New Tool For Visualization Research Articles

'Candidatus Liberibacter' Pathosystems at the Forefront of Agricultural and Biological Research Challenges.

'Candidatus Liberibacter' Pathosystems at the Forefront of Agricultural and Biological Research Challenges.

Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes

The assembled and annotated genomes for 16 inbred mouse strains (Lilue et al., Nat Genet 50:1574–1583, 2018) and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) (Thybert et al., Genome Res 28:448–459, 2018) are valuable resources for mouse genetics and comparative genomics. We developed the multiple genome viewer (MGV; http://www.informatics.jax.org/mgv) to support visualization, exploration, and comparison of genome annotations within and across these genomes. MGV displays chromosomal regions of user-selected genomes as horizontal tracks. Equivalent features across the genome tracks are highlighted using vertical ‘swim lane’ connectors. Navigation across the genomes is synchronized as a researcher uses the scroll and zoom functions. Researchers can generate custom sets of genes and other genome features to be displayed in MGV by entering genome coordinates, function, phenotype, disease, and/or pathway terms. MGV was developed to be genome agnostic and can be used to display homologous features across genomes of different organisms.

Cell Type-Specific Expression Analysis of the Inner Ear: A Technical Report.

The cellular diversity of the inner ear has presented a technical challenge in obtaining molecular insight into its development and function. The application of technological advancements in cell type-specific expression enable clinicians and researchers to leap forward from classic genetics to obtaining mechanistic understanding of congenital and acquired hearing loss. This understanding is essential for development of therapeutics to prevent and reverse diseases of the inner ear, including hearing loss. The objective of this study is to describe and compare the available tools for cell type-specific analysis of the ear, as a means to support decision making in study design. Three major approaches for cell type-specific analysis of the ear including fluorescence-activated cell sorting (FACS), ribosomal and RNA pulldown techniques, and single cell RNA-seq (scRNA-seq) are compared and contrasted using both published and original data. We demonstrate the strength and weaknesses of these approaches leading to the inevitable conclusion that to maximize the utility of these approaches, it is important to match the experimental approach with the tissue of origin, cell type of interest, and the biological question. Often, a combined approach (eg, cell sorting and scRNA-seq or expression analysis using 2 separate approaches) is required. Finally, new tools for visualization and analysis of complex expression data, such as the gEAR platform (umgear.org), collate cell type-specific gene expression from the ear field and provide unprecedented access to both clinicians and researchers. N/A Laryngoscope, 131:S1-S16, 2021.

Interactive ergonomic risk mapping: a practical approach for visual management of workplace ergonomics

Current studies identify an increasing need to develop enriched tools for ergonomic risk management that can foster an atmosphere enhancing commitment of all stakeholders to create a safe and heathy work environment using ergonomic principles. In this study, a new tool for visualization of ergonomic practices in the workplace is proposed. For developing this tool, an interactive ergonomic risk mapping (intERM) methodology is introduced consisting of five steps while integrating the company's strategic vision and helping to accommodate the impacts of changes in policy and regulatory context, economic and demographic environment, technology and employment context. The proposed systematic and practical methodology is demonstrated on a real-life example. This visual and interactive tool enables prompt identification of and reaction to ergonomic risks, anticipating changes for reducing/eliminating ergonomic risks, as well as increasing company-wide awareness for ergonomic risks and enhancing engagement and ownership of stakeholders.

Van Krevelen diagram visualization of high resolution-mass spectrometry metabolomics data with OpenVanKrevelen.

Van Krevelen (VK) diagrams provide a promising but uncommon solution to a number of challenges associated with the visualization of metabolomics data. VK diagrams are created by plotting H:C ratios against O:C ratios of the compounds in a chemical mixture. The aim of this manuscript is to present an open-source software tool and reference map that we have developed to make VK diagrams for visualization of metabolomics data. Software was created with a prompt-driven command line user interface and was written using Python 2.7. We empirically derived an accompanying map by plotting where compounds from seven biomolecule types fall within the VK plot space. We've created an easy to use, open source software tool named OpenVanKrevelen for making a range of VK diagrams that is available on GitHub: https://github.com/HegemanLab/VanKrevelenLocal . The empirical mapping approach has produced several improvements from previously published maps. OpenVanKrevelen provides the metabolomics community with access to a new tool for visualization of complex metabolomics datasets.

A Graphical Tool and Methods for Assessing Margin Definition From Daily Image Deformations

Estimating the proper margins for the planning target volume (PTV) could be a challenging task in cases where the organ undergoes significant changes during the course of radiotherapy treatment. Developments in image-guidance and the presence of onboard imaging technologies facilitate the process of correcting setup errors. However, estimation of errors to organ motions remain an open question due to the lack of proper software tools to accompany these imaging technological advances. Therefore, we have developed a new tool for visualization and quantification of deformations from daily images. The tool allows for estimation of tumor coverage and normal tissue exposure as a function of selected margin (isotropic or anisotropic). Moreover, the software allows estimation of the optimal margin based on the probability of an organ being present at a particular location. Methods based on swarm intelligence, specifically Ant Colony Optimization (ACO) are used to provide an efficient estimate of the optimal margin extent in each direction. ACO can provide global optimal solutions in highly nonlinear problems such as margin estimation. The proposed method is demonstrated using cases from gastric lymphoma with daily TomoTherapy megavoltage CT (MVCT) contours. Preliminary results using Dice similarity index are promising and it is expected that the proposed tool will be very helpful and have significant impact for guiding future margin definition protocols.

Visualization of Electron Paramagnetic Resonance Hyperfine Structure Coupling Pathways

The close relation between the EPR hyperfine coupling constant and NMR indirect spin-spin coupling constant is well-known. For example, the Karplus-type dependence of hyperfine constants on the dihedral angle, originally proposed for NMR spin-spin coupling, is widely used in pNMR studies. In the present work we propose a new tool for visualization of hyperfine coupling pathways based on our experience with visualization of NMR indirect spin-spin couplings. The plotted 3D-function is the difference between the total electron densities when the magnetic moment of the nucleus of interest changes its sign and as such is an observable from the physical point of view. It has been shown that it is proportional to the linear response of the spin density to the nuclear spin (i.e., magnetic moment). In contrast to the widely used visualization of spin density, our new approach depicts only the part of the electron cloud of a molecule that is affected by the interaction of the unpaired electron(s) with the desired nuclear magnetic moment. Because visualization of NMR spin-spin couplings and hyperfine interaction is based on the same ideas and done using similar techniques, it allows a direct comparison of the corresponding pathways for the two phenomena so as to analyze their resemblance and/or dissimilarity.

New Tool for Visualization of Time Series and Anomalies in Streaming Data

A new software tool for simultaneous visualization of multiple time dependent signals, featuring a novel and highly useful combination of capabilities, and published as an open source solution is presented in this paper. The tool is designed to meet the needs of its users who expect lightweight, interactive & intuitive use and ease of deployment in current setups, including live monitoring systems with anomaly detection, highlighting and streaming data processing abilities. The functionality and motivation for our system is derived from various signal analysis applications, our research activities related to design and evaluation of neural network models, and from systems for continuous monitoring and anomaly detection (e.g. in IT or medical domains), which is demonstrated on simple use case examples.

18F]FEBMP: Positron Emission Tomography Imaging of TSPO in a Model of Neuroinflammation in Rats, and in vitro Autoradiograms of the Human Brain.

We evaluated the efficacy of 2-[5-(4-[18F]fluoroethoxy-2-oxo-1,3-benzoxazol-3(2H)-yl)-N-methyl-N-phenylacetamide] ([18F]FEBMP) for positron emission tomography (PET) imaging of translocator protein (18 kDa, TSPO). Dissection was used to determine the distribution of [18F]FEBMP in mice, while small-animal PET and metabolite analysis were used for a rat model of focal cerebral ischemia. [18F]FEBMP showed high radioactivity uptake in mouse peripheral organs enriched with TSPO, and relatively high initial brain uptake (2.67 ± 0.12% ID/g). PET imaging revealed an increased accumulation of radioactivity in the infarcted striatum, with a maximum ratio of 3.20 ± 0.12, compared to non-injured striatum. Displacement with specific TSPO ligands lowered the accumulation levels in infarcts to those on the contralateral side. This suggests that the increased accumulation reflected TPSO-specific binding of [18F]FEBMP in vivo. Using a simplified reference tissue model, the binding potential on the infarcted area was 2.72 ± 0.27. Metabolite analysis in brain tissues showed that 83.2 ± 7.4% and 76.4 ± 2.1% of radioactivity was from intact [18F]FEBMP at 30 and 60 min, respectively, and that this ratio was higher than in plasma (8.6 ± 1.9% and 3.9 ± 1.1%, respectively). In vitro autoradiography on postmortem human brains showed that TSPO rs6971 polymorphism did not affect binding sites for [18F]FEBMP. These findings suggest that [18F]FEBMP is a promising new tool for visualization of neuroinflammation.

Understanding how pre-impact posture can affect injury outcome in side impact sled tests using a new tool for visualization of cadaver kinematics

The effect of posture and subject-specific factors on injury outcome is an active field of research in injury biomechanics, in particular in automotive safety research where post-mortem human subjects (PMHS) are used as surrogates. Current PMHS tests routinely include acquisition of the subjects׳ geometry and kinematics. However, combining these two datasets to better understand the injury mechanism is still a challenge. This study investigated the connection between pre-impact posture and resulting injuries in six previously published side impact sled tests (three with a rigid wall and three with an airbag) by creating three-dimensional kinematic animations (3DKA) of the tests. The 3DKA allow qualitative assessment of parameters related to posture and their possible effect on injury outcome. The orientation of the struck scapula and the lateral leaning of the torso were identified as potentially significant parameters. The ranges of variation in these parameters were quantified and compared to the number of rib fractures for each subject: the data suggested a correlation, but there was insufficient data for a probabilistic analysis. The 3DKA were published with this study and are freely available.

Visualization of system dynamics using phasegrams.

A new tool for visualization and analysis of system dynamics is introduced: the phasegram. Its application is illustrated with both classical nonlinear systems (logistic map and Lorenz system) and with biological voice signals. Phasegrams combine the advantages of sliding-window analysis (such as the spectrogram) with well-established visualization techniques from the domain of nonlinear dynamics. In a phasegram, time is mapped onto the x-axis, and various vibratory regimes, such as periodic oscillation, subharmonics or chaos, are identified within the generated graph by the number and stability of horizontal lines. A phasegram can be interpreted as a bifurcation diagram in time. In contrast to other analysis techniques, it can be automatically constructed from time-series data alone: no additional system parameter needs to be known. Phasegrams show great potential for signal classification and can act as the quantitative basis for further analysis of oscillating systems in many scientific fields, such as physics (particularly acoustics), biology or medicine.

HLA Class I Histamers: A New Tool for Visualization and Selection of Functionally Active Antigen-Specific CD8+ T Cells

HLA Class I Histamers: A New Tool for Visualization and Selection of Functionally Active Antigen-Specific CD8+ T Cells

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

SU‐GG‐J‐114: A Graphical Tool for Assessing Margin Definition from Daily Deformations

Purpose: Estimating the proper margins for the planned target volume (PTV) could be a challenging task in cases where the organ undergoes significant changes during the course of radiotherapy treatment. This is practically the case in stomach lymphoma, where the stomach can change significantly from day to day. A common practice is to add a constant l–2cm margin isotropically around the tumor volume based on planning CT scan. This might lead to some portions of stomach being under dosed or surrounding normal structures over‐dosed. The purpose of this work is to develop a tool that utilizes information from daily images to aid localization of these deformations and guide estimations of proper margins. Method and Materials: In this work, the stomach volume for each treatment fraction was delineated manually over the course of 6 weeks of fractionated treatment using daily Tomotherapy Mega voltage CT (MVCT) images from three patients. A software tool was developed to aid tracking variations in shape during therapy and record estimates of the probability by which an organ spends at any particular place. Accordingly, plots of estimated tumor coverage and excess irradiated normal tissue volumes as a function of margin could be generated. Results: Estimated stomach volumes for these cases were 429.2±67.7, 383.0±66.6, and 294.1±27.7 cc. Plots of tumor coverage and excess irradiated volume were created for each case. It was observed that with a margin of 1.5 cm over the original stomach, the entire union volume was covered. This margin resulted in about 500–800 cc of excess volume being irradiated for the three test cases. Conclusions: This work presented a new tool for visualization and quantification of daily deformations for isotropic and anisotropic margin definition guidance.

A Graphical Tool and Methods for Assessing Margin Definition From Daily Image Deformations

Estimating the proper margins for the planning target volume (PTV) could be a challenging task in cases where the organ undergoes significant changes during the course of radiotherapy treatment. Developments in image-guidance and the presence of onboard imaging technologies facilitate the process of correcting setup errors. However, estimation of errors due to organ motions remain an open question due to the lack of proper software tools to accompany these imaging technological advances. Therefore, we have developed a new tool for visualization and quantification of deformations from daily images. The tool allows for estimation of tumor coverage and normal tissue exposure as a function of selected margin (isotropic or anisotropic). Moreover, the software allows estimation of the optimal margin based on the probability of an organ being present at a particular location. Methods based on swarm intelligence, specifically Ant Colony Optimization (ACO) are used to provide an efficient estimate of the optimal margin extent in each direction. ACO can provide global optimal solutions in highly nonlinear problems such as margin estimation. The proposed method is demonstrated using cases from gastric lymphoma with daily TomoTherapy megavoltage CT (MVCT) contours. Preliminary results using the Dice similarity index are promising and it is expected that the proposed tool will be very helpful and have significant impact for guiding future margin definition protocols.

Large-scale human metabolic phenotyping and molecular epidemiological studies via 1H NMR spectroscopy of urine: investigation of borate preservation.

Borate is an antibacterial preservative widely used in clinical and large-scale epidemiological studies involving urine sample analysis. Since it readily forms covalent adducts and reversible complexes with hydroxyl and carboxylate groups, the effects of borate preservation in (1)H NMR-spectroscopy-based metabolic profiling of human urine samples have been assessed. Effects of various concentrations of borate (range 0-30 mM) on (1)H NMR spectra of urine were observed at sequential time points over a 12 month period. Consistent with known borate chemistry, the principal alterations in the (1)H resonance metabolite patterns were observed for compounds such as mannitol, citrate, and alpha-hydroxyisobutyrate and confirmed by ESI-MS analysis. These included line-broadening, T(1) and T(2) relaxation, and chemical shift changes consistent with complex formation and chemical exchange processes. To further investigate complexation behavior in the urinary metabolite profiles, a new tool for visualization of multicomponent relaxation variations in which the spectra were color-coded according to the T(1) and T(2) proton relaxation times respectively (T(1) or T(2) ordered projection spectroscopy, TOPSY) was also developed and applied. Addition of borate caused a general decrease in (1)H T(1) values, consistent with nonspecific effects such as solution viscosity changes. Minor changes in proton T(2) relaxation rates were observed for the most strongly complexing metabolites. From a molecular phenotyping and epidemiologic viewpoint, typical interpersonal biological variation was shown to be vastly greater than any variation introduced by the borate complexation, which had a negligible effect on the metabolic mapping and classification of samples. While caution is indicated in the assignment of biomarker signals where metabolites have diol groupings or where there are adjacent hydroxyl and carboxylate functions, it is concluded that borate preservation is "fit-for-purpose" for (1)H NMR-based epidemiological studies, since the essential biochemical classification features of the samples are robustly maintained.

The ST Compass: spatial visualization of ST-segment deviations and estimation of the ST injury vector

The current electrocardiogram criteria for the diagnosis of transmural myocardial ischemia focus on ST elevations, although anterior lead ST depression may be indicative of posterior ischemia. ST elevation and depression in different leads may be considered different projections of a common ST injury current directed toward areas of transmural ischemia. To facilitate vectorial analysis of ST deviations, we present the ST Compass—a new tool for visualization of ST deviations from standard 12-lead electrocardiograms. We also present a method to estimate a vector describing the magnitude and direction of the underlying ST injury current based on the observed ST deviations. In 2 cases of acute myocardial infarction, the ST deviation vectors form a clear pattern in the ST Compass, and the spatial direction of the ST injury current corresponds to the location of myocardial ischemia as confirmed by single-photon emission computed tomography imaging.

CHALLENGES AND INNOVATIONS IN REACTION ENGINEERING

The importance of reaction engineering in generating a myriad of products on which developed societies depend is outlined. The challenges of a political, economic, and technical nature that need to be addressed in rendering conversion of raw materials into desired products that are more environmentally friendly and sustainable are briefly discussed. It is shown that multiphase reactors are prevalent in all applications, and improvements in the reactor material and energy efficiencies lead to more environmentally benign processes. This requires, in addition to the selection of green process chemistry, systematic implementation of the multi-scale reaction engineering methodology to accomplish proper reactor type selection and scaleup for commercial applications. It is also illustrated that recent innovations in multiphase reaction engineering basically utilize two key concepts: process intensification (e.g., enhancement in mass and heat transfer rates) and simultaneous reaction and separation. Examples of these are discussed, such as micro-reactors, reactive distillation, etc. It is also shown that commercialization of bench-scale discoveries requires either scaleup in parallel or vertical scaleup. New tools for visualization of opaque multiphase flows and development of appropriate rational phenomenological multiphase reactor models for scaleup and design are also briefly discussed.

Visualizing evolution and impact of biomedical fields

We describe a new tool for visualization of biomedical scientific trends. The method captures variations in scientific impact over time to allow for a comparison of relative significance and evolution of fields similar to a financial market scorecard. The tool is available at SciTrends ( http://www.scitrends.net), depicting the evolution of almost 200 thousand biomedical fields in time. With millions of articles on thousands of topics published in biomedicine, we envision that only with such large-scale tools researchers can objectively understand the ever-changing interests in the biomedical sciences and make more informed decisions.

Visualization and Simulation in Scheduling

This paper deals with the representation of scheduling results and it introduces a new tool for visualization and simulation in time scheduling called VISIS. The purpose of this tool is to provide an environment for visualization, e.g. in production line scheduling. The simulation also proposes a way to simulate the influence of a schedule on a user defined system, e.g. for designing filters in digital signal processing. VISIS arises from representing scheduling results using the well-known Gantt chart. The application is implemented in the Matlab programming environment using Simulink and the Virtual Reality toolbox.