Adam Wójtowicz

RNA tertiary structure determination: NOE pathways construction by tabu search

MOTIVATION Liquid state nuclear magnetic resonance (NMR) spectroscopy has now been well established as a method for RNA tertiary structure determination. Most of the steps involved in the determination of RNA molecules are performed using computer programs. They however, do not apply to resonance assignment being the starting point of the whole procedure. We propose a tabu search algorithm as a tool for automating this step. Nuclear overhause effect (NOE) pathway, which determines the assignment, is constructed during an analysis of possible connections between resonances within aromatic/anomeric region of two-dimensional NOESY spectrum resulting from appropriate NMR experiment. RESULTS Computational tests demonstrate the superior performance of the tabu search algorithm as compared with the exact enumerative approach and genetic procedure applied to the experimental and simulated spectral data for RNA molecules. AVAILABILITY The software package can be obtained upon request from Marta Szachniuk.

Evolutionary approach to NOE paths assignment in RNA structure elucidation

Resonance assignment remains one of the hardest stages in RNA tertiary structure elucidation with the use of nuclear magnetic resonance spectroscopy. We propose an evolutionary algorithm being a tool for an automatic design of the procedure. NOE pathway, which determines the assignments, is constructed during an analysis of possible connections between resonances within aromatic/anomeric region of 2D-NOESY spectra. Computational tests demonstrate the performance of the genetic algorithm in comparison with the enumerative procedure applied for the experimental and simulated spectral data for RNA molecules.

Model for adaptable context-based biometric authentication for mobile devices

It becomes possible to take advantage of seamless biometric authentication on mobile devices due to increasing quality and quantity of built-in sensors, increasing processing power of the devices, and wireless connectivity. However, practical effectiveness of the biometric authentication application depends on user’s environment conditions that can decrease the accuracy of biometrics recognition or make the acquisition process undesirable for mobile user in a given moment, i.e., effectiveness depends on usage context. In this paper, context-based biometric authentication model for mobile devices is proposed. It enables determining the most accurate authentication method at the moment along with the most accurate form of interacting with a user w.r.t. authentication process. The generic model designed and verified with proof-of-concept implementation constitutes a foundation for building further adaptable and extensible multi-factor context-dependent systems for mobile authentication.

Computer Simulation of Prostate Cryoablation—Fast and Accurate Approximation of the Exact Solution

Objective. Cryosurgery is a minimally invasive cancer treatment that uses liquid nitrogen or supercooled argon to freeze and destroy tumors. To achieve complete ablation of the prostate, we have developed a computer program that can determine treatment effects by calculating iceball formation. This is based on a three-dimensional (3D) model of the patients prostate constructed from ultrasound images. The program predicts the best set of cryoablation parameters and cryoprobe spatial positions, then displays these parameters in graphical or numerical form. The objective of this work was to improve our prostate cryoablation modeling software by making its partial differential equation (PDE) solver more accurate and faster. Materials and Methods: CryoSim, our software package, accepts a set of acquired and processed 3D ultrasound images of the prostate, then models heat diffusion using numerical approximations of the heat equation. Results: We describe the latest version of the CryoSim software, which models cryoablation therapy. Solving the problems of low spatial resolution (now down to a fraction of a millimeter, as compared to 5 mm in the old version) and modeling cryosurgery in a short time (down to few minutes versus hours) provides a platform for proper planning of cryosurgery and a tool for the training of surgeons. Conclusion. Changes in the PDE solver algorithm produce more accurate results, leading to an improved visualization of the iceball, with a precision of a few mm and a significant decrease in computation time.

Secure User-Contributed 3D Virtual Environments

This chapter deals with the problem of access control in 3D virtual environments which are interactive, behavior-rich, multi-user, and based on user-contributed content. Traditional coarse-grained and geometry-centric privilege modeling methods are not sufficient for such environments. New methods are required that concern not only geometrical models, their relationships and structure, but also inter-object behavioral interactions. In this chapter, a method called Selective Semantic Modeling (SSM) is described. The SSM method enables modeling of privileges for behavioral objects with respect to their semantics. The SSM method is based on the concept of semantic operations, which are generated at run-time from the current content structure of a virtual environment and are applicable to the access control model as a part of a privilege. Semantic consistency of the privilege is guaranteed by a two-phase regeneration and validation mechanism, so that user privileges can be expressed in a precise, semantically accurate and flexible way.

Representing User Privileges in Object-Oriented Virtual Reality Systems

In virtual reality systems which are collaborative and dynamic, i.e. where at run-time mutually interactive objects can be added or removed in different contexts and where their behavior can be modified, the problem of data security and privacy protection is renewed. In such virtual worlds operations on objects should or should not be allowed to users playing particular roles with respect to inter-object interactions. In this paper a method called VR-PR is presented, where privileges are represented by pairs: object – semantic operations induced from object interactions. Semantic operations are generated using automatic analysis of the object method call graphs. Then they are used in the privilege creation and modification process. Privileges based on semantic operations are expressive, flexible and consistent with permanently evolving set of objects composing the virtual world, interactions between the objects, and a set of users.

Privacy-Preserving Protocol for Smart Space Services with Negotiable Comfort Preferences

In this paper an architecture and a protocol for secure and privacy-preserving service usage in smart spaces are presented. Comfort preferences that are defined and stored on end-users mobile devices are subject to negotiations. The approach relies on a single trusted party operating as a public service in the “security infrastructure as a service” model. It is designed to assure resilience against attacks on users privacy from the side of service providers (SPs), user’s attempts to use the services in an unauthorized manner, user’s attempts to violate payment policies, as well as payment authority’s attacks on privacy of users’ payment patterns. From the SP perspective, the proposed approach minimizes the risk of unauthorized service usage, or denial of service attacks. All players benefit from the fast and secure micropayments allowing for pay-per-use model implementation, which is natural in ubiquitous services usage scenarios.

Building Augmented Reality Presentations with Web 2.0 Tools

Augmented reality enables superimposing various kinds of computer generated content, such as interactive 2D and 3D multimedia objects, in real time, directly on a view of real objects. One of the application domains, which can particularly benefit from the use of AR techniques, is education. However, to enable widespread use of AR in education, simple and intuitive methods of preparation of learning content are required. In this paper, we propose an easy-to-use method of augmenting printed books with arbitrary multimedia content. A popular Moodle-based educational platform has been extended with a plugin enabling creation of AR presentations. In addition, an associated mobile application is provided, which helps teachers assign the presentations to book pages and enables students to access the content.

Semantic Exploration of Distributed AR Services

In this paper, we present a new approach to building large-scale ubiquitous augmented reality (AR) applications. Instead of fixed AR content, presented on specific places or objects, we propose the concept of a semantic network of distributed AR services contributed by different providers. These services have different roles and offer different content and functionality, but the synergy offered by such a diverse network of services opens new fields of application for AR systems. The services in our approach are modeled using well-established standards from the domain of business process modeling, but they are additionally annotated using semantic descriptions of the role and properties of particular services and their relationships, allowing meaningful selection of dynamic exploration paths by users with different interests, constraints and privileges. An indispensable element of such heterogeneous AR systems is proper consideration of security and privacy issues, which are also covered in this work.

Declarative GUI descriptions for device-independent applications

The increasing number and diversity of devices connected to the Internet open new research challenges in the field of cross-platform and device-independent applications. One of the approaches to this problem is the Device-Independent Architecture, which provides application logic and application data device independence. It enables also usage of user interface (UI) adaptation middleware to support application UI device independence. Potentially, device-independent descriptions of application UI can be implemented with existing user interface description languages (UIDLs). In this paper, we present an analysis of eight popular UIDLs that are assumed to be suitable for device-independent GUI descriptions, along with a summary of evaluation results and lessons learned. The selected UIDLs were employed to describe a set of GUI views based on an existing mobile application. The gathered results confirm our research hypothesis that the analyzed popular declarative UIDLs are not capable of describing mobile GUI in a device-independent manner. Therefore, using the knowledge gathered from the reported experiment, we propose a set of guidelines for an optimal device-independent UIDL.