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.     

The effect of emulsifiers,sugar, shortening and soya flour on the staling of barbari flat bread

A standard method has been developed to bake barbari flat-type bread. Instron was used to measure the hardness of the crumb of bread samples as a criterion of staling. Different combinations of emulsifiers, sugar, shortening and soya flour were added to the formula of barbari bread to find their effect on the retardation of hardness. Addition of soya flour increased the loaf weight but decreased its total organoleptic score. Added amounts of different additives tried in this experiment improved the hardness approximately to the same level. The best result was obtained by the addition of sodium stearoyl-2-lactylate and shortening.     

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.     

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.     

Molecular Subtyping of Invasive Breast Cancer Using a PAM50-Based Multigene Expression Test-Comparison with Molecular-Like Subtyping by Tumor Grade/Immunohistochemistry and Influence on Oncologist’s Decision on Systemic Therapy in a Real-World Setting

In intermediate risk hormone receptor (HR) positive, HER2 negative breast cancer (BC), the decision regarding adjuvant chemotherapy might be facilitated by multigene expression tests. In all, 142 intermediate risk BCs were investigated using the PAM50-based multigene expression test Prosigna® in a prospective multicentric study. In 119/142 cases, Prosigna® molecular subtyping was compared with local and two central (C1 and C6) molecular-like subtypes relying on both immunohistochemistry (IHC; HRs, HER2, Ki-67) and IHC + tumor grade (IHC+G) subtyping. According to local IHC, 35.4% were Luminal A-like and 64.6% Luminal B-like subtypes (local IHC+G subtype: 31.9% Luminal A-like; 68.1% Luminal B-like). In contrast to local and C1 subtyping, C6 classified >2/3 of cases as Luminal A-like. Pairwise agreement between Prosigna® subtyping and molecular-like subtypes was fair to moderate depending on molecular-like subtyping method and center. The best agreement was observed between Prosigna® (53.8% Luminal A; 44.5% Luminal B) and C1 surrogate subtyping (Cohen’s kappa = 0.455). Adjuvant chemotherapy was suggested to 44.2% and 88.6% of Prosigna® Luminal A and Luminal B cases, respectively. Out of all Luminal A-like cases (locally IHC/IHC+G subtyping), adjuvant chemotherapy was recommended if Prosigna® testing classified as Prosigna® Luminal A at high / intermediate risk or upgraded to Prosigna® Luminal B.     

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.