Non-pharmaceutical interventions to combat COVID-19 transmission have worked to slow the spread of the epidemic but can have high socio-economic costs. It is critical we understand the efficacy of nonpharmaceutical interventions to choose a safe exit strategy. Many current models are not suitable for assessing exit strategies because they do not account for epidemic resurgence when social distancing ends prematurely (e.g., statistical curve fits) nor permit scenario exploration in specific locations. We developed an SEIR-type mechanistic epidemiological model of COVID-19 dynamics to explore temporally variable non-pharmaceutical interventions. We provide an interactive tool and code to estimate the transmission parameter, β, and the effective reproduction number, R E . We fit the model to Santa Clara County, California, where an early epidemic start date and early shelter-in-place orders could provide a model for other regions. As of April 22, 2020, we estimate an R E of 0.982 (95% CI: 0.849 -1.107) in Santa Clara County. After June 1 (the end-date for Santa Clara County shelter-in-place as of April 27), we estimate a shift to partial social distancing, combined with rigorous testing and isolation of symptomatic individuals, is a viable alternative to indefinitely maintaining shelter-in-place. We also estimate that if Santa Clara County had waited one week longer before issuing shelter-in-place orders, 95 additional people would have died by April 22 (95% CI: 7 -283). Given early life-saving shelter-in-place orders in Santa Clara County, longer-term moderate social distancing and testing and isolation of symptomatic individuals have the potential to contain the size and toll of the COVID-19 pandemic in Santa Clara County, and may be effective in other locations.

Magnetic resonance (MR) images of the brain are of immense clinical and research utility. At the atomic and subatomic levels, the sources of MR signals are well understood. However, we lack a comprehensive understanding of the macromolecular correlates of MR signal contrast. To address this gap, we used genome-wide measurements to correlate gene expression with MR signal intensity across the cerebral cortex in the Allen Human Brain Atlas (AHBA). We focused on the ratio of T1-weighted and T2-weighted intensities (T1-w/T2-w ratio image), which is considered to be a useful proxy for myelin content. As expected, we found enrichment of positive correlations between myelin-associated genes and the ratio image, supporting its use as a myelin marker. Genome-wide, there was an association with protein mass, with genes coding for heavier proteins expressed in regions with high T1-w/T2-w values. Oligodendrocyte gene markers were strongly correlated with the T1-w/T2-w ratio, but this was not driven by myelin-associated genes. Mitochondrial genes exhibit the strongest relationship, showing higher expression in regions with low T1-w/T2-w ratio. This may be due to the pH gradient in mitochondria as genes up-regulated by pH in the brain were also highly correlated with the ratio. While we corroborate associations with myelin and synaptic plasticity, differences in the T1-w/T2-w ratio across the cortex are more strongly linked to molecule size, oligodendrocyte markers, mitochondria, and pH. We evaluate correlations between AHBA transcriptomic measurements and a group averaged T1-w/T2-w ratio image, showing agreement with in-sample results. Expanding our analysis to the whole brain results in strong positive T1-w/T2-w correlations for immune system, inflammatory disease, and microglia marker genes. Genes with negative correlations were enriched for neuron markers and synaptic plasticity genes. Lastly, our findings are similar when performed on T1-w or inverted T2-w intensities alone. These results provide a molecular characterization of MR contrast that will aid interpretation of future MR studies of the brain.

Inspired by data comics, this paper introduces a novel format for reporting controlled studies in the domain of humancomputer interaction (HCI). While many studies in HCI follow similar steps in explaining hypotheses, laying out a study design, and reporting results, many of these decisions are buried in blocks of dense scientific text. We propose leveraging data comics as study reports to provide an open and glanceable view of studies by tightly integrating text and images, illustrating design decisions and key insights visually, resulting in visual narratives that can be compelling to non-scientists and researchers alike. Use cases of data comics study reports range from illustrations for non-scientific audiences to graphical abstracts, study summaries, technical talks, textbooks, teaching, blogs, supplementary submission material, and inclusion in scientific articles. This paper provides examples of data comics study reports alongside a graphical repertoire of examples, embedded in a framework of guidelines for creating comics reports which was iterated upon and evaluated through a series of collaborative design sessions.

Mathematical models of epidemics are important tools for predicting epidemic dynamics and evaluating interventions. Yet, because early models are built on limited information, it is unclear how long they will accurately capture epidemic dynamics. Using a stochastic SEIR model of COVID-19 fitted to reported deaths, we estimated transmission parameters at different time points during the first wave of the epidemic (March–June, 2020) in Santa Clara County, California. Although our estimated basic reproduction number ( R 0 ) remained stable from early April to late June (with an overall median of 3.76), our estimated effective reproduction number ( R E ) varied from 0.18 to 1.02 in April before stabilizing at 0.64 on 27 May. Between 22 April and 27 May, our model accurately predicted dynamics through June; however, the model did not predict rising summer cases after shelter-in-place orders were relaxed in June, which, in early July, was reflected in cases but not yet in deaths. While models are critical for informing intervention policy early in an epidemic, their performance will be limited as epidemic dynamics evolve. This paper is one of the first to evaluate the accuracy of an early epidemiological compartment model over time to understand the value and limitations of models during unfolding epidemics.

Magnetic resonance (MR) images of the brain are of immense clinical and research utility. At the atomic and subatomic levels, the sources of MR signals are well understood. However, at the macromolecular scale, we lack a comprehensive understanding of what determines MR signal contrast. To address this gap, we used genome-wide measurements to correlate gene expression with MR signal intensity across the cortex in the Allen Human Brain Atlas. We focused on the ratio of T1-weighted and T2-weighted intensities (T1-w/T2-w) which is considered to be a useful proxy for myelin content. Positive correlations between myelin-associated genes and the ratio supported its use as a myelin marker. However, stronger correlations were observed for neurofilaments, and genes linked to the production of formaldehyde (which cross-links protein to create larger molecules). There was also an association with protein mass, with genes coding for heavier proteins expressed in regions with high T1-w/T2-w values. Oligodendrocyte gene markers were strongly correlated but this was not driven by myelin-associated genes, suggesting this signal is from non-myelinating satellite oligodendrocytes. We find the strongest support for the previous finding of high aerobic glycolysis in regions with low

BackgroundMental illness affects a significant portion of the worldwide population. Online mental health forums can provide a supportive environment for those afflicted and also generate a large amount of data which can be mined to predict mental health states using machine learning methods. ObjectiveWe benchmark multiple methods of text feature representation for social media posts and compare their downstream use with automated machine learning (AutoML) tools to triage content for moderator attention. MethodsWe used 1588 labeled posts from the CLPsych 2017 shared task collected from the Reachout.com forum (Milne et al., 2019). Posts were represented using lexicon based tools including VADER, Empath, LIWC and also used pre-trained artificial neural network models including DeepMoji, Universal Sentence Encoder, and GPT-1. We used TPOT and auto-sklearn as AutoML tools to generate classifiers to triage the posts. ResultsThe top-performing system used features derived from the GPT-1 model, which was finetuned on over 150,000 unlabeled posts from Reachout.com . Our top system had a macro averaged F1 score of 0.572, providing a new state-of-the-art result on the CLPsych 2017 task. This was achieved without additional information from meta-data or preceding posts. Error analyses revealed that this top system often misses expressions of hopelessness. We additionally present visualizations that aid understanding of the learned classifiers. ConclusionsWe show that transfer learning is an effective strategy for predicting risk with relatively little labeled data. We note that finetuning of pretrained language models provides further gains when large amounts of unlabeled text is available.

The Law of Common Fate from Gestalt psychology states that visual objects moving with the same velocity along parallel trajectories will be perceived by a human observer as grouped. However, the concept of common fate is much broader than mere velocity; in this paper we explore how common fate results from coordinated changes in luminance and size. We present results from a crowdsourced graphical perception study where we asked workers to make perceptual judgments on a series of trials involving four graphical objects under the influence of conflicting static and dynamic visual factors (position, size and luminance) used in conjunction. Our results yield the following rankings for visual grouping: motion > (dynamic luminance, size, luminance); dynamic size > (dynamic luminance, position); and dynamic luminance > size. We also conducted a follow-up experiment to evaluate the three dynamic visual factors in a more ecologically valid setting, using both a Gapminder-like animated scatterplot and a thematic map of election data.The results indicate that in practice the relative grouping strengths of these factors may depend on various parameters including the visualization characteristics and the underlying data. We discuss design implications for animated transitions in data visualization.

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