Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes

<b>Method:</b> Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory processes from time series data, and they have established themselves as a standard modelling tool in computational systems biology. The conventional approach is based on the assumption of a homogeneous Markov chain, and many recent research efforts have focused on relaxing this restriction. An approach that enjoys particular popularity is based on a combination of a DBN with a multiple changepoint process, and the application of a Bayesian inference scheme via reversible jump Markov chain Monte Carlo (RJMCMC). In the present article, we expand this approach in two ways. First, we show that a dynamic programming scheme allows the changepoints to be sampled from the correct conditional distribution, which results in improved convergence over RJMCMC. Second, we introduce a novel Bayesian clustering and information sharing scheme among nodes, which provides a mechanism for automatic model complexity tuning. <b>Results:</b> We evaluate the dynamic programming scheme on expression time series for Arabidopsis thaliana genes involved in circadian regulation. In a simulation study we demonstrate that the regularization scheme improves the network reconstruction accuracy over that obtained with recently proposed inhomogeneous DBNs. For gene expression profiles from a synthetically designed Saccharomyces cerevisiae strain under switching carbon metabolism we show that the combination of both: dynamic programming and regularization yields an inference procedure that outperforms two alternative established network reconstruction methods from the biology literature

Effect of sodium hyluronate added to topical corticosteroids in chronic rhinosinusitis with nasal polyposis

Available medical treatments for chronic rhinosinusitis (CRS) with nasal polyposis (CRSwNP) comprise systemic and topical therapies. Although topical corticosteroids are effective in the treatment of CRS, they are not completely devoid of adverse effects. Thus, care has to be taken when long-term treatments are prescribed. There is recent evidence that sodium hyaluronate (SH), the major component of many extracellular matrices, promotes tissue healing, including activation and moderation of the inflammatory responses, cell proliferation, migration, and angiogenesis

Documenting design decision rationale to improve individual and team design decision making: An experimental evaluation

Individual and team decision-making have crucial influence on the level of success of every software project. Even though several studies were already conducted, which concerned design decision rationale documentation approaches, a few of them focused on performances and evaluated them in laboratory. This paper proposes a technique to document design decision rationale, and evaluates experimentally the impact such a technique has on effectiveness and efficiency of individual/team decision-making in presence of requirement changes. The study was conducted as a controlled experiment. Fifty post-graduate Master students performed in the role of experiment subjects. Documented design decisions regarding the Ambient Intelligence paradigm constituted the experiment objects. Main results of the experiment show that, for both individual and team-based decision-making, effectiveness significantly improves, while efficiency remains unaltered, when decision-makers are allowed to use, rather not use, the proposed design rationale documentation technique. Copyright 2006 ACM

Developments in high-precision aspects of power converter control for LHC

The initial results from integration testing of the LHC magnet power converters revealed problems of lowfrequency noise, settling time, drift with time and temperature, thermal management and EMC. These problems originated in the use of DSP, the A/D converter (ADC), the DCCT and their respective environments. This paper reports the methods used to improve the performance through hardware and software modifications and the results achieved

One-side heating test and modeling of tubular receivers equipped with turbulence promoters for solar tower applications

Tubular receivers in central tower systems suffer the high mechanical stresses caused by the temperature gradient typically established along the tube and across its circumference due to the one-side heating. In the present work, the thermal behavior of three different absorber tubes is investigated both experimentally and numerically. The tubes, manufactured in Cr alloy 718 (Inconel®), were smooth or with repeated rib-roughness (annular or helical ribs), and were tested at the solar furnace SF60 of the Plataforma Solar de Almería (PSA) in 2017 within the international access program of SFERA II project, financed by the EU. The specific focus of the tests was the assessment of the role of turbulence promoters in reducing the peak wall temperature when a strong one-side heating is present, contributing to the reduction of the thermal gradients between the irradiated and the non-irradiated (back) side of the tube. The experimental results show that the use of turbulence promoters reduce the wall temperature with respect to the case of a smooth tube, as expected, although the comparison between the samples is not trivial in view of the change in the optical properties induced by the progressive oxidation of the irradiated surface. Computational Fluid Dynamic (CFD) 3D models have been developed for the three samples and they have proven the capability to very-well reproduce the experimental results. A fair comparison between the different simulated tubes in the same controlled conditions of one-side heating has been performed numerically, assessing quantitatively the temperature reduction induced by the turbulence promoters, and the best performance of the Inconel® tube equipped with helices

Experimental and numerical investigation of a porous receiver equipped with Raschig Rings for CSP applications

In the context of central solar tower systems, tubular receivers are among the most appealing absorber solutions: the absorbed solar radiation is transferred from the tube external surface to the heat transfer fluid (HTF) flowing within the absorber. In the case of air as HTF, very high temperatures of the coolant can be obtained in principle, thus increasing the efficiency of the downstream thermodynamic cycle. To explore the possible applicability of a porous medium made of Raschig Rings (RRs), already successfully adopted in the heat removal from the resonant cavity of a technological device, the gyrotron, where the heat flux can go up to 20–25 MW/m2 and removed by subcooled water, a mock-up of a planar receiver equipped with RRs has been tested in a solar furnace, using air as coolant. The test results are presented here and analyzed1. Furthermore, a numerical model of the mock-up, where the RRs are modeled in detail by the Discrete Element Method, is presented and its capability to reproduce the measured data demonstrated. The model shows, for the tested configuration, an enhancement of the heat transfer of a factor of ~5 with respect to a plain channel with the same envelope, and a Performance Evaluation Criteria of 2–2.5 when the device is compared to the same receiver configuration, but without RRs

High-precision performance testing of the LHC power converters

The magnet power converters for LHC were procured in three parts, power part, current transducers and control electronics, to enable a maximum of industrial participation in the manufacturing and still guarantee the very high precision (a few parts in 10-6) required by LHC. One consequence of this approach was several stages of system tests: factory reception tests, CERN reception tests, integration tests , short-circuit tests and commissioning on the final load in the LHC tunnel. The majority of the power converters for LHC have now been delivered, integrated into complete converter and high-precision performance testing is well advanced. This paper presents the techniques used for high-precision testing and the results obtained

QuickXsort: Efficient Sorting with n log n - 1.399n +o(n) Comparisons on Average

In this paper we generalize the idea of QuickHeapsort leading to the notion of QuickXsort. Given some external sorting algorithm X, QuickXsort yields an internal sorting algorithm if X satisfies certain natural conditions. With QuickWeakHeapsort and QuickMergesort we present two examples for the QuickXsort-construction. Both are efficient algorithms that incur approximately n log n - 1.26n +o(n) comparisons on the average. A worst case of n log n + O(n) comparisons can be achieved without significantly affecting the average case. Furthermore, we describe an implementation of MergeInsertion for small n. Taking MergeInsertion as a base case for QuickMergesort, we establish a worst-case efficient sorting algorithm calling for n log n - 1.3999n + o(n) comparisons on average. QuickMergesort with constant size base cases shows the best performance on practical inputs: when sorting integers it is slower by only 15% to STL-Introsort

Report of IRPA task group on the impact of the eye lens dose limits

In 2012 IRPA established a task group (TG) to identify key issues in the implementation of the revised eye lens dose limit. The TG reported its conclusions in 2013. In January 2015, IRPA asked the TG to review progress with the implementation of the recommendations from the early report and to collate current practitioner experience. This report presents the results of a survey on the view of the IRPA professionals on the new limit to the lens of the eye and on the wider issue of tissue reactions. Recommendations derived from the survey are presented. This report was approved by IRPA Executive Council on 31 January 2017