An investigation of the option space in conceptual building design for advanced building simulation

This article describes research conducted to gather empirical evidence on size, character and content of the option space in building design projects. This option space is the key starting point for the work of any climate engineer using building performance simulation who is supporting the design process. The underlying goal is to strengthen the role of advanced computing in building design, especially in the early conceptual stage, through a better integration of building performance simulation tools augmented with uncertainty analysis and sensitivity analysis. Better integration will need to assist design rather than automate design, allowing a spontaneous, creative and flexible process that acknowledges the expertise of the design team members. This research investigates and contrasts emergent option spaces and their inherent uncertainties in an artificial setting (student design studios) and in real-life scenarios (commercial design project case studies). The findings provide empirical evidence of the high variability of the option space that can be subjected to uncertainty analysis and sensitivity analysis.     

Knowledge assessment-practical example in testing

Knowledge assessment is inseparable part of current e-learning technologies. It can be used for self-assessment of students to give them feedback about their progress in a study or for an intermediate or final grading for tutors. However, knowledge tests are not developed with the adequate care. Author＇s experience in the area of knowledge assessment led to a confidence the ＂unstructured＂ testing is usually used in this process. It means that many of knowledge tests are not designed to reveal the reached level of knowledge. Moreover, testing suites are reviewed very seldom regarding their validity and items correlation. This paper presents experiences gained during the design and implementation of specific software focused on teaching several principles of the Unix-like operating systems. The structure of the specific assignment follows the Bloom＇s taxonomy of educational objectives.     

A cost-effective lexical acquisition process for large-scale thesaurus translation

Thesauri and controlled vocabularies facilitate access to digital collections by explicitly representing the underlying principles of organization. Translation of such resources into multiple languages is an important component for providing multilingual access. However, the specificity of vocabulary terms in most thesauri precludes fully-automatic translation using general-domain lexical resources. In this paper, we present an efficient process for leveraging human translations to construct domain-specific lexical resources. This process is illustrated on a thesaurus of 56,000 concepts used to catalog a large archive of oral histories. We elicited human translations on a small subset of concepts, induced a probabilistic phrase dictionary from these translations, and used the resulting resource to automatically translate the rest of the thesaurus. Two separate evaluations demonstrate the acceptability of the automatic translations and the cost-effectiveness of our approach.

DuD Recht

DuD Recht

DuD Recht     

Tracing pathway activities with kinase inhibitors and reverse phase protein arrays

Controlling aberrant protein kinase activity is a promising strategy for a variety of diseases, particularly cancer. Hence, the development of kinase inhibitors is currently a focal point for pharmaceutical research. In this study we utilize a chip-based reverse phase protein array (RPA) platform for profiling of kinase inhibitors in cell-based assays. In combination with the planar wave-guide technology the assay system has an absolute LOD down to the low zeptomole range. A431 cell lysates were analyzed for the activation state of key effectors in the epidermal growth factor (EGF) and insulin signaling pathways to validate this model for compound screening. A microtiter-plate format for growing, treating, and lysing cells was shown to be suitable for this approach, establishing the value of the technology as a screening tool for characterization of large numbers of kinase inhibitors against a wide variety of cellular signaling pathways. Moreover, the reverse array format allows rapid development of site-specific phosphorylation assays, since in contrast to ELISA type systems only a single antigen-specific antibody is required.     

The application of inductively coupled plasma mass spectrometry in clinical pharmacological oncology research

Metal-based anticancer agents are frequently used in the treatment of a wide variety of cancer types. The monitoring of these anticancer agents in biological samples is important to understand their pharmacokinetics, pharmacodynamics, and metabolism. In addition, determination of metals originating from anticancer agents is relevant to assess occupational exposure of health care personnel working with these drugs. The high sensitivity of inductively coupled plasma mass spectrometry (ICP-MS) has resulted in an increased popularity of this technique for the analysis of metal-based anticancer drugs. In addition to the quantitative analysis of the metal of interest in a sample, ICP-MS can be used as an ultrasensitive metal selective detector in combination with speciation techniques such as liquid chromatography. In the current review we provide a systematic survey of publications describing the analysis of platinum- and ruthenium-containing anticancer agents using ICP-MS, focused on the determination of total metal concentrations and on the speciation of metal compounds in biological fluids, DNA- and protein-adducts, and environmental samples. We conclude that ICP-MS is a powerful tool for the quantitative analysis of metal-based anticancer agents from multiple sample sources.     

Optimizing throughput and resource utilization using pipelining: Transformation based approach

A simple formulation of pipelining: Pipelining withN stages is equivalent to retiming where the number of delays on all inputs or all outputs, but not both, is increased byN is used as the basis for a convenient and efficient treatment of pipelining in the design of application specific computers.Pipelining according to the objective function (throughput or resource utilization) and the latency is introduced. For two polynomial complexity pipelining classes, optimal algorithms are presented. For two other classes both proofs of NP-completeness and efficient probabilistic algorithms are presented. Both theoretical and experimental properties of pipelining are discussed and a relationship with other transformations is explored. Due to similar formulations for both software pipelining and the pipelining presented here, all results can be easily modified for use in compilers for general purpose computers. We have also developed a polynomial complexity algorithm for determining the iteration bound.This work was done while the first author was at the University of California, Berkeley.     

State of the Art of Molecular Visualization in Immersive Virtual Environments

Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head-mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.