Alleviating batch effects in cell type deconvolution with SCCAF-D.

Cell type deconvolution methods can impute cell proportions from bulk transcriptomics data, revealing changes in disease progression or organ development. But benchmarking studies often use simulated bulk data from the same source as the reference, which limits its application scenarios. This study examines batch effects in deconvolution and introduces SCCAF-D, a computational workflow that ensures a Pearson Correlation Coefficient above 0.

Ultrasound Control of Genomic Regulatory Toolboxes for Cancer Immunotherapy.

There remains a critical need for the precise control of CRISPR (clustered regularly interspaced short palindromic repeats)-based technologies. Here, we engineer a set of inducible CRISPR-based tools controllable by focused ultrasound (FUS), which can penetrate deep and induce localized hyperthermia for transgene activation. We demonstrate the capabilities of FUS-inducible CRISPR, CRISPR activation (CRISPRa), and CRISPR epigenetic editor (CRISPRee) in modulating the genome and epigenome.

A brain cell atlas integrating single-cell transcriptomes across human brain regions.

While single-cell technologies have greatly advanced our comprehension of human brain cell types and functions, studies including large numbers of donors and multiple brain regions are needed to extend our understanding of brain cell heterogeneity. Integrating atlas-level single-cell data presents a chance to reveal rare cell types and cellular heterogeneity across brain regions. Here we present the Brain Cell Atlas, a comprehensive reference atlas of brain cells, by assembling single-cell data from 70 human and 103 mouse studies of the brain throughout major developmental stages across brain regions, covering over 26.

Discrimination of internal crack for rice seeds using near infrared spectroscopy.

It is an important thing to identify internal crack in seeds from normal seeds for evaluating the quality of rice seeds (Oryza sativa L.). In this study, non-destructive discrimination of internal crack in rice seeds using near infrared spectroscopy and chemometrics is proposed.

GateView: A Multi-Omics Platform for Gene Feature Analysis of Virus Receptors within Human Normal Tissues and Tumors.

Viruses are obligate intracellular parasites that rely on cell surface receptor molecules to complete the first step of invading host cells. The experimental method for virus receptor screening is time-consuming, and receptor molecules have been identified for less than half of known viruses. This study collected known human viruses and their receptor molecules.

Single Genomic Loci Labeling and Manipulation Using SIMBA System.

The SIMBA (Simultaneous Imaging and Manipulation of genomic loci by Biomolecular Assemblies) system is an innovative CRISPR-based imaging technique that leverages dCas9-SunTag and FRB-mCherry-HP1α, with scFv-FKBP acting as a bridge. This powerful system enables simultaneous visualization and manipulation of genomic loci. The dCas9-SunTag fusion protein allows for precise targeting of specific genomic sites, and the FRB-mCherry-HP1α fusion protein facilitates the condensation of chromatin at the targeted loci.

Abalone peptide increases stress resilience and cost-free longevity via SKN-1-governed transcriptional metabolic reprogramming in C. elegans.

A major goal of healthy aging is to prevent declining resilience and increasing frailty, which are associated with many chronic diseases and deterioration of stress response. Here, we propose a loss-or-gain survival model, represented by the ratio of cumulative stress span to life span, to quantify stress resilience at organismal level. As a proof of concept, this is demonstrated by reduced survival resilience in Caenorhabditis elegans exposed to exogenous oxidative stress induced by paraquat or with endogenous proteotoxic stress caused by polyglutamine or amyloid-β aggregation.

Integrative profiling of extrachromosomal circular DNA in placenta and maternal plasma provides insights into the biology of fetal growth restriction and reveals potential biomarkers.

Fetal growth restriction (FGR) is a placenta-mediated pregnancy complication that predisposes fetuses to perinatal complications. Maternal plasma cell-free DNA harbors DNA originating from placental trophoblasts, which is promising for the prenatal diagnosis and prediction of pregnancy complications. Extrachromosomal circular DNA (eccDNA) is emerging as an ideal biomarker and target for several diseases.

Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells.

Genome architecture and organization play critical roles in cell life. However, it remains largely unknown how genomic loci are dynamically coordinated to regulate gene expression and determine cell fate at the single cell level. We have developed an inducible system which allows Simultaneous Imaging and Manipulation of genomic loci by Biomolecular Assemblies (SIMBA) in living cells.

A wheat spike detection method based on Transformer.

Wheat spike detection has important research significance for production estimation and crop field management. With the development of deep learning-based algorithms, researchers tend to solve the detection task by convolutional neural networks (CNNs). However, traditional CNNs equip with the inductive bias of locality and scale-invariance, which makes it hard to extract global and long-range dependency.

Study on the Effect of Self-Made Lifei Dingchuan Decoction Combined with Western Medicine on Cough Variant Asthma.

Aims: To observe the clinical efficacy of self-made Lifei Dingchuan decoction combined with western medicine in the treatment of cough variant asthma (phlegm-heat accumulation in the lung syndrome).

Materials And Methods: The clinical data of 90 patients with cough variant asthma who were hospitalized in the Department of Respiratory Medicine of our hospital from January 2020 to April 2022 were selected as the research objects, and they were equally divided into the observation group and the reference group according to different treatment methods, 45 cases in each group. The group was treated with traditional montelukast sodium chewable tablet and salmeterol fluticasone mixed powder inhalation, and the observation group was treated with self-made Lifei Dingchuan decoction on the basis of the control group, saturation, pH, partial pressure of oxygen in arterial blood, partial pressure of carbon dioxide, length of stay, and hospitalization costs.

TD-Det: A Tiny Size Dense Aphid Detection Network under In-Field Environment.

It is well recognized that aphid infestation severely reduces crop yield and further leads to significant economic loss. Therefore, accurately and efficiently detecting aphids is of vital importance in pest management. However, most existing detection methods suffer from unsatisfactory performance without fully considering the aphid characteristics, including tiny size, dense distribution, and multi-viewpoint data quality.

Fast location and segmentation of high-throughput damaged soybean seeds with invertible neural networks.

Background: Fast identification of damaged soybean seeds has undeniable importance in seed sorting and food quality. Mechanical vibration is generally used in soybean seed sorting, but this can seriously damage soybean seeds. The convolutional neural network (CNN) is considered an effective method for location and segmentation tasks.

Integrated Analysis Reveals the Characteristics and Effects of SARS-CoV-2 Maternal-Fetal Transmission.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has caused a pandemic of coronavirus disease 2019 (COVID-19) and is threatening global health. SARS-CoV-2 spreads by air with a transmission rate of up to 15%, but the probability of its maternal-fetal transmission through the placenta is reported to be low at around 3.28%.

Engineering CAR T cells for enhanced efficacy and safety.

Despite its success in treating hematologic malignancies, chimeric antigen receptor (CAR) T cell therapy faces two major challenges which hinder its broader applications: the limited effectiveness against solid tumors and the nonspecific toxicities. To address these concerns, researchers have used synthetic biology approaches to develop optimization strategies. In this review, we discuss recent improvements on the CAR and other non-CAR molecules aimed to enhance CAR T cell efficacy and safety.

SARS-CoV-2 causes a significant stress response mediated by small RNAs in the blood of COVID-19 patients.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a serious impact on the world. In this study, small RNAs from the blood of COVID-19 patients with moderate or severe symptoms were extracted for high-throughput sequencing and analysis. Interestingly, the levels of a special group of tRNA-derived small RNAs (tsRNAs) were found to be dramatically upregulated after SARS-CoV-2 infection, particularly in coronavirus disease 2019 (COVID-19) patients with severe symptoms.

Control of the activity of CAR-T cells within tumours via focused ultrasound.

Focused ultrasound can deliver energy safely and non-invasively into tissues at depths of centimetres. Here we show that the genetics and cellular functions of chimeric antigen receptor T cells (CAR-T cells) within tumours can be reversibly controlled by the heat generated by short pulses of focused ultrasound via a CAR cassette under the control of a promoter for the heat-shock protein. In mice with subcutaneous tumours, locally injected T cells with the inducible CAR and activated via focused ultrasound guided by magnetic resonance imaging mitigated on-target off-tumour activity and enhanced the suppression of tumour growth, compared with the performance of non-inducible CAR-T cells.

Mass transfer from the rotor to the stator for improving the speed of the piezoelectric motor based on centrifugal force.

To improve the speed of a piezoelectric motor based on centrifugal force, a method is proposed on the basis of mass transfer from the rotor to the stator. Multi-degree-of-freedom vibration models are established before and after mass transfer. A mass of 150 g is transferred from the six-hole rotor to the stator.

Design and construction of chimeric linker library with controllable flexibilities for precision protein engineering.

Linkers play essential roles in the engineering of fusion proteins, and have been extensively demonstrated to affect protein properties such as expression level, solubility, and biological functions. For linker design and optimization, one of the key factors is the flexibility or rigidity of linkers, which describes the tendency of a linker to maintain a stable conformation when expressed, and can directly contribute to the physical distance between domains of a fusion protein. In this chapter, we discuss the design and engineering of linkers in fusion proteins, and describe a library-based method for optimization of linker flexibility.

ColorCells: a database of expression, classification and functions of lncRNAs in single cells.

Although long noncoding RNAs (lncRNAs) have significant tissue specificity, their expression and variability in single cells remain unclear. Here, we developed ColorCells (http://rna.sysu.

Optogenetic Control for Investigating Subcellular Localization of Fyn Kinase Activity in Single Live Cells.

Previous studies with various Src family kinase biosensors showed that the nuclear kinase activities are much suppressed compared to those in the cytosol, suggesting that these kinases are regulated differently in the nucleus and in the cytosol. In this study, using Fyn as an example, we first engineered a Fyn biosensor with a light-inducible nuclear localization signal to demonstrate that the Fyn kinase activity is significantly lower in the nucleus than in the cytosol. To understand how different equilibrium states between Fyn and the corresponding phosphatases are maintained in the cytosol and nucleus, we further engineered a Fyn kinase domain with light-inducible nuclear localization signal.

Engineering light-controllable CAR T cells for cancer immunotherapy.

T cells engineered to express chimeric antigen receptors (CARs) can recognize and engage with target cancer cells with redirected specificity for cancer immunotherapy. However, there is a lack of ideal CARs for solid tumor antigens, which may lead to severe adverse effects. Here, we developed a light-inducible nuclear translocation and dimerization (LINTAD) system for gene regulation to control CAR T activation.

Integrated Ultrafine Co Se in Carbon Nanofibers: An Efficient and Robust Bifunctional Catalyst for Oxygen Electrocatalysis.

Transition-metal selenides are emerging as alternative bifunctional catalysts for oxygen evolution reaction (OER) and oxygen reduction reaction (ORR); however, their activity and stability are still less than desirable. Herein, ultrafine Co Se nanoparticles encapsulated into carbon nanofibers (CNFs), Co Se@CNFs, is reported as an integrated bifunctional catalyst for OER and ORR. This catalyst exhibits a low OER potential of 1.

An AND-Gated Drug and Photoactivatable Cre- System for Spatiotemporal Control in Cell-Based Therapeutics.

While engineered chimeric antigen receptor (CAR) T cells have shown promise in detecting and eradicating cancer cells within patients, it remains difficult to identify a set of truly cancer-specific CAR-targeting cell surface antigens to prevent potentially fatal on-target off-tumor toxicity against other healthy tissues within the body. To help address this issue, we present a novel tamoxifen-gated photoactivatable split-Cre recombinase optogenetic system, called TamPA-Cre, that features high spatiotemporal control to limit CAR T cell activity to the tumor site. We created and optimized a novel genetic AND gate switch by integrating the features of tamoxifen-dependent nuclear localization and blue-light-inducible heterodimerization of Magnet protein domains (nMag, pMag) into split Cre recombinase.