Optimal variable identification for accurate detection of causal expression Quantitative Trait Loci with applications in heart-related diseases.

Gene expression plays a pivotal role in various diseases, contributing significantly to their mechanisms. Most GWAS risk loci are in non-coding regions, potentially affecting disease risk by altering gene expression in specific tissues. This expression is notably tissue-specific, with genetic variants substantially influencing it. However, accurately detecting the expression Quantitative Trait Loci (eQTL) is challenging due to limited heritability in gene expression, extensive linkage disequilibrium (LD), and multiple causal variants. The single variant association approach in eQTL analysis is limited by its susceptibility to capture the combined effects of multiple variants, and a bias towards common variants, underscoring the need for a more robust method to accurately identify causal eQTL variants. To address this, we developed an algorithm, CausalEQTL, which integrates L 0 +L 1 penalized regression with an ensemble approach to localize eQTL, thereby enhancing prediction performance precisely. Our results demonstrate that CausalEQTL outperforms traditional models, including LASSO, Elastic Net, Ridge, in terms of power and overall performance. Furthermore, analysis of heart tissue data from the GTEx project revealed that eQTL sites identified by our algorithm provide deeper insights into heart-related tissue eQTL detection. This advancement in eQTL mapping promises to improve our understanding of the genetic basis of tissue-specific gene expression and its implications in disease. The source code and identified causal eQTLs for CausalEQTL are available on GitHub: https://github.com/zhc-moushang/CausalEQTL.

A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data.

In recent years, the application of single-cell transcriptomics and spatial transcriptomics analysis techniques has become increasingly widespread. Whether dealing with single-cell transcriptomic or spatial transcriptomic data, dimensionality reduction and clustering are indispensable. Both single-cell and spatial transcriptomic data are often high-dimensional, making the analysis and visualization of such data challenging. Through dimensionality reduction, it becomes possible to visualize the data in a lower-dimensional space, allowing for the observation of relationships and differences between cell subpopulations. Clustering enables the grouping of similar cells into the same cluster, aiding in the identification of distinct cell subpopulations and revealing cellular diversity, providing guidance for downstream analyses. In this review, we systematically summarized the most widely recognized algorithms employed for the dimensionality reduction and clustering analysis of single-cell transcriptomic and spatial transcriptomic data. This endeavor provides valuable insights and ideas that can contribute to the development of novel tools in this rapidly evolving field.

MCU inhibition protects against intestinal ischemia‒reperfusion by inhibiting Drp1-dependent mitochondrial fission.

Intestinal ischemia‒reperfusion (IIR) injury is a common complication of surgery, but clear molecular insights and valuable therapeutic targets are lacking. Mitochondrial calcium overload is an early sign of various diseases and is considered a vital factor in ischemia‒reperfusion injury. The mitochondrial calcium uniporter (MCU), which is located on the inner mitochondrial membrane, is the primary mediator of calcium ion entry into the mitochondria. However, the specific mechanism of MCU in IIR injury remains to be clarified. In this study, we generated an IIR model using C57BL/6 mice and Caco-2 cells and found increases in the calcium levels and MCU expression following IIR injury. The specific inhibition of MCU markedly attenuated IIR injury. Moreover, MCU knockdown alleviates mitochondrial dysfunction by reducing oxidative stress and apoptosis. Mechanistically, MCU knockdown substantially reduced the translocation of Drp1 and thus its binding to Fis1 receptors, resulting in decreased mitochondrial fission. Taken together, our findings demonstrated that MCU is a novel upstream regulator of Drp1 in ischemia‒reperfusion and represents a predictive and therapeutic target for IIR.

Metatranscriptome and small RNA sequencing revealed a mixed infection of newly identified bymovirus and bean yellow mosaic virus on peas.

Peas (Pisum sativum L.) are widely cultivated in temperate regions and are susceptible hosts for various viruses across different families. The discovery and identification of new viruses in peas has significant implications for field disease management. Here, we identified a mixed infection of two viruses from field-collected peas exhibiting virus-like symptoms using metatranscriptome and small RNA sequencing techniques. Upon identification, one of the viruses was determined to be a newly isolated and discovered bymovirus from peas, named "pea bymovirus 1 (PBV1)". The other was identified as a novel variant of bean yellow mosaic virus (BYMV-HZ1). Subsequently, mechanical inoculation and RT-PCR assays confirmed that both viruses could be inoculated back onto peas and tobaccos, showing mixed infection by PBV1 and BYMV-HZ1. To our knowledge, this is the first isolation of a bymovirus from pea and the first documented case of mixed infection of peas by PBV1 and BYMV-HZ1 in China.

Novel artemisinin derivative P31 inhibits VEGF-induced corneal neovascularization through AKT and ERK1/2 pathways.

Corneal neovascularization (CoNV)is a major cause of blindness in many ocular diseases. Substantial evidence indicates that vascular endothelial growth factor (VEGF) plays an important role in the pathogenesis of corneal neovascularization. Previous evidence showed that artemisinin may inhibit angiogenesis through down regulation of the VEGF receptors. We designed and synthesized artemisinin derivatives, and validated their inhibitory effect on neovascularization in cell and animal models, and explored the mechanisms by which they exert an inhibitory effect on CoNV. Among these derivatives, P31 demonstrated significant anti-angiogenic effects in vivo and in vitro. Besides, P31 inhibited VEGF-induced HUVECs angiogenesis and neovascularization in rabbit model via AKT and ERK pathways. Moreover, P31 alleviated angiogenic and inflammatory responses in suture rabbit cornea. In conclusion, as a novel artemisinin derivative, P31 attenuates corneal neovascularization and has a promising application in ocular diseases.

Glutathione-depleting polyprodrug nanoparticle for enhanced photodynamic therapy and cascaded locoregional chemotherapy.

Nanomedicines that combine reactive oxygen species (ROS)-responsive polyprodrug and photodynamic therapy have shown great potential for improving treatment efficacy. However, the consumption of ROS by overexpressed glutathione in tumor cells is a major obstacle for achieving effective ROS amplification and prodrug activation. Herein, we report a polyprodrug-based nanoparticle that can realize ROS amplification and cascaded drug release. The nanoparticle can respond to the high level of hydrogen peroxide in tumor microenvironment, achieving self-destruction and release of quinone methide. The quinone methide depletes intracellular glutathione and thus decreases the antioxidant capacity of cancer cells. Under laser irradiation, a large amount of ROS will be generated to induce cell damage and prodrug activation. Therefore, the glutathione-depleting polyprodrug nanoparticles can efficiently inhibit tumor growth by enhanced photodynamic therapy and cascaded locoregional chemotherapy.

Anchorage performance of a new rebar bolt under different surrounding rock strength and borehole depth.

The theory and technology of rock bolting are fundamental research topics for strata control in civil and mining engineering. Rebar bolts are commonly used for roadway primary support in underground coal mine. To adapt to deep resource mining, a new left threaded rebar bolt has been developed. Compared to conventional rebar bolts, the result of installation test showed that the new bolt reduced of 41.5% and 57.9% in stirring resistance force and torque, respectively. In laboratory pullout tests, PVC and aluminum sleeves were used to simulate weak and medium strength surrounding rocks. The average peak pullout force, displacement at the peak load and energy absorption increased by 27%, 107% and 108%, respectively, using PVC sleeve; and increased by 113%, 109% and 212%, respectively, using aluminum sleeve. Field tests were conducted under soft coal, hard coal and medium strength rock geo-conditions. Different borehole depths were selected to precisely calculate the average anchorage performance of the new bolt. Results showed that the average peak pullout force of the new bolt increased by 37%, 38% and 28%, respectively, under different surrounding rock conditions. Moreover, based on on-site test results, the pullout curves in field-testing were summarised and classified into 6 different patterns, which were discussed from a viewpoint of causality mechanism. The research findings validate that the newly developed bolt has better anchorage performance compared to conventional rebar bolts, making it a new anchorage material for deep resource mining.

Numerical simulation of rock blasting under different in-situ stresses and joint conditions.

High primary rock stress can limit the generation of rock cracks caused by blasting, and blasting usually shows different rock breaking states under different primary rock stress conditions. There are a large number of naturally formed joints in rock mass, due to the limitations of laboratory tests, a numerical model of jointed rock mass was established using LS-DYNA software to investigate the evolution of blasting damage under various in-situ stresses and open joints. In this simulation, using the Lagrange-Euler (ALE) procedure and the equation of state (JWL) that defines explosive materials, the study considered different joint thicknesses (2cm, 4cm, and 6cm), joint angles (0°, 30°, 60°, and 90°), and in-situ stress conditions (lateral stress coefficients of 0.5, 1, and 2, with vertical in-situ stresses of 10MPa and 20MPa), through stress analysis and damage area comparison, the relationship between damage crack propagation and horizontal and vertical stress difference is explored. The research aimed to understand the mechanisms underlying crack initiation and propagation. The results show that: (1) The presence of joints exerts a barrier effect on the expansion and penetration of cracks. When explosion stress waves reach the joint surface, their propagation is impeded, leading to the diffusion of wing cracks at the joint ends. When the lateral stress coefficient and joint angle are the same, an increase in initial in-situ stress results in a reduction in the area of the blasting damage zone. (2) Under the same initial in-situ stress conditions, the area of the blasting damage zone initially increases and then decreases with an increasing joint angle. However, it remains larger than that without a joint, and there exists an optimal angle that maximizes the damage area. In the simulated conditions, the area of damage cracks is greatest when the joint angle is 60° dip angle. (3) The presence of initial in-situ stress has a certain impact on the initiation and expansion of blasting cracks. The degree and nature of this influence are not solely related to the lateral stress coefficient but also depend on the joint's angle and thickness. When in-situ stress is present, the initial in-situ stress field's pressure is not conducive to the initiation and propagation of blasting cracks. However, the existence of a joint has a noticeable guiding and promoting effect on crack propagation, and the pattern of crack propagation is influenced by both joint and in-situ stress conditions.

Health status monitoring of bridge cable and telescopic compensation device based on fiber grating sensing array.

Laying power cables along the bridge is a new way of laying submarine cables across the sea. Monitoring the health status of cables and their telescopic compensation devices is necessary. In this study, fiber grating sensing technology was used to monitor the strain, temperature, and vibration of the bridge cable of the Zhoushan-Daishan Bridge in Zhoushan, Zhejiang Province, and its compensation device. Two typhoons and one invasion event happened during the monitoring period. Temperature signals, strain signals, and time domain and time-frequency domain vibration signals were analyzed. The results showed that no fire hazards or risk of external damage were found with the bridge cable, and the monitoring system filled a gap in the in situ monitoring of the bridge cable in the Zhoushan-Daishan Bridge by the State Grid.

WY-14643, a novel antiplatelet and antithrombotic agent targeting the GPIbα receptor.

BACKGROUND AND PURPOSE: Hypolipidemia and platelet activation play key roles in atherosclerotic diseases. Pirinixic acid (WY-14643) was originally developed as a lipid-lowering drug. Here we focused on its antiplatelet and antithrombotic abilities and the underlying mechanism. EXPERIMENTAL APPROACH: The effects of WY-14643 on platelet aggregation was measured using a lumi-aggregometer. Clot retraction and spreading on fibrinogen were also assayed. PPARα-/- platelets were used to identify the target of WY-14643. The interaction between WY-14643 and glycoprotein Ibα (GPIbα) was detected using cellular thermal shift assay (CETSA), surface plasmon resonance (SPR) spectroscopy and molecular docking. GPIbα downstream signaling was examined by Western blot. The antithrombotic effect was investigated using mouse mesenteric arteriole thrombosis model. Mouse tail bleeding model was used to study its effect on bleeding side effects. KEY RESULTS: WY-14643 concentration-dependently inhibits human washed platelet aggregation, clot retraction, and spreading. Significantly, WY-14643 inhibits thrombin-induced activation of human washed platelets with an IC50 of 7.026 µM. The antiplatelet effect of WY-14643 is mainly dependent of GPIbα. CESTA, SPR and molecular docking results indicate that WY-14643 directly interacts with GPIbα and acts as a GPIbα antagonist. WY-14643 also inhibits phosphorylation of PLCγ2, Akt, p38, and Erk1/2 induced by thrombin. Noteworthily, 20 mg/kg oral administration of WY-14643 inhibits FeCl3-induced thrombosis of mesenteric arteries in mice similarly to clopidogrel without increasing bleeding. CONCLUSION AND IMPLICATIONS: WY-14643 is not only a PPARα agonist with lipid-lowering effect, but also an antiplatelet agent as a GPIbα antagonist. It may have more significant therapeutic advantages than current antiplatelet agents for the treatment of atherosclerotic thrombosis, which have lipid-lowering effects without bleeding side effects.

Lanosterol regulates abnormal amyloid accumulation in LECs through the mediation of cholesterol pathway metabolism.

Age-related cataract (ARC) is the predominant cause of global blindness, linked to the progressive aging of the lens, oxidative stress, perturbed calcium homeostasis, hydration irregularities, and modifications in crystallin proteins. Currently, surgical intervention remains the sole efficacious remedy, albeit carrying inherent risks of complications that may culminate in irreversible blindness. It is urgent to explore alternative, cost-effective, and uncomplicated treatment modalities for cataracts. Lanosterol has been widely reported to reverse cataracts, but the mechanism of action is not yet clear. In this study, we elucidated the mechanism through which lanosterol operates in the context of cataract reversal. Through the targeted suppression of sterol regulatory element-binding protein 2 (SREBP2) followed by lanosterol treatment, we observed the restoration of lipid metabolism disorders induced by SREBP2 knockdown in lens epithelial cells (LECs). Notably, lanosterol exhibited the ability to effectively counteract amyloid accumulation and cellular apoptosis triggered by lipid metabolism disorders. In summary, our findings suggest that lanosterol, a pivotal intermediate in lipid metabolism, may exert its therapeutic effects on cataracts by influencing lipid metabolism. This study shed light on the treatment and pharmaceutical development targeting Age-related Cataracts (ARC).

Temperature-Automated Calibration Methods for a Large-Area Blackbody Radiation Source.

High-precision temperature control of large-area blackbodies has a pivotal role in temperature calibration and thermal imaging correction. Meanwhile, it is necessary to correct the temperature difference between the radiating (surface of use) and back surfaces (where the temperature sensor is installed) of the blackbody during the testing phase. Moreover, large-area blackbodies are usually composed of multiple temperature control channels, and manual correction in this scenario is error-prone and inefficient. At present, there is no method that can achieve temperature-automated calibration for a large-area blackbody radiation source. Therefore, this article is dedicated to achieving temperature-automated calibration for a large-area blackbody radiation source. First, utilizing two calibrated infrared thermometers, the optimal temperature measurement location was determined using a focusing algorithm. Then, a three-axis movement system was used to obtain the true temperature at the same measurement location on a large-area blackbody surface from different channels. This temperature was subtracted from the blackbody's back surface. The temperature difference was calculated employing a weighted algorithm to derive the parameters for calibration. Finally, regarding experimental verification, the consistency error of the temperature measurement point was reduced by 85.4%, the temperature uniformity of the surface source was improved by 40.4%, and the average temperature measurement deviation decreased by 43.8%. In addition, this system demonstrated the characteristics of strong environmental adaptability that was able to perform temperature calibration under the working conditions of a blackbody surface temperature from 100 K to 573 K, which decreased the calibration time by 9.82 times.

Characterization of sub-nanosecond pulse compression based on frequency-detuning SBS.

High-frequency, high-power picosecond lasers have important and wide-ranging applications in laser ranging, optoelectronic countermeasures, and ultrafine industrial processing. Pulse compression based on stimulated Brillouin scattering (SBS) can achieve a highly efficient picosecond laser output, while improving the peak power and beam quality of the laser. In this paper, a generator-amplifier two-cell structure with frequency-detuning was proposed to achieve a pulse output that combines high compression ratio and high energy reflectivity. The experiment proved that under a pump pulse width of 15 ns and repetition frequency of 10 Hz, when the generator cell and amplifier cell media were selected as HT-230, the highest energy reflectivity of 46% and narrowest compression pulse width of 1.1 ns were achieved, and the pulse compression ratio was 13.6. When the amplifier cell was selected as FC-770 and the generator cell was selected as HT-230, an energy reflectivity of 52% and a compression pulse width of 840 ps could be achieved simultaneously, and the pulse compression ratio was 18.

Two different viral proteins suppress NUCLEAR FACTOR-YC-mediated antiviral immunity during infection in rice.

Plant viruses have multiple strategies to counter and evade the host's antiviral immune response. However, limited research has been conducted on the antiviral defense mechanisms commonly targeted by distinct types of plant viruses. In this study, we discovered that NUCLEAR FACTOR-YC (NF-YC) and NUCLEAR FACTOR-YA (NF-YA), 2 essential components of the NF-Y complex, were commonly targeted by viral proteins encoded by 2 different rice (Oryza sativa L.) viruses, rice stripe virus (RSV, Tenuivirus) and southern rice black streaked dwarf virus (SRBSDV, Fijivirus). In vitro and in vivo experiments showed that OsNF-YCs associate with OsNF-YAs and inhibit their transcriptional activation activity, resulting in the suppression of OsNF-YA-mediated plant susceptibility to rice viruses. Different viral proteins RSV P2 and SRBSDV SP8 directly disrupted the association of OsNF-YCs with OsNF-YAs, thereby suppressing the antiviral defense mediated by OsNF-YCs. These findings suggest an approach for conferring broad-spectrum disease resistance in rice and reveal a common mechanism employed by viral proteins to evade the host's antiviral defense by hindering the antiviral capabilities of OsNF-YCs.

NQO1-activated multifunctional theranostic probe for imaging-guided mitochondria-targeted photodynamic therapy and boosting immunogenic cell death.

NAD(P)H: quinine oxidoreductase (NQO1) is overexpressed in many types of cancer cells, and have been used as a biomarker for cancer diagnosis and targeted therapy. The development of activatable theranostic agents is highly desirable for precise cancer diagnosis and therapy. Herein, a NQO1-activated near-infrared multifunctional theranostic probe I-HCy-Q is successfully developed for imaging guided photodynamic therapy. The NIR fluorescence (λex/em = 685/703 nm) and capacity of reactive oxygen species generation are sensitive controllable by the level of NQO1, the linear detection range of NQO1 and limit of detection are 0.05-1.5 µg/mL and 5.66 ng/mL, respectively. On the one hand, I-HCy-Q can monitor the activity of NQO1 and distinguish the NQO1 positive cancer cells; on the other hand, the capacity of mitochondria-targeted photodynamic therapy makes I-HCy-Q an effective inducer of apoptosis and immunogenic cell death. Attribute to its complementary advantages, I-HCy-Q holds potential for the imaging and treatment of tumors in complex organisms.

Cell Reprogramming Strategies for Treating Osteoarthritis and Intervertebral Disc Degeneration.

Osteoarthritis (OA) and intervertebral disc degeneration (IVDD) are the most common degenerative bone and joint diseases, posing a major threat to patients' physical and mental health due to the occurrence of chronic pain and disability. Within this context, the absence of efficacious therapies has led to a growing interest in regenerative medicine. In particular, as a method that can erase the memory of differentiation and re-endow cells with pluripotency, cell reprogramming technologies have ushered in a new era of personalized therapy, which not only show great potential for the treatment of degenerative osteoarthropathies but also promise to achieve tissue regenerative and repair. However, compared to other areas of research, reprogramming technologies to treat OA and IVDD are still in the preliminary stages and require further investigation. This paper briefly introduces the characteristics of cell reprogramming; summarizes the pathological mechanisms of reprogramming to improves energy metabolism, aging, inflammation, oxidative stress, and immune imbalance in OA and IVDD under the background of microenvironment and immunity; highlights the significant advantages of reprogramming-derived cells compared to embryonic stem cells and mesenchymal stem cells, based on these advances, providing important strategies for its development and clinical application in OA and IVDD.

Clinical Features of Patients with Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disease and Isolated Seizure Symptoms.

Background: Myelin oligodendrocyte glycoprotein (MOG) antibody-associated encephalitis is a new clinical phenotype of inflammatory demyelinating diseases. Some MOG antibody-positive patients with central nervous system demyelinating events present with isolated seizures. However, there are gaps in the epidemiological knowledge regarding seizures with MOG antibody-associated encephalitis in adults. This study characterized the clinical features and treatment of MOG antibody-positive patients with isolated seizures. Methods: We reviewed all the patients admitted to Tianjin Huanhu Hospital between Jan. 1st 2017 and Jan. 1st 2022, to screen the MOG antibody-positive patients with isolated seizures, and collected the concerned patients' information regarding epidemiology, clinical presentations, laboratory and radiological characteristics, electroencephalogram (EEG), treatments, and prognoses. Results: We collected six MOG antibody-positive adult patients who had isolated symptomatic seizures. The mean age of the patients was 33 years (range, 29-40 years), and five (83.3%) were men. All patients presented with motor seizures, five (83.3%) had cognitive dysfunction, and only one (16.7%) had status epilepticus. Five (83.3%) patients had a good response to immunotherapy and antiseizure medications; only one had a sequela. The cerebrospinal fluid or serum anti-MOG antibody test turned negative over time. Discussion: The most common seizure type in patients with MOG antibody-associated encephalitis with isolated seizures was focal to bilateral tonic-clonic seizures, and most patients had a good prognosis. Adding antiseizure medications were beneficial for MOG antibody-positive patients with seizures. Relapses and sequelae were associated with low-dose, short-time, or delayed therapy, and wide-range demyelinating brain damage.

Immunomodulatory differences between mesenchymal stem cells from different oral tissues.

Mesenchymal stem cells (MSCs) have recently been identified as having potentially therapeutic immunomodulatory properties. MSCs isolated from different oral tissues have similar morphology and immunophenotypes, however, direct comparisons of their gene expression and immunomodulatory properties have not been conducted. We isolated alveolar bone-derived MSCs (aBMSCs), dental pulp stem cells (DPSCs) and gingiva-derived MSCs (GMSCs) from the same patients and compared their immunophenotypes and transcriptomes. Additionally, we compared their production of soluble immunomodulatory cytokines as well as their immunoregulatory properties in coculture with THP-1 human monocytic cells. RNA sequencing revealed distinct gene expression in DPSCs while aBMSCs and GMSCs had less differentially expressed genes. DPSCs also had significantly less secretion of osteopontin compared to aBMSCs and GMSCs. Finally, DPSCs did not exhibit an immunosuppresive effect on THP-1 cells to the same degree as aBMSCs and GMSCs. These findings demonstrate that MSCs from different oral tissues have distinct transcriptomes and immunoregulatory properties.

NEIL1 drives the initiation of colorectal cancer through transcriptional regulation of COL17A1.

Deficiency of DNA repair pathways drives the development of colorectal cancer. However, the role of the base excision repair (BER) pathway in colorectal cancer initiation remains unclear. This study shows that Nei-like DNA glycosylase 1 (NEIL1) is highly expressed in colorectal cancer (CRC) tissues and associated with poorer clinical outcomes. Knocking out neil1 in mice markedly suppresses tumorigenesis and enhances infiltration of CD8+ T cells in intestinal tumors. Furthermore, NEIL1 directly forms a complex with SATB2/c-Myc to enhance the transcription of COL17A1 and subsequently promotes the production of immunosuppressive cytokines in CRC cells. A NEIL1 peptide suppresses intestinal tumorigenesis in ApcMin/+ mice, and targeting NEIL1 demonstrates a synergistic suppressive effect on tumor growth when combined with a nuclear factor κB (NF-κB) inhibitor. These results suggest that combined targeting of NEIL1 and NF-κB may represent a promising strategy for CRC therapy.