Ribonuclease P (RNase P) RNA is converted to a Cd(2+)-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNase P cleavage site

To study the cleavage mechanism of bacterial Nase P RNA, we have synthesized precursor tRNA substrates carrying a single Rp- or Sp-phosphorothioate modification at the RNase P cleavage site. Both the Sp- and the Rp-diastereomer reduced the rate of processing by Escherichia coli RNase P RNA at least 1000-fold under conditions where the chemical step is rate-limiting. The Rp-modification had no effect and the Sp-modification had a moderate effect on precursor tRNA ground state binding to RNase P RNA. Processing of the Rp-diastereomeric substrate was largely restored in the presence of the "thiophilic" Cd2+ as the only divalent metal ion, demonstrating direct metal ion coordination to the (pro)-Rp substituent at the cleavage site and arguing against a specific role for Mg(2+)-ions at the pro-Sp oxygen. For the Rp-diastereomeric substrate, Hill plot analysis revealed a cooperative dependence upon [Cd2+] of nH = 1.8, consistent with a two-metal ion mechanism. In the presence of the Sp-modification, neither Mn2+ nor Cd2+ was able to restore detectable cleavage at the canonical site. Instead, the ribozyme promotes cleavage at the neighboring unmodified phosphodiester with low efficiency. Dramatic inhibition of the chemical step by both the Rp- and Sp-phosphorothioate modification is unprecedented among known ribozymes and points to unique features of transition state geometry in the RNase P RNA-catalyzed reaction.     

Controlling patterns of geospatial phenomena

Modeling spatially distributed phenomena in terms of its controlling factors is a recurring problem in geoscience. Most efforts concentrate on predicting the value of response variable in terms of controlling variables either through a physical model or a regression model. However, many geospatial systems comprises complex, nonlinear, and spatially non-uniform relationships, making it difficult to even formulate a viable model. This paper focuses on spatial partitioning of controlling variables that are attributed to a particular range of a response variable. Thus, the presented method surveys spatially distributed relationships between predictors and response. The method is based on association analysis technique of identifying emerging patterns, which are extended in order to be applied more effectively to geospatial data sets. The outcome of the method is a list of spatial footprints, each characterized by a unique “controlling pattern”—a list of specific values of predictors that locally correlate with a specified value of response variable. Mapping the controlling footprints reveals geographic regionalization of relationship between predictors and response. The data mining underpinnings of the method are given and its application to a real world problem is demonstrated using an expository example focusing on determining variety of environmental associations of high vegetation density across the continental United States.     

Information fusion for automotive applications – An overview

This article focusses on the fusion of information from various automotive sensors like radar, video, and lidar for enhanced safety and traffic efficiency. Fusion is not restricted to data from sensors onboard the same vehicle but vehicular communication systems allow to propagate and fuse information with sensor data from other vehicles or from the road infrastructure as well. This enables vehicles to perceive information from regions that are hardly accessible otherwise and represents the basis for cooperative driving maneuvers. While the Bayesian framework builds the basis for information fusion, automobile environments are characterized by their a priori unknown topology, i.e., the number, type, and structure of the perceived objects is highly variable. Multi-object detection and tracking methods are a first step to cope with this challenge. Obviously, the existence or non-existence of an object is of paramount importance for safe driving. Such decisions are highly influenced by the association step that assigns sensor measurements to object tracks. Methods that involve multiple sequences of binary assignments are compared with soft-assignment strategies. Finally, fusion based on finite set statistics that (theoretically) avoid an explicit association are discussed.     

The physiological mirror—a system for unconscious control of a virtual environment through physiological activity

This paper introduces a system for real-time physiological measurement, analysis, and metaphorical visualization within a virtual environment (VE). Our goal is to develop a method that allows humans to unconsciously relate to parts of an environment more strongly than to others, purely induced by their own physiological responses to the virtual reality (VR) displays. In particular, we exploit heart rate, respiration, and galvanic skin response in order to control the behavior of virtual characters in the VE. Such unconscious processes may become a useful tool for storytelling or assist guiding participants through a sequence of tasks in order to make the application more interesting, e.g., in rehabilitation. We claim that anchoring of subjective bodily states to a virtual reality (VR) can enhance a person’s sense of realism of the VR and ultimately create a stronger relationship between humans and the VR.     

Study on the replication quality of micro-structures in the injection molding process with dynamical tool tempering systems

The injection molding of micro-structures is a promising mass-production method for a broad range of materials. However, the replication quality of these structures depends significantly on the heat flow during the filling stage. In this paper, the filling and heat transfer of v-groove and random structures below 5 μm is investigated with the help of an AFM (atomic force microscope) and thermo couples. A numerical model is developed to predict the filling of surface structures during the filling and packing stage. The model implies the use of simple fully developed flow models taking the power-law material model into account. This permits investigation into which ways several processing parameters affect the polymer flow in the surface structures. The mold wall temperature, which has significant effects on the polymer flow, is varied by using a variothermal mold temperature control system to validate the model proposed.     

Improving component selection and monitoring with controlled experimentation and automated measurements

Context: A number of approaches have been proposed for the general problem of software component evaluation and selection. Most approaches come from the field of Component-Based Software Development (CBSD), tackle the problem of Commercial-off-the-shelf component selection and use goal-oriented requirements modelling and multi-criteria decision making techniques. Evaluation of the suitability of components is carried out largely manually and partly relies on subjective judgement. However, in dynamic, distributed environments with high demands for transparent selection processes leading to trustworthy, auditable decisions, subjective judgements and vendor claims are not considered sufficient. Furthermore, continuous monitoring and re-evaluation of components after integration is sometimes needed.Objective: This paper describes how an evidence-based approach to component evaluation can improve repeatability and reproducibility of component selection under the following conditions: (1) Functional homogeneity of candidate components and (2) High number of components and selection problem instances.Method: Our evaluation and selection method and tool empirically evaluate candidate components in controlled experiments by applying automated measurements. By analysing the differences to system-development-oriented scenarios, the paper shows how the process of utility analysis can be tailored to fit the problem space, and describes a method geared towards automated evaluation in an empirical setting. We describe tool support and a framework for automated measurements.We further present a taxonomy of decision criteria for the described scenario and discuss the data collection means needed for each category of criteria.Results: To evaluate our approach, we discuss a series of case studies in the area of digital preservation. We analyse the criteria defined in these case studies, classify them according to the taxonomy, and discuss the quantitative coverage of automated measurements.Conclusion: The results of the analysis show that an automated measurement, evaluation and selection framework is necessary and feasible to ensure trusted and repeatable decisions.     

IRIS: illustrative rendering for integral surfaces

Integral surfaces are ideal tools to illustrate vector fields and fluid flow structures. However, these surfaces can be visually complex and exhibit difficult geometric properties, owing to strong stretching, shearing and folding of the flow from which they are derived. Many techniques for non-photorealistic rendering have been presented previously. It is, however, unclear how these techniques can be applied to integral surfaces. In this paper, we examine how transparency and texturing techniques can be used with integral surfaces to convey both shape and directional information. We present a rendering pipeline that combines these techniques aimed at faithfully and accurately representing integral surfaces while improving visualization insight. The presented pipeline is implemented directly on the GPU, providing real-time interaction for all rendering modes, and does not require expensive preprocessing of integral surfaces after computation.