Inference and uncertainty quantification of stochastic gene expression via synthetic models

Estimating uncertainty in model predictions is a central task in quantitative biology. Biological models at the single-cell level are intrinsically stochastic and nonlinear, creating formidable challenges for their statistical estimation which inevitably has to rely on approximations that trade accuracy for tractability. Despite intensive interest, a sweet spot in this trade-off has not been found yet. We propose a flexible procedure for uncertainty quantification in a wide class of reaction networks describing stochastic gene expression including those with feedback. The method is based on creating a tractable coarse-graining of the model that is learned from simulations, a synthetic model, to approximate the likelihood function. We demonstrate that synthetic models can substantially outperform state-of-the-art approaches on a number of non-trivial systems and datasets, yielding an accurate and computationally viable solution to uncertainty quantification in stochastic models of gene expression.     

Dynamic stability of a rotating pre-twisted asymmetric cross-section Timoshenko beam subjected to an axial periodic force

A finite element model is presented to study the static and dynamic stability of a pre-twisted Timoshenko beam having asymmetric aerofoil cross-section subjected to an axial periodic force. The change in the effects of coupling due to centre of flexure distance from the centroid and the shear coefficient on the stability due to the pre-twist angle is considered. It is concluded from the results that the pre-twist angle has an influence on the effects of coupling and the shear coefficient.     

重振城市景观的的“乌托邦” 阿尔斯特图书馆和表演艺术学院

<正>阿尔斯特图书馆和表演艺术学院坐落在比利时阿尔斯特,由一栋8000m~2的砖结构建筑和一栋引人注目的 19世纪后期的历史建筑组成。项目的名称为"乌托邦",与托马斯莫尔的著作《乌托邦》同名,这本书是由阿尔斯特市民德克马滕斯首先出版。     

Determination of the Minimum Scan Size to Obtain Representative Textures by Electron Backscatter Diffraction

A new method for analyzing microstructure is proposed to evaluate the long-range dependence of texture. The proposed method calculates the average disorientation as a function of distance between data points as measured by electron backscatter diffraction patterns. This method gives a measure of clustering of texture and is used to evaluate accurately the effective grain size. This procedure in conjunction with Information theory is used to estimate a representative scan size for various materials. Analyses show that the optimal scan size depends on grain morphology and crystallographic texture. The results also indicate that on an average the optimal scan size needs to be 10 times the effective grain size.     

Structure–Activity Relationships and Molecular Docking of Novel Dihydropyrimidine‐Based Mitotic Eg5 Inhibitors

Dihydropyrimidine‐based compounds belong to the first discovered inhibitors of the human mitotic kinesin Eg5. Although they are used by many research groups as model compounds for chemical genetics, considerably less emphasis has been placed on the improvement of this type of inhibitor, with the exception of two recent studies. Dihydropyrimidines can be divided into class I (analogues that bind in the S configuration) and class II type inhibitors, which bind in the R configuration. Herein we report the synthesis and optimization of novel class II type dihydropyrimidines using a combination of in vitro and docking techniques.     

High speed CNC system design. Part I: jerk limited trajectory generation and quintic spline interpolation

Reference trajectory generation plays a key role in the computer control of machine tools. Generated trajectories must not only describe the desired tool path accurately, but must also have smooth kinematic profiles in order to maintain high tracking accuracy, and avoid exciting the natural modes of the mechanical structure or servo control system. Spline trajectory generation techniques have become widely adopted in machining aerospace parts, dies, and molds for this reason; they provide a more continuous feed motion compared to multiple linear or circular segments and result in shorter machining time, as well as better surface geometry. This paper presents a quintic spline trajectory generation algorithm that produces continuous position, velocity, and acceleration profiles. The spline interpolation is realized with a novel approach that eliminates feedrate fluctuations due to parametrization errors. Smooth accelerations and decelerations are obtained by imposing limits on the first and second time derivatives of feedrate, resulting in trapezoidal acceleration profiles along the toolpath. Finally, the reference trajectory generated with varying interpolation period is re-sampled at the servo loop closure period using fifth order polynomials, which enable the original kinematic profiles to be preserved. The proposed trajectory generation algorithm has been tested in machining a wing surface on a three axis milling machine, controlled with an in house developed open architecture CNC.     

Ein KI-Verfahren für das Kartenspiel Magic: The Gathering

Zusammenfassung  Das Projekt LOSER entwickelt eine künstliche Intelligenz für das Sammelkartenspiel ,,Magic: The Gathering“. Da dies viele verschiedene Teilprobleme aufweist, findet eine Vielzahl von Algorithmen Verwendung, die variabel umgesetzt werden, um Ver?nderungen der Spielregeln angemessen zu begegnen.     

Virtual CNC system. Part I. System architecture

The paper presents a comprehensive virtual simulation model of a realistic and modular CNC system. The Virtual CNC architecture represents an actual CNC, but with modular feed drives, sensors, motors, and amplifiers. The CNC software library includes a variety of trajectory interpolation and axis control laws. Constant, trapezoidal and cubic acceleration profiles can be selected as a trajectory generation module. The control laws can be selected ranging from a simple PID to complex Pole Placement, Generalized Predictive Control or Sliding Mode Controller with friction compensation. When the Virtual CNC is assembled, its performance can be tested using frequency and time domain response analyses, which are automated. The Virtual CNC includes both analytical tuning methods for linear controllers, as well as Fuzzy Logic based expert auto-tuning system for Adaptive Sliding Mode Control. The paper includes detailed experimental verification of the Virtual CNC.     

Chemical composition and physicochemical properties of tubera salep produced from some Orchidaceae species

Salep samples obtained from 10 different Orchidaceae spp., namely Dactylorhiza osmanica var. osmanica, Ophrys mammosa, Orchis anatolica, Orchis coriophora, Orchis italica, Orchis morio, Orchis palustris, Orchis simia, Orchis tridentata and Serapias vomeracea ssp. orientalis, in Anatolia, were analyzed for moisture, glucomannan, starch, protein, ash contents, pH and viscosity values. Depending on the species, the samples showed statistically significant differences in glucomannan, starch and viscosity values. It was observed that the salep samples obtained from the tubers of O. italica, O. morio, O. anatolica and O. tridentata and S. vomeracea ssp. orientalis, respectively, had higher glucomannan contents and viscosities. To ensure a supply of high-quality salep, the uncontrolled collection of tubers from the wild, especially the species O. italica, O. morio and O. anatolica, should be prevented, and research into methods of cultivation should be carried out.