J.R.; IJzerman, H.; John, M.S.; Joy-Gaba, J.A.; Kappes, H.B.; Krueger, L.E.; Kurtz, J.; Levitan, C.A.; Mallett, R.K.; Morris, W.L.; Nelson, A.J.; Nier, J.A.; Packard, G.; Pilati, R.; Rutchick, A.M.; Schmidt, K.; Skorinko, J.L.M.; Smith, R.; Steiner, T.G.; Storbeck, J.; Van Swol, L.M.; Thompson, D.; Veer, A.E. van 't; Vaughn, L.A.; Vranka, M.; Wichman, A.L.; Woodzicka, J.A.; Nosek, B.A.

    2014-01-01

    Although replication is a central tenet of science, direct replications are rare in psychology. This research tested variation in the replicability of 13 classic and contemporary effects across 36 independent samples totaling 6,344 participants. In the aggregate, 10 effects replicated consistently.

  13. Hepatitis B virus replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepadnaviruses, including human hepatitis B virus (HBV), replicate through reverse transcription of an RNA intermediate, the pregenomic RNA (pgRNA). Despite this kinship to retroviruses, there are fundamental differences beyond the fact that hepadnavirions contain DNA instead of RNA. Most peculiar is the initiation of reverse transcription: it occurs by protein-priming, is strictly committed to using an RNA hairpin on the pgRNA,ε, as template, and depends on cellular chaperones;moreover, proper replication can apparently occur only in the specialized environment of intact nucleocapsids.This complexity has hampered an in-depth mechanistic understanding. The recent successful reconstitution in the test tube of active replication initiation complexes from purified components, for duck HBV (DHBV),now allows for the analysis of the biochemistry of hepadnaviral replication at the molecular level. Here we review the current state of knowledge at all steps of the hepadnaviral genome replication cycle, with emphasis on new insights that turned up by the use of such cellfree systems. At this time, they can, unfortunately,not be complemented by three-dimensional structural information on the involved components. However, at least for the s RNA element such information is emerging,raising expectations that combining biophysics with biochemistry and genetics will soon provide a powerful integrated approach for solving the many outstanding questions. The ultimate, though most challenging goal,will be to visualize the hepadnaviral reverse transcriptase in the act of synthesizing DNA, which will also have strong implications for drug development.

  14. 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…

  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…

  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. 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.

  18. Putting the pieces together: an integrated model of program implementation.

    Science.gov (United States)

    Berkel, Cady; Mauricio, Anne M; Schoenfelder, Erin; Sandler, Irwin N

    2011-03-01

    Considerable evidence indicates that variability in implementation of prevention programs is related to the outcomes achieved by these programs. However, while implementation has been conceptualized as a multidimensional construct, few studies examine more than a single dimension, and no theoretical framework exists to guide research on the effects of implementation. We seek to address this need by proposing a theoretical model of the relations between the dimensions of implementation and outcomes of prevention programs that can serve to guide future implementation research. In this article, we focus on four dimensions of implementation, which we conceptualize as behaviors of program facilitators (fidelity, quality of delivery, and adaptation) and behaviors of participants (responsiveness) and present the evidence supporting these as predictors of program outcomes. We then propose a theoretical model by which facilitator and participant dimensions of implementation influence participant outcomes. Finally, we provide recommendations and directions for future implementation research.

  19. DNA computation model to solve 0-1 programming problem.

    Science.gov (United States)

    Zhang, Fengyue; Yin, Zhixiang; Liu, Bo; Xu, Jin

    2004-01-01

    0-1 programming problem is an important problem in opsearch with very widespread applications. In this paper, a new DNA computation model utilizing solution-based and surface-based methods is presented to solve the 0-1 programming problem. This model contains the major benefits of both solution-based and surface-based methods; including vast parallelism, extraordinary information density and ease of operation. The result, verified by biological experimentation, revealed the potential of DNA computation in solving complex programming problem.

  20. 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.

  1. A program of research in environmental modeling

    Science.gov (United States)

    1983-01-01

    A theoretical framework for the interpretation of satellite measurements of stratospheric temperature and trace gases is provided. This problem is quite complicated since the distributions of trace gases are dependent on dynamics and photochemistry. Therefore, the problem was attacked with models employing varying degrees of photochemical and dynamical complexity. The relationship between dynamics and trace gas transport and wave transience, dissipation and critical levels and the net (permanent) transport of trace gases, the role of photochemistry in trace gas transport, photochemistry and dynamics and altering the mean-zonal distribution of stratospheric ozone, and approximations to simplify the interpretation of observations and General Circulation Models are discussed.

  2. CoMD Implementation Suite in Emerging Programming Models

    Energy Technology Data Exchange (ETDEWEB)

    2014-09-23

    CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended to support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.

  3. Geometric model of robotic arc welding for automatic programming

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Geometric information is important for automatic programming of arc welding robot. Complete geometric models of robotic arc welding are established in this paper. In the geometric model of weld seam, an equation with seam length as its parameter is introduced to represent any weld seam. The method to determine discrete programming points on a weld seam is presented. In the geometric model of weld workpiece, three class primitives and CSG tree are used to describe weld workpiece. Detailed data structure is presented. In pose transformation of torch, world frame, torch frame and active frame are defined, and transformation between frames is presented. Based on these geometric models, an automatic programming software package for robotic arc welding, RAWCAD, is developed. Experiments show that the geometric models are practical and reliable.

  4. A new model for programming software in body sensor networks.

    Science.gov (United States)

    de A Barbosa, Talles M G; Sene, Iwens G; da Rocha, Adson F; de O Nascimento, Francisco A A; Carvalho, Joao L A; Carvalho, Hervaldo S

    2007-01-01

    A Body Sensor Network (BSN) must be designed to work autonomously. On the other hand, BSNs need mechanisms that allow changes in their behavior in order to become a clinically useful tool. The purpose of this paper is to present a new programming model that will be useful for programming BSN sensor nodes. This model is based on an intelligent intermediate-level compiler. The main purpose of the proposed compiler is to increase the efficiency in system use, and to increase the lifetime of the application, considering its requirements, hardware possibilities and specialist knowledge. With this model, it is possible to maintain the autonomous operation capability of the BSN and still offer tools that allow users with little grasp on programming techniques to program these systems.

  5. Endothelial cell culture model for replication of physiological profiles of pressure, flow, stretch, and shear stress in vitro.

    Science.gov (United States)

    Estrada, Rosendo; Giridharan, Guruprasad A; Nguyen, Mai-Dung; Roussel, Thomas J; Shakeri, Mostafa; Parichehreh, Vahidreza; Prabhu, Sumanth D; Sethu, Palaniappan

    2011-04-15

    The phenotype and function of vascular cells in vivo are influenced by complex mechanical signals generated by pulsatile hemodynamic loading. Physiologically relevant in vitro studies of vascular cells therefore require realistic environments where in vivo mechanical loading conditions can be accurately reproduced. To accomplish a realistic in vivo-like loading environment, we designed and fabricated an Endothelial Cell Culture Model (ECCM) to generate physiological pressure, stretch, and shear stress profiles associated with normal and pathological cardiac flow states. Cells within this system were cultured on a stretchable, thin (∼500 μm) planar membrane within a rectangular flow channel and subject to constant fluid flow. Under pressure, the thin planar membrane assumed a concave shape, representing a segment of the blood vessel wall. Pulsatility was introduced using a programmable pneumatically controlled collapsible chamber. Human aortic endothelial cells (HAECs) were cultured within this system under normal conditions and compared to HAECs cultured under static and "flow only" (13 dyn/cm(2)) control conditions using microscopy. Cells cultured within the ECCM were larger than both controls and assumed an ellipsoidal shape. In contrast to static control control cells, ECCM-cultured cells exhibited alignment of cytoskeletal actin filaments and high and continuous expression levels of β-catenin indicating an in vivo-like phenotype. In conclusion, design, fabrication, testing, and validation of the ECCM for culture of ECs under realistic pressure, flow, strain, and shear loading seen in normal and pathological conditions was accomplished. The ECCM therefore is an enabling technology that allows for study of ECs under physiologically relevant biomechanical loading conditions in vitro. © 2011 American Chemical Society

  6. Computer simulation modeling of abnormal behavior: a program approach.

    Science.gov (United States)

    Reilly, K D; Freese, M R; Rowe, P B

    1984-07-01

    A need for modeling abnormal behavior on a comprehensive, systematic basis exists. Computer modeling and simulation tools offer especially good opportunities to establish such a program of studies. Issues concern deciding which modeling tools to use, how to relate models to behavioral data, what level of modeling to employ, and how to articulate theory to facilitate such modeling. Four levels or types of modeling, two qualitative and two quantitative, are identified. Their properties are examined and interrelated to include illustrative applications to the study of abnormal behavior, with an emphasis on schizophrenia.

  7. 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.

  8. DNA replication origins in archaea

    OpenAIRE

    Zhenfang eWu; Jingfang eLiu; Haibo eYang; Hua eXiang

    2014-01-01

    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 ...

  9. On the scattering of DNA replication completion times

    Science.gov (United States)

    Meilikhov, E. Z.; Farzetdinova, R. M.

    2015-07-01

    Stochasticity of Eukaryotes' DNA replication should not lead to large fluctuations of replication times, which could result in mitotic catastrophes. Fundamental problem that cells face is how to be ensured that entire genome is replicated on time. We develop analytic approach of calculating DNA replication times, that being simplified and approximate, leads, nevertheless, to results practically coincident with those that were obtained by some sophisticated methods. In the framework of that model we consider replication times' scattering and discuss the influence of repair stopping on kinetics of DNA replication. Our main explicit formulae for DNA replication time t r ∝ ( N is the total number of DNA base pairs) is of general character and explains basic features of DNA replication kinetics.

  10. 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

    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...

  11. A Novel Nonlinear Programming Model for Distribution Protection Optimization

    NARCIS (Netherlands)

    Zambon, Eduardo; Bossois, Débora Z.; Garcia, Berilhes B.; Azeredo, Elias F.

    2009-01-01

    This paper presents a novel nonlinear binary programming model designed to improve the reliability indices of a distribution network. This model identifies the type and location of protection devices that should be installed in a distribution feeder and is a generalization of the classical optimizat

  12. Diet models with linear goal programming: impact of achievement functions

    NARCIS (Netherlands)

    Gerdessen, J.C.; Vries, de J.H.M.

    2015-01-01

    Background/Objectives: Diet models based on goal programming (GP) are valuable tools in designing diets that comply with nutritional, palatability and cost constraints. Results derived from GP models are usually very sensitive to the type of achievement function that is chosen. This paper aims to pr

  13. Details of Programming a Model of Children's Counting in ACTP.

    Science.gov (United States)

    Riley, Mary S.; Greeno, James G.

    Presented is an introduction to the operation and mechanics of the ACTP production system, a version of Anderson's (1976) ACT system. ACTP is already in use modeling geometry theorem proving and counting of a set of objects, and has been identified as a potentially useful programing framework for developing models of the cognitive processes used…

  14. Human Behavior Model Based Control Program for ACC Mobile Robot

    Directory of Open Access Journals (Sweden)

    Claudiu Pozna

    2006-07-01

    Full Text Available Present work is a part of the ACC autonomous car project. This paper will focuson the control program architecture. To design this architecture we will start from thehuman driver behavior model. Using this model we have constructed a three level controlprogram. Preliminary results are presented.

  15. A Primary Prevention Program: Teaching Models I and II.

    Science.gov (United States)

    Harlan, Nancy T; Tschiderer, Patricia A.

    Two teaching models of a service delivery program designed to prevent speech-language problems in lower socioeconomic children were compared. Specific goals included increasing mothers' awareness of the sensory input to which infants are responsive and increasing mothers' abilities to read infant nonverbal signals. In Model 1, two speech-language…

  16. 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…

  17. Modeling the complete Otto cycle: Preliminary version. [computer programming

    Science.gov (United States)

    Zeleznik, F. J.; Mcbride, B. J.

    1977-01-01

    A description is given of the equations and the computer program being developed to model the complete Otto cycle. The program incorporates such important features as: (1) heat transfer, (2) finite combustion rates, (3) complete chemical kinetics in the burned gas, (4) exhaust gas recirculation, and (5) manifold vacuum or supercharging. Changes in thermodynamic, kinetic and transport data as well as model parameters can be made without reprogramming. Preliminary calculations indicate that: (1) chemistry and heat transfer significantly affect composition and performance, (2) there seems to be a strong interaction among model parameters, and (3) a number of cycles must be calculated in order to obtain steady-state conditions.

  18. Use of a business excellence model to improve conservation programs.

    Science.gov (United States)

    Black, Simon; Groombridge, Jim

    2010-12-01

    The current shortfall in effectiveness within conservation biology is illustrated by increasing interest in "evidence-based conservation," whose proponents have identified the need to benchmark conservation initiatives against actions that lead to proven positive effects. The effectiveness of conservation policies, approaches, and evaluation is under increasing scrutiny, and in these areas models of excellence used in business could prove valuable. Typically, conservation programs require years of effort and involve rigorous long-term implementation processes. Successful balance of long-term efforts alongside the achievement of short-term goals is often compromised by management or budgetary constraints, a situation also common in commercial businesses. "Business excellence" is an approach many companies have used over the past 20 years to ensure continued success. Various business excellence evaluations have been promoted that include concepts that could be adapted and applied in conservation programs. We describe a conservation excellence model that shows how scientific processes and results can be aligned with financial and organizational measures of success. We applied the model to two well-documented species conservation programs. In the first, the Po'ouli program, several aspects of improvement were identified, such as more authority for decision making in the field and better integration of habitat management and population recovery processes. The second example, the black-footed ferret program, could have benefited from leadership effort to reduce bureaucracy and to encourage use of best-practice species recovery approaches. The conservation excellence model enables greater clarity in goal setting, more-effective identification of job roles within programs, better links between technical approaches and measures of biological success, and more-effective use of resources. The model could improve evaluation of a conservation program's effectiveness and may be

  19. 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.

  20. 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...

  1. Replication-Fork Dynamics

    NARCIS (Netherlands)

    Duderstadt, Karl E.; Reyes-Lamothe, Rodrigo; van Oijen, Antoine M.; Sherratt, David J.

    2014-01-01

    The proliferation of all organisms depends on the coordination of enzymatic events within large multiprotein replisomes that duplicate chromosomes. Whereas the structure and function of many core replisome components have been clarified, the timing and order of molecular events during replication re

  2. Coronavirus Attachment and Replication

    Science.gov (United States)

    1988-03-28

    synthesis during RNA replication of vesicular stomatitis virus. J. Virol. 49:303-309. Pedersen, N.C. 1976a. Feline infectious peritonitis: Something old...receptors on intestinal brush border membranes from normal host species were developed for canine (CCV), feline (FIPV), porcine (TGEV), human (HCV...gastroenteritis receptor on pig BBMs ...... ................. ... 114 Feline infectious peritonitis virus receptor on cat BBMs ... .............. 117 Human

  3. Constellation Program Life-cycle Cost Analysis Model (LCAM)

    Science.gov (United States)

    Prince, Andy; Rose, Heidi; Wood, James

    2008-01-01

    The Constellation Program (CxP) is NASA's effort to replace the Space Shuttle, return humans to the moon, and prepare for a human mission to Mars. The major elements of the Constellation Lunar sortie design reference mission architecture are shown. Unlike the Apollo Program of the 1960's, affordability is a major concern of United States policy makers and NASA management. To measure Constellation affordability, a total ownership cost life-cycle parametric cost estimating capability is required. This capability is being developed by the Constellation Systems Engineering and Integration (SE&I) Directorate, and is called the Lifecycle Cost Analysis Model (LCAM). The requirements for LCAM are based on the need to have a parametric estimating capability in order to do top-level program analysis, evaluate design alternatives, and explore options for future systems. By estimating the total cost of ownership within the context of the planned Constellation budget, LCAM can provide Program and NASA management with the cost data necessary to identify the most affordable alternatives. LCAM is also a key component of the Integrated Program Model (IPM), an SE&I developed capability that combines parametric sizing tools with cost, schedule, and risk models to perform program analysis. LCAM is used in the generation of cost estimates for system level trades and analyses. It draws upon the legacy of previous architecture level cost models, such as the Exploration Systems Mission Directorate (ESMD) Architecture Cost Model (ARCOM) developed for Simulation Based Acquisition (SBA), and ATLAS. LCAM is used to support requirements and design trade studies by calculating changes in cost relative to a baseline option cost. Estimated costs are generally low fidelity to accommodate available input data and available cost estimating relationships (CERs). LCAM is capable of interfacing with the Integrated Program Model to provide the cost estimating capability for that suite of tools.

  4. Using Virtual ATE Model to Migrate Test Programs

    Institute of Scientific and Technical Information of China (English)

    王晓明; 杨乔林

    1995-01-01

    Bacause of high development costs of IC (Integrated Circuit)test programs,recycling existing test programs from one kind of ATE (Automatic Test Equipment) to another or generating directly from CAD simulation modules to ATE is more and more valuable.In this paper,a new approach to migrating test programs is presented.A virtual ATE model based on object-oriented paradigm is developed;it runs Test C++ (an intermediate test control language) programs and TeIF(Test Inftermediate Format-an intermediate pattern),migrates test programs among three kinds of ATE (Ando DIC8032,Schlumberger S15 and GenRad 1732) and generates test patterns from two kinds of CAD 9Daisy and Panda) automatically.

  5. [Cancer screening in Hungary: World Bank supported model programs].

    Science.gov (United States)

    Bodó, M; Döbrössy, L; Liszka, G; Ottó, S; Péter, Z

    1997-07-13

    Since 1995, a model cancer screening program has been in operation in Hungary, the overall purpose of which is to promote the establishment of effective and efficient screening programs by means of adapting the internationally agreed principles of organized screening to the needs and opportunities in Hungary. The establishment and operation of a national population-based cancer registration system is an other aim of the Program. The model program--financed partly from a loan from the World Bank, partly from local funds provided by the Government of Hungary--is to develop standard procedure for cervical, breast and colorectal screening and to end up with tested recommendations for introduction of organized screening of proved effectiveness, integrated into the health care system, on country-wide service bases in Hungary.

  6. Modeling and prioritizing demand response programs in power markets

    Energy Technology Data Exchange (ETDEWEB)

    Aalami, H.A.; Moghaddam, M. Parsa; Yousefi, G.R. [Tarbiat Modares University, Tehran (Iran)

    2010-04-15

    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)

  7. 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.

  8. 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.

  9. From Mice to Men: research models of developmental programming

    OpenAIRE

    2013-01-01

    Developmental programming can be defined as a response to a specific challenge to the mammalian organism during a critical developmental time window that alters the trajectory of development with persistent effects on offspring phenotype and predisposition to future illness. We focus on the need for studies in relevant, well-characterized animal models in the context of recent research discoveries on the challenges, mechanisms and outcomes of developmental programming. We discuss commonalitie...

  10. Research on the Business English training model within MBA program

    OpenAIRE

    Natalia Yankovskaya; Olga Neklyudova

    2015-01-01

    The paper presents a brief summary of the research on the Business English training model within MBA program students. This study is devoted to the problem of developing a professional foreign language communicative competency of MBA program participants. A particular feature of additional MBA qualification is its international status which presupposes that its graduates (mid-level and top managers) should realize their professional tasks in a foreign language. The analysis of literary ...

  11. Deterministic Consistency: A Programming Model for Shared Memory Parallelism

    OpenAIRE

    Aviram, Amittai; Ford, Bryan

    2009-01-01

    The difficulty of developing reliable parallel software is generating interest in deterministic environments, where a given program and input can yield only one possible result. Languages or type systems can enforce determinism in new code, and runtime systems can impose synthetic schedules on legacy parallel code. To parallelize existing serial code, however, we would like a programming model that is naturally deterministic without language restrictions or artificial scheduling. We propose "...

  12. An Adaptive Neural Network Model for Nonlinear Programming Problems

    Institute of Scientific and Technical Information of China (English)

    Xiang-sun Zhang; Xin-jian Zhuo; Zhu-jun Jing

    2002-01-01

    In this paper a canonical neural network with adaptively changing synaptic weights and activation function parameters is presented to solve general nonlinear programming problems. The basic part of the model is a sub-network used to find a solution of quadratic programming problems with simple upper and lower bounds. By sequentially activating the sub-network under the control of an external computer or a special analog or digital processor that adjusts the weights and parameters, one then solves general nonlinear programming problems. Convergence proof and numerical results are given.

  13. Supplementary Educational Models in Canadian Neurosurgery Residency Programs.

    Science.gov (United States)

    Ryu, Won Hyung A; Chan, Sonny; Sutherland, Garnette R

    2017-03-01

    The proposed implementation of work hour restrictions has presented a significant challenge of maintaining the quality of resident education and ensuring adequate hands-on experience that is essential for novice surgeons. To maintain the level of resident surgical competency, revision of the apprentice model of surgical education to include supplementary educational methods, such as laboratory and virtual reality (VR) simulations, have become frequent topics of discussion. We aimed to better understand the role of supplementary educational methods in Canadian neurosurgery residency training. An online survey was sent to program directors of all 14 Canadian neurosurgical residency programs and active resident members of the Canadian Neurosurgical Society (N=85). We asked 16 questions focusing on topics of surgeon perception, current implementation and barriers to supplementary educational models. Of the 99 surveys sent, 8 out of 14 (57%) program directors and 37 out of 85 (44%) residents completed the survey. Of the 14 neurosurgery residency programs across Canada, 7 reported utilizing laboratory-based teaching within their educational plan, while only 3 programs reported using VR simulation as a supplementary teaching method. The biggest barriers to implementing supplementary educational methods were resident availability, lack of resources, and cost. Work-hour restrictions threaten to compromise the traditional apprentice model of surgical training. The potential value of supplementary educational methods for surgical education is evident, as reported by both program directors and residents across Canada. However, availability and utilization of laboratory and VR simulations are limited by numerous factors such as time constrains and lack of resources.

  14. 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.

  15. Immunogenicity and efficacy of intramuscular replication-defective and subunit vaccines against herpes simplex virus type 2 in the mouse genital model.

    Directory of Open Access Journals (Sweden)

    Simon Delagrave

    Full Text Available Herpes simplex virus type 2 (HSV-2 is a sexually transmitted virus that is highly prevalent worldwide, causing a range of symptoms that result in significant healthcare costs and human suffering. ACAM529 is a replication-defective vaccine candidate prepared by growing the previously described dl5-29 on a cell line appropriate for GMP manufacturing. This vaccine, when administered subcutaneously, was previously shown to protect mice from a lethal vaginal HSV-2 challenge and to afford better protection than adjuvanted glycoprotein D (gD in guinea pigs. Here we show that ACAM529 given via the intramuscular route affords significantly greater immunogenicity and protection in comparison with subcutaneous administration in the mouse vaginal HSV-2 challenge model. Further, we describe a side-by-side comparison of intramuscular ACAM529 with a gD vaccine across a range of challenge virus doses. While differences in protection against death are not significant, ACAM529 protects significantly better against mucosal infection, reducing peak challenge virus shedding at the highest challenge dose by over 500-fold versus 5-fold for gD. Over 27% (11/40 of ACAM529-immunized animals were protected from viral shedding while 2.5% (1/40 were protected by the gD vaccine. Similarly, 35% (7/20 of mice vaccinated with ACAM529 were protected from infection of their dorsal root ganglia while none of the gD-vaccinated mice were protected. These results indicate that measuring infection of the vaginal mucosa and of dorsal root ganglia over a range of challenge doses is more sensitive than evaluating survival at a single challenge dose as a means of directly comparing vaccine efficacy in the mouse vaginal challenge model. The data also support further investigation of ACAM529 for prophylaxis in human subjects.

  16. Genetic programming-based chaotic time series modeling

    Institute of Scientific and Technical Information of China (English)

    张伟; 吴智铭; 杨根科

    2004-01-01

    This paper proposes a Genetic Programming-Based Modeling(GPM)algorithm on chaotic time series. GP is used here to search for appropriate model structures in function space,and the Particle Swarm Optimization(PSO)algorithm is used for Nonlinear Parameter Estimation(NPE)of dynamic model structures. In addition,GPM integrates the results of Nonlinear Time Series Analysis(NTSA)to adjust the parameters and takes them as the criteria of established models.Experiments showed the effectiveness of such improvements on chaotic time series modeling.

  17. The Genomic Replication of the Crenarchaeal Virus SIRV2

    DEFF Research Database (Denmark)

    Martinez Alvarez, Laura

    of the crenarchaeal virus SIRV2, a model among archaeal viruses. SIRV2 was found to employ multiple replication mechanisms, with DNA synthesis starting by a strand-displacement mode that later derived in a rolling-circle replication from a circular intermediate. Interestingly, evidence for a secondary, bidirectional...... reinitiation events may partially explain the branched topology of the viral replication intermediates. We also analyzed the intracellular location of viral replication, showing the formation of viral peripheral replication centers in SIRV2-infected cells, where viral DNA synthesis and replication......-related proteins are concentrated. Our data indicates that the host DNA polymerase Dpo1 is also the viral replicative polymerase. Moreover, additional data suggests that other processes, such as translation, are also reorganized after infection. Based on our results, a model for the organization of viral...

  18. SISP : Simplified Interface for Stochastic Programming Establishing a hard link between mathematical programming modeling languages and SMPS codes

    CERN Document Server

    Condevaux Lanloy, Christian; King, A J

    2002-01-01

    The aim of this article is to propose a general approach to link a stochastic programming enabler to a mathematical programming modeling language. Modelers often choose to formulate their problems in well- tested, general purpose modeling languages such as GAMS and AMPL, but these modeling languages do not currently implement a natural syntax for stochastic programming. Specialized stochastic programming tools are available to efficiently generate and solve large-scale stochastic programs, but they lack many of the convenient features of the modeling languages. The lack of a well developed link between these tools and modeling languages prevents many modelers from accessing a powerful and convenient technique to take into account uncertainties. As an attempt to fill this gap, we will present SISP (Simplified Interface for Stochastic Programming), an interface between Algebraic Modeling Languages and specialized Stochastic Programming solvers, also known as SP solvers. 12 Refs.

  19. Physical properties of the benchmark models program supercritical wing

    Science.gov (United States)

    Dansberry, Bryan E.; Durham, Michael H.; Bennett, Robert M.; Turnock, David L.; Silva, Walter A.; Rivera, Jose A., Jr.

    1993-01-01

    The goal of the Benchmark Models Program is to provide data useful in the development and evaluation of aeroelastic computational fluid dynamics (CFD) codes. To that end, a series of three similar wing models are being flutter tested in the Langley Transonic Dynamics Tunnel. These models are designed to simultaneously acquire model response data and unsteady surface pressure data during wing flutter conditions. The supercritical wing is the second model of this series. It is a rigid semispan model with a rectangular planform and a NASA SC(2)-0414 supercritical airfoil shape. The supercritical wing model was flutter tested on a flexible mount, called the Pitch and Plunge Apparatus, that provides a well-defined, two-degree-of-freedom dynamic system. The supercritical wing model and associated flutter test apparatus is described and experimentally determined wind-off structural dynamic characteristics of the combined rigid model and flexible mount system are included.

  20. Understanding science teacher enhancement programs: Essential components and a model

    Science.gov (United States)

    Spiegel, Samuel Albert

    Researchers and practioners alike recognize that "the national goal that every child in the United States has access to high-quality school education in science and mathematics cannot be realized without the availability of effective professional development of teachers" (Hewson, 1997, p. 16). Further, there is a plethora of reports calling for the improvement of professional development efforts (Guskey & Huberman, 1995; Kyle, 1995; Loucks-Horsley, Hewson, Love, & Stiles, 1997). In this study I analyze a successful 3-year teacher enhancement program, one form of professional development, to: (1) identify essential components of an effective teacher enhancement program; and (2) create a model to identify and articulate the critical issues in designing, implementing, and evaluating teacher enhancement programs. Five primary sources of information were converted into data: (1) exit questionnaires, (2) exit surveys, (3) exit interview transcripts, (4) focus group transcripts, and (5) other artifacts. Additionally, a focus group was used to conduct member checks. Data were analyzed in an iterative process which led to the development of the list of essential components. The Components are categorized by three organizers: Structure (e.g., science research experience, a mediator throughout the program), Context (e.g., intensity, collaboration), and Participant Interpretation (e.g., perceived to be "safe" to examine personal beliefs and practices, actively engaged). The model is based on: (1) a 4-year study of a successful teacher enhancement program; (2) an analysis of professional development efforts reported in the literature; and (3) reflective discussions with implementors, evaluators, and participants of professional development programs. The model consists of three perspectives, cognitive, symbolic interaction, and organizational, representing different viewpoints from which to consider issues relevant to the success of a teacher enhancement program. These

  1. 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.

  2. ICU early physical rehabilitation programs: financial modeling of cost savings.

    Science.gov (United States)

    Lord, Robert K; Mayhew, Christopher R; Korupolu, Radha; Mantheiy, Earl C; Friedman, Michael A; Palmer, Jeffrey B; Needham, Dale M

    2013-03-01

    To evaluate the potential annual net cost savings of implementing an ICU early rehabilitation program. Using data from existing publications and actual experience with an early rehabilitation program in the Johns Hopkins Hospital Medical ICU, we developed a model of net financial savings/costs and presented results for ICUs with 200, 600, 900, and 2,000 annual admissions, accounting for both conservative- and best-case scenarios. Our example scenario provided a projected financial analysis of the Johns Hopkins Medical ICU early rehabilitation program, with 900 admissions per year, using actual reductions in length of stay achieved by this program. U.S.-based adult ICUs. Financial modeling of the introduction of an ICU early rehabilitation program. Net cost savings generated in our example scenario, with 900 annual admissions and actual length of stay reductions of 22% and 19% for the ICU and floor, respectively, were $817,836. Sensitivity analyses, which used conservative- and best-case scenarios for length of stay reductions and varied the per-day ICU and floor costs, across ICUs with 200-2,000 annual admissions, yielded financial projections ranging from -$87,611 (net cost) to $3,763,149 (net savings). Of the 24 scenarios included in these sensitivity analyses, 20 (83%) demonstrated net savings, with a relatively small net cost occurring in the remaining four scenarios, mostly when simultaneously combining the most conservative assumptions. A financial model, based on actual experience and published data, projects that investment in an ICU early rehabilitation program can generate net financial savings for U.S. hospitals. Even under the most conservative assumptions, the projected net cost of implementing such a program is modest relative to the substantial improvements in patient outcomes demonstrated by ICU early rehabilitation programs.

  3. Reversible Switching of Cooperating Replicators

    Science.gov (United States)

    Urtel, Georg C.; Rind, Thomas; Braun, Dieter

    2017-02-01

    How can molecules with short lifetimes preserve their information over millions of years? For evolution to occur, information-carrying molecules have to replicate before they degrade. Our experiments reveal a robust, reversible cooperation mechanism in oligonucleotide replication. Two inherently slow replicating hairpin molecules can transfer their information to fast crossbreed replicators that outgrow the hairpins. The reverse is also possible. When one replication initiation site is missing, single hairpins reemerge from the crossbreed. With this mechanism, interacting replicators can switch between the hairpin and crossbreed mode, revealing a flexible adaptation to different boundary conditions.

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

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth; Peleska, Jan

    2016-01-01

    , 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......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...

  5. 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.

  6. 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.

  7. Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Kai, Mihoko; Wang, Teresa S.-F

    2003-11-27

    Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Pol{kappa}). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development.

  8. Building enterprise reuse program--A model-based approach

    Institute of Scientific and Technical Information of China (English)

    梅宏; 杨芙清

    2002-01-01

    Reuse is viewed as a realistically effective approach to solving software crisis. For an organization that wants to build a reuse program, technical and non-technical issues must be considered in parallel. In this paper, a model-based approach to building systematic reuse program is presented. Component-based reuse is currently a dominant approach to software reuse. In this approach, building the right reusable component model is the first important step. In order to achieve systematic reuse, a set of component models should be built from different perspectives. Each of these models will give a specific view of the components so as to satisfy different needs of different persons involved in the enterprise reuse program. There already exist some component models for reuse from technical perspectives. But less attention is paid to the reusable components from a non-technical view, especially from the view of process and management. In our approach, a reusable component model--FLP model for reusable component--is introduced. This model describes components from three dimensions (Form, Level, and Presentation) and views components and their relationships from the perspective of process and management. It determines the sphere of reusable components, the time points of reusing components in the development process, and the needed means to present components in terms of the abstraction level, logic granularity and presentation media. Being the basis on which the management and technical decisions are made, our model will be used as the kernel model to initialize and normalize a systematic enterprise reuse program.

  9. Different rates of DNA replication at early versus late S-phase sections: multiscale modeling of stochastic events related to DNA content/EdU (5-ethynyl-2'deoxyuridine) incorporation distributions.

    Science.gov (United States)

    Li, Biao; Zhao, Hong; Rybak, Paulina; Dobrucki, Jurek W; Darzynkiewicz, Zbigniew; Kimmel, Marek

    2014-09-01

    Mathematical modeling allows relating molecular events to single-cell characteristics assessed by multiparameter cytometry. In the present study we labeled newly synthesized DNA in A549 human lung carcinoma cells with 15-120 min pulses of EdU. All DNA was stained with DAPI and cellular fluorescence was measured by laser scanning cytometry. The frequency of cells in the ascending (left) side of the "horseshoe"-shaped EdU/DAPI bivariate distributions reports the rate of DNA replication at the time of entrance to S phase while their frequency in the descending (right) side is a marker of DNA replication rate at the time of transition from S to G2 phase. To understand the connection between molecular-scale events and scatterplot asymmetry, we developed a multiscale stochastic model, which simulates DNA replication and cell cycle progression of individual cells and produces in silico EdU/DAPI scatterplots. For each S-phase cell the time points at which replication origins are fired are modeled by a non-homogeneous Poisson Process (NHPP). Shifted gamma distributions are assumed for durations of cell cycle phases (G1, S and G2 M), Depending on the rate of DNA synthesis being an increasing or decreasing function, simulated EdU/DAPI bivariate graphs show predominance of cells in left (early-S) or right (late-S) side of the horseshoe distribution. Assuming NHPP rate estimated from independent experiments, simulated EdU/DAPI graphs are nearly indistinguishable from those experimentally observed. This finding proves consistency between the S-phase DNA-replication rate based on molecular-scale analyses, and cell population kinetics ascertained from EdU/DAPI scatterplots and demonstrates that DNA replication rate at entrance to S is relatively slow compared with its rather abrupt termination during S to G2 transition. Our approach opens a possibility of similar modeling to study the effect of anticancer drugs on DNA replication/cell cycle progression and also to quantify other

  10. EVALUASI PROGRAM KONSELING DI SMP KOTA MALANG: DISCREPANCY MODEL

    Directory of Open Access Journals (Sweden)

    Wahyu Nanda Eka Saputra

    2015-12-01

    Full Text Available Penelitian ini bertujuan untuk  mengetahui kesenjangan antara performansi program konseling di SMP Kota Malang dengan standar yang telah ditentukan. Penelitian ini menggunakan standar dari Guidelines for Performance Based Professional School Counselor Evaluation. Standar tersebut berbunyi “konselor sekolah professional melaksanakan konseling pada siswa secara individual dan kelompok yang teridentifikasi kebutuhan dan masalahnya dan memerlukan bantuan”. Penelitian ini adalah penelitian evaluasi. Evaluasi yang dilakukan dalam penelitian ini menggunakan discrepancy model. Pendekatan yang digunakan adalah pendekatan sistem yang difokuskan pada perencanaan, pelaksanaan, dan evaluasi program konseling. Berdasarkan analisis hasil evaluasi, program konseling di SMP Kota Malang masih jauh dari standar. Hasil penelitian ini merekomendasikan kepada konselor untuk memperbaiki kualitas pelaksanaan program konseling, sehingga memberikan pengaruh positif bagi siswa.

  11. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    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...

  12. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    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...

  13. COMPLEX PROGRAMS FOR MODELING HIGHWAY: PARK, PROFILE AND COMPOSITION

    Directory of Open Access Journals (Sweden)

    M. Iu. Smirnov

    2014-01-01

    Full Text Available The main part of developing computer-aided design of roads are simulation systems to see the road in action. Modeling of the functioning of the road in such a simulation system - this test road design in the computer. This article describes three modules: PARK, PROFILE, COMPOSITION and comprising a set of process simulation programs functioning road. A significant increase in the accuracy of simulation results provides software parks established normative reference database of technical and economic parameters of vehicles belonging to the stream. Completeness framework allows continuous adjustment and constant up-dating of the parameters types of cars in different scales calculation excludes construction and operating costs in justifying economic calculations optimality design solutions and increases the reliability of evaluating the effectiveness of capital investments in the construction and reconstruction of roads. Optimization of the design solutions in general, as a single continuous sequence of combinations of elements contributes to road profile program that analyzes the geometric elements of the plan, longitudinal section, compressing the geometry information of the way for the subsequent modeling of the functioning of the road. Program PROFILE (and built on its basis BASIS program, PROFILE is a nexus between the projecting programs and programs that simulate traffic. Transport and road performance computer modeled for a particular stream of automobile. Technical and economic parameters of vehicles belonging to the flow (up to 20, which is sufficient for practical and research tasks and their percentage in the flow of the program selects COMPOSITION regulatory reference framework articulated earlier PARK module and writes them to a working file for their subsequent use module RIDE.

  14. A comprehensive operational semantics of the SCOOP programming model

    CERN Document Server

    Morandi, Benjamin; Meyer, Bertrand

    2011-01-01

    Operational semantics has established itself as a flexible but rigorous means to describe the meaning of programming languages. Oftentimes, it is felt necessary to keep a semantics small, for example to facilitate its use for model checking by avoiding state space explosion. However, omitting many details in a semantics typically makes results valid for a limited core language only, leaving a wide gap towards any real implementation. In this paper we present a full-fledged semantics of the concurrent object-oriented programming language SCOOP (Simple Concurrent Object-Oriented Programming). The semantics has been found detailed enough to guide an implementation of the SCOOP compiler and runtime system, and to detect and correct a variety of errors and ambiguities in the original informal specification and prototype implementation. In our formal specification, we use abstract data types with preconditions and axioms to describe the state, and introduce a number of special run-time operations to model the runti...

  15. 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.

  16. Model forest program: Year in review, 1992-1993

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    As part of the Green Plan, introduced by the Federal Government in late 1990, a network of model forests was developed to demonstrate the concept of sustainable forest management in practical terms on a working scale. This annual report describes the competitive site selection process, the forests involved in the project, program milestones, the operation of model forests, and highlights of the project. Financial data is included.

  17. Initiation of adenovirus DNA replication.

    OpenAIRE

    Reiter, T; Fütterer, J; Weingärtner, B; Winnacker, E L

    1980-01-01

    In an attempt to study the mechanism of initiation of adenovirus DNA replication, an assay was developed to investigate the pattern of DNA synthesis in early replicative intermediates of adenovirus DNA. By using wild-type virus-infected cells, it was possible to place the origin of adenovirus type 2 DNA replication within the terminal 350 to 500 base pairs from either of the two molecular termini. In addition, a variety of parameters characteristic of adenovirus DNA replication were compared ...

  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...

  19. Program Demand Cost Model for Alaskan Schools. Eighth Edition.

    Science.gov (United States)

    Morgan, Michael; Mearig, Tim; Coffee, Nathan

    The State of Alaska Department of Education has created a handbook for establishing budgets for the following three types of construction projects: new schools or additions; renovations; and combined new work and renovations. The handbook supports a demand cost model computer program that includes detailed renovation cost data, itemized by…

  20. Duals for classical inventory models via generalized geometric programming

    OpenAIRE

    Carlton H. Scott; Thomas R. Jefferson; Soheila Jorjani

    2004-01-01

    Inventory problems generally have a structure that can be exploited for computational purposes. Here, we look at the duals of two seemingly unrelated inventory models that suggest an interesting duality between discrete time optimal control and optimization over an ordered sequence of variables. Concepts from conjugate duality and generalized geometric programming are used to establish the duality.

  1. 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…

  2. 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…

  3. The Diversity Challenge: A Collection of Model Programs.

    Science.gov (United States)

    Mellander, Gustavo A., Ed.; Prochaska, Fred, Ed.

    Model programs designed to promote diversity within the West Valley-Mission Community College District (WVMCCD) in California are discussed and described in this report. First, an introductory chapter, "The Importance of Cultural Issues to Higher Education," by Gustavo A. Mellander and Fred Prochaska, reviews the diversity recommendations of the…

  4. DISTRIBUTED APPROACH to WEB PAGE CATEGORIZATION USING MAPREDUCE PROGRAMMING MODEL

    Directory of Open Access Journals (Sweden)

    P.Malarvizhi

    2011-12-01

    Full Text Available The web is a large repository of information and to facilitate the search and retrieval of pages from it,categorization of web documents is essential. An effective means to handle the complexity of information retrieval from the internet is through automatic classification of web pages. Although lots of automatic classification algorithms and systems have been presented, most of the existing approaches are computationally challenging. In order to overcome this challenge, we have proposed a parallel algorithm, known as MapReduce programming model to automatically categorize the web pages. This approach incorporates three concepts. They are web crawler, MapReduce programming model and the proposed web page categorization approach. Initially, we have utilized web crawler to mine the World Wide Web and the crawled web pages are then directly given as input to the MapReduce programming model. Here the MapReduce programming model adapted to our proposed web page categorization approach finds the appropriate category of the web page according to its content. The experimental results show that our proposed parallel web page categorization approach achieves satisfactory results in finding the right category for any given web page.

  5. A Context-Adaptive Model for Program Evaluation.

    Science.gov (United States)

    Lynch, Brian K.

    1990-01-01

    Presents an adaptable, context-sensitive model for ESL/EFL program evaluation, consisting of seven steps that guide an evaluator through consideration of relevant issues, information, and design elements. Examples from an evaluation of the Reading for Science and Technology Project at the University of Guadalajara, Mexico are given. (31…

  6. 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…

  7. The Arctic Climate Modeling Program: Professional Development for Rural Teachers

    Science.gov (United States)

    Bertram, Kathryn Berry

    2010-01-01

    The Arctic Climate Modeling Program (ACMP) offered yearlong science, technology, engineering, and math (STEM) professional development to teachers in rural Alaska. Teacher training focused on introducing youth to workforce technologies used in Arctic research. Due to challenges in making professional development accessible to rural teachers, ACMP…

  8. A Model for Using Triadic Supervision in Counselor Preparation Programs

    Science.gov (United States)

    Lawson, Gerard; Hein, Serge F.; Getz, Hildy

    2009-01-01

    The Council for Accreditation of Counseling and Related Educational Programs (2001) has approved the use of triadic supervision as an alternative to individual supervision in clinical instruction. However, literature describing this mode of supervision is very limited. A model for triadic supervision is described, including presession planning,…

  9. Advanced parallel programming models research and development opportunities.

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Zhaofang.; Brightwell, Ronald Brian

    2004-07-01

    There is currently a large research and development effort within the high-performance computing community on advanced parallel programming models. This research can potentially have an impact on parallel applications, system software, and computing architectures in the next several years. Given Sandia's expertise and unique perspective in these areas, particularly on very large-scale systems, there are many areas in which Sandia can contribute to this effort. This technical report provides a survey of past and present parallel programming model research projects and provides a detailed description of the Partitioned Global Address Space (PGAS) programming model. The PGAS model may offer several improvements over the traditional distributed memory message passing model, which is the dominant model currently being used at Sandia. This technical report discusses these potential benefits and outlines specific areas where Sandia's expertise could contribute to current research activities. In particular, we describe several projects in the areas of high-performance networking, operating systems and parallel runtime systems, compilers, application development, and performance evaluation.

  10. Solving linear integer programming problems by a novel neural model.

    Science.gov (United States)

    Cavalieri, S

    1999-02-01

    The paper deals with integer linear programming problems. As is well known, these are extremely complex problems, even when the number of integer variables is quite low. Literature provides examples of various methods to solve such problems, some of which are of a heuristic nature. This paper proposes an alternative strategy based on the Hopfield neural network. The advantage of the strategy essentially lies in the fact that hardware implementation of the neural model allows for the time required to obtain a solution so as not depend on the size of the problem to be solved. The paper presents a particular class of integer linear programming problems, including well-known problems such as the Travelling Salesman Problem and the Set Covering Problem. After a brief description of this class of problems, it is demonstrated that the original Hopfield model is incapable of supplying valid solutions. This is attributed to the presence of constant bias currents in the dynamic of the neural model. A demonstration of this is given and then a novel neural model is presented which continues to be based on the same architecture as the Hopfield model, but introduces modifications thanks to which the integer linear programming problems presented can be solved. Some numerical examples and concluding remarks highlight the solving capacity of the novel neural model.

  11. 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…

  12. 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…

  13. Control of DNA replication by anomalous reaction-diffusion kinetics

    Science.gov (United States)

    Bechhoefer, John; Gauthier, Michel

    2010-03-01

    DNA replication requires two distinct processes: the initiation of pre-licensed replication origins and the propagation of replication forks away from the fired origins. Experiments indicate that these origins are triggered over the whole genome at a rate I(t) (the number of initiations per unreplicated length per time) that increases throughout most of the synthesis (S) phase, before rapidly decreasing to zero at the end of the replication process. We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.

  14. Replication data collection highlights value in diversity of replication attempts

    Science.gov (United States)

    DeSoto, K. Andrew; Schweinsberg, Martin

    2017-01-01

    Researchers agree that replicability and reproducibility are key aspects of science. A collection of Data Descriptors published in Scientific Data presents data obtained in the process of attempting to replicate previously published research. These new replication data describe published and unpublished projects. The different papers in this collection highlight the many ways that scientific replications can be conducted, and they reveal the benefits and challenges of crucial replication research. The organizers of this collection encourage scientists to reuse the data contained in the collection for their own work, and also believe that these replication examples can serve as educational resources for students, early-career researchers, and experienced scientists alike who are interested in learning more about the process of replication. PMID:28291224

  15. Submicron Composite Mirror Replication (PDRT08-027) Project

    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...

  16. 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.

  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. Propeller aircraft interior noise model: User's manual for computer program

    Science.gov (United States)

    Wilby, E. G.; Pope, L. D.

    1985-01-01

    A computer program entitled PAIN (Propeller Aircraft Interior Noise) has been developed to permit calculation of the sound levels in the cabin of a propeller-driven airplane. The fuselage is modeled as a cylinder with a structurally integral floor, the cabin sidewall and floor being stiffened by ring frames, stringers and floor beams of arbitrary configurations. The cabin interior is covered with acoustic treatment and trim. The propeller noise consists of a series of tones at harmonics of the blade passage frequency. Input data required by the program include the mechanical and acoustical properties of the fuselage structure and sidewall trim. Also, the precise propeller noise signature must be defined on a grid that lies in the fuselage skin. The propeller data are generated with a propeller noise prediction program such as the NASA Langley ANOPP program. The program PAIN permits the calculation of the space-average interior sound levels for the first ten harmonics of a propeller rotating alongside the fuselage. User instructions for PAIN are given in the report. Development of the analytical model is presented in NASA CR 3813.

  19. 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.

  20. Gstat: a program for geostatistical modelling, prediction and simulation

    Science.gov (United States)

    Pebesma, Edzer J.; Wesseling, Cees G.

    1998-01-01

    Gstat is a computer program for variogram modelling, and geostatistical prediction and simulation. It provides a generic implementation of the multivariable linear model with trends modelled as a linear function of coordinate polynomials or of user-defined base functions, and independent or dependent, geostatistically modelled, residuals. Simulation in gstat comprises conditional or unconditional (multi-) Gaussian sequential simulation of point values or block averages, or (multi-) indicator sequential simulation. Besides many of the popular options found in other geostatistical software packages, gstat offers the unique combination of (i) an interactive user interface for modelling variograms and generalized covariances (residual variograms), that uses the device-independent plotting program gnuplot for graphical display, (ii) support for several ascii and binary data and map file formats for input and output, (iii) a concise, intuitive and flexible command language, (iv) user customization of program defaults, (v) no built-in limits, and (vi) free, portable ANSI-C source code. This paper describes the class of problems gstat can solve, and addresses aspects of efficiency and implementation, managing geostatistical projects, and relevant technical details.

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

    KAUST Repository

    Kaushik, Dinesh K.

    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.

  2. DNA Replication via Entanglement Swapping

    CERN Document Server

    Pusuluk, Onur

    2010-01-01

    Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Molecular biology assumes that function is explained by structure, the complementary geometries of molecules and weak intermolecular hydrogen bonds. However, both this assumption and its converse are possible if organic molecules and quantum circuits/protocols are considered as hardware and software of living systems that are co-optimized during evolution. In this paper, we try to model DNA replication as a multiparticle entanglement swapping with a reliable qubit representation of nucleotides. In the model, molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements.

  3. Anatomy of Mammalian Replication Domains

    Science.gov (United States)

    Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2017-01-01

    Genetic information is faithfully copied by DNA replication through many rounds of cell division. In mammals, DNA is replicated in Mb-sized chromosomal units called “replication domains.” While genome-wide maps in multiple cell types and disease states have uncovered both dynamic and static properties of replication domains, we are still in the process of understanding the mechanisms that give rise to these properties. A better understanding of the molecular basis of replication domain regulation will bring new insights into chromosome structure and function. PMID:28350365

  4. Development of SPAWM: selection program for available watershed models.

    Science.gov (United States)

    Cho, Yongdeok; Roesner, Larry A

    2014-01-01

    A selection program for available watershed models (also known as SPAWM) was developed. Thirty-three commonly used watershed models were analyzed in depth and classified in accordance to their attributes. These attributes consist of: (1) land use; (2) event or continuous; (3) time steps; (4) water quality; (5) distributed or lumped; (6) subsurface; (7) overland sediment; and (8) best management practices. Each of these attributes was further classified into sub-attributes. Based on user selected sub-attributes, the most appropriate watershed model is selected from the library of watershed models. SPAWM is implemented using Excel Visual Basic and is designed for use by novices as well as by experts on watershed modeling. It ensures that the necessary sub-attributes required by the user are captured and made available in the selected watershed model.

  5. SMART - a computer program for modelling stellar atmospheres

    CERN Document Server

    Aret, Anna; Poolamäe, Raivo; Sapar, Lili

    2013-01-01

    Program SMART (Spectra and Model Atmospheres by Radiative Transfer) has been composed for modelling atmospheres and spectra of hot stars (O, B and A spectral classes) and studying different physical processes in them (Sapar & Poolam\\"ae 2003, Sapar et al. 2007). Line-blanketed models are computed assuming plane-parallel, static and horizontally homogeneous atmosphere in radiative, hydrostatic and local thermodynamic equilibrium. Main advantages of SMART are its shortness, simplicity, user friendliness and flexibility for study of different physical processes. SMART successfully runs on PC both under Windows and Linux.

  6. Immune modelling and programming of a mobile robot demo

    Institute of Scientific and Technical Information of China (English)

    GONG Tao; CAI Zi-xing; HE Han-gen

    2006-01-01

    An artificial immune system was modelled with self/non-self selection to overcome abnormity in a mobile robot demo. The immune modelling includes the innate immune modelling and the adaptive immune modelling. The self/non-self selection includes detection and recognition, and the self/non-self detection is based on the normal model of the demo. After the detection, the non-self recognition is based on learning unknown non-self for the adaptive immunization. The learning was designed on the neural network or on the learning mechanism from examples. The last step is elimination of all the non-self and failover of the demo. The immunization of the mobile robot demo is programmed with Java to test effectiveness of the approach. Some worms infected the mobile robot demo, and caused the abnormity. The results of the immunization simulations show that the immune program can detect 100% worms,recognize all known Worms and most unknown worms, and eliminate the worms. Moreover, the damaged files of the mobile robot demo can all be repaired through the normal model and immunization. Therefore, the immune modelling of the mobile robot demo is effective and programmable in some anti-worms and abnormity detection applications.

  7. Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models.

    Science.gov (United States)

    Pope, Bernard J; Fitch, Blake G; Pitman, Michael C; Rice, John J; Reumann, Matthias

    2011-01-01

    Future multiscale and multiphysics models must use the power of high performance computing (HPC) systems to enable research into human disease, translational medical science, and treatment. Previously we showed that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message passing processes (e.g. the message passing interface (MPI)) with multithreading (e.g. OpenMP, POSIX pthreads). The objective of this work is to compare the performance of such hybrid programming models when applied to the simulation of a lightweight multiscale cardiac model. Our results show that the hybrid models do not perform favourably when compared to an implementation using only MPI which is in contrast to our results using complex physiological models. Thus, with regards to lightweight multiscale cardiac models, the user may not need to increase programming complexity by using a hybrid programming approach. However, considering that model complexity will increase as well as the HPC system size in both node count and number of cores per node, it is still foreseeable that we will achieve faster than real time multiscale cardiac simulations on these systems using hybrid programming models.

  8. FBH1 Catalyzes Regression of Stalled Replication Forks

    DEFF Research Database (Denmark)

    Fugger, Kasper; Mistrik, Martin; Neelsen, Kai J

    2015-01-01

    DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression...... a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks....... of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity...

  9. 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

  10. From Mice to Men: research models of developmental programming.

    Science.gov (United States)

    Rabadán-Diehl, C; Nathanielsz, P

    2013-02-01

    Developmental programming can be defined as a response to a specific challenge to the mammalian organism during a critical developmental time window that alters the trajectory of development with persistent effects on offspring phenotype and predisposition to future illness. We focus on the need for studies in relevant, well-characterized animal models in the context of recent research discoveries on the challenges, mechanisms and outcomes of developmental programming. We discuss commonalities and differences in general principles of developmental programming as they apply to several species, including humans. The consequences of these differences are discussed. Obesity, metabolic disorders and cardiovascular diseases are associated with the highest percentage of morbidity and mortality worldwide. Although many of the causes are associated with lifestyle, high-energy diets and lack of physical activity, recent evidence has linked developmental programming to the epidemic of metabolic diseases. A better understanding of comparative systems physiology of mother, fetus and neonate using information provided by rapid advances in molecular biology has the potential to improve the lifetime health of future generations by providing better women's health, diagnostic tools and preventative and therapeutic interventions in individuals exposed during their development to programming influences.

  11. Characterization and modeling of fast programming bits in flash EEPROM

    Science.gov (United States)

    Nkansah, F.; Hatalis, M.; Olasupo, K.

    2000-11-01

    The effects of flash EEPROM floating gate (FG) morphology on the generation and density of fast programming bits in a 2Mbit flash EEPROM array has been characterized. These fast programming bits exhibit identical subthreshold characteristics similar to that of a normal bit after UV erase, thus establishing that the initial charge stored on the FG of both fast and normal bit is the same. Experimental results clearly indicates that the fast programming phenomena result from an interaction of the programming process with the FG polysilicon microstructure. An in-depth experimentation previously reported, reveals that the FG poly deposition and doping processes are crucial for controlling the desired Fowler-Nordheim tunneling. A correlation is established between the fast bit density observed in the memory arrays, the FG polysilicon grain size and tunneling field enhancement factor μ( Rc). A compact model of the fast programming bit memory threshold voltage as a function of the effective FG polysilicon grain area factor Geff, and tunneling field enhancement factor μ( Rc) has been developed for the first time.

  12. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.

    Science.gov (United States)

    Löb, D; Lengert, N; Chagin, V O; Reinhart, M; Casas-Delucchi, C S; Cardoso, M C; Drossel, B

    2016-04-07

    DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

  13. 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.

  14. 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...

  15. THE SEPARATION OF URANIUM ISOTOPES BY GASEOUS DIFFUSION: A LINEAR PROGRAMMING MODEL,

    Science.gov (United States)

    URANIUM, ISOTOPE SEPARATION), (*GASEOUS DIFFUSION SEPARATION, LINEAR PROGRAMMING ), (* LINEAR PROGRAMMING , GASEOUS DIFFUSION SEPARATION), MATHEMATICAL MODELS, GAS FLOW, NUCLEAR REACTORS, OPERATIONS RESEARCH

  16. 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

  17. 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....... It is illustrated by means of a case study from the railway domain, how this can be achieved, using concepts from the theory of institutions. This also enables the utilisation of verification tools in different formalisms, despite the fact that these tools are usually developed for one specific formal method....

  18. 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.

  19. 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

  20. A Hybrid Program Projects Selection Model for Nonprofit TV Stations

    Directory of Open Access Journals (Sweden)

    Kuei-Lun Chang

    2015-01-01

    Full Text Available This study develops a hybrid multiple criteria decision making (MCDM model to select program projects for nonprofit TV stations on the basis of managers’ perceptions. By the concept of balanced scorecard (BSC and corporate social responsibility (CSR, we collect criteria for selecting the best program project. Fuzzy Delphi method, which can lead to better criteria selection, is used to modify criteria. Next, considering the interdependence among the selection criteria, analytic network process (ANP is then used to obtain the weights of them. To avoid calculation and additional pairwise comparisons of ANP, technique for order preference by similarity to ideal solution (TOPSIS is used to rank the alternatives. A case study is presented to demonstrate the applicability of the proposed model.

  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. 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.

  3. From Safety Critical Java Programs to Timed Process Models

    DEFF Research Database (Denmark)

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

    2015-01-01

    built and the tools have been used to analyse a number of systems for properties such as worst case execution time, schedulability and energy optimization [12–14,19,34,36,38]. In this paper we will elaborate on the theoretical underpinning of the translation from Java programs to timed automata models...... frameworks, we have in recent years pursued an agenda of translating hard-real-time embedded safety critical programs written in the Safety Critical Java Profile [33] into networks of timed automata [4] and subjecting those to automated analysis using the UPPAAL model checker [10]. Several tools have been...... and briefly summarize some of the results based on this translation. Furthermore, we discuss future work, especially relations to the work in [16,24] as Java recently has adopted first class higher order functions in the form of lambda abstractions....

  4. Unifying Model-Based and Reactive Programming within a Model-Based Executive

    Science.gov (United States)

    Williams, Brian C.; Gupta, Vineet; Norvig, Peter (Technical Monitor)

    1999-01-01

    Real-time, model-based, deduction has recently emerged as a vital component in AI's tool box for developing highly autonomous reactive systems. Yet one of the current hurdles towards developing model-based reactive systems is the number of methods simultaneously employed, and their corresponding melange of programming and modeling languages. This paper offers an important step towards unification. We introduce RMPL, a rich modeling language that combines probabilistic, constraint-based modeling with reactive programming constructs, while offering a simple semantics in terms of hidden state Markov processes. We introduce probabilistic, hierarchical constraint automata (PHCA), which allow Markov processes to be expressed in a compact representation that preserves the modularity of RMPL programs. Finally, a model-based executive, called Reactive Burton is described that exploits this compact encoding to perform efficIent simulation, belief state update and control sequence generation.

  5. Optimizing Marine Corps Personnel Assignments Using an Integer Programming Model

    Science.gov (United States)

    2012-12-01

    would assist the Monitors in the assignment process. Though these studies contain very thorough analyses, they differ from the approach taken in this...thesis in that they do not look into using a low cost, yet very efficient, decision modeling approach of integer programming as a method of...2012 BAH Rates-with Dependents. Defense Travel Mangement Office. (2011, December). 2012 BAH Rates-without Dependents. M ileage C ost 1 Per D iem

  6. Replicated Spectrographs in Astronomy

    CERN Document Server

    Hill, Gary J

    2014-01-01

    As telescope apertures increase, the challenge of scaling spectrographic astronomical instruments becomes acute. The next generation of extremely large telescopes (ELTs) strain the availability of glass blanks for optics and engineering to provide sufficient mechanical stability. While breaking the relationship between telescope diameter and instrument pupil size by adaptive optics is a clear path for small fields of view, survey instruments exploiting multiplex advantages will be pressed to find cost-effective solutions. In this review we argue that exploiting the full potential of ELTs will require the barrier of the cost and engineering difficulty of monolithic instruments to be broken by the use of large-scale replication of spectrographs. The first steps in this direction have already been taken with the soon to be commissioned MUSE and VIRUS instruments for the Very Large Telescope and the Hobby-Eberly Telescope, respectively. MUSE employs 24 spectrograph channels, while VIRUS has 150 channels. We compa...

  7. 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.

  8. The Viral Polymerase Inhibitor 2 '-C-Methylcytidine Inhibits Norwalk Virus Replication and Protects against Norovirus-Induced Diarrhea and Mortality in a Mouse Model

    OpenAIRE

    2013-01-01

    Human noroviruses are a major cause of food-borne illness, accountable for 50% of all-etiologies outbreaks of acute gastroenteritis (in both developing and developed countries). There is no vaccine or antiviral drug for the prophylaxis or treatment of norovirus-induced gastroenteritis. We recently reported the inhibitory effect of 2'-C-methylcytidine (2CMC), a hepatitis C virus polymerase inhibitor, on the in vitro replication of murine norovirus (MNV). Here we evaluated the inhibitory effect...

  9. Modelling dynamic programming problems by generalized d-graphs

    CERN Document Server

    Kátai, Zoltán

    2010-01-01

    In this paper we introduce the concept of generalized d-graph (admitting cycles) as special dependency-graphs for modelling dynamic programming (DP) problems. We describe the d-graph versions of three famous single-source shortest algorithms (The algorithm based on the topological order of the vertices, Dijkstra algorithm and Bellman-Ford algorithm), which can be viewed as general DP strategies in the case of three different class of optimization problems. The new modelling method also makes possible to classify DP problems and the corresponding DP strategies in term of graph theory.

  10. Modeling dietary influences on offspring metabolic programming in Drosophila melanogaster.

    Science.gov (United States)

    Brookheart, Rita T; Duncan, Jennifer G

    2016-09-01

    The influence of nutrition on offspring metabolism has become a hot topic in recent years owing to the growing prevalence of maternal and childhood obesity. Studies in mammals have identified several factors correlating with parental and early offspring dietary influences on progeny health; however, the molecular mechanisms that underlie these factors remain undiscovered. Mammalian metabolic tissues and pathways are heavily conserved in Drosophila melanogaster, making the fly an invaluable genetic model organism for studying metabolism. In this review, we discuss the metabolic similarities between mammals and Drosophila and present evidence supporting its use as an emerging model of metabolic programming.

  11. A fuzzy goal programming model for biodiesel production

    Science.gov (United States)

    Lutero, D. S.; Pangue, EMU; Tubay, J. M.; Lubag, S. P.

    2016-02-01

    A fuzzy goal programming (FGP) model for biodiesel production in the Philippines was formulated with Coconut (Cocos nucifera) and Jatropha (Jatropha curcas) as sources of biodiesel. Objectives were maximization of feedstock production and overall revenue and, minimization of energy used in production and working capital for farming subject to biodiesel and non-biodiesel requirements, and availability of land, labor, water and machine time. All these objectives and constraints were assumed to be fuzzy. Model was tested for different sets of weights. Results for all sets of weights showed the same optimal allocation. Coconut alone can satisfy the biodiesel requirement of 2% per volume.

  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. Modelling parallel programs and multiprocessor architectures with AXE

    Science.gov (United States)

    Yan, Jerry C.; Fineman, Charles E.

    1991-01-01

    AXE, An Experimental Environment for Parallel Systems, was designed to model and simulate for parallel systems at the process level. It provides an integrated environment for specifying computation models, multiprocessor architectures, data collection, and performance visualization. AXE is being used at NASA-Ames for developing resource management strategies, parallel problem formulation, multiprocessor architectures, and operating system issues related to the High Performance Computing and Communications Program. AXE's simple, structured user-interface enables the user to model parallel programs and machines precisely and efficiently. Its quick turn-around time keeps the user interested and productive. AXE models multicomputers. The user may easily modify various architectural parameters including the number of sites, connection topologies, and overhead for operating system activities. Parallel computations in AXE are represented as collections of autonomous computing objects known as players. Their use and behavior is described. Performance data of the multiprocessor model can be observed on a color screen. These include CPU and message routing bottlenecks, and the dynamic status of the software.

  14. 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.

  15. Aerosol measurement program strategy for global aerosol backscatter model development

    Science.gov (United States)

    Bowdle, David A.

    1985-01-01

    The purpose was to propose a balanced program of aerosol backscatter research leading to the development of a global model of aerosol backscatter. Such a model is needed for feasibility studies and systems simulation studies for NASA's prospective satellite-based Doppler lidar wind measurement system. Systems of this kind measure the Doppler shift in the backscatter return from small atmospheric aerosol wind tracers (of order 1 micrometer diameter). The accuracy of the derived local wind estimates and the degree of global wind coverage for such a system are limited by the local availability and by the global scale distribution of natural aerosol particles. The discussions here refer primarily to backscatter model requirements at CO2 wavelengths, which have been selected for most of the Doppler lidar systems studies to date. Model requirements for other potential wavelengths would be similar.

  16. Aerosol measurement program strategy for global aerosol backscatter model development

    Science.gov (United States)

    Bowdle, David A.

    1985-01-01

    The purpose was to propose a balanced program of aerosol backscatter research leading to the development of a global model of aerosol backscatter. Such a model is needed for feasibility studies and systems simulation studies for NASA's prospective satellite-based Doppler lidar wind measurement system. Systems of this kind measure the Doppler shift in the backscatter return from small atmospheric aerosol wind tracers (of order 1 micrometer diameter). The accuracy of the derived local wind estimates and the degree of global wind coverage for such a system are limited by the local availability and by the global scale distribution of natural aerosol particles. The discussions here refer primarily to backscatter model requirements at CO2 wavelengths, which have been selected for most of the Doppler lidar systems studies to date. Model requirements for other potential wavelengths would be similar.

  17. 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....

  18. Self-replication with magnetic dipolar colloids.

    Science.gov (United States)

    Dempster, Joshua M; Zhang, Rui; Olvera de la Cruz, Monica

    2015-10-01

    Colloidal self-replication represents an exciting research frontier in soft matter physics. Currently, all reported self-replication schemes involve coating colloidal particles with stimuli-responsive molecules to allow switchable interactions. In this paper, we introduce a scheme using ferromagnetic dipolar colloids and preprogrammed external magnetic fields to create an autonomous self-replication system. Interparticle dipole-dipole forces and periodically varying weak-strong magnetic fields cooperate to drive colloid monomers from the solute onto templates, bind them into replicas, and dissolve template complexes. We present three general design principles for autonomous linear replicators, derived from a focused study of a minimalist sphere-dimer magnetic system in which single binding sites allow formation of dimeric templates. We show via statistical models and computer simulations that our system exhibits nonlinear growth of templates and produces nearly exponential growth (low error rate) upon adding an optimized competing electrostatic potential. We devise experimental strategies for constructing the required magnetic colloids based on documented laboratory techniques. We also present qualitative ideas about building more complex self-replicating structures utilizing magnetic colloids.

  19. Synchronization of DNA array replication kinetics

    Science.gov (United States)

    Manturov, Alexey O.; Grigoryev, Anton V.

    2016-04-01

    In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

  20. 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.

  1. Coordination between chromosome replication, segregation, and cell division in Caulobacter crescentus

    DEFF Research Database (Denmark)

    Jensen, Rasmus Bugge

    2006-01-01

    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 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...

  2. Efficient usage of Adabas replication

    CERN Document Server

    Storr, Dieter W

    2011-01-01

    In today's IT organization replication becomes more and more an essential technology. This makes Software AG's Event Replicator for Adabas an important part of your data processing. Setting the right parameters and establishing the best network communication, as well as selecting efficient target components, is essential for successfully implementing replication. This book provides comprehensive information and unique best-practice experience in the field of Event Replicator for Adabas. It also includes sample codes and configurations making your start very easy. It describes all components ne

  3. Solving the Telomere Replication Problem

    Science.gov (United States)

    Maestroni, Laetitia; Matmati, Samah; Coulon, Stéphane

    2017-01-01

    Telomeres are complex nucleoprotein structures that protect the extremities of linear chromosomes. Telomere replication is a major challenge because many obstacles to the progression of the replication fork are concentrated at the ends of the chromosomes. This is known as the telomere replication problem. In this article, different and new aspects of telomere replication, that can threaten the integrity of telomeres, will be reviewed. In particular, we will focus on the functions of shelterin and the replisome for the preservation of telomere integrity. PMID:28146113

  4. Program package for constructing analytical models of industrial robots

    Energy Technology Data Exchange (ETDEWEB)

    Vukobratovich, M.; Kirchanskiy, N.

    Complex multidimensional nonlinear dynamic systems are controlled with the use of control computers differing in their complexity, from large ones at the level of the modeling of the dynamics of the system and synthesis of the control algorithm to microcomputers directly controlling the system. One of the main decisive problems in controlling an industrial robot is the generation of a dynamic on-line model. For this purpose, a separate microcomputer or several computers operating in the multiprocessor mode are used. The existing methods of robot dynamics simulation which are based on the equations of Newton-Euler, Lagrange and others require a large number of numerical operations and they cannot be realized in real time: the time spent on the construction of a model is several times greater than that acceptable for the computer. This is explained by the following factors: complexity of the mathematical model, the use of a high-level language for programming, the desire to construct an algorithm of a general kind, which leads to high redundancy of numerical operations; the use of recursion relations, which excludes the possibility of performing parallel operations during the realization in a computer. Special characteristics of the construction of a program system which is to a considerable degree free of the above drawbacks is considered below. Instead of directly constructing a model in the numerical form on the basis of one of the approaches of classical mechanics, the concept of constructing a model in symbols is proposed here. It is possible to show that in this way it is possible to obtain a compact mathematical model which requires fewer numerical operations (multiplication, addition) for its realization by two orders in comparison with the methods used earlier. 9 references, 2 tables.

  5. Evaluation of medical education virtual program: P3 model

    Directory of Open Access Journals (Sweden)

    RITA REZAEE

    2016-10-01

    Full Text Available Introduction: 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. Methods: 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. Results: 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. Conclusion: 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.

  6. Evaluation of Medical Education virtual Program: P3 model

    Science.gov (United States)

    REZAEE, RITA; SHOKRPOUR, NASRIN; BOROUMAND, MARYAM

    2016-01-01

    Introduction: 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. Methods: 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. Results: 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). Conclusion: 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. PMID:27795971

  7. An optimal replication strategy for data grid systems

    Institute of Scientific and Technical Information of China (English)

    JIANG Jianjin; YANG Guangwen

    2007-01-01

    Data access latency is an important metric of system performance in data grid.By means of efficient replication strategy,the amount of data transferred in a wide area network will decrease,and the average access latency of data will decrease ultimately.The motivation of our research is to solve the optimized replica distribution problem in a data grid;that is,the system should utilize many replicas for every data with storage constraints to minimize the average access latency of data.This paper proposes a model of replication strategy in federated data grid and gives the optimized solution.The analysis results and simulation results show that the optimized replication strategy proposed in this paper is superior to LRU caching strategy,uniform replication strategy,proportional replication strategy and square root replication strategy in terms of wide area network bandwidth requirement and in the average access latency of data.

  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. A stochastic dynamic programming model for stream water quality management

    Indian Academy of Sciences (India)

    P P Mujumdar; Pavan Saxena

    2004-10-01

    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 (FDM) developed by us in an earlier study is used to compute the system performance measure required in the SDP model. The state of the system in a season is defined by streamflows at the headwaters during the season and the initial DO deficit at some pre-specified checkpoints. The random variation of streamflows is included in the SDP model through seasonal transitional probabilities. The decision vector consists of seasonal fraction-removal levels for the effluent dischargers. Uncertainty due to imprecision (fuzziness) associated with water quality goals is addressed using the concept of fuzzy decision. Responses of pollution control agencies to the resulting end-of-season DO deficit vector and that of dischargers to the fraction-removal levels are treated as fuzzy, and modelled with appropriate membership functions. Application of the model is illustrated with a case study of the Tungabhadra river in India.

  10. 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.

  11. A model to design effective Production Improvement Programs

    Directory of Open Access Journals (Sweden)

    T. Bautista

    2010-04-01

    Full Text Available The objective of this paper is to present a model to design effective Production Improvement Programs (PIP in order tocontribute in the solution of the problematic situations generally faced by the Mexican manufacturing micro, small and mediumsizedenterprises (M‐SME. In this proposal, we imply that facilitating their development is a natural way to improve theirperformance, especially in terms of productive efficiency. The study picked up empirical evidence from the ProcessesReengineering Workshop (PRW, one of the leading services of the National Committee of Productivity and TechnologicalInnovation (NCPTI which is considered a Mexican successful case. We show through a comparative analysis that it is possible tohave better programs when they follow a continuous improvement process involving the owner of the firm and workforceparticipation. Furthermore, we suggest a series of methods for planning, structuring and improvement according to theimitative, tacit and qualitative M‐SME specific competence.

  12. Fetal developmental programing: insights from human studies and experimental models.

    Science.gov (United States)

    Lopes, Gisele Aparecida Dionísio; Ribeiro, Vinícius Luís Bertotti; Barbisan, Luís Fernando; Marchesan Rodrigues, Maria Aparecida

    2017-03-01

    Environmental factors, particularly nutrition during pregnancy and early life can influence the risk of chronic diseases in later life. The underlying mechanism, termed "programing", postulates that an environmental stimulus during a critical window of time, early in life, has a permanent effect on subsequent structure and function of the organism. In this study we review the concept of fetal programing on chronic diseases and the proposed hypotheses for the association between early development and later disease, including epigenetic variation. We concentrate on specific aspects of maternal nutrition, particularly under-nutrition and over-nutrition, in humans and animal models. An adequate maternal nutrition during pregnancy is crucial for the health outcome of the offspring at adulthood.

  13. 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.

  14. Replication Attack Mitigations for Static and Mobile WSN

    CERN Document Server

    Manjula, V; 10.5121/ijnsa.2011.3210

    2011-01-01

    Security is important for many sensor network applications. Wireless Sensor Networks (WSN) are often deployed in hostile environments as static or mobile, where an adversary can physically capture some of the nodes. once a node is captured, adversary collects all the credentials like keys and identity etc. the attacker can re-program it and replicate the node in order to eavesdrop the transmitted messages or compromise the functionality of the network. Identity theft leads to two types attack: clone and sybil. In particularly a harmful attack against sensor networks where one or more node(s) illegitimately claims an identity as replicas is known as the node replication attack. The replication attack can be exceedingly injurious to many important functions of the sensor network such as routing, resource allocation, misbehavior detection, etc. This paper analyzes the threat posed by the replication attack and several novel techniques to detect and defend against the replication attack, and analyzes their effect...

  15. The Evolution of Cartography Graduate Programs and the Development of New Graduate Programs in Cartography: An Assessment of Models.

    Science.gov (United States)

    Steinke, Theodore R.

    This paper traces the historical development of cartography graduate programs, establishes an evolutionary model, and evaluates the model to determine if it has some utility today for the development of programs capable of producing highly skilled cartographers. Cartography is defined to include traditional cartography, computer cartography,…

  16. Tank System Integrated Model: A Cryogenic Tank Performance Prediction Program

    Science.gov (United States)

    Bolshinskiy, L. G.; Hedayat, A.; Hastings, L. J.; Sutherlin, S. G.; Schnell, A. R.; Moder, J. P.

    2017-01-01

    Accurate predictions of the thermodynamic state of the cryogenic propellants, pressurization rate, and performance of pressure control techniques in cryogenic tanks are required for development of cryogenic fluid long-duration storage technology and planning for future space exploration missions. This Technical Memorandum (TM) presents the analytical tool, Tank System Integrated Model (TankSIM), which can be used for modeling pressure control and predicting the behavior of cryogenic propellant for long-term storage for future space missions. Utilizing TankSIM, the following processes can be modeled: tank self-pressurization, boiloff, ullage venting, mixing, and condensation on the tank wall. This TM also includes comparisons of TankSIM program predictions with the test data andexamples of multiphase mission calculations.

  17. Probabilistic Constraint Programming for Parameters Optimisation of Generative Models

    CERN Document Server

    Zanin, Massimiliano; Sousa, Pedro A C; Cruz, Jorge

    2015-01-01

    Complex networks theory has commonly been used for modelling and understanding the interactions taking place between the elements composing complex systems. More recently, the use of generative models has gained momentum, as they allow identifying which forces and mechanisms are responsible for the appearance of given structural properties. In spite of this interest, several problems remain open, one of the most important being the design of robust mechanisms for finding the optimal parameters of a generative model, given a set of real networks. In this contribution, we address this problem by means of Probabilistic Constraint Programming. By using as an example the reconstruction of networks representing brain dynamics, we show how this approach is superior to other solutions, in that it allows a better characterisation of the parameters space, while requiring a significantly lower computational cost.

  18. Synchronizing production and air transportation scheduling using mathematical programming models

    Science.gov (United States)

    Zandieh, M.; Molla-Alizadeh-Zavardehi, S.

    2009-08-01

    Traditional scheduling problems assume that there are always infinitely many resources for delivering finished jobs to their destinations, and no time is needed for their transportation, so that finished products can be transported to customers without delay. So, for coordination of these two different activities in the implementation of a supply chain solution, we studied the problem of synchronizing production and air transportation scheduling using mathematical programming models. The overall problem is decomposed into two sub-problems, which consists of air transportation allocation problem and a single machine scheduling problem which they are considered together. We have taken into consideration different constraints and assumptions in our modeling such as special flights, delivery tardiness and no delivery tardiness. For these purposes, a variety of models have been proposed to minimize supply chain total cost which encompass transportation, makespan, delivery earliness tardiness and departure time earliness tardiness costs.

  19. A Timing Evaluator for C Programs Generated by the Model System.

    Science.gov (United States)

    1987-12-01

    the C programming language in its automatic generation of C programs from the input MODEL language specification Theretore. though the MTE is primarily...program (the MODEL compiler), it is known beforehand that not all of the features of the C programming language will be used and the MTE has been

  20. 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

  1. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase

    Science.gov (United States)

    Lõoke, Marko; Maloney, Michael F.; Bell, Stephen P.

    2017-01-01

    Activation of the Mcm2–7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2–7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2–7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2–7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. PMID:28270517

  2. Generalized fish life-cycle poplulation model and computer program

    Energy Technology Data Exchange (ETDEWEB)

    DeAngelis, D. L.; Van Winkle, W.; Christensen, S. W.; Blum, S. R.; Kirk, B. L.; Rust, B. W.; Ross, C.

    1978-03-01

    A generalized fish life-cycle population model and computer program have been prepared to evaluate the long-term effect of changes in mortality in age class 0. The general question concerns what happens to a fishery when density-independent sources of mortality are introduced that act on age class 0, particularly entrainment and impingement at power plants. This paper discusses the model formulation and computer program, including sample results. The population model consists of a system of difference equations involving age-dependent fecundity and survival. The fecundity for each age class is assumed to be a function of both the fraction of females sexually mature and the weight of females as they enter each age class. Natural mortality for age classes 1 and older is assumed to be independent of population size. Fishing mortality is assumed to vary with the number and weight of fish available to the fishery. Age class 0 is divided into six life stages. The probability of survival for age class 0 is estimated considering both density-independent mortality (natural and power plant) and density-dependent mortality for each life stage. Two types of density-dependent mortality are included. These are cannibalism of each life stage by older age classes and intra-life-stage competition.

  3. OpenMP Programming for a Global Inverse Model

    Directory of Open Access Journals (Sweden)

    Ping Wang

    2002-01-01

    Full Text Available The objective of our investigation is to establish robust inverse algorithms to convert GRACE gravity and ICESat altimetry mission data into global current and past surface mass variations. To assess separation of global sources of change and to evaluate spatio-temporal resolution and accuracy statistically from full posterior covariance matrices, a high performance version of a global simultaneous grid inverse algorithm is essential. One means to accomplish this is to implement a general, well-optimized, parallel global model on massively parallel supercomputers. In our present work, an efficient parallel version of a global inverse program has been implemented on the Origin 2000 using the OpenMP programming model. In this paper, porting a sequential global code to a shared-memory computing system is discussed; several efficient strategies to optimize the code are reported; well-optimized scientific libraries are used; detailed parallel implementation of the global model is reported; performance data of the code are analyzed. Scaling performance on a shared-memory system is also discussed. The parallel version software gives good speedup and dramatically reduces total data processing time.

  4. Modelling Alcoholism as a Contagious Disease: A Mathematical Model with Awareness Programs and Time Delay

    Directory of Open Access Journals (Sweden)

    Shuang-Hong Ma

    2015-01-01

    Full Text Available A dynamic alcohol consumption model with awareness programs and time delay is formulated and analyzed. The aim of this model is to capture the effects of awareness programs and time delay in controlling the alcohol problems. We introduce awareness programs by media in the model as a separate class with growth rate of the cumulative density of them being proportional to the number of mortalities induced by heavy drinking. Susceptible population will isolate themselves and avoid contact with the heavy drinkers or become aware of risk of heavy drinking and decline to drink due to such programs. In particular, we incorporate time delay because the nonconsumer population will take a period of time to become an alcohol consumer. We find that the model has two equilibria: one without alcohol problems and one where alcohol problems are endemic in population. The model analysis shows that though awareness programs cannot eradicate alcohol problems, they are effective measures in controlling the alcohol problems. Further, we conclude that the time delay in alcohol consumption habit which develops in susceptible population may result in Hopf bifurcation by increasing the value of time delay. Some numerical simulation results are also given to support our theoretical predictions.

  5. Boolean Variables in Economic Models Solved by Linear Programming

    Directory of Open Access Journals (Sweden)

    Lixandroiu D.

    2014-12-01

    Full Text Available The article analyses the use of logical variables in economic models solved by linear programming. Focus is given to the presentation of the way logical constraints are obtained and of the definition rules based on predicate logic. Emphasis is also put on the possibility to use logical variables in constructing a linear objective function on intervals. Such functions are encountered when costs or unitary receipts are different on disjunct intervals of production volumes achieved or sold. Other uses of Boolean variables are connected to constraint systems with conditions and the case of a variable which takes values from a finite set of integers.

  6. 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.

  7. 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.

  8. 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

    2014-01-01

    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. PMID:24954939

  9. 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.

  10. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    Directory of Open Access Journals (Sweden)

    Hendro Nindito

    2014-01-01

    Full Text Available 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 MySQL running on Linux as the destination. The method applied in this research is prototyping in which the processes of development and testing can be done interactively and repeatedly. The key result of this research is that the replication technology applied, which is called Oracle GoldenGate, can successfully manage to do its task in replicating data in real-time and heterogeneous platforms.

  11. 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.

  12. 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.

  13. The Compass Model to plan faculty development programs

    Directory of Open Access Journals (Sweden)

    Mohamed Mostafa Al-Eraky

    2012-05-01

    Full Text Available Faculty development is an imperative if institutions are to develop professional and competent teachers, educators, researchers and leaders. Planning of faculty development currently focuses on meeting the perceived needs of staff and their interests. We would like to propose the Compass Model as a conceptual framework to plan faculty development, which was inspired by the interplay between intrinsic and extrinsic forces for learning, as outlined in the Self-Determination Theory (SDT. In planning faculty development, the Compass Model acknowledges four agendas (directions from various stakeholders: Strategies (N, Competencies (E, Resources (S and Wish lists (W. The model then describes four avenues for faculty development offerings (quadrants: Foundation (NE, Innovation (SE, Response (SW and Motivation (NW (i.e. outputs, activities. The model was compared theoretically with another approach to faculty development planning. It was then piloted as a quality measure for a current program to check for omissions or missed opportunities. We plan to use it in a multi-center study to compare approaches in faculty development planning in different contexts. We hope our model assists faculty developers to consider all stakeholders’ agendas when planning faculty development, beyond the current standard customer-based approach.

  14. BWR Refill-Reflood Program, Task 4. 7 - model development: TRAC-BWR component models

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, Y K; Parameswaran, V; Shaug, J C

    1983-09-01

    TRAC (Transient Reactor Analysis Code) is a computer code for best-estimate analysis for the thermal hydraulic conditions in a reactor system. The development and assessment of the BWR component models developed under the Refill/Reflood Program that are necessary to structure a BWR-version of TRAC are described in this report. These component models are the jet pump, steam separator, steam dryer, two-phase level tracking model, and upper-plenum mixing model. These models have been implemented into TRAC-B02. Also a single-channel option has been developed for individual fuel-channel analysis following a system-response calculation.

  15. Genetic Programming Modeling and Complexity Analysis of the Magnetoencephalogram of Epileptic Patients

    Science.gov (United States)

    Georgopoulos, Efstratios F.; Adamopoulos, Adam V.; Likothanassis, Spiridon D.

    In this work MagnetoEncephaloGram (MEG) recordings of epileptic patients are modeled using a genetic programming approach. This is the first time that genetic programming is used to model MEG signal. Numerous experiments were conducted giving highly successful results. It is demonstrated that genetic programming can produce very simple nonlinear models that fit with great accuracy the observed data of MEG.

  16. 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%.

  17. A Cooperation-planning Model Based on Bilevel Programming Decision

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jianfeng; ZHOU Lei; BAO Zhenqiang; BIAN Wenyu; LI Xiangqing

    2006-01-01

    This paper is based on a resource constrained active network project; the constraint of the local resource and the time constraint of the cooperation resource are considered simultaneously. And the respective benefit of the manager and cooperation partners is also considered simultaneously. And a cooperation-planning model based on bilevel multi-objective programming is designed, according to the due time and total cost. And an extended CNP based on the permitted range for resource and time requests is presented. A larger task set in scheduling cycle is on the permitting for the request of cooperation resource and time while the task manager itself may be permitted biding for tasks. As a result, the optimization space for the cooperation planning is enlarged. So not every bidding task is successfully bid by invitee, and the task manager itself takes on some bidding tasks. Finally, the genetic algorithm is given and the validity and feasibility of the model is proved by a case.

  18. Semantic network based component organization model for program mining

    Institute of Scientific and Technical Information of China (English)

    王斌; 张尧学; 陈松乔

    2003-01-01

    Based on the definition of component ontology, an effective component classification mechanism and a facet named component relationship are proposed. Then an application domain oriented, hierarchical component organization model is established. At last a hierarchical component semantic network (HCSN) described by ontology interchange language(OIL) is presented and then its function is described. Using HCSN and cooperating with other components retrieving algorithms based on component description, other components information and their assembly or composite modes related to the key component can be found. Based on HCSN, component directory library is catalogued and a prototype system is constructed. The prototype system proves that component library organization based on this model gives guarantee to the reliability of component assembly during program mining.

  19. A stochastic model of translation with -1 programmed ribosomal frameshifting

    Science.gov (United States)

    Bailey, Brenae L.; Visscher, Koen; Watkins, Joseph

    2014-02-01

    Many viruses produce multiple proteins from a single mRNA sequence by encoding overlapping genes. One mechanism to decode both genes, which reside in alternate reading frames, is -1 programmed ribosomal frameshifting. Although recognized for over 25 years, the molecular and physical mechanism of -1 frameshifting remains poorly understood. We have developed a mathematical model that treats mRNA translation and associated -1 frameshifting as a stochastic process in which the transition probabilities are based on the energetics of local molecular interactions. The model predicts both the location and efficiency of -1 frameshift events in HIV-1. Moreover, we compute -1 frameshift efficiencies upon mutations in the viral mRNA sequence and variations in relative tRNA abundances, predictions that are directly testable in experiment.

  20. Using a visual programming language to bridge the cognitive gap between a novice's mental model and program code

    Science.gov (United States)

    Smith, Bryan J.

    Current research suggests that many students do not know how to program very well at the conclusion of their introductory programming course. We believe that a reason novices have such difficulties learning programming is because engineering novices often learn through a lecture format where someone with programming knowledge lectures to novices, the novices attempt to absorb the content, and then reproduce it during exams. By primarily appealing to programming novices who prefer to understand visually, we research whether programming novices understand programming better if computer science concepts are presented using a visual programming language than if these programs are presented using a text-based programming language. This method builds upon previous research that suggests that most engineering students are visual learners, and we propose that using a flow-based visual programming language will address some of the most important and difficult topics to novices of programming. We use an existing flow-model tool, RAPTOR, to test this method, and share the program understanding results using this theory.

  1. Energy consumption model over parallel programs implemented on multicore architectures

    Directory of Open Access Journals (Sweden)

    Ricardo Isidro-Ramirez

    2015-06-01

    Full Text Available In High Performance Computing, energy consump-tion is becoming an important aspect to consider. Due to the high costs that represent energy production in all countries it holds an important role and it seek to find ways to save energy. It is reflected in some efforts to reduce the energy requirements of hardware components and applications. Some options have been appearing in order to scale down energy use and, con-sequently, scale up energy efficiency. One of these strategies is the multithread programming paradigm, whose purpose is to produce parallel programs able to use the full amount of computing resources available in a microprocessor. That energy saving strategy focuses on efficient use of multicore processors that are found in various computing devices, like mobile devices. Actually, as a growing trend, multicore processors are found as part of various specific purpose computers since 2003, from High Performance Computing servers to mobile devices. However, it is not clear how multiprogramming affects energy efficiency. This paper presents an analysis of different types of multicore-based architectures used in computing, and then a valid model is presented. Based on Amdahl’s Law, a model that considers different scenarios of energy use in multicore architectures it is proposed. Some interesting results were found from experiments with the developed algorithm, that it was execute of a parallel and sequential way. A lower limit of energy consumption was found in a type of multicore architecture and this behavior was observed experimentally.

  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.

    2016-08-01

    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. 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.

  4. 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

  5. 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.

  6. Development of primary cell cultures from mud crab, Scylla serrata, and their potential as an in vitro model for the replication of white spot syndrome virus.

    Science.gov (United States)

    Deepika, A; Makesh, M; Rajendran, K V

    2014-01-01

    Primary cell cultures were developed from haemocytes and testis of Scylla serrata. Haemocytes were collected from live animals and cultured in double-strength L-15 medium (2× L-15) prepared in crab saline, supplemented with 5% foetal bovine serum and antibiotic-antimycotic solution (penicillin 100 U/mL, streptomycin 100 μg/mL and amphotericin B 0.25 μg/mL) with osmolality adjusted to 894 mOsm/kg. The haemocytes adhered within 2 h after seeding and showed proliferation up to 72 h. The disaggregated testis tissue fragments were seeded in 3× L-15 supplemented with non-essential amino acid mixture, lipid concentrate and antibiotic-antimycotic solution, with osmolality adjusted to 1,035 mOsm/kg with crab saline. Cells from the testis could be subcultured and maintained up to 21 d as suspension culture. Different dilutions of white spot syndrome virus (WSSV) inoculum (known virus copy number) prepared from infected Penaeus monodon were inoculated in the cultured cells, and the cytopathic effects like detachment, rounding of cells and clear areas of depleted cells were observed after 48 h in haemocyte cultures. However, WSSV-exposed testis cells did not show any obvious change until 72 h post-infection. WSSV was detected in both haemocyte and testis cultures at different time-points of infection by conventional and real-time PCR using WSSV-specific primers. The transcripts of WSSV were found to be much higher in haemocytes than in testis culture. The virus harvested from the cultured haemocytes after three passages could infect healthy P. monodon. The present study showed that mud crab haemocyte culture can support WSSV replication, and it can be used as an in vitro tool for WSSV replication.

  7. 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......, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator....

  8. The Psychology of Replication and Replication in Psychology.

    Science.gov (United States)

    Francis, Gregory

    2012-11-01

    Like other scientists, psychologists believe experimental replication to be the final arbiter for determining the validity of an empirical finding. Reports in psychology journals often attempt to prove the validity of a hypothesis or theory with multiple experiments that replicate a finding. Unfortunately, these efforts are sometimes misguided because in a field like experimental psychology, ever more successful replication does not necessarily ensure the validity of an empirical finding. When psychological experiments are analyzed with statistics, the rules of probability dictate that random samples should sometimes be selected that do not reject the null hypothesis, even if an effect is real. As a result, it is possible for a set of experiments to have too many successful replications. When there are too many successful replications for a given set of experiments, a skeptical scientist should be suspicious that null or negative findings have been suppressed, the experiments were run improperly, or the experiments were analyzed improperly. This article describes the implications of this observation and demonstrates how to test for too much successful replication by using a set of experiments from a recent research paper.

  9. Regulation of Replication Recovery and Genome Integrity

    DEFF Research Database (Denmark)

    Colding, Camilla Skettrup

    Preserving genome integrity is essential for cell survival. To this end, mechanisms that supervise DNA replication and respond to replication perturbations have evolved. One such mechanism is the replication checkpoint, which responds to DNA replication stress and acts to ensure replication pausing...

  10. 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.

  11. 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…

  12. Modeling multi-clocked data-flow programs using the Generic Modeling Environment

    OpenAIRE

    Brunette, Christian; Talpin, Jean-Pierre; Besnard, Loïc; Gautier, Thierry

    2006-01-01

    International audience; This paper presents Signal-Meta, the metamodel designed for the synchronous data-flow language Signal. It relies on the Generic Modeling Environment (GME), a configurable object-oriented toolkit that supports the creation of domain-specific modeling and program synthesis environments. The graphical description constitutes the base to build multi-clock environments, and a good front-end for the Polychrony platform. To complete this frontend, we develop a tool that trans...

  13. An integer programming model for assigning students to elective courses

    Directory of Open Access Journals (Sweden)

    Ivo Beroš

    2015-10-01

    Full Text Available This paper deals with the problem of assigning students to elective courses according to their preferences. This process of assigning students to elective courses according to their preferences often places before academic institutions numerous obstacles, the most typical being a limited number of students who can be assigned to any particular class. Furthermore, due to financial or technical reasons, the maximum number of the elective courses is determined in advance, meaning that the institution decides which courses to conduct. Therefore, the expectation that all the students will be assigned to their first choice of courses is not realistic (perfect satisfaction. This paper presents an integer programming model that maximizes the total student satisfaction in line with a number of different constraints. The measure of student satisfaction is based on a student's order of preference according to the principle: the more a choice is met the higher the satisfaction. Following the basic model, several versions of the models are generated to cover possible real-life situations, while taking into consideration the manner student satisfaction is measured, as well as the preference of academic institution within set technical and financial constraints. The main contribution of the paper is introducing the concept of the minimal student satisfaction level that reduces the number of students dissatised with the courses to which they were assigned.

  14. 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...... with their chronological age and present health status, help define their current rate of aging and contribute to establish personalized therapy plans to reduce, counteract or even avoid the appearance of aging biomarkers....

  15. NASA Space Radiation Program Integrative Risk Model Toolkit

    Science.gov (United States)

    Kim, Myung-Hee Y.; Hu, Shaowen; Plante, Ianik; Ponomarev, Artem L.; Sandridge, Chris

    2015-01-01

    NASA Space Radiation Program Element scientists have been actively involved in development of an integrative risk models toolkit that includes models for acute radiation risk and organ dose projection (ARRBOD), NASA space radiation cancer risk projection (NSCR), hemocyte dose estimation (HemoDose), GCR event-based risk model code (GERMcode), and relativistic ion tracks (RITRACKS), NASA radiation track image (NASARTI), and the On-Line Tool for the Assessment of Radiation in Space (OLTARIS). This session will introduce the components of the risk toolkit with opportunity for hands on demonstrations. The brief descriptions of each tools are: ARRBOD for Organ dose projection and acute radiation risk calculation from exposure to solar particle event; NSCR for Projection of cancer risk from exposure to space radiation; HemoDose for retrospective dose estimation by using multi-type blood cell counts; GERMcode for basic physical and biophysical properties for an ion beam, and biophysical and radiobiological properties for a beam transport to the target in the NASA Space Radiation Laboratory beam line; RITRACKS for simulation of heavy ion and delta-ray track structure, radiation chemistry, DNA structure and DNA damage at the molecular scale; NASARTI for modeling of the effects of space radiation on human cells and tissue by incorporating a physical model of tracks, cell nucleus, and DNA damage foci with image segmentation for the automated count; and OLTARIS, an integrated tool set utilizing HZETRN (High Charge and Energy Transport) intended to help scientists and engineers study the effects of space radiation on shielding materials, electronics, and biological systems.

  16. 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

  17. Pedagogy and Processes for a Computer Programming Outreach Workshop--The Bridge to College Model

    Science.gov (United States)

    Tangney, Brendan; Oldham, Elizabeth; Conneely, Claire; Barrett, Stephen; Lawlor, John

    2010-01-01

    This paper describes a model for computer programming outreach workshops aimed at second-level students (ages 15-16). Participants engage in a series of programming activities based on the Scratch visual programming language, and a very strong group-based pedagogy is followed. Participants are not required to have any prior programming experience.…

  18. Computer programs for forward and inverse modeling of acoustic and electromagnetic data

    Science.gov (United States)

    Ellefsen, Karl J.

    2011-01-01

    A suite of computer programs was developed by U.S. Geological Survey personnel for forward and inverse modeling of acoustic and electromagnetic data. This report describes the computer resources that are needed to execute the programs, the installation of the programs, the program designs, some tests of their accuracy, and some suggested improvements.

  19. 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.

  20. Overview of the NRL DPF program: Experiment and Modeling

    Science.gov (United States)

    Richardson, A. S.; Jackson, S. L.; Angus, J. R.; Giuliani, J. L.; Swanekamp, S. B.; Schumer, J. W.; Mosher, D.

    2016-10-01

    Charged particle acceleration in imploding plasmas is an important phenomenon which occurs in various natural and laboratory plasmas. A new research project at the Naval Research Laboratory (NRL) has been started to investigate this phenomenon both experimentally-in a dense plasma focus (DPF) device-and theoretically using analytical and computational modeling. The DPF will be driven by the high-inductance (607 nH) Hawk pulsed-power generator, with a rise time of 1.2 μs and a peak current of 665 kA. In this poster we present an overview of the research project, and some preliminary results from fluid simulations of the m = 0 instability in an idealized DPF pinch. This work was supported by the Naval Research Laboratory Base Program.

  1. Plasmid Rolling-Circle Replication.

    Science.gov (United States)

    Ruiz-Masó, J A; MachóN, C; Bordanaba-Ruiseco, L; Espinosa, M; Coll, M; Del Solar, G

    2015-02-01

    Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start de novo DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.

  2. A Transactional Asynchronous Replication Scheme for Mobile Database Systems

    Institute of Scientific and Technical Information of China (English)

    丁治明; 孟小峰; 王珊

    2002-01-01

    In mobile database systems, mobility of users has a significant impact on data replication. As a result, the various replica control protocols that exist today in traditional distributed and multidatabase environments are no longer suitable. To solve this problem, a new mobile database replication scheme, the Transaction-Level Result-Set Propagation (TLRSP)model, is put forward in this paper. The conflict detection and resolution strategy based on TLRSP is discussed in detail, and the implementation algorithm is proposed. In order to compare the performance of the TLRSP model with that of other mobile replication schemes, we have developed a detailed simulation model. Experimental results show that the TLRSP model provides an efficient support for replicated mobile database systems by reducing reprocessing overhead and maintaining database consistency.

  3. Termination of DNA replication forks: "Breaking up is hard to do".

    Science.gov (United States)

    Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

    2015-01-01

    To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

  4. COMPLEX PROGRAMS FOR MODELING HIGHWAY: WAY AND STREAM

    Directory of Open Access Journals (Sweden)

    A. V. Skrypnikov

    2014-01-01

    Full Text Available The complexity of the operation of the road caused by continuously varying from picket to picket road conditions caused by a variety of parameters projected (existing road , the variety of types of cars, their technical and economic parameters , a variety of climatic and weather conditions required to develop a complex simulation programs . This paper describes a set of programs that form the core of the subsystem "driver-vehicle-road environment". Optimization of the design solutions developed modules contribute WAY type and columns, not using indicators averaged transport - road performance, and detailed process model of functioning of the road. WAY module provides continuous sequence modeling perception of road elements mechanical subsystem "road-car " (by continuous formation and solution of the equations of motion and the characteristics of this mode. WAY module (with module PARK brings the technical contradiction between the 20-year term of road design and use of existing practices in their justification of design decisions technical parameters of cars today. The complexity of the operation of the road due to the random nature of traffic demanded inclusion in the computer -aided design of roads STREAM module. STREAM module allows to obtain simulation results of a random process, sufficient to optimize the design decisions in general and in the areas of local variation of the plan, longitudinal section, the way the situation, etc. Varie ty of road conditions possible to classify on the specifics of the formation of the flow regimes. This builds on the results of study of the process of movement of cars in the stream.

  5. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

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

    2016-01-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment...... 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...... 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...

  6. USP7 is a SUMO deubiquitinase essential for DNA replication.

    Science.gov (United States)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia; Lopez-Contreras, Andres J; Ruppen, Isabel; Murga, Matilde; Muñoz, Javier; Mendez, Juan; Fernandez-Capetillo, Oscar

    2016-04-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment 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 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 inhibitors as anticancer agents.

  7. 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…

  8. 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…

  9. The component model of infrastructure: a practical approach to understanding public health program infrastructure.

    Science.gov (United States)

    Lavinghouze, S René; Snyder, Kimberly; Rieker, Patricia P

    2014-08-01

    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.

  10. 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.

  11. Preliminary results on molecular modeling of asphaltenes using structure elucidation programs in conjunction with molecular simulation programs

    Energy Technology Data Exchange (ETDEWEB)

    Kowalewski, I.; Vandenbroucke, M.; Huc, A.Y.; Taylor, M.J.; Faulon, J.L. [Institut Francais du Petrole, Rueil-Malmaison (France). Division Geologie-Geochimie

    1996-01-01

    Molecular modeling using structure elucidation programs in conjunction with molecular simulation programs has been performed on asphaltene molecules, the heaviest fraction of crude oil, in order to obtain a chemical model allowing the tentative study of their physicochemical properties. Boscan asphaltenes (Venezuela) derived from a marine source rock have been analysed. The different steps of this molecular modeling are described. First, a 3-D chemical representation of Boscan asphaltene is defined from an analytical data set. Second, the results of molecular dynamic simulations indicate that only a few stable conformations are possible due to the high reticulation of the model of the asphaltene unit obtained. 42 refs., 6 figs., 9 tabs.

  12. Stress responses and replication of plasmids in bacterial cells

    Directory of Open Access Journals (Sweden)

    Wegrzyn Alicja

    2002-05-01

    Full Text Available Abstract Plasmids, DNA (or rarely RNA molecules which replicate in cells autonomously (independently of chromosomes as non-essential genetic elements, play important roles for microbes grown under specific environmental conditions as well as in scientific laboratories and in biotechnology. For example, bacterial plasmids are excellent models in studies on regulation of DNA replication, and their derivatives are the most commonly used vectors in genetic engineering. Detailed mechanisms of replication initiation, which is the crucial process for efficient maintenance of plasmids in cells, have been elucidated for several plasmids. However, to understand plasmid biology, it is necessary to understand regulation of plasmid DNA replication in response to different environmental conditions in which host cells exist. Knowledge of such regulatory processes is also very important for those who use plasmids as expression vectors to produce large amounts of recombinant proteins. Variable conditions in large-scale fermentations must influence replication of plasmid DNA in cells, thus affecting the efficiency of recombinant gene expression significantly. Contrary to extensively investigated biochemistry of plasmid replication, molecular mechanisms of regulation of plasmid DNA replication in response to various environmental stress conditions are relatively poorly understood. There are, however, recently published studies that add significant data to our knowledge on relations between cellular stress responses and control of plasmid DNA replication. In this review we focus on plasmids derived from bacteriophage λ that are among the best investigated replicons. Nevertheless, recent results of studies on other plasmids are also discussed shortly.

  13. 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

    2014-03-01

    Intervention studies in participatory ergonomics (PE) are often difficult to interpret due to limited descriptions of program planning and evaluation. 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. 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. 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. © 2013 Wiley Periodicals, Inc.

  14. Development of a Logic Model to Guide Evaluations of the ASCA National Model for School Counseling Programs

    Science.gov (United States)

    Martin, Ian; Carey, John

    2014-01-01

    A logic model was developed based on an analysis of the 2012 American School Counselor Association (ASCA) National Model in order to provide direction for program evaluation initiatives. The logic model identified three outcomes (increased student achievement/gap reduction, increased school counseling program resources, and systemic change and…

  15. 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.

  16. Concurrent Constraint Programming: A Language and Its Execution Model

    Institute of Scientific and Technical Information of China (English)

    廖乐健; 曹元大

    2003-01-01

    To overcome inefficiency in traditional logic programming, a declarative programming language COPS is designed based on the notion of concurrent constraint programming (CCP). The improvement is achieved by the adoption of constraint-based heuristic strategy and the introduction of deterministic components in the framework of CCP. Syntax specification and an operational semantic description are presented.

  17. 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......-like, artificial, molecular aggregate (i.e. protocell) that has been proposed by Steen Rasussen and coworkers and is currently pursued both experimentally and computationally in interdisciplinary international research projects. We develop a space-time continuous physically motivated simulation framework based...... computational models. This allows us to address key issues of the replicating subsystems – container, genome, and metabolism – both individually and in mutual coupling. We analyze each step in the life-cycle of the molecular aggregate, and a final integrated simulation of the entire life-cycle is prepared. Our...

  18. Choreography of bacteriophage T7 DNA replication.

    Science.gov (United States)

    Lee, Seung-Joo; Richardson, Charles C

    2011-10-01

    The replication system of phage T7 provides a model for DNA replication. Biochemical, structural, and single-molecule analyses together provide insight into replisome mechanics. A complex of polymerase, a processivity factor, and helicase mediates leading strand synthesis. Establishment of the complex requires an interaction of the C-terminal tail of the helicase with the polymerase. During synthesis the complex is stabilized by other interactions to provide for a processivity of 5 kilobase (kb). The C-terminal tail also interacts with a distinct region of the polymerase to captures dissociating polymerase to increase the processivity to >17kb. The lagging strand is synthesized discontinuously within a loop that forms and resolves during each cycle of Okazaki fragment synthesis. The synthesis of a primer as well as the termination of a fragment signal loop resolution.

  19. Competition and cooperation in dynamic replication networks.

    Science.gov (United States)

    Dadon, Zehavit; Wagner, Nathaniel; Alasibi, Samaa; Samiappan, Manickasundaram; Mukherjee, Rakesh; Ashkenasy, Gonen

    2015-01-07

    The simultaneous replication of six coiled-coil peptide mutants by reversible thiol-thioester exchange reactions is described. Experimental analysis of the time dependent evolution of networks formed by the peptides under different conditions reveals a complex web of molecular interactions and consequent mutant replication, governed by competition for resources and by autocatalytic and/or cross-catalytic template-assisted reactions. A kinetic model, first of its kind, is then introduced, allowing simulation of varied network behaviour as a consequence of changing competition and cooperation scenarios. We suggest that by clarifying the kinetic description of these relatively complex dynamic networks, both at early stages of the reaction far from equilibrium and at later stages approaching equilibrium, one lays the foundation for studying dynamic networks out-of-equilibrium in the near future.

  20. 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.

  1. Inhibiting NAD+-dependent DNA ligase activity with 2-(cyclopentyloxy)-5'-deoxyadenosine (CPOdA) offers a new tool for DNA replication and repair studies in the model archaeon Haloferax volcanii.

    Science.gov (United States)

    Giroux, Xavier; MacNeill, Stuart A

    2015-11-01

    DNA ligases play an essential role in many aspects of DNA metabolism in all three domains of life. The haloarchaeal organism Haloferax volcanii encodes both ATP- and NAD(+)-dependent DNA ligase enzymes designated LigA and LigN, respectively. Neither LigA nor LigN alone is required for cell viability but they share an essential function, most likely the ligation of Okazaki fragments during chromosome replication. Here we show that 2-(cyclopentyloxy)-5'-deoxyadenosine (referred to as CPOdA), originally developed as a inhibitor of bacterial NAD(+)-dependent DNA ligases, is a potent inhibitor of the growth of Hfx. volcanii cells expressing LigN alone, causing chromosome fragmentation and cell death, while cells expressing LigA are unaffected. Growth inhibition occurs at significantly lower CPOdA concentrations (MIC ≤ 50 ng ml(-1)) than those required for inhibition of bacterial growth (≥2 μg ml(-1)). CPOdA has the potential to become a vital tool in DNA replication and repair studies in this important model organism.

  2. 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, Tus......, to specific DNA sequences called Ter. Here, we demonstrate that Tus-Ter modules also induce polar RF pausing when engineered into the Saccharomyces cerevisiae genome. This heterologous RF barrier is distinct from a number of previously characterized, protein-mediated, RF pause sites in yeast, as it is neither...

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

    Directory of Open Access Journals (Sweden)

    Richard McElreath

    Full Text Available 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.

  4. 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.

  5. 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.

  6. Support for Programming Models in Network-on-Chip-based Many-core Systems

    DEFF Research Database (Denmark)

    Rasmussen, Morten Sleth

    and scalability in an image processing application with the aim of providing insight into parallel programming issues. The second part proposes and presents the tile-based Clupea many-core architecture, which has the objective of providing configurable support for programming models to allow different programming......This thesis addresses aspects of support for programming models in Network-on- Chip-based many-core architectures. The main focus is to consider architectural support for a plethora of programming models in a single system. The thesis has three main parts. The first part considers parallelization...

  7. 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.

  8. Mutation at Expanding Front of Self-Replicating Colloidal Clusters

    CERN Document Server

    Tanaka, Hidenori; Brenner, Michael P

    2016-01-01

    We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through the bath in the form of Fisher waves. Our model reflects existing colloidal systems, but is simple enough to allow simulation of many generations and thereby the first study of evolutionary dynamics in an artificial system. By introducing spatially localized mutations in the replication rules, we show that the mutated cluster population can survive and spread with the expanding front in circular sectors of the colony.

  9. Mutation at Expanding Front of Self-Replicating Colloidal Clusters

    Science.gov (United States)

    Tanaka, Hidenori; Zeravcic, Zorana; Brenner, Michael P.

    2016-12-01

    We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through the bath in the form of Fisher waves. Our model reflects existing colloidal systems, but is simple enough to allow simulation of many generations and thereby the first study of evolutionary dynamics in an artificial system. By introducing spatially localized mutations in the replication rules, we show that the mutated cluster population can survive and spread with the expanding front in circular sectors of the colony.

  10. Simulation Studies in Data Replication Strategies

    Institute of Scientific and Technical Information of China (English)

    HarveyB.Newman; IosifC.Legrand

    2001-01-01

    The aim of this work is to present the simulation studies in evaluating different data replication strategies between Regional Centers.The simulation Framework developed within the "Models of Networked Analysis at Rgional Centers”(MONARC) project,as a design and optimization tool for large scale distributed systems,has been used for these modeling studies.Remote client-serer access to database servers as well as ftp-like data transfers have been ralistically simulated and the performance and limitations are presented as a function of the characteristics of the protocol used and the network parameters.

  11. 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…

  12. Modeling a phosphorus credit trading program in an agricultural watershed.

    Science.gov (United States)

    Corrales, Juliana; Naja, G Melodie; Bhat, Mahadev G; Miralles-Wilhelm, Fernando

    2014-10-01

    Water quality and economic models were linked to assess the economic and environmental benefits of implementing a phosphorus credit trading program in an agricultural sub-basin of Lake Okeechobee watershed, Florida, United States. The water quality model determined the effects of rainfall, land use type, and agricultural management practices on the amount of total phosphorus (TP) discharged. TP loadings generated at the farm level, reaching the nearby streams, and attenuated to the sub-basin outlet from all sources within the sub-basin, were estimated at 106.4, 91, and 85 mtons yr(-)(1), respectively. Almost 95% of the TP loadings reaching the nearby streams were attributed to agriculture sources, and only 1.2% originated from urban areas, accounting for a combined TP load of 87.9 mtons yr(-)(1). In order to compare a Least-Cost Abatement approach to a Command-and-Control approach, the most cost effective cap of 30% TP reduction was selected, and the individual allocation was set at a TP load target of 1.6 kg ha(-1) yr(-1) (at the nearby stream level). The Least-Cost Abatement approach generated a potential cost savings of 27% ($1.3 million per year), based on an optimal credit price of $179. Dairies (major buyer), ornamentals, row crops, and sod farms were identified as potential credit buyers, whereas citrus, improved pastures (major seller), and urban areas were identified as potential credit sellers. Almost 81% of the TP credits available for trading were exchanged. The methodology presented here can be adapted to deal with different forms of trading sources, contaminants, or other technologies and management practices. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Logic Models for Program Design, Implementation, and Evaluation: Workshop Toolkit. REL 2015-057

    Science.gov (United States)

    Shakman, Karen; Rodriguez, Sheila M.

    2015-01-01

    The Logic Model Workshop Toolkit is designed to help practitioners learn the purpose of logic models, the different elements of a logic model, and the appropriate steps for developing and using a logic model for program evaluation. Topics covered in the sessions include an overview of logic models, the elements of a logic model, an introduction to…

  14. Review of the ATLAS B0 model coil test program

    CERN Document Server

    Dolgetta, N; Acerbi, E; Berriaud, C; Boxman, H; Broggi, F; Cataneo, F; Daël, A; Delruelle, N; Dudarev, A; Foussat, A; Haug, F; ten Kate, H H J; Mayri, C; Paccalini, A; Pengo, R; Rivoltella, G; Sbrissa, E

    2004-01-01

    The ATLAS B0 model coil has been extensively tested, reproducing the operational conditions of the final ATLAS Barrel Toroid coils. Two test campaigns have taken place on B0, at the CERN facility where the individual BT coils are about to be tested. The first campaign aimed to test the cool-down, warm-up phases and to commission the coil up to its nominal current of 20.5 kA, reproducing Lorentz forces similar to the ones on the BT coil. The second campaign aimed to evaluate the margins above the nominal conditions. The B0 was tested up to 24 kA and specific tests were performed to assess: the coil temperature margin with respect to the design value, the performance of the double pancake internal joints, static and dynamic heat loads, behavior of the coil under quench conditions. The paper reviews the overall test program with emphasis on second campaign results not covered before. 10 Refs.

  15. The Capra Research Program for Modelling Extreme Mass Ratio Inspirals

    CERN Document Server

    Thornburg, Jonathan

    2011-01-01

    Suppose a small compact object (black hole or neutron star) of mass $m$ orbits a large black hole of mass $M \\gg m$. This system emits gravitational waves (GWs) that have a radiation-reaction effect on the particle's motion. EMRIs (extreme--mass-ratio inspirals) of this type will be important GW sources for LISA; LISA's data analysis will require highly accurate EMRI GW templates. In this article I outline the "Capra" research program to try to model EMRIs and calculate their GWs \\textit{ab initio}, assuming only that $m \\ll M$ and that the Einstein equations hold. Here we treat the EMRI spacetime as a perturbation of the large black hole's "background" (Schwarzschild or Kerr) spacetime and use the methods of black-hole perturbation theory, expanding in the small parameter $m/M$. The small body's motion can be described either as the result of a radiation-reaction "self-force" acting in the background spacetime or as geodesic motion in a perturbed spacetime. Several different lines of reasoning lead to the (s...

  16. Mathematical Model and Programming in VBA Excel for Package Calculation

    Directory of Open Access Journals (Sweden)

    João Daniel Reis Lessa

    2016-05-01

    Full Text Available The industrial logistics is a fundamental pillar for the survival of companies in the actual increasingly competitive market. It is not exclusively about controlling the flow of external material between suppliers and the company, but for developing a detailed study of how to plan, control, handle and package those materials as well. Logistics activities must ensure the maximum efficiency in using corporate resources once they do not add value to the final product. The creation of a logistic plan, for each piece of the company’s production, has to adapt the demand parameters, seasonal or not, in the timeline. Thus, the definition of packaging (transportation and consumption must adjust in accordance with the demand, in order to allow the logistic planning to work, constantly, with order of economy batches. The packaging calculation for each part in every demand can become well complicated due to the large amount of parts in the production process. Automating the calculation process for choosing the right package for each piece is an effective method in logistics planning. This article will expose a simple and practical mathematical model for automating the packaging calculation and a logic program, created in Visual Basic language in the Excel software, used for creating graphic designs that show how the packages are being filled.

  17. FBH1 Catalyzes Regression of Stalled Replication Forks

    Directory of Open Access Journals (Sweden)

    Kasper Fugger

    2015-03-01

    Full Text Available DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity, is required for early phosphorylation of ATM substrates such as CHK2 and CtIP as well as hyperphosphorylation of RPA. These phosphorylations occur prior to apparent DNA double-strand break formation. Furthermore, FBH1-dependent signaling promotes checkpoint control and preserves genome integrity. We propose a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks.

  18. 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.

  19. A Generalised Concept of Dominance in Linear Programming Models

    OpenAIRE

    Drynan, Ross G.

    1987-01-01

    The notion of dominance most familiar to agricultural economists is perhaps the decision theoretic concept entailed in comparing one risky prospect to others. But dominance concepts are also relevant in the linear programming context, for example in identifying redundant constraints. In this note, the standard concept of dominance in linear programming is generalized by defining dominance with respect to differing levels of information about the programming problem.

  20. Development of a program to fit data to a new logistic model for microbial growth.

    Science.gov (United States)

    Fujikawa, Hiroshi; Kano, Yoshihiro

    2009-06-01

    Recently we developed a mathematical model for microbial growth in food. The model successfully predicted microbial growth at various patterns of temperature. In this study, we developed a program to fit data to the model with a spread sheet program, Microsoft Excel. Users can instantly get curves fitted to the model by inputting growth data and choosing the slope portion of a curve. The program also could estimate growth parameters including the rate constant of growth and the lag period. This program would be a useful tool for analyzing growth data and further predicting microbial growth.