A new tool for annotating scientific animations and supporting scientific dialogue.

A new interactive annotation interface supports a detailed molecular animation of the SARS-CoV-2 life cycle. With this tool, users can interactively explore the data used to create the animation and engage in scientific discourse through comments and questions.

Network Architecture of Gap Junctional Coupling among Parallel Processing Channels in the Mammalian Retina.

Gap junctions are ubiquitous throughout the nervous system, mediating critical signal transmission and integration, as well as emergent network properties. In mammalian retina, gap junctions within the Aii amacrine cell-ON cone bipolar cell (CBC) network are essential for night vision, modulation of day vision, and contribute to visual impairment in retinal degenerations, yet neither the extended network topology nor its conservation is well established. Here, we map the network contribution of gap junctions using a high-resolution connectomics dataset of an adult female rabbit retina. Gap junctions are prominent synaptic components of ON CBC classes, constituting 5%-25% of all axonal synaptic contacts. Many of these mediate canonical transfer of rod signals from Aii cells to ON CBCs for night vision, and we find that the uneven distribution of Aii signals to ON CBCs is conserved in rabbit, including one class entirely lacking direct Aii coupling. However, the majority of gap junctions formed by ON CBCs unexpectedly occur between ON CBCs, rather than with Aii cells. Such coupling is extensive, creating an interconnected network with numerous lateral paths both within, and particularly across, these parallel processing streams. Coupling patterns are precise with ON CBCs accepting and rejecting unique combinations of partnerships according to robust rulesets. Coupling specificity extends to both size and spatial topologies, thereby rivaling the synaptic specificity of chemical synapses. These ON CBC coupling motifs dramatically extend the coupled Aii-ON CBC network, with implications for signal flow in both scotopic and photopic retinal networks during visual processing and disease.SIGNIFICANCE STATEMENT Electrical synapses mediated by gap junctions are fundamental components of neural networks. In retina, coupling within the Aii-ON CBC network shapes visual processing in both the scotopic and photopic networks. In retinal degenerations, these same gap junctions mediate oscillatory activity that contributes to visual impairment. Here, we use high-resolution connectomics strategies to identify gap junctions and cellular partnerships. We describe novel, pervasive motifs both within and across classes of ON CBCs that dramatically extend the Aii-ON CBC network. These motifs are highly specific with implications for both signal processing within the retina and therapeutic interventions for blinding conditions. These findings highlight the underappreciated contribution of coupling motifs in retinal circuitry and the necessity of their detection in connectomics studies.

Community-Based Measurements Reveal Unseen Differences during Air Pollution Episodes.

Short-term exposure to fine particulate matter (PM2.5) pollution is linked to numerous adverse health effects. Pollution episodes, such as wildfires, can lead to substantial increases in PM2.5 levels. However, sparse regulatory measurements provide an incomplete understanding of pollution gradients. Here, we demonstrate an infrastructure that integrates community-based measurements from a network of low-cost PM2.5 sensors with rigorous calibration and a Gaussian process model to understand neighborhood-scale PM2.5 concentrations during three pollution episodes (July 4, 2018, fireworks; July 5 and 6, 2018, wildfire; Jan 3-7, 2019, persistent cold air pool, PCAP). The firework/wildfire events included 118 sensors in 84 locations, while the PCAP event included 218 sensors in 138 locations. The model results accurately predict reference measurements during the fireworks (n: 16, hourly root-mean-square error, RMSE, 12.3-21.5 µg/m3, n(normalized)RMSE: 14.9-24%), the wildfire (n: 46, RMSE: 2.6-4.0 µg/m3; nRMSE: 13.1-22.9%), and the PCAP (n: 96, RMSE: 4.9-5.7 µg/m3; nRMSE: 20.2-21.3%). They also revealed dramatic geospatial differences in PM2.5 concentrations that are not apparent when only considering government measurements or viewing the US Environmental Protection Agency's AirNow visualizations. Complementing the PM2.5 estimates and visualizations are highly resolved uncertainty maps. Together, these results illustrate the potential for low-cost sensor networks that combined with a data-fusion algorithm and appropriate calibration and training can dynamically and with improved accuracy estimate PM2.5 concentrations during pollution episodes. These highly resolved uncertainty estimates can provide a much-needed strategy to communicate uncertainty to end users.

Patterns of distributive environmental inequity under different PM2.5 air pollution scenarios for Salt Lake County public schools.

Previous studies have cataloged social disparities in air pollution exposure in US public schools with respect to race/ethnicity and socioeconomic status. These studies rely upon chronic, averaged measures of air pollution, which fosters a static conception of exposure disparities. This paper examines PM2.5 exposure disparities in Salt Lake County (SLC), Utah public schools under three different PM2.5 scenarios-relatively clean air, a moderate winter persistent cold air pool (PCAP), and a major winter PCAP-with respect to race/ethnicity, economic deprivation, student age, and school type. We pair demographic data for SLC schools (n = 174) with modelled PM2.5 values, obtained from a distributed network of sensors placed through a community-university partnership. Results from generalized estimating equations controlling for school district clustering and other covariates reveal that patterns of social inequality vary under different PM2.5 pollution scenarios. Charter schools and schools serving economically deprived students experienced disproportionate exposure during relatively clean air and moderate PM2.5 PCAP conditions, but those inequalities attenuated under major PCAP conditions. Schools with higher proportions of racial/ethnic minority students were unequally exposed under all PM2.5 pollution scenarios, reflecting the robustness of racial/ethnic disparities in exposure. The findings speak to the need for policy changes to protect school-aged children from environmental harm in SLC and elsewhere.

Outcomes of an electronic social network intervention with neuro-oncology patient family caregivers.

INTRODUCTION: Informal family caregivers (FCG) are an integral and crucial human component in the cancer care continuum. However, research and interventions to help alleviate documented anxiety and burden on this group is lacking. To address the absence of effective interventions, we developed the electronic Support Network Assessment Program (eSNAP) which aims to automate the capture and visualization of social support, an important target for overall FCG support. This study seeks to describe the preliminary efficacy and outcomes of the eSNAP intervention. METHODS: Forty FCGs were enrolled into a longitudinal, two-group randomized design to compare the eSNAP intervention in caregivers of patients with primary brain tumors against controls who did not receive the intervention. Participants were followed for six weeks with questionnaires to assess demographics, caregiver burden, anxiety, depression, and social support. Questionnaires given at baseline (T1) and then 3-weeks (T2), and 6-weeks (T3) post baseline questionnaire. RESULTS: FCGs reported high caregiver burden and distress at baseline, with burden remaining stable over the course of the study. The intervention group was significantly less depressed, but anxiety remained stable across groups. CONCLUSIONS: With the lessons learned and feedback obtained from FCGs, this study is the first step to developing an effective social support intervention to support FCGs and healthcare providers in improving cancer care.

Feasibility of implementing an electronic social support and resource visualization tool for caregivers in a neuro-oncology clinic.

PURPOSE: The goals of this study were to assess the feasibility of a web-based application-electronic Social Network Assessment Program (eSNAP)-to automate the capture and visualization of family caregiver social network data of neuro-oncology patients. METHODS: Caregivers were recruited from a neuro-oncology clinic at an NCI-designated comprehensive cancer center. Participants completed baseline questionnaires on a laptop in clinic assessing demographic characteristics. After baseline, participants were randomly assigned to either create a social network visualization using eSNAP (intervention) or to usual care (control) condition. Those who used eSNAP provided likeability/usability data. All participants were asked to complete follow-up questionnaires at 3 and 6 weeks after baseline to determine feasibility of longitudinal study. RESULTS: We recruited 40 caregivers of patients with primary malignant brain tumor to participate in this study. Participants rated eSNAP usability and likeability highly, indicating that eSNAP would help them consider their available social support. At 3 weeks, 90% of participants completed questionnaires and 82.5% completed questionnaires at 6 weeks. CONCLUSIONS: There is a need to encourage family caregivers of patients with primary malignant brain tumor to engage their existing social network resources to help alleviate caregiver burden. Our findings suggest that our web-based application to address this issue is feasible to implement with high usability and likeability. This pilot study identified minor changes to the intervention to improve effectiveness and has implications for future research in this understudied population. TRIAL REGISTRATION: clinicaltrials.gov, protocol number NCT03026699.

A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of equivalent cells.

Transitioning to a Commercial Dashboarding System: Socio-Technical Observations and Opportunities.

Many long-established, traditional manufacturing businesses are becoming more digital and data-driven to improve their production. These companies are embracing visual analytics in these transitions through their adoption of commercial dashboarding systems. Although a number of studies have looked at the technical challenges of adopting these systems, very few have focused on the socio-technical issues that arise. In this paper, we report on the results of an interview study with 17 participants working in a range of roles at a long-established, traditional manufacturing company as they adopted Microsoft Power BI. The results highlight a number of socio-technical challenges the employees faced, including difficulties in training, using and creating dashboards, and transitioning to a modern digital company. Based on these results, we propose a number of opportunities for both companies and visualization researchers to improve these difficult transitions, as well as opportunities for rethinking how we design dashboarding systems for real-world use.

Data Hunches: Incorporating Personal Knowledge into Visualizations.

The trouble with data is that it frequently provides only an imperfect representation of a phenomenon of interest. Experts who are familiar with their datasets will often make implicit, mental corrections when analyzing a dataset, or will be cautious not to be overly confident about their findings if caveats are present. However, personal knowledge about the caveats of a dataset is typically not incorporated in a structured way, which is problematic if others who lack that knowledge interpret the data. In this work, we define such analysts' knowledge about datasets as data hunches. We differentiate data hunches from uncertainty and discuss types of hunches. We then explore ways of recording data hunches, and, based on a prototypical design, develop recommendations for designing visualizations that support data hunches. We conclude by discussing various challenges associated with data hunches, including the potential for harm and challenges for trust and privacy. We envision that data hunches will empower analysts to externalize their knowledge, facilitate collaboration and communication, and support the ability to learn from others' data hunches.

Exploring the Personal Informatics Analysis Gap: "There's a Lot of Bacon".

Personal informatics research helps people track personal data for the purposes of self-reflection and gaining self-knowledge. This field, however, has predominantly focused on the data collection and insight-generation elements of self-tracking, with less attention paid to flexible data analysis. As a result, this inattention has led to inflexible analytic pipelines that do not reflect or support the diverse ways people want to engage with their data. This paper contributes a review of personal informatics and visualization research literature to expose a gap in our knowledge for designing flexible tools that assist people engaging with and analyzing personal data in personal contexts, what we call the personal informatics analysis gap. We explore this gap through a multistage longitudinal study on how asthmatics engage with personal air quality data, and we report how participants: were motivated by broad and diverse goals; exhibited patterns in the way they explored their data; engaged with their data in playful ways; discovered new insights through serendipitous exploration; and were reluctant to use analysis tools on their own. These results present new opportunities for visual analysis research and suggest the need for fundamental shifts in how and what we design when supporting personal data analysis.

Genome-wide synteny through highly sensitive sequence alignment: Satsuma.

MOTIVATION: Comparative genomics heavily relies on alignments of large and often complex DNA sequences. From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes). RESULTS: Satsuma addresses all three issues through novel strategies: (i) cross-correlation, implemented via fast Fourier transform; (ii) a match scoring scheme that eliminates almost all false hits; and (iii) an asynchronous 'battleship'-like search that allows for aligning two entire fish genomes (470 and 217 Mb) in 120 CPU hours using 15 processors on a single machine. AVAILABILITY: Satsuma is part of the Spines software package, implemented in C++ on Linux. The latest version of Spines can be freely downloaded under the LGPL license from http://www.broadinstitute.org/science/programs/genome-biology/spines/.

Insights From Experiments With Rigor in an EvoBio Design Study.

Design study is an established approach of conducting problem-driven visualization research. The academic visualization community has produced a large body of work for reporting on design studies, informed by a handful of theoretical frameworks, and applied to a broad range of application areas. The result is an abundance of reported insights into visualization design, with an emphasis on novel visualization techniques and systems as the primary contribution of these studies. In recent work we proposed a new, interpretivist perspective on design study and six companion criteria for rigor that highlight the opportunities for researchers to contribute knowledge that extends beyond visualization idioms and software. In this work we conducted a year-long collaboration with evolutionary biologists to develop an interactive tool for visual exploration of multivariate datasets and phylogenetic trees. During this design study we experimented with methods to support three of the rigor criteria: ABUNDANT, REFLEXIVE, and TRANSPARENT. As a result we contribute two novel visualization techniques for the analysis of multivariate phylogenetic datasets, three methodological recommendations for conducting design studies drawn from reflections over our process of experimentation, and two writing devices for reporting interpretivist design study. We offer this work as an example for implementing the rigor criteria to produce a diverse range of knowledge contributions.

HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models.

We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment-using clicks on nodes, links, or icons-with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e. g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that-in addition to their annotational role-also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.

MulteeSum: a tool for comparative spatial and temporal gene expression data.

Cells in an organism share the same genetic information in their DNA, but have very different forms and behavior because of the selective expression of subsets of their genes. The widely used approach of measuring gene expression over time from a tissue sample using techniques such as microarrays or sequencing do not provide information about the spatial position within the tissue where these genes are expressed. In contrast, we are working with biologists who use techniques that measure gene expression in every individual cell of entire fruitfly embryos over an hour of their development, and do so for multiple closely-related subspecies of Drosophila. These scientists are faced with the challenge of integrating temporal gene expression data with the spatial location of cells and, moreover, comparing this data across multiple related species. We have worked with these biologists over the past two years to develop MulteeSum, a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed--it is the first tool to support comparisons across multiple such data sets. MulteeSum is part of a general and flexible framework we developed with our collaborators that is built around multiple summaries for each cell, allowing the biologists to explore the results of computations that mix spatial information, gene expression measurements over time, and data from multiple related species or organisms. We justify our design decisions based on specific descriptions of the analysis needs of our collaborators, and provide anecdotal evidence of the efficacy of MulteeSum through a series of case studies.

MizBee: a multiscale synteny browser.

In the field of comparative genomics, scientists seek to answer questions about evolution and genomic function by comparing the genomes of species to find regions of shared sequences. Conserved syntenic blocks are an important biological data abstraction for indicating regions of shared sequences. The goal of this work is to show multiple types of relationships at multiple scales in a way that is visually comprehensible in accordance with known perceptual principles. We present a task analysis for this domain where the fundamental questions asked by biologists can be understood by a characterization of relationships into the four types of proximity/location, size, orientation, and similarity/strength, and the four scales of genome, chromosome, block, and genomic feature. We also propose a new taxonomy of the design space for visually encoding conservation data. We present MizBee, a multiscale synteny browser with the unique property of providing interactive side-by-side views of the data across the range of scales supporting exploration of all of these relationship types. We conclude with case studies from two biologists who used MizBee to augment their previous automatic analysis work flow, providing anecdotal evidence about the efficacy oft he system for the visualization of syntenic data, the analysis of conservation relationships, and the communication of scientific insights.

Criteria for Rigor in Visualization Design Study.

We develop a new perspective on research conducted through visualization design study that emphasizes design as a method of inquiry and the broad range of knowledge-contributions achieved through it as multiple, subjective, and socially constructed. From this interpretivist position we explore the nature of visualization design study and develop six criteria for rigor. We propose that rigor is established and judged according to the extent to which visualization design study research and its reporting are INFORMED, REFLEXIVE, ABUNDANT, PLAUSIBLE, RESONANT, and TRANSPARENT. This perspective and the criteria were constructed through a four-year engagement with the discourse around rigor and the nature of knowledge in social science, information systems, and design. We suggest methods from cognate disciplines that can support visualization researchers in meeting these criteria during the planning, execution, and reporting of design study. Through a series of deliberately provocative questions, we explore implications of this new perspective for design study research in visualization, concluding that as a discipline, visualization is not yet well positioned to embrace, nurture, and fully benefit from a rigorous, interpretivist approach to design study. The perspective and criteria we present are intended to stimulate dialogue and debate around the nature of visualization design study and the broader underpinnings of the discipline.

Rod-cone crossover connectome of mammalian bipolar cells.

The basis of cross-suppression between rod and cone channels has long been an enigma. Using rabbit retinal connectome RC1, we show that all cone bipolar cell (BC) classes inhibit rod BCs via amacrine cell (AC) motifs (C1-6); that all cone BC classes are themselves inhibited by AC motifs (R1-5, R25) driven by rod BCs. A sparse symmetric AC motif (CR) is presynaptic and postsynaptic to both rod and cone BCs. ON cone BCs of all classes drive inhibition of rod BCs via motif C1 wide-field GABAergic ACs (γACs) and motif C2 narrow field glycinergic ON ACs (GACs). Each rod BC receives ≈10 crossover AC synapses and each ON cone BC can target ≈10 or more rod BCs via separate AC processes. OFF cone BCs mediate monosynaptic inhibition of rod BCs via motif C3 driven by OFF γACs and GACs and disynaptic inhibition via motifs C4 and C5 driven by OFF wide-field γACs and narrow-field GACs, respectively. Motifs C4 and C5 form halos of 60-100 inhibitory synapses on proximal dendrites of AI γACs. Rod BCs inhibit surrounding arrays of cone BCs through AII GAC networks that access ON and OFF cone BC patches via motifs R1, R2, R4, R5 and a unique ON AC motif R3 that collects rod BC inputs and targets ON cone BCs. Crossover synapses for motifs C1, C4, C5, and R3 are 3-4× larger than typical feedback synapses, which may be a signature for synaptic winner-take-all switches. J. Comp. Neurol. 527:87-116, 2019. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Volume MLS ray casting.

The method of Moving Least Squares (MLS) is a popular framework for reconstructing continuous functions from scattered data due to its rich mathematical properties and well-understood theoretical foundations. This paper applies MLS to volume rendering, providing a unified mathematical framework for ray casting of scalar data stored over regular as well as irregular grids. We use the MLS reconstruction to render smooth isosurfaces and to compute accurate derivatives for high-quality shading effects. We also present a novel, adaptive preintegration scheme to improve the efficiency of the ray casting algorithm by reducing the overall number of function evaluations, and an efficient implementation of our framework exploiting modern graphics hardware. The resulting system enables high-quality volume integration and shaded isosurface rendering for regular and irregular volume data.

Particle-based sampling and meshing of surfaces in multimaterial volumes.

Methods that faithfully and robustly capture the geometry of complex material interfaces in labeled volume data are important for generating realistic and accurate visualizations and simulations of real-world objects. The generation of such multimaterial models from measured data poses two unique challenges: first, the surfaces must be well-sampled with regular, efficient tessellations that are consistent across material boundaries; and second, the resulting meshes must respect the nonmanifold geometry of the multimaterial interfaces. This paper proposes a strategy for sampling and meshing multimaterial volumes using dynamic particle systems, including a novel, differentiable representation of the material junctions that allows the particle system to explicitly sample corners, edges, and surfaces of material intersections. The distributions of particles are controlled by fundamental sampling constraints, allowing Delaunay-based meshing algorithms to reliably extract watertight meshes of consistently high-quality.