Ultrasensitive Method Enables Liquid Biopsy for the Precise Detection of Circulating MicroRNAs.

Due to invasive and serial examinations of bioactive molecules, liquid biopsy (LB) has emerged as a rapid and reliable solution for early disease detection and monitoring. Developing portable devices with high specificity and sensitivity for LB is highly valuable. To realize a generalized approach to increase the sensitivity of LB, we developed an ultrasensitive diagnostic biochip based on the amplification of miRNA by recombinase polymerase amplification and the significant enhancement of fluorescence signals by photonic crystal (PC) materials. The PCs-RPA biochip has a detection limit as low as 0.24 aM, a wide linear range of 8 orders of magnitude, and excellent specificity. Such advantages realize the accurate detection of circulating miRNAs with very low content in clinical serum samples for the precise diagnosis of nonsmall cell lung cancer.

Utilizing Epigenetic Modification as a Reactive Handle To Regulate RNA Function and CRISPR-Based Gene Regulation.

The current methods to control RNA functions in living conditions are limited. The new RNA-controlling strategy presented in this study involves utilizing 5-formylcytidine (f5C)-directed base manipulation. This study shows that malononitrile and pyridine boranes can effectively manipulate the folding, small molecule binding, and enzyme recognition of f5C-bearing RNAs. We further demonstrate the efficiency of f5C-directed reactions in controlling two different clustered regularly interspaced short palindromic repeat (CRISPR) systems. Although further studies are needed to optimize the efficiency of these reactions in vivo, this small molecule-based approach presents exciting new opportunities for regulating CRISPR-based gene expression and other applications.

Antibody-Free Fluorine-Assisted Metabolic Sequencing of RNA N4-Acetylcytidine.

N4-Acetylcytidine (ac4C) has been found to affect a variety of cellular and biological processes. For a mechanistic understanding of the roles of ac4C in biology and disease, we present an antibody-free, fluorine-assisted metabolic sequencing method to detect RNA ac4C, called "FAM-seq". We successfully applied FAM-seq to profile ac4C landscapes in human 293T, HeLa, and MDA cell lines in parallel with the reported acRIP-seq method. By comparison with the classic ac4C antibody sequencing method, we found that FAM-seq is a convenient and reliable method for transcriptome-wide mapping of ac4C. Because this method holds promise for detecting nascent RNA ac4C modifications, we further investigated the role of ac4C in regulating chemotherapy drug resistance in chronic myeloid leukemia. The results indicated that drug development or combination therapy could be enhanced by appreciating the key role of ac4C modification in cancer therapy.

4-Thiouridine-Enhanced Peroxidase-Generated Biotinylation of RNA.

Peroxidase-generated proximity labeling is in widespread use to study subcellular proteomes and the protein interaction networks in living cells, but the development of subcellular RNA labeling is limited. APEX-seq has emerged as a new method to study subcellular RNA in living cells, but the labeling of RNA still has room to improve. In this work, we describe 4-thiouridine (s4 U)-enhanced peroxidase-generated biotinylation of RNA with high efficiency. The incorporation of s4 U could introduce additional sites for RNA labeling, enhanced biotinylation was observed on monomer, model oligo RNA and total RNA. Through the s4 U metabolic approach, the in vivo RNA biotinylation efficiency by peroxidase catalysis was also dramatically increased, which will benefit RNA isolation and study for the spatial transcriptome.

Specific stabilization of DNA G-quadruplex structures with a chemically modified complementary probe.

The DNA G-quadruplex is an important higher-order structure formed from guanine-rich DNA sequences. There are many molecules which can stabilize this structure. However, the selectivity of these ligands to different G-quadruplexes was not satisfactory. Herein, we designed and synthesized a chemically modified G-quadruplex probe, Razo-DNA, for the unique stabilization of the G-quadruplex. Razo-DNA consists of two fragments: The first is an organic molecular moiety which can stabilize G-quadruplex structures, and the second is a DNA molecule that is complementary with a sequence adjacent to the guanine-rich sequence of targeted DNA. Further studies showed that Razo-DNA could precisely stabilize the targeted DNA G-quadruplex structures in vitro.

Simultaneous and Sensitive Detection of Multisite 5-Methylcytosine Including Non-CpG Sites at Single-5mC-Resolution.

The methylation status of multiplexed methylcytosine sites can be simultaneously monitored by ligation-depended PCR assay. The ability of quantitative detection of multiplexed sites in one PCR reaction makes it a good choice for detecting methylation at both CpG and non-CpG sites for research and diagnosis of disease compared with others. The assay can determine as low as 20 aM methylated DNA and has been successfully applied to the genomic DNA sample derived from cancer cell lines.

Mapping medical image-text to a joint space via masked modeling.

Recently, masked autoencoders have demonstrated their feasibility in extracting effective image and text features (e.g., BERT for natural language processing (NLP) and MAE in computer vision (CV)). This study investigates the potential of applying these techniques to vision-and-language representation learning in the medical domain. To this end, we introduce a self-supervised learning paradigm, multi-modal masked autoencoders (M3AE). It learns to map medical images and texts to a joint space by reconstructing pixels and tokens from randomly masked images and texts. Specifically, we design this approach from three aspects: First, taking into account the varying information densities of vision and language, we employ distinct masking ratios for input images and text, with a notably higher masking ratio for images; Second, we utilize visual and textual features from different layers for reconstruction to address varying levels of abstraction in vision and language; Third, we develop different designs for vision and language decoders. We establish a medical vision-and-language benchmark to conduct an extensive evaluation. Our experimental results exhibit the effectiveness of the proposed method, achieving state-of-the-art results on all downstream tasks. Further analyses validate the effectiveness of the various components and discuss the limitations of the proposed approach. The source code is available at https://github.com/zhjohnchan/M3AE.

Induced Mesenchymal Stem Cells-Small Extracellular Vesicles Alleviate Post-stroke Cognitive Impairment by Rejuvenating Senescence of Neural Stem Cells.

Ischemic stroke is typified by hypoxia and a cascade of pathophysiological events, including metabolic dysfunction, ionic dysregulation, excitotoxicity, inflammatory infiltration, and oxidative stress. These ultimately result in neuronal apoptosis or necrosis with constrained neuroregenerative capabilities. In this study, neural stem cells (NSCs) under conditions of oxygen-glucose deprivation (OGD) in vitro and following middle cerebral artery occlusion (MCAO) in vivo were explored. Transcriptome sequencing revealed a decline in NSC differentiation and neurogenesis after OGD exposure, which was related to cellular senescence. This observation was corroborated by increased senescence markers in the MCAO mouse model, reduction in NSC numbers, and decline in neurogenesis. Importantly, iMSC-sEVs (induced mesenchymal stem cells-small extracellular vesicles) have the therapeutic potential to alleviate NSC senescence and rejuvenate their regenerative capacities both in vitro and in vivo. Moreover, iMSC-sEVs contribute to the recovery of cognitive function and synapse loss caused by MCAO.

Macrophage WNK1 senses intracellular hypo-chlorine to regulate vulnerability to sepsis attack during hypochloremia.

Sepsis is one of the leading causes of death in critical patients worldwide and its occurrence is related to the excessive activation of macrophages. Chloride loss worsens the prognosis of patients with sepsis but the underlying mechanism is currently unclear. In this study, we founded that macrophages deficient in intracellular Cl- secrete more inflammatory cytokines such as IL-1ß, IL-6 and TNF-α compared with control group. The intracellular chloride level decreased in WNK1 deficiency or activity inhibited macrophages with more severe inflammatory response after LPS treatment. Remimazolam, as classic GABAa receptor agonist, alleviates excessive inflammation cascade by promoting macrophage chloride influx during sepsis progression. Collectively, this study proves that macrophage WNK1 acts as a negative regulator of inflammatory response by sensing chloride to maintain intracellular chloride balance during sepsis coupled with hypochloremia.

Neuronal HIPK2-HDAC3 axis regulates mitochondrial fragmentation to participate in stroke injury and post-stroke anxiety like behavior.

Post-stroke anxiety (PSA) seriously affects the prognosis of patients, which is an urgent clinical problem to be addressed. However, the pathological mechanism of PSA is largely unclear. Here, we found that neuronal HIPK2 expression was upregulated in the ischemic lesion after stroke. The upregulation of HIPK2 promotes Drp1 oligomerization through the HDAC3-dependent pathway, leading to excessive mitochondrial damage. This subsequently triggers the release of cellular cytokines such as IL-18 from neurons under ischemic stress. Microglia are capable of responding to IL-18, which promotes their activation and enhances their phagocytosis, ultimately resulting in the loss of synapses and neurons, thereby exacerbating the pathological progression of PSA. HIPK2 knockdown or inhibition suppresses excessive pruning of neuronal synapses by activated microglia in the contralateral vCA1 region to compromise inactivated anxiolytic pBLA-vCA1Calb1+ circuit, relieving anxiety-like behavior after stroke. Furthermore, we discovered that early remimazolam administration can remodel HIPK2-HDAC3 axis, ameliorating the progression of PSA. In conclusion, our study revealed that the neuronal HIPK2-HDAC3 axis in the ischemic focus regulates mitochondrial fragmentation to balance inflammation stress reservoir to participate in anxiety susceptibility after stroke.

Adsorption and recovery of phosphate using sodium carbonate as co-precipitant synthesized La&Zr dual-metal modified material: Adsorption mechanism and practical application.

Adsorption methods offer efficient recovery of phosphorus from water bodies. Modification adsorption materials combining lanthanum (La) and zirconium (Zr) dual-metal immobilized via co-precipitation method have been widely applied in the adsorption and recovery of phosphate. Meanwhile, sodium carbonate (Na2CO3) is gradually replacing sodium hydroxide (NaOH) as the mainstream co-precipitant for immobilizing metals into supporting matrices due to its excellent performance and environmental friendliness. However, the adsorption mechanisms of materials synthesized with different co-precipitants and the synergistic effects between dual-metal components are not well understood, which is not conducive to the further optimization of dual-metal adsorption materials. In this study, anion exchange resin was utilized as the supporting matrices, and La&Zr dual-metal-modified materials, La&Zr-CO32- and La&Zr-OH-, were prepared using Na2CO3 and NaOH as co-precipitants, respectively. The results indicate that La&Zr-CO32- exhibits superior performance in phosphate adsorption and recovery, with adsorption capacity and recovery efficiency reaching 36.28 mg/g and 82.59%, respectively. Additionally, this material demonstrates strong stability in reuse, phosphate selectivity, and a wide pH applicability range. La&Zr-CO32- achieves phosphate adsorption through surface electrostatic affinity, ligand exchange, and intraspherical complexation, whereas La&Zr-OH- primarily relies on electrostatic adsorption on the surface and interior of the material. Synergistic effects between La and Zr result in enhanced adsorption performance of the dual-metal material compared to individual metals. Specifically, phosphate adsorption is predominantly governed by La, while the presence of Zr further enhances ligand exchange between lattice oxygen and metals. Simultaneously, Zr doping enhances the phosphate recovery capacity and reusability of the materials. Continuous flow adsorption results from actual water bodies demonstrate that La&Zr-CO32- is more suitable for the removal and recovery of phosphate in water treatment engineering. This study provides a theoretical basis and technical support for the adsorption and recovery of phosphate using dual-metal-modified materials.

Targeting non-B-form DNA in living cells.

Under certain conditions, repetitive DNA motifs have the potential to adopt non-B-form DNA structures, such as hairpins, triplexes, Z-DNA, quadruplexes, and i-motifs. Some non-B-form DNAs have been proposed to cause mutations and, consequently, participate in several biologically important processes, including regulation, evolution, and human disease. Advancement in the knowledge of specific interactions between molecules and non-B-form DNAs at the molecular level in living cells is important for understanding their biological functions. In this review, we describe the latest studies on molecules that target non-B-form DNAs in vivo, with a focus on Z-DNA, G-quadruplexes, triplexes, i-motifs, and hairpins.

Comprehensive Visual Question Answering on Point Clouds through Compositional Scene Manipulation.

Visual Question Answering on 3D Point Cloud (VQA-3D) is an emerging yet challenging field that aims at answering various types of textual questions given an entire point cloud scene. To tackle this problem, we propose the CLEVR3D, a large-scale VQA-3D dataset consisting of 171K questions from 8,771 3D scenes. Specifically, we develop a question engine leveraging 3D scene graph structures to generate diverse reasoning questions, covering the questions of objects' attributes (i.e., size, color, and material) and their spatial relationships. Through such a manner, we initially generated 44K questions from 1,333 real-world scenes. Moreover, a more challenging setup is proposed to remove the confounding bias and adjust the context from a common-sense layout. Such a setup requires the network to achieve comprehensive visual understanding when the 3D scene is different from the general co-occurrence context (e.g., chairs always exist with tables). To this end, we further introduce the compositional scene manipulation strategy and generate 127K questions from 7,438 augmented 3D scenes, which can improve VQA-3D models for real-world comprehension. Built upon the proposed dataset, we baseline several VQA-3D models, where experimental results verify that the CLEVR3D can significantly boost other 3D scene understanding tasks. Our code and dataset are publicly available at https://github.com/yanx27/CLEVR3D.

Short-Term Monitoring of Graft Regeneration in Partial Liver Transplantation Recipients.

BACKGROUND Liver regeneration after partial liver transplantation, including living donor liver transplantation and split liver transplantation, is important for successful transplantation. MATERIAL AND METHODS We retrospectively analyzed 68 patients who underwent partial liver transplantation and calculated their regeneration index (RI)-based difference in postoperative and preoperative liver volume. We collected clinical data of donors and recipients and analyzed the correlation between clinical characteristics and RI. According to the above results, the generalized estimating equation (GEE) model included white blood cell count (WBC), neutrophils, lymphocytes, platelets, prothrombin time (PT), and activated partial thromboplastin time (APTT) on Days 1, 3, and 7 after LT and was used to predict the RI. RESULTS The mean RI was 40%, which was used as the cutoff value to divide all patients to the high-RI group and the low-RI group. The percentage of Child-Pugh C patients was 44% in the high-RI group, which was significantly more than that (21%) in the low-RI group (P=0.038). Among the postoperative monitoring parameters, neutrophil (P=0.044) and platelet (P=0.036) levels declined in the high-RI group on Day 3, while APTT was higher on Day 1 compared to the low-RI group. The predictive model based on GEE analysis achieved a good effect, with the area under the receiver operating characteristic curve on Day 1 (0.681; 95% CI, 0.556-0.807) and Day 3 (0.705; 95% CI, 0.578-0.832) showing significant differences (P=0.010 and 0.004, respectively). CONCLUSIONS The combination of decreased counts of WBC, neutrophils, lymphocytes, and platelets, as well as elevated PT and APTT on Day 3 after LT showed a good capability to predict a higher rate of liver regeneration after partial liver transplantation.

Revealing the Grain-Boundary-Cracking Induced Capacity Decay of a High-Voltage LiCoO2 at 4.6 V.

During a practical battery manufacture process, the LiCoO2 (LCO) electrodes are usually rolled with high pressure to achieve better performance, including reducing electrode polarization, increasing compact density, enhancing mechanical toughness, etc. In this work, a high-voltage LCO (HV-LCO) is achieved via modulating a commercialized LCO with an Al/F enriched and spinel reinforced surface structure. We reveal that the rolling can more or less introduce risk of grain-boundary-cracking (GBC) inside the HV-LCO and accelerate the capacity decay when cycled at 3-4.6 V vs Li/Li+. In particular, the concept of interface structure is proposed to explain the reason for the deteriorated cycle stability. As the GBC is generated, the interface structure of HV-LCO alters from a surface spinel phase to a hybrid of surface spinel plus boundary layer phases, leading to the exposure of some the nonprotective layer phase against the electrolyte. This alternation causes serious bulk structure damage upon cycles, including expanding GBC among the primary crystals, forming intragranular cracks and inactive spinel phases inside the bulk regions, etc., eventually leading to the deteriorated cycle stability. Above all, we realize that it is far from enough to achieve a eligible high-voltage LCO via only applying surface modification. This work provides a new insight for developing more advanced LCO cathodes.

Chrysanthemum sporopollenin: A novel vaccine delivery system for nasal mucosal immunity.

Objective: Mucosal immunization was an effective defender against pathogens. Nasal vaccines could activate both systemic and mucosal immunity to trigger protective immune responses. However, due to the weak immunogenicity of nasal vaccines and the lack of appropriate antigen carriers, very few nasal vaccines have been clinically approved for human use, which was a major barrier to the development of nasal vaccines. Plant-derived adjuvants are promising candidates for vaccine delivery systems due to their relatively safe immunogenic properties. In particular, the distinctive structure of pollen was beneficial to the stability and retention of antigen in the nasal mucosa. Methods: Herein, a novel wild-type chrysanthemum sporopollenin vaccine delivery system loaded with a w/o/w emulsion containing squalane and protein antigen was fabricated. The unique internal cavities and the rigid external walls within the sporopollenin skeleton construction could preserve and stabilize the inner proteins. The external morphological characteristics were suitable for nasal mucosal administration with high adhesion and retention. Results: Secretory IgA antibodies in the nasal mucosa can be induced by the w/o/w emulsion with the chrysanthemum sporopollenin vaccine delivery system. Moreover, the nasal adjuvants produce a stronger humoral response (IgA and IgG) compared to squalene emulsion adjuvant. Mucosal adjuvant benefited primarily from prolongation of antigens in the nasal cavity, improvement of antigen penetration in the submucosa and promotion of CD8+ T cells in spleen. Disccusion: Based on effective delivering both the adjuvant and the antigen, the increase of protein antigen stability and the realization of mucosal retention, the chrysanthemum sporopollenin vaccine delivery system has the potential to be a promising adjuvant platform. This work provide a novel idea for the fabrication of protein-mucosal delivery vaccine.

Fluorescent DNA labeling by N-mustard analogues of S-adenosyl-L-methionine.

Azide and alkyne-functionalized N-mustard analogues of S-adenosyl-L-methionine have been synthesized and were demonstrated to undergo efficient methyltransferase-dependent DNA alkylation by M.TaqI and M.HhaI. Subsequent labeling of the DNA with a fluorophore was carried out using copper-catalyzed azide-alkyne cycloaddition chemistry and was visualized by fluorescence scanning. This work demonstrates the utility of functionalized N-mustard analogues as biochemical tools to study biological methylation and offers a facile way to site-selectively label substrates of DNA methyltransferases.

In situ gelation strategy based on ferrocene-hyaluronic acid organic copolymer biomaterial for exudate management and multi-modal wound healing.

Exudate management remains a major concern in slow or non-healing wound management. Therefore, there is a need to devise a massive exudate-absorbing, exudate-locking, and stable extracellular matrix structure-maintaining functional wound dressing. Inspired by metal-organic frameworks, we chemically introduced sandwich ferrocene (Fc) into hyaluronic acid (HA) to fabricate an innovative metal Fc-HA organic copolymer (FHoC) as the skeleton material for in situ gelation, which was then gently compressed into a pre-hydrogel patch (FHoCP). Fc promoted the rearrangement of polymer chains to form additional microcrystalline and hydrophobic regions, which improved hydrogel transition and the exudate-locking ability. Thus, the simple composition FHoCP(5) absorbed 150 times its weight of water and maintained a firm three-dimensional network, which contributed to reducing inflammation and acted as a physical barrier against hemostasis and anti-bacterial invasion. Meanwhile, multi-modal processes, including fibroblast migration, angiogenesis, and antibacterial effects, were integrated into the gelled FHoCP(5) guided by Fe to promote wound healing. This study suggested that FHoC biomaterial could accelerate the closure of chronic wounds. We believe that this unique FHoCP(5)-based in situ gelation strategy could provide a solid drug-loaded scaffold for cell or adjunctive drug therapies, which holds great potential for the development of multifunctional biomaterials. STATEMENT OF SIGNIFICANCE: Hydrogels that absorb excessive exudates while maintaining stable ECM-like network as well as exert multimodal wound healing activities are ideal dressings for accelerating chronic wound contraction. Herein, we reported an innovative metal ferrocene-hyaluronic acid organic copolymer patch (FHoCP) and FHoCP-mediated in situ gelation strategy. Ferrocene (Fc) induced in situ gelation by promoting polymer chain rearrangement, acting as a physical barrier for hemostasis and anti-bacterial invasion, and absorbing massive exudates, resulting in reducing delayed inflammation. As the structural core, rigid Fc enhanced the stability of the hydrogel backbone, and hydrophobic Fc improved fibroblast migration. In addition, Fe2+ chemically inhibited bacteria and increased angiogenesis. These results indicated the potential of FHoCP-based hydrogel for application in clinical skin reconstruction.

From highly enantioselective catalytic reaction of 1,3-diynes with aldehydes to facile asymmetric synthesis of polycyclic compounds.

(S)-1,1'-Binaphth-2-ol (BINOL) in combination with ZnEt(2), Ti(O(i)Pr)(4), and biscyclohexylamine was found to catalyze the highly enantioselective (83-95% ee) addition of various 1,3-diynes to aldehydes of diverse structures. This method provides a convenient pathway to generate a number of optically active dienediynes as the acyclic precursors to polycyclic compounds. The chiral dienediynes undergo highly chemoselective Pauson-Khand (PK) cycloaddition in benzaldehyde by using [Rh(cod)Cl](2) as the catalyst in the presence of rac-BINAP. High diastereoselectivity (up to >20:1) has also been achieved with the chiral dienediyne substrates containing a bulky substituent adjacent to the chiral center. In the presence of the Grubbs II catalyst, ring-closing enyne metathesis of the PK cycloaddition products led to the formation of the desired 5,5,7- and 5,5,8-fused tricyclic compounds. Further highly diastereoselective Diels-Alder reaction of a 5,5,7-tricyclic compound with maleic anhydride produced a 5,5,7,6-polycyclic product. The asymmetric synthesis of polycyclic compounds from optically active dienediynes has established a novel and efficient synthetic route to the structural framework of many biologically significant molecules.

Module-scale analysis of low-salt-rejection reverse osmosis: Design guidelines and system performance.

Low-salt-rejection reverse osmosis (LSRRO) is a novel reverse osmosis (RO)-based technology that can highly concentrate brines using moderate operating pressures. In this study, we investigate the performance of LSRRO membrane modules and systems using module-scale analysis. Specifically, we correlate the observed salt rejection of an LSRRO module with the water and salt permeabilities of the RO membrane. We then elaborate the impact of membrane properties and operating conditions on the performance of a 2-stage LSRRO, providing design guidelines for LSRRO systems. We further compare the performance of 2-stage and 3-stage LSRRO systems, showing that an LSRRO system with more stages is not always favored due to a larger energy consumption. The performance of a 3-stage LSRRO in treating different feed solutions for minimal/zero liquid discharge (MLD/ZLD) applications is then evaluated. Based on our results, when treating feed waters with a relatively low salinity (e.g., 0.1 M or ∼5,800 mg L-1 NaCl), the 3-stage LSRRO can achieve a concentrated brine that can be directly sent to the thermal brine crystallizers (i.e., brine concentration > 4 M or ∼240,000 mg L-1 NaCl), and the corresponding specific energy consumption (SEC) is only ∼3 kWh m-3. When treating feed waters with a relatively high salinity (e.g., 0.6 M or ∼35,000 mg L-1 NaCl), the brine from the 3-stage LSRRO can be ∼80 % more concentrated compared to that from conventional RO, while the corresponding SEC does not exceed 6 kWh m-3. Our results demonstrate that LSRRO can substantially advance minimal/zero liquid discharge (MLD/ZLD) applications because it can significantly minimize the use of thermal brine concentrators. We conclude with a discussion on the practicability of LSRRO and highlight future research needs.