[Clinical outcome of combined over-the-top reconstruction with modified Lemaire procedure in one-stage revision anterior cruciate ligament reconstruction]

Objective: To investigate the clinical effect of over-the-top (OTT) reconstruction of the anterior cruciate ligament (ACL) combined with the modified Lemaire technique in one-stage ACL revision. Methods: It's a retrospective study. The clinical data of 37 patients who underwent one-stage revision of ACL using OTT combined with modified Lemaire technique from April 2020 to May 2023 in the Department of Sports Medicine of Xinhua Hospital Affiliated to Dalian University were retrospectively analyzed. There were 28 males and 9 females with a mean age of (32.7±5.7) years. The postoperative knee function and surgical revision effect were evaluated by subjective and objective evaluation indexes of the knee joint before and 3 months and 24 months after surgery. The subjective evaluation indexes included the International Knee Documentation Committee (IKDC) score, Lysholm score, and Tegner score; and the objective evaluation indexes included the anterior-posterior static displacement distance of the tibia, tibia-femur relative rotation angle, the Lachman test, the axial shift test, and the ratio of the loss of muscle strength of the lower limb. Results: At the final follow-up, all patients returned to pre-injury motor level, with significant improvements in IKDC scores (45.3±6.8 preoperatively, 67.5±4.7 and 93.2±2.3 at 3 months and 2 years after the operation, respectively), Lysholm scores (57.2±2.6 preoperatively, 72.6±2.9 and 89.7±3.7 at 3 months and 2 years after the operation, respectively), and Tegner scores (3.1±0.7 preoperatively, 4.9±0.6 and 5.8±1.3 at 3 months and 2 years after the operation, respectively) (all P<0.001). The anterior-posterior static displacement distance of the tibia reduced significantly [from (5.2±0.5) mm before the operation to (1.4±0.5) mm at 2 years postoperatively) (P<0.001)]; and the relative rotation angle of the tibia-femur restored to the normal physiological range, it was reduced from 6.2°±1.2° before the operation to 1.7°±0.3° 2 years after (P<0.001). The Lachman test and axial shift test at 2 years postoperatively were all negative. The muscle strength loss ratio of the affected lower limb was significantly better than that before the operation (P<0.001). Conclusion: The use of OTT reconstruction combined with modified Lemaire technique for revision of ACL in patients with ACL reconstruction failure can circumvent the tunnel problem for one-stage revision and better restore the stability and function of the knee joint, with ideal clinical results.

MRI-based radiomics model to preoperatively predict mesenchymal transition subtype in high-grade serous ovarian cancer

AIM

To develop a magnetic resonance imaging (MRI)-based radiomics model for the preoperative identification of mesenchymal transition (MT) subtype in high-grade serous ovarian cancer (HGSOC).

MATERIALS AND METHODS

One hundred and eighty-nine patients with histopathologically confirmed HGSOC were enrolled retrospectively. Among the included patients, 55 patients were determined as the MT subtype and the remaining 134 were non-MT subtype. After extracting a total of 204 features from T2-weighted imaging (T2WI) and contrast-enhanced (CE)-T1WI images, the Mann-Whitney U-test, Spearman correlation test, and Boruta algorithm were adopted to select the optimal feature set. Three classifiers, including logistic regression (LR), support vector machine (SVM), and random forest (RF), were trained to develop radiomics models. The performance of established models was evaluated from three aspects: discrimination, calibration, and clinical utility.

RESULTS

Seven radiomics features relevant to MT subtypes were selected to build the radiomics models. The model based on the RF algorithm showed the best performance in predicting MT subtype, with areas under the curves (AUCs) of 0.866 (95 % confidence interval [CI]: 0.797-0.936) and 0.852 (95 % CI: 0.736-0.967) in the training and testing cohorts, respectively. The calibration curves, supported with Brier scores, indicated very good consistency between observation and prediction. Decision curve analysis (DCA) showed that the RF-based model could provide more net benefit, which suggested favorable utility in clinical application.

CONCLUSION

The RF-based radiomics model provided accurate identification of MT from the non-MT subtype and may help facilitate personalised management of HGSOC.

Near-infrared Light-Induced Polymerizations: Mechanisms and Applications

Photopolymerizations have garnered significant attention in polymer science due to their low polymerization temperature, high production efficiency, environmental friendliness, and spatial controllability. Despite these merits, the poor penetration and severe chemical damage from ultraviolet/visible (UV/Vis) light resources pose significant barriers to their success in conventional photopolymerizations. A recent breakthrough involving the utilization of near-infrared (NIR) laser with long wavelength has been exploited for diverse applications. With the combination of a NIR photosensitizer (PS), NIR-induced photopolymerizations have been successfully developed to alleviate the challenges in conventional methods. The enhancement of penetration depth and safety of NIR-induced photopolymerizations can contribute significantly to improving the efficiency of polymerization for production of intricate structures across various scales. In this concept, the typical types of PSs and polymerization mechanisms (PMs) within the NIR-induced photopolymerization systems have been classified in detail. Additionally, the applications of various polymers achieved by NIR-induced photopolymerizations are summarized. Furthermore, research directions and future challenges of this field are also discussed comprehensively.

E2F1-mediated Up-regulation of NCAPG Promotes Hepatocellular Carcinoma Development by Inhibiting Pyroptosis

Background and Aims

As a subunit of the condensin complex, NCAPG has an important role in maintaining chromosome condensation, but its biological function and regulatory mechanism in hepatocellular carcinoma (HCC) remains undefined.

Methods

The prognostic ability of NCAPG in HCC patients was examined by univariate and multivariate Cox regression analysis. ROC curves were plotted to compare the predictive ability of NCAPG and AFP. Double luciferase reporter system, and ChIP were used to investigate transcriptional potential of E2F1 to NCAPG. Pyroptosis was observed by scanning electron microscopy. Protein expression of NCAPG, E2F1, and major proteins constituting NLRP3 inflammasome was determined by western blotting and ELISA. An in vivo tumor formation assay was conducted to verify the in vitro results.

Results

Up-regulated NCAPG was identified in HCC tissues compared with adjacent tissue and high NCAPG was positively correlated with poor prognosis. Serum NCAPG mRNA level was a prognostic factor in HCC patients and also a diagnostic factor with higher predictive ability compared with AFP [AUROC 0.766 (95% CI: 0.650-0.881) vs. 0.649 (95% CI 0.506-0.793)]. HBx transfection resulted in concomitant up-regulation of E2F1 and NCAPG. E2F1 significantly increased the activity of luciferase reporter fused with NCAPG reporter, and the interaction of E2F1 and NCAPG gene was confirmed by ChIP. Silencing of E2F1 resulted in significant down-regulation of NCAPG. Knockdown of NCAPG promote pyroptosis mediated by NLRP3 inflammasome activation in multiple HCC cell lines and also suppressed tumorigenesis in vitro.

Conclusions

We identified a novel role of NCAPG in the regulation of NLRP3 inflammasome-mediated pyroptosis, which was regulated by its upstream transactivator, E2F1. The role of E2F1-NCAPG-NLRP3 regulation of pyroptosis network may be a potential target in HCC treatment.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.

[Analysis of public health risks associated with pathogenic fungi in China]

At present, the public health risks caused by pathogenic fungi are greater in China and have attracted great attention from disease control departments. Due to the difficulty in diagnosing fungal infections, the public health risk of pathogenic fungi is currently hidden in the unexplained pneumonia/encephalitis/fever syndrome and is not effectively appreciated. From the public health perspective, the mainly focused fungal pathogens include highly pathogenic fungi (including dimorphic fungi and dematiaceous fungi), pathogenic fungi that cause regional aggregation infections, and drug-resistant pathogenic fungi. However, due to the lack of systematic monitoring data, the disease burden related to pathogenic fungi cannot be accurately quantified and evaluated. Therefore, to effectively reduce the serious harm of fungal infections to the public, systematic monitoring of pathogenic fungi should be carried out nationally.

Systemic analysis of the prognostic significance and interaction network of miR-26b-3p in cholangiocarcinoma

MicroRNAs (miRNAs) reportedly play significant roles in the progression of various cancers and hold huge potential as both diagnostic tools and therapeutic targets. Given the ongoing uncertainty surrounding the precise functions of several miRNAs in cholangiocarcinoma (CCA), this research undertakes a comprehensive analysis of CCA data sourced from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The present study identified a novel miRNA, specifically miR-26b-3p, which exhibited prognostic value for individuals with CCA. Notably, miR-26b-3p was upregulated within CCA samples, with an inverse correlation established with patient prognosis (Hazard Ratio = 8.19, p = 0.018). Through a combination of functional enrichment analysis, analysis of the LncRNA-miR-26b-3p-mRNA interaction network, and validation by qRT PCR and western blotting, this study uncovered the potential of miR-26b-3p in potentiating the malignant progression of CCA via regulation of essential genes (including PSMD14, XAB2, SLC4A4) implicated in processes such as endoplasmic reticulum (ER) stress and responses to misfolded proteins. Our findings introduce novel and valuable insights that position miR-26b-3p-associated genes as promising biomarkers for the diagnosis and treatment of CCA.

Temporal Structures in Positron Spectra and Charge-Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic positron fluxes in the rigidity range from 1.00 to 41.9 GV based on 3.4×10^{6} positrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The positron fluxes show distinctly different time variations from the electron fluxes at short and long timescales. A hysteresis between the electron fluxes and the positron fluxes is observed with a significance greater than 5σ at rigidities below 8.5 GV. On the contrary, the positron fluxes and the proton fluxes show similar time variation. Remarkably, we found that positron fluxes are modulated more than proton fluxes with a significance greater than 5σ for rigidities below 7 GV. These continuous daily positron fluxes, together with AMS daily electron, proton, and helium fluxes over an 11-year solar cycle, provide unique input to the understanding of both the charge-sign and mass dependencies of cosmic rays in the heliosphere.

Clinical-Radiomics Nomogram for Risk Prediction of Esophageal Fistula in Patients with Esophageal Squamous Cell Carcinoma Treated by IMRT or VMAT

PURPOSE/OBJECTIVE(S)

This study aimed to analyze the predictive factors of esophageal fistula (EF) in patients with esophageal squamous cell carcinoma (ESCC) receiving intensity-modulated radiotherapy (IMRT) or Volumetric Modulated Arc Therapy (VMAT), and to establish a prediction model for risk prediction of EF.

MATERIALS/METHODS

A total of 479 patients with ESCC treated with IMRT or VMAT from 2013 to 2020 in Xijing hospital were retrospectively analyzed. A total of 43 patients with EF and 129 patients without EF were included in the analysis by 1:3 propensity score matching (time of diagnosis, gender). The clinical risk factors associated with EF were obtained based on univariate logistic regression analysis. Radiomic features were extracted and selected from pre-treatment contrast-enhance computed tomography (CT) to construct radiomic signature. The clinical-radiomics nomogram was constructed based on multivariate stepwise logistic regression. The classification performance of the model was evaluated based on 100 times of 5-fold cross validation.

RESULTS

The median OS of the 172 patients included in the analysis was 27.8 months (range 1.3-104.9m), and the median OS of EF patients was lower than that of non-EF patients with 13.1 months (range 1.3-65.3m) vs 49.4 months (range 4.0-104.9m, p<0.001). A total of 1158 radiomics features were extracted and 8 radiomics features were finally selected. The area under the receiver operating characteristic curve (AUC) value of radiomic signature calculated by selected features for predicting EF was 0.794, and it also had the prognostic ability of OS risk stratification (median OS:17.6vs 46.6m, p<0.001). Multivariate analysis showed that the tumor length, tumor volume, T stage, lymphocyte rate and grade 4 esophagus stenosis were related to EF, and the AUC value of clinical nomogram for predicting EF was 0.849. The clinical-radiomics nomogram had the best performance in predicting EF with an AUC value of 0.896.

CONCLUSION

The clinical-radiomics nomogram can predict the risk of EF in ESCC patients, and be helpful for individualized treatment of esophageal cancer.

Association of Parental Status and Gender with Burden of Multidisciplinary Tumor Boards

PURPOSE/OBJECTIVE(S)

Tumor boards are an integral part of the management of patients with cancer. However, there is limited data investigating the burden of tumor boards on physicians. Our objective was to determine what physician-related, and tumor board-related factors associate with higher burden.

MATERIALS/METHODS

Tumor board start times were collected by email from 22 National Cancer Institute-designated cancer centers and/or U.S. World and News Report Top 40 hospitals for cancer. Tumor board burden was assessed by a cross-sectional convenience survey posted on social media and by email to Cedars-Sinai Medical Center cancer physicians between March 3, 2022, and April 3, 2022. Tumor board burden was measured on a 4-point scale (1, not at all; 2, slightly; 3, moderately; 4, very burdensome). Univariable and multivariable analyses were performed using a probabilistic index model.

RESULTS

The timing of 392 tumor boards was collected from 22 institutions. The most common tumor board start time was at or before 0730 (24.6%). Surveys were completed by 111 physicians, of which 52.3% identified as women and 42.3% as men. Reported specialties were radiation oncology (39.6%), medical oncology (18.0%), surgery (15.3%), radiology (12.6%), and pathology (9.9%). On average, 41.4% attended ≥3 hours/week total of tumor boards and 1-2 hours/week of early/late tumor boards (defined as starting before 0800 or 1700 or after). Overall, 37.8% reported tumor boards were at least moderately burdensome. On multivariable analysis, radiology/pathology specialty (probability 0.68; 95% confidence interval [CI], 0.54-0.79; p = 0.015), attending ≥3 hours/week of tumor boards (probability 0.68; 95% CI, 0.58-0.76; p<.001), and having ≥2 children (probability 0.65; 95% CI, 0.52-0.77; p = 0.029), were associated with higher burden. Early/late tumor boards were frequently considered burdensome (20.7% moderately, 29.7% very burdensome). On multivariable analysis, identifying as a woman (probability 0.69; 95% CI, 0.57-0.78; p = 0.003) and having children (probability 0.75; 95% CI, 0.62-0.84; p<.001) remained associated with a higher level of burden from early/late tumor boards. Further, parents frequently reported that early/late tumor boards negatively affected childcare (55.8%), feeding and/or sleep logistics (33.8%), and overall family dynamics (63.7%).

CONCLUSION

Identifying as a woman and having children were associated with a higher level of burden from early/late tumor boards. The negative impact of early/late tumor boards on overall family dynamics, including children feeding, sleeping, and childcare logistics, was commonly reported by parents. Having ≥2 children, attending ≥3 hours/week of tumor boards, and radiology/pathology specialty were associated with a higher level of burden overall. Future strategies should aim to decrease burden, particularly the disparate impact on parents and women.

4D-MRI Guided Stereotactic Body Radiation Therapy for Unresectable Colorectal Liver Metastases

PURPOSE/OBJECTIVE(S)

This study evaluated the feasibilities and outcomes following four-dimensional magnetic resonance imaging (4D-MRI) guided stereotactic body radiation therapy (SBRT) for unresectable colorectal liver metastases (CRLM).

MATERIALS/METHODS

From March 2018 to January 2022, we identified 76 unresectable CRLM patients with 123 lesions who received 4D-MRI guided SBRT in our institution. 4D-MRI simulation with or without abdominal compression was conducted for all patients. The prescription dose was 50-65 Gy in 5-12 fractions. The image quality of computed tomography (CT) and MRI were compared using the Clarity Score. Clinical outcomes and toxicity profiles were evaluated.

RESULTS

The 4D-MRI significantly improved the image quality compared with CT images (mean Clarity Score: 1.67 vs 2.88, P < 0.001). The abdominal compression significantly reduced motions in cranial-caudal direction (P = 0.03) with 2 phase T2 weighted images assessing tumor motion. The median follow-up time was 12.5 months. For 98 lesions assessed for best response, the complete response, partial response and stable disease rate were 57.1 %, 30.6 % and 12.2 %, respectively. The local control (LC) rate at 2 year was 97.3%. 46.1% of patients experienced grade 1-2 toxicities and only 2.6% patients experienced grade 3 hematologic toxicities.

CONCLUSION

The 4D-MRI technique allowed precise target delineation and motion tracking in unresectable CRLM patients. High LC rate and mild toxicities were achieved. This study provided evidence for using 4D-MRI guided SBRT as an alternative treatment in unresectable CRLM.

New Limits on Exotic Spin-Dependent Interactions at Astronomical Distances

Exotic spin-dependent interactions involving new light particles address key questions in modern physics. Interactions between polarized neutrons (n) and unpolarized nucleons (N) occur in three forms: g_{S}^{N}g_{P}^{n}σ·r, g_{V}^{N}g_{A}^{n}σ·v, and g_{A}^{N}g_{A}^{n}σ·v×r, where σ is the spin and g's are the corresponding coupling constants for scalar, pseudoscalar, vector, and axial-vector vertexes. If such interactions exist, the Sun and Moon could induce sidereal variations of effective fields in laboratories. By analyzing existing data from laboratory measurements on Lorentz and CPT violation, we derive new experimental upper limits on these exotic spin-dependent interactions at astronomical ranges. Our limits on g_{S}^{N}g_{P}^{n} surpass the previous combined astrophysical-laboratory limits, setting the most stringent experimental constraints to date. We also report new constraints on vector-axial-vector and axial-axial-vector interactions at astronomical scales, with vector-axial-vector limits improved by ∼12 orders of magnitude. We extend our analysis to Hari Dass interactions and obtain new constraints.

Pan-cancer analysis reveals that G6PD is a prognostic biomarker and therapeutic target for a variety of cancers

Background

Despite accumulating evidence revealing that Glucose-6-phosphate dehydrogenase (G6PD) is highly expressed in many tumor tissues and plays a remarkable role in cancer tumorigenesis and progression, there is still a lack of G6PD pan-cancer analysis. This study was designed to analyze the expression status and prognostic significance of G6PD in pan-cancer.

Methods

G6PD expression data were obtained from multiple data resources including the Genotype-Tissue Expression, the Cancer Genome Atlas, and the Tumor Immunity Estimation Resource. These data were used to assess the G6PD expression, prognostic value, and clinical characteristics. The ESTIMATE algorithms were used to analyze the association between G6PD expression and immune-infiltrating cells and the tumor microenvironment. The functional enrichment analysis was also performed across pan-cancer. In addition, the GDSC1 database containing 403 drugs was utilized to explore the relationship between drug sensitivity and G6PD expression levels. Furthermore, we also performed clinical validation and in vitro experiments to further validate the role of G6PD in hepatocellular carcinoma (HCC) cells and its correlation with prognosis. The R software was used for statistical analysis and data visualization.

Results

G6PD expression was upregulated in most cancers compared to their normal counterparts. The study also revealed that G6PD expression was a prognostic indicator and high levels of G6PD expression were correlated with worse clinical prognosis including overall survival, disease-specific survival, and progression-free interval in multiple cancers. Furthermore, the G6PD level was also related to cancer immunity infiltration in most of the cancers, especially in KIRC, LGG, and LIHC. In addition to this, G6PD expression was positively related to pathological stages of KIRP, BRCA, KIRC, and LIHC. Functional analysis and protein-protein interactions network results revealed that G6PD was involved in metabolism-related activities, immune responses, proliferation, and apoptosis. Drug sensitivity analysis showed that IC50 values of most identified anti-cancer drugs were positively correlated with the G6PD expression. Notably, in vitro functional validation showed that G6PD knockdown attenuated the phenotypes of proliferation in HCC.

Conclusion

G6PD may serve as a potential prognostic biomarker for cancers and may be a potential therapeutic target gene for tumor therapy.

Pulmonary interleukin 1 beta/serum amyloid A3 axis promotes lung metastasis of hepatocellular carcinoma by facilitating the pre-metastatic niche formation

BACKGROUND

Increasing evidence suggests a vital role of the pre-metastatic niche in the formation of distant metastasis of many cancers. However, how the pre-metastatic niche is formed and promotes pulmonary metastasis of hepatocellular carcinoma (HCC) remains unknown.

METHODS

Orthotopic liver tumor models and RNA-Seq were used to identify dysregulated genes in the pre-metastatic lung. Il1b knockout (Il1b^-/-) mice and lentivirus-mediated gene knockdown/overexpression were utilized to demonstrate the role of interleukin 1 beta (IL-1β)/serum amyloid A3 (SAA3) in the pre-metastatic niche formation and pulmonary metastasis. The potential molecular mechanisms were investigated by RNA-Seq, real-time quantitative PCR (qPCR), western blotting, immunohistochemistry (IHC), flow cytometry, luciferase reporter assay, double immunofluorescent staining and H&E staining.

RESULTS

Accumulation of myeloid cells and upregulation of IL-1β were observed in the pre-metastatic lung of orthotopic liver tumor models. Myeloid cells accumulation and pulmonary metastasis were suppressed in Il1b^-/- mice and Il1r1-silencing mice. Mechanistically, SAA3 and matrix metallopeptidase 9 (MMP9) were identified as potential downstream targets of IL-1β. Overexpression of SAA3 in the lungs of Il1b^-/- mice restored myeloid cells accumulation and pulmonary metastasis of the orthotopic HCC xenografts. Moreover, alveolar macrophages-derived IL-1β dramatically enhanced SAA3 expression in alveolar epithelial cells in an NF-κB dependent manner and increased MMP9 levels in an autocrine manner. Furthermore, SAA3 recruited myeloid cells to the lung without affecting the expression of MMP9 in myeloid cells.

CONCLUSIONS

Our study suggests a key role of pulmonary IL-1β and SAA3 in creating a permissive lung pre-metastatic niche by enhancing MMP9 expression and recruiting myeloid cells, respectively, thus promoting pulmonary metastasis of HCC.

Properties of Cosmic-Ray Sulfur and Determination of the Composition of Primary Cosmic-Ray Carbon, Neon, Magnesium, and Sulfur: Ten-Year Results from the Alpha Magnetic Spectrometer

We report the properties of primary cosmic-ray sulfur (S) in the rigidity range 2.15 GV to 3.0 TV based on 0.38×10^{6} sulfur nuclei collected by the Alpha Magnetic Spectrometer experiment (AMS). We observed that above 90 GV the rigidity dependence of the S flux is identical to the rigidity dependence of Ne-Mg-Si fluxes, which is different from the rigidity dependence of the He-C-O-Fe fluxes. We found that, similar to N, Na, and Al cosmic rays, over the entire rigidity range, the traditional primary cosmic rays S, Ne, Mg, and C all have sizeable secondary components, and the S, Ne, and Mg fluxes are well described by the weighted sum of the primary silicon flux and the secondary fluorine flux, and the C flux is well described by the weighted sum of the primary oxygen flux and the secondary boron flux. The primary and secondary contributions of the traditional primary cosmic-ray fluxes of C, Ne, Mg, and S (even Z elements) are distinctly different from the primary and secondary contributions of the N, Na, and Al (odd Z elements) fluxes. The abundance ratio at the source for S/Si is 0.167±0.006, for Ne/Si is 0.833±0.025, for Mg/Si is 0.994±0.029, and for C/O is 0.836±0.025. These values are determined independent of cosmic-ray propagation.

Temporal Structures in Electron Spectra and Charge Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic electron fluxes in the rigidity interval from 1.00 to 41.9 GV based on 2.0×10^{8} electrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The electron fluxes exhibit variations on multiple timescales. Recurrent electron flux variations with periods of 27 days, 13.5 days, and 9 days are observed. We find that the electron fluxes show distinctly different time variations from the proton fluxes. Remarkably, a hysteresis between the electron flux and the proton flux is observed with a significance of greater than 6σ at rigidities below 8.5 GV. Furthermore, significant structures in the electron-proton hysteresis are observed corresponding to sharp structures in both fluxes. This continuous daily electron data provide unique input to the understanding of the charge sign dependence of cosmic rays over an 11-year solar cycle.

Tumor necrosis factor-α-inducible protein 8-like protein 3 (TIPE3): a novel prognostic factor in colorectal cancer

BACKGROUND

To explore the correlation of tumor necrosis factor-α-induced protein 8-like protein 3 (TIPE3) expressions in colorectal cancer (CRC) with tumor-immune infiltration and patient prognosis.

METHODS

Formalin-fixed paraffin-embedded tumor samples from CRC patients (n = 110) were used in this study. Immunohistochemistry staining of TIPE3 and three prognostic immune biomarkers (CD8, CD20, and CD66b) was conducted in the tumor tissues and adjacent normal tissues. A Cox regression analysis of univariate and multivariate variables was performed to assess the correlation between TIPE3 and patient prognosis.

RESULT

We found that TIPE3 was mainly expressed in the cytoplasm, with a small amount in the nucleus. The expression of TIPE3 in tumor tissues is significantly higher than in adjacent normal tissues, and it is significantly correlated with the survival rate of patients in tumor tissues (p = 0.0038) and adjacent normal tissues (p<0.0001). Patients with a high TIPE3 expression had a lower survival rate, while patients with a low TIPE3 expression had a higher survival rate. Univariate regression analysis showed that the TIPE3 expression in tumor tissues (p = 0.007), the TIPE3 expression in adjacent normal tissues (p<0.001), the number of CD8+ T cells in tumor tissues (p = 0.020), the number of CD20+ B cells in tumor tissues (p = 0.023), the number of CD20+ B cells in adjacent normal tissues (p = 0.023), the number of CD66b+ neutrophils in tumor tissues (p = 0.005), the number of CD66b+ neutrophils in adjacent normal tissues (p<0.001), lymphatic metastasis (p = 0.010), TNM stage (p = 0.013), and tumor grade (p = 0.027) were significantly correlated with overall survival (OS). These prognostic factors were then subjected to multivariate regression analysis, and the results showed that the expression of TIPE3, the number of CD8+ T cells, and the number of CD66b+ neutrophils were prognostic factors affecting the OS rate of CRC patients.

CONCLUSION

We found that the TIPE3 protein is upregulated in CRC cancer tissues and is correlated with survival rate.

Classification and survival prediction in early-stage cirrhosis by gene expression profiling

Liver cirrhosis has been increasingly diagnosed at an early stage owing to the non-invasive diagnostic techniques. However, it is difficult to identify patients at high risk of disease progression. Screening cirrhotic patients with poor prognosis who are most in need of surveillance is still challenging. Gene expression data GSE15654 and GSE14520 were downloaded for performing unsupervised clustering analysis. The prognostic differences between the different clusters were explored by Cox regression. Integrative analysis of gene expression signature, immune cell enrichments and clinical characterization was performed for different clusters. Two distinctive subclasses were identified in HCV-related GSE15654, and Kaplan-Meier analysis indicated that subtype 2 had lower survival rates than subtype 1 (p = 0.0399). Further analysis revealed subtype 2 had a higher density of follicular T helper cells, resting natural killer cells and M0, M2 macrophages while subtype 1 with a higher fraction of naive B cells, memory B cells, resting memory CD 4 T cells, activated natural killer cells and monocytes. 226 differentially expressed genes were identified between the two subtypes, and Reactome analysis showed the mainly enriched pathways were biological oxidations and fatty acid metabolism. Five hub genes (AKT1, RPS16, CDC42, CCND1 and PCBP2) and three significant modules were extracted from the PPI network. The results were validated in HBV-related GSE14520 cohort. We identified two subtypes of patients with different prognosis for hepatitis C-related early-stage liver cirrhosis. Bioinformatics analysis of the gene expression and immune cell profile may provide fresh insight into understanding the prognosis difference.

Classification of colorectal cancer into clinically relevant subtypes based on genes and mesenchymal cells

BACKGROUND

Most studies on subtype identification of colorectal cancer (CRC) were based on expressions of either genes or immune cells. However, few studies have hitherto used the combination of genes with immune and stroma cells for subtype identification.

METHODS

Dataset GSE17536 was obtained from the Gene Expression Omnibus (GEO) database. The xCell algorithm was used to estimate the composition and density of 64 cell types, including immune and stroma cell types. Clustering analysis was then conducted on the top 3000 most variable genes from a total of 20,174 genes for CRC subtype identification. We employed the ensemble method of Similarity network fusion and 112 Consensus Clustering (SNF-CC) for cancer subtype identification. Reactome pathway analysis was conducted to identify the impact of the representative genes on prognosis. The results were validated in independent gene expression data from dataset GSE17537.

RESULTS

In this study, we identified 3 clinically relevant subtypes and their representative genes, immune and stroma cells. Moreover, we confirmed the correlation of these subtypes with their clinical characteristics. The representative genes of the subtype with poor prognosis correlated with extracellular matrix structural constituent, while the subtype with good prognosis correlated with Toll-like receptor signaling pathway or chemokine signaling pathway. However, different subtypes were associated with distinct cell subtypes; the subtype with poor prognosis had a high abundance of fibroblasts and endothelial cells; the subtype with median prognosis had a higher abundance of immune cells, such as CD4 + T-cell, Th2 cells and aDC; the subtype with good prognosis had a higher abundance of NKT.

CONCLUSION

This study highlights the utility of immune and innate cells, especially during gene analysis, to provide the theoretical basis for personalized treatment in colorectal cancer patients.

Hydrogen sulfide protects against ischemic heart failure by inhibiting RIP1/RIP3/MLKL-mediated necroptosis

The aim of the present study was to explore whether hydrogen sulfide (H2S) protects against ischemic heart failure (HF) by inhibiting the necroptosis pathway. Mice were randomized into Sham, myocardial infarction (MI), MI + propargylglycine (PAG) and MI + sodium hydrosulfide (NaHS) group, respectively. The MI model was induced by ligating the left anterior descending coronary artery. PAG was intraperitoneally administered at a dose of 50 mg/kg/day for 4 weeks, and NaHS at a dose of 4mg/kg/day for the same period. At 4 weeks after MI, the following were observed: A significant decrease in the cardiac function, as evidenced by a decline in ejection fraction (EF) and fractional shortening (FS); an increase in plasma myocardial injury markers, such as creatine kinase-MB (CK-MB) and cardiac troponin I (cTNI); an increase in myocardial collagen content in the heart tissues; and a decrease of H2S level in plasma and heart tissues. Furthermore, the expression levels of necroptosis-related markers such as receptor interacting protein kinase 1 (RIP1), RIP3 and mixed lineage kinase domain-like protein (MLKL) were upregulated after MI. NaHS treatment increased H2S levels in plasma and heart tissues, preserving the cardiac function by increasing EF and FS, decreasing plasma CK-MB and cTNI and reducing collagen content. Additionally, NaHS treatment significantly downregulated the RIP1/RIP3/MLKL pathway. While, PAG treatment aggravated cardiac function by activated the RIP1/RIP3/MLKL pathway. Overall, the present study concluded that H2S protected against ischemic HF by inhibiting RIP1/RIP3/MLKL-mediated necroptosis which could be a potential target treatment for ischemic HF.

An early novel prognostic model for predicting 80-day survival of patients with COVID-19

The outbreak of the novel coronavirus disease 2019 (COVID-19) has had an unprecedented impact worldwide, and it is of great significance to predict the prognosis of patients for guiding clinical management. This study aimed to construct a nomogram to predict the prognosis of COVID-19 patients. Clinical records and laboratory results were retrospectively reviewed for 331 patients with laboratory-confirmed COVID-19 from Huangshi Hospital of Traditional Chinese Medicine (TCM) (Infectious Disease Hospital) and Third Affiliated Hospital of Sun Yat-sen University. All COVID-19 patients were followed up for 80 days, and the primary outcome was defined as patient death. Cases were randomly divided into training (n=199) and validation (n=132) groups. Based on baseline data, we used statistically significant prognostic factors to construct a nomogram and assessed its performance. The patients were divided into Death (n=23) and Survival (n=308) groups. Analysis of clinical characteristics showed that these patients presented with fever (n=271, 81.9%), diarrhea (n=20, 6.0%) and had comorbidities (n=89, 26.9.0%). Multivariate Cox regression analysis showed that age, UREA and LDH were independent risk factors for predicting 80-day survival of COVID-19 patients. We constructed a qualitative nomogram with high C-indexes (0.933 and 0.894 in the training and validation groups, respectively). The calibration curve for 80-day survival showed optimal agreement between the predicted and actual outcomes. Decision curve analysis revealed the high clinical net benefit of the nomogram. Overall, our nomogram could effectively predict the 80-day survival of COVID-19 patients and hence assist in providing optimal treatment and decreasing mortality rates.

PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform

Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG.SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG.SV is freely accessible via https://www.biosino.org/pggsv.

Association between immune checkpoint inhibitors and vascular endothelial growth factor targeted therapy with cardiovascular events

Background

The use of immune checkpoint inhibitors (ICI) has been associated with a 3-fold higher risk for cardiovascular events as compared to cancer patients who did not receive ICI. Therapies targeting vascular endothelial growth factor (VEGF) have also been associated with a wide range of cardiovascular events. The combination use of ICIs and VEGF inhibitors is currently approved as a treatment for patients with renal-cell carcinoma, hepatocellular carcinoma, non-small cell lung cancer, and endometrial cancer. Data are lacking whether the combination of ICIs and VEGF-targeted therapy is associated with an additional increase in cardiovascular events.

Purpose

To evaluate whether the combination use of ICI and VEGF targeted therapies are associated with a higher risk of cardiovascular events as compared to ICI therapy alone, we performed a retrospective matched case-control study.

Methods

Cases received both ICI and VEGF-targeted therapy (n=157), and control patients (n=157) only received ICI therapy. The primary outcome was a composite of cardiovascular events (myocardial infarction, coronary revascularization, ischemic stroke, deep venous thrombosis, and pulmonary embolism). Patients were censored at time of first event or at last date of follow up. Cox proportional hazard regression analysis was performed to calculate hazard ratio (HR) with 95% confidence interval (CI), counting only the first cardiovascular event.

Results

Baseline characteristics for the cases and controls are shown in Table 1. Overall cases (combination ICI and VEGF inhibitor) and controls (ICI alone) were not different with respect to age, type of cancer, and a prior history of any cardiovascular event. Cases received more ICI cycles as compared to controls (median of 7 [4–17] cycles vs. 4 [2–10] cycles, P&lt;0.001). Cases also had a longer follow-up time (334 [127–663] days vs. 201 [60–564] days, P=0.008) as compared to the control group. As compared to ICI alone, a similar risk for a composite cardiovascular event was observed in those who received both ICI and VEGF-targeted therapy (HR, 0.70 [95% CI, 0.39–1.25]; P=0.23, Table 1). In total, 21/157 patients had a composite cardiovascular event among the cases, who received the combination of ICI and VEGF inhibitor (9 DVT, one MI, 9 PE, two ischemic strokes) as compared to 25/157 among the controls, who received ICI alone (14 DVT, 3 MI, 7 PE, one ischemic stroke). The median time to event was not different between the two groups (126 [98–260] days vs. 145 [28–205] days, P=0.47).

Conclusion

We found that among 157 patients who received a combination of ICI and VEGF-targeted therapy and 157 matched control patients who only received ICI therapy, the risk for cardiovascular events was not different between the two groups.

Funding Acknowledgement

Type of funding sources: Public grant(s) – EU funding.

Trajectory of pulmonary congestion by lung ultrasound in patients with acute myocardial infarction and association with cardiac structure and function

Background

The PARADISE-MI trial examined the efficacy of sacubitril/valsartan in patients with acute myocardial infarction (AMI) complicated by reduced left ventricular ejection fraction (LVEF), pulmonary congestion or both. Little is known about the trajectory and echocardiographic correlates of pulmonary congestion in this population.

Purpose

We sought to assess the trajectory of pulmonary congestion using lung ultrasound (LUS) and its association with cardiac structure and function in a subset of patients enrolled in PARADISE- MI.

Methods

Participants underwent 8-zone LUS at baseline and 8 months. B-lines were quantified offline, blinded to treatment group, clinical findings, timepoint and outcomes by a core laboratory. Paired t-tests, chi-squared tests, and linear regression analyses were conducted.

Results

Among 152 patients (median age 65 years, 32% women, 35% obese, mean LVEF 41%), any B-lines were detectable in 87%, the median sum of B-lines in 8 zones was 4 [IQR 2–8], and 67% had ≥3 B-lines indicative of congestion. Greater number of B-lines at baseline was associated with larger left atrial (LA) size, higher E/e' and E/A ratios, greater degree of mitral regurgitation, worse right ventricular (RV) systolic function, and higher tricuspid regurgitation velocity (P trend &lt;0.05 for all) (Figure 1). Among 115 patients with 8-month LUS data, there was a significant decline in number of B-lines from baseline (mean ± SD: −1.6±7.3; p=0.018). Adjusted for baseline, B-lines at follow-up were on average 6 (95% CI: 3, 9) higher in a patient who experienced an intercurrent heart failure (HF) event than a non-HF patient (p=0.001). Among 75 patients with ≥3 B-lines at baseline, a decrease in B-lines to &lt;3, indicating decongestion, occurred in 37% and was similar in the sacubitril/valsartan and ramipril groups (36% vs. 39%, p=0.83).

Conclusions

In this post-AMI cohort, sonographic B-lines, indicating pulmonary congestion, were common at baseline and were significantly higher at follow-up in those who developed HF. Worse pulmonary congestion at baseline was associated with prognostically important echocardiographic markers of LV filling pressure, pulmonary pressure, and RV function.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Novartis

Identification of molecular subtypes in lung adenocarcinoma based on DNA methylation and gene expression profiling—a bioinformatic analysis

Background

Molecular typing based on deoxyribonucleic acid (DNA) methylation and gene expression can extend understandings of the molecular mechanisms involved in lung adenocarcinoma (LUAD) and enhance current diagnostic, treatment, and prognosis prediction approaches.

Methods

Gene expression and DNA methylation data sets of LUAD were obtained from The Cancer Genome Atlas (TCGA), and the differential gene and methylation expression levels were analyzed.

Results

We successfully divided the LUAD samples into 2 clinically relevant subtypes with significantly different survival times and tumor stages according to the transcriptome and methylation data. We found significant differences in the survival status, age, gender, tumor stage, node stage, and clinical stage between the 2 subtypes. The hub genes identified in the subnetworks, including NCAPG, CCNB1, DLGAP5, HLA-DQA1, HLA-DPA1, HLA-DPB1, SFTP, SCGBA1A, and SFTPD, were correlated with the cell cycle and immune system. The Gene Ontology annotation of the hub genes showed that the biological processes included organelle fission mitotic nuclear division, and sister chromatid segregation. The cellular components included chromosomal region, spindle, and kinetochore. The molecular functions included tubulin-binding, microtubule-binding, and DNA replication origin binding. The Kyoto Encyclopedia of Genes and Genomes signaling pathways related to the hub genes mainly included the cell cycle, human T-cell leukemia virus (type 1) infection, inflammatory bowel disease, and the intestinal immune network for immunoglobulin A production. The clinical stage difference was also confirmed in the validation group using the GSE32863 data set.

Conclusions

Our findings extend understandings of the pathogenesis of LUAD and can be used to improve current diagnosis, treatment, and prognosis prediction strategies.

[Microfocal prostate cancer: a clinicopathological analysis of 206 cases]

Objective: To investigate the clinical and pathological features and prognosis of patients with microfocal prostate adenocarcinoma. Methods: Clinical and pathological data of the patients diagnosed with microfocal adenocarcinoma on prostate biopsy at the West China Hospital from 2013 to 2019 were collected. Microfocal adenocarcinoma was defined as follows: Gleason score of 3+3=6, total number of the cores ≥10, number of the positive cores ≤2, and proportion of the tumor in each positive core<50%. Clinicopathological parameters, treatment plans and follow-up data were collected. Pathological information of the biopsy and radical resection specimens was used to analyze the correlation between pathological parameters in the biopsy report and adverse pathological features of radical resection specimens, including increased Gleason score, capsule invasion, positive surgical margin and perineural invasion. Results: A total of 206 cases of microfocal adenocarcinoma were diagnosed on prostate biopsies from 2013 to 2019, accounting for 6.7% of all adenocarcinoma cases. There were 139 cases of 1 positive core and 67 cases of 2 positive cores. Patients with microfocal adenocarcinoma were younger than those with non-microfocal adenocarcinoma (69 years versus 71 years, P<0.001). Compared with patients with non-microfocal adenocarcinoma, the pre-biopsy total prostate specific antigen (tPSA) and free prostate specific antigen (fPSA) levels in patients with microfocal adenocarcinoma were both lower (11.2 μg/L² versus 23.7 μg/L²; 1.4 μg/L² versus 3.0 μg/L², P<0.001), the fPSA/tPSA level was higher (12.9% versus 10.7%, P<0.05), the prostate volume was larger (38.9 mL versus 34.3 mL, P<0.05), and the PSA density was lower (0.3 μg/L² versus 0.8 μg/L², P<0.001). 130 patients underwent radical prostatectomy, 30 patients chose active monitoring, 31 patients chose endocrine or radiation therapy, and 15 patients were lost to follow-up. Three patients in the active surveillance group underwent radical prostatectomy for disease progression after 21-39 months observation. Biochemical relapses occurred in two patients in the radical prostatectomy group. The remaining patients have no disease progression or recurrence at present. Compared with radical prostatectomy specimens, Gleason score in the biopsy material was increased in 64/115 patients (55.7%). Among resection excision specimens, 14 cases (12.2%) had extraprostatic extension (EPE), 35 cases (30.4%) had perineural invasion, and 16 cases (13.9%) had a positive margin. Univariate and multivariate analyses showed that low fPSA/tPSA ratio and 2 positive cores were independent risk factors for Gleason score increase in the radical prostatectomy specimens. A low fPSA/tPSA ratio was an independent risk factor for perineural invasion. Low fPSA/tPSA ratio and low prostate volume were associated with a positive margin in radical prostatectomy specimens. Conclusions: In this study, patients diagnosed with microfocal adenocarcinoma on prostate biopsy account for a high proportion of the patients with increased Gleason score in the radical prostatectomy specimens, and there is a certain proportion of adverse pathological features in the radical specimens. Therefore, for the patients with only a small amount of low-grade adenocarcinoma found in biopsy, PSA levels and PSA density should be taken into consideration in treatment selection.

Properties of Daily Helium Fluxes

We present the precision measurement of 2824 daily helium fluxes in cosmic rays from May 20, 2011 to October 29, 2019 in the rigidity interval from 1.71 to 100 GV based on 7.6×10^{8} helium nuclei collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The helium flux and the helium to proton flux ratio exhibit variations on multiple timescales. In nearly all the time intervals from 2014 to 2018, we observed recurrent helium flux variations with a period of 27 days. Shorter periods of 9 days and 13.5 days are observed in 2016. The strength of all three periodicities changes with time and rigidity. In the entire time period, we found that below ∼7  GV the helium flux exhibits larger time variations than the proton flux, and above ∼7  GV the helium to proton flux ratio is time independent. Remarkably, below 2.4 GV a hysteresis between the helium to proton flux ratio and the helium flux was observed at greater than the 7σ level. This shows that at low rigidity the modulation of the helium to proton flux ratio is different before and after the solar maximum in 2014.

A Comprehensive Analysis of HAVCR1 as a Prognostic and Diagnostic Marker for Pan-Cancer

Hepatitis A virus cellular receptor (HAVCR1) is a type-1 integral membrane glycoprotein that plays a key role in immunity and renal regeneration and is abnormally expressed in various tumor types. Nonetheless, the function of HAVCR1 in pan-cancer remains unknown. In this study, we comprehensively analyzed the expression and promoter methylation level of HAVCR1 and assessed the immune cell infiltration, correlation between stromal and immune cell admixture, CD (Cluster of Differentiation) and HAVCR1 expression and prognostic value of HAVCR1 mRNA expression in Liver hepatocellular carcinoma (LIHC) and Pancreatic adenocarcinoma (PAAD). Our results showed that HAVCR1 was overexpressed while the promoter methylation of HAVCR1 was decreased in Liver hepatocellular carcinoma and Pancreatic adenocarcinoma. HAVCR1 was associated with increased infiltration of B cells, CD8 cells, macrophages, neutrophils and Dendritic cells in Liver hepatocellular carcinoma and Pancreatic adenocarcinoma. HAVCR1 expression was positively correlated with the immune, stromal and estimate scores of Pancreatic adenocarcinoma and the stromal and estimate scores of Liver hepatocellular carcinoma. Furthermore, HAVCR1 expression was correlated with other immune molecules such as HHLA2 (Human endogenous retrovirus-H long terminal repeat-associating protein 2), CD44 and TNFRSF4 (TNF Receptor Superfamily Member 4) in Liver hepatocellular carcinoma and Pancreatic adenocarcinoma. During Kaplan-Meier analysis, high HAVCR1 expression in Liver hepatocellular carcinoma and Pancreatic adenocarcinoma correlated with poor survival. A marginally significant p-value (p = 0.051) was obtained when the relationship between HAVCR1 expression in Liver hepatocellular carcinoma and prognosis was analyzed, attributed to the small sample size. Overall, we provided compelling evidence that HAVCR1 could be a prognostic and diagnostic marker for Liver hepatocellular carcinoma and Pancreatic adenocarcinoma.

A simple and practical microRNA-based nomogram to predict metastatic HCC

Background:

Notwithstanding that unprecedented scientific progress has been achieved over the years, there is no established microRNA-based model for predicting hepatocellular carcinoma (HCC) metastasis. To this end, we aimed to develop a simple model based on the expression of miRNAs to identify patients at high risk of metastatic HCC.

Methods:

HCC datasets with metastasis data were acquired from the Gene Expression Omnibus (GEO) database, and samples were randomly divided into training (n=169) and validation (n=72) groups. Based on the expression of miRNAs in the training group, we developed a predictive nomogram for metastatic HCC. We evaluated its performance using the area under the receiver operating characteristic curve (AUC), calibration curve, decision curve and clinical impact curve analysis.

Results:

By applying the absolute shrinkage and selection operator regression (LASSO) and multivariate logistic regression, we found that the expression of miR-30c, miR-185, and miR-323 were independent predictors of metastatic HCC. These miRNAs were used to construct a nomogram that yielded good performance in predicting metastasis in training (AUC 0.869 [95% CI 813-0.925], sensitivity 92.7%, specificity 57.8%) and validation groups (0.821 [CI 0.720-0.923], sensitivity 94.7%, specificity 60%). The calibration curve showed a good agreement between actual and predicted outcomes. Decision curve analysis showed a high clinical net benefit of nomogram predictions for our patients. Moreover, higher total scores of our nomogram were associated with dead patients. In addition, functional enrichment analysis showed that the predicted target genes of these 3 miRNAs correlated with tumor metastasis-associated terms, such as filopodium, and identified their related hub genes.

Conclusions:

Our easy-to-use nomogram could assist in identifying HCC patients at high risk of metastasis, which offers valuable information for clinical treatment.

Expression and Regulatory Network Analysis of Function of Small Nucleolar RNA Host Gene 4 in Hepatocellular Carcinoma

BACKGROUND AND AIMS

Long non-coding RNA small nucleolar RNA host genes (SNHGs) play a critical role in the occurrence and development of tumors. In this study, we aimed to investigate the role of SNHG4 in hepatocellular carcinoma (HCC) and its underlining mechanism.

METHODS

Datasets were acquired from The Cancer Genome Atlas (TCGA) database. lncLocator 2.0 was used to identify the distribution of SNHG4 in HCC cells. Gene expression, Kaplan-Meier survival, microRNA and transcription factor target analyses were performed with the University of Alabama Cancer (UALCAN) Database, Kaplan-Meier Plotter, LinkedOmics, WebGestalt and gene set enrichment analysis, respectively. Gene Ontology and pathway enrichment analyses and assessment of RNA binding proteins were performed by R software, circlncRNAnet and Encyclopedia of RNA Interactomes (ENCORI). In addition, CirclncRNAnet and ENCORI were used to find the correlation between SNHG4 and important proteins, while the prognostic value was assessed with the Human Protein Atlas database and Kaplan-Meier Plotter.

RESULTS

Expression of SNHG4 in HCC is higher in HCC tissue than in normal healthy liver tissues and is mainly distributed in the nucleus. SNHG4 positively correlated with poor prognosis (p<0.01 for overall survival and recurrence-free survival). Functional enrichment analysis revealed SNHG4 involvement with regulation of ribosomal RNA synthesis and the RNA processing and surveillance pathway. SNHG4 is closely associated with miR-154 and miR-206, transcription factor target E2F family and the signaling pathway for MAPK/ERK and mTOR. U2 auxiliary factor 2 (U2AF2) showed strong correlation with SNHG4, while low-expression of U2AF2 showed good prognosis.

CONCLUSIONS

Based on our findings, we infer SNHG4 may play a role in the formation of HCC via regulation of tumor-related pathways.

Machine learning-based screening of the diagnostic genes and their relationship with immune-cell infiltration in patients with lung adenocarcinoma

Background

Methods

Results

Conclusions

Differential Gene Sets Profiling in Gram-Negative and Gram-Positive Sepsis

Background

The host response to bacterial sepsis is reported to be nonspecific regardless of the causative pathogen. However, newer paradigms indicated that the host response of Gram-negative sepsis may be different from Gram-positive sepsis, and the difference has not been clearly clarified. The current study aimed to explore the difference by identifying the differential gene sets using the genome-wide technique.

Methods

The training dataset GSE6535 and the validation dataset GSE13015 were used for bioinformatics analysis. The distinct gene sets of sepsis with different infections were screened using gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA). The intersection gene sets based on the two algorithms were confirmed through Venn analysis. Finally, the common gene sets between GSE6535 and GSE13015 were determined by GSEA.

Results

Two immunological gene sets in GSE6535 were identified based on GSVA, which could be used to discriminate sepsis caused by Gram-positive, Gram-negative, or mixed infection. A total of 19 gene sets were obtained in GSE6535 through Venn analysis based on GSVA and GSEA, which revealed the heterogeneity of Gram-negative and Gram-positive sepsis at the molecular level. The result was also verified by analysis of the validation set GSE13015, and 40 common differential gene sets were identified between dataset GSE13015 and dataset GSE6535 by GSEA.

Conclusions

The identified differential gene sets indicated that host response may differ dramatically depending on the inciting organism. The findings offer new insight to investigate the pathophysiology of bacterial sepsis.

The Immune Landscape of Hepatitis B Virus-Related Acute Liver Failure by Integration Analysis

Hepatitis B virus-related acute liver failure (HBV-ALF) is a common type of liver failure, associated with high short-term mortality and morbidity rates. However, the immune landscape of HBV-ALF and its correlation with cell death are currently unknown. Based on 3 Gene Expression Omnibus data sets, infiltrated immune cells were quantified by single-sample gene set enrichment analysis method. The expression levels of immune genes and the abundance of immune cells in liver failure were compared with those in normal liver. The enrichment scores of cell death gene sets from Kyoto Encyclopedia of Genes and Genomes (KEGG) were calculated by gene set variation analysis method, and a protein-protein interaction (PPI) network was constructed using Cytoscape. Besides 21 differentially expressed immune genes, we identified 11 types of differentially infiltrated immune cells in HBV-ALF compared with normal liver. Enriched pathways of these immune genes mainly consisted of chemokine receptors, chemokine binding, interleukin-10 signaling, and TNFs bind their physiological receptors by Reactome pathway analysis. In addition, the enrichment scores of apoptosis and necroptosis pathway instead of autophagy and ferroptosis were increased in liver failure compared with normal liver. PPI network and gene cluster analysis of immune genes and apoptosis and necroptosis genes suggested that hub genes were mainly related to immune response and apoptosis. In summary, our study offers a conceptual framework to understand the immune landscape of HBV-ALF, which might help to improve prognosis.

Periodicities in the Daily Proton Fluxes from 2011 to 2019 Measured by the Alpha Magnetic Spectrometer on the International Space Station from 1 to 100 GV

We present the precision measurement of the daily proton fluxes in cosmic rays from May 20, 2011 to October 29, 2019 (a total of 2824 days or 114 Bartels rotations) in the rigidity interval from 1 to 100 GV based on 5.5×10^{9} protons collected with the Alpha Magnetic Spectrometer aboard the International Space Station. The proton fluxes exhibit variations on multiple timescales. From 2014 to 2018, we observed recurrent flux variations with a period of 27 days. Shorter periods of 9 days and 13.5 days are observed in 2016. The strength of all three periodicities changes with time and rigidity. The rigidity dependence of the 27-day periodicity is different from the rigidity dependences of 9-day and 13.5-day periods. Unexpectedly, the strength of 9-day and 13.5-day periodicities increases with increasing rigidities up to ∼10  GV and ∼20  GV, respectively. Then the strength of the periodicities decreases with increasing rigidity up to 100 GV.

Prognostic Value of Inflammatory Indicators in Chronic Hepatitis B Patients With Significant Liver Fibrosis: A Multicenter Study in China

Diagnosis of significant liver fibrosis is essential to facilitate the optimal treatment decisions and improve prognosis in patients with chronic hepatitis B (CHB). We aimed to evaluate the value of inflammatory indicators and construct a nomogram that effectively predicts significant liver fibrosis among CHB patients. 563 CHB patients from two centers in China from 2014 to 2019 were divided into three cohorts (development, internal validation, and independent validation cohorts), assigned into cases with significant fibrosis (liver fibrosis stages ≥2) and those without. Multiple biochemical and serological inflammatory indicators were investigated. Inflammatory indicators, Alanine aminotransferase (ALT) and aspartate aminotransferase (AST), were significantly associated with significant liver fibrosis in CHB patients but limited predictive performance, and then we combined them with prothrombin time activity percentage (PTA) and liver stiffness measurement (LSM) were identified by multivariate logistic regression analysis. Based on these factors, we constructed the nomogram with excellent performance. The area under the receiver operating characteristic curve (AUROC) for the nomogram in the development, internal validation, and independent validation cohorts were 0.860, 0.877, and 0.811, respectively. Our nomogram based on ALT and AST that had excellent performance in predicting significant fibrosis of CHB patients were constructed.

Pericardial disease in patients treated with immune checkpoint inhibitors

Background

There are limited data on the occurrence, associations and outcomes of pericardial effusions and pericarditis after treatment with immune checkpoint inhibitors (ICIs).

Purpose

To evaluate incidence of pericardial disease in patients treated with an ICI.

Methods

This was a retrospective study at a single academic center that compared 2842 consecutive patients who received ICIs with 2699 age- and cancer-type matched patients with metastatic disease who did not receive ICI (design 1). A pericardial event was defined as a composite outcome of pericarditis and new or worsening moderate or large pericardial effusion. The endpoints were obtained through chart review and were blindly adjudicated. To identify risk factors associated with a pericardial event, in a second analysis, we also compared patients who developed an event on an ICI to patients treated with an ICI who did not develop a pericardial event (design 2). Cox proportional hazard model and logistical regression analysis were performed to study the association between ICI use and pericardial disease as well as pericardial disease and mortality. An additional 6-week landmark analysis was performed to account for lead-time bias.

Results

There were 42 pericardial events in the patients treated with ICI (n=2842) over 193 days (interquartile range 64 to 411) with an incidence rate of 1.57 events per 100 person-years. There was a 4-fold increase in the risk for pericarditis or a pericardial effusion among patients on an ICI compared to controls not treated with ICI after adjusting for potential confounders (hazard ratio [HR] 4.37, 95% confidence interval [CI] 2.09–9.14, p&lt;0.001). Patients who developed pericardial disease while on an ICI had a trend for increased all-cause mortality (HR 1.53, 95% CI 0.99–2.36, p=0.05) compared to those who did not develop pericardial disease. When comparing those who developed pericardial disease after ICI treatment to those who did not, a higher dose of corticosteroid pre-ICI (&gt;0.7 mg/kg prednisone) was associated with increased risk of pericardial disease (HR 2.56, 95% CI 1.00–6.57, p=0.049).

Conclusions

ICI use was associated with an increased risk for development of pericardial disease among cancer patients and a pericardial event on an ICI was associated with a trend towards increased mortality.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): National Institutes of Health/National Heart, Lung, and Blood Institute; a gift from A. Curt Greer and Pamela Kohlberg

Erratum: Properties of a New Group of Cosmic Nuclei: Results from the Alpha Magnetic Spectrometer on Sodium, Aluminum, and Nitrogen [Phys. Rev. Lett. 127, 021101 (2021)]

This corrects the article DOI: 10.1103/PhysRevLett.127.021101.

Incidence and risk factors of female urinary incontinence: a 4-year longitudinal study among 24 985 adult women in China

OBJECTIVE

To estimate the incidence of urinary incontinence (UI), including its subtypes stress UI (SUI), urgency UI (UUI) and mixed UI (MUI), and to examine risk factors for de novo SUI and UUI in Chinese women.

DESIGN

Nationwide longitudinal study.

SETTING

Six geographic regions of China.

PARTICIPANTS

Women aged ≥20 years old were included using a multistage, stratified, cluster sampling method.

METHODS

This study was conducted between May 2014 and March 2016, with follow up in 2018. Data on demographics, medical history, lifestyle and physiological and anthropometric information were collected.

MAIN OUTCOME MEASUREMENTS

Incidence, rate ratio (RR).

RESULTS

Analyses included 24 985 women (mean age 41.9 years).The follow-up response rate was 55.5%, median follow-up time was 3.7 years. The standardised incidences of UI, SUI, UUI and MUI were 21.2, 13.1, 3.0 and 5.1 per 1000 person-years, respectively. Risk factors for de novo SUI included delivery pattern (vaginal spontaneous delivery RR 2.12, 95% CI 1.62-2.78 and instrumental delivery RR 3.30, 95% CI 1.99-5.45), high body mass index (BMI) (overweight RR 1.52, 95% CI 1.33-1.74 and obesity RR 1.67, 95% CI 1.32-2.11), cigarette smoking (RR 1.54, 95% CI 1.12-2.12), chronic cough (RR 1.44, 95% CI 1.17-1.76), diabetes (RR 1.33, 95% CI 1.10-1.60) and older age (50-59 years RR 1.49, 95% CI 1.16-1.90 and 60-69 years RR 1.61, 95% CI 1.22-2.13).The risk factors significantly associated with de novo UUI were age (RR increased from 1.21, 95% CI 0.74-1.99, at 30-39 years to 6.3, 95% CI 3.85-10.30, at >70 years) and diabetes (RR 1.48, 95% CI 1.05-2.09).

CONCLUSIONS

The incidence of female UI is 21.2 per 1000 person-years in China. Delivery (vaginal spontaneous delivery, instrumental delivery), high BMI, cigarette smoking, chronic cough, diabetes and older age were risk factors.

TWEETABLE ABSTRACT

The incidence of female urinary incontinence was 21.2 per 1000 person-years in China. Delivery, BMI, diabetes and old age are risk factors.

U-Shaped Relationship of Low-Density Lipoprotein Cholesterol With Risk of Severe COVID-19 From a Multicenter Pooled Analysis

Low-density lipoprotein cholesterol (LDL-C) is a well-known risk factor for coronary heart disease but protects against infection and sepsis. We aimed to disclose the exact association between LDL-C and severe 2019 novel coronavirus disease (COVID-19). Baseline data were retrospectively collected for 601 non-severe COVID-19 patients from two centers in Guangzhou and one center in Shenzhen, and patients on admission were medically observed for at least 15 days to determine the final outcome, including the non-severe group (n = 460) and the severe group (severe and critical cases) (n = 141). Among 601 cases, 76 (12.65%) received lipid-lowering therapy; the proportion of patients taking lipid-lowering drugs in the severe group was higher than that in the non-severe group (22.7 vs. 9.6%). We found a U-shaped association between LDL-C level and risk of severe COVID-19 using restricted cubic splines. Using univariate logistic regression analysis, odds ratios for severe COVID-19 for patients with LDL-C ≤1.6 mmol/L (61.9 mg/dL) and above 3.4 mmol/L (131.4 mg/dL) were 2.29 (95% confidence interval 1.12–4.68; p = 0.023) and 2.02 (1.04–3.94; p = 0.039), respectively, compared to those with LDL-C of 2.81–3.40 mmol/L (108.6–131.4 mg/dL); following multifactorial adjustment, odds ratios were 2.61 (1.07–6.37; p = 0.035) and 2.36 (1.09–5.14; p = 0.030). Similar results were yielded using 0.3 and 0.5 mmol/L categories of LDL-C and sensitivity analyses. Both low and high LDL-C levels were significantly associated with higher risk of severe COVID-19. Although our findings do not necessarily imply causality, they suggest that clinicians should pay more attention to lipid-lowering therapy in COVID-19 patients to improve clinical prognosis.