Fast Learning Radiance Fields by Shooting Much Fewer Rays

Learning radiance fields has shown remarkable results for novel view synthesis. The learning procedure usually costs lots of time, which motivates the latest methods to speed up the learning procedure by learning without neural networks or using more efficient data structures. However, these specially designed approaches do not work for most of radiance fields based methods. To resolve this issue, we introduce a general strategy to speed up the learning procedure for almost all radiance fields based methods. Our key idea is to reduce the redundancy by shooting much fewer rays in the multi-view volume rendering procedure which is the base for almost all radiance fields based methods. We find that shooting rays at pixels with dramatic color change not only significantly reduces the training burden but also barely affects the accuracy of the learned radiance fields. In addition, we also adaptively subdivide each view into a quadtree according to the average rendering error in each node in the tree, which makes us dynamically shoot more rays in more complex regions with larger rendering error. We evaluate our method with different radiance fields based methods under the widely used benchmarks. Experimental results show that our method achieves comparable accuracy to the state-of-the-art with much faster training.Comment: Accepted by lEEE Transactions on lmage Processing 2023. Project Page: https://zparquet.github.io/Fast-Learning . Code: https://github.com/zParquet/Fast-Learnin

Cancer-associated fibroblast related gene signature in Helicobacter pylori-based subtypes of gastric carcinoma for prognosis and tumor microenvironment estimation in silico analysis

IntroductionGastric cancer (GC) remains the major constituent of cancer-related deaths and a global public health challenge with a high incidence rate. Helicobacter pylori (HP) plays an essential role in promoting the occurrence and progression of GC. Cancer-associated fibroblasts (CAFs) are regarded as a significant component in the tumor microenvironment (TME), which is related to the metastasis of GC. However, the regulation mechanisms of CAFs in HP-related GC are not elucidated thoroughly.MethodsHP-related genes (HRGs) were downloaded from the GSE84437 and TCGA-GC databases. The two databases were combined into one cohort for training. Furthermore, the consensus unsupervised clustering analysis was obtained to sort the training cohort into different groups for the identification of differential expression genes (DEGs). Weighted correlation network analysis (WGCNA) was performed to verify the correlation between the DEGs and cancer-associated fibroblasts which were key components in the tumor microenvironment. The least absolute shrinkage and selection operator (LASSO) was executed to find cancer-associated fibroblast-related differential expression genes (CDEGs) for the further establishment of a prognostic model.Results and discussionIn this study, 52 HP-related genes (HRGs) were screened out based on the GSE84437 and TCGA-GC databases. A total of 804 GC samples were analyzed, respectively, and clustered into two HP-related subtypes. The DEGs identified from the two subtypes were proved to have a relationship with TME. After WGCNA and LASSO, the CAFs-related module was identified, from which 21 gene signatures were confirmed. Then, a CDEGs-Score was constructed and its prediction efficiency in GC patients was conducted for validation. Overall, a highly precise nomogram was established for enhancing the adaptability of the CDEGs-Score. Furthermore, our findings revealed the applicability of CDEGs-Score in the sensitivity of chemotherapeutic drugs. In general, our research provided brand-new possibilities for comprehending HP-related GC, evaluating survival, and more efficient therapeutic strategies

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, and limited types of evolutionary events. Here, we provide an alternative way to resolve phylogenetic problems based on analyses of real genome data. We use phylogenetic signals from all types of genome level evolutionary events, and overcome the conflicting issues existing in traditional phylogenetic approaches. Further, we build an automated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolution real yeast genome datasets. Comparison results with recent studies and publications show that we reconstruct very accurate and robust phylogenies and ancestors. Finally, we identify and analyze the conserved syntenic blocks among reconstructed ancestral genomes and present yeast species

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Chromatin Architectural Changes during Cellular Senescence and Aging

Chromatin 3D structure is highly dynamic and associated with many biological processes, such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer development, cellular senescence, and aging. Recently, by using chromosome conformation capture technologies, tremendous findings have been reported about the dynamics of genome architecture, their associated proteins, and the underlying mechanisms involved in regulating chromatin spatial organization and gene expression. Cellular senescence and aging, which involve multiple cellular and molecular functional declines, also undergo significant chromatin structural changes, including alternations of heterochromatin and disruption of higher-order chromatin structure. In this review, we summarize recent findings related to genome architecture, factors regulating chromatin spatial organization, and how they change during cellular senescence and aging

Non-Cooperative LEO Satellite Orbit Determination Using Single Station for Space-Based Opportunistic Positioning

Space-based opportunistic positioning is a crucial component of resilient positioning, navigation, and timing (PNT) systems, and it requires the acquisition of orbit information for non-cooperative low Earth orbit (LEO) satellites. Traditional methods for orbit determination (OD) of non-cooperative LEO satellites have difficulty in achieving a balance between reliability, hardware costs, and availability duration. To address these challenges, this study proposes a framework for single-station orbit determination of non-cooperative LEO satellites. By utilizing signals of opportunity (SOPs) captured by a single ground station, the system performs initial orbit determination (IOD), precise orbit determination (POD), and orbit prediction (OP), enabling the long-term determination of satellite positions and velocities. Under the proposed framework, the reliability and real-time performance are dependent on the initial orbit determination and the orbit calculation based on the dynamical model. To achieve initial orbit determination, a three-step algorithm is designed. (1) An improved search method is employed to estimate a coarse orbit using single-pass Doppler measurements. (2) Data association is conducted to obtain multi-pass Doppler observations. (3) The least squares (LS) is implemented to determine the initial orbit using the associated multi-pass Doppler measurements and the coarse orbit. Additionally, to enhance computational efficiency, two fast orbit calculation algorithms are devised. These algorithms leverage the numerical stability of the Runge–Kutta integrator to reduce computations and exploit the strong correlation among nearby time intervals of orbits with small eccentricities to minimize redundant calculations, thereby achieving orbit calculation efficiently. Finally, through positioning experiments, the determined orbits are demonstrated to have accuracy comparable to that of two-line elements (TLE) updated by the North American Aerospace Defense Command (NORAD)