ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.

Nanopore selective sequencing allows the targeted sequencing of DNA of interest using computational approaches rather than experimental methods such as targeted multiplex polymerase chain reaction or hybridization capture. Compared to sequence-alignment strategies, deep learning (DL) models for classifying target and nontarget DNA provide large speed advantages. However, the relatively low accuracy of these DL-based tools hinders their application in nanopore selective sequencing. Here, we present a DL-based tool named ReadCurrent for nanopore selective sequencing, which takes electric currents as inputs. ReadCurrent employs a modified very deep convolutional neural network (VDCNN) architecture, enabling significantly lower computational costs for training and quicker inference compared to conventional VDCNN. We evaluated the performance of ReadCurrent across 10 nanopore sequencing datasets spanning human, yeasts, bacteria, and viruses. We observed that ReadCurrent achieved a mean accuracy of 98.57% for classification, outperforming four other DL-based selective sequencing methods. In experimental validation that selectively sequenced microbial DNA from human DNA, ReadCurrent achieved an enrichment ratio of 2.85, which was higher than the 2.7 ratio achieved by MinKNOW using the sequence-alignment strategy. In summary, ReadCurrent can rapidly classify target and nontarget DNA with high accuracy, providing an alternative in the toolbox for nanopore selective sequencing. ReadCurrent is available at https://github.com/Ming-Ni-Group/ReadCurrent.

Integration of multiomics features for blood-based early detection of colorectal cancer.

BACKGROUND: Early detection of colorectal cancer (CRC) significantly enhances patient outcomes. Conventional CRC screening tools, like endoscopy and stool-based tests, have constraints due to their invasiveness or suboptimal patient adherence. Recently, liquid biopsy employing plasma cell-free DNA (cfDNA) has emerged as a potential noninvasive screening technique for various malignancies. METHODS: In this research, we harnessed the Mutation Capsule Plus (MCP) technology to profile an array of genomic characteristics from cfDNA procured from a single blood draw. This profiling encompassed DNA methylation, the 5' end motif, copy number variation (CNV), and genetic mutations. An integrated model built upon selected multiomics biomarkers was trained using a cohort of 93 CRC patients and 96 healthy controls. RESULTS: This model was subsequently validated in another cohort comprising 89 CRC patients and 95 healthy controls. Remarkably, the model achieved an area under the curve (AUC) of 0.981 (95% confidence interval (CI), 0.965-0.998) in the validation set, boasting a sensitivity of 92.1% (95% CI, 84.5%-96.8%) and a specificity of 94.7% (95% CI, 88.1%-98.3%). These numbers surpassed the performance of any single genomic feature. Importantly, the sensitivities reached 80% for stage I, 89.2% for stage II, and were 100% for stages III and IV. CONCLUSION: Our findings underscore the clinical potential of our multiomics liquid biopsy test, indicating its prospective role as a noninvasive method for early-stage CRC detection. This multiomics approach holds promise for further refinement and broader clinical application.

High Refractive Index Imaging Buffer for Dual-Color 3D SMLM Imaging of Thick Samples.

The current limitations of single-molecule localization microscopy (SMLM) in deep tissue imaging, primarily due to depth-dependent aberrations caused by refractive index (RI) mismatch, present a significant challenge in achieving high-resolution images at greater depths. To extend the imaging depth, we optimized the imaging buffer of SMLM with the RI matched to that of the objective immersion medium and systematically evaluated five different RI-matched buffers, focusing on their impact on the blinking behavior of red-absorbing dyes and the quality of reconstructed super-resolution images. Particularly, we found that clear unobstructed brain imaging cocktails-based imaging buffer could match the RI of oil and was able to clear the tissue samples. With the help of the RI-matched imaging buffers, we showed high-quality dual-color 3D SMLM images with imaging depths ranging from a few micrometers to tens of micrometers in both cultured cells and sectioned tissue samples. This advancement offers a practical and accessible method for high-resolution imaging at greater depths without the need for specialized optical equipment or expertise.

High-Coupled Magnetic-Levitation Hybrid Nanogenerator with Frequency Multiplication Effect for Wireless Water Level Alarm.

Hybrid nanogenerators (HNGs) represent a promising avenue for water energy harvesting, yet their commercial viability faces hurdles such as limited power output, poor coupling, and constrained operational lifespans. Here, a highly coupled triboelectric-electromagnetic magnetic-levitation hybrid nanogenerator (ML-HNG) is introduced that shows great potential for water energy harvesting. The ML-HNG fulfills the challenges of high power output, strong coupling, and long operational lifespans. During the contact-separation process of the triboelectric nanogenerator (TENG), the changing magnetic flux in the electromagnetic generator's coils generates a potential difference between the coils and Cu electrodes. The unique design of the ML-HNG employs a shared coil electrode configuration, which enhances the coupling without adding extra volume. This integration allows the ML-HNG to achieve multi-frequency vibrations and multiple output cycles per external longitudinal movement, a phenomenon known as the frequency multiplication effect. With an average power density of 1.69 W m-3 in water, the ML-HNG provides continuous power for a thermo-hygrometer and can quickly drive a wireless water level alarm system within a minute. This groundbreaking hybrid nanogenerator design holds significant promise for the efficient and consistent harvesting of low-frequency ocean wave energy, marking a substantial advancement in blue energy technology.

Substrate calibration method of a computer-generated hologram based on ray propagation in a three-dimensional model.

In interferometry with a computer-generated hologram (CGH), the substrate error of the CGH limits its high-precision aspheric measurement application. The propagation form of the substrate error is still ambiguous although 0th-order calibration can partly correct it. We established the ray propagation in a three-dimensional model in order to solve the ambiguity of substrate error propagation. This method shows the modulation process of the CGH substrate error on the transmitted wavefront for the first time, until now, to the best of our knowledge. The experiments show that the propagation of the substrate error can be accurately analyzed, and the CGH design efficiency also is significantly improved after applying this method.

An Accesss to 4,5,6-Trisubstituted Pyrimidines from 2H-Azirines and α-Isocyanoacetates or α-Isocyanoacetamides Enabled by 1,3-Dipolar [3 + 2] Cycloaddition/Ring-Expanding/Oxidative Aromatization Process.

The products containing pyrimidine scaffolds exhibit various important physiological and biological activities. To date, the strategies to generate 4,5,6-trisubstituted pyrimidines were not reported. Here, a copper-catalyzed reaction of 2H-azirines with α-isocyanoacetates or α-isocyanoacetamides has been developed, rapidly preparing 4,5,6-trisubstituted pyrimidines. The mechanistic results reveal that this strategy underwent a formal 1, 3-dipolar [3 + 2] cycloaddition/ring-expanding/oxidative aromatization procedure to construct the desired pyrimidines.

Cu(I)-Catalyzed Three-Component Annulation for the Synthesis of 3-Acyl Imidazo[1, 5-a]Pyridines from 2-Pyridinyl-Substituted p-Quinone Methides, Terminal Alkynes, and TsN3 Using O2 as the Oxygen Source.

Currently, most conventional methods to achieve imidazo[1,5-a]pyridines have limitations for the synthesis of 3-acyl imidazo[1,5-a]pyridines. Herein, a novel and efficient Cu(I)-catalyzed three-component annulation method for the synthesis of valuable 3-acyl imidazo[1,5-a]pyridines by the reaction of 2-pyridinyl-substituted p-QMs, terminal alkynes, and TsN3 in the presence of O2 under mild conditions have successfully been developed. The investigation indicated that molecular oxygen (O2) and TsN3, respectively, serving as oxygen and nitrogen sources, were essential for the successful completion of the reaction system.

Luminescent Metal-Organic Framework-Based Fluorescent Sensor Array for Screening and Discrimination of Bisphenols.

Extensive applications of bisphenols in industrial products have led to their release into aquatic environments, causing a great threat to human health due to their endocrine-disrupting effects, whereas existing methods are difficult to implement the rapid and high-throughput detection of multiple bisphenols. To circumvent this issue, we constructed a sensor array using two luminescent metal-organic frameworks (LMOFs) (Zr-BUT-12 and Ga-MIL-61) for the rapid discrimination of six bisphenol contaminants (BPA, BPS, BPB, BPF, BPAF, and TBBPA). Wherein, Zr-BUT-12 and Ga-MIL-61 exhibited different fluorescence-emission properties and good luminescent stability. Interestingly, bisphenols with different structures had diverse quenching effects on the fluorescence intensity of Zr-BUT-12 and Ga-MIL-61 via the adsorptive interaction, resulting in unique fluorescent fingerprints. Based on pattern recognition methods, different bisphenols were successfully identified, with the limit of detection in the range of 1.59-16.7 ng/mL for six bisphenols. More importantly, the developed sensor array could be effectively utilized for distinguishing different ratios of mixed bisphenols, which was further applied for bisphenol discrimination in real water samples. Consequently, our finding provides a promising strategy for the simultaneous recognition of multiple bisphenols, which encourages the development of a sensor array for the detection of multiple contaminants in environmental monitoring and food safety.

One-pot formal [3 + 2] annulation of 2-pyridinyl-substituted p-quinone methides and arynes for the synthesis of 3-aryl pyrido[1,2-a]indoles.

An efficient and metal-free method for the synthesis of 3-aryl pyrido[1,2-a]indoles from aryne intermediates and 2-pyridinyl-substituted p-QMs was successfully developed under ambient conditions. The reaction offered a novel and practical protocol to access some diverse functional molecules in good to excellent yields. The proposed mechanism indicated that the reaction proceeded via a formal [3 + 2] cycloaddition step.

Elastic Self-Recovering Hybrid Nanogenerator for Water Wave Energy Harvesting and Marine Environmental Monitoring.

To achieve large-scale development of triboelectric nanogenerators (TENGs) for water wave energy harvesting and powering the colossal sensors widely distributed in the ocean, facile and scalable TENGs with high output are urgently required. Here, an elastic self-recovering hybrid nanogenerator (ES-HNG) is proposed for water wave energy harvesting and marine environmental monitoring. The elastic skeletal support of the ES-HNG is manufactured using three-dimensional (3D) printing technology, which is more conducive to the large-scale integration of the ES-HNG. Moreover, the combination of a TENG and an electromagnetic generator (EMG) optimizes the utilization of device space, leading to enhanced energy harvesting efficiency. Experimental results demonstrate that the TENG achieves a peak power output of 42.68 mW, and the EMG reaches a peak power output of 4.40 mW. Furthermore, various marine environment monitoring sensors, such as a self-powered wireless meteorological monitoring system, a wireless alarm system, and a water quality monitoring pen, have been successfully powered by the sophisticated ES-HNG. This work introduces an ES-HNG for water wave energy harvesting, which demonstrates potential in marine environment monitoring and offers a new solution for the sustainable development of the marine internet of things.

A Point Cloud Graph Neural Network for Protein-Ligand Binding Site Prediction.

Predicting protein-ligand binding sites is an integral part of structural biology and drug design. A comprehensive understanding of these binding sites is essential for advancing drug innovation, elucidating mechanisms of biological function, and exploring the nature of disease. However, accurately identifying protein-ligand binding sites remains a challenging task. To address this, we propose PGpocket, a geometric deep learning-based framework to improve protein-ligand binding site prediction. Initially, the protein surface is converted into a point cloud, and then the geometric and chemical properties of each point are calculated. Subsequently, the point cloud graph is constructed based on the inter-point distances, and the point cloud graph neural network (GNN) is applied to extract and analyze the protein surface information to predict potential binding sites. PGpocket is trained on the scPDB dataset, and its performance is verified on two independent test sets, Coach420 and HOLO4K. The results show that PGpocket achieves a 58% success rate on the Coach420 dataset and a 56% success rate on the HOLO4K dataset. These results surpass competing algorithms, demonstrating PGpocket's advancement and practicality for protein-ligand binding site prediction.

Clostridium butyricum inhibits epithelial-mesenchymal transition of intestinal carcinogenesis through downregulating METTL3.

Colorectal cancer (CRC) is related to gut microbiota dysbiosis, especially butyrate-producing bacteria reduction. Our previous study suggested that administration of Clostridium butyricum, a butyrate-producing bacterium, exerts a crucial effect against CRC, however the potential mechanism is not clear. We first found that methyltransferase-like 3 (METTL3) showed a positive correlation with proliferation, epithelial-mesenchymal transition (EMT), DNA repair, metastasis, and invasion in a database analysis. The expression of METTL3 gradually increased from human normal colon tissue, to adenoma, and carcinoma, and was positively correlated with E-cadherin and CD34 levels. Overexpression of METTL3 promoted the proliferation, migration, and invasion of CRC cells and induced vasculogenic mimicry (VM) formation. Clostridium butyricum could downregulate METTL3 expression in CRC cells and decrease the expression of vimentin and vascular endothelial growth factor receptor 2 to reduce EMT and VM formation. Clostridium butyricum alleviated the pro-oncogenic effect of METTL3 overexpressing plasmid in CRC cells. The anti-EMT effect on METTL3 reduction of C. butyricum could be blunted by knocking down G-protein coupled receptor 43. Moreover, C. butyricum prevented EMT and VM and inhibited tumor metastasis in nude mice. Accordingly, C. butyricum could inhibit EMT and VM formation of intestinal carcinogenesis through downregulating METTL3. These findings broaden our understanding of probiotics supplement in CRC prevention and treatment.

Lotus Leaf Derived NiS/Carbon Nanofibers/Porous Carbon Heterogeneous Structures for Strong and Broadband Microwave Absorption.

Developing composite materials with the synergistic effects of heterogeneous structures and multiple components is considered as a promising strategy to achieve high-performance electromagnetic wave (EMW) absorbers. To further satisfy the demand of broadband and strong microwave absorption, a novel NiS/carbon nanofibers (CNFs)/porous carbon composite is successfully synthesized by hydrothermal and chemical vapor deposition using lotus leaves as a biomass carbon source. A few carbon nanotubes (CNTs) and uniformly dispersed Ni nanocrystals have also been found in the hybrid. Benefiting from the porous structure derived from lotus leaves, the combination of dielectric NiS, conductive carbon nanomaterials, and magnetic Ni nanoparticles, together with the three-dimensional conductive network of CNFs and CNTs, the remarkable EMW absorption properties with a minimum reflection loss up to -67.65 dB have been achieved at merely 2.32 mm. Besides, the widest effective absorption band can reach 5.9 GHz with a thin thickness of 2.07 mm, covering almost the entire Ku band. In addition, under the incident angle of 31°, the radar cross-section reduction value of LNSF-600 can reach 42.88 dBm2. Therefore, this work provides an efficient and facile method for manufacturing outstanding biomass-derived EMW absorbers.

Auxin biosynthesis maintains embryo identity and growth during BABY BOOM-induced somatic embryogenesis.

Somatic embryogenesis is a type of plant cell totipotency where embryos develop from nonreproductive (vegetative) cells without fertilization. Somatic embryogenesis can be induced in vitro by auxins, and by ectopic expression of embryo-expressed transcription factors like the BABY BOOM (BBM) AINTEGUMENTA-LIKE APETALA2/ETHYLENE RESPONSE FACTOR domain protein. These different pathways are thought to converge to promote auxin response and biosynthesis, but the specific roles of the endogenous auxin pathway in somatic embryogenesis induction have not been well-characterized. Here we show that BBM transcriptionally regulates the YUCCA3 (YUC3) and YUC8 auxin biosynthesis genes during BBM-mediated somatic embryogenesis in Arabidopsis (Arabidopsis thaliana) seedlings. BBM induced local and ectopic YUC3 and YUC8 expression in seedlings, which coincided with increased DR5 auxin response and indole-3-acetic acid (IAA) biosynthesis and with ectopic expression of the WOX2 embryo reporter. YUC-driven auxin biosynthesis was required for BBM-mediated somatic embryogenesis, as the number of embryogenic explants was reduced by ca. 50% in yuc3 yuc8 mutants and abolished after chemical inhibition of YUC enzyme activity. However, a detailed YUC inhibitor time-course study revealed that YUC-dependent IAA biosynthesis is not required for the re-initiation of totipotent cell identity in seedlings. Rather, YUC enzymes are required later in somatic embryo development for the maintenance of embryo identity and growth. This study resolves a long-standing question about the role of endogenous auxin biosynthesis in transcription factor-mediated somatic embryogenesis and also provides an experimental framework for understanding the role of endogenous auxin biosynthesis in other in planta and in vitro embryogenesis systems.

Multidimensional stitching method with wavelength tuned interferometry and unconstrained support tooling for large-thin parallel plate.

Limited by measurement methods, measuring the surfaces and thickness of large thin parallel plates has been challenging. In this paper, we propose a multi-dimensional stitching method using thickness alignment (MSuTA), which use the sub-aperture stitching method based on the phenomenon of parallel plate self-interference with wavelength-tuned interferometer (WTI) for measuring the surfaces and thickness of large thin parallel plates. We establish the stitching correction model based on Legendre polynomial to separate the aberrations caused by the elastic deformation of the thin plate in the unconstrained support tooling by analyzing the influence of the stress state of the thin plate with unconstrained three-point support. The stitching experiment has carried out on 6.3 mm thick, 6-inch parallel plates that the stitching residual is better than 0.35 nm RMS. Compared with 12-inch vertical interferometer, the surfaces and thickness deviation are better than 0.8 nm RMS, and the 36 standard Legendre polynomial coefficient deviation are better than 2.5 nm. Moreover, MSuTA can improves the lateral resolution of the measurement by nearly four times, allowing for a display of more comprehensive surface information. The stitching method proposed in this paper will be widely applied in the manufacture and measurement of large thin parallel plates, and provide reference for the elastic deformation analysis of the thin optical elements in the unconstrained support tooling.

One-Step Protocol for the Synthesis of Cyanoacrylates Promoted by Elemental Sulfur from p-Quinone Methides and Cyanoacetates under Basic Conditions.

Cyanoacrylates have a wide range of biological activities and are extensively applied in production and daily life. Classic synthetic routes to cyanoacrylates have many limitations. Herein, we demonstrate an elemental sulfur-promoted method for the synthesis of ß,ß-diaryl cyanoacrylates by a tandem 1,6-Michael addition/oxidation/elimination process from p-QMs and cyanoacetates under optimal conditions. The effective protocol has good substrate scopes and yields, and the ratio of inseparable E/Z isomers of cyanoacrylates is also determined by 1HNMR.

Lewis Acid-Catalyzed Remote Site-Selective Ring Deconstruction of Cyclobuteno[a]naphthalene-4-ones to Access Unsymmetric 1,1-Diarylated Olefins.

A catalytic site-selective ring deconstruction of cyclobuteno[a]naphthalene-4-ones with alcohols is reported, enabling the direct production of a wide range of unsymmetric 1,1-diarylated olefins with good yields and complete regioselectivity. The late-stage application of these resulting terminal olefins demonstrates great possibilities to apply this strategy to complex molecules. The protocol features good functional group compatibility, broad substrate scope, and controllable site selectivity.

DMSO-promoted direct δ-selective arylation of p-quinone methenylpiperidine bearinides to generate fuchsones under metal-free conditions by employing p-QMs themselves or substituted phenols as aryl sources.

Fuchsones have wide applications in modern society. Present methods for generating fuchsones have many disadvantages and there are significant limitations for further exploration of fuchsone applications. Herein, we describe a DMSO-promoted direct δ-selective arylation of p-QMs to synthesize symmetrical and unsymmetrical fuchsones under metal-free conditions by employing p-QMs themselves or substituted phenols as aryl sources. As unprecedented methods, these novel strategies present a great advantage and significance for further exploration of fuchsones and the development of new applications.

Mitofusin-2 mediates cannabidiol-induced neuroprotection against cerebral ischemia in rats.

Cannabidiol (CBD) reportedly exerts protective effects against many psychiatric disorders and neurodegenerative diseases, but the mechanisms are poorly understood. In this study, we explored the molecular mechanism of CBD against cerebral ischemia. HT-22 cells or primary cortical neurons were subjected to oxygen-glucose deprivation insult followed by reoxygenation (OGD/R). In both HT-22 cells and primary cortical neurons, CBD pretreatment (0.1, 0.3, 1 µM) dose-dependently attenuated OGD/R-induced cell death and mitochondrial dysfunction, ameliorated OGD/R-induced endoplasmic reticulum (ER) stress, and increased the mitofusin-2 (MFN2) protein level in HT-22 cells and primary cortical neurons. Knockdown of MFN2 abolished the protective effects of CBD. CBD pretreatment also suppressed OGD/R-induced binding of Parkin to MFN2 and subsequent ubiquitination of MFN2. Overexpression of Parkin blocked the effects of CBD in reducing MFN2 ubiquitination and reduced cell viability, whereas overexpressing MFN2 abolished Parkin's detrimental effects. In vivo experiments were conducted on male rats subjected to middle cerebral artery occlusion (MCAO) insult, and administration of CBD (2.5, 5 mg · kg-1, i.p.) dose-dependently reduced the infarct volume and ER stress in the brains. Moreover, the level of MFN2 within the ischemic penumbra of rats was increased by CBD treatment, while the binding of Parkin to MFN2 and the ubiquitination of MFN2 was decreased. Finally, short hairpin RNA against MFN2 reversed CBD's protective effects. Together, these results demonstrate that CBD protects brain neurons against cerebral ischemia by reducing MFN2 degradation via disrupting Parkin's binding to MFN2, indicating that MFN2 is a potential target for the treatment of cerebral ischemia.

Electroencephalographic slowdowns during sleep are associated with cognitive impairment in patients who have obstructive sleep apnea but no dementia.

OBJECTIVES: To research the relationship between quantitative electroencephalogram (qEEG) and impaired cognitive function patients who have obstructive sleep apnea (OSA) but no dementia. METHODS: Subjects who complained of snoring between March 2020 and April 2021 in the Sleep Medicine Center of Weihai Municipal Hospital were included. All subjects underwent overnight in-laboratory polysomnography (PSG) and were assessed using a neuropsychological scale. Standard fast fourier transform (FFT) was used to obtain the electroencephalogram (EEG) power spectral density curve, and to calculate the delta, theta, alpha, and beta relative power and the ratio between slow and fast frequencies. Binary logistic regression was used to assess the risk factors for cognitive impairment in patients who had OSA but no dementia. Correlation analysis was performed to determine the relationship between qEEG and cognitive impairment. RESULTS: A total of 175 participants without dementia who met the inclusion criteria were included in this study. There were 137 patients with OSA, including 76 with mild cognitive impairment (OSA + MCI), 61 without mild cognitive impairment (OSA-MCI), and 38 participants without OSA (non-OSA). The relative theta power in the frontal lobe in stage 2 of non-rapid eye movement sleep (NREM 2) in OSA + MCI was higher than that in OSA-MCI (P = 0.038) and non-OSA (P = 0.018). Pearson correlation analysis showed that the relative theta power in the frontal lobe in NREM 2 was negatively correlated with Mini-Mental State Examination (MMSE) scores, Montreal Cognitive Assessment (MoCA) Beijing version scores, and MoCA subdomains scores (visual executive function, naming, attention, language, abstraction, delayed recall and orientation) outside language. CONCLUSIONS: In patients who had OSA but no dementia, the EEG slower frequency power increased. The relative theta power in the frontal lobe in NREM 2 was associated with MCI of patients with OSA. These results suggest that the slowing of theta activity may be one of the neurophysiological changes in the early stage of cognitive impairment in patients with OSA.