Optimizing 5'UTRs for mRNA-delivered gene editing using deep learning.

mRNA therapeutics are revolutionizing the pharmaceutical industry, but methods to optimize the primary sequence for increased expression are still lacking. Here, we design 5'UTRs for efficient mRNA translation using deep learning. We perform polysome profiling of fully or partially randomized 5'UTR libraries in three cell types and find that UTR performance is highly correlated across cell types. We train models on our datasets and use them to guide the design of high-performing 5'UTRs using gradient descent and generative neural networks. We experimentally test designed 5'UTRs with mRNA encoding megaTALTM gene editing enzymes for two different gene targets and in two different cell lines. We find that the designed 5'UTRs support strong gene editing activity. Editing efficiency is correlated between cell types and gene targets, although the best performing UTR was specific to one cargo and cell type. Our results highlight the potential of model-based sequence design for mRNA therapeutics.

Model and Property Analysis for a Ball-Hinged Three-Degree-of-Freedom Piezoelectric Spherical Motor.

Multi-degree-of-freedom piezoelectric motors have the advantages of high torque and resolution, simple structure, and direct drive, which are widely used in robot wrist joints, deep-sea mechanisms, medical equipment, and space mechanisms. To solve the problems of high force/torque coupling degree and ball low stator and rotor bonding strength of the traditional traveling wave type three-degree-of-freedom piezoelectric spherical motor, a new structure of ball-hinged piezoelectric spherical motor is proposed. Through coordinate transformation and force analysis, the driven mathematical model of the spherical motor is given. The model shows that the three degrees of freedom of the motor are coupled with each other. According to the mathematical model of the spherical motor, the mechanical properties of the motor are analyzed by the computer simulation. The results show that the stalling torque coefficient kt has a linear relationship with the friction coefficient ε and the stator preload Fc, has a nonlinear relationship with the stator radius R and the rotor radius r, and increases with the increase of R and decreases with the increase of r. The no-load speed of motor ωn is not related to the friction coefficient ε and the stator preload Fc, and increases with the increase of R and decreases with the increase of r. The anisotropic characteristics of torque and speed of a spherical motor are further analyzed, which lays a theoretical foundation for the drive control of a spherical motor.

Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells.

Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell-type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell-type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell-type-specific cis-regulatory changes. We find that cell-type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell-type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.

Photoredox-Catalyzed Divergent Radical Cascade Annulations of 1,6-Enynes via Pyridine N-Oxide-Promoted Vinyl Radical Generation.

The divergent organophotoredox-catalyzed radical cascade annulation reactions of 1,6-enynes were developed. A series of cyclopropane-fused hetero- and carbo-bicyclic, tricyclic, and spiro-tetracyclic compounds were facilely synthesized from a broad scope of 1,6-enynes and 2,6-lutidine N-oxide under mild and metal-free conditions with blue light-emitting diode light irradiation. The cascade annulation reaction occurs with the intermediacy of a ß-oxyvinyl radical, which is produced from photocatalytically generated pyridine N-oxy radical addition to the carbon-carbon triple bond.

Unraveling FOXO3a and USP18 Functions in Idiopathic Pulmonary Fibrosis through Single-Cell RNA Sequencing of Mouse and Human Lungs.

Background Idiopathic pulmonary fibrosis (IPF) is identified as a chronic, progressive lung disease, predominantly marked by enhanced fibroblast proliferation and excessive deposition of extracellular matrix. The intricate interactions between diverse molecular pathways in fibroblasts play a crucial role in driving the pathogenesis of IPF. Methods This research is focused on elucidating the roles of FOXO3a, a transcription factor, and USP18, a ubiquitin-specific protease, in modulating fibroblast functionality in the context of IPF. FOXO3a is well-known for its regulatory effects on cellular responses, including apoptosis and oxidative stress, while USP18 is generally associated with protein deubiquitination. Results Our findings highlight that FOXO3a acts as a critical regulator in controlling fibroblast activation and differentiation, illustrating its vital role in the pathology of IPF. Conversely, USP18 seems to promote fibroblast proliferation and imparts resistance to apoptosis, thereby contributing to the exacerbation of fibrotic processes. The synergistic dysregulation of both FOXO3a and USP18 in fibroblasts was found to significantly contribute to the fibrotic alterations characteristic of IPF. Conclusion Deciphering the complex molecular interactions between FOXO3a and USP18 in fibroblasts provides a deeper understanding of IPF pathogenesis and unveils novel therapeutic avenues, offering a promising potential for not just halting but potentially reversing the progression of this debilitating disease.

Deleted in lymphocytic leukemia 2 (DLEU2): a possible biomarker that holds promise for future diagnosis and treatment of cancer

The mechanism of deleted in lymphocytic leukemia 2 (DLEU2)-long non-coding RNA in tumors has become a major point of interest in recent research related to the occurrence and development of a variety of tumors. Recent studies have shown that the long non-coding RNA DLEU2 (lncRNA-DLEU2) can cause abnormal gene or protein expression by acting on downstream targets in cancers. At present, most lncRNA-DLEU2 play the role of oncogenes in different tumors, which are mostly associated with tumor characteristics, such as proliferation, migration, invasion, and apoptosis. The data thus far show that because lncRNA-DLEU2 plays an important role in most tumors, targeting abnormal lncRNA-DLEU2 may be an effective treatment strategy for early diagnosis and improving the prognosis of patients. In this review, we integrated lncRNA-DLEU2 expression in tumors, its biological functions, molecular mechanisms, and the utility of DLEU2 as an effective diagnostic and prognostic marker of tumors. This study aimed to provide a potential direction for the diagnosis, prognosis, and treatment of tumors using lncRNA-DLEU2 as a biomarker and therapeutic target (AU)

Experimental and Simulation Study on Welding Characteristics and Parameters of Gas Metal Arc Welding for Q345qD Thick-Plate Steel.

The welding and construction processes for H-type thick-plate bridge steel involve complex multi-pass welding processes, which make it difficult to ensure its welding performance. Accordingly, it is crucial to explore the inherent correlations between the welding process parameters and welding quality, and apply them to welding robots, eliminating the instability in manual welding. In order to improve welding quality, the GMAW (gas metal arc welding) welding process parameters are simulated, using the Q345qD bridge steel flat joint model. Four welds with X-shaped grooves are designed to optimize the parameters of the welding current, welding voltage, and welding speed. The optimal welding process parameters are investigated through thermal-elastic-plastic simulation analysis and experimental verification. The results indicate that, when the welding current is set to 230 A, the welding voltage to 32 V, and the welding speed to 0.003 m/s, the maximum deformation of the welded plate is 0.52 mm, with a maximum welding residual stress of 345 MPa. Both the simulation results of multi-pass welding, and the experimental tests meet the welding requirements, as they show no excessive stress or strain. These parameters can be applied to building large steel-frame bridges using welding robots, improving the quality of welded joints.

Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells.

Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell type-specific cis-regulatory changes. We find that cell type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.

Deleted in lymphocytic leukemia 2 (DLEU2): a possible biomarker that holds promise for future diagnosis and treatment of cancer.

The mechanism of deleted in lymphocytic leukemia 2 (DLEU2)-long non-coding RNA in tumors has become a major point of interest in recent research related to the occurrence and development of a variety of tumors. Recent studies have shown that the long non-coding RNA DLEU2 (lncRNA-DLEU2) can cause abnormal gene or protein expression by acting on downstream targets in cancers. At present, most lncRNA-DLEU2 play the role of oncogenes in different tumors, which are mostly associated with tumor characteristics, such as proliferation, migration, invasion, and apoptosis. The data thus far show that because lncRNA-DLEU2 plays an important role in most tumors, targeting abnormal lncRNA-DLEU2 may be an effective treatment strategy for early diagnosis and improving the prognosis of patients. In this review, we integrated lncRNA-DLEU2 expression in tumors, its biological functions, molecular mechanisms, and the utility of DLEU2 as an effective diagnostic and prognostic marker of tumors. This study aimed to provide a potential direction for the diagnosis, prognosis, and treatment of tumors using lncRNA-DLEU2 as a biomarker and therapeutic target.

SEACU-Net: Attentive ConvLSTM U-Net with squeeze-and-excitation layer for skin lesion segmentation.

BACKGROUND AND OBJECTIVE: Accurate segmentation of skin lesions is a pivotal step in dermoscopy image classification, which provides a powerful means for dermatologists to diagnose skin diseases. However, due to blurred boundaries, low contrast between the lesion and its surrounding skin, and changes in color and shape, most existing segmentation methods still face great challenges in obtaining receptive fields and extracting image feature information. To settle the above issues, we construct a new framework, named SEACU-Net, to analyze and segment skin lesion images. METHODS: Inspired by the U-Net, we utilize dense convolution blocks to obtain more discriminative information. Then, at each encoding and decoding stage, a channel and spatial squeeze & excitation layer are designed after each convolution, to adaptively enhance useful information features and suppress low-value ones from different feature channels. In addition, the attention mechanism is integrated into the convolutional long short-term memory (ConvLSTM) structure, which improves sensitivity and prediction accuracy. Furthermore, this network introduces a novel loss based on binary cross-entropy and Jaccard losses, which can ensure more balanced segmentation. RESULTS: The proposed method is applied to the ISIC 2017 and 2018 publicly image databases, then obtains a better performance in Dice, Jaccard, and Accuracy, with 89.11% and 87.58% Dice value, 80.50% and 78.12% Jaccard value, 95.01%, and 93.60% Accuracy value, respectively. CONCLUSION: The results of quantitative and qualitative experiments show that our method reaches high-performance skin lesion segmentation, and can help radiologists make radiotherapy treatment plans in clinical practice.

Transcriptome diversity is a systematic source of variation in RNA-sequencing data.

RNA sequencing has been widely used as an essential tool to probe gene expression. While standard practices have been established to analyze RNA-seq data, it is still challenging to interpret and remove artifactual signals. Several biological and technical factors such as sex, age, batches, and sequencing technology have been found to bias these estimates. Probabilistic estimation of expression residuals (PEER), which infers broad variance components in gene expression measurements, has been used to account for some systematic effects, but it has remained challenging to interpret these PEER factors. Here we show that transcriptome diversity-a simple metric based on Shannon entropy-explains a large portion of variability in gene expression and is the strongest known factor encoded in PEER factors. We then show that transcriptome diversity has significant associations with multiple technical and biological variables across diverse organisms and datasets. In sum, transcriptome diversity provides a simple explanation for a major source of variation in both gene expression estimates and PEER covariates.

Magnetoelastic Coupled Wave Diffraction and Dynamic Stress Intensity Factor in Graded Piezomagnetic Composites with a Cylindrical Aperture.

A theoretical method is developed to study the magnetoelastic coupled wave and dynamic stress intensity around a cylindrical aperture in exponential graded piezomagnetic materials. By employing the decoupling technique, the coupled magnetoelastic governing equations are decomposed. Then the analytic solutions of elastic wave fields and magnetic fields are presented by using the wave function expansion method. By satisfying the boundary conditions of the aperture, the mode coefficients, and the analytic solutions of dynamic stress intensity factors are determined. The numerical examples of the dynamic stress intensity factor near the aperture are presented. The numerical results indicate that the incident wave number, the piezomagnetic properties, and the nonhomogeneous parameter of materials highly influence the dynamic stress around the aperture.

FOXO3a is stabilized by USP18-mediated de-ISGylation and inhibits TGF-ß1-induced fibronectin expression.

FOXO3a belongs to a family of transcription factors characterized by a conserved forkhead box DNA-binding domain. It has been known to regulate various cellular processes including cell proliferation, apoptosis and differentiation. Post-translational modifications of FOXO3a and their roles in the regulation of FOXO3a activity have been well-documented. FOXO3a can be phosphorylated, acetylated and ubiquitinated, however, the ISGylation of FOXO3a has not been reported. Protein overexpression, ISGylation and half-life were measured to determine the post-translational modification of FOXO3a. Human fibroblast cells were treated with transforming growth factor (TGF)-ß1 to determine the role of FOXO3a ISGylation in TGF-ß1 signaling. FOXO3a's half-life is around 3.7 hours. Inhibition of the proteasome, not lysosome, extends its half-life. ISGylation, but not ubiquitination of FOXO3a, is increased in the presence of the proteasome inhibitor. Overexpression of ISG15 increases FOXO3a degradation, while overexpression of USP18 stabilizes FOXO3a through de-ISGylation. These results suggest that FOXO3a is degraded in the ISGylation and proteasome system, which can be reversed by USP18, an ISG15-specific deubiquitinase. This study reveals a new molecular mechanism by which ISGylation regulates FOXO3a degradation. Furthermore, we show that the overexpression of FOXO3a attenuated TGF-ß1-induced fibronectin expression in human lung fibroblast cells without altering Smad2/3 expression and activation. FOXO3a can be ISGylated, which can regulate FOXO3a stability. USP18/FOXO3a pathway is a potential target for treating TGF-ß1-mediated fibrotic diseases such as idiopathic pulmonary fibrosis.

Bis(imino)pyridine iron complexes for catalytic carbene transfer reactions.

The bis(imino)pyridine iron complex, for the first time, is developed as an effective metal carbene catalyst for carbene transfer reactions of donor-acceptor diazo compounds. Its broad catalytic capability is demonstrated by a range of metal carbene reactions, from cyclopropanation, cyclopropenation, epoxidation, and Doyle-Kirmse reaction to O-H insertion, N-H insertion, and C-H insertion reactions. The asymmetric cyclopropanation of styrene and methyl phenyldiazoacetate was successfully achieved by the new chiral bis(imino)pyridine iron catalyst, which delivers a new gateway for the development of chiral iron catalysis for metal carbene reactions.

Human 5' UTR design and variant effect prediction from a massively parallel translation assay.

The ability to predict the impact of cis-regulatory sequences on gene expression would facilitate discovery in fundamental and applied biology. Here we combine polysome profiling of a library of 280,000 randomized 5' untranslated regions (UTRs) with deep learning to build a predictive model that relates human 5' UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5' UTRs that accurately direct specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,212 truncated human 5' UTRs and 3,577 naturally occurring variants and show that the model predicts ribosome loading of these sequences. Finally, we provide evidence of 45 single-nucleotide variants (SNVs) associated with human diseases that substantially change ribosome loading and thus may represent a molecular basis for disease.

Thermal Wave Scattering by an Elliptic Subsurface Hole Buried in a Block, Based on the Non-Fourier Equation.

With the application to engineering practice, the study of the scattering of thermal waves using innovative and comprehensive methods is becoming increasingly important. The thermal wave scattering by an elliptic subsurface hole in a block with two boundaries is discussed based on the non-Fourier heat conduction equation, employing the complex function method and the conformal mapping method, and a general solution for the thermal wave scattering is given. The numerical results of temperature distributions around a subsurface hole are presented and the effects of geometrical and physical parameters on the temperature distributions were analyzed. The wave number, the shape and position of the hole, the scale of the block, and the frequency of the heat load were found to have great effects on distributions and variations of temperature. The findings of this study could be helpful in providing better understandings of infrared thermal wave imaging, the physical inverse problem, and the evaluation of internal holes in materials.

ortho-Alkylation of Pyridine N-Oxides with Alkynes by Photocatalysis: Pyridine N-Oxide as a Redox Auxiliary.

A photocatalyzed ortho-alkylation of pyridine N-oxide with ynamides and arylacetylenes has been developed, which yields a series of α-(2-pyridinyl) benzyl amides/ketones. Mechanistic studies, including electrochemical studies, radical-trapping experiments, and Stern-Volmer fluorescence quenching studies demonstrate that pyridine N-oxide serves as both a redox auxiliary and radical acceptor to achieve the mild photocatalytic single-electron oxidation of carbon-carbon triple bonds with the generation of a cationic vinyl radical intermediate.

Modeling and Efficiency Analysis of a Piezoelectric Energy Harvester Based on the Flow Induced Vibration of a Piezoelectric Composite Pipe.

This paper proposes and investigates a piezoelectric energy harvesting system based on the flow induced vibration of a piezoelectric composite cantilever pipe. Dynamic equations for the proposed energy harvester are derived considering the fluid-structure interaction and piezoelectric coupling vibration. Linear global stability analysis of the fluid-solid-electric coupled system is done using the numerical continuation method to find the neutrally stable vibration mode of the system. A measure of the energy harvesting efficiency of the system is proposed and analyzed. A series of simulations are conducted to throw light upon the influences of mass ratio, dimensionless electromechanical coupling, and dimensionless connected resistance upon the critical reduced velocity and the normalized energy harvesting efficiency. The results provide useful guidelines for the practical design of piezoelectric energy harvester based on fluid structure interaction and indicate some future topics to be investigated to optimize the device performance.

Muscarinic suppression of ATP-sensitive K+ channels mediated by the M3/Gq/11/phospholipase C pathway contributes to mouse ileal smooth muscle contractions.

ATP-sensitive K+ (KATP) channels are expressed in gastrointestinal smooth muscles, and their activity is regulated by muscarinic receptor stimulation. However, the physiological significance and mechanisms of muscarinic regulation of KATP channels are not fully understood. We examined the effects of the KATP channel opener cromakalim and the KATP channel blocker glibenclamide on electrical activity of single mouse ileal myocytes and on mechanical activity in ileal segment preparations. To explore muscarinic regulation of KATP channel activity and its underlying mechanisms, the effect of carbachol (CCh) on cromakalim-induced KATP channel currents ( IKATP) was studied in myocytes of M2 or M3 muscarinic receptor-knockout (KO) and wild-type (WT) mice. Cromakalim (10 µM) induced membrane hyperpolarization in single myocytes and relaxation in segment preparations from WT mice, whereas glibenclamide (10 µM) caused membrane depolarization and contraction. CCh (100 µM) induced sustained suppression of IKATP in cells from both WT and M2KO mice. However, CCh had a minimal effect on IKATP in M3KO and M2/M3 double-KO cells. The Gq/11 inhibitor YM-254890 (10 µM) and PLC inhibitor U73122 (1 µM), but not the PKC inhibitor calphostin C (1 µM), markedly decreased CCh-induced suppression of IKATP in WT cells. These results indicated that KATP channels are constitutively active and contribute to the setting of resting membrane potential in mouse ileal smooth muscles. M3 receptors inhibit the activity of these channels via a Gq/11/PLC-dependent but PKC-independent pathways, thereby contributing to membrane depolarization and contraction of smooth muscles. NEW & NOTEWORTHY We systematically investigated the regulation of ATP-sensitive K+ channels by muscarinic receptors expressed on mouse ileal smooth muscles. We found that M3 receptors inhibit the activity of ATP-sensitive K+ channels via a Gq/11/PLC-dependent, but PKC-independent, pathway. This muscarinic suppression of ATP-sensitive K+ channels contributes to membrane depolarization and contraction of smooth muscles.

Exogenous NAD(+) administration significantly protects against myocardial ischemia/reperfusion injury in rat model.

Acute myocardial infarction is one of the leading causes for death around the world. Although essential for successful interventional therapy, it is inevitably complicated by reperfusion injury. Thus effective approaches to reduce ischemia/reperfusion (I/R) injury are still critically needed. To test our hypothesis that intravenous administration of NAD(+) can attenuate I/R injury by reducing apoptotic damage and enhancing antioxidant capacity, we used a rat mode of myocardial I/R. Our study found that administration of 10-20 mg/kg NAD(+) can dose dependently reduce myocardial infarct induced by I/R, with an approximately 85% reduction of the infarct at the dosage of 20 mg/kg NAD(+). We further found that the injection of NAD(+) can significantly decrease I/R-induced apoptotic damage in the heart: NAD(+) administration can both decrease the TUNEL signals, Bax, cleaved caspase-3 levels and increase the Bcl-XL levels in the rats that are subjected to myocardial I/R injury. NAD(+) administration can also significantly attenuate I/R-induced decreases in SOD activity and SOD-2 protein levels in the hearts. NAD(+) can profoundly decrease myocardial I/R injury at least partially by attenuating apoptotic damage and enhancing the antioxidant capacity, thus suggesting that NAD(+) may become a promising therapeutic agent for myocardial I/R injury.