DPNN-ac4C: A Dual-Path Neural Network with self-attention mechanism for identification of N4­acetylcytidine (ac4C) in mRNA.

MOTIVATION: The modification of N4-acetylcytidine (ac4C) in RNA is a conserved epigenetic mark that plays a crucial role in post-transcriptional regulation, mRNA stability, and translation efficiency. Traditional methods for detecting ac4C modifications are laborious and costly, necessitating the development of efficient computational approaches for accurate identification of ac4C sites in mRNA. RESULTS: We present DPNN-ac4C, a dual-path neural network with a self-attention mechanism for the identification of ac4C sites in mRNA. Our model integrates embedding modules, bidirectional GRU networks, convolutional neural networks, and self-attention to capture both local and global features of RNA sequences. Extensive evaluations demonstrate that DPNN-ac4C outperforms existing models, achieving an AUROC of 91.03%, accuracy of 82.78%, MCC of 65.78%, and specificity of 84.78% on an independent test set. Moreover, DPNN-ac4C exhibits robustness under the Fast Gradient Method (FGM) attack, maintaining a high level of accuracy in practical applications. AVAILABILITY AND IMPLEMENTATION: The model code and dataset are publicly available on GitHub (https://github.com/shock1ng/DPNN-ac4C).

Selective targeting of parallel G-quadruplex structure using L-RNA aptamer.

G-quadruplexes (G4) are special nucleic acid structures with diverse conformational polymorphisms. Selective targeting of G-quadruplex conformations and regulating their biological functions provide promising therapeutic intervention. Despite the large repertoire of G4-binding tools, only a limited number of them can specifically target a particular G4 conformation. Here, we introduce a novel method, G4-SELEX-Seq and report the development of the first L-RNA aptamer, L-Apt12-6, with high binding selectivity to parallel G4 over other nucleic acid structures. Using parallel dG4 c-kit 1 as an example, we demonstrate the strong binding affinity between L-Apt12-6 and c-kit 1 dG4 in vitro and in cells, and notably report the applications of L-Apt12-6 in controlling DNA replication and gene expression. Our results suggest that L-Apt12-6 is a valuable tool for targeting parallel G-quadruplex conformation and regulating G4-mediated biological processes. Furthermore, G4-SELEX-Seq can be used as a general platform for G4-targeting L-RNA aptamers selection and should be applicable to other nucleic acid structures.

Simultaneous improvement of the sensitivity and resolution of CPT magnetometers based on phase delay and differential method.

We report a method to enhance the sensitivity of coherent population trapping (CPT) magnetometers using a combination of left-handed and right-handed circularly polarized light phase-delay detection and a differential detection scheme. The approach can achieve a four third-fold enhancement of the CPT dispersion signal slope and a three-fold reduction in noises. The proposed method experimentally exhibits a four third-fold magnetic field resolution enhancement in CPT open-loop measurements, and the differential method could achieve a sensitivity of 1 p T/H z at 10 Hz and a sensitivity of 0.4 p T/H z at 50-100 Hz in the CPT closed-loop measurement, which is a four-fold sensitivity enhancement compared to the single-transmitted CPT magnetometer.

Visualization of ligand-induced c-MYC duplex-quadruplex transition and direct exploration of the altered c-MYC DNA-protein interactions in cells.

Ligand-Induced duplex-quadruplex transition within the c-MYC promoter region is one of the most studied and advanced ideas for c-MYC regulation. Despite its importance, there is a lack of methods for monitoring such process in cells, hindering a better understanding of the essence of c-MYC G-quadruplex as a drug target. Here we developed a new fluorescent probe ISCH-MYC for specific c-MYC G-quadruplex recognition based on GTFH (G-quadruplex-Triggered Fluorogenic Hybridization) strategy. We validated that ISCH-MYC displayed distinct fluorescence enhancement upon binding to c-MYC G-quadruplex, which allowed the duplex-quadruplex transition detection of c-MYC G-rich DNA in cells. Using ISCH-MYC, we successfully characterized the induction of duplex to G-quadruplex transition in the presence of G-quadruplex stabilizing ligand PDS and further monitored and evaluated the altered interactions of relevant transcription factors Sp1 and CNBP with c-MYC G-rich DNA. Thus, our study provides a visualization strategy to explore the mechanism of G-quadruplex stabilizing ligand action on c-MYC G-rich DNA and relevant proteins, thereby empowering future drug discovery efforts targeting G-quadruplexes.

UItra-low friction and edge-pinning effect in large-lattice-mismatch van der Waals heterostructures.

Two-dimensional heterostructures are excellent platforms to realize twist-angle-independent ultra-low friction due to their weak interlayer van der Waals interactions and natural lattice mismatch. However, for finite-size interfaces, the effect of domain edges on the friction process remains unclear. Here we report the superlubricity phenomenon and the edge-pinning effect at MoS2/graphite and MoS2/hexagonal boron nitride van der Waals heterostructure interfaces. We found that the friction coefficients of these heterostructures are below 10-6. Molecular dynamics simulations corroborate the experiments, which highlights the contribution of edges and interface steps to friction forces. Our experiments and simulations provide more information on the sliding mechanism of finite low-dimensional structures, which is vital to understand the friction process of laminar solid lubricants.

Review and prospects of targeted therapies for Spleen tyrosine kinase (SYK).

Spleen tyrosine kinase (SYK) is a non-receptor tyrosine kinase. The dysregulation of SYK is closely related to the occurrence and development of allergic diseases, autoimmune diseases and cancer. SYK has become an attractive target for drug discovery due to its important biological functions. This article reviews the biological function of SYK, the relationship between SYK and disease, and therapies targeting SYK. In addition, inspired by new technologies such as proteolysis targeting chimeras (PROTACs) and phosphatase recruiting chimeras (PHORCs), we propose the development of new therapeutic approaches for targeting SYK, such as SYK PROTACs and SYK PHORCs, which may overcome deficiencies of existing methods.

Nonaqueous Electroextraction with Tunable Selectivity for Direct, Fast, and Exhaustive Enrichment of Per- and Polyfluoroalkyl Acids from Oils and Food Contact Materials.

Widespread concerns have been raised due to the ever-increasing number of novel per- and polyfluoroalkyl acids (PFAAs) and the ever-decreasing level of legacy PFAAs. Most analytical methods for PFAAs suffer from a narrow range of analyzable PFAAs, insufficient sensitivity, poor performance for oil samples, and defective quantification without internal standards or blank matrices. To solve these challenges, a highly selective method for multiple PFAAs from oils and food contact materials (FCMs) was developed based on nonaqueous electroextraction (NE). Through theoretical derivation and experimental investigation, the selectivity of NE was discovered to be tunable, and the range of extractable analytes could be tuned by adjusting the dielectric constant of the sample solution. For PFAAs, the selectivity was attributed to the pKa-based differential migration mechanism, as PFAAs exhibited less variable pKa values in different solvents compared to interference components. The method achieved nonmatrix-matched calibration without internal standards and integration of sample cleanup, selective extraction, and exhaustive enrichment into a fast and convenient operation. The method provided low limits of detection (0.002-0.03 µg·kg-1), satisfactory accuracy (88.0-107.8%), and RSDs (<11.7%). Migration experiments from 33 FCMs to oils were further investigated. PFBS (<0.05-2.34 µg·kg-1) and PFBA (<0.2-0.398 µg·kg-1) were detected from most FCMs. This was the first attempt at PFAA analysis as well as oil sample analysis using an electric field-assisted extraction technique and also the first report on PFAA migration from FCMs into edible oils.

An RNA G-Quadruplex Structure within the ADAR 5'UTR Interacts with DHX36 Helicase to Regulate Translation.

RNA G-quadruplex (rG4) structures in the 5' untranslated region (5'UTR) play crucial roles in fundamental cellular processes. ADAR is an important enzyme that binds to double-strand RNA and accounts for the conversion of Adenosine to Inosine in RNA editing. However, so far there is no report on the formation and regulatory role of rG4 on ADAR expression. Here, we identify and characterize a thermostable rG4 structure within the 5'UTR of the ADAR1 mRNA and demonstrate its formation and inhibitory role on translation in reporter gene and native gene constructs. We reveal rG4-specific helicase DHX36 interacts with this rG4 in vitro and in cells under knockdown and knockout conditions by GTFH (G-quadruplex-triggered fluorogenic hybridization) probes and modulates translation in an rG4-dependent manner. Our results further substantiate the rG4 structure-DHX36 protein interaction in cells and highlight rG4 to be a key player in controlling ADAR1 translation.

Nonaqueous Miscible Liquid-Liquid Electroextraction for Fast Exhaustive Enrichment of Ultratrace Analytes by an Exponential Transfer and Deceleration Mechanism.

Conventional electrical-field-assisted sample preparation (EFASP) methods rely on analyte transfer between immiscible phases and require at least one aqueous phase in contact with the electrode. In this paper, we report a novel nonaqueous miscible liquid-liquid electroextraction (NMLEE) technique that enables fast exhaustive enrichment of ultratrace analytes from a milliliter-level donor in a vial to a microliter-level acceptor in a tube. Miscible nonaqueous solvents are used for the donor and acceptor to overcome common EFASP problems such as high charge or mass transfer resistance, loss of analytes in the membrane phase, water electrolysis, back-extraction, bubble generation, and difficulties in the application of high voltage for fast migration. According to theoretical derivation and experimental verification results, the concentrations of analytes in the donor and their migration velocity in the acceptor both decrease exponentially with time, and the extraction recovery correlates linearly with the current variation. These mechanisms result in efficient enrichment by forming an analyte-enriched zone and allow the extraction progress and recovery to be monitored and estimated based on the current variation. NMLEE was coupled with liquid chromatography-mass spectrometry to analyze 10 amphetamine-type drugs, atropine, nortriptyline, and methadone in blood and urine samples. This method provided low limits of detection (0.003-0.1 ng·mL-1), satisfactory extraction recoveries (89.6-104.1%), and RSDs (<12.3% for intraday and <8.8% for interday), which met the requirements of the ICH guidelines. This study may contribute to the further development of EFASP methods for effective ultratrace analyses in forensic science.

Bending-loss-resistant distributed Brillouin curvature sensor based on an erbium-doped few-mode fiber.

We developed a bending-loss-resistant distributed Brillouin curvature sensor based on an erbium-doped few-mode fiber (Er-FMF) and differential pulse-width pair Brillouin optical time-domain analysis. With Er ion amplification compensating for bending-induced optical loss, radii in the ∼0.3 to 2.02 cm range could be monitored correctly. The corresponding Brillouin frequency shift variations were in the range of 91.7 to 9 MHz, which agrees well with theoretical calculations. The sensitivity of the Er-FMF device increased inversely with the bending radius, with the optimal sensitivity of 292.7 MHz/cm obtained at a radius of 0.3 cm. To the best of our knowledge, this is the smallest radius of curvature detected and highest sensitivity reported to date, indicating potential applications in distributed sharp-bend sensing, such as intelligent robotics and structural health monitoring.

Structural superlubricity in 2D van der Waals heterojunctions.

Structural superlubricity is a fundamentally important research topic in the area of tribology. Van der Waals heterojunctions of 2D materials are an ideal system for achieving structural superlubricity and possessing potentially a wide range of applications in the future due to their ultra-flat and incommensurate crystal interfaces. Here we briefly introduce the origin and mechanism of structural superlubricity and summarize the representative experimental results, in which the coefficient of friction has achieved the order of 10-5. Furthermore, we analyze the factors affecting structural superlubricity of 2D materials, including dynamic reconstruction of interfaces, edge effects, interfacial adsorption, etc, and give a perspective on how to realize the macroscopic expansion and where it can be applied in practice.

Recent advances in fluorescent probes for G-quadruplex nucleic acids.

G-quadruplexes are non-canonical nucleic acid structures formed by guanine-rich DNA or RNA sequences. In recent decades, an increasing number of evidences have suggested that G-quadruplexes are associated with a wide range of biological events. Therefore, to further study the function and distribution of G-quadruplexes, developing new probes is an essential part of G-quadruplexes research. In the review, several examples of chemical fluorescent probes for G-quadruplexes developed in recent years are highlighted. These probes are promising tools for future G-quadruplex studies, which display outstanding selectivity and capability of cell imaging.

High-Fidelity, High-Scalability Two-Qubit Gate Scheme for Superconducting Qubits.

High-quality two-qubit gate operations are crucial for scalable quantum information processing. Often, the gate fidelity is compromised when the system becomes more integrated. Therefore, a low-error-rate, easy-to-scale two-qubit gate scheme is highly desirable. Here, we experimentally demonstrate a new two-qubit gate scheme that exploits fixed-frequency qubits and a tunable coupler in a superconducting quantum circuit. The scheme requires less control lines, reduces cross talk effect, and simplifies calibration procedures, yet produces a controlled-Z gate in 30 ns with a high fidelity of 99.5%, derived from the interleaved randomized benchmarking method. Error analysis shows that gate errors are mostly coherence limited. Our demonstration paves the way for large-scale implementation of high-fidelity quantum operations.

Tracking the Dynamic Folding and Unfolding of RNA G-Quadruplexes in Live Cells.

Because of the absence of methods for tracking RNA G-quadruplex dynamics, especially the folding and unfolding of this attractive structure in live cells, understanding of the biological roles of RNA G-quadruplexes is so far limited. Herein, we report a new red-emitting fluorescent probe, QUMA-1, for the selective, continuous, and real-time visualization of RNA G-quadruplexes in live cells. The applications of QUMA-1 in several previously intractable applications, including live-cell imaging of the dynamic folding, unfolding, and movement of RNA G-quadruplexes and the visualization of the unwinding of RNA G-quadruplexes by RNA helicase have been demonstrated. Notably, our real-time results revealed the complexity of the dynamics of RNA G-quadruplexes in live cells. We anticipate that the further application of QUMA-1 in combination with appropriate biological and imaging methods to explore the dynamics of RNA G-quadruplexes will uncover more information about the biological roles of RNA G-quadruplexes.

In-situ growth of covalent organic framework on stainless steel needles as solid-phase microextraction probe coupled with electrospray ionization mass spectrometry for rapid and sensitive determination of tricyclic antidepressants in biosamples.

Tricyclic antidepressants (TCAs) including amitriptyline (AT), doxepin (DOX) and nortriptyline (NT) are the first-line drugs for the clinical treatment of depression; however, monitoring TCA concentrations in biological fluids and tissues is necessary to improve therapeutic effect and determine the cause of death in patients. It is of great significance to develop a rapid and sensitive method for real-time monitoring of TCAs in various biosamples. In this work, we fabricated a novel covalent organic framework (COF) based solid-phase microextraction (SPME) probe by an in-situ step-by-step strategy, which was obtained by sequentially modifying 1,3,5-tri (4-aminophenyl) benzene (TPB) and 2, 5-divinylbenzaldehyde (DVA) on the surface of polydopamine layer. The TPB-DVA-COF-SPME probe possessed high specific surface area (1244 m2·g - 1), regular pores (3.23 nm), good hydrophobicity and stability, resulting in efficient enrichment for TCAs. Furthermore, the combination of TPB-DVA-COF-SPME probe and ambient electrospray ionization mass spectrometry system (ESI/MS) was firstly proposed for rapid and sensitive determination of TCAs in biosamples. As a result, the developed method exhibited low limits of detection (LODs) (0.1-0.5 µg∙L - 1), high enrichment factors (39-218), and low relative standard deviations (RSDs) for one probe (1.2-3.8%) and probe-to-probe (2.0-3.7%). Benefiting from these outstanding performance, TPB-DVA-COF-SPME probe was further successfully applied to biosamples (i.e., serum, liver, kidney, and brain) with excellent reusability, indicating the promising applicability of the TPB-DVA-COF-SPME-ESI/MS as a powerful tool for drug monitoring.

Risk factors for the development of bronchiolitis obliterans in children after suffering from adenovirus pneumonia.

Introduction: Bronchiolitis obliterans (BO) is an irreversible chronic obstructive lung disease in small airways. The aim of this study was to identify the relevant risk factors for the development of BO in children after suffering from adenovirus (ADV) pneumonia. Methods: An observational cohort study that included 112 children suffering from ADV pneumonia in our institution from March 2019 to March 2020 was performed. We divided the children into a BO group and a non-BO group based on whether they did develop BO or not. Univariate analysis and multivariate logistic regression analysis were applied to identify risk factors for the development of BO. The prediction probability model was evaluated by receiver operating characteristic (ROC) curve analysis. Results: Twenty-eight children (25%) did develop BO after suffering from ADV pneumonia, while 84 children did not. Respiratory support (OR 6.772, 95% CI 2.060-22.260, P = 0.002), extended length of wheezing days (OR 1.112, 95% CI 1.040-1.189, P = 0.002) and higher lactic dehydrogenase (LDH) levels (OR 1.002, 95% CI 1.000-1.003, P = 0.012) were independently associated with the development of BO. The predictive value of this prediction probability model was validated by the ROC curve, with an area under the curve of 0.870 (95% CI 0.801-0.939, P < 0.001), a standard error of 0.035, a maximum Youden's index of 0.608, a sensitivity of 0.929, and a specificity of 0.679. Conclusions: After suffering an ADV pneumonia, children who have needed respiratory support, had a longer length of wheezing days or had higher LDH levels are more likely to develop BO.

Neutrophil autophagy and NETosis in COVID-19: perspectives.

The COVID-19 pandemic has caused substantial losses worldwide in people's lives, health, and property. Currently, COVID-19 is still prominent worldwide without any specific drug treatment. The SARS-CoV-2 pathogen is the cause of various systemic diseases, mainly acute pneumonia. Within the pathological process, neutrophils are recruited to infected sites, especially in the lungs, for the first stage of removing invading SARS-CoV-2 through a range of mechanisms. Macroautophagy/autophagy, a conserved autodegradation process in neutrophils, plays a crucial role in the neutrophil phagocytosis of pathogens. NETosis refers to neutrophil cell death, while auto-inflammatory factors and antigens release NETs. This review summarizes the latest research progress and provides an in-depth explanation of the underlying mechanisms of autophagy and NETosis in COVID-19. Furthermore, after exploring the relationship between autophagy and NETosis, we discuss potential targets and treatment options. This review keeps up with the latest research on COVID-19 from neutrophil autophagy and NETosis with a new perspective, which can guide the urgent development of antiviral drugs and provide guidance for the clinical treatment of COVID-19.Abbreviations: AKT1: AKT serine/threonine kinase 1; AMPK: AMP-activated protein kinase; AP: autophagosome; ARDS: acute respiratory distress syndrome; ATG: autophagy related; BECN1: beclin 1; cfDNA: cell-free DNA; COVID-19: coronavirus disease 2019; CQ: chloroquine; DMVs: double-membrane vesicles; ELANE/NE: elastase, neutrophil expressed; F3: coagulation factor III, tissue factor; HCQ: hydroxychloroquine; MAP1LC3/LC3: microtubule associated protein 1 light chain of 3; MPO: myeloperoxidase; MTORC1: mechanistic target of rapamycin kinase complex 1; NETs: neutrophil traps; NSP: nonstructural protein; PI3K: class I phosphoinositide 3-kinase; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; ROS: reactive oxygen species; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; SKP2: S-phase kinase associated protein 2; TCC: terminal complement complex; ULK1: unc-51 like.

Ultrasound-assisted micellar cleanup coupled with large-volume-injection enrichment for the analysis of polar drugs in blood and zebrafish samples.

A novel ultrasound-assisted micellar cleanup strategy (UAMC) coupled with large volume injection (LVI) high performance liquid chromatography (HPLC) method was proposed and successfully applied to the analysis of cefathiamidine in complex biological samples such as whole blood, plasma, serum and even zebrafish, a challenging positive real sample. Based on the micelle-biomacromolecule interaction, the phase-separation feature of surfactant micelles and ultrasound cavitation, UAMC possessed an impressive matrix cleanup capability and could rapidly reach distribution equilibrium (approximately 2 min), which enabled simultaneous sample cleanup and analyte extraction within 8 min. Due to the high cleanup efficiency of UAMC, large volume of pretreated samples could be injected for analysis without peak broadening, impurity interference and column degradation. Thus, online analyte enrichment could be automatically performed to significantly improve method sensitivity by the column-switching LVI-HPLC system, a commercial HPLC system with small modifications. The UAMC-LVI-HPLC method creatively integrated sample cleanup, analyte extraction and on-column enrichment into simple operation. In addition, the UAMC-LVI-HPLC method enabled non-matrix-matched analysis of cefathiamidine in complex biological samples. This feature was helpful to address the problems caused by conventional matrix-matched or internal standard calibration methods, such as matrix bias, increased workload, limited availability of suitable blank matrices and the use of expensive internal standards. The method had low limits of detections (e.g., 0.0051 mg/L and 0.038 µg/g), wide linear ranges (0.030-100 mg/L and 0.15-489 µg/g), good linear correlation (R2 = 0.9999), satisfactory accuracy (97.6-109.7%) and excellent intra- and interday precision (0.5-4.9%). Thus, UAMC-LVI-HPLC is expected to be a promising candidate for bioanalysis in therapeutic drug monitoring or pharmacokinetic and toxicology studies in the future.

Wafer-Scale Oxygen-Doped MoS2 Monolayer.

Monolayer MoS2 is an emergent 2D semiconductor for next-generation miniaturized and flexible electronics. Although the high-quality monolayer MoS2 is already available at wafer scale, doping of it uniformly remains an unsolved problem. Such doping is of great importance in view of not only tailoring its properties but also facilitating many potential large-scale applications. In this work, the uniform oxygen doping of 2 in wafer-scale monolayer MoS2 (MoS2- x Ox ) with tunable doping levels is realized through an in situ chemical vapor deposition process. Interestingly, ultrafast infrared spectroscopy measurements and first-principles calculations reveal a reduction of bandgaps of monolayer MoS2- x Ox with increased oxygen-doping levels. Field-effect transistors and logic devices are also fabricated based on these wafer-scale MoS2- x Ox monolayers, and excellent electronic performances are achieved, exhibiting promise of such doped MoS2 monolayers.

A simple, versatile, and automated pulse-diffusion-focusing strategy for sensitive milliliter-level-injection HILIC-MS/MS analysis of hydrophilic toxins.

The measurement of trace hydrophilic toxins in complex aqueous-rich matrices is a daunting challenge. To address this analytical bottleneck, pulse diffusion focusing (PDF), a novel sample injection technique for hydrophilic interaction chromatography-tandem mass spectrometry (HILIC-MS/MS), was developed. Theoretical and experimental investigations of the mechanism and key parameters revealed that the pulse-injection approach, assisted by solvent diffusion, efficiently solved the volume overload problem. This milliliter-level-injection HILIC-MS/MS technique was reported for the first time herein, and provided a significant enhancement in sensitivity compared to the conventional injection method, in addition to being an efficient approach to address the solvent incompatibility of off-line sample preparation and HILIC. The automated PDF-HILIC-MS/MS system was obtained by slightly modifying a commercial LC-MS/MS instrument in an easy and economical manner. The efficiency of the system was demonstrated through the detection of trace tetrodotoxin contents in plasma and urine samples. Low limits of detection (i.e., 0.65 and 2.2 ng·mL-1) were obtained using the simplified sample preparation method. The recoveries were in the range 91-113.3 % with intra-day and inter-day precisions of ≤9.6 %. Further experimental results proved the method to be versatile for various hydrophilic toxins.