Bimodal Visualization of Industrial X-Ray and Neutron Computed Tomography Data.

Advanced manufacturing creates increasingly complex objects with material compositions that are often difficult to characterize by a single modality. Our collaborating domain scientists are going beyond traditional methods by employing both X-ray and neutron computed tomography to obtain complementary representations expected to better resolve material boundaries. However, the use of two modalities creates its own challenges for visualization, requiring either complex adjustments of bimodal transfer functions or the need for multiple views. Together with experts in nondestructive evaluation, we designed a novel interactive bimodal visualization approach to create a combined view of the co-registered X-ray and neutron acquisitions of industrial objects. Using an automatic topological segmentation of the bivariate histogram of X-ray and neutron values as a starting point, the system provides a simple yet effective interface to easily create, explore, and adjust a bimodal visualization. We propose a widget with simple brushing interactions that enables the user to quickly correct the segmented histogram results. Our semiautomated system enables domain experts to intuitively explore large bimodal datasets without the need for either advanced segmentation algorithms or knowledge of visualization techniques. We demonstrate our approach using synthetic examples, industrial phantom objects created to stress bimodal scanning techniques, and real-world objects, and we discuss expert feedback.

Migration and diffusion of unsteady-state flow of volatile organic compounds on activated carbon adsorption beds under reverse ventilation.

Despite increasing attention to the influence of unsteady-state volatile organic compounds (VOCs) on the adsorption of activated carbon, studies in this regard are rare. Therefore, in this study, an investigation into the migration and diffusion of unsteady-state VOCs on activated carbon adsorption beds under reverse ventilation was conducted. Here, reverse clean air was introduced when the activated carbon bed reached the penetration point. The influence of reverse ventilation temperature, reverse superficial gas velocity, activated carbon filling height, and different ventilation modes on the adsorption of unsteady toluene by activated carbon were studied. Our experimental results show that when the reverse ventilation temperature increased from 20 °C to 60 °C, the quasi-first-order desorption rate constant increased from 0.00356 min-1 to 0.00807 min-1, an increase in the reverse superficial gas velocity led to a higher rate constant, and at greater reverse superficial gas velocities, the stripping capacity increased. It was observed that the maximum stripping capacity was achieved at a reverse superficial gas velocity of 0.3 m/s. For different activated carbon filling heights, following reverse ventilation, the stripping capacity of a 5 cm and 30 cm activated carbon bed accounted for 41.43% and 65.85% of the original adsorption capacity, respectively. The study concludes that concentration of toluene first increased and then decreased with time under forward ventilation, whereas the concentration gradually decreased under reverse ventilation.

Tailored approach to study Legionella infection using a lattice light sheet microscope (LLSM).

Legionella is a genus of ubiquitous environmental pathogens found in freshwater systems, moist soil, and composted materials. More than four decades of Legionella research has provided important insights into Legionella pathogenesis. Although standard commercial microscopes have led to significant advances in understanding Legionella pathogenesis, great potential exists in the deployment of more advanced imaging techniques to provide additional insights. The lattice light sheet microscope (LLSM) is a recently developed microscope for 4D live cell imaging with high resolution and minimum photo-damage. We built a LLSM with an improved version for the optical layout with two path-stretching mirror sets and a novel reconfigurable galvanometer scanner (RGS) module to improve the reproducibility and reliability of the alignment and maintenance of the LLSM. We commissioned this LLSM to study Legionella pneumophila infection with a tailored workflow designed over instrumentation, experiments, and data processing methods. Our results indicate that Legionella pneumophila infection is correlated with a series of morphological signatures such as smoothness, migration pattern and polarity both statistically and dynamically. Our work demonstrates the benefits of using LLSM for studying long-term questions in bacterial infection. Our free-for-use modifications and workflow designs on the use of LLSM system contributes to the adoption and promotion of the state-of-the-art LLSM technology for both academic and commercial applications.

The migration and diffusion of unsteady-state VOCs flow on activated carbon adsorption beds.

ABSTRACTTraditionally, in engineering applications, VOC (volatile organic compound) emissions are usually under non-steady states due to intermittent emissions and concentration fluctuations, which adversely affects the stable and reliable operation of many existing purification systems and may constitute a safety hazard. However, previous studies on VOC adsorption by adsorbents have mostly focused on the adsorption performance and properties of different modified adsorbents. Few studies of VOC adsorption have focused on adsorption or movement for unsteady-state VOCs using activated carbon adsorption beds. This study investigated three common and important factors (load time ratio, load mode and no-load flow rate) that affect the adsorption of unsteady-state VOCs by activated carbon. This allowed the migration and movement of VOCs between activated carbon adsorption beds under different factors to be analyzed, which provides important insights in understanding VOC adsorption and can promote the development of homogeneous buffering technology for non-steady state VOCs. In addition, this information provides support for the development of pollution control processes for tidal VOCs discharge airflows that result from storage and transportation operations, and also provides parameters that could support practical applications of activated carbon to adsorb unsteady-state VOCs.

Multiscale Unfolding: Illustratively Visualizing the Whole Genome at a Glance.

We present Multiscale Unfolding, an interactive technique for illustratively visualizing multiple hierarchical scales of DNA in a single view, showing the genome at different scales and demonstrating how one scale spatially folds into the next. The DNA's extremely long sequential structure-arranged differently on several distinct scale levels-is often lost in traditional 3D depictions, mainly due to its multiple levels of dense spatial packing and the resulting occlusion. Furthermore, interactive exploration of this complex structure is cumbersome, requiring visibility management like cut-aways. In contrast to existing temporally controlled multiscale data exploration, we allow viewers to always see and interact with any of the involved scales. For this purpose we separate the depiction into constant-scale and scale transition zones. Constant-scale zones maintain a single-scale representation, while still linearly unfolding the DNA. Inspired by illustration, scale transition zones connect adjacent constant-scale zones via level unfolding, scaling, and transparency. We thus represent the spatial structure of the whole DNA macro-molecule, maintain its local organizational characteristics, linearize its higher-level organization, and use spatially controlled, understandable interpolation between neighboring scales. We also contribute interaction techniques that provide viewers with a coarse-to-fine control for navigating within our all-scales-in-one-view representations and visual aids to illustrate the size differences. Overall, Multiscale Unfolding allows viewers to grasp the DNA's structural composition from chromosomes to the atoms, with increasing levels of "unfoldedness," and can be applied in data-driven illustration and communication.

Vivern-A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures.

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality (VR) was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions.

Unified Nanotechnology Format: One Way to Store Them All.

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

Adenita: interactive 3D modelling and visualization of DNA nanostructures.

DNA nanotechnology is a rapidly advancing field, which increasingly attracts interest in many different disciplines, such as medicine, biotechnology, physics and biocomputing. The increasing complexity of novel applications requires significant computational support for the design, modelling and analysis of DNA nanostructures. However, current in silico design tools have not been developed in view of these new applications and their requirements. Here, we present Adenita, a novel software tool for the modelling of DNA nanostructures in a user-friendly environment. A data model supporting different DNA nanostructure concepts (multilayer DNA origami, wireframe DNA origami, DNA tiles etc.) has been developed allowing the creation of new and the import of existing DNA nanostructures. In addition, the nanostructures can be modified and analysed on-the-fly using an intuitive toolset. The possibility to combine and re-use existing nanostructures as building blocks for the creation of new superstructures, the integration of alternative molecules (e.g. proteins, aptamers) during the design process, and the export option for oxDNA simulations are outstanding features of Adenita, which spearheads a new generation of DNA nanostructure modelling software. We showcase Adenita by re-using a large nanorod to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

[Operation and Maintenance of Cost-Effective Volatile Organic Compounds Abatement Alternatives].

Presently, volatile organic compounds (VOCs) pollution control in China has entered the deep-water zone, facing difficult challenges. The cost-effectiveness of VOCs abatement alternatives will determine the final environmental benefits. Screening of abatement alternatives with good cost-effectiveness and performance is important to form a sound basis for VOCs emission abatement work to create sustainable and stable alternatives. In this study, 12 typical emission scenarios are set up based on the emission characteristics of pollution sources, such as emission concentration, airflow volume, continuous or intermittent emissions, and fluctuations in concentration. Based on these typical scenarios, the operation costs of current mainstream emission abatement alternatives is estimated, and a cost-effectiveness comparison is made using the unit abatement cost (UAC, yuan·kg-1, VOCs) as the index. The results obtained can provide a reference for choosing appropriate VOCs abatement alternatives according to the characteristics of VOCs emission. Results show that for low concentration VOCs, the UAC of emission abatement is normally more than 8 yuan·kg-1. The concentration in the process plays an important role in reducing UAC. Therefore, the reasonable collection of VOCs gas, resulting in smaller emission volume and higher concentration, has a significant impact on the subsequent emission abatement cost-effectiveness. Enhancing the classification collection of VOCs to improve resource attributes of the recovered VOCs liquid is also an effective way to improve the cost effectiveness of VOCs abatement.

Scale Trotter: Illustrative Visual Travels Across Negative Scales.

We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels-the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out-instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.

Multiscale Molecular Visualization.

We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.

How wastewater with different nutrient levels influences microbial degradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in anaerobic sediments.

While wastewater and polybrominated diphenyl ethers (PBDEs) are commonly both discharged into aquatic ecosystems, little information is known about how wastewaters with different nutrient levels impact on microbial degradation of PBDEs. In this study, we used an anaerobic microcosm experiment to examine how the removal rates of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) from contaminated sediment varied when exposed to three wastewaters with different nutrient properties, namely livestock wastewater (LS), municipal sewage (MS), and shrimp pond wastewater (SP), and to determine the microbial controls on removal processes. We found that BDE-47 degraded relatively rapidly in MS, which had low carbon and nitrogen concentrations, but degraded much more slowly in LS and SP, which had relatively high nutrient concentrations. The variations in BDE-47 removal in different wastewater were related to iron reduction rates and the abundances of organohalide-respiring bacteria (OHRB). The community compositions of both total bacteria and OHRB from the family Dehalococcoidaceae differed significantly among the wastewater treatments. Compared with other treatments, some bacterial groups with PBDE degradation abilities were more abundant in MS where the PBDE-degradation efficiencies were higher. Our results should help support evaluations of the bioremediation potential of sites that are contaminated with both halogenated organic compounds and nutrient-rich wastewater.

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures.

We present an approach to represent DNA nanostructures in varying forms of semantic abstraction, describe ways to smoothly transition between them, and thus create a continuous multiscale visualization and interaction space for applications in DNA nanotechnology. This new way of observing, interacting with, and creating DNA nanostructures enables domain experts to approach their work in any of the semantic abstraction levels, supporting both low-level manipulations and high-level visualization and modifications. Our approach allows them to deal with the increasingly complex DNA objects that they are designing, to improve their features, and to add novel functions in a way that no existing single-scale approach offers today. For this purpose we collaborated with DNA nanotechnology experts to design a set of ten semantic scales. These scales take the DNA's chemical and structural behavior into account and depict it from atoms to the targeted architecture with increasing levels of abstraction. To create coherence between the discrete scales, we seamlessly transition between them in a well-defined manner. We use special encodings to allow experts to estimate the nanoscale object's stability. We also add scale-adaptive interactions that facilitate the intuitive modification of complex structures at multiple scales. We demonstrate the applicability of our approach on an experimental use case. Moreover, feedback from our collaborating domain experts confirmed an increased time efficiency and certainty for analysis and modification tasks on complex DNA structures. Our method thus offers exciting new opportunities with promising applications in medicine and biotechnology.

Placenta Maps: In Utero Placental Health Assessment of the Human Fetus.

The human placenta is essential for the supply of the fetus. To monitor the fetal development, imaging data is acquired using (US). Although it is currently the gold-standard in fetal imaging, it might not capture certain abnormalities of the placenta. (MRI) is a safe alternative for the in utero examination while acquiring the fetus data in higher detail. Nevertheless, there is currently no established procedure for assessing the condition of the placenta and consequently the fetal health. Due to maternal respiration and inherent movements of the fetus during examination, a quantitative assessment of the placenta requires fetal motion compensation, precise placenta segmentation and a standardized visualization, which are challenging tasks. Utilizing advanced motion compensation and automatic segmentation methods to extract the highly versatile shape of the placenta, we introduce a novel visualization technique that presents the fetal and maternal side of the placenta in a standardized way. Our approach enables physicians to explore the placenta even in utero. This establishes the basis for a comparative assessment of multiple placentas to analyze possible pathologic arrangements and to support the research and understanding of this vital organ. Additionally, we propose a three-dimensional structure-aware surface slicing technique in order to explore relevant regions inside the placenta. Finally, to survey the applicability of our approach, we consulted clinical experts in prenatal diagnostics and imaging. We received mainly positive feedback, especially the applicability of our technique for research purposes was appreciated.