Hypervalent iodine catalysis enabled iterative multi-fluorination: not just a simple alternative for the electrochemical approach.

Unlike the well-established fluoroalkylation, the direct incorporation of multiple fluorine atoms into small molecules iterative fluorinations has been much less investigated. Herein, we report a hypervalent iodine catalytically selective multi-fluorination in which the fluorination degree is controlled by the delicate balance between the HF/amine ratios. The and of hypervalent iodine catalysis and the previously established electrochemical approach in the iterative multi-fluorinations are also provided.

LinRace: cell division history reconstruction of single cells using paired lineage barcode and gene expression data.

Lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for inference of cell lineage and cell types at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expressions are emerging. Effectively incorporating the gene expression data requires a reasonable model of how gene expression data changes along generations of divisions.

scMultiSim: simulation of single cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.

Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities.

CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics.

Motivation: Gene regulatory networks (GRNs) in a cell provide the tight feedback needed to synchronize cell actions. However, genes in a cell also take input from, and provide signals to other neighboring cells. These cell-cell interactions (CCIs) and the GRNs deeply influence each other.

LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data.

Understanding how single cells divide and differentiate into different cell types in developed organs is one of the major tasks of developmental and stem cell biology. Recently, lineage tracing technology using CRISPR/Cas9 genome editing have enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for the reconstruction of the cell division tree, and even the detection of cell types and differentiation trajectories at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expression data are emerging, aiming to improve the accuracy of lineage reconstruction.

Outstanding Electrochemical Performance of Ni-Rich Concentration-Gradient Cathode Material LiNiCoMnO for Lithium-Ion Batteries.

The full-concentrationgradient LiNiCoMnO (CG-LNCM), consisting of core Ni-rich LiNiCoO, transition zone LiNiCoMnO and outmost shell LiNiCoMnO was prepared by a facile co-precipitation method and high-temperature calcination. CG-LNCM was then investigated with an X-ray diffractometer, ascanning electron microscope, a transmission electron microscope, and electrochemical measurements. The results demonstrate that CG-LNCM has a lower cation mixing of Li and Ni and larger Li diffusion coefficients than concentration-constant LiNiCoMnO (CC-LNCM).

LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data.

Understanding how single cells divide and differentiate into different cell types in developed organs is one of the major tasks of developmental and stem cell biology. Recently, lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for the reconstruction of the cell division tree, and even the detection of cell types and differentiation trajectories at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expression data are emerging, aiming to improve the accuracy of lineage reconstruction.

scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks.

Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities.

Diastereoselective Synthesis of Dihydrobenzofuran-Fused Spiroindolizidines via Double-Dearomative [3 + 2] Cycloadditions.

Spiroindolizidine oxindoles represent a kind of privileged scaffold in many biologically active natural alkaloids. 2,3-Dihydrobenzofuran derivatives exhibit significant bioactivities in a variety of pharmaceuticals. Herein, we assembled these two privileged fragments into a small molecule via double-dearomative [3 + 2] cycloadditions with pyridinium ylides and 2-nitrobenzofurans.

TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history.

Recently, lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes, which allows for the reconstruction of the cell division tree and makes it possible to reconstruct ancestral cell types and trace the origin of each cell type. Meanwhile, trajectory inference methods are widely used to infer cell trajectories and pseudotime in a dynamic process using gene expression data of present-day cells. Here, we present TedSim (single-cell temporal dynamics simulator), which simulates the cell division events from the root cell to present-day cells, simultaneously generating two data modalities for each single cell: the lineage barcode and gene expression data.

Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics.

The recent advance of single-cell copy number variation (CNV) analysis plays an essential role in addressing intratumor heterogeneity, identifying tumor subgroups and restoring tumor-evolving trajectories at single-cell scale. Informative visualization of copy number analysis results boosts productive scientific exploration, validation and sharing. Several single-cell analysis figures have the effectiveness of visualizations for understanding single-cell genomics in published articles and software packages.

Unintended changes in ocular biometric parameters during a 6-month follow-up period after FS-LASIK and SMILE.

Background: Corneal refractive surgery has become reliable for correcting refractive errors, but it can induce unintended ocular changes that alter refractive outcomes. This study is to evaluate the unintended changes in ocular biometric parameters over a 6-month follow-up period after femtosecond laser-assisted laser in situ keratomileusis (FS-LASIK) and small incision lenticule extraction (SMILE).

Methods: 156 consecutive myopic patients scheduled for FS-LASIK and SMILE were included in this study.

Oviz-Bio: a web-based platform for interactive cancer genomics data visualization.

Genetics data visualization plays an important role in the sharing of knowledge from cancer genome research. Many types of visualization are widely used, most of which are static and require sufficient coding experience to create. Here, we present Oviz-Bio, a web-based platform that provides interactive and real-time visualizations of cancer genomics data.

Effectiveness of the Goldmann Applanation Tonometer, the Dynamic Contour Tonometer, the Ocular Response Analyzer and the Corvis ST in Measuring Intraocular Pressure following FS-LASIK.

: To test the performance of the four tonometers in providing IOP measurements that were free of the effects of corneal biomechanics changes caused by refractive surgery.: Four tonometers were employed to provide IOP measurements for 65 participants who accepted Femtosecond laser-assisted LASIK (FS-LASIK). The measurements included GAT-IOP by the Goldmann Applanation Tonometer, DCT-IOP by the Dynamic Contour Tonometer, Goldmann-correlated IOP (ORA-IOPg) and corneal-compensated IOP (ORA-IOPcc) by the Ocular Response Analyzer, and uncorrected IOP (CVS-IOP) and biomechanically corrected IOP (CVS-bIOP) by the Corvis ST.

MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals.

Background: Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation.

Results: Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages.

miR-326 functions as a tumor suppressor in human prostatic carcinoma by targeting Mucin1.

Accumulating evidence suggests that microRNA-326 (miR-326) serves as a tumor suppressor in the initiation and progression of several human malignancies. However, the biological function and underlying molecular mechanism of miR-326 in prostatic carcinoma (PCa) remains largely unknown. In the present study, we found that miR-326 expression level was significantly downregulated in both primary PCa and castration-resistant PCa (CRPC) tissue samples as detected by qRT-PCR.

Over-expression of a poor prognostic marker in prostate cancer: AQP5 promotes cells growth and local invasion.

Background: The aquaporins (AQPs), water channel proteins, are known playing a major role in transcellular and transepithelial water movement; they also exhibit several properties related to tumor development. The aim of the present study is to elucidate whether the expression of AQP5 is a strong prognostic biomarker for prostate cancer, and the potential role in the progression of prostate cancer cells.

Methods: AQP5 expression was measured in 60 prostate cancer tissues and cells (both PC-3 and LNCaP) by immunohistochemistry and immunofluorescence assay.