Online Abelian Pattern Matching

Ejaz T, Rahmann S, Stoye J. Online Abelian Pattern Matching. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld. Bielefeld: Technische Fakultät der Universität Bielefeld; 2008.An abelian pattern describes the set of strings that comprise of the same combination of characters. Given an abelian pattern P and a text T [Epsilon] [Sigma]^n, the task is to find all occurrences of P in T, i.e. all substrings S = T_i...T_j such that the frequency of each character in S matches the specified frequency of that character in P. In this report we present simple online algorithms for abelian pattern matching, and give a lower bound for online algorithms which is [Omega](n)

Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

During the last decade, computational methods, which were for the most part developed to study protein-ligand interactions and especially to discover, design and develop drugs by and for medicinal chemists, have been successfully applied in a variety of food science applications [1,2]. It is now clear, in fact, that drugs and nutritional molecules behave in the same way when binding to a macromolecular target or receptor, and that many of the approaches used so extensively in medicinal chemistry can be easily transferred to the fields of food science. For instance, nuclear receptors are common targets for a number of drug molecules and could be, in the same way, affected by the interaction with food or food-like molecules. Thus, key computational medicinal chemistry methods like molecular dynamics can be used to decipher protein flexibility and to obtain stable models for docking and scoring in food-related studies, and virtual screening is increasingly being applied to identify molecules with potential to act as endocrine disruptors, food mycotoxins, and new nutraceuticals [3,4,5]. All of these methods and simulations are based on protein-ligand interaction phenomena, and represent the basis for any subsequent modification of the targeted receptor's or enzyme's physiological activity. We describe here the energetics of binding of biological complexes, providing a survey of the most common and successful algorithms used in evaluating these energetics, and we report case studies in which computational techniques have been applied to food science issues. In particular, we explore a handful of studies involving the estrogen receptors for which we have a long-term interest

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Investigating Precise Control in Spatial Interactions: Proxemics, Kinesthetics, and Analytics

Augmented and Virtual Reality (AR/VR) technologies have reshaped the way in which we perceive the virtual world. In fact, recent technological advancements provide experiences that make the physical and virtual worlds almost indistinguishable. However, the physical world affords subtle sensorimotor cues which we subconsciously utilize to perform simple and complex tasks in our daily lives. The lack of this affordance in existing AR/VR systems makes it difficult for their mainstream adoption over conventional $2D$ user interfaces. As a case in point, existing spatial user interfaces (SUI) lack the intuition to perform tasks in a manner that is perceptually familiar to the physical world. The broader goal of this dissertation lies in facilitating an intuitive spatial manipulation experience, specifically for motor control. We begin by investigating the role of proximity to an action on precise motor control in spatial tasks. We do so by introducing a new SUI called the Clock-Maker's Work-Space (CMWS), with the goal of enabling precise actions close to the body, akin to the physical world. On evaluating our setup in comparison to conventional mixed-reality interfaces, we find CMWS to afford precise actions for bi-manual spatial tasks. We further compare our SUI with a physical manipulation task and observe similarities in user behavior across both tasks. We subsequently narrow our focus on studying precise spatial rotation. We utilize haptics, specifically force-feedback (kinesthetics) for augmenting fine motor control in spatial rotational task. By designing three kinesthetic rotation metaphors, we evaluate precise rotational control with and without haptic feedback for 3D shape manipulation. Our results show that haptics-based rotation algorithms allow for precise motor control in 3D space, also, help reduce hand fatigue. In order to understand precise control in its truest form, we investigate orthopedic surgery training from the point of analyzing bone-drilling tasks. We designed a hybrid physical-virtual simulator for bone-drilling training and collected physical data for analyzing precise drilling action. We also developed a Laplacian based performance metric to help expert surgeons evaluate the resident training progress across successive years of orthopedic residency