Encoding folding paths of RNA switches

RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and intermolecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.Comment: 9 pages, 6 figure

DFT and BIST of a multichip module for high-energy physics experiments

Engineers at Politecnico di Torino designed a multichip module for high-energy physics experiments conducted on the Large Hadron Collider. An array of these MCMs handles multichannel data acquisition and signal processing. Testing the MCM from board to die level required a combination of DFT strategie

Cluster Computing and the Power of Edge Recognition

We study the robustness--the invariance under definition changes--of the cluster class CL#P [HHKW05]. This class contains each #P function that is computed by a balanced Turing machine whose accepting paths always form a cluster with respect to some length-respecting total order with efficient adjacency checks. The definition of CL#P is heavily influenced by the defining paper's focus on (global) orders. In contrast, we define a cluster class, CLU#P, to capture what seems to us a more natural model of cluster computing. We prove that the naturalness is costless: CL#P = CLU#P. Then we exploit the more natural, flexible features of CLU#P to prove new robustness results for CL#P and to expand what is known about the closure properties of CL#P. The complexity of recognizing edges--of an ordered collection of computation paths or of a cluster of accepting computation paths--is central to this study. Most particularly, our proofs exploit the power of unique discovery of edges--the ability of nondeterministic functions to, in certain settings, discover on exactly one (in some cases, on at most one) computation path a critical piece of information regarding edges of orderings or clusters

Caught in the Middle: Empowerment in Middle Managers

Citation: Doty, N. (2017) Caught in the Middle: Empowerment in Middle Managers. Unpublished manuscript, Kansas State University, Manhattan, KS.Kirmser Undergraduate Research Award - Individual Non-Freshman Category, grand prizePrevious studies on the topic of middle management focus on how these specific managers drive the organizations they are a part of, how they motivate their subordinates to work effectively and efficiently, how middle managers create excitement, and how their leadership style helps their followers find purpose in their work. And yet, little is done to flesh out how these strong MMs are created, what motivates them, and how they succeed in their position (Kominis & Emmanuel, 2007). These MMs are the “basis of strategic renewal” in bettering an ever-changing organizational environment and, conversely, can even “sabotage implementation efforts” in the changing strategy of the workplace (Mantere, 2008, p. 294). This paper aims to discover what factors influence the empowerment of middle managers for the purpose of better understanding and development of MMs in organizational and workplace structures. Motivation is the influence on a person’s “direction, vigor and persistence of action” (Rajhans, 2012, p. 82). The current literature on the subjects of management, motivation, and work performance focus on the topics of role expectations, and empowerment, and are typically viewed through the theoretical lenses of structural empowerment and psychological empowerment, which are outlined below

An efficient numerical method for shakedown analysis

The algorithm proposed in [9] for incremental elastoplasticity is extended and applied to shakedown analysis. Using the three field mixed finite element proposed in [22] a series of mathematical programming problems or steps, obtained from the application of the proximal point algorithm to the static shakedown theorem, are obtained. Each step is solved by an Equality Constrained Sequential Quadratic Programming (EC-SQP) tech- nique that allows a consistent linearization of the equations improving the computational efficiency

Three-dimensional cell to tissue assembly process

The present invention relates a 3-dimensional cell to tissue and maintenance process, more particularly to methods of culturing cells in a culture environment, either in space or in a gravity field, with minimum fluid shear stress, freedom for 3-dimensional spatial orientation of the suspended particles and localization of particles with differing or similar sedimentation properties in a similar spatial region

Statistical Analysis of Bus Networks in India

Through the past decade the field of network science has established itself as a common ground for the cross-fertilization of exciting inter-disciplinary studies which has motivated researchers to model almost every physical system as an interacting network consisting of nodes and links. Although public transport networks such as airline and railway networks have been extensively studied, the status of bus networks still remains in obscurity. In developing countries like India, where bus networks play an important role in day-to-day commutation, it is of significant interest to analyze its topological structure and answer some of the basic questions on its evolution, growth, robustness and resiliency. In this paper, we model the bus networks of major Indian cities as graphs in \textit{L}-space, and evaluate their various statistical properties using concepts from network science. Our analysis reveals a wide spectrum of network topology with the common underlying feature of small-world property. We observe that the networks although, robust and resilient to random attacks are particularly degree-sensitive. Unlike real-world networks, like Internet, WWW and airline, which are virtual, bus networks are physically constrained. The presence of various geographical and economic constraints allow these networks to evolve over time. Our findings therefore, throw light on the evolution of such geographically and socio-economically constrained networks which will help us in designing more efficient networks in the future.Comment: Submitted to PLOS ON