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Search Results: 1 - 10 of 8876 matches for " Ben Calderhead "
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Riemannian Manifold Hamiltonian Monte Carlo
Mark Girolami,Ben Calderhead,Siu A. Chin
Mathematics , 2009,
Abstract: The paper proposes a Riemannian Manifold Hamiltonian Monte Carlo sampler to resolve the shortcomings of existing Monte Carlo algorithms when sampling from target densities that may be high dimensional and exhibit strong correlations. The method provides a fully automated adaptation mechanism that circumvents the costly pilot runs required to tune proposal densities for Metropolis-Hastings or indeed Hybrid Monte Carlo and Metropolis Adjusted Langevin Algorithms. This allows for highly efficient sampling even in very high dimensions where different scalings may be required for the transient and stationary phases of the Markov chain. The proposed method exploits the Riemannian structure of the parameter space of statistical models and thus automatically adapts to the local manifold structure at each step based on the metric tensor. A semi-explicit second order symplectic integrator for non-separable Hamiltonians is derived for simulating paths across this manifold which provides highly efficient convergence and exploration of the target density. The performance of the Riemannian Manifold Hamiltonian Monte Carlo method is assessed by performing posterior inference on logistic regression models, log-Gaussian Cox point processes, stochastic volatility models, and Bayesian estimation of parameter posteriors of dynamical systems described by nonlinear differential equations. Substantial improvements in the time normalised Effective Sample Size are reported when compared to alternative sampling approaches. Matlab code at \url{http://www.dcs.gla.ac.uk/inference/rmhmc} allows replication of all results.
Bayesian Solution Uncertainty Quantification for Differential Equations
Oksana A. Chkrebtii,David A. Campbell,Ben Calderhead,Mark A. Girolami
Statistics , 2013,
Abstract: We explore the use of probability models for uncertainty arising from discretization of system states defined implicitly by ordinary or partial differential equations. Accounting for this uncertainty is vital for characterising potential inferential bias incurred when likelihoods are constructed based on a numerical approximation over a finite discretization grid. A formalism for inferring fixed but a priori unknown model trajectories is proposed within the forward problem through Bayesian updating of sequentially refined prior models conditional on model interrogations. A one-step-ahead sampling scheme for interrogating the model is studied in detail, its consistency and first order convergence properties are proved. The proposed approach is demonstrated to capture the functional structure and magnitude of the discretization error, while attaining computational scaling of the same order as traditional first order numerical methods, and providing a formal statistical trade-off between accuracy and discretization grid size. Examples illustrate the flexibility of this framework to deal with a wide variety of models that include initial value, delay, and boundary value ordinary differential equations, as well as partial differential equations. Finally, the discussion outlines a wide range of emerging research themes in the new field of probabilistic numerics that naturally follow from the work presented.
Ten Simple Rules for Effective Computational Research
James M. Osborne ,Miguel O. Bernabeu,Maria Bruna,Ben Calderhead,Jonathan Cooper,Neil Dalchau,Sara-Jane Dunn,Alexander G. Fletcher,Robin Freeman,Derek Groen,Bernhard Knapp,Greg J. McInerny,Gary R. Mirams,Joe Pitt-Francis,Biswa Sengupta,David W. Wright,Christian A. Yates,David J. Gavaghan,Stephen Emmott,Charlotte Deane
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003506
R2: Information or Noise? Textual Analysis Based on SSE E-Interaction  [PDF]
Ben Wang
Open Journal of Business and Management (OJBM) , 2019, DOI: 10.4236/ojbm.2019.72054
Abstract: The question whether R2 represents information or noise is still a fundamental question in the study of stock price synchronicity. There are two main difficulties. Firstly, the trait information of a company is hard to measure; Secondly, the investors’ sophistication is ignored when we discuss the effectiveness of market. Through the study of Chinese SSE E-interaction platform and the measurement by textual analysis method, this article argues that the improvement of investors’ sophistication has negative association with stock price synchronicity. This result is more salient in companies with lower opacity or with higher corporate governance. This paper contributes to the deepen understanding of stock price synchronicity and new method of measuring trait information of companies.
Multiplex RT-PCR Amplification of HIV Genes to Create a Completely Autologous DC-Based Immunotherapy for the Treatment of HIV Infection
Irina Tcherepanova, Jason Harris, Aijing Starr, Jaclyn Cleveland, Helen Ketteringham, David Calderhead, Joe Horvatinovich, Don Healey, Charles A. Nicolette
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001489
Abstract: Background Effective therapy for HIV-infected individuals remains an unmet medical need. Promising clinical trials with dendritic cell (DC)-based immunotherapy consisting of autologous DC loaded with autologous virus have been reported, however, these approaches depend on large numbers of HIV virions to generate sufficient doses for even limited treatment regimens. Methodology/Principal Findings The present study describes a novel approach for RT-PCR amplification of HIV antigens. Previously, RT-PCR amplification of autologous viral sequences has been confounded by the high mutation rate of the virus which results in unreliable primer-template binding. To resolve this problem we developed a multiplex RT-PCR strategy that allows reliable strain-independent amplification of highly polymorphic target antigens from any patient and requires neither viral sequence data nor custom-designed PCR primers for each individual. We demonstrate the application of our RT-PCR process to amplify translationally-competent RNA encoding regions of Gag, Vpr, Rev and Nef. The products amplified using this method represent a complex mixture of autologous antigens encoded by viral quasispecies. We further demonstrate that DCs electroporated with in vitro-transcribed HIV RNAs are capable of stimulating poly-antigen-specific CD8+ T cell responses in vitro. Conclusion/Significance This study describes a strategy to overcome patient to patient viral diversity enabling strain-independent RT-PCR amplification of RNAs encoding sequence divergent quasispecies of Gag, Vpr, Rev and Nef from small volumes of infectious plasma. The approach allows creation of a completely autologous therapy that does not require advance knowledge of the HIV genomic sequences, does not have yield limitations and has no intact virus in the final product. The simultaneous use of autologous viral antigens and DCs may provoke broad patient-specific immune responses that could potentially induce effective control of viral loads in the absence of conventional antiretroviral drug therapy.
Ectopic expression of a truncated CD40L protein from synthetic post-transcriptionally capped RNA in dendritic cells induces high levels of IL-12 secretion
Irina Y Tcherepanova, Melissa D Adams, Xiaorong Feng, Atsushi Hinohara, Joe Horvatinovich, David Calderhead, Don Healey, Charles A Nicolette
BMC Molecular Biology , 2008, DOI: 10.1186/1471-2199-9-90
Abstract: Site-directed mutagenesis of each of the first five in-frame methionine codons in the CD40L coding sequence demonstrated that DCs expressing a truncated CD40L protein initiated from the second methionine codon secreted the highest levels of IL-12. In addition, a post-transcriptional method of capping was utilized for final modification of the CD40L RNA. This method enzymatically creates a type I cap structure identical to that found in most eukaryotic mRNAs, in contrast to the type 0 cap incorporated using the conventional co-transcriptional capping reaction.The combination of knocking out the first initiation methionine and post-transcriptional capping of the CD40L RNA allowed for approximately a one log increase in IL-12 levels by the transfected DCs. We believe this is a first report describing improved protein expression of post-transcriptionally capped RNA in DCs. The post-transcriptional capping which allows generation of a type I cap may have broad utility for optimization of protein expression from RNA in DCs and other cell types.RNA transfection into Dendritic Cells (DCs) is widely employed to achieve antigen expression [1]. RNA-transfected DCs are potent immune stimulators that have been tested in several clinical trials in cancer patients [2]. Transfection of DCs with RNA has several advantages over other platforms of antigen delivery such as DNA or viral vector-encoded antigens. Conditions may be optimized for cytoplasmic delivery of the RNA and together with transient expression and rapid degradation it may contribute to the safety of DC-based immunotherapy.Successful protein expression from transfected RNA depends on transfection efficiency, translation competence, and stability of the transfected RNA. A 5' cap structure and 3' poly(A) tail are essential components for RNA translation in eukaryotic cells. Mockey et. al. demonstrated that a poly(A) tail of 100 nucleotides and a 5'ARCA cap analogue act synergistically to produce high protein expression i
Using Labor Market Stocks to Identify Labor Market Flow Nissim Ben David  [PDF]
Ben-David Nissim
Modern Economy (ME) , 2011, DOI: 10.4236/me.2011.22021
Abstract: A technique that permits the calculation of the flow of agents between and within labor market states is pre-sented. A statistical agency having collected data on those flows easiest to collect and together with data on employment, unemployment and being out of the labor force, will be able to calculate the rest of the flows. The contribution of this paper is in suggesting an easy process which overcomes the difficulties statistical agencies usually have in collecting flow data.
The Rise and Fall of the Hydrophobic Effect in Protein Folding and Protein-Protein Association, and Molecular Recognition  [PDF]
Arieh Ben-Naim
Open Journal of Biophysics (OJBIPHY) , 2011, DOI: 10.4236/ojbiphy.2011.11001
Abstract: In the beginning everything was explained in Biochemistry in terms of hydrogen-bonds (HB). Then, the devastating blow, known as the HB-inventory argument came; hydrogen bonding with water molecules compete with intramolecular hydrogen-bonds. As a result, the HBs paradigm fell from grace. The void created was immediately filled by Kauzmann’s idea of hydrophobic (HφO) effect which reigned supreme in biochemical literature for over 50 years (1960-2010). Cracks in the HB-inventory argument on one hand, and doubts about the adequacy of Kauzmann’s model for the HφO effect, have led to a comeback of the HBs, along with a host of new hydrophilic (HφI) effects. The HφO effects lost much of its power - which it never really had - in explaining protein folding and protein-protein association. Instead, the more powerful and richer repertoire of HφI effects took over the reins. The interactions also offered simple and straightforward answers to the problems of protein folding, and protein-protein association.
Some No Longer Unknowns in Science  [PDF]
Arieh Ben-Naim
Open Journal of Biophysics (OJBIPHY) , 2012, DOI: 10.4236/ojbiphy.2012.21001
Abstract: Three out of 125 “big questions of science”, can now be claimed to have been answered. All of these questions involve water; its structure, its role in protein folding and its role in protein-protein association.
Experimentation of a Plane Solar Integrated Collector Storage Water Heater  [PDF]
Romdhane Ben Slama
Energy and Power Engineering (EPE) , 2012, DOI: 10.4236/epe.2012.42010
Abstract: In order to popularize the use of the solar-water heaters, especially in the residential and tertiary sectors with the third world, it appears to be necessary to reduce their cost while improving their performances. It is the object of this integrated storage collector thus created and tested in the south of Tunisia. It is simply made up of a tank playing the double part of solar absorber and storage tank of warm water, of a glazing to profit from the greenhouse effect and of an insulating case. Its measured energy performances, by the method of input-output proves its effectiveness to produce hot water, in spite of its simplicity of manufacture, usage and maintenance. Indeed a temperature of water exceeding 70?C is reached towards the afternoon True Solar Time, and for an efficiency of 7%. Thus, this type of collector with integrated storage is entirely satisfactory and could be available to larger mass.
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