Associations between COVID-19 risk, multiple environmental exposures, and housing conditions: A study using individual-level GPS-based real-time sensing data.

Few studies have used individual-level data to explore the association between COVID-19 risk with multiple environmental exposures and housing conditions. Using individual-level data collected with GPS-tracking smartphones, mobile air-pollutant and noise sensors, an activity-travel diary, and a questionnaire from two typical neighborhoods in a dense and well-developed city (i.e., Hong Kong), this study seeks to examine 1) the associations between multiple environmental exposures (i.e., different types of greenspace, PM2.5, and noise) and housing conditions (i.e., housing types, ownership, and overcrowding) with individuals' COVID-19 risk both in residential neighborhoods and along daily mobility trajectories; 2) which social groups are disadvantaged in COVID-19 risk through the perspective of the neighborhood effect averaging problem (NEAP). Using separate multiple linear regression and logistical regression models, we found a significant negative association between COVID-19 risk with greenspace (i.e., NDVI) both in residential areas and along people's daily mobility trajectories. Meanwhile, we also found that high open space and recreational land exposure and poor housing conditions were positively associated with COVID-19 risk in high-risk neighborhoods, and noise exposure was positively associated with COVID-19 risk in low-risk neighborhoods. Further, people with work places in high-risk areas and poor housing conditions were disadvantaged in COVID-19 risk.

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

A real-time heart rate estimation framework based on a facial video while wearing a mask.

BACKGROUND: The imaging photoplethysmography (iPPG) method is a non-invasive, non-contact measurement method that uses a camera to detect physiological indicators. On the other hand, wearing a mask has become essential today when COVID-19 is rampant, which has become a new challenge for heart rate (HR) estimation from facial videos recorded by a camera. OBJECTIVE: The aim is to propose an iPPG-based method that can accurately estimate HR with or without a mask. METHODS: First, the facial regions of interest (ROI) were divided into two sub-ROIs, and the original signal was obtained through spatial averaging with different weights according to the result of judging whether wearing a mask or not, and the CDF, which emphasizes the main component signal, was combined with the improved POS suitable for real-time HR estimation to obtain the noise-removed BVP signal. RESULTS: For self-collected data while wearing a mask, MAE, RMSE, and ACC were 1.09 bpm, 1.44 bpm, and 99.08%, respectively. CONCLUSION: Experimental results show that the proposed framework can estimate HR stably in real-time in both cases of wearing a mask or not. This study expands the application range of HR estimation based on facial videos and has very practical value in real-time HR estimation in daily life.

Testing big data in a big crisis: Nowcasting under COVID-19.

During the COVID-19 pandemic, economists have struggled to obtain reliable economic predictions, with standard models becoming outdated and their forecasting performance deteriorating rapidly. This paper presents two novelties that could be adopted by forecasting institutions in unconventional times. The first innovation is the construction of an extensive data set for macroeconomic forecasting in Europe. We collect more than a thousand time series from conventional and unconventional sources, complementing traditional macroeconomic variables with timely big data indicators and assessing their added value at nowcasting. The second novelty consists of a methodology to merge an enormous amount of non-encompassing data with a large battery of classical and more sophisticated forecasting methods in a seamlessly dynamic Bayesian framework. Specifically, we introduce an innovative "selection prior" that is used not as a way to influence model outcomes, but as a selecting device among competing models. By applying this methodology to the COVID-19 crisis, we show which variables are good predictors for nowcasting Gross Domestic Product and draw lessons for dealing with possible future crises.

Spatiotemporal Bayesian estimation of the number of under-reported COVID-19 cases in Victoria Australia.

Having an estimate of the number of under-reported cases is crucial in determining the true burden of a disease. In the COVID-19 pandemic, there is a great need to quantify the true disease burden by capturing the true incidence rate to establish appropriate measures and strategies to combat the disease. This study investigates the under-reporting of COVID-19 cases in Victoria, Australia, during the third wave of the pandemic as a result of variation in geographic area and time. It is aimed to determine potential under-reported areas and generate the true picture of the disease in terms of the number of cases. A two-tiered Bayesian hierarchical model approach is employed to estimate the true incidence and detection rates through Bayesian model averaging. The proposed model goes beyond testing inequality across areas by looking into other covariates such as weather, vaccination rates, and access to vaccination and testing centres, including interactions and variations between space and time. This model aims for parsimony yet allows a broader range of scope to capture the underlying dynamic of the reported COVID-19 cases. Moreover, it is a data-driven, flexible, and generalisable model to a global context such as cross-country estimation and across time points under strict pandemic conditions.

Bayesian Model Averaging to Account for Model Uncertainty in Estimates of a Vaccine's Effectiveness.

Purpose: Vaccine effectiveness (VE) studies are often conducted after the introduction of new vaccines to ensure they provide protection in real-world settings. Control of confounding is often needed during the analyses, which is most efficiently done through multivariable modeling. When many confounders are being considered, it can be challenging to know which variables need to be included in the final model. We propose an intuitive Bayesian model averaging (BMA) framework for this task. Patients and Methods: Data were used from a matched case-control study that aimed to assess the effectiveness of the Lyme vaccine post-licensure. Cases were residents of Connecticut, 15-70 years of age with confirmed Lyme disease. Up to 2 healthy controls were matched to each case subject by age. All participants were interviewed, and medical records were reviewed to ascertain immunization history and evaluate potential confounders. BMA was used to systematically search for potential models and calculate the weighted average VE estimate from the top subset of models. The performance of BMA was compared to three traditional single-best-model-selection methods: two-stage selection, stepwise elimination, and the leaps and bounds algorithm. Results: The analysis included 358 cases and 554 matched controls. VE ranged between 56% and 73% and 95% confidence intervals crossed zero in <5% of all candidate models. Averaging across the top 15 models, the BMA VE was 69% (95% CI: 18-88%). The two-stage, stepwise, and leaps and bounds algorithm yielded VE of 71% (95% CI: 21-90%), 73% (95% CI: 26-90%), and 74% (95% CI: 27-91%), respectively. Conclusion: This paper highlights how the BMA framework can be used to generate transparent and robust estimates of VE. The BMA-derived VE and confidence intervals were similar to those estimated using traditional methods. However, by incorporating model uncertainty into the parameter estimation, BMA can lend additional rigor and credibility to a well-designed study.