Morin protects chicks with T-2 toxin poisoning by decreasing heterophil extracellular traps, oxidative stress and inflammatory response

1. Fusarium tritici widely exists in a variety of grain feeds. The T-2 toxin is the main hazardous component produced by Fusarium tritici, making a serious hazard to poultry industry. Morin, belonging to the flavonoid family, can be extracted from mulberry plants and possesses anticancer, antioxidant and anti-inflammatory compounds, but whether morin protects chicks with T-2 toxin poisoning remains unclear. This experiment firstly established a chick model of T-2 toxin poisoning and then investigated the protective effects and mechanism of morin against T-2 toxin in chicks.2. The function of liver and kidney was measured by corresponding alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), blood urea nitrogen (BUN), creatinine (Cre) and uric acid (UA) kits. Histopathological changes were observed by haematoxylin-eosin staining. The status of oxidative stress was measured by MDA, SOD, CAT, GSH and GSH-PX kits. The mRNA levels of TNF-α, COX-2, IL-1β, IL-6, caspase-1, caspase-3 and caspase-11 were measured by quantitative real-time PCR. Heterophil extracellular trap (HET) release was analysed by immunofluorescence and fluorescence microplate.3. The model with T-2 toxin poisoning in chicks was successfully established. Morin significantly decreased T-2 toxin-induced ALT, AST, ALP, BUN, Cre and UA, and improved T-2 toxin-induced liver cell rupture, liver cord disorder and kidney interstitial oedema. Oxidative stress analysis showed that morin ameliorated T-2 toxin-induced damage by reducing malondialdehyde (MDA), increasing superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and glutathione peroxidase (GSH-PX). The qRT-PCR analysis showed that morin reduced T-2 toxin-induced mRNA expressions of TNF-α, COX-2, IL-1β, IL-6, caspase-1, caspase-3 and caspase-11. Moreover, morin significantly reduced the release of T-2 toxin-induced HET in vitro and in vivo.4. Morin can protect chicks from T-2 toxin poisoning by decreasing HETs, oxidative stress and inflammatory responses, which make it a useful compound against T-2 toxin poisoning in poultry feed.

Massively parallel CRISPR off-target detection enables rapid off-target prediction model building

BACKGROUND

CRISPR (clustered regularly interspaced short palindromic repeats) genome editing holds tremendous potential in clinical translation. However, the off-target effect has always been a major concern.

METHODS

Here, we have developed a novel sensitive and specific off-target detection method, AID-seq (adaptor-mediated off-target identification by sequencing), that can comprehensively and faithfully detect the low-frequency off targets generated by different CRISPR nucleases (including Cas9 and Cas12a).

FINDINGS

Based on AID-seq, we developed a pooled strategy to simultaneously identify the on/off targets of multiple gRNAs, as well as using mixed human and human papillomavirus (HPV) genomes to screen the most efficient and safe targets from 416 HPV gRNA candidates for antiviral therapy. Moreover, we used the pooled strategy with 2,069 single-guide RNAs (sgRNAs) at a pool size of about 500 to profile the properties of our newly discovered CRISPR, FrCas9. Importantly, we successfully built an off-target detection model using these off-target data via the CRISPR-Net deep learning method (area under the receiver operating characteristic curve [AUROC] = 0.97, area under the precision recall curve [AUPRC] = 0.29).

CONCLUSIONS

To our knowledge, AID-seq is the most sensitive and specific in vitro off-target detection method to date. And the pooled AID-seq strategy can be used as a rapid and high-throughput platform to select the best sgRNAs and characterize the properties of new CRISPRs.

FUNDING

This work was supported by The National Natural Science Foundation of China (grant nos. 32171465 and 82102392), the General Program of Natural Science Foundation of Guangdong Province of China (grant no. 2021A1515012438), Guangdong Basic and Applied Basic Research Foundation (grant no. 2020A1515110170), and the National Ten Thousand Plan-Young Top Talents of China (grant no. 80000-41180002).

VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns

Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein-Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 virus genotypes and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover integration patterns; and (3) a statistics interface for a comprehensive investigation of genotype-specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at https://www.vis-atlas.tech/.

HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription

Human papillomavirus (HPV) integration is a critical step in cervical cancer development; however, the oncogenic mechanism at the genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of six HPV-positive and three HPV-negative cell lines. Through HPV integration detection, super-enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. We identified seven high-ranking cellular SEs generated by HPV integration in total (the HPV breakpoint-induced cellular SEs, BP-cSEs), leading to intra-chromosomal and inter-chromosomal regulation of chromosomal genes. The pathway analysis revealed that the dysregulated chromosomal genes were correlated to cancer-related pathways. Importantly, we demonstrated that BP-cSEs existed in the HPV-human hybrid ecDNAs, explaining the above transcriptional alterations. Our results suggest that HPV integration generates cellular SEs that function as ecDNA to regulate unconstrained transcription, expanding the tumorigenic mechanism of HPV integration and providing insights for developing new diagnostic and therapeutic strategies.

Targeting Diagnosis of High-Risk Papillary Thyroid Carcinoma Using Ultrasound Contrast Agent With the BRAFV600E Mutation: An Experimental Study

OBJECTIVE

High-risk papillary thyroid carcinoma (PTC) patients with BRAF mutation have lymph node and distant metastases and poor prognosis. Therefore, this study aims to develop a targeted ultrasound contrast agent for the BRAF^V600E mutation to screen high-risk PTC at early stage.

METHODS

The targeted lipid nanobubbles carrying BRAF^V600E antibody were prepared using thin film hydration-sonication and avidin-biotin binding methods. The physicochemical properties and stability of the targeted nanobubbles were detected by transmission electron microscopy, atomic force microscopy, and confocal laser scanning microscopy. The target binding abilities of the targeted nanobubbles in the PTC cells (B-CPAP) overexpressed mutant BRAF^V600E were evaluated by immunofluorescence staining, quantitative real-time polymerase chain reaction, western blot, and fluorescence microscopy. After PTC tumor models overexpressed mutant BRAF^V600E were established, the enhanced images of targeted lipid nanobubbles and untargeted lipid nanobubbles on PTC tumors in nude mice were observed using contrast-enhanced ultrasound imaging.

RESULTS

The targeted lipid nanobubbles revealed uniform, round morphology, and good stability with a nanoscale size. Besides, BRAF^V600E monoclonal antibody was observed to be combined on the surface of lipid nanobubbles. Furthermore, the targeted nanobubbles had a good targeting diagnosis ability in PTC cells with BRAF^V600E overexpression. Moreover, the targeted nanobubbles had better ultrasound enhancement and peak intensity of the time-intensity curve (P < .001) in PTC tumors with BRAF^V600E overexpression as compared to the untargeted lipid nanobubbles.

CONCLUSION

The targeted lipid nanobubbles carrying BRAF^V600E antibody could be regarded as a potential targeted ultrasound contrast agent for the diagnosis of high-risk PTC.

Retraction Note: Combination therapy with metformin and IL-12 to inhibit the growth of hepatic carcinoma by promoting apoptosis and autophagy in HepG2-bearing mice

The article "Combination therapy with metformin and IL-12 to inhibit the growth of hepatic carcinoma by promoting apoptosis and autophagy in HepG2-bearing mice, by Z. Jin, B.-X. Jia, L.-D. Tan, Q.-M. Chen, Y.-H. Liu, published in Eur Rev Med Pharmacol Sci 2020; 24 (23): 12368-12379-DOI: 10.26355/eurrev_202012_24031-PMID: 33336757" has been retracted by the authors as they cannot ensure the reliability of the manuscript due to inaccuracies in the conclusions and in the experiment (the cell migration and invasion assay along with the cell cycle arrest assay are missing). The Publisher apologizes for any inconvenience this may cause https://www.europeanreview.org/article/24031.

Differential diagnosis and feature visualization for thyroid nodules using computer-aided ultrasonic diagnosis system: initial clinical assessment

BACKGROUND

To assess the diagnostic efficacy of the computer-aided ultrasonic diagnosis system (CAD system) in differentiating benign and malignant thyroid nodules.

METHODS

The images of 296 thyroid nodules were included in validation sets. The diagnostic efficacy of the CAD system was compared with that of junior physicians and senior physicians, as well as that of the combination diagnosis of the CAD system with junior physicians. The diagnostic efficacy of the CAD system for different sizes of thyroid nodules was compared.

RESULTS

The diagnostic sensitivity and accuracy of the CAD system were higher than those of junior physicians (83.4% vs. 72.2%, 73.0% vs. 69.6%), but the diagnostic specificity of the CAD system was lower than that of junior physicians (62.1% vs. 66.9%). The diagnostic accuracy of the CAD system was lower than that of senior physicians (73.0% vs. 83.8%). However, the combination diagnosis of the CAD system with junior physicians had higher accuracy (81.8%) and AUC (0.842) than those of either the CAD system or junior physicians alone, and comparable diagnostic performance with those of senior physicians. The Kappa was 0.635 in the combination diagnosis of the CAD system with junior physicians, showing good consistency with the pathological results. The accuracy (76.4%) of the CAD system was the highest for nodules of 1-2 cm.

CONCLUSION

The CAD system can effectively assist physicians to identify malignant and benign thyroid nodules, reduce the overdiagnosis and overtreatment of thyroid nodules, avoid unnecessary invasive fine needle aspiration, and improve the diagnostic accuracy of junior physicians.

Spatiotemporal evolution of online attention to vaccines since 2011: An empirical study in China

Since the outbreak of Coronavirus Disease 2019 (COVID-19), the Chinese government has taken a number of measures to effectively control the pandemic. By the end of 2021, China achieved a full vaccination rate higher than 85%. The Chinese Plan provides an important model for the global fight against COVID-19. Internet search reflects the public's attention toward and potential demand for a particular thing. Research on the spatiotemporal characteristics of online attention to vaccines can determine the spatiotemporal distribution of vaccine demand in China and provides a basis for global public health policy making. This study analyzes the spatiotemporal characteristics of online attention to vaccines and their influencing factors in 31 provinces/municipalities in mainland China with Baidu Index as the data source by using geographic concentration index, coefficient of variation, GeoDetector, and other methods. The following findings are presented. First, online attention to vaccines showed an overall upward trend in China since 2011, especially after 2016. Significant seasonal differences and an unbalanced monthly distribution were observed. Second, there was an obvious geographical imbalance in online attention to vaccines among the provinces/municipalities, generally exhibiting a spatial pattern of “high in the east and low in the west.” Low aggregation and obvious spatial dispersion among the provinces/municipalities were also observed. The geographic distribution of hot and cold spots of online attention to vaccines has clear boundaries. The hot spots are mainly distributed in the central-eastern provinces and the cold spots are in the western provinces. Third, the spatiotemporal differences in online attention to vaccines are the combined result of socioeconomic level, socio-demographic characteristics, and disease control level.

Global Trade Pattern of Medical Devices and China's Trade Position: Based on Data From 2001 to 2020

To depict the evolution of the global trade of medical devices, this study analyzes the spatiotemporal evolution characteristics of global and China's trade patterns of medical devices from 2001 to 2020 based on data from the World Bank and United Nations Commodity Trade Statistics Database, and thereby investigates the status quo of global and China's medical device trade, as well as changes in China's position in the global medical device trade. The findings are as follows. First, the total global trade volume of medical devices is generally on the rise, showing closer network connections. Despite some changes in trade position, the core countries in the global medical device trade network are relatively fixed. The intermediate position of core trading countries has been weakened on the whole, whereas exporting countries have generally assumed an enhanced central position. Communities with geographical proximity have been formed in the global medical device trade network, including two large communities, the Asian-European countries and the Pacific Rim countries, and one small community, the South American countries. Second, with its rapidly growing trade volume of medical devices with other countries, China has now become the fourth largest medical device trading country in the world. Its number of import and export partners has remained relatively stable and continued to increase. Its export markets are relatively concentrated, and a tripartite pattern of import sources has been formed. China has established extensive interdependent relations and almost no one-way dependent relations in the medical device trade. Among its major trading partners for medical devices, the interdependence of China with developed countries/regions, such as European and American countries and Japan, has generally deepened.

Peripheral nerve defects repaired with autogenous vein grafts filled with platelet-rich plasma and active nerve microtissues and evaluated by novel multimodal ultrasound techniques

BACKGROUND

Developing biocompatible nerve conduits that accelerate peripheral nerve regeneration, lengthening and functional recovery remains a challenge. The combined application of nerve microtissues and platelet-rich plasma (PRP) provides abundant Schwann cells (SCs) and various natural growth factors and can compensate for the deficiency of SCs in the nerve bridge, as well as the limitations of applying a single type of growth factor. Multimodal ultrasound evaluation can provide additional information on the stiffness and microvascular flow perfusion of the tissue. This study was designed to investigate the effectiveness of a novel tissue-engineered nerve graft composed of an autogenous vein, nerve microtissues and PRP in reconstructing a 12-mm tibial nerve defect and to explore the value of multimodal ultrasound techniques in evaluating the prognosis of nerve repair.

METHODS

In vitro, nerve microtissue activity was first investigated, and the effects on SC proliferation, migration, factor secretion, and axonal regeneration of dorsal root ganglia (DRG) were evaluated by coculture with nerve microtissues and PRP. In vivo, seventy-five rabbits were equally and randomly divided into Hollow, PRP, Micro-T (Microtissues), Micro-T + PRP and Autograft groups. By analysing the neurological function, electrophysiological recovery, and the comparative results of multimodal ultrasound and histological evaluation, we investigated the effect of these new nerve grafts in repairing tibial nerve defects.

RESULTS

Our results showed that the combined application of nerve microtissues and PRP could significantly promote the proliferation, secretion and migration of SCs and the regeneration of axons in the early stage. The Micro-T + PRP group and Autograft groups exhibited the best nerve repair 12 weeks postoperatively. In addition, the changes in target tissue stiffness and microvascular perfusion on multimodal ultrasound (shear wave elastography; contrast-enhanced ultrasonography; Angio PlaneWave UltrasenSitive, AngioPLUS) were significantly correlated with the histological results, such as collagen area percentage and VEGF expression, respectively.

CONCLUSION

Our novel tissue-engineered nerve graft shows excellent efficacy in repairing 12-mm defects of the tibial nerve in rabbits. Moreover, multimodal ultrasound may provide a clinical reference for prognosis by quantitatively evaluating the stiffness and microvescular flow of nerve grafts and targeted muscles.

Non-homologous dsODN increases the mutagenic effects of CRISPR-Cas9 to disrupt oncogene E7 in HPV positive cells

Genome editing tools targeting high-risk human papillomavirus (HPV) oncogene could be a promising therapeutic strategy for the treatment of HPV-related cervical cancer. We aimed to improve the editing efficiency and detect off-target effects concurrently for the clinical translation strategy by using CRISPR-Cas9 system co-transfected with 34nt non-homologous double-stranded oligodeoxynucleotide (dsODN). We firstly tested this strategy on targeting the Green Fluorescent Protein (GFP) gene, of which the expression is easily observed. Our results showed that the GFP+ cells were significantly decreased when using GFP-sgRNAs with dsODN, compared to using GFP-sgRNAs without donors. By PCR and Sanger sequencing, we verified the dsODN integration into the break sites of the GFP gene. And by amplicon sequencing, we observed that the indels% of the targeted site on the GFP gene was increased by using GFP-sgRNAs with dsODN. Next, we went on to target the HPV18 E7 oncogene by using single E7-sgRNA and multiplexed E7-sgRNAs respectively. Whenever using single sgRNA or multiplexed sgRNAs, the mRNA expression of HPV18 E7 oncogene was significantly decreased when adding E7-sgRNAs with dsODN, compared to E7-sgRNAs without donor. And the indels% of the targeted sites on the HPV18 E7 gene was markedly increased by adding dsODN with E7-sgRNAs. Finally, we performed GUIDE-Seq to verify that the integrated dsODN could serve as the marker to detect off-target effects in using single or multiplexed two sgRNAs. And we detected fewer on-target reads and off-target sites in multiplexes compared to the single sgRNAs when targeting the GFP and the HPV18 E7 genes. Together, CRISPR-Cas9 system co-transfected with 34nt dsODN concurrently improved the editing efficiency and monitored off-target effects, which might provide new insights in the treatment of HPV infections and related cervical cancer.

FrCas9 is a CRISPR/Cas9 system with high editing efficiency and fidelity

Genome editing technologies hold tremendous potential in biomedical research and drug development. Therefore, it is imperative to discover gene editing tools with superior cutting efficiency, good fidelity, and fewer genomic restrictions. Here, we report a CRISPR/Cas9 from Faecalibaculum rodentium, which is characterized by a simple PAM (5'-NNTA-3') and a guide RNA length of 21-22 bp. We find that FrCas9 could achieve comparable efficiency and specificity to SpCas9. Interestingly, the PAM of FrCas9 presents a palindromic sequence, which greatly expands its targeting scope. Due to the PAM sequence, FrCas9 possesses double editing-windows for base editor and could directly target the TATA-box in eukaryotic promoters for TATA-box related diseases. Together, our results broaden the understanding of CRISPR/Cas-mediated genome engineering and establish FrCas9 as a safe and efficient platform for wide applications in research, biotechnology and therapeutics.

Gene knock-out chain reaction enables high disruption efficiency of HPV18 E6/E7 genes in cervical cancer cells

A genome editing tool targeting the high-risk human papillomavirus (HPV) oncogene is a promising therapeutic strategy to treat HPV-related cervical cancer. To improve gene knockout efficiency, we developed a gene knockout chain reaction (GKCR) method for continually generating mutagenic disruptions and used this method to disrupt the HPV18 E6 and E7 genes. We verified that the GKCR Cas9/guide RNA (gRNA) cassettes could integrated into the targeted loci via homology-independent targeted insertion (HITI). The qPCR results revealed that the GKCR method enabled a relatively higher Cas9/gRNA cassette insertion rate than a control method (the common CRISPR-Cas9 strategy). Tracking of Indels by DEcomposition (TIDE) assay results showed that the GKCR method produced a significantly higher percentage of insertions or deletions (indels) in the HPV18 E6 and E7 genes. Furthermore, by targeting the HPV18 E6/E7 oncogenes, we found that the GKCR method significantly upregulated the P53/RB proteins and inhibited the proliferation and motility of HeLa cells. The GKCR method significantly improved the gene knockout efficiency of the HPV18 E6/E7 oncogenes, which might provide new insights into treatment of HPV infection and related cervical cancer.

The comparison of ZFNs, TALENs, and SpCas9 by GUIDE-seq in HPV-targeted gene therapy

Zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR-associated Cas9 endonucleases are three major generations of genome editing tools. However, no parallel comparison about the efficiencies and off-target activity of the three nucleases has been reported, which is critical for the final clinical decision. We for the first time developed the genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) method in ZFNs and TALENs with novel bioinformatics algorithms to evaluate the off-targets. By targeting human papillomavirus 16 (HPV16), we compared the performance of ZFNs, TALENs, and SpCas9 in vivo. Our data showed that ZFNs with similar targets could generate distinct massive off-targets (287–1,856), and the specificity could be reversely correlated with the counts of middle “G” in zinc finger proteins (ZFPs). We also compared the TALENs with different N-terminal domains (wild-type [WT]/αN/βN) and G recognition modules (NN/NH) and found the design (αN or NN) to improve the efficiency of TALEN inevitably increased off-targets. Finally, our results showed that SpCas9 was more efficient and specific than ZFNs and TALENs. Specifically, SpCas9 had fewer off-target counts in URR (SpCas9, n = 0; TALEN, n = 1; ZFN, n = 287), E6 (SpCas9, n = 0; TALEN, n = 7), and E7 (SpCas9, n = 4; TALEN, n = 36). Taken together, we suggest that for HPV gene therapies, SpCas9 is a more efficient and safer genome editing tool. Our off-target data could be used to improve the design of ZFNs and TALENs, and the universal in vivo off-target detection pipeline for three generations of artificial nucleases provided useful tools for genome engineering-based gene therapy.

Contrast agent retention features in contrast-enhanced ultrasound: diagnostic performance for the prediction of papillary thyroid carcinoma

PURPOSE

To report a new feature of contrast-enhanced ultrasound (CEUS) and its diagnostic performance for the prediction of papillary thyroid carcinoma (PTC).

METHODS

This retrospective study was conducted from October 2018 to March 2019, including 276 patients with 308 thyroid nodules who underwent CEUS examinations prior to surgery (90 patients, 122 nodules) or fine needle aspiration (186 patients, 186 nodules). Quantitative analysis of CEUS features was performed using time-intensity curves. After surgery, tissue sections stained with HE and an anti-CD34 primary antibody were used to characterize the cell number and microvessel density. The nodules were divided into retention and non-retention groups.

RESULTS

There were 168 malignant nodules and 140 benign nodules. The contrast-agent retention (CAR) feature was only observed in 52 papillary carcinomas. The CAR feature showed the sensitivity of 30.9% albeit the high specificity of 100%, for the diagnosis of thyroid cancers. The maximum slope coefficient of the washout index was significantly lower in the retention group than in the non-retention group (P < 0.001). The enhancement intensity during the late stage of enhancement index was significantly higher in the retention group than in the non-retention group (P < 0.001). The cell number and microvessel density in nodules with CAR features were higher (P < 0.001, P = 0.004).

CONCLUSION

The combination of the retention pattern of the CEUS observed herein with other CEUS features may be a useful tool to improve the diagnostic of the PTC.

Combining tumor deposits with the number of lymph node metastases to improve the prognostic accuracy in stage III colon cancer: a post hoc analysis of the CALGB/SWOG 80702 phase III study (Alliance)☆

BACKGROUND

In colon cancer, tumor deposits (TD) are considered in assigning prognosis and staging only in the absence of lymph node metastasis (i.e. stage III pN1c tumors). We aimed to evaluate the prognostic value of the presence and the number of TD in patients with stage III, node-positive colon cancer.

PATIENTS AND METHODS

All participants from the CALGB/SWOG 80702 phase III trial were included in this post hoc analysis. Pathology reports were reviewed for the presence and the number of TD, lymphovascular and perineural invasion. Associations with disease-free survival (DFS) and overall survival (OS) were evaluated by multivariable Cox models adjusting for sex, treatment arm, T-stage, N-stage, lymphovascular invasion, perineural invasion and lymph node ratio.

RESULTS

Overall, 2028 patients were included with 524 (26%) TD-positive and 1504 (74%) TD-negative tumors. Of the TD-positive patients, 80 (15.4%) were node negative (i.e. pN1c), 239 (46.1%) were pN1a/b (<4 positive lymph nodes) and 200 (38.5%) were pN2 (≥4 positive lymph nodes). The presence of TD was associated with poorer DFS [adjusted hazard ratio (aHR) = 1.63, 95% CI 1.33-1.98] and OS (aHR = 1.59, 95% CI 1.24-2.04). The negative effect of TD was observed for both pN1a/b and pN2 groups. Among TD-positive patients, the number of TD had a linear negative effect on DFS and OS. Combining TD and the number of lymph node metastases, 104 of 1470 (7.1%) pN1 patients were re-staged as pN2, with worse outcomes than patients confirmed as pN1 (3-year DFS rate: 65.4% versus 80.5%, P = 0.0003; 5-year OS rate: 87.9% versus 69.1%, P = <0.0001). DFS was not different between patients re-staged as pN2 and those initially staged as pN2 (3-year DFS rate: 65.4% versus 62.3%, P = 0.4895).

CONCLUSION

Combining the number of TD and the number of lymph node metastases improved the prognostication accuracy of tumor-node-metastasis (TNM) staging.

Notoginsenoside R1 protects hypoxia-reoxygenation deprivation-induced injury by upregulation of miR-132 in H9c2 cells

BACKGROUND

Myocardial ischemia/reperfusion injury (IRI) is a common perioperative complication of heart and great vessels surgery, aggravating the original myocardial damage and seriously affecting the postoperative recovery of cardiac function. The aim of this study was to reveal the functional effects and potential mechanisms of notoginsenoside R1 (NG-R1) in myocardial cells injured by hypoxia-reoxygenation (H/R).

METHODS

The rat cardiomyocyte line H9c2 was subjected to H/R with or without NG-R1 treatment. The levels of miR-132 and HBEGF in the cell were altered by microRNA or short-hairpin RNA transfection. Cell viability, apoptosis, lactate dehydrogenase (LDH) and malondialdehyde (MDA) were monitored. Dual luciferin was used to detect the relationship between miR-132 and HBEGF.

RESULTS

NG-R1 (20 μM) had no impact on H9c2 cells, but cell viability was significantly reduced at 80 μM. NG-R1 (20 μM) protected H9c2 cells against H/R-induced cell damage, accompanied by increased cell viability, reduced cell apoptosis, and downregulation of LDH and MDA. Furthermore, the level of miR-132 was decreased in response to H/R exposure but then increased after NG-R1 treatment. When miR-132 was overexpressed, H/R-induced cell damage could be recovered. Downregulation of miR-132 limited the protective effect of NG-R1 on H/R damage. We also found that HBEGF was a direct target of miR-132. The expression of HBEGF was increased upon H/R damage, and this increase was reversed after NG-R1 treatment.

CONCLUSIONS

This study demonstrated that NG-R1 markedly protected H9c2 cells against H/R-induced damage via upregulation of miR-132 and downregulation of its target protein HBEGF.

Long non-coding RNA plasmacytoma variant translocation 1 (PVT1) promotes glioblastoma multiforme progression via regulating miR-1301-3p/TMBIM6 axis

OBJECTIVE

To explore whether plasmacytoma variant translocation 1 (PVT1) could regulate glioblastoma multiforme (GBM) progression via microRNA-1301-3p (miR-1301-3p) and transmembrane BAX inhibitor motif containing 6 (TMBIM6) axis.

MATERIALS AND METHODS

Expression patterns of PVT1 and RMBIM6 in GBM patients were analyzed using GEPIA, an online gene expression analysis tool. Levels of PVT1 in GBM cells and normal cells were analyzed with quantitative real-time PCR method. Cell Counting Kit-8 (CCK-8), transwell invasion assay, and flow cytometry assay were applied to detect cell viability and apoptosis. Connections of PVT1 or TMBIM6 with miR-1301-3p were validated with bioinformatic tool and luciferase activity reporter assay.

RESULTS

PVT1 was significantly expressed in GBM tissues and cells. PVT1 promotes GBM cell proliferation and invasion but inhibits apoptosis in vitro. TMBIM6 was significantly expressed in GBM tissues. The knockdown of TMBIM6 reversed the stimulation effects of PVT1 on GBM cell malignancy behaviors with miR-1301-3p as a bridge.

CONCLUSIONS

Collectively, we showed PVT1 elevated TMBIM6 expression mediated by miR-1301-3p and thus to promote GBM progression.

Factors associated with health-related quality of life in papillary thyroid microcarcinoma patients undergoing radiofrequency ablation: a cross-sectional prevalence study

PURPOSE

To explore the association of demographic characteristics, clinical symptoms and the fear of the disease progression factors with the physical and mental summary components of the health-related of life (HRQoL) of the papillary thyroid microcarcinoma (PTMC) patients undergoing radiofrequency ablation (RFA).

METHODS

123 PTMC survivors undergoing RFA were enrolled in this study from October 2019 to March 2020. Demographic, clinical symptoms and the fear of the disease progression data were collected. SF-36, THYCA-QoL and FoP-Q-SF were used to evaluate the HRQoL of patients, clinical symptoms and the fear of disease progression. A multivariate regression model was performed to evaluate the association between the independent variable and the HRQoL variable.

RESULTS

The average self-reported HRQoL score was 81.17 ± 15.48 for the PCS and 73.40 ± 18.03 for the MCS. The multivariate linear regression model shows that the factors related to a poorer PCS were dependent for the female patients, the symptoms of neuromuscular and the throat/mouth, the fear of disease progression; the psychological disorder, symptoms of throat/mouth, inability to concentrate were related to worse scores for the MCS. The condition that was most strongly related to a poorer HRQoL (in both PCS and MCS) was the fear of their physical health.

CONCLUSIONS

The factors related to significantly worse HRQoL scores across PCS and MCS for PTMC survivors include the female gender, the symptoms of neuromuscular and the throat/mouth, the psychological disorder, inability to concentrate, and the fear of their own physical health. Identification, management, and prevention of these factors are critical to improving the HRQoL of patients.

DeepEBV: A deep learning model to predict Epstein-Barr virus (EBV) integration sites

MOTIVATION

Epstein-Barr virus (EBV) is one of the most prevalent DNA oncogenic viruses. The integration of EBV into the host genome has been reported to play an important role in cancer development. The preference of EBV integration showed strong dependence on the local genomic environment, which enables the prediction of EBV integration sites.

RESULTS

An attention-based deep learning model, DeepEBV, was developed to predict EBV integration sites by learning local genomic features automatically. First, DeepEBV was trained and tested using the data from the dsVIS database. The results showed that DeepEBV with EBV integration sequences plus Repeat peaks and 2 fold data augmentation performed the best on the training dataset. Furthermore, the performance of the model was validated in an independent dataset. In addition, the motifs of DNA-binding proteins could influence the selection preference of viral insertional mutagenesis. Furthermore, the results showed that DeepEBV can predict EBV integration hotspot genes accurately. In summary, DeepEBV is a robust, accurate and explainable deep learning model, providing novel insights into EBV integration preferences and mechanisms.

AVAILABILITY

DeepEBV is available as open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepEBV.gitSupplementary information  Supplementary data are available at Bioinformatics online.

Discovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity

ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While ASH1L represents an attractive drug target, developing ASH1L inhibitors is challenging, as the catalytic SET domain adapts an inactive conformation with autoinhibitory loop blocking the access to the active site. Here, by applying fragment-based screening followed by medicinal chemistry and a structure-based design, we developed first-in-class small molecule inhibitors of the ASH1L SET domain. The crystal structures of ASH1L-inhibitor complexes reveal compound binding to the autoinhibitory loop region in the SET domain. When tested in MLL leukemia models, our lead compound, AS-99, blocks cell proliferation, induces apoptosis and differentiation, downregulates MLL fusion target genes, and reduces the leukemia burden in vivo. This work validates the ASH1L SET domain as a druggable target and provides a chemical probe to further study the biological functions of ASH1L as well as to develop therapeutic agents.

SK2 channel deletion reduces susceptibility to bupivacaine-induced cardiotoxicity in mouse

Bupivacaine is frequently used for regional anesthesia and postoperative analgesia. However, an inadvertent intravenous injection can cause severe cardiotoxicity, manifesting as arrhythmia, hypotension, and even cardiac asystole. The mechanism of bupivacaine-mediated cardiotoxicity remains unclear. SK2 knockout mice (SK) and wild-type mice (WT) were divided into four groups, with 12 mice per group. We determined the difference in bupivacaine cardiotoxicity between SK2 knockout and WT mice by measuring the time to the first arrhythmia (T_arrhythmia) and the time to asystole (T_asystole). Secondary indicators of cardiotoxicity were the time from the beginning of bupivacaine infusion to 20% prolongation of the QT interval (T_QT) and the time to 20% widening of the QRS complex (T_QRS). T_arrhythmia and T_asystole were significantly longer in the SK-bupi group than in the WT-bupi group (both P < 0.05). T_QT and T_QRS were longer in the SK-bupi group than in the WT-bupi group (all P < 0.05). The time to 25%, 50%, and 75% reduction in HR in the SK-bupi group was significantly longer than in the WT-bupi group (all P < 0.05). Knocking out the SK2 channel can reduce bupivacaine-induced cardiotoxicity in the mouse.

MiR-219-5p inhibits prostate cancer cell growth and metastasis by targeting HMGA2

OBJECTIVE

To investigate the expression of micro ribonucleic acid (miR)-219-5p in prostate cancer (PCa), its influences on the biological functions of PCa, and its mechanism.

PATIENTS AND METHODS

The expression differences of miR-219-5p and high mobility group protein A2 (HMGA2) in 30 pairs of PCa tissues and para-carcinoma tissues were detected via quantitative Real Time-Polymerase Chain Reaction (qRT-PCR), and the difference in miR-219-5p expression in PCa cell lines and normal prostatic epithelial cells was also determined via qRT-PCR. The human PC-3 cells were divided into negative control group and miR-219-5p overexpression group. Methyl thiazolyl tetrazolium (MTT) and colony formation assays were adopted to detect the cell proliferative ability, and flow cytometry was applied to determine the cell apoptosis. The expression of apoptosis-related proteins was measured via Western blotting, and the invasive and migratory abilities of the cells were examined through wound-healing and transwell assays. Bioinformatics prediction software and luciferase reporter assay were employed to verify the targets that might be controlled by miR-219-5p. Rescue experiment was conducted to clarify whether the inhibitory effects of miR-219-5p on the growth and metastasis of PC-3 cells depend on the inhibition of HMGA2.

RESULTS

It was shown in qRT-PCR results that the expression level of miR-219-5p was downregulated remarkably in PCa tissues and cell lines, but overexpressed miR-219-5p could repress the proliferation and promote the apoptosis of PC-3 cells notably. The results of wound-healing and transwell assays indicated that overexpressed miR-219-5p was able to suppress the invasion and metastasis of PC-3 cells. According to Western blotting results, overexpressed miR-219-5p could up-regulate the expressions of pro-apoptotic proteins [Bax, cleaved-caspase-3 and cleaved-poly-ADP-ribose-polymerase (PARP)] and reverse the epithelial-mesenchymal transition (EMT) of PCa cells. It was predicted via the bioinformatics software that HMGA2 gene might be a target gene of miR-219-5p. The Dual-Luciferase reporter assay confirmed that there was a direct regulatory relationship between miR-219-5p and HMGA2. The rescue experiment manifested that overexpressed HMGA2 could reverse the inhibition of miR-219-5p on the growth and metastasis of PC-3 cells.

CONCLUSIONS

MiR-219-5p suppresses the growth and metastasis abilities of prostate cancer cells by directly repressing the expression of HMGA2.

Apelin-13 protects the lungs from ischemia-reperfusion injury by attenuating inflammatory and oxidative stress

Apelin has been reported to regulate mitochondrial function in myocardial ischemia-reperfusion injury and cerebral ischemia-reperfusion injury. However, the role of apelin-13 in lung ischemia-reperfusion injury (LIRI) remains unclear. This study established an experimental rat model to evaluate the underlying mechanisms of apelin-13 on LIRI. Twenty-four rats were randomly divided to sham operation group (group SM), ischemia/reperfusion group (group IR), and apelin-13 treatment group (group APL). The effects of apelin-13 on LIRI were determined histologically using H&E staining, while the wet/dry weight ratio was used to assess lung edema caused by LIRI. Inflammatory cytokines were also detected in Bronchoalveolar lavage (BAL) fluid by ELISA. The protein expression of UCP2 and the morphological changes of mitochondria were determined by western blotting and electromicroscopy, respectively. The results demonstrated the structural damage of lung tissues and lung edema in group IR. An increased level of inflammatory cytokines including IL-1β, IL-6 and TNF-α was observed in rats with LIRI using ELISA. After that, oxidative stress and morphological damage of mitochondria were also shown in group IR. Yet, the application of apelin-13 reversed all these deleterious effects in group APL. The protective effects of apelin-13 were indicated by decreased reactive oxygen species (ROS) and elevated UCP2 expression levels in rats. In conclusion, this study revealed that apelin-13 had protective effects against LIRI via attenuating lung edema, the production of inflammatory cytokines, oxidative stress and mitochondrial dysfunction.

Ablation of small conductance calcium-activated potassium type-2 channel (SK2) delays occurrence of bupivacaine-induced cardiotoxicity in isolated mouse hearts

Bupivacaine is frequently used for conducting regional anesthesia. When accidentally injected or excessively absorbed into circulation, bupivacaine can induce severe arrhythmia and potentially lead to cardiac arrest. The specific mechanisms underlying this cardiotoxicity, however, remain to be clarified. We transfected HEK-293 cells to express the small conductance calcium-activated potassium type-2 channel (SK2), and used a whole-cell patch clamp method in order to explore how bupivacaine affected these channels. We subsequently used SK2 knockout mice to explore the relevance of SK2 channels in bupivacaine-induced cardiotoxicity in isolating mouse hearts, mounting them on a Langendorff apparatus, and perfusing them with bupivacaine. Using this system, arrhythmia, asystole, and cardiac functions were monitored. We observed dose-dependent inhibition of SK2 channels by bupivacaine: half-maximal inhibitory concentration (IC50) value = 18.6 μM (95% CI 10.8-32.1). When SK2 knockout (SK2 -/-) or wild-type (WT) mice were perfused with Krebs-Henseleit buffer (KHB), we did not observe any instances of arrhythmia. When SK2 -/- mice or WT were perfused with KHB containing bupivacaine (40 μM), the time to arrhythmia (Tarrhythmia) and time to asystole (Tasystole) were both significantly longer in SK2 -/- mice relative to WT mice (P < 0.001). Similarly, SK2 -/- mice exhibited a significantly longer time to 25%, 50%, and 75% reductions in heart rate (HR) and rate-pressure product (RPP) relative to WT mice following bupivacaine perfusion (P < 0.001). These results reveal that bupivacaine was able to mediate a dose-dependent inhibition of SK2 channels in HEK-293 cells, and deletion of SK2 channels can delay bupivacaine-induced cardiotoxicity in isolated mouse hearts.

Diagnosis of thyroid cancer using a TI-RADS-based computer-aided diagnosis system: a multicenter retrospective study

OBJECTIVE

The purpose of this study was to use a computer-aided diagnosis (CAD) system based on the Thyroid Imaging, Reporting, and Data System (TI-RADS) to improve the diagnostic performance of thyroid cancer by analyzing clinical ultrasound imaging data.

METHODS

A retrospective diagnostic study of ultrasound image sets was conducted at five hospitals in China. A CAD system based on TI-RADS was applied in this study, and the diagnostic performance of CAD system was tested through multi-center data. The performance of the CAD system was compared with the consensus of three experienced radiologists. The interobserver agreement for cancer diagnosis was calculated between the CAD system and the consensus of the three experienced radiologists.

RESULTS

The CAD system performed well in the diagnosis of thyroid cancer, with an area under the curve (AUC) value of 0.902 (95% CI: 0.884-0.918), and obtained results similar to those of the three experienced radiologists. The CAD system performed better in the internal test set than in the external test set (AUC: 0.930 vs 0.877, respectively). The performance of the CAD system in the diagnosis of thyroid cancer for nodules of different sizes (<1 cm, 1-2 cm and ≥2 cm) was basically similar (accuracy: 84.6% vs 85% vs 84.2%). The CAD system can recognize 15 ultrasound features of thyroid nodules, most of which reached the level of 3 experienced radiologists (12/15, 85%).

CONCLUSION

The CAD system achieved an improved AUC and similar sensitivity and specificity in the diagnosis of thyroid cancer compared with the consensus of experienced radiologists.

The quality of life in papillary thyroid microcarcinoma patients undergoing lobectomy or total thyroidectomy: A cross-sectional study

OBJECTIVE

Papillary thyroid microcarcinoma (PTMC) has a good prognosis and a long survival time, surgery is the common treatment including total thyroidectomy (TT) and unilateral lobectomy (LT), but recent studies showed that TT does not show an advantage over LT for PTMC in preventing cancer recurrence and reducing mortality. Given this, the health-related quality of life (HRQoL) has become one of the important factors that physicians must consider when making treatment decisions. The aim of this study was to compare the HRQoL of patients between undergoing TT and LT.

METHODS

From October 2019 to December 2019, 69 PTMC patients were enrolled in our study, including 34 in the LT group and 35 in the TT group, respectively. We used three questionnaires which included the 36-item short-form health survey (SF-36), thyroid cancer-specific quality of life (THYCA-QOL), and Fear of Progression Questionnaire-Short Form (FoP-Q-SF) for each patient to evaluate their scores of HRQoL.

RESULTS

According to the SF-36, the scores of the domain for the role limitation due to physical problems, emotional problems, and social function (RP, RE, and SF) as well as Physical Component Summary (PCS) and Mental Component Summary (MCS) showed a significant negative linear association between the LT group and TT group: RP (coefficient [coef]: -33.953 [confidence interval (CI) -51.187 to -16.720], p < 0.001, RE (coef: -21.633 [CI -39.500 to -3.766], p = 0.018), SF (coef: -10.169 [CI -19.586 to -0.752], p = 0.035)and PCS (coef: -10.571 [CI -17.768 to -3.373], p = 0.005), MCS (coef: -10.694 [CI -19.465 to -1.923], p = 0.018). The THYCA-QOL showed that the scores of the TT group were higher than that of the LT group in the problem of scar (coef: 16.245 [CI 1.697 to 30.794], p = 0.029 according to the multivariate analysis), suggesting a higher level of complaint in the TT group. There was no statistically significant difference in the scores of FoP-Q-SF between the two groups.

CONCLUSIONS

In patients with PTMC, LT offers an advantage over TT in terms of HRQoL, which supports the role of LT as an alternative strategy to TT.

The prognostic value of quantitating and localizing F-18 FDG uptake in cardiac sarcoidosis

BACKGROUND

There is no identified level of FDG uptake in cardiac sarcoidosis (CS) associated with increased risk of arrhythmias, conduction disease, heart failure, or death. We aim to utilize standardized uptake value (SUV) quantitation and localization to identify patients at increased risk of cardiac events.

METHODS AND RESULTS

F18-FDG PET/CT with MPI was used in CS diagnosis (N = 67). Mean and max SUV were measured and grouped as basal, mid, and apical disease. Post-scan ventricular tachycardia, AICD placement, complete heart block, pacemaker placement, atrial fibrillation, heart failure, and cardiac-related hospital admissions were recorded (mean follow up 2.98 ± 2 years). Poisson regression analysis revealed that max SUV, mean SUV, as well as mean basal SUV, and LVEF were significantly associated with total cardiac events. Max SUV odds ratio (OR) = 1.068 (95% CI 1.024-1.114, P = 0.002), mean SUV OR = 1.059 (95% CI 1.008-1.113, P = 0.023), mean SUV OR = 1.061 (95% CI 1.012-1.112, P = 0.014), scan LVEF OR = 0.731 (95% CI 0.664-0.805, P < 0.001).

CONCLUSIONS

SUV at time of CS diagnosis has significant associations with future cardiac events. Patients with higher SUV, particularly in basal segments, are at increased risk of events. Further studies are needed to identify treatment methods utilizing risk stratification of CS.

Combination therapy with metformin and IL-12 to inhibit the growth of hepatic carcinoma by promoting apoptosis and autophagy in HepG2-bearing mice

OBJECTIVE

To investigate the effects and mechanism of metformin (Met) combined the interleukin-12 (IL-12) on inhibiting hepatoma HepG2 cell proliferation via in vitro and in vivo assays.

MATERIALS AND METHODS

MTT assay was used to detect inhibitory effects of Met, IL-12 alone or combination on HepG2 cells proliferation. Half inhibitory concentration (IC50) and combination index (CI) were also calculated. Anti-tumor effects of combination or monotherapy on the HepG2-bearing mice were investigated and protein expression levels of apoptosis, as well as the Akt/mTOR/STAT3 signaling pathway-related factors were detected by Western blot.

RESULTS

MTT results showed that the inhibitory effect of Met combined with IL-12 on HepG2 cell proliferation was significantly enhanced (both p<0.01) compared with monomer therapy group with a significant synergistic effect (CI<1). The apoptosis rate of HepG2 cells treated with Met combined with IL-12 were 88.12±7.15% and significantly higher than the others (all p<0.01). Moreover, combination treatment significantly suppressed hepatoma growth and increased the survival rate of HepG2-bearing mice without evident body weight loss. Western blot analysis showed that Met combined with IL-12 significantly increased the expression of autophagy-related marker proteins, downregulated the protein expression levels of Bcl-2, p-Akt, p-mTOR, p-STAT3, upregulated the expression level of BAX in both HepG2 cells and tumor tissues.

CONCLUSIONS

Met combined with IL-12 exhibited a synergistic antitumor effect on hepatoma HepG2 cells, and the mechanism may be related to its common inhibition of Akt/mTOR/STAT3 signaling pathway and increase of autophagy in HepG2-bearing mice.

[Factors Affecting Quality of Life of Patients Undergoing Radiofrequency Ablation for Papillary Thyroid Microcarcinoma]

Objective To evaluate the factors affecting health-related quality of life (HRQoL) of patients with thyroid papillary microcarcinoma (PTMC) after ultrasound-guided radiofrequency ablation (RFA).Methods The clinical data of 100 patients with PTMC who underwent reexamination after RFA in the Ultrasound Department of our center from October to December 2019 were retrospectively analyzed.Demographic information was collected.SF-36 and Thyroid Cancer-specific Health-related Quality of Life Questionnaire scales were used to assess patients' quality of life and thyroid-related specific symptoms.The SF-36 scale includes two general domains including physical component summary (PCS) and mental component summary (MCS).The impacts of demographic characteristics and thyroid-related symptoms after RFA on PCS and MCS scores were further analyzed.Results Univariate analysis and correlation analysis showed that the PCS scores in quality of life of PTMC patients were related to sex, neuromuscular, voice, concentration, sympathetic nerve, and throat/mouth complaints, psychological state, sensory symptoms, scar, chills, tingling, and headache (all P<0.1);and the MCS scores were associated with education level, residence, neuromuscular, voice, concentration, sympathetic nerve, and throat/mouth complains, psychological state, sensory symptoms, scar, chills, tingling, and headache (all P<0.1).Multivariate regression analysis showed that the PCS scores were only associated with sex and the neuromuscular and throat/mouth complains and the psychological state.The regression equation was:PCS=110.367-8.025×sex-0.213×psychological state-0.280×neuromuscular complain-0.278×throat/mouth complain.In contrast, the MCS scores were only associated with the psychological state and the throat/mouth and concentration complains, with the regression equation being:MCS=91.323-0.237×psychological state-0.437×throat/mouth-0.304×concentration.Conclusions The main risk factors affecting the quality of life of PTMC patients after ultrasound-guided RFA were female gender, psychological burden, lack of attention, and symptoms in neuromuscular system and throat/mouth.Therefore, preoperative explanations should be made according to the relevant symptoms that the patients may report, and psychological interventions should be offered after RFA to improve the quality of life of PTMC patients after treatment.

Frequency of cardiac arrhythmias in older adults: findings from the subclinical atrial fibrillation and risk of ischemic stroke (SAFARIS) study

Background

Prolonged monitoring of cardiac rhythm has been used in patients with symptomatic arrhythmias and to assess for atrial fibrillation (AF) after cryptogenic stroke, but not in the general population and especially in older adults.

Purpose

To evaluate the frequency of arrhythmias in a community-based cohort of older adults through 14-days continuous cardiac monitoring using a patch-based device.

Methods

Cardiac rhythm was analyzed in 533 participants free of AF and congestive heart failure (CHF) from the tri-ethnic (white, black, Hispanic) Subclinical Atrial Fibrillation and Risk of Ischemic Stroke (SAFARIS) study. AF, supraventricular tachycardia (SVT, defined as 4 beats or more), premature atrial (PACs) and ventricular (PVCs) contractions, ventricular tachycardia (VT, defined as 4 beats or more), sinus pauses (SP) and atrio-ventricular blocks (AVB) were analyzed. Gender, age and race-ethnic differences were examined.

Results

Mean age was 77.2±6.8 years (198 men, 335 women). Recording duration was over 10 days in 91%, and over 13 days in 84%. AF was present in 10 participants (1.9%), atrial flutter in 1 (0.2%). Other arrhythmias are reported in the Table. SP (1.9%) and high-degree AVB (Mobitz II: 0.6%; 3rd degree: 0.9%) were rare. No significant race-ethnic differences were observed.

Conclusion

In older adults without history of stroke or CHF, prolonged rhythm monitoring revealed moderate frequency of AF, but higher than expected frequencies of AF-predisposing conditions such as SVT and frequent PACs. VT episodes were relatively frequent, whereas SP and AVB were less frequent than commonly believed. Most arrhythmias were more frequent in the oldest; ventricular arrhythmias were more common in men than in women.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): NINDS R01 NS083874

DeepHPV: a deep learning model to predict human papillomavirus integration sites

Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism. Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: huzheng1998@163.com, liangjiuxing@m.scnu.edu.cn, lizheyzy@163.com.

Phase transitions in the classical exchange-anisotropic Kitaev-Heisenberg model

The Kitaev model on the honeycomb lattice has been receiving substantial attention due to the discovery of quantum spin liquid state associated with this model. Consequently, its classical partners such as the Kitaev-Heisenberg (KH) model and associated phase transitions become concerned. Specifically, an intermediate Kosterlitz-Thouless (KT) phase engaged in the transition from the high-temperature (T) disordered state to the low-T sixfold degenerate state is predicted in the isotropic KH model [Phys. Rev. Lett. 109, 187201 (2012)10.1103/PhysRevLett.109.187201], but so far no sufficient experimental proof has been reported. In this work, we consider an essential extension of this KH model on the honeycomb lattice by including the Kitaev exchange anisotropy that is non-negligible in realistic materials. The associated phase transitions are thus investigated using the Monte Carlo simulations. It is found that such an anisotropy will result in a degradation of the sixfold degeneracy of the ground state in the isotropic KH model down to the fourfold or twofold degenerate ground state, and the finite-T phase transitions will also be modified remarkably. Interestingly, the intermediate KT phase can be suppressed by this Kitaev exchange anisotropy. This work thus provides a more realistic description of the physics ingredient with the KH model and presents a possible explanation on absence of the intermediate phase in real materials where the Kitaev exchange anisotropy can be more or less available.

[Construction of urban scale-free network model and its epidemiological significance in the prevention and control of COVID-19]

COVID-19 is a public health emergency currently. In this study, a scale-free network model is established based on the Spring Migration data in 2020.The cities is clustered into three different modules. The epidemic of the cities in the black module was the most serious, followed by the red and the cyan. The black module contains 9 cities in Zhejiang province and 8 cities in Guangdong province, most of them located in the southeast coastal economic belt. These cities should be the key cities for epidemic prevention and control.

[Quantitative Evaluation of Sciatic Nerve Crush Injury with Conventional Ultrasound Combined with Shear-wave Elastography in Rabbit Models]

Objective To explore the value of conventional ultrasound combined with shear-wave elastography in the quantitative evaluation of sciatic nerve crush injury in rabbit models. Methods Forty healthy male New Zealand white rabbits were randomly divided into four groups (n=10 in each group):three crush injury (CI) groups (2,4,and 8 weeks after crush) and control group (without injury). The thickness and stiffness of the crushed sciatic nerves and denervated triceps surae muscles were measured at different time points and compared with histopathologic parameters. Inter-reader variability was assessed with intraclass correlation coefficients. Results Compared with the control group,the inner diameters of the sciatic nerves significantly increased in the 2-week CI group [(1.65±0.34) mm vs. (0.97±0.15) mm,P=0.00] but recovered to the nearly normal level in the 8-week CI group [(1.12±0.18) mm vs. (0.97±0.15) mm,P=0.06];however,compared with control group [(8.75±1.02)kPa],the elastic modulus of the nerves increased significantly in all the CI groups [2-week:(14.77±2.53) kPa;4-week:(19.12±3.46) kPa;and 8-week:(28.39±5.26) kPa;all P=0.00];pathologically,massive hyperplasia of collagen fibers were found in the nerve tissues. The thickness of denervated triceps surae muscle decreased gradually,and the elastic modulus decreased 2 weeks after injury but increased gradually in the following 6 weeks;pathologically,massive hyperplasia of collagen fibers and adipocytes infiltration were visible,along with decreased muscle wet-weight ratio and muscle fiber cross-sectional area. The inter-reader agreements were good. Conclusion Conventional ultrasound combined with shear-wave elastography is feasible for the quantitative evaluation of the morphological and mechanical properties of crushed nerves and denervated muscles.