Optimization of degenerate oligonucleotide primed PCR for amplification of microdissected chromosome segments

The degenerate oligonucleotide primer of sequence, 5\u27 CCGACTCGAGNNNNNNATGTGG 3\u27, contains a specific 3\u27 hexanucleotide , a central random hexanucleotide and an Xhol site towards it\u27s 5\u27 end. This degenerate primer (Telenius et al, 1992) has been developed for the amplification and subsequent cloning of any source of target DNA, particularly the human chromosome, in a process termed degenerate oligonucleotide primed PGR (DOP-PCR). In the present study, bacteriophage lambda DNA was employed as a model target DNA to test a variety of DOPPCR procedures. To achieve the highest efficiency, different concentrations of primer and Taq DNA polymerase and also a variety of PGR program cycles were tested. After achieving the optimal concentration of the DOP primer and Taq DNA polymerase, two different protocols were investigated. The first reUes on low-temperature pre-amplification of the target DNA by modified T7 DNA polymerase (Sequenase) and uses the amphfied segments for a subsequent amplification catalysed by Taq DNA polymerase. With this protocol, amplified DNA was obtained with down to 0.2 pg DNA of template. The other procedure employs Taq DNA polymerase for all stages of amphfication. We have developed a modified form of this strategy by boosting Taq DNA polymerase in the middle of the amphfication program. This modification increases the efficiency and sensitivity of the procedure and enables us to ampUfy as little as 0.02 pg DNA. The latter method should be of considerable value for amphfication of DNA from a wide variety of sources, particularly human chromosomes, since it should reduce to a minimum the number of dissected chromosome fragments required. In fact, following the completion of this work, the method has been successfully applied to the analysis of a human chromosome translocation in collaboratio

On the Bayesian estimation of jump-diffusion models in finance

The jump-diffusion framework introduced by Duffie et al. (2000) encompasses most one factor models used in finance. Due to the model complexity of this framework, the particle filter (e.g., Hurn et al., 2015; Jacobs & Liu, 2018) and combinations of Gibbs and Metropolis-Hastings samplers (e.g., Eraker et al., 2003; Eraker, 2004) have been the tools of choice for its estimation. However, Bégin & Boudreault (2020) recently showed that the discrete nonlinear filter (DNF) of Kitagawa (1987) can also be used for fast and accurate maximum likelihood estimation of jump-diffusion models. In this project report, we combine the DNF with Markov chain Monte Carlo (MCMC) methods for Bayesian estimation in the spirit of the particle MCMC algorithm of Andrieu et al. (2010). In addition, we show that derivative prices (i.e., European option prices) can be easily included into the DNF’s likelihood evaluations, which allows for efficient joint Bayesian estimation

Adsorption of imidazole on Au(111) surface: Dispersion corrected density functional study

We use density functional theory in the generalized gradient approximation to study the adsorption of imidazole on the Au(111) surface and account for dispersion effect using Grimme's empirical dispersion correction technique. Our results show that the adsorption energy of imidazole depends on the slab size and on the adsorption site. In agreement with other studies, we find the largest adsorption energy for imidazole on a top site of Au(111). However, we also note that the adsorption energy at other sites is substantial

Understanding of matrix embedding: a theoretical spectroscopic study of CO interacting with Ar clusters, surfaces and matrices

Through benchmark studies, we explore the performance of PBE density functional theory, with and without Grimme's dispersion correction (DFT-D3), in predicting spectroscopic properties for molecules interacting with rare gas matrices. Here, a periodic-dispersion corrected model of matrix embedding is used for the first time. We use PBE-D3 to determine the equilibrium structures and harmonic vibrational frequencies of carbon monoxide in interaction with small Ar clusters (CO–Arn, n = 1, 2, 3), with an Ar surface and embedded in an Ar matrix. Our results show a converging trend for both the vibrational frequencies and binding energies when going from the gas-phase to a fully periodic approach describing CO embedding in Ar. This trend is explained in terms of solvation effects, as CO is expected to alter the structure of the Ar matrix. Due to a competition between CO–Ar interactions and Ar–Ar interactions, perturbations caused by the presence of CO are found to extend over several Å in the matrix. Accordingly, it is mandatory to fully relax rare gas matrices when studying their interaction with embedded molecules. Moreover, we show that the binding energy per Ar is almost constant (∼−130 cm−1 atom−1) regardless of the environment of the CO molecule. Finally, we show that the concentration of the solute into the cold matrix influences the spectroscopic parameters of molecules embedded into cold matrices. We suggest hence that several cautions should be taken before comparing these parameters to gas phase measurements and to theoretical data of isolated species

Extracting User Interest Center Based on a Semantic User Profile

Abstract—The fundamental purpose of a personalized information retrieval system is to provide relevant results to the specific need of the user. The selection of interesting documents to a user is done on the basis of his area of interest, inferred from the information about the user or his user profile. Thus the calculation of the interest center is one of the essential elements for a relevant research. On one hand, information retrieval systems converge to a semantic representation of user profiles. On the other hand, they do not take into account the semantic links between the concepts (meaning of the word) when defining the center of interest.In this paper we use a graphical representation of the user profile based on ontology. Thus we were able to use the power of mathematical calculations of graphs to deduce the interest’s centers of the user

Une méthode variationelle en temps pour le couplage de schémas hétérogènes en dynamique transitoire

International audienceCet article présente très succinctement les derniers résultats de l'équipe sur le cou-plage de codes en dynamique. La méthode proposée est très générale et elle est basée sur une vision faible de l'intégration temporelle des équations d'équilibre dynamique. Cette manière de comprendre les algorithmes de calcul en dynamique permet de mettre en place une stratégie de couplage qui assure que le couplage ne perturbe en aucune façon les bilans d'énergie des sous do-maines assemblés. Il en résulte que la méthode proposée permet d'assembler des sous domaines ou des codes différenets utilisant leur propre intégrateur temporel, leur propre maillage, et leur propre pas de temps. Un exemple est proposé pour illustrer le propos

Architects Requirements of Decision Support Tools to deliver Low Impact Housing Design in the UK: Insights and Recommendations

The construction industry is facing increasing pressure to address environmental performance earlier in the design process. For United Kingdom (UK) buildings, design is perceived to be the key in delivering the low carbon agenda. Hence, a fundamental change to designers’ approach in designing for low impact buildings is needed. A mixed method approach comprising of questionnaires to sustainable architectural practices were combined with interviews of architects in practice and academia. This is necessary to identify the gaps in the current use of Building Performance Energy Simulation (BPES) tools as design- decision support for architects, towards recommending the requirements of new generation architects’ friendly tools for the early and detail stages of the design process to deliver the sustainable housing design in the UK. The results indicate a limited number of architects use BPES tools; that is, until the later stage of the design process. Moreover, there is need to focus on tool development for architects decision-making process, especially at the conceptual stage, where major decision are taken. Thus, the study focuses on recommending requirements of architects’ friendly tools, fit for their design-decision making at various stages of the design process. As architectural design decisions vary significantly in terms of accuracy, flexibility, and the level of detail, the study recommends that: at the early stages of the process, where relatively minimal information is available, flexibility and approximation in BPES tools is more approximate to support design decisions. Nevertheless, as the design develops, and more information becomes available, precision and higher levels of detail in BPES tools are required. Keywords: Building Performance Energy Simulation Tools, Decision Making, Low Impact Buildings, Royal Institute of British Architects, Sustainability