Multi-Modal Interfaces for Sensemaking of Graph-Connected Datasets

The visualization of hypothesized evolutionary processes is often shown through phylogenetic trees. Given evolutionary data presented in one of several widely accepted formats, software exists to render these data into a tree diagram. However, software packages commonly in use by biologists today often do not provide means to dynamically adjust and customize these diagrams for studying new hypothetical relationships, and for illustration and publication purposes. Even where these options are available, there can be a lack of intuitiveness and ease-of-use. The goal of our research is, thus, to investigate more natural and effective means of sensemaking of the data with different user input modalities. To this end, we experimented with different input modalities, designing and running a series of prototype studies, ultimately focusing our attention on pen-and-touch. Through several iterations of feedback and revision provided with the help of biology experts and students, we developed a pen-and-touch phylogenetic tree browsing and editing application called PhyloPen. This application expands on the capabilities of existing software with visualization techniques such as overview+detail, linked data views, and new interaction and manipulation techniques using pen-and-touch. To determine its impact on phylogenetic tree sensemaking, we conducted a within-subject comparative summative study against the most comparable and commonly used state-of-the-art mouse-based software system, Mesquite. Conducted with biology majors at the University of Central Florida, each used both software systems on a set number of exercise tasks of the same type. Determining effectiveness by several dependent measures, the results show PhyloPen was significantly better in terms of usefulness, satisfaction, ease-of-learning, ease-of-use, and cognitive load and relatively the same in variation of completion time. These results support an interaction paradigm that is superior to classic mouse-based interaction, which could have the potential to be applied to other communities that employ graph-based representations of their problem domains

Mapping regions of equifinality in the parameter space: A method to evaluate inverse estimates and to plan experimental boundary conditions

Breakthrough curves of column outflow experiments are frequently used to identify parameters of reactive transport in porous media. However, inverse techniques coincide often with uniqueness problems, i.e. more than a single parameter set can reproduce the breakthrough curve equally well – a problem, which is termed equifinality. In this study, maps of regions with reliable parameter estimates were created applying numerical case studies with systematically varied parameters and boundary conditions. This was carried out by comparing the numerically produced breakthrough curves from forward simulations of the advection dispersion equation including equilibrium and non-equilibrium sorption (two-site/two-region model). Mapping of regions of uniqueness in the parameter space can help to improve the reliability of inverse simulations in two ways. On the one hand, regions of uniqueness depend on the boundary conditions of the experiment. Consequently, if the correct experimental boundary conditions – such as flow velocity, number and duration of percolation intervals and flow interruptions – are chosen, uniqueness problems can be avoided a priori. All what is required are some a priori information on the target compounds and materials and maps of regions of uniqueness for different experimental designs. On the other hand parameter estimates can be plotted into such maps a posteriori, to be able to evaluate whether equifinal solutions exist. are required, then an appropriate experimental design can be selected using maps of uniqueness

Highlights from the SoilCAM project: Soil Contamination, Advanced integrated characterisation and time-lapse Monitoring

The SoilCAM project (Soil Contamination, Advanced integrated characterisation and time-lapse Monitoring 2008-2012, EU-FP7-212663) is aimed at improving current methods for monitoring contaminant distribution and biodegradation in the subsurfac

Characterization of reactive transport by 3-D electrical resistivity tomography (ERT) under unsaturated conditions

The leaching of nitrate from intensively used arable soil is of major concern in many countries. In this study, we show how time lapse electrical resistivity tomography (ERT) can be used to characterize spatially heterogeneous processes of ion production, consumption, and transport in soils. A controlled release fertilizer was introduced into an undisturbed soil core in a laboratory lysimeter and subjected to infiltration events. The production of ions resulting from processes associated with nitrification and their transport through the soil core was observed by time lapse ERT and analysis of seepage water samples from a multicompartment sampler. ERT images show development and propagation of a high-conductivity plume from the fertilizer source zone. Molar amounts of nitrate produced in and exported from the soil core could be well reproduced by time lapse ERT using a spatial moment analysis. Furthermore, we observed that several shape measures of local breakthrough-curves (BTCs) of seepage water conductivity and nitrate derived by effluent analyses and BTCs of bulk conductivity derived by ERT are highly correlated, indicating the preservation of spatial differences of the plume breakthrough in the ERT data. Also differences between nitrate breakthrough and a conservative tracer breakthrough can be observed by ERT. However, the estimation of target ion concentrations by ERT is error bound and the smoothing algorithm of the inversion masks spatial conductivity differences. This results in difficulties reproducing spatial differences of ion source functions and variances of travel times. Despite the observed limitations, we conclude that time lapse ERT can be qualitatively and quantitatively informative with respect to processes affecting the fate of nitrate in arable soils

Characterization of reactive transport by 3-D electrical resistivity tomography (ERT) under unsaturated conditions

The leaching of nitrate from intensively used arable soil is of major concern in many countries. In this study, we show how time lapse electrical resistivity tomography (ERT) can be used to characterize spatially heterogeneous processes of ion production, consumption, and transport in soils. A controlled release fertilizer was introduced into an undisturbed soil core in a laboratory lysimeter and subjected to infiltration events. The production of ions resulting from processes associated with nitrification and their transport through the soil core was observed by time lapse ERT and analysis of seepage water samples from a multicompartment sampler. ERT images show development and propagation of a high-conductivity plume from the fertilizer source zone. Molar amounts of nitrate produced in and exported from the soil core could be well reproduced by time lapse ERT using a spatial moment analysis. Furthermore, we observed that several shape measures of local breakthrough-curves (BTCs) of seepage water conductivity and nitrate derived by effluent analyses and BTCs of bulk conductivity derived by ERT are highly correlated, indicating the preservation of spatial differences of the plume breakthrough in the ERT data. Also differences between nitrate breakthrough and a conservative tracer breakthrough can be observed by ERT. However, the estimation of target ion concentrations by ERT is error bound and the smoothing algorithm of the inversion masks spatial conductivity differences. This results in difficulties reproducing spatial differences of ion source functions and variances of travel times. Despite the observed limitations, we conclude that time lapse ERT can be qualitatively and quantitatively informative with respect to processes affecting the fate of nitrate in arable soils

The distribution of organic contaminant in aged tar-oil contaminated soils

One of the most common soil contamination sources in Germany are former manufactured gas plants. Many of them were destroyed during the World War II or abandoned in late XXth century. As the result a lot of potentially fertile soils were contaminated with specific viscous tar oil wastes. We studied a small tar oil waste basin. The age of the contamination was assessed to be at least 30 years. Natural attenuation processes resulted in formation of three soil layers. The upper layer (about 7cm in thickness) was rooted by weak grass vegetation and had features of newly formed humic-like organic matter. The total petroleum hydrocarbon (TPH) content was 28 mg/g. Below this layer (7-15 cm) we observed the most contaminated stratum with 90 mg/g TPH. The layer underneath (15-22 cm) had smaller concentrations of 16 mg/g TPH. Underlying strata had no visual evidence of contamination. Microbial biomass analyses showed that the most contaminated layer had 2-3 times more bacteria than the control soils. We suppose that during the aging processes a new microbial consortium capable of transforming high-molecular weight hydrocarbons has developed. Optical and FTIR-microscopy allowed us to observe the microstructure of contaminated soils. The tar oil formed dense spherical aggregates within the soil, which contained almost no mineral phase. Root channels and macropores were identified as preferential pathflows for the viscous tar oil, as they seemed to be coated with hydrocarbons even in less contaminated underlayers. We presume that open pores could initially act as remediation spots with aerobic conditions. Future oil migration might clog these pores, cease oxidation processes and slow down the remediation. High contents of total Fe and both dithionite-extractable and oxalate-extractable Fe as well as the occurrence of large siderite crystals in the most contaminated layer suggested that there might be isolated zones with anaerobic conditions to support this assumption

Analysis of TPV Network Losses (a Presentation)

This talk focuses on the theoretical analysis of electrical losses associated with electrically networking large numbers of TPV cells to produce high power TPV power generators