Head up, foot down : object words orient attention to the objects' typical location

Many objects typically occur in particular locations, and object words encode these spatial associations. We tested whether such object words (e.g., head, foot) orient attention toward the location where the denoted object typically occurs (i.e., up, down). Because object words elicit perceptual simulations of the denoted objects (i.e., the representations acquired during actual perception are reactivated), we predicted that an object word would interfere with identification of an unrelated visual target subsequently presented in the object's typical location. Consistent with this prediction, three experiments demonstrated that words denoting objects that typically occur high in the visual field hindered identification of targets appearing at the top of the display, whereas words denoting low objects hindered target identification at the bottom of the display. Thus, object words oriented attention to and activated perceptual simulations in the objects' typical locations. These results shed new light on how language affects perception

Visual and spatial audio mismatching in virtual environments

This paper explores how vision affects spatial audio perception in virtual reality. We created four virtual environments with different reverb and room sizes, and recorded binaural clicks in each one. We conducted two experiments: one where participants judged the audio-visual match, and another where they pointed to the click direction. We found that vision influences spatial audio perception and that congruent audio-visual cues improve accuracy. We suggest some implications for virtual reality design and evaluation

uAnalyze: web-based high-resolution DNA melting analysis with comparison to thermodynamic predictions

pre-printAbstract-uAnalyzeSM is a web-based tool for analyzing high-resolution melting data of PCR products. PCR product sequence is input by the user and recursive nearest neighbor thermodynamic calculations used to predict a melting curve similar to uMELT (http://www.dna.utah.edu/umelt/umelt.html). Unprocessed melting data are input directly from LightScanner-96, LS32, or HR-1 data files or via a generic format for other instruments. A fluorescence discriminator identifies low intensity samples to prevent analysis of data that cannot be adequately normalized. Temperature regions that define fluorescence background are initialized by prediction and optionally adjusted by the user. Background is removed either as an exponential or by linear baseline extrapolation. The precision or, "curve spread," of experimental melting curves is quantified as the average of the maximum helicity difference of all curve pairs. Melting curve accuracy is quantified as the area or "2D offset" between the average experimental and predicted melting curves. Optional temperature overlay (temperature shifting) is provided to focus on curve shape. Using 14 amplicons of CYBB, the mean þ= standard deviation of the difference between experimental and predicted fluorescence at 50 percent helicity was 0:04 þ = 0:48C. uAnalyze requires Flash, is not browser specific and can be accessed at http://www.dna.utah.edu/uv/uanalyze.html

uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application

ManuscriptuMeltSM is a flexible web-based tool for predicting DNA melting curves and denaturation profiles of PCR products. The user defines an amplicon sequence and chooses a set of thermodynamic and experimental parameters that include nearest-neighbor stacking energies, loop entropy effects, cation (monovalent and Mg++) concentrations and a temperature range. Using an accelerated partition function algorithm along with chosen parameter values, uMelt interactively calculates and visualizes the mean helicity and the dissociation probability at each sequence position at temperatures within the temperature range. Predicted curves display the mean helicity as a function of temperature or as derivative plots. Predicted profiles display stability as a function of sequence position either as 50% helicity temperatures or as the helicity probability at specific temperatures. The loss of helicity associated with increasing temperature may be viewed dynamically to visualize domain formation within the molecule. Results from fluorescent high-resolution melting experiments match the number of predicted melting domains and their relative temperatures. However, the absolute melting temperatures vary with the selected thermodynamic parameters and current libraries do not account for the rapid melting rates and helix stabilizing dyes used in fluorescent melting experiments. uMelt provides a convenient platform for simulation and design of high-resolution melting assays

Heterozygote PCR product melting curve prediction

pre-printMelting curve prediction of PCR products is limited to perfectly complementary strands. Multiple domains are calculated by recursive nearest-neighbor thermodynamics. However, the melting curve of an amplicon containing a heterozygous single nucleotide variant (SNV) after PCR is the composite of four duplexes: two matched homoduplexes and two mismatched heteroduplexes. To better predict the shape of composite heterozygote melting curves, 52 experimental curves were compared to brute force in silico predictions varying two parameters simultaneously: the relative contribution of heteroduplex products and an ionic scaling factor for mismatched tetrads. Heteroduplex products contributed 25.7 +/- 6.7% to the composite melting curve, varying from 23-28% for different SNV classes. The effect of ions on mismatch tetrads scaled to 76-96% of normal (depending on SNV class) and averaged 88 +/-16.4%. Based on uMelt (www.dna.utah.edu/umelt/umelt.html) with an expanded nearest neighbor thermodynamic set that UU IR Author Manuscript UU IR Author Manuscript University of Utah Institutional Repository Author Manuscript HETEROZYGOTE PCR PRODUCT MELTING CURVE PREDICTION 2 includes mismatched base pairs, uMelt HETS calculates helicity as a function of temperature for homoduplex and heteroduplex products, as well as the composite curve expected from heterozygotes. It is an interactive web tool for efficient genotyping design, heterozygote melting curve prediction, and quality control of melting curve experiments. The application was developed in Actionscript and can be found online at http://www.dna.utah.edu/hets/

Understanding Death : Creating Student Opportunities for Meaningful Emotional Expression in the Science Classroom

Understanding death as natural and integral to life cycles has been considered crucial and relevant in science teaching. The concept of death not only defines the physical end of life but also the end of a cycle and the beginnings of transformation. Adopting a broader definition of death thus empowers educators to directly address the affect and emotion that occurs for all students

Laboratory driven, lean-to-adaptive prototyping in Parallel for Web software project identification and application development in health science research

Journal ArticleClinical research laboratories, bioinformatics core facilities, and health science organizations often rely on heavy planning based software development models to propose, build, and distribute software as a consumable product. Projects in non-agile software life cycles tend to have rigid ?plan-design-build? milestones, increasing the amount of time needed for software development completion. Though the classic software development approach is needed for large-scale and organizational projects, clinical research laboratories can expedite software development while maintaining quality by using lean prototyping as a condition of project advancement to a committed adaptive software development cycle. Software projects benefit from an agile methodology due to the active and changing requirements often guided by experimental data driven models. We describe a lean to adaptive method used in parallel with laboratory bench work to develop quality software quickly that meets the requirements of a fast-paced research environment and reducing time to production, providing immediate value to the end user, and limiting unnecessary development practices in favor of results

Atlas in the Cloud

This report describes the research, system analysis, design methodology, and testing procedures that were used to create a Cloud-based robotics development kit. The goal of this project was to utilize Cloud computing resources in support of the Worcester Polytechnic Institute-Carnegie Mellon University DARPA Robotics Challenge team. The following report begins with background on the underlying technologies and the DARPA Robotics Challenge. The report includes a systems analysis and design methodology. User feedback informed subsequent revision of the original design. The report ends with implementation details, testing, and the results achieved by the system