Construction of a Cities Evolution Tree, with Applications

China has been experiencing urbanization at an unprecedented rate over the last two decades. This study analyzes the impact of urbanization on land occupation. Cities are clustered by their functions and development stages, which is illustrated by a cluster tree, a dynamic tree that depicts the evolution of cities. The evolution tree in one year is used to predict the state of a city in a future time period. Another application of the evolution tree is to predict urban-type relevant phenomena, such as urban occupation. It is found that comprehensive cities, business cities, and manufacturing cities have higher urban expansion rates than tourist cities, with a few exceptions that focus on both industry and tourism. Meanwhile, the speed and extent of city land growth are dominated by industrialization stages and economic patterns, as well as leap-development. The methodology presented in this study is especially suitable for identifying transition paths of a stochastic process in a complex dataset of 253 cities in China

Lightweight Delegated Subset Test with Privacy Protection

Singapore Management Universit

Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma

Table summarizing the RNA-seq results. Differential gene expression results in BAP1-knockdown compared to control OCM-1A cells are shown from the RNA-seq data. Each row gives the unique Ensembl identifier, gene name, and description for each gene, as well as the log of the fold change (logFC), average expression, adjusted p-value, and linear fold change. (XLSX 1392 kb

On the seasonal variations of ocean bottom pressure in the world oceans

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cheng, X., Ou, N., Chen, J., & Huang, R. X. On the seasonal variations of ocean bottom pressure in the world oceans. Geoscience Letters, 8(1), (2021): 29, https://doi.org/10.1186/s40562-021-00199-3.Seasonal variability of the ocean bottom pressure (OBP) in the world oceans is investigated using 15 years of GRACE observations and a Pressure Coordinate Ocean Model (PCOM). In boreal winter, negative OBP anomalies appear in the northern North Pacific, subtropical South Pacific and north of 40 °S in the Indian Ocean, while OBP anomaly in the Southern Ocean is positive. The summer pattern is opposite to that in winter. The centers of positive (negative) OBP signals have a good coherence with the mass convergence/divergence due to Ekman transport, indicating the importance of wind forcing. The PCOM model reproduces the observed OBP quite well. Sensitivity experiments indicate that wind forcing dominates the regional OBP seasonal variations, while the contributions due to heat flux and freshwater flux are unimportant. Experiments with daily sea level pressure (SLP) forcing suggest that at high frequencies the non-static effect of SLP is not negligible.This research was supported by the National Key R&D Program of China (2018YFA0605702), Natural Science Foundation of China (Grant nos. 41522601, 41876002, 41876224)

Identification of novel pathways and immune profiles related to sarcopenia

IntroductionSarcopenia is a progressive deterioration of skeletal muscle mass strength and function.MethodsTo uncover the underlying cellular and biological mechanisms, we studied the association between sarcopenia's three stages and the patient's ethnicity, identified a gene regulatory network based on motif enrichment in the upregulated gene set of sarcopenia, and compared the immunological landscape among sarcopenia stages.ResultsWe found that sarcopenia (S) was associated with GnRH, neurotrophin, Rap1, Ras, and p53 signaling pathways. Low muscle mass (LMM) patients showed activated pathways of VEGF signaling, B-cell receptor signaling, ErbB signaling, and T-cell receptor signaling. Low muscle mass and physical performance (LMM_LP) patients showed lower enrichment scores in B-cell receptor signaling, apoptosis, HIF-1 signaling, and the adaptive immune response pathways. Five common genes among DEGs and the elastic net regression model, TTC39DP, SLURP1, LCE1C, PTCD2P1, and OR7E109P, were expressed between S patients and healthy controls. SLURP1 and LCE1C showed the highest expression levels among sarcopenic Chinese descent than Caucasians and Afro-Caribbeans. Gene regulatory analysis of top upregulated genes in S patients yielded a top-scoring regulon containing GATA1, GATA2, and GATA3 as master regulators and nine predicted direct target genes. Two genes were associated with locomotion: POSTN and SLURP1. TTC39DP upregulation was associated with a better prognosis and stronger immune profile in S patients. The upregulation of SLURP1 and LCE1C was associated with a worse prognosis and weaker immune profile.ConclusionThis study provides new insight into sarcopenia's cellular and immunological prospects and evaluates the age and sarcopenia-related modifications of skeletal muscle

Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus

Retroviral reverse transcriptase (RT) of Moloney murine leukemia virus (MoMLV) is expressed in the form of a large Gag–Pol precursor protein by suppression of translational termination in which the maximal efficiency of stop codon read-through depends on the interaction between MoMLV RT and peptidyl release factor 1 (eRF1). Here, we report the crystal structure of MoMLV RT in complex with eRF1. The MoMLV RT interacts with the C-terminal domain of eRF1 via its RNase H domain to sterically occlude the binding of peptidyl release factor 3 (eRF3) to eRF1. Promotion of read-through by MoMLV RNase H prevents nonsense-mediated mRNA decay (NMD) of mRNAs. Comparison of our structure with that of HIV RT explains why HIV RT cannot interact with eRF1. Our results provide a mechanistic view of how MoMLV manipulates the host translation termination machinery for the synthesis of its own proteins

Optimization of Green and Hardness Protection Technology of Frozen Green Pepper

To diminish the browning and tissue softening issues of green pepper dishes in the freezing/thawing processes, salt, trehalose and calcium chloride were used to treat thawed green peppers, and the hardness, drip loss rate, chlorophyll content, sensory evaluation and microstructure of thawed green peppers were measured to verify the effect of process green protection and hard preservation. A single factor experiment was used to screen the optimum range of each factor and response surface methodology was chosen to obtain the optimum process parameter combination. Results showed that the optimum process for protecting green and hardness properties of green pepper was as follows: Blanching green pepper at 100 ℃ for 5 s, the mass fraction of salt in the blanching solution was 0.50%, immersed in cold water for 15 min, the mass fraction of trehalose was 0.51%, and the mass fraction of calcium chloride was 0.25%. Under this process condition, compared with the control group, the color difference of green pepper in the treatment group was reduced by 3.98, the hardness was increased by 20.37%, the juice loss rate was decreased by 40.29%, the chlorophyll content and sensory score were increased by 102.70% and 88%, respectively. Through the scanning electron microscopy, it was found that the treated green pepper cell wall was more complete and maintained a better cell structure. This process can effectively maintain the color and taste of green pepper after thawing, which can provide data support for the research of green and hardness preservation technology of frozen green pepper prefabricated vegetables

Pycallingcards: An integrated environment for visualizing, analyzing, and interpreting Calling Cards data

MOTIVATION: Unraveling the transcriptional programs that control how cells divide, differentiate, and respond to their environments requires a precise understanding of transcription factors\u27 (TFs) DNA-binding activities. Calling cards (CC) technology uses transposons to capture transient TF binding events at one instant in time and then read them out at a later time. This methodology can also be used to simultaneously measure TF binding and mRNA expression from single-cell CC and to record and integrate TF binding events across time in any cell type of interest without the need for purification. Despite these advantages, there has been a lack of dedicated bioinformatics tools for the detailed analysis of CC data. RESULTS: We introduce Pycallingcards, a comprehensive Python module specifically designed for the analysis of single-cell and bulk CC data across multiple species. Pycallingcards introduces two innovative peak callers, CCcaller and MACCs, enhancing the accuracy and speed of pinpointing TF binding sites from CC data. Pycallingcards offers a fully integrated environment for data visualization, motif finding, and comparative analysis with RNA-seq and ChIP-seq datasets. To illustrate its practical application, we have reanalyzed previously published mouse cortex and glioblastoma datasets. This analysis revealed novel cell-type-specific binding sites and potential sex-linked TF regulators, furthering our understanding of TF binding and gene expression relationships. Thus, Pycallingcards, with its user-friendly design and seamless interface with the Python data science ecosystem, stands as a critical tool for advancing the analysis of TF functions via CC data. AVAILABILITY AND IMPLEMENTATION: Pycallingcards can be accessed on the GitHub repository: https://github.com/The-Mitra-Lab/pycallingcards