A contrastive learning approach to integrate spatial transcriptomics and histological images.

The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, we present ConGcR, a contrastive learning-based model for integrating gene expression, spatial location, and tissue morphology for data representation and spatial tissue architecture identification. Graph convolution and ResNet were used as encoders for gene expression with spatial location and histological image inputs, respectively. We further enhanced ConGcR with a graph auto-encoder as ConGaR to better model spatially embedded representations. We validated our models using 16 human brains, four chicken hearts, eight breast tumors, and 30 human lung spatial transcriptomics samples. The results showed that our models generated more effective embeddings for obtaining tissue architectures closer to the ground truth than other methods. Overall, our models not only can improve tissue architecture identification's accuracy but also may provide valuable insights and effective data representation for other tasks in spatial transcriptome analyses.

Ketogenic diet time-dependently prevents NAFLD through upregulating the expression of antioxidant protein metallothionein-2.

BACKGROUND & AIMS: The past few decades have witnessed a rapid growth in the prevalence of nonalcoholic fatty liver disease (NAFLD). While the ketogenic diet (KD) is considered for managing NAFLD, the safety and efficacy of the KD on NAFLD has been a controversial topic. Here, we aimed to investigate the effect of KD of different durations on metabolic endpoints in mice with NAFLD and explore the underlying mechanisms. METHODS: NAFLD mice were fed with KD for 1, 2, 4 and 6 weeks, respectively. The blood biochemical indexes (blood lipids, AST, ALT and etc.) and liver fat were measured. The LC-MS/MS based proteomic analysis was performed on liver tissues. Metallothionein-2 (MT2) was knocked down with adeno-associated virus (AAV) or small interfering RNA (siRNA) in NAFLD mice and AML-12 cells, respectively. H&E, BODIPY and ROS staining were performed to examine lipid deposition and oxidative stress. Furthermore, MT2 protein levels, nucleus/cytoplasm distribution and DNA binding activity of peroxisome proliferators-activated receptors α (PPARα) were evaluated. RESULTS: KD feeding for 2 weeks showed the best improvement on NAFLD phenotype. Proteomic analysis revealed that MT2 was a key candidate for different metabolic endpoints of NAFLD affected by different durations of KD feeding. MT2 knockdown in NAFLD mice blocked the effects of 2 weeks of KD feeding on HFD-induced steatosis. In mouse primary hepatocytes and AML-12 cells, MT2 protein levels were induced by ß-hydroxybutyric acid (ß-OHB). MT2 Knockdown blunted the effects of ß-OHB on alleviating PA-induced lipid deposition. Mechanistically, 2 weeks of KD or ß-OHB treatment reduced oxidative stress and upregulated the protein levels of MT2 in nucleus, which subsequently increased its DNA binding activity and PPARα protein expression. CONCLUSIONS: Collectively, these findings indicated that KD feeding prevented NAFLD in a time dependent manner and MT2 is a potential target contributing to KD improvement on steatosis.

Online sequential analysis of volatile and semivolatile organic compounds in water matrices by double robotic sample preparations and dual-channel mono and comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry system.

The monitoring of organic compounds in aquatic matrices poses challenges due to its complexity and time-intensive nature. To address these challenges, we introduce a novel approach utilizing a dual-channel mono (1D) and comprehensive two-dimensional (2D) gas chromatography coupled with time-of-flight mass spectrometry (GC × GC-TOFMS) system, integrated with a robotic pretreatment platform, for online monitoring of both volatile organic compounds (VOCs) and semivolatile organic compounds (SVOCs) in water matrices. Employing the robotic platform, we establish a suite of online liquid-liquid extraction (LLE) pretreatment processes for water samples, marking the first instance of such procedures. Leveraging the automatic headspace (HS) module, dual robotic preparations of HS and LLE are sequentially executed to extract VOCs and SVOCs from water matrices. The GC × GC-TOFMS system is distinguished by its dual-channel analytical column configuration, facilitating sequential analysis of VOCs in GC-TOFMS mode and SVOCs in GC × GC-TOFMS mode. Quantitative detection of 55 target VOCs and 104 SVOCs is achieved in a water sample using the instrument system. Our method demonstrates excellent correlation coefficients ranging from 0.990 to 1.000, method detection limits ranging from 0.08 to 4.78 µg L-1, relative standard deviations below 19.3 %, and recovery rates ranging from 50.0 % to 124.0 %. To validate the online monitoring capabilities of our system, we assess target SVOCs at three different concentration levels over a 3-day period. Most compounds exhibit recovery rates ranging from 70.0 % to 130.0 %. Furthermore, we apply our method to analyze a real water sample, successfully identifying over 100 target and nontarget VOCs/SVOCs, including alcohols, aldehydes, ketones, acids, esters, and phenols. These results highlight the efficacy of the proposed analysis system, capable of conducting two distinct analyses in automatic sequence, thereby enhancing the efficiency and accuracy of organic compound analysis in water matrices.

Phyllanthus emblica Linn: A comprehensive review of botany, traditional uses, phytonutrients, health benefits, quality markers, and applications.

Phyllanthus emblica Linn is not only an edible fruit with high nutritional value, but also a medicinal plant with multiple bioactivities. It is widely used in clinical practice with functions of clearing heat, cooling blood, digesting food, strengthening stomach, promoting fluid production, and relieving cough. This review summarized a wide variety of phytonutrients, including nutritional components (mineral elements, amino acids, vitamins, polysaccharides, unsaturated free fatty acids) and functional components (phenolic acids (1-34), tannins (35-98), flavonoids (99-141), sterols (142-159), triterpenoids (160-175), lignans (176-183), alkaloids (184-197), alkanes (198-212), aromatic micromolecules (213-222), other compounds (223-239)). The isolated compounds and the various extracts of P. emblica Linn presented a diverse spectrum of biological activities such as anti-oxidant, anti-cancer, anti-inflammatory, anti-bacterial, hepatoprotective, hypoglycemic, anti-atherosclerosis, neuroprotective, enhancing immunity, anti-fatigue, anti-myocardial fibrosis. The quality markers of P. emblica Linn were predicted and analyzed based on traditional medicinal properties, traditional efficacy, plant genealogy and chemical component characteristics, biogenic pathway of chemical components, measurability of chemical components, transformation characteristics of polyphenolic components, homologous characteristics of medicine and food, compound compatibility environment, and clinical applications. This review also summarized and prospected applications of P. emblica Linn in beverages, preserved fruits, fermented foods, etc. However, the contents of mechanism, structure-activity relationship, quality control, toxicity, extraction, processing of P. emblica Linn are not clear, and are worth further studies in the future.

The Role of Ki-67 in HR+/HER2- Breast Cancer: A Real-World Study of 956 Patients.

Objective: This study determined the cut-off value of Ki-67 expression and discussed the interaction between Ki-67 and histological grade, further explored the prognostic role of Ki-67 in hormone receptor-positive and human epidermal growth factor receptor 2 negative (HR+/HER2-) breast cancer;. Materials and Methods: We assessed the Ki-67 expression of 956 patients with HR+/HER2 breast cancer diagnosed in the General Hospital of Ningxia Medical University from 2015 to 2019 by immunohistochemistry (IHC), The disease-free survival (DFS) was defined as the time from postoperative to the first local recurrence, distant metastasis or death of the disease. The follow-up by means of inpatient or outpatient medical records and telephone. Results: 22.5% was used as the cut-off for low/high Ki-67 expression in HR+/HER2- breast cancer. Compared with the value of 14%, which is commonly used in clinic at present, the consistency of the two values is moderate (Kappa = 0.484, P<0.001). The expression of Ki-67 was increased with the grade. (Median: G1:10%; G2:20%; G3:40%. Mean: G1:13%; G2:23%; G3:39%, P <0.001). Survival analysis was based on all patients for a median of 51 months (24-89 months), 63 cases had recurrence or metastasis during the follow-up, which 21 cases had low expression of Ki-67 and 42 cases had high expression. The patients with Ki-67 ≥ 22.5% had a 2.969 higher risk of early recurrence and metastasis than the patients with Ki-67 < 22.5%. There were 4 cases of local recurrence, 7 cases of regional lymph node metastasis, and 52 cases of distant metastasis in all patients, the common distant metastases were bone, liver, and lung, and rare metastases were adrenal gland, bone marrow, and pericardium. Conclusion: In HR+/HER2- breast cancer, patients with Ki-67 > 22.5% have a worse prognosis and are more likely to have early recurrence and metastasis.

A novel U-tied semi-manual anastomosis in totally laparoscopic colectomy.

TECHNIQUE: We describe improvements to the previously proposed "U-tied anastomosis" with the aim of broadening its indications, especially in left hemicolectomy. After bowel mobilization and vascular ligation, the proximal and distal colon were aligned in a U-shape using a ligature. An anastomosis was constructed using a linear stapler through the common enterotomies. Following resection of the bowel using laparoscopic coagulation shears, the common opening was closed using 3-0 barbed sutures. RESULTS: Eight consecutive patients underwent colectomy using the U-tied semi-manual technique between May and July 2023. In all cases, the U-tied procedures were completed using one cartridge and two sutures. No complications or mortality were observed after one month of follow-up. CONCLUSIONS: The U-tied semi-manual anastomosis is a straightforward and effective method for intracorporeal anastomosis. The simplified reconstruction technique of U-tied series, together with the minimization of technique variability, results in consistent outcomes when performed by surgeons with different levels of experience. The streamlined process enhances the homogeneity of the intracorporeal anastomosis while reducing cartridge use.

A rapid identification method for soft tissue markers of dentofacial deformities based on heatmap regression.

OBJECTIVE: The purpose of this study was to construct a facial deformity dataset and a network model based on heatmap regression for the recognition of facial soft tissue landmarks to provide a basis for clinicians to perform cephalometric analysis of soft tissue. MATERIALS AND METHODS: A 34-point face marker detection model, the Back High-Resolution Network (BHR-Net), was constructed based on the heatmap regression algorithm, and a custom dataset of 1780 facial detection images for orthognathic surgery was collected. The mean normalized error (MNE) and 10% failure rate (FR10%) were used to evaluate the performance of BHR-Net, and a test set of 50 patients was used to verify the accuracy of the landmarks and their measurement indicators. The test results were subsequently validated in 30 patients. RESULTS: Both the MNE and FR10% of BHR-Net were optimal compared with other models. In the test set (50 patients), the accuracy of the markers excluding the nose root was 86%, and the accuracy of the remaining markers reached 94%. In the model validation (30 patients), using the markers detected by BHR-Net, the diagnostic accuracy of doctors was 100% for Class II and III deformities, 100% for the oral angle plane, and 70% for maxillofacial asymmetric deformities. CONCLUSIONS: BHR-Net, a network model based on heatmap regression, can be used to effectively identify landmarks in maxillofacial multipose images, providing a reliable way for clinicians to perform cephalometric measurements of soft tissue objectively and quickly.

Radiofrequency radiation reshapes tumor immune microenvironment into antitumor phenotype in pulmonary metastatic melanoma by inducing active transformation of tumor-infiltrating CD8+ T and NK cells.

Immunosuppression by the tumor microenvironment is a pivotal factor contributing to tumor progression and immunotherapy resistance. Priming the tumor immune microenvironment (TIME) has emerged as a promising strategy for improving the efficacy of cancer immunotherapy. In this study we investigated the effects of noninvasive radiofrequency radiation (RFR) exposure on tumor progression and TIME phenotype, as well as the antitumor potential of PD-1 blockage in a model of pulmonary metastatic melanoma (PMM). Mouse model of PMM was established by tail vein injection of B16F10 cells. From day 3 after injection, the mice were exposed to RFR at an average specific absorption rate of 9.7 W/kg for 1 h per day for 14 days. After RFR exposure, lung tissues were harvested and RNAs were extracted for transcriptome sequencing; PMM-infiltrating immune cells were isolated for single-cell RNA-seq analysis. We showed that RFR exposure significantly impeded PMM progression accompanied by remodeled TIME of PMM via altering the proportion and transcription profile of tumor-infiltrating immune cells. RFR exposure increased the activation and cytotoxicity signatures of tumor-infiltrating CD8+ T cells, particularly in the early activation subset with upregulated genes associated with T cell cytotoxicity. The PD-1 checkpoint pathway was upregulated by RFR exposure in CD8+ T cells. RFR exposure also augmented NK cell subsets with increased cytotoxic characteristics in PMM. RFR exposure enhanced the effector function of tumor-infiltrating CD8+ T cells and NK cells, evidenced by increased expression of cytotoxic molecules. RFR-induced inhibition of PMM growth was mediated by RFR-activated CD8+ T cells and NK cells. We conclude that noninvasive RFR exposure induces antitumor remodeling of the TIME, leading to inhibition of tumor progression, which provides a promising novel strategy for TIME priming and potential combination with cancer immunotherapy.

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment.

Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown, in part due to technical barriers in dissecting the tumor microenvironment (TME) in high detail. Herein, we applied multiplexed ion beam imaging (MIBI) spatial pro-teomics on 6 EBV-positive and 14 EBV-negative cHL samples. We identify key TME features that distinguish between EBV-positive and EBV-negative cHL, including the relative predominance of memory CD8 T cells and increased T-cell dysfunction as a function of spatial proximity to HRS cells. Building upon a larger multi-institutional cohort of 22 EBV-positive and 24 EBV-negative cHL samples, we orthogonally validated our findings through a spatial multi-omics approach, coupling whole transcriptome capture with antibody-defined cell types for tu-mor and T-cell populations within the cHL TME. We delineate contrasting transcriptomic immunological signatures between EBV-positive and EBV-negative cases that differently impact HRS cell proliferation, tumor-immune interactions, and mecha-nisms of T-cell dysregulation and dysfunction. Our multi-modal framework enabled a comprehensive dissection of EBV-linked reorganization and immune evasion within the cHL TME, and highlighted the need to elucidate the cellular and molecular fac-tors of virus-associated tumors, with potential for targeted therapeutic strategies.

Targeting metabolic sensing switch GPR84 on macrophages for cancer immunotherapy.

INTRODUCTION: As one of the major components of the tumor microenvironment, tumor-associated macrophages (TAMs) possess profound inhibitory activity against T cells and facilitate tumor escape from immune checkpoint blockade therapy. Converting this pro-tumorigenic toward the anti-tumorigenic phenotype thus is an important strategy for enhancing adaptive immunity against cancer. However, a plethora of mechanisms have been described for pro-tumorigenic differentiation in cancer, metabolic switches to program the anti-tumorigenic property of TAMs are elusive. MATERIALS AND METHODS: From an unbiased analysis of single-cell transcriptome data from multiple tumor models, we discovered that anti-tumorigenic TAMs uniquely express elevated levels of a specific fatty acid receptor, G-protein-coupled receptor 84 (GPR84). Genetic ablation of GPR84 in mice leads to impaired pro-inflammatory polarization of macrophages, while enhancing their anti-inflammatory phenotype. By contrast, GPR84 activation by its agonist, 6-n-octylaminouracil (6-OAU), potentiates pro-inflammatory phenotype via the enhanced STAT1 pathway. Moreover, 6-OAU treatment significantly retards tumor growth and increases the anti-tumor efficacy of anti-PD-1 therapy. CONCLUSION: Overall, we report a previously unappreciated fatty acid receptor, GPR84, that serves as an important metabolic sensing switch for orchestrating anti-tumorigenic macrophage polarization. Pharmacological agonists of GPR84 hold promise to reshape and reverse the immunosuppressive TME, and thereby restore responsiveness of cancer to overcome resistance to immune checkpoint blockade.

Uncut Roux-en-Y reconstruction after distal gastrectomy for gastric cancer.

BACKGROUND: Choosing an optimal reconstruction method is pivotal for patients with gastric cancer undergoing distal gastrectomy. The uncut Roux-en-Y reconstruction, a variant of the conventional Roux-en-Y approach (or variant of the Billroth II reconstruction), employs uncut devices to occlude the afferent loop of the jejunum. This modification is designed to mitigate postgastrectomy syndrome and enhance long-term functional outcomes. However, the comparative benefits and potential harms of this approach compared to other reconstruction techniques remain a topic of debate. OBJECTIVES: To assess the benefits and harms of uncut Roux-en-Y reconstruction after distal gastrectomy in patients with gastric cancer. SEARCH METHODS: We searched CENTRAL, PubMed, Embase, WanFang Data, China National Knowledge Infrastructure, and clinical trial registries for published and unpublished trials up to November 2023. We also manually reviewed references from relevant systematic reviews identified by our search. We did not impose any language restrictions. SELECTION CRITERIA: We included randomised controlled trials (RCTs) and quasi-RCTs comparing uncut Roux-en-Y reconstruction versus other reconstructions after distal gastrectomy for gastric cancer. The comparison groups encompassed other reconstructions such as Billroth I, Billroth II (with or without Braun anastomosis), and Roux-en-Y reconstruction. DATA COLLECTION AND ANALYSIS: We used standard Cochrane methodological procedures. The critical outcomes included health-related quality of life at least six months after surgery, major postoperative complications within 30 days after surgery according to the Clavien-Dindo Classification (grades III to V), anastomotic leakage within 30 days, changes in body weight (kg) at least six months after surgery, and incidence of bile reflux, remnant gastritis, and oesophagitis at least six months after surgery. We used the GRADE approach to evaluate the certainty of the evidence. MAIN RESULTS: We identified eight trials, including 1167 participants, which contributed data to our meta-analyses. These trials were exclusively conducted in East Asian countries, predominantly in China. The studies varied in the types of uncut devices used, ranging from 2- to 6-row linear staplers to suture lines. The follow-up periods for long-term outcomes spanned from 3 months to 42 months, with most studies focusing on a 6- to 12-month range. We rated the certainty of evidence from low to very low. Uncut Roux-en-Y reconstruction versus Billroth II reconstruction In the realm of surgical complications, very low-certainty evidence suggests that uncut Roux-en-Y reconstruction compared with Billroth II reconstruction may make little to no difference to major postoperative complications (risk ratio (RR) 0.98, 95% confidence interval (CI) 0.24 to 4.05; I² = 0%; risk difference (RD) 0.00, 95% CI -0.04 to 0.04; I² = 0%; 2 studies, 282 participants; very low-certainty evidence) and incidence of anastomotic leakage (RR 0.64, 95% CI 0.29 to 1.44; I² not applicable; RD -0.00, 95% CI -0.03 to 0.02; I² = 32%; 3 studies, 615 participants; very low-certainty evidence). We are very uncertain about these results. Focusing on long-term outcomes, low- to very low-certainty evidence suggests that uncut Roux-en-Y reconstruction compared with Billroth II reconstruction may make little to no difference to changes in body weight (mean difference (MD) 0.04 kg, 95% CI -0.84 to 0.92 kg; I² = 0%; 2 studies, 233 participants; low-certainty evidence), may reduce the incidence of bile reflux into the remnant stomach (RR 0.67, 95% CI 0.55 to 0.83; RD -0.29, 95% CI -0.43 to -0.16; number needed to treat for an additional beneficial outcome (NNTB) 4, 95% CI 3 to 7; 1 study, 141 participants; low-certainty evidence), and may have little or no effect on the incidence of remnant gastritis (RR 0.27, 95% CI 0.01 to 5.06; I2 = 78%; RD -0.15, 95% CI -0.23 to -0.07; I2 = 0%; NNTB 7, 95% CI 5 to 15; 2 studies, 265 participants; very low-certainty evidence). No studies reported on quality of life or the incidence of oesophagitis. Uncut Roux-en-Y reconstruction versus Roux-en-Y reconstruction In the realm of surgical complications, very low-certainty evidence suggests that uncut Roux-en-Y reconstruction compared with Roux-en-Y reconstruction may make little to no difference to major postoperative complications (RR 4.74, 95% CI 0.23 to 97.08; I² not applicable; RD 0.01, 95% CI -0.02 to 0.04; I² = 0%; 2 studies, 256 participants; very low-certainty evidence) and incidence of anastomotic leakage (RR 0.34, 95% CI 0.05 to 2.08; I² = 0%; RD -0.02, 95% CI -0.06 to 0.02; I² = 0%; 2 studies, 213 participants; very low-certainty evidence). We are very uncertain about these results. Focusing on long-term outcomes, very low-certainty evidence suggests that uncut Roux-en-Y reconstruction compared with Roux-en-Y reconstruction may increase the incidence of bile reflux into the remnant stomach (RR 10.74, 95% CI 3.52 to 32.76; RD 0.57, 95% CI 0.43 to 0.71; NNT for an additional harmful outcome (NNTH) 2, 95% CI 2 to 3; 1 study, 108 participants; very low-certainty evidence) and may make little to no difference to the incidence of remnant gastritis (RR 1.18, 95% CI 0.69 to 2.01; I² = 60%; RD 0.03, 95% CI -0.03 to 0.08; I² = 0%; 3 studies, 361 participants; very low-certainty evidence) and incidence of oesophagitis (RR 0.82, 95% CI 0.53 to 1.26; I² = 0%; RD -0.02, 95% CI -0.07 to 0.03; I² = 0%; 3 studies, 361 participants; very low-certainty evidence). We are very uncertain about these results. Data were insufficient to assess the impact on quality of life and changes in body weight. AUTHORS' CONCLUSIONS: Given the predominance of low- to very low-certainty evidence, this Cochrane review faces challenges in providing definitive clinical guidance. We found the majority of critical outcomes may be comparable between the uncut Roux-en-Y reconstruction and other methods, but we are very uncertain about most of these results. Nevertheless, it indicates that uncut Roux-en-Y reconstruction may reduce the incidence of bile reflux compared to Billroth-II reconstruction, albeit with low certainty. In contrast, compared to Roux-en-Y reconstruction, uncut Roux-en-Y may increase bile reflux incidence, based on very low-certainty evidence. To strengthen the evidence base, further rigorous and long-term trials are needed. Additionally, these studies should explore variations in surgical procedures, particularly regarding uncut devices and methods to prevent recanalisation. Future research may potentially alter the conclusions of this review.

Ketogenic diet ameliorates high-fat diet-induced insulin resistance in mouse skeletal muscle by alleviating endoplasmic reticulum stress.

OBJECTIVE: Ketogenic diets (KD) have been shown to alleviate insulin resistance (IR) by exerting anti-lipogenic and insulin sensitizing effects in the liver through a variety of pathways. The present study sought to investigate whether a ketogenic diet also improves insulin sensitization in skeletal muscle cells through alleviating endoplasmic reticulum stress. METHODS: High-fat diet-induced IR mice were allowed to a 2-week ketogenic diet. Insulin resistance and glucose tolerance were evaluated through GTT, ITT, and HOMA-IR. The C2C12 myoblasts exposed to palmitic acid were used to evaluate the insulin sensitization effects of ß-hydroxybutyric acid (ß-OHB). Molecular mechanisms concerning ER stress signaling activation and glucose uptake were assessed. RESULTS: The AKT/GSK3ß pathway was inhibited, ER stress signaling associated with IRE1, PERK, and BIP was activated, and the number of Glut4 proteins translocated to membrane decreased in the muscle of HFD mice. However, all these changes were reversed after 2 weeks of feeding on a ketogenic diet. Consistently in C2C12 myoblasts, the AKT/GSK3ß pathway was inhibited by palmitic acid (PA) treatment. The endoplasmic reticulum stress-related proteins, IRE1, and BIP were increased, and the number of Glut4 proteins on the cell membrane decreased. However, ß-OHB treatment alleviated ER stress and improved the glucose uptake of C2C12 cells. CONCLUSION: Our data reveal that KD ameliorated HFD-induced insulin resistance in skeletal muscle, which was partially mediated by inhibiting endoplasmic reticulum stress. The insulin sensitization effect of ß-OHB is associated with up regulation of AKT/GSK3ß pathway and the increase in the number of Glut4 proteins on the cell membrane.

Detecting and genotyping high-risk human papillomavirus among male patients during 2015-2023 in Beijing, China.

Few studies focused on human papillomavirus (HPV) in male patients. This study aimed to explore the detection rate and genotyping of HPV among male patients in Beijing to provide a reference for formulating prevention strategies for HPV infection. The cross-sectional study was conducted in Beijing Chaoyang Hospital from November 2015 to March 2023. It covered male patients from the urology and dermatology departments. Fifteen high-risk HPV genotypes were detected by the multiplex real-time polymerase chain reaction method. The overall detection rate of HPV was 25.19% (1288/5114, 95% confidence interval [CI] 24.00%-26.38%), of which the single infection rate was 16.99% (869/5114, 95% CI 15.97%-18.05%) and the co-infection rate was 8.19% (419/5114, 95% CI 7.46%-8.98%). The detection rate of HPV was 40.77% (521/1278), 35.58% (58/163), 32.69% (101/309), 31.91% (60/188), 12.63% (299/2367), and 32.35% (131/405) among male patients with balanitis, warts, rash, urethritis, prostatitis, and other urinary inflammation, respectively (P < 0.001). The top five HPV genotypes were HPV-52, HPV-58, HPV-16, HPV-51, and HPV-66. After the first positive HPV test, the proportion of male patients who turned negative was 22.47% within 3 months, 26.40% within 3-6 months, 24.72% within 6-12 months, 17.98% within 12-24 months, and 8.43% more than 24 months. The detection rate of HPV was high among male patients from the urology and dermatology departments in Beijing, which should be considered to develop HPV vaccines with better prevention effects.

Preventing lower limb lymphedema after pelvic lymphadenectomy with progressive resistance exercise training: A randomized controlled trial.

Objective: This study aimed to assess the efficacy of a self-designed progressive resistance exercise training program for preventing the development of lower limb lymphedema. Methods: An open-label randomized controlled trial was conducted in patients who underwent radical surgery for cervical cancer treatment in our department between October 7, 2019, and October 7, 2021. The participants were randomly assigned to one of three groups: progressive resistance exercise training, graduated compression stocking, and control group. Results: A total of 267 patients were enrolled (89 in each group). The incidence of lower limb lymphedema was 9.0% (n = 8) in the progressive resistance exercise training group, 28.1% (n = 25) in the graduated compression stocking group, and 42.7% (n = 38) in the control group. Over the 2-year follow-up period, the risk of lower limb lymphedema was significantly lower in the progressive resistance exercise training group than in the control group, with a hazard ratio (HR) (95% confidence interval [CI]) of 0.156 (0.073-0.335). The study was underpowered to demonstrate a statistically significant reduction in risk in the graduated compression stocking group, with an HR (95% CI) of 0.624 (0.376-1.033). Conclusions: Progressive resistance exercise training is an effective strategy for preventing lower limb lymphedema after pelvic lymphadenectomy for cervical cancer. It imposes no additional economic burden and can be performed conveniently without the need for dedicated exercise facilities. This makes it particularly accessible to patients in developing countries, allowing them to exercise at their convenience. Trial registration: ChiCTR1800014905.

Midline and off-midline wound closure methods after surgical treatment for pilonidal sinus.

BACKGROUND: Pilonidal sinus disease is a common and debilitating condition. Surgical treatment remains the mainstay for managing chronic disease, with options including midline and off-midline wound closure methods. However, the optimal approach remains uncertain. Recent developments in tension-free midline techniques require further exploration. OBJECTIVES: To assess the effects of midline and off-midline wound closure methods for pilonidal sinus, and to determine the optimal off-midline flap procedures. SEARCH METHODS: In June 2022, we searched the Cochrane Wounds Specialised Register, CENTRAL, MEDLINE, Embase, CINAHL Plus EBSCO, and clinical trials registries. We also scanned the reference lists of included studies, as well as reviews, meta-analyses, and health technology reports. We applied no language, publication date, or study setting restrictions. SELECTION CRITERIA: We included parallel RCTs involving participants undergoing midline closure without flap techniques and off-midline closure for pilonidal sinus treatment. We excluded quasi-experimental studies and studies that enroled participants presenting with an abscess. DATA COLLECTION AND ANALYSIS: We followed standard Cochrane methodology. The critical outcomes included wound healing (time to wound healing, proportion of wounds healed), recurrence rate, wound infection, wound dehiscence, time to return to work, and quality of life. We assessed biases in these outcomes utilising the Cochrane risk of bias 2 tool and appraised evidence certainty via the GRADE approach. MAIN RESULTS: We included 33 studies with 3667 analysed participants. The median or average age of the participants across the included studies ranged from 21.0 to 34.2 years, with a predominant male representation. Geographically, the trials were primarily conducted in the Middle East. We identified nine intervention comparisons. In this abstract, we focus on and present the summarised findings for the three primary comparisons. Off-midline closure versus conventional midline closure Off-midline closure probably reduces the time to wound healing (mean difference (MD) -5.23 days, 95% confidence interval (CI) -7.55 to -2.92 days; 3 studies, 300 participants; moderate-certainty evidence). However, there may be little to no difference between the two methods in the proportion of wounds healed (100% versus 88.5%, risk ratio (RR) 1.13, 95% CI 0.92 to 1.39; 2 studies, 207 participants; very low-certainty evidence). Off-midline closure probably results in lower rates of recurrence (1.5% versus 6.8%, RR 0.22, 95% CI 0.11 to 0.45; 13 studies, 1492 participants; moderate-certainty evidence) and wound infection (3.8% versus 11.7%, RR 0.32, 95% CI 0.22 to 0.49; 13 studies, 1568 participants; moderate-certainty evidence), and may lower rates of wound dehiscence (3.9% versus 8.9%, RR 0.44, 95% CI 0.27 to 0.71; 11 studies, 1389 participants; low-certainty evidence). Furthermore, off-midline closure may result in a reduced time to return to work (MD -3.72 days, 95% CI -6.11 to -1.33 days; 6 studies, 820 participants; low-certainty evidence). There were no data available for quality of life. Off-midline closure versus tension-free midline closure Off-midline closure may reduce the time to wound healing (median 14 days in off-midline closure versus 51 days in tension-free midline closure; 1 study, 116 participants; low-certainty evidence) and increase wound healing rates at three months (94.7% versus 76.4%, RR 1.24, 95% CI 1.06 to 1.46; 1 study, 115 participants; low-certainty evidence), but may result in little to no difference in rates of recurrence (5.4% versus 7.8%, RR 0.69, 95% CI 0.30 to 1.61; 6 studies, 551 participants; very low-certainty evidence), wound infection (2.8% versus 6.4%, RR 0.44, 95% CI 0.16 to 1.17; 6 studies, 559 participants; very low-certainty evidence), and wound dehiscence (2.5% versus 3.0%, RR 0.82, 95% CI 0.17 to 3.84; 3 studies, 250 participants; very low-certainty evidence) compared to tension-free midline closure. Furthermore, off-midline closure may result in longer time to return to work compared to tension-free midline closure (MD 3.00 days, 95% CI 1.52 to 4.48 days; 1 study, 60 participants; low-certainty evidence). There were no data available for quality of life. Karydakis flap versus Limberg flap Karydakis flap probably results in little to no difference in time to wound healing compared to Limberg flap (MD 0.36 days, 95% CI -1.49 to 2.22; 6 studies, 526 participants; moderate-certainty evidence). Compared to Limberg flap, Karydakis flap may result in little to no difference in the proportion of wounds healed (80.0% versus 66.7%, RR 1.20, 95% CI 0.77 to 1.86; 1 study, 30 participants; low-certainty evidence), recurrence rate (5.1% versus 4.5%, RR 1.14, 95% CI 0.61 to 2.14; 9 studies, 890 participants; low-certainty evidence), wound infection (7.9% versus 5.1%, RR 1.55, 95% CI 0.90 to 2.68; 8 studies, 869 participants; low-certainty evidence), wound dehiscence (7.4% versus 6.2%, RR 1.20, 95% CI 0.41 to 3.50; 7 studies, 776 participants; low-certainty evidence), and time to return to work (MD -0.23 days, 95% CI -5.53 to 5.08 days; 6 studies, 541 participants; low-certainty evidence). There were no data available for quality of life. AUTHORS' CONCLUSIONS: This Cochrane review examines the midline and off-midline wound closure options for pilonidal sinus, predominantly based on young adult studies. Off-midline flap procedures demonstrate there may be benefits over conventional midline closure for pilonidal sinus, with various off-midline flap techniques. When off-midline flap closures were compared to tension-free midline closure, low-certainty evidence indicated there may be improved wound healing and increased time to return to work for off-midline closure, whilst very low-certainty evidence indicated there may be no evidence of a difference in other outcomes. There may be no evidence of an advantage found amongst the off-midline techniques evaluated. The choice of either procedure is likely to be based on a clinician's preference, experience, patient characteristics, and the patients' preferences. To more accurately determine the benefits and potential harms of these closure techniques, further large-scale and meticulously-designed trials are essential. Specifically, there is a pressing need for more studies addressing the paediatric population, in addition to adult studies.

mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is highly transmissible and evades pre-established immunity. Messenger RNA (mRNA) vaccination against ancestral strain spike protein can induce intact T-cell immunity against the Omicron variant, but efficacy of booster vaccination in patients with late-stage lung cancer on immune-modulating agents including anti-programmed cell death protein 1(PD-1)/programmed death-ligand 1 (PD-L1) has not yet been elucidated. METHODS: We assessed T-cell responses using a modified activation-induced marker assay, coupled with high-dimension flow cytometry analyses. Peripheral blood mononuclear cells (PBMCs) were stimulated with various viral peptides and antigen-specific T-cell responses were evaluated using flow cytometry. RESULTS: Booster vaccines induced CD8+ T-cell response against the ancestral SARS-CoV-2 strain and Omicron variant in both non-cancer subjects and patients with lung cancer, but only a marginal induction was detected for CD4+ T cells. Importantly, antigen-specific T cells from patients with lung cancer showed distinct subpopulation dynamics with varying degrees of differentiation compared with non-cancer subjects, with evidence of dysfunction. Notably, female-biased T-cell responses were observed. CONCLUSION: We conclude that patients with lung cancer on immunotherapy show a substantial qualitative deviation from non-cancer subjects in their T-cell response to mRNA vaccines, highlighting the need for heightened protective measures for patients with cancer to minimize the risk of breakthrough infection with the Omicron and other future variants.

MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer.

Rare cell populations are key in neoplastic progression and therapeutic response, offering potential intervention targets. However, their computational identification and analysis often lag behind major cell types. To fill this gap, we introduce MarsGT: Multi-omics Analysis for Rare population inference using a Single-cell Graph Transformer. It identifies rare cell populations using a probability-based heterogeneous graph transformer on single-cell multi-omics data. MarsGT outperforms existing tools in identifying rare cells across 550 simulated and four real human datasets. In mouse retina data, it reveals unique subpopulations of rare bipolar cells and a Müller glia cell subpopulation. In human lymph node data, MarsGT detects an intermediate B cell population potentially acting as lymphoma precursors. In human melanoma data, it identifies a rare MAIT-like population impacted by a high IFN-I response and reveals the mechanism of immunotherapy. Hence, MarsGT offers biological insights and suggests potential strategies for early detection and therapeutic intervention of disease.

A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset.

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors. SIGNIFICANCE: Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.

Case Report: Laparoscopy-assisted resection for intra-abdominal gossypiboma masquerading as a jejunal tumor (with video).

Introduction: Intra-abdominal gossypiboma, a cotton-based retained foreign body after an abdominal surgery, is associated with various clinical manifestations and complications. Its infrequent occurrence and unpredictability make its early diagnosis particularly challenging. We herein present an atypical case of intra-abdominal gossypiboma mistaken for a jejunal tumor. Case presentation: A 33-year-old female presented to the emergency room with an acute episode of progressive abdominal pain and distention, nausea, and vomiting for 20 hours. She had undergone an urgent cesarean section due to fetal tachycardia seven years prior. The initial diagnosis of small bowel obstruction (SBO) due to a jejunal tumor was established by computed tomography. Subsequent to successful medical management of the SBO, a laparoscopy-assisted resection of the mass and the adherent jejunal segment was conducted, culminating in a primary side-to-side jejunojejunostomy. Examination of the excised tissue revealed an approximately spherical fibrous mass, 6 × 6 × 5 cm in dimension, embedded in the jejunal wall, housing a 20 × 20-cm gauze. Postoperative recovery and routine follow-up ensued without complications. Conclusion: In light of this case, the need for clinicians to maintain an elevated awareness and suspicion of gossypiboma should be accentuated when evaluating an intra-abdominal mass, especially in patients with a prior history of high-risk laparotomy. Laparoscopic surgery stands out as a technically proficient and minimally invasive strategy for diagnosing and treating intra-abdominal gossypiboma. Besides, it is imperative to emphasize the importance of meticulous surgical procedures and postoperative protocols to prevent such oversights, reaffirming the need for consistent intraoperative counts and checks of surgical items.