scLTNN: an innovative tool for automatically visualizing single-cell trajectories.

Motivation: Cellular state identification and trajectory inference enable the computational simulation of cell fate dynamics using single-cell RNA sequencing data. However, existing methods for constructing cell fate trajectories demand substantial computational resources or prior knowledge of the developmental process.

Results: Here, based on the discovery of the consistent expression distribution of highly variable genes, we create a new tool named scRNA-seq latent time neural network (scLTNN) by combining an artificial neural network with a distribution model.

Neuroprotective effects of mesenchymal stromal cells in mouse models of Alzheimer's Disease: The Mediating role of gut microbes and their metabolites via the Microbiome-Gut-Brain axis.

The intricacy and multifaceted nature of Alzheimer's disease (AD) necessitate therapies that target multiple aspects of the disease. Mesenchymal stromal cells (MSCs) emerge as potential agents to mitigate AD symptoms; however, whether their therapeutic efficacy involves modulation of gut microbiota and the microbiome-gut-brain axis (MGBA) remains unexplored. In this study, we evaluated the effects of three distinct MSCs types-derived from the umbilical cord (UCMSC), dental pulp (SHED), and adipose tissue (ADSC)-in an APP/PS1 mouse model of AD.

Network-based pharmacology and UHPLC-Q-Exactive-Orbitrap-MS reveal granule's mechanism in reducing cellular inflammation in COVID-19.

Introduction: The outbreak of SARS-CoV-2, leading to COVID-19, poses a major global health threat. While specific treatments and vaccines are under development, Traditional Chinese Medicine (TCM) has historically been effective against pandemics, including viral pneumonias. Our study explores the efficacy and mechanisms of Jinhua Qinggan Granules (JHQG) in treating COVID-19.

OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing.

Single-cell sequencing is frequently affected by "omission" due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly "omitted" cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of "omitted" cells within single-cell RNA sequencing datasets.

A Network Pharmacology-based Study on the Anti-aging Properties of Traditional Chinese Medicine Sisheng Bulao Elixir.

Background: Traditional Chinese Medicine (TCM) has a rich history of use in preventing senescence for millennia in China. Nonetheless, a systematic method to study the antiaging properties and the underlying molecular mechanism of TCM remains absent.

Objective: The objective of this study is to decipher the anti-aging targets and mechanisms of Sisheng Bulao Elixir (SBE) using a systematic approach based on a novel aging database and network pharmacology.

Too Many Cooks: Exploring How Graphical Perception Studies Influence Visualization Recommendations in Draco.

Findings from graphical perception can guide visualization recommendation algorithms in identifying effective visualization designs. However, existing algorithms use knowledge from, at best, a few studies, limiting our understanding of how complementary (or contradictory) graphical perception results influence generated recommendations. In this paper, we present a pipeline of applying a large body of graphical perception results to develop new visualization recommendation algorithms and conduct an exploratory study to investigate how results from graphical perception can alter the behavior of downstream algorithms.

Stem cells from human exfoliated deciduous teeth rejuvenate the liver in naturally aged mice by improving ribosomal and mitochondrial proteins.

Background Aims: Aging is accompanied by a decline in cellular proteome homeostasis, mitochondrial, and metabolic function. Mesenchymal stromal cell (MSC) therapies have been reported to extend lifespan and delay some age-related pathologies, yet the anti-aging rate and mechanisms remain unclear. Here, we investigated the effects and mechanism by transplantation of stem cells from human exfoliated deciduous teeth (SHED) into the naturally aged mice model.

Regulatory factor identification for genes in zebrafish by causal inference.

Activation of genes is critical for mesoderm and endoderm induction. Our previous study reported that zebrafish genes / and / are coordinately regulated by maternal Eomesa, Hwa-activated β-catenin (Hwa/β-catenin) signaling, and Nodal autoregulation (Nodal/Smad2) signaling. However, the exact contribution and underlying mechanisms are still elusive.

Phosphate sequestration by lanthanum-layered rare earth hydroxides through multiple mechanisms while avoiding the attenuation effect from sediment particles in lake water.

Lanthanum-based adsorbents have been used extensively to capture phosphate from wastewater. However, the attenuation effect that arises from the coexistence of sediment and humic acid is the major drawback in practical applications. The Lanthanum-layered rare earth hydroxides (LRHs)-Cl (La-LRH-Cl) was synthesized and achieved high elemental phosphorus (P) adsorption capacity (138.

Composition of intestinal flora affects the risk relationship between Alzheimer's disease/Parkinson's disease and cancer.

An increasing number of epidemiological studies have shown that there is a significant inverse relationship between the onset of Alzheimer's disease/Parkinson's disease (AD/PD) and cancer, but the mechanism is still unclear. Considering that intestinal flora can connect them, we tried to explain this phenomenon from the intestinal flora. This review briefly introduced the relationship among AD/PD, cancer, and intestinal flora, studied metabolites or components of the intestinal flora and the role of intestinal barriers and intestinal hormones in AD/PD and cancer.

Stem cells from human exfoliated deciduous teeth affect mitochondria and reverse cognitive decline in a senescence-accelerated mouse prone 8 model.

Background Aims: Stem cell therapy is a novel therapy being explored for AD. The molecular mechanism of its effect is still unclear. The authors investigated the effects and mechanism by injection of SHEDs into an AD mouse model.

An Evaluation-Focused Framework for Visualization Recommendation Algorithms.

Although we have seen a proliferation of algorithms for recommending visualizations, these algorithms are rarely compared with one another, making it difficult to ascertain which algorithm is best for a given visual analysis scenario. Though several formal frameworks have been proposed in response, we believe this issue persists because visualization recommendation algorithms are inadequately specified from an evaluation perspective. In this paper, we propose an evaluation-focused framework to contextualize and compare a broad range of visualization recommendation algorithms.

ERgene: Python library for screening endogenous reference genes.

In gene expression analysis, sample differences and experimental operation differences are common, but sometimes, these differences will cause serious errors to the results or even make the results meaningless. Finding suitable internal reference genes efficiently to eliminate errors is a challenge. Aside from the need for high efficiency, there is no package for screening endogenous genes available in Python.

Establishment and validation of a drug-target microarray for SARS-CoV-2.

COVID-19 has become one of the worst epidemic in the world, currently already more than four million people have been infected, which probably co-exist with human beings, and has a significant impact on the global economy and political order. In the process of fighting against the epidemic in China, the clinical value of a variety of herbal medicines has been recognized and written into the clinical application guide. However, their effective molecular mechanism and potential targets are still not clear.

High-throughput screening suggests glutathione synthetase as an anti-tumor target of polydatin using human proteome chip.

Polydatin (PD) is a bio-active ingredient with known anti-tumor effects. However, its specific protein targets yet have not been systematically screened, and the molecular anti-tumor mechanism is still unclear. Here, proteomic-chip was efficiently used to screen potential targets of PD.

Tuning of Persulfate Activation from a Free Radical to a Nonradical Pathway through the Incorporation of Non-Redox Magnesium Oxide.

Nonradical-based advanced oxidation processes for pollutant removal have attracted much attention due to their inherent advantages. Herein we report that magnesium oxides (MgO) in CuOMgO/FeO not only enhanced the catalytic properties but also switched the free radical peroxymonosulfate (PMS)-activated process into the O based nonradical process. CuOMgO/FeO catalyst exhibited consistent performance in a wide pH range from 5.

Zeta potential-assisted sorption of uranyl tricarbonate complex from aqueous solution by polyamidoxime-functionalized colloidal particles.

Uranium(vi) is one of the main sources in nuclear energy but can cause severe effects to human health and the environment, therefore it is important to develop a new method and materials for uranium capture. A novel approach is reported here for efficient uranium sorption by polyamidoxime-functionalized colloids with zeta potential-assistance. Specifically, colloidal particles were prepared via emulsion polymerization with (3-acrylamidopropyl)trimethyl-ammonium chloride (MAPTAC).