Single-structure 3-axis Lorentz force magnetometer based on an AlN-on-Si MEMS resonator.

This work presents a single-structure 3-axis Lorentz force magnetometer (LFM) based on an AlN-on-Si MEMS resonator. The operation of the proposed LFM relies on the flexible manipulation of applied excitation currents in different directions and frequencies, enabling the effective actuation of two mechanical vibration modes in a single device for magnetic field measurements in three axes. Specifically, the excited out-of-plane drum-like mode at 277 kHz is used for measuring the x- and y-axis magnetic fields, while the in-plane square-extensional mode at 5.4 MHz is used for measuring the z-axis magnetic field. The different configurations of applied excitation currents ensure good cross-interference immunity among the three axes. Compared to conventional capacitive LFMs, the proposed piezoelectric LFM utilizes strong electromechanical coupling from the AlN layer, which allows it to operate at ambient pressure with a high sensitivity. To understand and analyze the measured results, a novel equivalent circuit model for the proposed LFM is also reported in this work, which serves to separate the effect of Lorentz force from the unwanted capacitive feedthrough. The demonstrated 3-axis LFM exhibits measured magnetic responsivities of 1.74 ppm/mT, 1.83 ppm/mT and 6.75 ppm/mT in the x-, y- and z-axes, respectively, which are comparable to their capacitive counterparts.

Influence of preoperative urine culture and bacterial species on urogenital sepsis after ureteral flexible lithotripsy in patients with upper urinary tract stones.

Objective: This retrospective study aims to identify risk factors for urogenic sepsis in patients with upper urinary tract stones following ureteral flexible lithotripsy (FURL). Additionally, we analyze the clinical characteristics of bacterial infections post-surgery. Methods: A total of 759 patients who underwent FURL at the Urology Department of Zunyi Medical University were included. Univariate and multivariate Logistic regression analyses were conducted to identify independent risk factors for urogenic sepsis post-FURL. The distribution of bacteria based on preoperative urine cultures was also analyzed. Statistical analysis was performed using R4.2.2 software. Results: Of the 759 patients, positive preoperative urine culture, urine nitrite positivity, urine white blood cell count (WBC) ≥ 200 cells/µL, residual stones, and neutrophil-to-lymphocyte ratio (NLR) were found to be independent risk factors for urogenic sepsis after FURL. Among the 164 patients with positive preoperative urine cultures, 32 developed urogenic sepsis post-surgery, with 68.75% having positive preoperative cultures. The leading pathogens causing postoperative urogenic sepsis were Escherichia coli (E. coli), Enterococcus faecium, Proteus mirabilis, and Klebsiella pneumoniae. The probabilities of progression to urogenic sepsis were as follows: E. coli 19% (n = 12), Enterococcus faecium 43% (n = 3), Proteus mirabilis 33.3% (n = 1), and Klebsiella pneumoniae 33.3% (n = 1). The ages of affected patients were 47.17 ± 13.2, 53.7, 41, and 79 years, respectively. Rates of comorbid diabetes were 36.4, 66.7, 50, 100%, with nitrite positivity rates at 72.7, 33.3, 50, 0%. Ten female patients were infected with E. coli, while patients infected with Klebsiella pneumoniae had an NLR of 7.62. Conclusion: Positive preoperative urine culture, urine nitrite positivity, urine WBC ≥ 200 cells/µL, residual stones, and NLR are independent risk factors for urogenic sepsis after FURL. Escherichia coli is the predominant pathogen post-FURL, with notable female prevalence and nitrite-positive urine in infections. Enterococcus faecium infections are associated with diabetes.

Intraoperative fat embolism syndrome associated with implantation of titanium sacroiliac joint fusion implants: a report of two cases.

Background: For patients undergoing long-construct fusion surgeries, simultaneous sacroiliac joint (SIJ) fusion is a growing trend in spine surgery. Some options for posterior SIJ fusion include 3D-printed triangular titanium implants or self-harvesting SIJ screws. Both implants require fixation within the sacrum and ileum. Fat embolism syndrome is a rare but known complication of lumbar pedicle instrumentation but has never been reported in association with SIJ fusion, regardless of implant type. We report the first two known cases of fat embolism associated with placement of SIJ fusion devices during long construct posterior spine fusion. Case Description: Case 1-a 50-year-old female with multiple previous spine surgeries complicated by osteomyelitis/diskitis that was successfully eradicated, underwent T10-pelvis posterior spinal fusion (PSF), L4 pedicle-subtracting-osteotomy, and bilateral SIJ fusion. During implantation of each SIJ fusion device, the patient's hemodynamic status deteriorated necessitating vasopressor support, intravenous fluid bolus, and hyperventilation, but quickly resolved. The case was completed without further issue, and she had an uneventful post-operative course. Case 2-a 71-year-old female with a past medical history of ankylosing spondylitis, previous L2-L5 PSF, rheumatoid arthritis on chronic steroids, underwent a T9-pelvis PSF, bilateral SIJ fusion, L4 pedicle subtraction osteotomy, T10-L1 Smith Peterson osteotomies. After implantation of the second SIJ fusion device, she became hypotensive and tachycardic, pulses were absent, and cardiopulmonary resuscitation was initiated. Pulses returned quickly, the index surgery was terminated, and she was transferred to the intensive care unit (ICU). In the ICU she was quickly weaned off the ventilator on post-operative day 1. On post-operative day 4, the patient returned to the operating room for completion of the surgery and had an extended, but uneventful, recovery afterwards. Conclusions: We report on the first two known cases of fat embolism syndrome occurring immediately after implantation of SIJ fusion devices. Spine surgeons should be aware of this rare, but potentially fatal, complication. Collaboration with the anesthesia team and optimization of the patient's hemodynamic status prior to implantation may help prevent catastrophic complications.

Comprehensive analysis of fibroblast activation protein expression across 23 tumor indications: insights for biomarker development in cancer immunotherapies.

Introduction: Fibroblast activation protein (FAP) is predominantly upregulated in various tumor microenvironments and scarcely expressed in normal tissues. Methods: We analyzed FAP across 1216 tissue samples covering 23 tumor types and 70 subtypes. Results: Elevated FAP levels were notable in breast, pancreatic, esophageal, and lung cancers. Using immunohistochemistry and RNAseq, a correlation between FAP gene and protein expression was found. Evaluating FAP's clinical significance, we assessed 29 cohorts from 12 clinical trials, including both mono and combination therapies with the PD-L1 inhibitor atezolizumab and chemotherapy. A trend links higher FAP expression to poorer prognosis, particularly in RCC, across both treatment arms. However, four cohorts showed improved survival with high FAP, while in four others, FAP had no apparent survival impact. Conclusions: Our results emphasize FAP's multifaceted role in therapy response, suggesting its potential as a cancer immunotherapy biomarker.

Associations between postoperative anaemia and unplanned readmission to hospital after major surgery: a retrospective cohort study†.

BACKGROUND: Anaemia following major surgery may be associated with unplanned readmission to hospital. However, the severity-response relationship between the degree of anaemia at discharge and the risk of unplanned readmission is poorly defined. We aimed to describe the severity-response relationship between haemoglobin concentration at the time of discharge and the risk of unplanned readmission in a cohort of patients undergoing different types of major surgery. METHODS: We performed a retrospective cohort study in a single tertiary health service, including all patients who underwent major surgery (orthopaedic, abdominal, cardiac or thoracic) between 1 May 2011 and 1 February 2022. The primary outcome was unplanned readmission to hospital in the 90 days following discharge after the index surgical procedure. These complex, non-linear relationships were modelled with restricted cubic splines. RESULTS: We identified 22,134 patients and included 14,635 in the primary analysis, of whom 1804 (12%) experienced at least one unplanned readmission. The odds of unplanned readmission rose when the discharge haemoglobin concentration was < 100 g.l-1 (p < 0.001). On subgroup analysis, the haemoglobin threshold below which odds of readmission began to increase appeared to be higher in patients undergoing emergency surgery (110 g.l-1; p < 0.001) compared with elective surgery. Declining discharge haemoglobin concentration was associated with increased odds ratios (95%CI) of unplanned readmission in patients undergoing orthopaedic (1.08 (1.01-1.15), p = 0.03), abdominal (1.13 (1.07-1.19), p < 0.001) and thoracic (1.12 (1.01-1.24), p = 0.03) procedures, but not cardiac surgery (1.09 (0.99-1.19), p = 0.07). CONCLUSIONS: Our findings suggest that a haemoglobin concentration < 100 g.l-1 following elective procedures and < 110 g.l-1 following emergency procedures, at the time of hospital discharge after major surgery, was associated with unplanned readmission. Future interventional trials that aim to treat postoperative anaemia and reduce unplanned readmission should include patients with discharge haemoglobin below these thresholds.

Improving SLAM Techniques with Integrated Multi-Sensor Fusion for 3D Reconstruction.

Simultaneous Localization and Mapping (SLAM) poses distinct challenges, especially in settings with variable elements, which demand the integration of multiple sensors to ensure robustness. This study addresses these issues by integrating advanced technologies like LiDAR-inertial odometry (LIO), visual-inertial odometry (VIO), and sophisticated Inertial Measurement Unit (IMU) preintegration methods. These integrations enhance the robustness and reliability of the SLAM process for precise mapping of complex environments. Additionally, incorporating an object-detection network aids in identifying and excluding transient objects such as pedestrians and vehicles, essential for maintaining the integrity and accuracy of environmental mapping. The object-detection network features a lightweight design and swift performance, enabling real-time analysis without significant resource utilization. Our approach focuses on harmoniously blending these techniques to yield superior mapping outcomes in complex scenarios. The effectiveness of our proposed methods is substantiated through experimental evaluation, demonstrating their capability to produce more reliable and precise maps in environments with variable elements. The results indicate improvements in autonomous navigation and mapping, providing a practical solution for SLAM in challenging and dynamic settings.

Mendelian randomization of circulating proteome identifies IFN-γ as a druggable target in aplastic anemia.

BACKGROUND: Aplastic anemia (AA) is a kind of bone marrow failure (BMF) characterized by pancytopenia with hypoplasia/aplasia of bone marrow. Immunosuppressive therapy and bone marrow transplantation are effective methods to treat severe aplastic anemia. However, the efficacy is limited by complications and the availability of suitable donors. This study aimed to determine whether any circulating druggable protein levels may have causal effects on AA and provide potential novel drug targets for AA. METHODS: Genetic variants strongly associated with circulating druggable protein levels to perform Mendelian randomization (MR) analyses were used. The effect of these druggable protein levels on AA risk was measured using the summary statistics from a large-scale proteomic genome-wide association study (GWAS) and FinnGen database ( https://www.finngen.fi/en/access_results ). Multivariable MR analyses were performed to statistically adjust for potential confounders, including platelet counts, reticulocyte counts, neutrophil counts, and proportions of hematopoietic stem cells. RESULTS: The data showed that higher level of circulating IFN-γ levels was causally associated with AA susceptibility. The causal effects of circulating IFN-γ levels on the AA were broadly consistent, when adjusted for platelet counts, reticulocyte counts, neutrophil counts and proportions of hematopoietic stem cells. CONCLUSIONS: High levels of circulating IFN-γ levels might increase the risk of AA and might provide a potential novel target for AA.

Pro-cancer role of CD276 as a novel biomarker for clear cell renal cell carcinoma.

OBJECTIVE: Renal cell carcinoma (RCC) is a common malignant tumor with a high incidence in males and the elderly, and clear cell RCC (ccRCC) is the most common RCC subtype. ccRCC is highly metastatic with a poor prognosis. Therefore, it is crucial to obtain a detailed understanding of the molecular mechanism of ccRCC and to identify suitable biomarkers to realize early diagnosis and improve prognosis. METHODS: We analyzed data from the Cancer Genome Atlas, investigated the overall differential expression of CD276 in ccRCC, and evaluated the influence of CD276 on patient survival and prognosis. We also performed gene set enrichment analysis (GSEA) and pathway enrichment analysis and investigated cell infiltration and drug responsiveness to further assess the regulatory effect of CD276 on ccRCC. Furthermore, we verified CD276 expression in RCC cell lines and control cell lines. RESULTS: The CD276 expression level in ccRCC samples was higher than that in corresponding samples adjacent to the tumors. Moreover, high CD276 expression levels were positively correlated with poor prognosis in patients with RCC. GSEA revealed that CD276 was significantly involved in immune-related pathways, and the level of CD276 expression was confirmed as associated with immune cell infiltration to some extent. Notably, some drugs were predicted to act on CD276, and this was confirmed by molecular docking. Furthermore, high levels of CD276 expression in RCC cell lines were verified. CONCLUSION: CD276 expression was significantly increased in ccRCC tissues and cells and positively correlated with patient prognosis. CD276 is a potential prognostic biomarker of ccRCC. Overall, this study provides a potential therapeutic strategy for ccRCC.

Genetic interactions reveal distinct biological and therapeutic implications in breast cancer.

Co-occurrence and mutual exclusivity of genomic alterations may reflect the existence of genetic interactions, potentially shaping distinct biological phenotypes and impacting therapeutic response in breast cancer. However, our understanding of them remains limited. Herein, we investigate a large-scale multi-omics cohort (n = 873) and a real-world clinical sequencing cohort (n = 4,405) including several clinical trials with detailed treatment outcomes and perform functional validation in patient-derived organoids, tumor fragments, and in vivo models. Through this comprehensive approach, we construct a network comprising co-alterations and mutually exclusive events and characterize their therapeutic potential and underlying biological basis. Notably, we identify associations between TP53mut-AURKAamp and endocrine therapy resistance, germline BRCA1mut-MYCamp and improved sensitivity to PARP inhibitors, and TP53mut-MYBamp and immunotherapy resistance. Furthermore, we reveal that precision treatment strategies informed by co-alterations hold promise to improve patient outcomes. Our study highlights the significance of genetic interactions in guiding genome-informed treatment decisions beyond single driver alterations.

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In the clinical diagnosis and treatment of children with short stature, mental health issues merit special attention. It is widely acknowledged that the psychological well-being of children with short stature is lower than that of their peers with normal height. Therefore, during the diagnosis, treatment, and care of short stature, it is crucial to actively monitor the mental health of these children, promptly identify potential psychological and behavioral issues, and intervene accordingly. Such measures play a positive role in enhancing the quality of life of these children and improving their physical and mental health. This article analyses and discusses the current state of psychological assessment and psycho-behavioral interventions for children with short stature, aiming to provide insights for improving their mental health.

Use of Dixon in magnetic resonance breast contrast-enhanced T1 weighted high-resolution imaging for mastectomy patients at 3T: A prospective study in single center.

BACKGROUND: For patients with complete breast resection, conventional contrast-enhanced T1-weighted imaging (CE-T1WI) with frequency-selective spectral attenuated inversion recovery (SPAIR) provides limited fat suppression on the postoperative side due to the uneven skin surface, inhomogeneous tissue environment, and frequency-selective feature of the SPAIR scheme, leading to difficulties in precise diagnosis. This study aimed to investigate the image quality and performance of the Dixon method compared with SPAIR in breast high-resolution CE-T1WI for mastectomy patients. MATERIALS AND METHODS: Sixty female patients who had not performed any breast surgeries were randomly selected retrospectively as the control group. Postmastectomy female patients were enrolled to undergone high-resolution CE-T1WI with SPAIR and Dixon breast scans. Subjective scores were rated using a 5-point scale. Objective parameters, including contrast-to-noise ratio (CNR), edge sharpness, and signal uniformity were measured and calculated. The Wilcoxon rank-sum test and Kappa statistic were used. RESULTS: A total of 114 consecutive postmastectomy patients were included. Subjective scores of T1WI-SPAIR in the control group were all significantly better than those with SPAIR on the postoperative side of mastectomy patients (P < 0.01). Dixon outperformed SPAIR with significantly better subjective scores in regards to uniformity and degree of fat-suppression, anatomical structures depiction, lesion conspicuity, and axillary visibility (p < 0.05) in both post- and non-operative sides and bilateral axillary areas through the paired comparison. The objective parameters of Dixon were significantly better than those of SPAIR. CONCLUSION: The Dixon method provided better image uniformity and higher fat suppression efficiency, and showed significant advantages in delineating the anatomical structures, with better axillary and lesion visibilities, especially on the completely removed breast side.

The Epidemiology, Management and Therapeutic Outcomes of Subdural Empyema in Neonates with Acute Bacterial Meningitis.

Background: Subdural empyema is one of the more serious complications of bacterial meningitis and therapeutic challenges to clinicians. We aimed to evaluate the clinical characteristics, treatment, and outcome of subdural empyema in neonates with bacterial meningitis. Methods: A retrospective cohort study was conducted in two medical centers in Taiwan that enrolled all cases of neonates with subdural empyema after bacterial meningitis between 2003 and 2020. Results: Subdural empyema was diagnosed in 27 of 153 (17.6%) neonates with acute bacterial meningitis compared with cases of meningitis without subdural empyema. The demographics and pathogen distributions were comparable between the study group and the controls, but neonates with subdural empyema were significantly more likely to have clinical manifestations of fever (85.2%) and seizure (81.5%) (both p values < 0.05). The cerebrospinal fluid results of neonates with subdural empyema showed significantly higher white blood cell counts, lower glucose levels and higher protein levels (p = 0.011, 0.003 and 0.006, respectively). Neonates with subdural empyema had a significantly higher rate of neurological complications, especially subdural effusions and periventricular leukomalacia. Although the final mortality rate was not increased in neonates with subdural empyema when compared with the controls, they were often treated much longer and had a high rate of long-term neurological sequelae. Conclusions: Subdural empyema is not uncommon in neonates with acute bacterial meningitis and was associated with a high risk of neurological complications, although it does not significantly increase the final mortality rate. Close monitoring of the occurrence of subdural empyema is required, and appropriate long-term antibiotic treatment after surgical intervention may lead to optimized outcomes.

60Co-γ Irradiation-Induced Shift and Polarity Reversal in the Triboelectric Series of Poly(ether sulfone)s.

The sensitivity of triboelectric nanogenerators (TENGs) to the surface charge density highlights the significance of triboelectric materials and their modifications. Efforts have been directed toward developing effective strategies for increasing the surface charge density, expanding the potential applications of TENGs. This study proposes the use of irradiation technology for grafting to modify the electron-donating capability of poly(ether sulfone) (PES), thereby affording a dual benefit of enhancing the surface charge density and inducing a shift in the position of PES from negative to positive within the triboelectric series. The TENG based on grafted PES has resulted in a significant 3-fold increase in surface charge density compared to that of pristine PES, reaching 263 µC m-2. The surface charge density can be further increased to 502 µC m-2 through charge pumping. Notably, irradiation technology presents advantages over chemical grafting methods, particularly in terms of sustainability and environmental friendliness. This innovative approach shows great potential in advancing the domain of TENGs.

Novel STAT3 oligonucleotide compounds suppress tumor growth and overcome the acquired resistance to sorafenib in hepatocellular carcinoma.

Signal transducer and activator of transcription 3 (STAT3) plays an important role in the occurrence and progression of tumors, leading to resistance and poor prognosis. Activation of STAT3 signaling is frequently detected in hepatocellular carcinoma (HCC), but potent and less toxic STAT3 inhibitors have not been discovered. Here, based on antisense technology, we designed a series of stabilized modified antisense oligonucleotides targeting STAT3 mRNA (STAT3 ASOs). Treatment with STAT3 ASOs decreased the STAT3 mRNA and protein levels in HCC cells. STAT3 ASOs significantly inhibited the proliferation, survival, migration, and invasion of cancer cells by specifically perturbing STAT3 signaling. Treatment with STAT3 ASOs decreased the tumor burden in an HCC xenograft model. Moreover, aberrant STAT3 signaling activation is one of multiple signaling pathways involved in sorafenib resistance in HCC. STAT3 ASOs effectively sensitized resistant HCC cell lines to sorafenib in vitro and improved the inhibitory potency of sorafenib in a resistant HCC xenograft model. The developed STAT3 ASOs enrich the tools capable of targeting STAT3 and modulating STAT3 activity, serve as a promising strategy for treating HCC and other STAT3-addicted tumors, and alleviate the acquired resistance to sorafenib in HCC patients. A series of novel STAT3 antisense oligonucleotide were designed and showed potent anti-cancer efficacy in hepatocellular carcinoma in vitro and in vivo by targeting STAT3 signaling. Moreover, the selected STAT3 ASOs enhance sorafenib sensitivity in resistant cell model and xenograft model.

Protein degradation of Lsd1 is mediated by Bre1 yet opposed by Lsd1-interacting lncRNAs during fly follicle development.

Tissue development, homeostasis, and repair all require efficient progenitor expansion. Lysine-specific demethylase 1 (Lsd1) maintains plastic epigenetic states to promote progenitor proliferation while overexpressed Lsd1 protein causes oncogenic gene expression in cancer cells. However, the precise regulation of Lsd1 protein expression at the molecular level to drive progenitor differentiation remains unclear. Here, using Drosophila melanogaster oogenesis as our experimental system, we discovered molecular machineries that modify Lsd1 protein stability in vivo. Through genetic and biochemical analyses, an E3 ubiquitin ligase, Bre1, was identified as required for follicle progenitor differentiation, likely by mediating Lsd1 protein degradation. Interestingly, specific Lsd1-interacting long non-coding RNAs (LINRs) were found to antagonize Bre1-mediated Lsd1 protein degradation. The intricate interplay discovered among the Lsd1 complex, LINRs and Bre1 provides insight into how Lsd1 protein stability is fine-tuned to underlie progenitor differentiation in vivo.

A Novel Three-Point Localization Method for Bladder Volume Estimation.

The measurement of bladder volume is crucial for the diagnosis and treatment of urinary system diseases. Ultrasound imaging, with its non-invasive, radiation-free, and repeatable scanning capabilities, has become the preferred method for measuring residual urine volume. Nevertheless, it still faces some challenges, including complex imaging methods leading to longer measurement times and lower spatial resolution. Here, we propose a novel three-point localization method that does not require ultrasound imaging to calculate bladder volume. A corresponding triple-element ultrasound probe has been designed based on this method, enabling the ultrasound probe to transmit and receive ultrasound waves in three directions. Furthermore, we utilize the Hilbert Transform algorithm to extract the envelope of the ultrasound signal to enhance the efficiency of bladder volume measurements. The experiment indicates that bladder volume estimation can be completed within 5 s, with a relative error rate of less than 15%. These results demonstrate that this novel three-point localization method offers an effective approach for bladder volume measurement in patients with urological conditions.

High-Frequency Workpiece Image Recognition Model Integrating Multi-Level Network Structure.

High-frequency workpieces have the characteristics of complex intra-class textures and small differences between classes, leading to the problem of low recognition rates when existing models are applied to the recognition of high-frequency workpiece images. We propose in this paper a novel high-frequency workpiece image recognition model that uses EfficientNet-B1 as the basic network and integrates multi-level network structures, designated as ML-EfficientNet-B1. Specifically, a lightweight mixed attention module is first introduced to extract global workpiece image features with strong illumination robustness, and the global recognition results are obtained through the backbone network. Then, the weakly supervised area detection module is used to locate the locally important areas of the workpiece and is introduced into the branch network to obtain local recognition results. Finally, the global and local recognition results are combined in the branch fusion module to achieve the final recognition of high-frequency workpiece images. Experimental results show that compared with various image recognition models, the proposed ML-EfficientNet-B1 model has stronger adaptability to illumination changes, significantly improves the performance of high-frequency workpiece recognition, and the recognition accuracy reaches 98.3%.

Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction.

Binding affinity prediction of three-dimensional (3D) protein-ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches usually transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and then use graph neural networks (GNNs) to predict its binding affinity. However, the node and edge features of the 2D graph are extracted based on invariant local coordinate systems of the 3D complex. As a result, these approaches can not fully learn the global information of the complex, such as the physical symmetry and the topological information of bonds. To address these issues, we propose a novel Equivariant Line Graph Network (ELGN) for binding affinity prediction of 3D protein-ligand complexes. The proposed ELGN firstly adds a super node to the 3D complex, and then builds a line graph based on the 3D complex. After that, ELGN uses a new E(3)-equivariant network layer to pass the messages between nodes and edges based on the global coordinate system of the 3D complex. Experimental results on two real datasets demonstrate the effectiveness of ELGN over several state-of-the-art baselines.

Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning.

MOTIVATION: Single-cell clustering plays a crucial role in distinguishing between cell types, facilitating the analysis of cell heterogeneity mechanisms. While many existing clustering methods rely solely on gene expression data obtained from single-cell RNA sequencing techniques to identify cell clusters, the information contained in mono-omic data is often limited, leading to suboptimal clustering performance. The emergence of single-cell multi-omics sequencing technologies enables the integration of multiple omics data for identifying cell clusters, but how to integrate different omics data effectively remains challenging. In addition, designing a clustering method that performs well across various types of multi-omics data poses a persistent challenge due to the data's inherent characteristics. RESULTS: In this paper, we propose a graph-regularized multi-view ensemble clustering (GRMEC-SC) model for single-cell clustering. Our proposed approach can adaptively integrate multiple omics data and leverage insights from multiple base clustering results. We extensively evaluate our method on five multi-omics datasets through a series of rigorous experiments. The results of these experiments demonstrate that our GRMEC-SC model achieves competitive performance across diverse multi-omics datasets with varying characteristics. AVAILABILITY AND IMPLEMENTATION: Implementation of GRMEC-SC, along with examples, can be found on the GitHub repository: https://github.com/polarisChen/GRMEC-SC.

Dual RNA sequencing of Helicobacter pylori and host cell transcriptomes reveals ontologically distinct host-pathogen interaction.

Helicobacter pylori is a highly successful pathogen that poses a substantial threat to human health. However, the dynamic interaction between H. pylori and the human gastric epithelium has not been fully investigated. In this study, using dual RNA sequencing technology, we characterized a cytotoxin-associated gene A (cagA)-modulated bacterial adaption strategy by enhancing the expression of ATP-binding cassette transporter-related genes, metQ and HP_0888, upon coculturing with human gastric epithelial cells. We observed a general repression of electron transport-associated genes by cagA, leading to the activation of oxidative phosphorylation. Temporal profiling of host mRNA signatures revealed the downregulation of multiple splicing regulators due to bacterial infection, resulting in aberrant pre-mRNA splicing of functional genes involved in the cell cycle process in response to H. pylori infection. Moreover, we demonstrated a protective effect of gastric H. pylori colonization against chronic dextran sulfate sodium (DSS)-induced colitis. Mechanistically, we identified a cluster of propionic and butyric acid-producing bacteria, Muribaculaceae, selectively enriched in the colons of H. pylori-pre-colonized mice, which may contribute to the restoration of intestinal barrier function damaged by DSS treatment. Collectively, this study presents the first dual-transcriptome analysis of H. pylori during its dynamic interaction with gastric epithelial cells and provides new insights into strategies through which H. pylori promotes infection and pathogenesis in the human gastric epithelium. IMPORTANCE: Simultaneous profiling of the dynamic interaction between Helicobacter pylori and the human gastric epithelium represents a novel strategy for identifying regulatory responses that drive pathogenesis. This study presents the first dual-transcriptome analysis of H. pylori when cocultured with gastric epithelial cells, revealing a bacterial adaptation strategy and a general repression of electron transportation-associated genes, both of which were modulated by cytotoxin-associated gene A (cagA). Temporal profiling of host mRNA signatures dissected the aberrant pre-mRNA splicing of functional genes involved in the cell cycle process in response to H. pylori infection. We demonstrated a protective effect of gastric H. pylori colonization against chronic DSS-induced colitis through both in vitro and in vivo experiments. These findings significantly enhance our understanding of how H. pylori promotes infection and pathogenesis in the human gastric epithelium and provide evidence to identify targets for antimicrobial therapies.