Unsupervised cryo-EM data clustering through adaptively constrained K-means algorithm

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.Comment: 35 pages, 14 figure

Visualizing the impact of Covid-19 vaccine passports on pedestrian access to metro stations in Hong Kong

Pedestrian infrastructures in Hong Kong enable multilevel city life in a vertical metropolis plagued by land scarcity. Public spaces integrated into pedestrian networks play an indispensable role in neighbourhood accessibility. We visualize the impact of the Covid-19 vaccine passport (VP) restrictions on the use of public space on pedestrian accessibility to all 97 metro stations in Hong Kong. Pedestrians without a vaccine passport (PwoVP) need to walk significantly longer alternative routes. Specifically, VP-related access restrictions to indoor walkways have doubled the shortest travel time for PwoVP and a 50% reduction in accessibility of two-thirds of stations

Unsupervised Multi-view Pedestrian Detection

With the prosperity of the video surveillance, multiple cameras have been applied to accurately locate pedestrians in a specific area. However, previous methods rely on the human-labeled annotations in every video frame and camera view, leading to heavier burden than necessary camera calibration and synchronization. Therefore, we propose in this paper an Unsupervised Multi-view Pedestrian Detection approach (UMPD) to eliminate the need of annotations to learn a multi-view pedestrian detector via 2D-3D mapping. 1) Firstly, Semantic-aware Iterative Segmentation (SIS) is proposed to extract unsupervised representations of multi-view images, which are converted into 2D pedestrian masks as pseudo labels, via our proposed iterative PCA and zero-shot semantic classes from vision-language models. 2) Secondly, we propose Geometry-aware Volume-based Detector (GVD) to end-to-end encode multi-view 2D images into a 3D volume to predict voxel-wise density and color via 2D-to-3D geometric projection, trained by 3D-to-2D rendering losses with SIS pseudo labels. 3) Thirdly, for better detection results, i.e., the 3D density projected on Birds-Eye-View from GVD, we propose Vertical-aware BEV Regularization (VBR) to constraint them to be vertical like the natural pedestrian poses. Extensive experiments on popular multi-view pedestrian detection benchmarks Wildtrack, Terrace, and MultiviewX, show that our proposed UMPD approach, as the first fully-unsupervised method to our best knowledge, performs competitively to the previous state-of-the-art supervised techniques. Code will be available

Generation of energetic He atom beams by a pulsed positive corona discharge

Time-of-flight measurements were made of neutral helium atom beams extracted from a repetitive, pulsed, positive-point corona discharge. Two strong neutral peaks, one fast and one slow, were observed, accompanied by a prompt photon peak and a fast ion peak. All peaks were correlated with the pulsing of the discharge. The two types of atoms appear to be formed by different mechanisms at different stages of the corona discharge. The fast atoms had energies of 190 eV and were formed at the onset of the pulsing, approximately 0.7 µs before the maximum of the photon peak. The slow peak, composed of electronically metastable He atoms, originated 30–50 µs after the photon pulse, and possessed a nearly thermal velocity distribution. The velocity distribution was typical of an undisturbed supersonic expansion with a stagnation temperature of 131 K and a speed ratio of 3.6. Peak intensities and velocities were measured as a function of source voltage, stagnation pressure, and skimmer voltage

Hepatic Carboxylesterase 1 Is Induced by Glucose and Regulates Postprandial Glucose Levels

Metabolic syndrome, characterized by obesity, hyperglycemia, dyslipidemia and hypertension, increases the risks for cardiovascular disease, diabetes and stroke. Carboxylesterase 1 (CES1) is an enzyme that hydrolyzes triglycerides and cholesterol esters, and is important for lipid metabolism. Our previous data show that over-expression of mouse hepatic CES1 lowers plasma glucose levels and improves insulin sensitivity in diabetic ob/ob mice. In the present study, we determined the physiological role of hepatic CES1 in glucose homeostasis. Hepatic CES1 expression was reduced by fasting but increased in diabetic mice. Treatment of mice with glucose induced hepatic CES1 expression. Consistent with the in vivo study, glucose stimulated CES1 promoter activity and increased acetylation of histone 3 and histone 4 in the CES1 chromatin. Knockdown of ATP-citrate lyase (ACL), an enzyme that regulates histone acetylation, abolished glucose-mediated histone acetylation in the CES1 chromatin and glucose-induced hepatic CES1 expression. Finally, knockdown of hepatic CES1 significantly increased postprandial blood glucose levels. In conclusion, the present study uncovers a novel glucose-CES1-glucose pathway which may play an important role in regulating postprandial blood glucose levels