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Abstract The increasing utilization of mouse models in human neuroscience research places higher demands on computational methods to translate findings from the mouse brain to the human one. In this study, we develop BrainAlign, a self-supervised learning approach, for the whole brain alignment of spatial transcriptomics (ST) between humans and mice. BrainAlign encodes spots and genes simultaneously in two separated shared embedding spaces by a heterogeneous graph neural network. We demonstrate that BrainAlign could integrate cross-species spots into the embedding space and reveal the conserved brain regions supported by ST information, which facilitates the detection of homologous regions between humans and mice. Genomic analysis further presents gene expression connections between humans and mice and reveals similar expression patterns for marker genes. Moreover, BrainAlign can accurately map spatially similar homologous regions or clusters onto a unified spatial structural domain while preserving their relative positions.

Abstract N-type polycrystalline SnSe is considered as a highly promising candidates for thermoelectric applications due to facile processing, machinability, and scalability. However, existing efforts do not enable a peak ZT value exceeding 2.0 in n-type polycrystalline SnSe. Here, we realized a significant ZT enhancement by leveraging the synergistic effects of divacancy defect and introducing resonance level into the conduction band. The resonance level and increased density of states resulting from tungsten boost the Seebeck coefficient. The combination of the enhanced electrical conductivity (achieved by increasing carrier concentration through WCl6 doping and Se vacancies) and large Seebeck coefficient lead to a high power factor. Microstructural analyses reveal that the co-existence of divacancy defects (Se vacancies and Sn vacancies) and endotaxial W- and Cl-rich nanoprecipitates scatter phonons effectively, resulting in ultralow lattice conductivity. Ultimately, a record-high peak ZT of 2.2 at 773 K is achieved in n-type SnSe0.92 + 0.03WCl6.

Abstract Whole-body regeneration of planarians is a natural wonder but how it occurs remains elusive. It requires coordinated responses from each cell in the remaining tissue with spatial awareness to regenerate new cells and missing body parts. While previous studies identified new genes essential to regeneration, a more efficient screening approach that can identify regeneration-associated genes in the spatial context is needed. Here, we present a comprehensive three-dimensional spatiotemporal transcriptomic landscape of planarian regeneration. We describe a pluripotent neoblast subtype, and show that depletion of its marker gene makes planarians more susceptible to sub-lethal radiation. Furthermore, we identified spatial gene expression modules essential for tissue development. Functional analysis of hub genes in spatial modules, such as plk1, shows their important roles in regeneration. Our three-dimensional transcriptomic atlas provides a powerful tool for deciphering regeneration and identifying homeostasis-related genes, and provides a publicly available online spatiotemporal analysis resource for planarian regeneration research.

For high frequency noise, a new $ 2n $-th order cascade extended state observer with dynamic dead-zone structure is proposed in this paper. Dead zone dynamic consists of two parts. One is to "trim" the effect of noise by cutting off the part that falls in the dead zone. The other part pushes the dead zone amplitude to converge to 0 as soon as possible to ensure the convergence of the estimation error. Moreover, in the cascade structure, the high-gain parameter grows only to a second power, thus avoiding excessive amplification of the measurement noise and solving numerical implementation problems. The design procedure ensures that the extended state observer is input-to-state stable. Numerical simulations show the improvement in terms of total disturbance estimation and noise attenuation. The frequency-domain analysis of the proposed ESO using the describing function method investigates the effect of the dead zone nonlinear parameter on the performance of a closed-loop system.

Abstract Site investigation, deformation monitoring, laboratory test, and theoretical calculations were used to analyze the evolution details of a large expressway roadside landslide during the start-up sliding process. The monitoring results show that the initial deformation and failure occurred on the protective wall at the slope toe, then gradually developed to the upper part of the slope, and finally led to tensile cracks at the slope trailing edge. Accelerated deformation of the slope support structures, such as the protective wall at the slope toe, the anti-slide pile, and the anchor cable, were observed during the continuous extreme rainfall. The infiltrated rainwater can change the weight, the osmotic pressure, the anti-sliding force, the sliding force of the sliding mass, and further soften the fully weathered tuff soil and reduce its strength, resulting in the landslide occurrence. Block the slope surface runoff is an effective measure to reduce the landslide risk. The current analysis will be helpful to the prevention, control, and emergency disposal of similar landslides.

IntroductionThis study was designed to investigate the effect of running exercise on improving bone health in aging mice and explore the role of the SIRT1 in regulating autophagy and osteogenic differentiation of Bone marrow Mesenchymal Stem Cells (BMSCs).MethodsTwelve-month-old male C57BL/6J mice were used in this study as the aging model and were assigned to treadmill running exercise for eight weeks. Non-exercise male C57BL/6J mice of the same old were used as aging control and five-month-old mice were used as young controls. BMSCs were isolated from mice and subjected to mechanical stretching stimulation in vitro.ResultsThe results showed that aging mice had lower bone mass, bone mineral density (BMD), and autophagy than young mice, while running exercise improved BMD and bone mass as well as upregulated autophagy in bone cells. Mechanical loading increased osteogenic differentiation and autophagy in BMSCs, and knockdown of SIRT1 in BMSCs demonstrated that SIRT1-regulated autophagy involved the mechanical loading activation of osteogenic differentiation.ConclusionTaken together, this study revealed that exercise improved bone health during aging by activating bone formation, which can be attributed to osteogenic differentiation of BMSCs through the activation of SIRT1-mediated autophagy. The mechanisms underlying this effect may involve mechanical loading.

An increase in trade policy uncertainty raises policymakers’ concerns, as it can be harmful to investments and growth globally. This study examines the impact of reducing trade policy uncertainty on export product quality. Based on the ASEAN–China Free Trade Area (ACFTA), the difference-in-difference, two-way fixed, and triple difference methods were used to conduct benchmark tests. The results show that reducing trade policy uncertainty improves export product quality. Social capital has strengthened the role of the changing trade environments. The results were robust after the PSM-DID, placebo test, and deletion of outliers. Furthermore, the role of social capital is incorporated into the regression model. From the perspective of informal internal systems, this study expands the theoretical view of regional trade integration research and answers the current trade strategy adjustment and export transformation policy concerns.

Articular cartilage degeneration has been proved to cause a variety of joint diseases, among which osteoarthritis is the most typical. Osteoarthritis is characterized by articular cartilage degeneration and persistent pain, which affects the quality of life of patients as well as brings a heavy burden to society. The occurrence and development of osteoarthritis is related to the disorder of the subchondral bone microenvironment. Appropriate exercise can improve the subchondral bone microenvironment, thus playing an essential role in preventing and treating osteoarthritis. However, the exact mechanism whereby exercise improves the subchondral bone microenvironment remains unclear. There is biomechanical interaction as well as biochemical crosstalk between bone and cartilage. And the crosstalk between bone and cartilage is the key to bone-cartilage homeostasis maintenance. From the perspective of biomechanical and biochemical crosstalk between bone and cartilage, this paper reviews the effects of exercise-mediated bone-cartilage crosstalk on the subchondral bone microenvironment, aiming to provide a theoretical basis for the prevention and treatment of degenerative bone diseases.

Breakthrough technologies for spatially resolved transcriptomics have enabled genome-wide profiling of gene expressions in captured locations. Here the authors integrate gene expressions and spatial locations to identify spatial domains using an adaptive graph attention auto-encoder.

Abstract The exploration of single‐cell 3D genome maps reveals that chromatin domains are indeed physical structures presenting in single cells, and domain boundaries vary from cell to cell. However, systematic analysis of the association between regulatory factor binding and elements and the formation of chromatin domains in single cells has not yet emerged. To this end, a hierarchical chromatin domain structure identification algorithm (named as HiCS) is first developed from individual single‐cell Hi‐C maps, with superior performance in both accuracy and efficiency. The results suggest that in addition to the known CTCF‐cohesin complex, Polycomb, TrxG, pluripotent protein families, and other multiple factors also contribute to shaping chromatin domain boundaries in single embryonic stem cells. Different cooperation patterns of these regulatory factors drive genomic position categories with differential preferences forming boundaries, and the most extensive six types of retrotransposons are differentially distributed in these genomic position categories with preferential localization. The above results suggest that these different retrotransposons within genomic regions interplay with regulatory factors navigating the preference of genomic positions forming boundaries, driving the formation of higher‐order chromatin structures, and thus regulating cell functions in single mouse embryonic stem cells.

This paper studies the distribution characteristics of acoustic emission (AE) events in supporting roadways under different dynamic load conditions through numerical simulation and theoretical analysis. According to the principle of AE numerical simulation, the roadway model is established by FLAC3D software, and the supporting structure of the bolt cable is established by editing the Fish function. According to the model dynamic load application criterion, the relationship between the peak velocity of the particle, the distance from the source center to the dynamic impact damage point, and the dynamic load intensity is introduced. The velocity-distance-energy relationship is deduced from the relationship to determine the magnitude of the dynamic load energy. The simulation results show that the intensity of the dynamic load source and the distance of the dynamic load source directly impact the AE events. The larger the dynamic load intensity and the closer to the dynamic load source, the more concentrated the AE events. The roadway has a blocking effect on the transmission of the dynamic load stress waves. According to this characteristic, the roadway can be protected by a high-pressure relief roadway. Rock lithology greatly influences the transmission of dynamic load stress waves and the number of AE events. When the dynamic load stress wave passes through the rock strata of different lithologies, the attenuation of the dynamic load energy and the number of AE events are large. However, when the dynamic load stress wave passes through the rock strata of the same lithology, the attenuation of the dynamic load energy and AE events is small. The surrounding rock structure in the bottom corner area of the roadway is susceptible to disturbance from dynamic load sources above the roadway. The results are greatly significant for studying the AE characteristics of support roadways with disturbance-typeimpact failure.

Deregulation of Pol III products causes a range of diseases, including neural diseases and cancers. However, the factors and mechanisms that modulate Pol III-directed transcription remain to be found, although massive advances have been achieved. Here, we show that STAT3 positively regulates the activities of Pol III-dependent transcription and cancer cell growth. RNA-seq analysis revealed that STAT3 inhibits the expression of TP73, a member of the p53 family. We found that TP73 is not only required for the regulation of Pol III-directed transcription mediated by STAT3 but also independently suppresses the synthesis of Pol III products. Mechanistically, TP73 can disrupt the assembly of TFIIIB subunits and inhibit their occupancies at Pol III target loci by interacting with TFIIIB subunit TBP. MiR-106a-5p can activate Pol III-directed transcription by targeting the TP73 mRNA 3’ UTR to reduce TP 73 expression. We show that STAT3 activates the expression of miR-106a-5p by binding to the miRNA promoter, indicating that the miR-106a-5p links STAT3 with TP73 to regulate Pol III-directed transcription. Collectively, these findings indicate that STAT3 functions as a positive regulator in Pol III-directed transcription by controlling the miR-106a-5p/TP73 axis.

The predicted age difference (PAD) between an individual’s predicted brain age and chronological age has been commonly viewed as a meaningful phenotype relating to aging and brain diseases. However, the systematic bias appears in the PAD achieved using machine learning methods. Recent studies have designed diverse bias correction methods to eliminate it for further downstream studies. Strikingly, here we demonstrate that bias still exists in the PAD of samples with the same age even after kind of correction. Therefore, current PAD may not be taken as a reliable phenotype and more investigations are needed to solve this fundamental defect. To this end, we propose an age-level bias correction method and demonstrate its efficacy in numerical experiments.

Background: We aimed to characterize the relationship between the serum 25-hydroxyvitamin D concentration and the circulating lipid concentrations of patients with NAFLD in the Hulunbuir region of China. Methods: One hundred fifty-six patients, who were diagnosed with NAFLD in the Physical Examination Department of the Second Clinical College of Inner Mongolia University for the Nationalities between January 2021 and March 2023, were recruited as NAFLD group, and 160 healthy people were recruited as a control group during the same period. The serum 25(OH)VitD, TBIL, TG, TC, LDL-C, HDL-C, AST, ALT, GGT, and FPG activities of the participants were measured, and hepatic ultrasonography was performed. Results: The BMI of the NAFLD group was higher than of the control group (p < 0.05). The serum 25(OH)VitD3 (p < 0.05) and the HDL-C concentrations of the NAFLD group were lower than those of the normal control group. However, the AST (p < 0.05), ALT (p < 0.05), and GGT (p < 0.05) activities, and the serum TG (p < 0.05), TC (p < 0.05), LDL-C (p < 0.05), and the fasting glucose (p < 0.05) concentrations of the NAFLD group were higher than those of the normal control group. The serum 25(OH)VitD3 concentrations of the NAFLD group significantly correlated negatively with BMI (r = -0.302, p < 0.01), TG (r = -0.221, p < 0.05), and fasting glucose (r = -0.236, p < 0.05). The BMI, TG, and fasting glucose of vitamin D-deficient participants were higher than of the participants with adequate or insufficient levels of vitamin D (p < 0.05). Finally, the BMI of vitamin D-deficient participants was higher than of those with an adequate vitamin D status (p < 0.05). Conclusions: A deficiency of 25(OH)VitD is more common in people from the Hulunbuir region of China than elsewhere. In addition, the vitamin D status is significantly associated with NAFLD; as the serum vitamin D concentration decreases, patients with NAFLD show greater dyslipidemia and hyperglycemia and a higher BMI. [ABSTRACT FROM AUTHOR]

Abstract Background Venous thromboembolism (VTE) is one of the leading complications in glioma patients. Neutrophil extracellular traps (NETs) have been reported to play a critical role in the physiopathology of cancer. We aimed to investigate the presence and potential role of NETs in the hypercoagulable state in glioma patients. Moreover, we evaluated the interaction between NETs and endothelial cells (ECs) in glioma patients. Methods The plasma levels of NETs were detected by enzyme‐linked immunosorbent assay. The NET procoagulant activity was performed based on fibrin formation assays. The NET generation and NET‐treated ECs in vitro were observed by confocal microscopy. Activated platelets (PLTs) and PLT‐neutrophil aggregates were detected by flow cytometry. Results Plasma NET markers were significantly higher in stage III/IV glioma patients than in stage I/II glioma patients and healthy subjects. PLTs from glioma patients tended to induce NET formation than those from healthy subjects. NETs contributed to the hypercoagulable state in glioma patients. After ECs were incubated with NETs isolated from stage III/IV glioma patients, they lost their intercellular connections and were converted into procoagulant phenotypes. Combining DNase I and activated protein C markedly decreased endothelial dysfunction. Conclusions Our results showed the interaction between NETs and hypercoagulability in glioma patients. Targeting NETs may be a potential therapeutic and prevention direction for thrombotic complications in glioma patients.

Abstract Background Severe carotid stenosis is a common cause of stroke. In addition, previous clinical studies revealed that patients symptomatic of carotid stenosis suffer from increased episodes of stroke compared with their asymptomatic counterparts. However, the mechanism underlying these differences in the recurrence of stroke remains unclear. Objective The present study aimed to evaluate the levels of neutrophil extracellular traps (NETs) in the plasma of patients with severe carotid stenosis and investigate whether NETs induced procoagulant activity (PCA) in severe carotid stenosis. The study also sought to investigate the interactions between platelets or endothelial cells (ECs) and NETs. Methods The levels of NETs in plasma were quantified using enzyme‐linked immunosorbent assay (ELISA). In addition, NETting neutrophils and neutrophil‐platelet aggregates were detected through flow cytometry. On the other hand, the morphology of NETs formation and endothelial cells were analyzed through confocal microscopy. Finally, the procoagulant activity (PCA) of NETs and endothelial cells were assessed through ELISA and fibrin formation. Results Patients with symptomatic carotid stenosis patients had significantly higher levels of NETs markers compared with their asymptomatic counterparts and healthy subjects. In addition, increased levels of neutrophil‐platelet aggregates induced the generation of NETs in patients with symptomatic carotid stenosis. Moreover, NETs contributed to PCA through tissue factor (TF), in patients with carotid stenosis. Furthermore, NETs disrupted the endothelial barrier and converted endothelial cells (ECs) into PCA to enhance the PCA in patients with carotid stenosis. Conclusions The current study revealed differences in the levels of NETs in the plasma of symptomatic and asymptomatic patients suffering from carotid stenosis. The study also uncovered the interaction between NETs and thrombogenicity in carotid stenosis. Therefore, inhibiting NETs may be a potential biomarker and therapeutic target for recurring stroke in severe carotid stenosis.

Abstract Site-directed mutagenesis for large plasmids is a difficult task that cannot easily be solved by the conventional methods used in many laboratories. In this study, we developed an effective method for Site-directed Mutagenesis for Large Plasmids (SMLP) based on a PCR technique. The SMLP method combines several effective approaches, including a high-efficiency DNA polymerase for the large DNA amplification, two independent PCR reactions and a fast recombinational ligation. Using this method, we have achieved a variety of mutants for the filamin A gene (7.9 kb) cloned in the pcDNA (5.4 kb) or the pLV-U6-CMV-EGFP (9.4 kb) plasmids, indicating that this method can be applied to site-directed mutagenesis for the plasmids up to 17.3 kb. We show that the SMLP method has a greater advantage than the conventional methods tested in this study, and this method can be applied to substitution, deletion, and insertion mutations for both large and small plasmids as well as the assembly of three fragments from PCR reactions. Altogether, the SMLP method is simple, effective, and beneficial to the laboratories that require completing the mutagenesis of large plasmids.

Bone homeostasis involves bone formation and bone resorption, which are processes that maintain skeletal health. Oxidative stress is an independent risk factor, causing the dysfunction of bone homeostasis including osteoblast-induced osteogenesis and osteoclast-induced osteoclastogenesis, thereby leading to bone-related diseases, especially osteoporosis. Autophagy is the main cellular stress response system for the limination of damaged organelles and proteins, and it plays a critical role in the differentiation, apoptosis, and survival of bone cells, including bone marrow stem cells (BMSCs), osteoblasts, osteoclasts, and osteocytes. High evels of reactive oxygen species (ROS) induced by oxidative stress induce autophagy to protect against cell damage or even apoptosis. Additionally, pathways such as ROS/FOXO3, ROS/AMPK, ROS/Akt/mTOR, and ROS/JNK/c-Jun are involved in the regulation of oxidative stress-induced autophagy in bone cells, including osteoblasts, osteocytes and osteoclasts. This review discusses how autophagy regulates bone formation and bone resorption following oxidative stress and summarizes the potential protective mechanisms exerted by autophagy, thereby providing new insights regarding bone remodeling and potential therapeutic targets for osteoporosis.