Experimental techniques using optically enabled ring oscillators

We present a method for characterizing transceiver performance in parallel optical data links. By establishing a bidirectional link between two optically enabled chips, the conditions for a ring oscillator are made possible. We propose this technique as a means of measuring the sensitivity of transceiver latency to controlled variables such as temperature, optical output power, supply voltage, and device misalignment. This method is noninvasive and independent of the packaging, circuit topology, and optical medium used. The technique is demonstrated experimentally, and results are compared with a simulation.     

Fast-Fourier-domain delay line for in vivo optical coherence tomography with a polygonal scanner

We demonstrate in vivo optical coherence tomography using a Fourier-domain optical delay line constructed with a commercially available polygonal scanner. The 20-faceted polygonal mirror array, capable of scanning at rates up to 15 kHz, is implemented at 4 kHz to acquire 500 x 500 pixel images at 8 frames/s with a signal-to-noise ratio of 80 dB. Features of this delay line include scalability to high repetition rates, 98.6% linearity in group delay over 2 mm, and bandwidth support exceeding 150 nm. Images are obtained in an animal model (Xenopus laevis), and limitations due to phase-delay nonlinearity and polygon asymmetry are discussed.     

Genomic mining for complex disease traits with “random chemistry”

Our rapidly growing knowledge regarding genetic variation in the human genome offers great potential for understanding the genetic etiology of disease. This, in turn, could revolutionize detection, treatment, and in some cases prevention of disease. While genes for most of the rare monogenic diseases have already been discovered, most common diseases are complex traits, resulting from multiple gene–gene and gene-environment interactions. Detecting epistatic genetic interactions that predispose for disease is an important, but computationally daunting, task currently facing bioinformaticists. Here, we propose a new evolutionary approach that attempts to hill-climb from large sets of candidate epistatic genetic features to smaller sets, inspired by Kauffman’s “random chemistry” approach to detecting small auto-catalytic sets of molecules from within large sets. Although the algorithm is conceptually straightforward, its success hinges upon the creation of a fitness function able to discriminate large sets that contain subsets of interacting genetic features from those that don’t. Here, we employ an approximate and noisy fitness function based on the ReliefF data mining algorithm. We establish proof-of-concept using synthetic data sets, where individual features have no marginal effects. We show that the resulting algorithm can successfully detect epistatic pairs from up to 1,000 candidate single nucleotide polymorphisms in time that is linear in the size of the initial set, although success rate degrades as heritability declines. Research continues into seeking a more accurate fitness approximator for large sets and other algorithmic improvements that will enable us to extend the approach to larger data sets and to lower heritabilities.     

An improved topographic mapping technique from airborne lidar: application in a forested hillside

We developed a robust method to reconstruct a digital terrain model (DTM) by classifying raw light detection and ranging (lidar) points into ground and non-ground points with the help of the Progressive Terrain Fragmentation (PTF) method. PTF applies iterative steps for searching terrain points by approximating terrain surfaces using the triangulated irregular network (TIN) model constructed from ground return points. Instead of using absolute slope or offset distance, PTF uses orthogonal distance and relative angle between a triangular plane and a node. Due to this characteristic, PTF was able to classify raw lidar points into ground and non-ground points on a heterogeneous steep forested area with a small number of parameters. We tested this approach by using a lidar data set covering a part of the Angelo Coast Range Reserve on the South Fork of the Eel River in Mendocino County, California, USA. We used systematically positioned 16 reference plots to determine the optimal parameter that can be used to separate ground and non-ground points from raw lidar point clouds. We tested at different admissible hillslope angles (15° to 20°), and the minimum total error (1.6%) was acquired at the angle value of 18°. Because classifying raw lidar points into ground and non-ground points is the basis for other types of analyses, we expect that our study will provide more accurate terrain approximation and contribute to improving the extraction of other forest biophysical parameters.     

Experiencing Nature: Embodying Animals in Immersive Virtual Environments Increases Inclusion of Nature in Self and Involvement With Nature

Immersive virtual environments (IVEs) produce simulations that mimic unmediated sensory experiences. 3 experiments (N = 228) tested how different modalities increase environmental involvement by allowing users to inhabit the body of animals in IVEs or watch the experience on video. Embodying sensory‐rich experiences of animals in IVEs led to greater feeling of embodiment, perception of being present in the virtual world, and interconnection between the self and nature compared to video. Heightened interconnection with nature elicited greater perceptions of imminence of the environmental risk and involvement with nature, which persisted for 1 week. Although the effect sizes were small to moderate, findings suggest that embodied experiences in IVEs may be an effective tool to promote involvement with environmental issues.     

Thermal Annealing and Propagation of Shockley Stacking Faults in 4H-SiC PiN Diodes

Stacking faults within 4H-SiC PiN diodes are known to be detrimental to device operation. Here, we present electroluminescence (EL) images of 4H-SiC PiN diodes providing evidence that electrically and optically stimulated Shockley stacking fault (SSF) propagation is a reversible process at temperatures as low as 210°C. Optical beam induced current (OBIC) images taken following complete optical stressing of a PiN diode and that lead to a small number of completely propagated SSFs provide evidence that such defects propagate across the n–/p+ interface and continue to grow throughout the p+ layer. These observations bring about questions regarding the validity of the currently accepted driving force mechanism for SSF propagation.     

Spatial modeling for groundwater arsenic levels in North Carolina

To examine environmental and geologic determinants of arsenic in groundwater, detailed geologic data were integrated with well water arsenic concentration data and well construction data for 471 private wells in Orange County, NC, via a geographic information system. For the statistical analysis, the geologic units were simplified into four generalized categories based on rock type and interpreted mode of deposition/emplacement. The geologic transitions from rocks of a primary pyroclastic origin to rocks of volcaniclastic sedimentary origin were designated as polylines. The data were fitted to a left-censored regression model to identify key determinants of arsenic levels in groundwater. A Bayesian spatial random effects model was then developed to capture any spatial patterns in groundwater arsenic residuals into model estimation. Statistical model results indicate (1) wells close to a transition zone or fault are more likely to contain detectible arsenic; (2) welded tuffs and hydrothermal quartz bodies are associated with relatively higher groundwater arsenic concentrations and even higher for those proximal to a pluton; and (3) wells of greater depth are more likely to contain elevated arsenic. This modeling effort informs policy intervention by creating three-dimensional maps of predicted arsenic levels in groundwater for any location and depth in the area.     

Examining cognitive function across the lifespan using a mobile application

Many studies conducted in a laboratory or university setting are limited by funding, personnel, space, and time constraints. In the present study, we introduce a method of data collection using a mobile application that circumvents these typical experiment administration issues. Using the application, we examined cross-sectional age differences in cognitive function. We obtained data from more than 15,000 participants and replicated specific patterns of age-related differences in cognition. Using a subset of these participants, we also examined the processing speed account of age-related cognitive differences, and the association of exercise and leisure activity with cognitive function across the lifespan. We discuss the relative advantages and disadvantages of data collection with a mobile application, and provide recommendations for the use of this method in research.     

The Chinese Room: Visualization and Interaction to Understand and Correct Ambiguous Machine Translation

We present The Chinese Room , a visualization interface that allows users to explore and interact with a multitude of linguistic resources in order to decode and correct poor machine translations. The target users of The Chinese Room are not bilingual and are not familiar with machine translation technologies. We investigate the ability of our system to assist such users in decoding and correcting faulty machine translations. We found that by collaborating with our application, end-users can overcome many difficult translation errors and disambiguate translated passages that were otherwise baffling. We also examine the utility of our system to machine translation researchers. Anecdotal evidence suggests that The Chinese Room can help such researchers develop better machine translation systems.