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Yang Xi,1,* Yu-Qin Deng,1,2,* Han-Da Li,1 Wo-Er Jiao,1 Jin Chen,2 Jian-Jun Chen,3 Ze-Zhang Tao1,2 1Department of Otolaryngology, Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, People’s Republic of China; 2Institute of Otolaryngology, Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, People’s Republic of China; 3Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Ze-Zhang Tao, Department of Otolaryngology, Head and Neck Surgery Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060, Hubei, People’s Republic of China, Tel +86 13907141892, Fax +86 27 88043958, Email taozezhang696@163.com Jian-Jun Chen, Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Jianghan District, Wuhan, 430060, Hubei, People’s Republic of China, Tel +86 13659851719, +86 27 85726300, Email ylly80331@163.comPurpose: Up to now, there is no generally accepted biomarker to indicate the clinical response of immunotherapy. This study mainly analyzed the correlation between eosinophil cationic protein-myeloperoxidase (ECP-MPO) test papers and other immunotherapy indices in subcutaneous immunotherapy of dust mites and to explore whether the test paper can be used as an auxiliary index to quickly evaluate the efficacy of immunotherapy.Patients and methods: This study included 53 participants who received subcutaneous immunotherapy at the allergy clinic of Renmin Hospital of Wuhan University and 28 control participants. Six visits were conducted during a prospective study over one year. The results of the ECP-MPO test paper, nasal secretion eosinophil smear and count, nasal secretion ECP concentration, and clinical symptom scores were collected during five follow-up visits after the start of subcutaneous immunotherapy. Th1/Th2/Th17 cytokines, chemokines, IgE, IgG4 against dust mite components, and ECP concentrations were detected in the serum of participants at baseline, six months, and one year after subcutaneous immunotherapy.Results: The ECP test paper is not only easy to operate, but also can effectively and quickly detect the concentrations of ECP in the nasal secretion and diagnose allergic rhinitis. Symptom score is an important index for evaluating clinical immune efficacy, during subcutaneous immunotherapy, the ECP test paper showed a positive correlation with the symptom score. Simultaneously, during immunotherapy, the changes in the chromogenic grading of the test paper were synchronized with the changes in inflammatory cytokines and eosinophilic chemokines in Th2 cells of serum dust mite IgE. The sIgG4 against dust mites weakly negatively correlated with the concentration of ECP in nasal secretions and the color classification of the ECP test paper.Conclusion: The ECP-MPO test paper has a certain correlation with subcutaneous immunotherapy markers of allergic rhinitis, indicating that the ECP test paper may become an auxiliary biomarker to replace other complex laboratory tests.Keywords: dust mites, ECP-MPO test paper, subcutaneous immunotherapy, allergic rhinitis

Yang Xi,1,* Yu-Qin Deng,1,2,* Han-Da Li,1 Wo-Er Jiao,1 Jin Chen,2 Jian-Jun Chen,3 Ze-Zhang Tao1,2 1Department of Otolaryngology, Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, People’s Republic of China; 2Institute of Otolaryngology, Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, People’s Republic of China; 3Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Ze-Zhang Tao, Department of Otolaryngology, Head and Neck Surgery Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060, Hubei, People’s Republic of China, Tel +86 13907141892, Fax +86 27 88043958, Email taozezhang696@163.com Jian-Jun Chen, Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Jianghan District, Wuhan, 430060, Hubei, People’s Republic of China, Tel +86 13659851719, Fax +86 27 85726300, Email ylly80331@163.comPurpose: To develop and evaluate the effectiveness/clinical application of an eosinophil cationic protein-myeloperoxidase (ECP-MPO) test paper before and after treatment in patients with allergic rhinitis (AR).Patients and Methods: We included 40 controls and 106 AR patients who were enrolled in the Allergy Clinic of Renmin Hospital of Wuhan University. Total IgE, specific IgE and skin prick test (SPT) were detected in all participants. AR patients were treated with oral cetirizine hydrochloride for 14 days. The ECP-MPO test paper results, nasal secretion smear and eosinophil counts, rhinoconjunctivitis total nasal symptom score (TNSS), quality of life questionnaire (RQLQ), visual analogue scale (VAS), serum Th1/Th2/Th17 cytokine, and chemokine data were collected pre- and post-treatment. ECP concentrations in nasal secretions were assessed by ELISA. Pearson correlation test and Kappa consistency test were used for statistical analysis.Results: The post-treatment colour grade of the ECP-MPO test paper was lower in AR patients than the pre-treatment grade. The chromogenic grade correlated positively with the ECP concentration and the eosinophil count in nasal secretions both before and after treatment. Positive ECP-MPO test paper results were consistent with positive SPT, Der p-IgE and Der f-IgE result (Kappa values, 0.843, 0.810, 0.795, respectively). The pre- and post-treatment chromogenic grades correlated positively with the TNSS (r1=0· 691; r2=0· 539), RQLQ (r1=0· 783; r2=0· 625), and VAS (r1=0· 703; r2=0· 682) scores in AR patients.Conclusion: The ECP-MPO test paper can effectively detect ECP in nasal secretions, and its results are consistent with those from the SPT, Der p-IgE and Der f-IgE result. Its chromogenic grade can reflect the symptom severity and specific cytokine and chemokine levels in AR patients.Keywords: allergic rhinitis, eosinophil cationic protein, nasal secretion, cytokine, chemokine

Xiaoyuan Liu,1 Huandong Li,2 Fang Luo,1 Lei Zhang,3 Ruquan Han,1 Baoguo Wang41Department of Anesthesiology, Beijing Tiantan Hospital, Capital Medical University, 2Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 3Department of Neuroradiology, Beijing Neurosurgical Institute, 4Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, People’s Republic of ChinaBackground: The default mode network (DMN) is closely associated with the maintenance of alertness and cognitive functions. This study aimed to observe the changes in DMN induced by increasing doses of propofol and progressively deepening sedation.Methods: Twelve healthy subjects were selected; they received target-controlled infusion of propofol (1.0 and 3.0 µg/mL of plasma) and underwent functional magnetic resonance imaging before sedation and when they achieved light and deep sedation states. The average degree, average shortest path length, global efficiency, local efficiency, and clustering coefficient of DMN were assessed to study the overall and internal changes of DMN with gradual changes in alertness level, as well as the relationship between thalamus and DMN. Meanwhile, basic vital signs and respiratory inhibition were recorded.Results: DMN parameters were gradually inhibited with decreasing level of alertness, the differences were significant between light sedation and awake states (all P

Abstract ZnO nano/microstructures have been formed by thermal evaporation method using ZnO powders mixed with carbon group elements (C, Si, Ge, Sn, or Pb) as the reducing agent. For cases of mixed precursors of ZnO/C, ZnO/Si, and ZnO/Ge, the pure ZnO nano/microstructures are realized, while for ZnO/Sn (ZnO/Pb) systems, the phase of Pb2O3(Zn2SnO4) generally are represented in the ZnO products. The appearance of Pb2O3(Zn2SnO4) is attributed to the lower melting point and higher vapor pressure of Sn (Pb) in the heating and evaporation processes. The morphologies and sizes of the products are controlled by adjusting the growth regions and/or introducing gaseous argon. Room temperature (RT) photoluminescence spectra indicate that the intensity (peak position) of the ultraviolet emission is increased (redshift) due to the existence of Zn2SnO4 phase in the ZnO products. The Pb2O3(Zn2SnO4) phase in ZnO nano/microstructures plays a important role in enhancing the saturation magnetizations of RT ferromagnetism with respect to the case of pure ZnO products fabricated by the precursor of mixed ZnO and graphite.

Macrophage polarization is vital to mounting a host defense or repairing tissue in various liver diseases. Excessive activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome is related to the orchestration of inflammation and alcohol-associated liver disease (ALD) pathology. Rab GTPases play critical roles in regulating vesicular transport. In this study we investigated the role of Rab11b in ALD, aiming to identify effective therapeutic targets. Here, we first demonstrated a decreased expression of Rab11b in macrophages from ALD mice. Knockdown of Rab11b by macrophage-specific adeno-associated virus can alleviate alcohol induced liver inflammation, injury and steatosis. We found that LPS and alcohol stimulation promoted Rab11b transferring from the nucleus to the cytoplasm in bone marrow-derived macrophages (BMDM) cells. Rab11b specifically activated the NLRP3 inflammasome in BMDMs and RAW264.7 cells to induce M1 macrophage polarization. Rab11b overexpression in BMDMs inhibited autophagic flux, leading to the suppression of LC3B-mediated NLRP3 degradation. We conclude that impaired Rab11b could alleviate alcohol-induced liver injury via autophagy-mediated NLRP3 degradation., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Shanghai Institute of Materia Medica, Chinese Academy of Sciences and Chinese Pharmacological Society.)

Background: The effect of nonalcoholic fatty liver disease (NAFLD) on the efficacy of nucleoside analogues (NAs) in antiviral therapy for patients with chronic hepatitis B (CHB) remains controversial., Aim: To investigate the influence of NAFLD on virological response in CHB patients undergoing NAs treatment., Methods: Logistic regression analysis was conducted on a cohort of 465 CHB patients from two hospitals to determine whether NAFLD was a risk factor for adverse reactions to NAs. CHB patients were followed up for more than 28 months after initial antiviral treatment, and further validation was performed using different viral load populations., Results: NAFLD was identified as an independent risk factor for partial virological response following antiviral therapy with NAs (odds ratio = 1.777, P = 0.017). In our subsequent analysis focusing on CHB patients with high viral load, the NAFLD group exhibited significantly longer virus shedding time and lower proportion of the complete virological response compared with the non-NAFLD group (16.8 ± 6.1 vs 13.0 ± 6.8, P < 0.05). During the 24-month period of antiviral treatment with NAs, hepatitis B virus (HBV) DNA levels decreased slowly in the NAFLD group, and the negative conversion rate of HBV was notably lower than that observed in non-NAFLD group ( P = 0.001). Similar results were obtained when analyzing patients with low baseline HBV viral load within the NAFLD group., Conclusion: Coexistence of NAFLD may diminish virological response among CHB patients receiving antiviral treatment with NAs., Competing Interests: Conflict-of-interest statement: The authors declare that they have no conflict of interest., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)

Background: The gold standard of care for patients with severe peripheral nerve injury is autologous nerve grafting; however, autologous nerve grafts are usually limited for patients because of the limited number of autologous nerve sources and the loss of neurosensory sensation in the donor area, whereas allogeneic or xenografts are even more limited by immune rejection. Tissue-engineered peripheral nerve scaffolds, with the morphology and structure of natural nerves and complex biological signals, hold the most promise as ideal peripheral nerve "replacements"., Aim: To prepare allogenic peripheral nerve scaffolds using a low-toxicity decellularization method, and use human umbilical cord mesenchymal stem cells (hUC-MSCs) as seed cells to cultivate scaffold-cell complexes for the repair of injured peripheral nerves., Methods: After obtaining sciatic nerves from New Zealand rabbits, an optimal acellular scaffold preparation scheme was established by mechanical separation, varying lyophilization cycles, and trypsin and DNase digestion at different times. The scaffolds were evaluated by hematoxylin and eosin (HE) and luxol fast blue (LFB) staining. The maximum load, durability, and elastic modulus of the acellular scaffolds were assessed using a universal material testing machine. The acellular scaffolds were implanted into the dorsal erector spinae muscle of SD rats and the scaffold degradation and systemic inflammatory reactions were observed at 3 days, 1 week, 3 weeks, and 6 weeks following surgery to determine the histocompatibility between xenografts. The effect of acellular scaffold extracts on fibroblast proliferation was assessed using an MTT assay to measure the cytotoxicity of the scaffold residual reagents. In addition, the umbilical cord from cesarean section fetuses was collected, and the Wharton's jelly (WJ) was separated into culture cells and confirm the osteogenic and adipogenic differentiation of mesenchymal stem cells (MSCs) and hUC-MSCs. The cultured cells were induced to differentiate into Schwann cells by the antioxidant-growth factor induction method, and the differentiated cells and the myelinogenic properties were identified., Results: The experiments effectively decellularized the sciatic nerve of the New Zealand rabbits. After comparing the completed acellular scaffolds among the groups, the optimal decellularization preparation steps were established as follows: Mechanical separation of the epineurium, two cycles of lyophilization-rewarming, trypsin digestion for 5 hours, and DNase digestion for 10 hours. After HE staining, no residual nuclear components were evident on the scaffold, whereas the extracellular matrix remained intact. LFB staining showed a significant decrease in myelin sheath composition of the scaffold compared with that before preparation. Biomechanical testing revealed that the maximum tensile strength, elastic modulus, and durability of the acellular scaffold were reduced compared with normal peripheral nerves. Based on the histocompatibility test, the immune response of the recipient SD rats to the scaffold New Zealand rabbits began to decline3 weeks following surgery, and there was no significant rejection after 6 weeks. The MTT assay revealed that the acellular reagent extract had no obvious effects on cell proliferation. The cells were successfully isolated, cultured, and passaged from human umbilical cord WJ by MSC medium, and their ability to differentiate into Schwann-like cells was demonstrated by morphological and immunohistochemical identification. The differentiated cells could also myelinate in vitro ., Conclusion: The acellular peripheral nerve scaffold with complete cell removal and intact matrix may be prepared by combining lyophilization and enzyme digestion. The resulting scaffold exhibited good histocompatibility and low cytotoxicity. In addition, hUC-MSCs have the potential to differentiate into Schwann-like cells with myelinogenic ability following in vitro induction., Competing Interests: Conflict-of-interest statement: The authors declare no competing interests., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)

Motivation: Isoforms spliced from the same gene may carry distinct biological functions. Therefore, annotating functions at the isoform level provides valuable insights into the functional diversity of genomes. Since experimental approaches for determining isoform functions are time- and cost-demanding, computational methods have been proposed. In this case, multi-omics data integration helps enhance the model performance, providing complementary insights for isoform functions. However, current methods underperform in leveraging diverse omics data, primarily due to the limited power to integrate the heterogeneous feature domains. Besides, among the multi-omics data, isoform-isoform interactions (IIIs) are a key data source, as isoforms interact with each other to perform functions. Unfortunately, IIIs remain largely underutilized in isoform function predictions until now., Results: We introduce CrossIsoFun, a multi-omics data analysis framework for isoform function prediction. CrossIsoFun combines omics-specific and cross-omics learning for data integration and function prediction. In detail, CrossIsoFun uses a graph convolutional network (GCN) as the omics-specific classifier for each data source. The initial label predictions from GCNs are forwarded to the View Correlation Discovery Network (VCDN) and processed as a cross-omics integrative representation. The representation is then used to produce final predictions of isoform functions. In addition, an antoencoder within a cycle-consistency generative adversarial network (cycleGAN) is designed to generate IIIs from PPIs and thereby enrich the interactomics data. Our method outperforms the state-of-the-art methods on three tissue-naive datasets and 15 tissue-specific datasets with mRNA expression, sequence, and PPI data. The prediction of CrossIsoFun is further validated by its consistency with subcellular localization and isoform-level annotations with literature support., Availability and Implementation: CrossIsoFun is freely available at https://github.com/genemine/CrossIsoFun., (© The Author(s) 2024. Published by Oxford University Press.)

Alzheimer's disease (AD) is a complex disease with its genetic etiology not fully understood. Gene network-based methods have been proven promising in predicting AD genes. However, existing approaches are limited in their ability to model the nonlinear relationship between networks and disease genes, because (i) any data can be theoretically decomposed into the sum of a linear part and a nonlinear part, (ii) the linear part can be best modeled by a linear model since a nonlinear model is biased and can be easily overfit, and (iii) existing methods do not separate the linear part from the nonlinear part when building the disease gene prediction model. To address the limitation, we propose linear model-integrated graph convolutional network (LIMO-GCN), a generic disease gene prediction method that models the data linearity and nonlinearity by integrating a linear model with GCN. The reason to use GCN is that it is by design naturally suitable to dealing with network data, and the reason to integrate a linear model is that the linearity in the data can be best modeled by a linear model. The weighted sum of the prediction of the two components is used as the final prediction of LIMO-GCN. Then, we apply LIMO-GCN to the prediction of AD genes. LIMO-GCN outperforms the state-of-the-art approaches including GCN, network-wide association studies, and random walk. Furthermore, we show that the top-ranked genes are significantly associated with AD based on molecular evidence from heterogeneous genomic data. Our results indicate that LIMO-GCN provides a novel method for prioritizing AD genes., (© The Author(s) 2024. Published by Oxford University Press.)

Background: Currently, there is a lack of evidence for the long-term bioprosthetic valve durability of patients with bicuspid aortic valve (BAV) following transcatheter aortic valve replacement (TAVR)., Methods and Results: This study aimed to evaluate hemodynamic outcome, structural valve deterioration, and bioprosthetic valve failure during long-term follow-up after TAVR in patients with BAV versus patients with tricuspid aortic valve (TAV). Patients with BAV and TAV who underwent TAVR between 2012 and 2020, with echocardiography followed for at least 3 years, were included. Baseline characteristics, long-term valve hemodynamic performance, structural valve deterioration, and bioprosthetic valve failure were compared between patients with BAV and TAV. A total of 170 patients with BAV and 145 patients with TAV were included. The mean duration of follow-up for patients with BAV and TAV was 5.2±1.8 and 5.0±1.7 years. No significant differences were observed in the rates of structural valve deterioration and bioprosthetic valve failure between patients with BAV and TAV: structural valve deterioration, BAV 20 (11.8%) versus TAV 16 (11.0%) at last follow-up ( P =0.861); bioprosthetic valve failure, BAV 3 (1.8%) versus TAV 7 (4.8%) at last follow-up ( P =0.196). More than moderate intravalvular aortic regurgitation (1.8% versus 4.8%, P =0.196) and paravalvular leak (6.5% versus 3.4%, P =0.305) were rare in both patients with BAV and patients with TAV., Conclusions: This study indicated satisfactory long-term valve durability of TAVR in patients with BAV. Comparable hemodynamic outcome, structural valve deterioration, and bioprosthetic valve failure could be achieved in patients with BAV and TAV during long-term follow-up after TAVR.

Introduction: Metabolic dysfunction-associated steatotic liver disease (MASLD) frequently confers an increased risk of vascular thrombosis; however, the marketed antiplatelet drugs are investigated for the prevention and treatment of MASLD in patients with these coexisting diseases., Methods: To determine whether clopidogrel could ameliorate high-fat diet (HFD)-induced hepatic steatosis in mice and how it works, mice were fed on normal diet or HFD alone or in combination with or without clopidogrel for 14 weeks, and primary mouse hepatocytes were treated with palmitate/oleate alone or in combination with the compounds examined for 24 h. Body weight, liver weight, insulin resistance, triglyceride and total cholesterol content in serum and liver, histological morphology, transcriptomic analysis of mouse liver, and multiple key MASLD-associated genes and proteins were measured, respectively., Results and Discussion: Clopidogrel mitigated HFD-induced hepatic steatosis (as measured with oil red O staining and triglyceride kit assay) and reduced elevations in serum aminotransferases, liver weight, and the ratio of liver to body weight. Clopidogrel downregulated the expression of multiple critical lipogenic ( Acaca / Acacb , Fasn , Scd1 , Elovl6 , Mogat1 , Pparg , Cd36 , and Fabp4 ), profibrotic ( Col1a1 , Col1a2 , Col3a1 , C ol4a1 , Acta2 , and Mmp2 ), and proinflammatory ( Ccl2 , Cxcl2 , Cxcl10 , Il1a , Tlr4 , and Nlrp3 ) genes, and enhanced phosphorylation of AMPK and ACC. However, compound C (an AMPK inhibitor) reversed enhanced phosphorylation of AMPK and ACC in clopidogrel-treated primary mouse hepatocytes and alleviated accumulation of intracellular lipids. We concluded that clopidogrel may prevent and/or reverse HFD-induced hepatic steatosis in mice, suggesting that clopidogrel could be repurposed to fight fatty liver in patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Tai, Shao, Zheng, Jiang, Han, Yin, Li, Ji, Mi, Yang, Feng, Duan and Xie.)

ETV6::ABL1 is a rare fusion gene that found in MPN, ALL, and AML. It has a complex and diverse formation mechanism due to the reciprocal orientations of the ETV6 and ABL1 genes relative to the centromeres. NPM1 is frequently mutated in adult AML, often accompanied by FLT3-ITD, which suggests molecular synergisms in AML pathogenesis. Previous reports on ETV6::ABL1 mostly focus on FLT3-ITD. In this study, we present a case of AML with ETV6::ABL1, along with NPM1 and FLT3-ITD. The patient showed a rapid increase in primitive cells at the initial stage, along with the presence of immature granulocytes and erythrocytes. Through cytogenetic analysis, fluorescence in situ hybridization (FISH), and RNA-seq, we elucidated the mechanism behind the formation of the ETV6::ABL1 fusion gene. Despite conventional chemotherapy failure and rapid tumor proliferation, we attempted to add FLT3 inhibitor sorafenib to the treatment, along with chemotherapy bridging to haploidentical transplantation. After haplo-HSCT, a combination of sorafenib and dasatinib was administered as maintenance therapy. The patient achieved complete remission (CR) and maintained it for 11 months. The intricate genetic landscape observed in this case presents diagnostic dilemmas and therapeutic challenges, emphasizing the importance of a comprehensive understanding of its implications for disease classification, risk stratification, and treatment selection., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

This study aimed to determine changes in the hydrolysis of vicagrel, a substrate drug of arylacetamide deacetylase (Aadac) and carboxylesterase 2 (Ces2), in P-glycoprotein (P-gp)-deficient or P-gp-inhibited mice and to elucidate the mechanisms involved.Male wild-type (WT) and P-gp knock-out (KO) mice were used to investigate the systemic exposure of vicagrel thiol active metabolite H4 and platelet response to vicagrel, and the mRNA and protein expression levels of intestinal Aadac and Ces2. Moreover, WT mice were administered vicagrel alone or in combination with elacridar (a potent P-gp inhibitor) to determine drug-drug interactions.Compared with WT mice, P-gp KO mice exhibited significant increases in the systemic exposure of H4, the protein expression levels of intestinal Aadac and Ces2, and inhibition of ADP-induced platelet aggregation by vicagrel. Further, the H4 exposure was positively correlated with intestinal Aadac protein expression levels but did not vary with short-term inhibition of P-gp efflux activity by elacridar.P-gp-deficient mice, rather than elacridar-treated mice, exhibited significant upregulation of intestinal Aadac and Ces2 and thus, enhanced metabolic activation of and platelet response to vicagrel, suggesting that the metabolic activation of vicagrel may vary with P-gp deficiency, not P-gp inhibition, in mice.

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate rare cell types and achieve accurate identification. We benchmark scCAD on 25 real-world scRNA-seq datasets, demonstrating its superior performance compared to 10 state-of-the-art methods. In-depth case studies across diverse datasets, including mouse airway, brain, intestine, human pancreas, immunology data, and clear cell renal cell carcinoma, showcase scCAD's efficiency in identifying rare cell types in complex biological scenarios. Furthermore, scCAD can correct the annotation of rare cell types and identify immune cell subtypes associated with disease, thereby offering valuable insights into disease progression., (© 2024. The Author(s).)

The effective isolation of rare target cells, such as circulating tumor cells, from whole blood is still challenging due to the lack of a capturing surface with strong target-binding affinity and non-target-cell resistance. Here we present a solution leveraging the flexibility of bacterial virus (phage) nanofibers with their sidewalls displaying target circulating tumor cell-specific aptamers and their ends tethered to magnetic beads. Such flexible phages, with low stiffness and Young's modulus, can twist and adapt to recognize the cell receptors, energetically enhancing target cell capturing and entropically discouraging non-target cells (white blood cells) adsorption. The magnetic beads with flexible phages can isolate and count target cells with significant increase in cell affinity and reduction in non-target cell absorption compared to magnetic beads having rigid phages. This differentiates breast cancer patients and healthy donors, with impressive area under the curve (0.991) at the optimal detection threshold (>4 target cells mL -1 ). Immunostaining of captured circulating tumor cells precisely determines breast cancer subtypes with a diagnostic accuracy of 91.07%. Our study reveals the power of viral mechanical attributes in designing surfaces with superior target binding and non-target anti-fouling., (© 2024. The Author(s).)

Motivation: Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited., Results: Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of employing hypergraphs for representing annotated gene sets. Second, we validate the accuracy of DISHyper-predicted cancer genes using functional validation results and multiple independent functional genomics data. Third, our model predicts 44 novel cancer genes, and subsequent analysis shows their significant associations with multiple types of cancers. Overall, our study provides a new perspective for discovering cancer genes and reveals previously undiscovered cancer genes., Availability and Implementation: DISHyper is freely available for download at https://github.com/genemine/DISHyper., (© The Author(s) 2024. Published by Oxford University Press.)

Objectives: Idiopathic inflammatory myopathies (IIMs) are a group of heterogeneous autoimmune diseases. Intron retention (IR) serves as an important post-transcriptional and translational regulatory mechanism. This study aims to identify changes in IR profiles in IIM subtypes, investigating their influence on proteins and their correlations with clinical features., Methods: RNA sequencing and liquid chromatography-tandem mass spectrometry were performed on muscle tissues obtained from 174 patients with IIM and 19 controls, following QC procedures. GTFtools and iREAD software were used for IR identification. An analysis of differentially expressed IRs (DEIs), exons and proteins was carried out using edgeR or DEP. Functional analysis was performed with clusterProfiler, and SPIRON was used to assess splicing factors., Results: A total of 6783 IRs located in 3111 unique genes were identified in all IIM subtypes compared with controls. IIM subtype-specific DEIs were associated with the pathogenesis of respective IIM subtypes. Splicing factors YBX1 and HSPA2 exhibited the most changes in dermatomyositis and immune-mediated necrotising myopathy. Increased IR was associated with reduced protein expression. Some of the IIM-specific DEIs were correlated with clinical parameters (skin rash, MMT-8 scores and muscle enzymes) and muscle histopathological features (myofiber necrosis, regeneration and inflammation). IRs in IFIH1 and TRIM21 were strongly correlated with anti-MDA5+ antibody, while IRs in SRP14 were associated with anti-SRP+ antibody., Conclusion: This study revealed distinct IRs and specific splicing factors associated with IIM subtypes, which might be contributing to the pathogenesis of IIM. We also emphasised the potential impact of IR on protein expression in IIM muscles., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

Objective: Prostate cancer (PCa) is the most common malignant tumor in the male genitourinary system. Once PCa has metastasized, it is very difficult to cure. The purpose of this study was to investigate the prognostic risk factor analysis of patients with different prostate-specific antigen (PSA) levels in distant metastatic PCa. At the same time, we construct effective models for predicting the survival rate of prostate cancer patients., Patients and Methods: Data on prostate cancer patients with the presence of distant metastases were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. PCa patients with distant metastases were categorized into two groups based on PSA levels, one with PSA <20 ng/mL and the other with PSA ≥20 ng/mL. Univariate and multivariate COX regression analyses were used to identify independent factors affecting the prognosis of the patients. A nomogram was constructed using the independent prognostic factors, and the results were evaluated using calibration curves, timeROC curves, and Kaplan-Meier curves., Results: In the PSA <20 ng/mL group, there were a total of 1,832 patients. COX regression analysis showed that age, marital status, N stage, grade, Gleason score, and medical household income inflation were independent prognostic factors for overall survival (OS) in patients. In addition, we found that age, marital status, N stage, bone metastasis, grade, and Gleason score were independent prognostic factors for cancer-specific survival (CSS) in patients. In the PSA ≥20 ng/mL group, there were a total of 5,314 patients. It was found that age, ethnicity, marital status, bone metastasis, first malignant primary indicator, grade, Gleason score, and medical household income inflation were patients' independent prognostic factors for OS. For CSS, we found that age, ethnicity, marital status, T stage, radiotherapy, bone metastasis, Gleason score, and Median household income inflation were independent prognostic factors. Constructing a nomogram can accurately predict the prognosis of this group of patients., Conclusions: We found different independent prognostic factors for different PSA levels in patients with distant metastatic PCa. A new nomogram was constructed to predict OS and CSS in patients, which helps in clinical-assisted decision-making.

Objective: To explore the effect of Kümmell's disease with kyphosis on the sagittal morphology of the spine-pelvis., Methods: A retrospective analysis of 34 patients of Kümmell's disease with kyphosis （Kümmell group） admitted from August 2015 to September 2022, including 10 males and 24 females with an average age of （71.1±8.5） years old. A control group of 37 asymptomatic population aged （69.3±6.7） years old was matched. Spinal-pelvic sagittal parameters were measured on the anterior-posterior and lateral X-rays of the whole spine in the standing position, including segmental kyphosis（SK） or thoracolumbar kyphosis（TLK）, thoracic kyphosis（TK）, lumbar lordosis（LL）, pelvic incidence（PI）, pelvic tilt（PT）, sacral slope（SS）, sagittal vertical axis（SVA）, T1 pelvic angle（TPA） and PI-LL. Vertebral wedge angle（WA） in Kümmell was measured and differences in parameters among groups were analyzed and the relationship between spino-pelvic parameters and WA, SK were also investigated., Results: TK, SK, PT, SVA, TPA and PI-LL in Kümmell group were significantly larger than those in control group （ P <0.05）, LL and SS in Kümmell group were significantly decreased than those in control group （ P <0.05）, and there was no significant difference in PI between two groups （ P >0.05）. In Kümmell group, WA（30.8±5.9）° showed a positive correlation with SK and TK（ r =0.366, 0.597, P <0.05）, and SK was significantly correlated with LL and SS（ r =0.539, -0.591, P <0.05）. Strong positive correlation between LL and PI, SS, SVA, TPA, PI-LL were also confirmed in patients with Kümmell with kyphosis（ r =0.559, 0.741, -0.273, -0.356, -0.882, P <0.05）., Conclusion: Patients with Kümmell with kyphosis not only have segmental kyphosis, but also changes the overall spinal-pelvic sagittal parameters, including loss of lumbar lordosis, pelvic retrorotation, trunk forward tilt. The surgical treatment of Kümmell disease should not only pay attention to the recovery of the height of the collapsed vertebra, but also focus on the overall balance of the spine-pelvic sagittal plane for patients with kyphosis.

Drug response prediction is essential for drug development and disease treatment. One key question in predicting drug response is the representation of molecules, which has been greatly advanced by artificial intelligence (AI) techniques in recent years. In this review, we first describe different types of representation methods, pinpointing their key principles and discussing their limitations. Thereafter we discuss potential ways how these methods could be further developed. We expect that this review will provide useful guidance for researchers in the community., Competing Interests: Declaration of competing interest None declared., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Graph learning methods have achieved noteworthy performance in disease diagnosis due to their ability to represent unstructured information such as inter-subject relationships. While it has been shown that imaging, genetic and clinical data are crucial for degenerative disease diagnosis, existing methods rarely consider how best to use their relationships. How best to utilize information from imaging, genetic and clinical data remains a challenging problem. This study proposes a novel graph-based fusion (GBF) approach to meet this challenge. To extract effective imaging-genetic features, we propose an imaging-genetic fusion module which uses an attention mechanism to obtain modality-specific and joint representations within and between imaging and genetic data. Then, considering the effectiveness of clinical information for diagnosing degenerative diseases, we propose a multi-graph fusion module to further fuse imaging-genetic and clinical features, which adopts a learnable graph construction strategy and a graph ensemble method. Experimental results on two benchmarks for degenerative disease diagnosis (Alzheimers Disease Neuroimaging Initiative and Parkinson's Progression Markers Initiative) demonstrate its effectiveness compared to state-of-the-art graph-based methods. Our findings should help guide further development of graph-based models for dealing with imaging, genetic and clinical data.

Municipal solid waste incineration fly ash (MSWIFA) can be reused as a positive additive to strengthen soft soil. In this study, MSWIFA was initially used as a supplementary solidification material in combination with ordinary Portland cement to prepare fly ash cement-stabilized soil (FACS) with silty sand and silty clay, respectively. The ratio of MWSIFA to total mass was 5%, 10%, and 15%, and the cement content was set as 10% and 15%. The mechanical properties of FACS were evaluated by unconfined compressive strength test. The heavy metal-leaching test was conducted to estimate the environmental risk of FACS. The scanning electron microscope was used to test the micro-structure of FACS. The X-ray diffraction was performed to analyze material composition of FACS. The result indicates that the collaborative solidification of soft soil with MSWIFA and cement is feasible. Regarding the silty clay, the FA had positive effects on the silty clay in the service age (between 50 and 100% with 15% MSWIFA), as the MSWIFA reformulated the initial silty clay structure, resulting in interconnection and pore fill between particles. It can be founded that C-S-H and ettringite are the main products of MSWIFA and cement hydration, which are formed by the hydration of C3S and C2S. Regarding the silty sand, the MSWIFA decreased the peak strength (between 35 and 48% with 15% MSWIFA) but increased the ductility of the stabilized cement. Under the same mix proportions, the leaching toxicities of Zn and Pb in FACS of silty clay were obviously lower than were those of silty sand. Generally, the leaching concentrations of tested metals under all the mix proportions were well below the limit value set by GB 18598-2019 for hazardous waste landfill. Thus, the reuse of MSWIFA in cement-stabilized soil would be one of the effective methods in soft soil treatment and solid waste reduction., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Objective: Clear cell renal cell carcinoma (ccRCC) is the most common type of cancer, and its molecular pathogenesis is unclear. In this study, we investigated the prognostic value of essential meiotic endonuclease 1 (EME1) in kidney renal clear cell carcinoma (KIRC)., Materials and Methods: We downloaded the RNA-Seq expression of 526 KIRC tissues and 72 normal tissues from the TCGA database and the corresponding clinical data. The gene expression profiles associated with four clear cell renal cell carcinomas were downloaded from the GEO database for analysis. The expression of EME1 in clear renal cell carcinoma and its correlation with the clinical baseline data were analyzed. Kaplan-Meier survival curve analysis was performed to assess the relationship between EME1 and patient survival. Enrichment analysis was performed to elucidate the possible functions of EME1. We also analyzed the relationship between the EME1 expression and immune infiltration through TIMER2.0 and TISIDB online databases as well as the relationship between EME1 and common immune checkpoints., Results: EME1 was identified as a risk factor for overall survival in clear cell renal cell carcinoma with a hazard ratio of 3.201 (95% confidence interval: 2.430-4.215; p < 0.001). EME1 was highly expressed in KIRC compared to that in normal tissues (p < 0.001) and in the worse TNM stages and late stages (stage 3/4) (p < 0.001). High EME1 expression was strongly associated with the advanced T stage (p = 0.003), advanced N stage (p = 0.002), and advanced M stage (p = 0.006). Research data on KIRC were simultaneously collected and analyzed from the GEO database, including GSE40435, GSE53000, GSE68417, and GSE53757. EME1 predicted the survival status in KIRC patients (AUC = 0.62). We further established a nomogram including the correlation between the high and low EME1 expression, and EME1 was found to contribute to the prediction of the probability of patient survival with a c-index = 0.796. Kaplan-Meier analysis revealed a lower likelihood of survival with a high EME1 expression (p < 0.001). In addition, further bioinformatics analysis suggested that EME1 may be associated with the extent of immune infiltration in KIRC., Conclusions: An increased expression of EME1 in KIRC is thus associated with advanced clinicopathological features, possibly acting as a potential biomarker of poor prognosis in KIRC.

By recombining natural cell signaling systems and further reprogramming cell functions, use of genetically engineered cells and bacteria as therapies is an innovative emerging concept. However, the inherent properties and structures of the natural signal sensing and response pathways constrain further development. We present a universal DNA-based sensing toolbox on the cell surface to endow new signal sensing abilities for cells, control cell states, and reprogram multiple cell functions. The sensing toolbox contains a triangular-prismatic-shaped DNA origami framework and a sensing core anchored inside the internal confined space to enhance the specificity and efficacy of the toolbox. As a proof of principle, the sensing toolbox uses the customizable sensing core with signal sensing switches and converters to recognize unconventional signal inputs, deliver functional components to cells, and then control cell responses, including specific tumor cell death, immune cell disinhibition and adhesion, and bacterial expression. This work expands the diversity of cell sensing signals and reprograms biological functions by constructing nanomechanical-natural hybrid cells, providing new strategies for engineering cells and bacteria in diagnosis and treatment applications.

The clustered regularly interspaced short palindromic repeats (CRISPR/Cas12a) system has exhibited great promise in the rapid and sensitive molecular diagnostics for its trans-cleavage property. However, most CRISPR/Cas system-based detection methods are designed for nucleic acids and require target preamplification to improve sensitivity and detection limits. Here, we propose a generic crRNA switch circuit-regulated CRISPR/Cas sensor for the sensitive detection of various targets. The crRNA switch is engineered and designed in a blocked state but can be activated in the presence of triggers, which are target-induced association DNA to initiate the trans-cleavage activity of Cas12a for signal reporting. Additionally, RNase H is introduced to specifically hydrolyze RNA duplexed with the DNA trigger, resulting in the regeneration of the trigger to activate more crRNA switches. Such a combination provides a generic and sensitive strategy for the effective sensing of the p53 sequence, thrombin, and adenosine triphosphate. The design is incorporated with nucleic acid nanotechnology and extensively broadens the application scope of the CRISPR technology in biosensing.

Context: 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is a typical insensitive energetic material. It can be used in explosive formulations, such as PBX-9502 and LX-17-0. TATB is an intriguing and unusual explosive for another reason: it crystallizes into a wide array of planar hydrogen bonds, forming a graphite-like layered structure. Therefore, TATB is one of the important research objects, and its surface structure needs to be deeply understood. In this research work, the electronic and energetic properties of TATB (001) surface are explored., Methods: In this paper, the structural, electronic, energetic properties and impact sensitivity of TATB (001) surface structure at 0 and -3 GPa along with x-axis were calculated in this study using the first-principles calculations. The calculations in this paper are performed in the CASTEP code, which is based on the density functional theory with the first-principles calculation method using the plan-wave pseudopotential approach. The exchange-correlation interaction was adopted by the generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) functional. The DFT-D method with the Grimme correction accurately models van der Waals interactions. To model the surface structures of TATB, the planar slab method was employed. We constructed TATB (001) periodic slabs including three layers with a 15-Å vacuum layer., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

It is important to identify disease-associated genes for studying the pathogenic mechanism of complex diseases. Recently, models for disease gene prediction are dominantly based on molecular expression data and networks, including gene expression, protein expression, co-expression networks, protein-protein interaction networks, etc. One limitation of these methods is that they do not consider the knowledge of annotated gene sets representing known pathways or functionally-related sets of genes. In this study, we propose a new approach to predict disease-associated genes by integrating annotated gene sets data from the Molecular Signature Database (MSigDB). It first represents and integrates the different types of annotated gene sets in the MSigDB database in the form of the signal matrix. It then uses the signal matrix as the gene feature to train the disease gene prediction model. We compare our method with existing methods in predicting genes for five complex diseases. The results show that our method is superior to other methods. Further, we perform a case study on autism spectrum disorder (ASD). We find that ASD predictions are associated with ASD based on the statistical analysis of biological networks and independent ASD studies. The source code, prediction results and datasets are publicly available on https://github.com/genemine/GSI.git.

Exosomes derived from human bone marrow mesenchymal stem cells (MSC-Exo) are characterized by easy expansion and storage, low risk of tumor formation, low immunogenicity, and anti-inflammatory effects. The therapeutic effects of MSC-Exo on ischemic stroke have been widely explored. However, the underlying mechanism remains unclear. In this study, we established a mouse model of ischemic brain injury induced by occlusion of the middle cerebral artery using the thread bolt method and injected MSC-Exo into the tail vein. We found that administration of MSC-Exo reduced the volume of cerebral infarction in the ischemic brain injury mouse model, increased the levels of interleukin-33 (IL-33) and suppression of tumorigenicity 2 receptor (ST2) in the penumbra of cerebral infarction, and improved neurological function. In vitro results showed that astrocyte-conditioned medium of cells deprived of both oxygen and glucose, to simulate ischemia conditions, combined with MSC-Exo increased the survival rate of primary cortical neurons. However, after transfection by IL-33 siRNA or ST2 siRNA, the survival rate of primary cortical neurons was markedly decreased. These results indicated that MSC-Exo inhibited neuronal death induced by oxygen and glucose deprivation through the IL-33/ST2 signaling pathway in astrocytes. These findings suggest that MSC-Exo may reduce ischemia-induced brain injury through regulating the IL-33/ST2 signaling pathway. Therefore, MSC-Exo may be a potential therapeutic method for ischemic stroke., Competing Interests: None

Single-cell clustering is a critical step in biological downstream analysis. The clustering performance could be effectively improved by extracting cell-type-specific genes. The state-of-the-art feature selection methods usually calculate the importance of a single gene without considering the information contained in the gene expression distribution. Moreover, these methods ignore the intrinsic expression patterns of genes and heterogeneity within groups of different mean expression levels. In this work, we present a Feature sElection method based on gene Expression Decomposition (FEED) of scRNA-seq data, which selects informative genes to enhance clustering performance. First, the expression levels of genes are decomposed into multiple Gaussian components. Then, a novel gene correlation calculation method is proposed to measure the relationship between genes from the perspective of distribution. Finally, a permutation-based approach is proposed to determine the threshold of gene importance to obtain marker gene subsets. Compared with state-of-the-art feature selection methods, applying FEED on various scRNA-seq datasets including large datasets followed by different common clustering algorithms results in significant improvements in the accuracy of cell-type identification. The source codes for FEED are freely available at https://github.com/genemine/FEED., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Aim: To evaluate whether a novel tyrosine kinase inhibitor nintedanib could inhibit basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF) simultaneously for retinal vascular disease in vivo ., Methods: After a laser induced rabbit retinal vein occlusion (RVO) model was made, 0.5 mg of nintedanib was injected intravitreally in the left eye on the third day while the right eye was as a control. Intracameral samples were taken on the day before laser treatment and days 1, 3, 7, 14, 21, and 28 after treatment. Enzyme-linked immunosorbent assay (ELISA) was used to test the bFGF and VEGF-A concentrations in the aqueous humor., Results: Both bFGF and VEGF-A rose significantly on the third day after laser treatment in both eyes. In the control eye the bFGF concentration peaked on the 14 th day while the VEGF-A concentration dropped rapidly soon after the third day. After nintadanib injection in the study eye, both bFGF and VEGF-A showed a significant reduction on the 4 th day (7 th day after laser treatment) when compared to the control eye, and kept on low level in the following several weeks., Conclusion: Intravitreal injection of nintedanib can inhibit the expression of bFGF and VEGF in the process of RVO model to a certain extent, which is expected to become a new method for the treatment of retinal vascular diseases or fibrotic diseases., (International Journal of Ophthalmology Press.)

Background: Diabetic retinopathy (DR) is currently recognized as one of the most serious diabetic microangiopathies and a major cause of adult blindness. Commonly used clinical approaches include etiological control, microvascular improvement, and surgical intervention, but they are ineffective and have many side effects. Oral Chinese medicine (OCM) has been used for thousands of years to treat DR and is still widely used today, but it is unclear which OCM is more effective for DR., Aim: To estimate relative effectiveness and safety profiles for different classes of OCMs for DR, and provide rankings of the available OCMs., Methods: The search time frame was from the creation of the database to January 2023. RevMan 5.3 and Stata 14.0 software were used to perform the systematic review and Network meta-analyses (NMA)., Results: A total of 107 studies and 9710 patients were included, including 4767 cases in the test group and 4973 cases in the control group. Based on previous studies and clinical reports, and combined with the recommendations of Chinese guidelines for the prevention and treatment of DR, 9 OCMs were finally included in this study, namely Compound Xueshuantong Capsules, Qiming Granules, Compound Danshen Dripping Pills, Hexue Mingmu Tablets (HXMM), Qiju Dihuang Pills (QJDH), Shuangdan Mingmu Capsules (SDMM), Danggui Buxue Decoction (DGBX), Xuefu Zhuyu Decoction and Buyang Huanwu Decoction. When these nine OCMs were analyzed in combination with conventional western medicine treatment (CT) compared with CT alone, the NMA results showed that HXMM + CT has better intervention effect on the overall efficacy of DR patients, HXMM + CT has better effect on improving patients' visual acuity, SDMM + CT has better effect on inhibiting vascular endothelial growth factor, DGBX + CT has better effect on reducing fundus hemorrhage area, HXMM + CT has better effect on reducing fasting blood glucose, and QJDH + CT has better effect on reducing glycated hemoglobin. When there are not enough clinical indicators for reference, SDMM + CT or HXMM + CT treatments can be chosen because they are effective for more indicators and demonstrate multidimensional efficacy., Conclusion: This study provides evidence that combining OCMs with CT leads to better outcomes in all aspects of DR compared to using CT alone. Based on the findings, we highly recommend the use of SDMM or HXMM for the treatment of DR. These two OCMs have demonstrated outstanding efficacy across multiple indicators., Competing Interests: Conflict-of-interest statement: All authors have no conflict of interest of any kind., (©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.)

Gastrin-releasing peptide (GRP) binds to its receptor (GRP receptor [GRPR]) to regulate multiple biological processes, but the function of GRP/GRPR axis in acute kidney injury (AKI) remains unknown. In the present study, GRPR is highly expressed by tubular epithelial cells (TECs) in patients or mice with AKI, while histone deacetylase 8 may lead to the transcriptional activation of GRPR. Functionally, we uncovered that GRPR was pathogenic in AKI, as genetic deletion of GRPR was able to protect mice from cisplatin- and ischemia-induced AKI. This was further confirmed by specifically deleting the GRPR gene from TECs in GRPR Flox/Flox//KspCre mice. Mechanistically, we uncovered that GRPR was able to interact with Toll-like receptor 4 to activate STAT1 that bound the promoter of MLKL and CCL2 to induce TEC necroptosis, necroinflammation, and macrophages recruitment. This was further confirmed by overexpressing STAT1 to restore renal injury in GRPR Flox/Flox/KspCre mice. Concurrently, STAT1 induced GRP synthesis to enforce the GRP/GRPR/STAT1 positive feedback loop. Importantly, targeting GRPR by lentivirus-packaged small hairpin RNA or by treatment with a novel GRPR antagonist RH-1402 was able to inhibit cisplatin-induced AKI. In conclusion, GRPR is pathogenic in AKI and mediates AKI via the STAT1-dependent mechanism. Thus, targeting GRPR may be a novel therapeutic strategy for AKI., Competing Interests: Declaration of interests The authors declare that they have no competing interests., (Copyright © 2023 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.)

Motivation: A single gene may yield several isoforms with different functions through alternative splicing. Continuous efforts are devoted to developing machine-learning methods to predict isoform functions. However, existing methods do not consider the relevance of each feature to specific functions and ignore the noise caused by the irrelevant features. In this case, we hypothesize that constructing a feature selection framework to extract the function-relevant features might help improve the model accuracy in isoform function prediction., Results: In this article, we present a feature selection-based approach named IsoFrog to predict isoform functions. First, IsoFrog adopts a reversible jump Markov Chain Monte Carlo (RJMCMC)-based feature selection framework to assess the feature importance to gene functions. Second, a sequential feature selection procedure is applied to select a subset of function-relevant features. This strategy screens the relevant features for the specific function while eliminating irrelevant ones, improving the effectiveness of the input features. Then, the selected features are input into our proposed method modified domain-invariant partial least squares, which prioritizes the most likely positive isoform for each positive MIG and utilizes diPLS for isoform function prediction. Tested on three datasets, our method achieves superior performance over six state-of-the-art methods, and the RJMCMC-based feature selection framework outperforms three classic feature selection methods. We expect this proposed methodology will promote the identification of isoform functions and further inspire the development of new methods., Availability and Implementation: IsoFrog is freely available at https://github.com/genemine/IsoFrog., (© The Author(s) 2023. Published by Oxford University Press.)

Social biotic colonies often perform intricate tasks by interindividual communication and cooperation. Inspired by these biotic behaviors, a DNA nanodevice community is proposed as a universal and scalable platform. The modular nanodevice as the infrastructure of platform contains a DNA origami triangular prism framework and a hairpin-swing arm machinery core. By coding and decoding a signal domain on the shuttled output strand in different nanodevices, an orthogonal inter-nanodevice communication network is established to connect multi-nanodevices into a functional platform. The nanodevice platform enables implementation of diverse tasks, including signal cascading and feedback, molecular input recording, distributed logic computing, and modeling of simulation for virus transmission. The nanodevice platform with powerful compatibility and programmability presents an elegant example of the combination of the distributed operation of multiple devices and the complicated interdevice communication network, and may become a new generation of intelligent DNA nanosystems., (© 2023 Wiley-VCH GmbH.)

Circular RNA (circRNA) has been implicated in liver fibrosis and modulated by multiple elusive molecular mechanisms, while the effects of N 6 -methyladenosine (m 6 A) modification on circRNA are still elusive. Herein, we identify circIRF2 from our circRNA sequencing data, which decreased in liver fibrogenesis stage and restored in resolution stage, indicating that dysregulated circIRF2 may be closely associated with liver fibrosis. Gain/loss-of-function analysis was performed to evaluate the effects of circIRF2 on liver fibrosis at both the fibrogenesis and resolution in vivo. Ectopic expression of circIRF2 attenuated liver fibrogenesis and HSCs activation at the fibrogenesis stage, whereas downregulation of circIRF2 impaired mouse liver injury repair and inflammation resolution. Mechanistically, YTHDF2 recognized m 6 A-modified circIRF2 and diminished circIRF2 stability, partly accounting for the decreased circIRF2 in liver fibrosis. Microarray was applied to investigate miRNAs regulated by circIRF2, our data elucidate cytoplasmic circIRF2 may directly harbor miR-29b-1-5p and competitively relieve its inhibitory effect on FOXO3, inducing FOXO3 nuclear translocation and accumulation. Clinically, circIRF2 downregulation was prevalent in liver fibrosis patients compared with healthy individuals. In summary, our findings offer a novel insight into m 6 A modification-mediated regulation of circRNA and suggest that circIRF2 may be an exploitable prognostic marker and/or therapeutic target for liver fibrosis., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Colonization and extinction at local and regional scales, and gains and losses of patches are important processes in the spatiotemporal dynamics of metacommunities. However, analytical challenges remain in quantifying such spatiotemporal dynamics when species extinction-colonization and patch gain and loss processes act simultaneously. Recent advances in network analysis show great potential in disentangling the roles of colonization, extinction, and patch dynamics in metacommunities. Here, we developed a species-patch network approach to quantify metacommunity dynamics including (i) temporal changes in network structure, and (ii) temporal beta diversity of species-patch links and its components that reflect species extinction-colonization and patch gain and loss. Application of the methods to simulated datasets demonstrated that the approach was informative about metacommunity assembly processes. Based on three empirical datasets, our species-patch network approach provided additional information about metacommunity dynamics through distinguishing the effects of species colonization and extinction at different scales from patch gains and losses and how specific environmental factors related to species-patch network structure. In conclusion, our species-patch network framework provides effective methods for monitoring and revealing long-term metacommunity dynamics by quantifying gains and losses of both species and patches under local and global environmental change., (© 2023 John Wiley & Sons Ltd.)

Objective: To explore the effects of morphological changes such as vertebral wedge deformation and disc degeneration (collapse) on adult thoracolumbar/lumbar degenerative kyphosis(TL/LDK) deformity., Methods: A retrospective analysis of 32 patients with spinal TL/LDK deformity admitted from August 2015 to December 2020, including 8 males and 24 females, aged 48 to 75(60.3±12.4) years old. On the long-cassette standing upright lateral radiographs, the coronal Cobb angle, sagittal thoracic lumbar/lumbar kyphosis angle(KA) of spine were measured, and the height and wedge parameters of apex vertebral(AV) and two vertebrae(AV-1, AV-2, AV+1, AV+2) above and below AV and the intervertebrae and the intervertebral disc(AV-1D, AV-2D, AV+1D, AV+2D) were evaluated, involving anterior vertebral body height(AVH), posterior vertebral body height(PVH), vertebral wedge angle(VWA), ratio of vertebral wedging(RVW), anterior disc height(ADH), posterior disc height(PDH), disc wedge angle(DWA), ratio of disc wedging(RDW), and DWA/KA., Results: The average angle of kyphosis was (44.2±19.1)°. A significant decrease in anterior height of vertebral was observed compared to the posterior height of vertebral( P <0.005). There was no significant difference in anterior and posterior height of discs. The vertebral wedging ratio/contribution ratio:AV-2(14.98±10.95)%/(14.21±8.08)%, AV-1(21.08±12.39)%/(18.09±7.38)%, AV(26.94±11.94)%/(25.52±8.64)%, AV+1(24.19±8.42)%/(20.82±8.69)%, AV+2(20.56±7.80)%/(15.60±9.71)%, total contribution(94.23±22.25)%, the disc wedging ratio/contribution ratio:AV-2D(2.88±2.57)%/(5.27±4.11)%, AV-1D(1.98±1.41)%/(2.29±2.16)%, AV+1D(-5.54±3.75)%/(-0.57±0.46)%, AV+2D(-8.27±4.62)%/(-1.22±1.11)%, total contribution (5.77±4.79)%. And the contribution rate of AV was significantly higher than that of adjacent vertebral( P <0.05)., Conclusion: The vertebral body and intervertebral disc shape both have influence on thoracolumbar kyphosis. However, the contribution of vertebral morphometry to the angle of TL/LDK deformity is relatively more important than the disc. The contribution of the wedge change of the AV to the TL/LDK deformity is particularly significant.