We report that color and depth, as well as form, are recovered in tandem with seeing motion. The stimulus, consisting of multiple frames, was designed to keep all aspects, except color, of the binocular images identical. In still view, rivalry occurs due to the unmatched color of some corresponding image elements in the two eyes. When frames--created by translating color assignments and nothing else--are rapidly cycled, a colored object is seen moving in depth. In natural scenes the same mechanisms may be used to reconstruct depth, color, and form of hidden objects so that they can be seen as if in plain view.

RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of the CTD affects clustering are not entirely known. In this work, we studied the concentrated solutions of two heptapeptide repeat (2CTD) models at different phosphorylation patterns and protein and ion concentrations using all-atom molecular dynamics simulations to investigate clustering behavior and molecular interactions driving the cluster formation. Our results show that salt concentration and phosphorylation patterns play an important role in determining the clustering pattern, specifically at low protein concentrations. The balance between inter- and intrapeptide interactions and counterion coordination together impact the clustering behavior upon phosphorylation.

In an effect we call color from motion (CFM), apparent motion is accompanied by subjective color spread seen in physically achromatic regions. Here we report that physical lights can cancel the subjective color seen in CFM. As measured by cancellation, the saturation of the subjective color spread increases as the luminance of the test elements increase. Without luminance differences between test and surround elements, chromaticity differences alone can result in the perception of subjective color spread. In this case, subjective color spread is seen without seeing a subjective contour, suggesting that CFM does not require contour formation and that color - independent of contour - can be recovered in tandem with seeing motion. There are two modes in which CFM is perceived, either (1) as a localized change of illumination, a colored spotlight or shadow, moving over a textured surface or (2) as a moving, colored object seen through holes in an occluding surface. The mode in which CFM is seen depends on figural cues and on regional differences in luminance contrast between the chromatic elements and the achromatic background. Regions with distinct figural cues are always seen as moving; and CFM is seen in the first mode if the regions are of lower luminance contrast and in the second mode if the regions are of higher luminance contrast. Without figural cues, the regions of lower luminance contrast are always seen to move and CFM is seen in the first mode.

BACKGROUND: Social determinants of health (SDOH) are becoming increasingly recognised as mediators of human health. In the setting of metabolic dysfunction-associated steatotic liver disease (MASLD), most of the literature on SDOH relates to individual-level risk factors. However, there are very limited data on neighbourhood-level SDOH in MASLD. AIM: To assess whether SDOH impact fibrosis progression in patients who already have MASLD. METHODS: This was a retrospective cohort study of patients with MASLD seen at Michigan Medicine. The primary predictors were two neighbourhood-level SDOH, disadvantage and affluence. The primary outcomes were mortality, incident liver-related events (LREs) and incident cardiovascular disease (CVD). We modelled these outcomes using Kaplan-Meier statistics for mortality and competing risk analyses for LREs and CVD, using a 1-year landmark. RESULTS: We included 15,904 patients with MASLD with median follow-up of 63 months. Higher affluence was associated with lower risk of overall mortality (hazard ratio 0.49 [0.37-0.66], p < 0.0001 for higher vs. lower quartile), LREs (subhazard ratio 0.60 [0.39-0.91], p = 0.02) and CVD (subhazard ratio 0.71 [0.57-0.88], p = 0.0018). Disadvantage was associated with higher mortality (hazard ratio 2.08 [95% confidence interval 1.54-2.81], p < 0.0001 for the highest vs. lowest quartile) and incident CVD (subhazard ratio 1.36 [95% confidence interval 1.10-1.68], p < 0.0001). These findings were robust across several sensitivity analyses. DISCUSSION: Neighbourhood-level SDOH are associated with mortality, incidence of LREs and incident CVD in patients with steatotic liver disease. Interventions aimed at disadvantaged neighbourhoods may improve clinical outcomes.

OBJECTIVE: Although it is established that structural damage of the meniscus is linked to knee osteoarthritis (OA) progression, the predisposition to future development of OA because of geometric meniscal shapes is plausible and unexplored. This study aims to identify common variations in meniscal shape and determine their relationships to tissue morphology, OA onset, and longitudinal changes in cartilage thickness. METHODS: A total of 4,790 participants from the Osteoarthritis Initiative data set were studied. A statistical shape model was developed for the meniscus, and shape scores were evaluated between a control group and an OA incidence group. Shape features were then associated with cartilage thickness changes over 8 years to localize the relationship between meniscus shape and cartilage degeneration. RESULTS: Seven shape features between the medial and lateral menisci were identified to be different between knees that remain normal and those that develop OA. These include length-width ratios, horn lengths, root attachment angles, and concavity. These at-risk shapes were linked to unique cartilage thickness changes that suggest a relationship between meniscus geometry and decreased tibial coverage and rotational imbalances. Additionally, strong associations were found between meniscal shape and demographic subpopulations, future tibial extrusion, and meniscal and ligamentous tears. CONCLUSION: This automatic method expanded upon known meniscus characteristics that are associated with the onset of OA and discovered novel shape features that have yet to be investigated in the context of OA risk.

Performance testing is a standard practice for evolving systems to detect performance issues proactively. It samples various performance metrics that will be compared with a stable baseline to judge whether the measurement data is abnormal. This type of comparative analysis requires domain expertise, which can take experienced performance analysts days to conduct. In an effort to build an automatic solution for a leading data warehousing company to improve the comparative performance analysis efficiency, we implemented machine learning approaches proposed by existing research. But the initial result has a 86% false negative rate on average, which means the majority of performance defects would be missed. To investigate causes for this unsatisfying result, we take a step back to revisit the performance data itself and find several important data related issues that are overlooked by existing work. In this paper, we discuss in detail these issues and share our hindsights to address them. With the new learning scheme we devise, we are able to reduce the false negative rate to as low as 16% and achieve a balanced accuracy of 0.91, which enables the analysis engine to be practically adopted.

Pre-2018 CSE ID: CS2015-1014

Cartilage thickness change is a well-documented biomarker of osteoarthritis pathogenesis. However, there is still much to learn about the spatial and temporal patterns of cartilage thickness change in health and disease. In this study, we develop a novel analysis method for elucidating such patterns using a functional connectivity approach. Descriptive statistics are reported for 1186 knees that did not develop osteoarthritis during the 8 years of observation, which we present as a model of cartilage thickness change related to healthy aging. Within the control population, patterns vary greatly between male and female subjects, while body mass index (BMI) has a more moderate impact. Finally, several differences are shown between knees that did and did not develop osteoarthritis. Some but not all significance appears to be accounted for by differences in sex, BMI, and knee alignment. With this work, we present the connectome as a novel tool for studying spatiotemporal dynamics of tissue change.

The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.