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Abstract Clinical proteomics analysis is of great significance for analyzing pathological mechanisms and discovering disease-related biomarkers. Using computational methods to accurately predict disease types can effectively improve patient disease diagnosis and prognosis. However, how to eliminate the errors introduced by peptide precursor identification and protein identification for pathological diagnosis remains a major unresolved issue. Here, we develop a powerful end-to-end deep learning model, termed “MS1Former”, that is able to classify hepatocellular carcinoma tumors and adjacent non-tumor (normal) tissues directly using raw MS1 spectra without peptide precursor identification. Our model provides accurate discrimination of subtle m/z differences in MS1 between tumor and adjacent non-tumor tissue, as well as more general performance predictions for data-dependent acquisition, data-independent acquisition, and full-scan data. Our model achieves the best performance on multiple external validation datasets. Additionally, we perform a detailed exploration of the model’s interpretability. Prospectively, we expect that the advanced end-to-end framework will be more applicable to the classification of other tumors.

Abstract Osteoporosis is a major degenerative metabolic bone disease that threatens the life and health of postmenopausal women. Owing to limitations in detection methods and prevention strategy awareness, the purpose of osteoporosis treatment is more to delay further deterioration rather than to fundamentally correct bone mass. We aimed to clarify the pathogenesis of postmenopausal osteoporosis and optimize treatment plans. Our experiments were based on previous findings that oxidative stress mediates bone metabolism imbalance after oestrogen deficiency. Through energy metabolism-targeted metabolomics, we revealed that purine metabolism disorder is the main mechanism involved in inducing oxidative damage in bone tissue, which was verified via the use of machine-learning data from human databases. Xanthine and xanthine oxidase were used to treat osteoblasts to construct a purine metabolism disorder model. The activity and differentiation ability of osteoblasts decreased after X/XO treatment. Transcriptomic sequencing indicated that autophagic flux damage was involved in purine metabolism-induced oxidative stress in osteoblasts. Additionally, we performed serum metabolomics combined with network pharmacology to determine the pharmacological mechanism of metformin in the treatment of postmenopausal osteoporosis. HPRT1 was the potential target filtered from the hub genes, and FoxO1 signalling was the key pathway mediating the effect of metformin in osteoblasts. We also revealed that SIRT3-mediated deacetylation promoted the nuclear localization of FoxO1 to increase the expression of HPRT1. HPRT1 upregulation promoted purine anabolism and prevented the accumulation of ROS caused by purine catabolism to reverse oxidative damage in osteoblasts. We propose that purine metabolism disorder-induced oxidative stress is important for the pathogenesis of postmenopausal osteoporosis. The therapeutic mechanism of metformin should be confirmed through subsequent drug optimization and development studies to improve bone health in postmenopausal women.

Abstract Zeolite molecular sieves are potential adsorbents for wastewater treatment, characterized by high efficiency, simple process, easy regeneration, and low treatment cost. In this study, zeolite A molecular sieves were prepared using coal fly ash (CFA), which is an effective method for the utilization of CFA. The results showed that the CFA-based zeolite molecular sieves synthesized under optimized conditions exhibited excellent adsorption and removal rates (> 40%) for ammonia–nitrogen in wastewater of different concentrations and properties. The analysis of adsorption kinetics revealed that the adsorption process followed pseudo-second-order kinetics model, indicating that the adsorption of ammonia–nitrogen on zeolite is primarily controlled by chemisorption rather than physisorption. The adsorption process can be divided into two stages, with a higher adsorption rate and a smaller diffusion boundary layer thickness in the first stage, and a lower adsorption rate and an increased diffusion boundary layer thickness in the second stage. This indicates that as the adsorption proceeds, the internal diffusion resistance within the particles gradually increases, leading to a decrease in the adsorption rate until reaching equilibrium, where both the diffusion and adsorption become stable. The adsorption isotherms of ammonia–nitrogen on zeolite A conformed to the assumptions of the Langmuir model, suggesting that the adsorption mechanism primarily involves uniform monolayer adsorption on the surface without intermolecular interactions.

Abstract Osteoarthritis (OA) is a common joint disease associated with the aging of the population, and it reduces the quality of life of patients. It is characterized by the destruction of articular cartilage and the secretion of inflammatory cytokines. Owing to the unclear pathogenesis of OA, current treatment methods have significant limitations. Oxidative stress has been revealed to play an important role in the development of OA. Our experiments indicated that the levels of GSH decreased and the level of MDA increased in chondrocytes, which induced ferroptosis in chondrocytes in OA. We also revealed that ferroptosis was the main mechanism of cartilage destruction caused by the addition of the ferroptosis activator erastin and the ferroptosis inhibitor ferrostatin-1. NOX1 is the main modulator of oxidative stress by increasing the generation of reactive oxidative species (ROS). We suppressed the expression of NOX1 in chondrocytes through cell transfection. The expression of collagen II and MMP13, and the secretion of IL-1β and TNF-α were reversed. An increase in the mitochondrial membrane potential and a decrease in the level of intracellular ROS indicate an improvement in oxidative damage. Additionally, we determined the effect of the Nrf2/HO-1 pathway on NOX1-mediated chondrocyte injury. We found that NOX1 inhibited the expression of Nrf2/HO-1, but the activation of Nrf2 improved the oxidative damage to chondrocytes in vivo and vitro. This study revealed that NOX1-mediated oxidative stress induces chondrocyte ferroptosis by inhibiting the Nrf2/HO-1 pathway. Our findings contribute to revealing the pathogenesis of OA, providing targets for drug design and optimizing the clinical treatment of OA.

Abstract Background Pneumoconiosis has a significant impact on the quality of patient survival. This study aims to evaluate the performance and application value of improved Unet network technology in the recognition and segmentation of lesion areas of lung CT images in patients with pneumoconiosis. Methods A total of 1212 lung CT images of patients with pneumoconiosis were retrospectively included. The improved Unet network was used to identify and segment the CT image regions of the patients’ lungs, and the image data of the granular regions of the lungs were processed by the watershed and region growing algorithms. After random sorting, 848 data were selected into the training set and 364 data into the validation set. The experimental dataset underwent data augmentation and were used for model training and validation to evaluate segmentation performance. The segmentation results were compared with FCN-8s, Unet network (Base), Unet (Squeeze-and-Excitation, SE + Rectified Linear Unit, ReLU), and Unet + + networks. Results In the segmentation of lung CT granular region with the improved Unet network, the four evaluation indexes of Dice similarity coefficient, positive prediction value (PPV), sensitivity coefficient (SC) and mean intersection over union (MIoU) reached 0.848, 0.884, 0.895 and 0.885, respectively, increasing by 7.6%, 13.3%, 3.9% and 6.4%, respectively, compared with those of Unet network (Base), and increasing by 187.5%, 249.4%, 131.9% and 51.0%, respectively, compared with those of FCN-8s, and increasing by 14.0%, 31.2%, 4.7% and 9.7%, respectively, compared with those of Unet network (SE + ReLU), while the segmentation performance was also not inferior to that of the Unet + + network. Conclusions The improved Unet network proposed shows good performance in the recognition and segmentation of abnormal regions in lung CT images in patients with pneumoconiosis, showing potential application value for assisting clinical decision-making.

Abstract Background Spinal intradural tumors are rare and heterogeneous in histological type, aggressiveness, and symptomatology, and there is a lack of data about them. This study investigated the epidemiological features of spinal intradural tumors. Methods This retrospective analysis included patients with spinal intradural tumors who underwent surgical treatment at the Myelopathy and Spondylosis Ward Beijing Jishuitan Hospital between January 2012 and December 2022. Results This study included 1321 patients [aged 47.19 ± 14.90 years, 603 (45.65%) males] with spinal intradural tumors. The most common histological subtype was schwannoma [n = 511 (38.68%)], followed by spinal meningioma [n = 184 (13.93%)] and ependymoma [n = 101 (7.65%)]. Fifteen (1.14%) patients were diagnosed with metastatic spinal intradural tumors as a presentation of another primary cancer type. The spinal intradural tumors were mostly found in the lumbar region [n = 436 (33.01%)], followed by the thoracic vertebrae [n = 390 (29.52%)], cervical vertebrae [n = 154 (11.66%)], and thoracolumbar region [n = 111 (8.40%)]. Schwannomas mostly affected the lumbar region [n = 256 (52.64%)], spinal meningiomas in the thoracic region [n = 153 (83.15)], and ependymomas in the lumbar region [56 (55.45%)]. The de novo metastases were mostly found in the lumbar region [n = 8 (53.33%)]. Conclusion According to the results of our single-center study, the most common spinal intradural tumor in Northern China is schwannoma, followed by spinal meningioma and ependymoma.

The development of effective cancer treatments is a popular in contemporary medical research. Immunotherapy, the fourth most common cancer treatment method, relies on activating autoimmune function to eradicate tumors and exhibits advantages such as a good curative effect and few side effects. In recent years, tumor vaccines that activate the stimulator of interferon genes (STING) pathway are being actively researched in the field of immunotherapy; however, their application is still limited because of the rapid clearance rate of tumor-related lymph nodes and low efficiency of antigen presentation. The rise of nanomedicine has provided new opportunities for solving these problems. By preparing materials with adjuvant effects nanoparticles, the small size of nanoparticles can be exploited to enable the entry of vaccines into tumor-related lymph nodes to accurately deliver STING agonists and activate the immune response. Based on this, this paper reviews various types of nano-adjuvants based on metals, platinum chemotherapy drugs, camptothecin derivatives, deoxyribonucleic acid, etc. and highlights the transformation prospects of these nano-adjuvants in tumor vaccines to provide a reference for promoting the development of nano-medicine and tumor vaccinology.

We reviewed research on SARS-CoV-2 and influenza virus detection on surfaces, their persistence under various conditions, and response to disinfectants. Viral contamination in community and healthcare settings was analyzed, emphasizing survival on surfaces influenced by temperature, pH, and material. Findings showed higher concentrations enhance survivability at room temperature, whereas stability increases at 4°C. Both viruses decline in low pH and high heat, with influenza affected by salinity. On various material surfaces, SARS-CoV-2 and influenza viruses demonstrate considerable variations in survival durations, and SARS-CoV-2 is more stable than influenza virus. On the skin, both virus types can persist for ≥2 h. Next, we delineated the virucidal efficacy of disinfectants against SARS-CoV-2 and influenza viruses. In daily life, exposure to ethanol (70%), isopropanol (70%), bleach (10%), or hydrogen peroxide (1–3%) for 15–30 min can effectively inactive various SARS-CoV-2 variants. Povidone-iodine (1 mg/mL, 1 min) or cetylpyridinium chloride (0.1 mg/mL, 2 min) may be used to inactive different SARS-CoV-2 variants in the mouth. Chlorine disinfectants (500 mg/L) or ultraviolet light (222 nm) can effectively inhibit different SARS-CoV-2 variants in public spaces. In conclusion, our study provides a scientific basis and practical guidance for reduction of viral persistence (retention of infectivity) on surfaces and environmental cleanliness.

In 2009, severe fever with thrombocytopenia syndrome virus (SFTSV), also known as the Dabie bandavirus (DBV), was first discovered in Henan, China. It is a tick-borne zoonotic virus with a fatality rate ranging from 6% to 30%. Currently, we lack safe and effective vaccines or antiviral drugs to treat SFTSV infection. Therefore, the development of a specific, sensitive, and cost-effective detection method is crucial. Using inactivated SFTSV and recombinant SFTSV nucleocapsid protein (SFTSV-NP), we repeatedly immunized mice with different adjuvants and obtained two monoclonal antibodies against SFTSV-NP, which were used to develop a colloidal gold immunochromatographic assay (ICA) rapid test kit for SFTSV. Compared with nucleic acid testing (gold standard), the ICA test strips are 97.67% accurate in testing clinical serum samples (36 cases of clinical serum samples and seven cases of whole blood samples). The test kit was 100% accurate in detecting different SFTSV strains. No false-positive results were generated when detecting other arboviruses. Therefore, our developed SFTSV test kit conveniently, rapidly, and effectively detects SFTSV.

One of the most prevalent pathological types of Primary Liver Cancer (PLC) is the Hepatocellular Carcinoma (HCC) poses a global health issue. The high recurrence and metastasis rate of HCC, coupled with a low 5-year survival rate, result in a bleak prognosis. Exosomes, small extracellular vesicles released by various cells, contain diverse non-coding RNA molecules, including circular RNAs (circRNAs), which play a significant role in intercellular communication and can impact HCC progression. Studies have revealed the potential clinical applications of exosomal circRNAs as biomarkers and therapeutic targets for HCC. These circRNAs can be transferred via exosomes to nearby non-cancerous cells, thereby regulating HCC progression and influencing malignant phenotypes, such as cell proliferation, invasion, metastasis, and drug resistance. This review provides a comprehensive overview of the identified exosomal circRNAs, highlighting their potential as non-invasive biomarkers for HCC, and suggesting new perspectives for HCC diagnosis and treatment. The circRNA from exosomal organelles promotes metastasis and immune scape because of their unique chirality which is different from the Biomolecular Homochirality.

Actinobacillus pleuropneumoniae, a significant respiratory pig pathogen, is causing substantial losses in the global swine industry. The resistance spectrum of A. pleuropneumoniae is expanding, and multidrug resistance is a severe issue. Horizontal gene transfer (HGT) plays a crucial role in the development of the bacterial genome by facilitating the dissemination of resistance determinants. However, the horizontal transfer of resistance genes via A. pleuropneumoniae-derived outer membrane vesicles (OMVs) has not been previously reported. In this study, we used Illumina NovaSeq and PacBio SequeI sequencing platforms to determine the whole genome sequence of A. pleuropneumoniae GD2107, a multidrug-resistant (MDR) isolate from China. We detected a plasmid in the isolate named pGD2107-1; the plasmid was 5,027 bp in size with 7 putative open reading frames (ORF) and included the floR resistance genes. The carriage of resistance genes in A. pleuropneumoniae OMVs was identified using a polymerase chain reaction (PCR) assay, and then we thoroughly evaluated the influence of OMVs on the horizontal transfer of drug-resistant plasmids. The transfer of the plasmid to recipient bacteria via OMVs was confirmed by PCR. In growth competition experiments, all recipients carrying the pGD2107-1 plasmid exhibited a fitness cost compared to the corresponding original recipients. This study revealed that OMVs could mediate interspecific horizontal transfer of the resistance plasmid pGD2107-1 into Escherichia coli recipient strains and significantly enhance the resistance of the transformants. In summary, A. pleuropneumoniae-OMVs play the pivotal role of vectors for dissemination of the floR gene spread and may contribute to more antimicrobial resistance gene transfer in other Enterobacteriaceae.

Abstract A comprehensive understanding of the transient characteristics in solid oxide cells (SOCs) is crucial for advancing SOC technology in renewable energy storage and conversion. However, general formulas describing the relationship between SOC transients and multiple parameters remain elusive. Through comprehensive numerical analysis, we find that the thermal and gaseous response times of SOCs upon rapid electrical variations are on the order of two characteristic times (τ h and τ m), respectively. The gaseous response time is approximately 1τ m, and the thermal response time aligns with roughly 2τ h. These characteristic times represent the overall heat and mass transfer rates within the cell, and their mathematical relationships with various SOC design and operating parameters are revealed. Validation of τ h and τ m is achieved through comparison with an in-house experiment and existing literature data, achieving the same order of magnitude for a wide range of electrochemical cells, showcasing their potential use for characterizing transient behaviors in a wide range of electrochemical cells. Moreover, two examples are presented to demonstrate how these characteristic times can streamline SOC design and control without the need for complex numerical simulations, thus offering valuable insights and tools for enhancing the efficiency and durability of electrochemical cells.

Streptococcus suis serotype 2 (S. suis 2) is a zoonotic pathogen that clinically causes severe swine and human infections (such as meningitis, endocarditis, and septicemia). In order to cause widespread diseases in different organs, S. suis 2 must colonize the host, break the blood barrier, and cause exaggerated inflammation. In the last few years, most studies have focused on a single virulence factor and its influences on the host. Membrane vesicles (MVs) can be actively secreted into the extracellular environment contributing to bacteria-host interactions. Gram-negative bacteria-derived outer membrane vesicles (OMVs) were recently shown to activate host Caspase-11-mediated non-canonical inflammasome pathway via deliverance of OMV-bound lipopolysaccharide (LPS), causing host cell pyroptosis. However, little is known about the effect of the MVs from S. suis 2 (Gram-positive bacteria without LPS) on cell pyroptosis. Thus, we investigated the molecular mechanism by which S. suis 2 MVs participate in endothelial cell pyroptosis. In this study, we used proteomics, electron scanning microscopy, fluorescence microscope, Western blotting, and bioassays, to investigate the MVs secreted by S. suis 2. First, we demonstrated that S. suis 2 secreted MVs with an average diameter of 72.04 nm, and 200 proteins in MVs were identified. Then, we showed that MVs were transported to cells via mainly dynamin-dependent endocytosis. The S. suis 2 MVs activated NLRP3/Caspase-1/GSDMD canonical inflammasome signaling pathway, resulting in cell pyroptosis, but it did not activate the Caspase-4/-5 pathway. More importantly, endothelial cells produce large amounts of reactive oxygen species (ROS) and lost their mitochondrial membrane potential under induction by S. suis 2 MVs. The results in this study suggest for the first time that MVs from S. suis 2 were internalized by endothelial cells via mainly dynamin-dependent endocytosis and might promote NLRP3/Caspase-1/GSDMD pathway by mitochondrial damage, which produced mtDNA and ROS under induction, leading to the pyroptosis of endothelial cells.

Renal fibrosis is a devastating consequence of progressive chronic kidney disease, representing a major public health challenge worldwide. The underlying mechanisms in the pathogenesis of renal fibrosis remain unclear, and effective treatments are still lacking. Renal tubular epithelial cells (RTECs) maintain kidney function, and their dysfunction has emerged as a critical contributor to renal fibrosis. Cellular quality control comprises several components, including telomere homeostasis, ubiquitin-proteasome system (UPS), autophagy, mitochondrial homeostasis (mitophagy and mitochondrial metabolism), endoplasmic reticulum (ER, unfolded protein response), and lysosomes. Failures in the cellular quality control of RTECs, including DNA, protein, and organelle damage, exert profibrotic functions by leading to senescence, defective autophagy, ER stress, mitochondrial and lysosomal dysfunction, apoptosis, fibroblast activation, and immune cell recruitment. In this review, we summarize recent advances in understanding the role of quality control components and intercellular crosstalk networks in RTECs, within the context of renal fibrosis.

Summary: Background: Toripalimab, a novel PD-1 antibody, is approved for treatment of multiple solid tumors; however, its neoadjuvant use with chemotherapy for triple-negative breast cancer (TNBC) remains unevaluated. Additionally, induction chemotherapy followed by de-escalation of neoadjuvant immunotherapy remains underexplored. Therefore, we conducted a phase II trial investigating a novel neoadjuvant chemoimmunotherapy regimen including de-escalation of immunotherapy for early-stage TNBC. Methods: Chemotherapy and anti-PD-1 therapy were sequentially administered in a neoadjuvant setting to female patients with histologically confirmed stage II–III TNBC between June 9, 2020, and March 24, 2022. Patients received neoadjuvant therapy with four cycles of epirubicin-cyclophosphamide every 2 weeks, followed by toripalimab (240 mg) every 3 weeks plus nab-paclitaxel weekly for 12 weeks. The primary endpoint was total pathological complete response (tpCR; ypT0/is ypN0). Key secondary endpoints included breast pCR (bpCR; ypT0/is), event-free survival and biomarker analysis. Safety was also assessed. This study was registered with ClinicalTrials.gov (NCT04418154). Findings: Among 70 enrolled patients (median age, 51 years; 62.9% stage III), 66 completed treatment without progression and subsequently underwent surgery. The percentages of patients with a tpCR and bpCR were 39 of 70 (55.7%, 95% confidence interval [CI]: 43.3–67.6) and 41 of 70 (58.6%, 95% CI 46.2–70.2), respectively. Sixteen (22.9%) patients experienced grade ≥3 adverse events (AEs), frequently neutropenia (12, 17.1%) and leukopenia (11, 15.7%). The most common immune-related AE was hypothyroidism (5, 7.1%, all grade 1–2). Interpretation: Including 12 weeks of toripalimab in neoadjuvant chemotherapy conferred encouraging activity and manageable toxicity in patients with early TNBC, and this regimen warrants further investigation. Funding: National Natural Science Foundation of China, Junshi Biosciences, and Jiangsu Hengrui Pharmaceuticals.

Abstract The late‐stage union of Pangea was associated with the convergence of Siberia with Laurussia, but the exact timing remains unclear. The orogenic duration of the Kazakhstan block can provide geochronological constraints as it connects Siberia, Baltica, and Tarim. Zircon petrochronology offers a reliable approach for ascertaining the lifespan of an ancient orogen. In this study, we explore three phases of magmatism recorded in detrital zircons from late Paleozoic and Mesozoic sandstone‐siltstones in Western Tianshan, that is, 400–470 Ma, 320–380 Ma, and 280–320 Ma. Based on their age‐propagated Hf isotopes, melt SiO2 contents, and crustal thicknesses, our findings suggest that the southern limb of Kazakhstan underwent the early Paleozoic amalgamation of microcontinents with arcs, the late Paleozoic maturation of an Andean‐like continental arc, and the late Carboniferous collision of Kazakhstan with the Junggar oceanic basin and the Tarim craton. Such characteristics manifest the long‐term orogenic progression of Kazakhstan. Combining published timelines and paleolatitudes of major orogens and blocks, we propose that the Kazakhstan block welded northeastern Pangea along with the cessation of these orogenic activities around it. Consequently, by docking Kazakhstan with surrounding cratons, the fundamental configuration of Pangea could have been established in the late Carboniferous.