Visual perception and mixed-initiative interaction for assisted visualization design

This paper describes the integration of perceptual guidelines from human vision with an AI-based mixed-initiative search strategy. The result is a visualization assistant called ViA, a system that collaborates with its users to identify perceptually salient visualizations for large, multidimensional datasets. ViA applies knowledge of low-level human vision to: (1) evaluate the effectiveness of a particular visualization for a given dataset and analysis tasks; and (2) rapidly direct its search towards new visualizations that are most likely to offer improvements over those seen to date. Context, domain expertise, and a high-level understanding of a dataset are critical to identifying effective visualizations. We apply a mixed-initiative strategy that allows ViA and its users to share their different strengths and continually improve ViA's understanding of a user's preferences. We visualize historical weather conditions to compare ViA's search strategy to exhaustive analysis, simulated annealing, and reactive tabu search, and to measure the improvement provided by mixed-initiative interaction. We also visualize intelligent agents competing in a simulated online auction to evaluate ViA's perceptual guidelines. Results from each study are positive, suggesting that ViA can construct high-quality visualizations for a range of real-world datasets.     

Mass spectrometric techniques for label-free high-throughput screening in drug discovery

High-throughput screening (HTS) is an important tool for finding active compounds to initiate medicinal chemistry programs in pharmaceutical discovery research. Traditional HTS methods rely on fluorescent or radiolabeled reagents and/or coupling assays to permit quantitation of enzymatic target inhibition or activation. Mass spectrometry-based high-throughput screening (MS-HTS) is an alternative that is not susceptible to the limitations imposed by labeling and coupling enzymes. MS-HTS offers a selective and sensitive analytical method for unlabeled substrates and products. Furthermore, method development times are reduced without the need to incorporate labels or coupling assays. MS-HTS also permits screening of targets that are difficult or impossible to screen by other techniques. For example, enzymes that are challenging to purify can lead to the nonspecific detection of structurally similar components of the impure enzyme or matrix of membraneous enzymes. The high selectivity of tandem mass spectrometry (MS/MS) enables these screens to proceed with low levels of background noise to sensitively discover interesting hits even with relatively weak activity. In this article, we describe three techniques that we have adapted for large-scale (approximately 175,000 sample) compound library screening, including four-way parallel multiplexed electrospray liquid chromatography tandem mass spectrometry (MUX-LC/MS/MS), four-way parallel staggered gradient liquid chromatography tandem mass spectrometry (LC/MS/MS), and eight-way staggered flow injection MS/MS following 384-well plate solid-phase extraction (SPE). These methods are capable of analyzing a 384-well plate in 37 min, with typical analysis times of less than 2 h. The quality of the MS-HTS approach is demonstrated herein with screening data from two large-scale screens.     

Dimensional changes during solvent-induced crystallization of poly(ethylene terephthalate) films

The sample dimensional changes accompanying diffusion with induced crystallization in amorphous poly(ethylene terephthalate) (PET) films are analyzed. Initially, the film's lateral area remains practically constant, but near the end of the process, it increases rapidly, consistent with non-Fickian models for diffusion. The ultimate relative thickness increase is about double that for the lateral dimension, implying that plastic deformation in the thickness direction accompanies the sorption. Plots of fractional area increase (ΔA/ΔA_∞) vs. fractional weight gain (W/W_∞) indicate severe softening of the polymer by the penetrant.     

Pentadiagonal alternating-direction-implicit finite-difference time-domain method for two-dimensional Schrödinger equation

In this paper, we have proposed a pentadiagonal alternating-direction-implicit (Penta-ADI) finite-difference time-domain (FDTD) method for the two-dimensional Schrödinger equation. Through the separation of complex wave function into real and imaginary parts, a pentadiagonal system of equations for the ADI method is obtained, which results in our Penta-ADI method. The Penta-ADI method is further simplified into pentadiagonal fundamental ADI (Penta-FADI) method, which has matrix-operator-free right-hand-sides (RHS), leading to the simplest and most concise update equations. As the Penta-FADI method involves five stencils in the left-hand-sides (LHS) of the pentadiagonal update equations, special treatments that are required for the implementation of the Dirichlet’s boundary conditions will be discussed. Using the Penta-FADI method, a significantly higher efficiency gain can be achieved over the conventional Tri-ADI method, which involves a tridiagonal system of equations.     

A Multi‐Autonomous Underwater Vehicle System for Autonomous Tracking of Marine Life

This paper presents a multi‐autonomous underwater vehicle system capable of cooperatively and autonomously tracking and following marine targets (i.e., fish) tagged with an acoustic transmitter. The AUVs have been equipped with stereo‐hydrophones that receive signals broadcasted by the acoustic transmitter tags to enable real‐time calculation of bearing‐to‐tag and distance‐to‐tag measurements. These measurements are shared between AUVs via acoustic modem and fused within each AUV's particle filter for estimating the target's position. The AUVs use a leader/follower multi‐AUV control system to enable the AUVs to drive toward the estimated target state by following collision‐free paths. Once within the local area of the target, the AUVs circumnavigate the target state until it moves to another area. The system builds on previous work by incorporating a new SmartTag package that can be attached to an individual's dorsal fin. The SmartTag houses a full inertial measurement unit (INU), video logger, acoustic transmitter, and timed release mechanism. After real‐time AUV tracking experiments, the SmartTag is recovered. Logged IMU data are fused with logged AUV‐obtained acoustic tag measurements within a particle filter to improve state estimation accuracy. This improvement is validated through a series of multi‐AUV shark and boat tracking experiments conducted at Santa Catalina Island, California. When compared with previous work that did not use the SmartTag package, results demonstrated a decrease in mean position estimation error of 25–75%, tag orientation estimation errors dropped from 80° to 30° , the sensitivity of mean position error with respect to distance to the tag was less by a factor of 50, and the sensitivity of mean position error with respect to acoustic signal reception frequency to the tag was 25 times less. These statistics demonstrate a large improvement in the system's robustness when the SmartTag package is used.     

Water soluble polymeric nanofibres for rapid flocculation and enhanced dewatering of mature fine tailings

Water-soluble polymer flocculants have been used to efficiently release entrapped water in oil sands tailings by bridging fine particles to create large heavier flocs which can then settle faster and release water more efficiently. Due to their initial interaction with the fine particles suspended in tailings, polymer nanofibres may perform better than their parent polymers because of the entire surface of the nanofibres being fully accessible to the fine particles. In this work, commercially available poly(acrylamide-co-diallyl dimethylammonium chloride) was chosen as a basis for this study. Initial settling rate, supernatant turbidity, water recovery, capillary suction time, and solids content were measured to determine the effect of polymer nanofibres on solid-liquid separation. The solid forms of the polymer (either as nanofibre or powder) perform better than the polymer solution in each test, with optimum dosages of 5 wt% mature fine tailings (MFT) loading. Nanofibres could achieve settling rates of 60 m/h, while the other forms were only able to achieve 42 m/h. Additionally, the turbidity of the supernatant obtained after flocculation with nanofibres was 15 nephelometric turbidity units (NTU), while the polymer solution and powder produced turbidites of 162 NTU and 70 NTU, respectively. In addition, polymer nanofibres and powders generated larger flocs compared to the polymer solution, which produced small, homogenized flocs.     

A Flavanone and Two Phenolic Acids from Chrysanthemum morifolium with Phytotoxic and Insect Growth Regulating Activity

Leaves of Chrysanthemum morifolium cv. Ramat were extracted sequentially with hexane, ethyl acetate, and methanol. The methanol fraction, when incorporated into artificial diet was found to reduce the growth of cabbage looper (Trichoplusia ni Hubner) larvae at concentrations between 500 and 5000 ppm of diet. Fractionation of the methanol extract on a Sephadex column yielded five fractions, three of which reduced the weight of larvae relative to the control. One fraction was analyzed using high performance liquid chromatography (HPLC) and found to contain three main constituents. These compounds were purified using a combination of gel permeation chromatography on Sephadex LH20 and HPLC, and analyzed by 1H and 13CNMR as well as undergoing chemical and physical analyses. The compounds were identified as: 1, chlorogenic acid (5-O-caffeoylquinic acid); 2, 3,5-O-dicaffeoylquinic acid; and 3, 3', 4',5-trihydroxyflavanone7-O-glucuronide (eriodictyol7-O-glucuronide). At concentrations between 100 to 1000 ppm these compounds reduced both growth and photosynthesis of Lemna gibba L. with the order of efficacy being: flavanone > chlorogenic acid > 3,5-O-dicaffeoylquinic acid. Furthermore, when incorporated separately into artificial diet these compounds, at 10 to 1000 ppm, enhanced or reduced growth of the cabbage looper (Trichoplusia ni) and gypsy moth (Lymantria dispar L.).     

Nitrogen dynamics during till and no-till pasture restoration sequences in Rondônia,Brazil

The clearing of tropical rain forest in the Amazon basin has created large areas of cattle pasture that are now declining in productivity. Practices adopted by ranchers to restore productivity to degraded pastures have the potential to alter soil N availability and gaseous N losses from soils. We examined how soil inorganic N pools, net N mineralization and net nitrification rates, nitrification potential and NO and N₂O emissions from soils of a degraded pasture responded to the following restoration treatments: (1) soil tillage followed by replanting of grass and fertilization, (2) no-till application of non-selective herbicide, planting of rice, harvest followed by no-till replanting of grass and fertilization, and (3) the same no-till sequence with soybeans instead of rice. Tillage increased soil NH₄⁺ and NO₃^? pools but NH₄⁺ and NO₃^? pools remained relatively constant in the control and no-till treatments. Cumulative rates of net N mineralization and net nitrification during the first 6 months after treatment varied widely but were hightest in the tilled treatment. Emissions of NO and N₂O fluxes increased with tillage and with N fertilization. There were no clear relationships among rates of N fertilizer application, net N mineralization, net nitrification, NO, N₂O and total N oxide emissions. Our results indicate that pasture restoration sequences involving tilling and fertilizing will increase emissions of N oxides, but the magnitude of the increase is likely to differ based on timing of fertilizer application relative to the presence of plants and the magnitude of plant N demand. Emissions of N oxides appear to be decreased by the use of restoration sequences that minimize reductions in pasture grass cover.