[Interaction between implants and natural teeth in patients with severe periodontitis:a retrospective study]

Objective: To evaluate the clinical outcomes after implant restoration in the posterior region of severe periodontitis patients and to investigate the factors of natural tooth affecting the implant from the perspective of improving natural periodontal health, which may provide a reference for clinical practice. Methods: Fifty-three patients with severe periodontitis who visited the Department of Periodontology at the Affiliated Stomatological Hospital of China Medical University from June 2014 to June 2023 and completed posterior implant treatment with single crown were included, among which were 16 males and 37 females, aged (52.2±8.0) years old, with a total of 136 implants, 135 adjacent natural teeth in the edentulous area. We retrospectively compared the changes of probing depth (PD), bleeding on probing (BOP) and tooth mobility (TM) before and after implant placement. Besides, we explored the effects of the natural periodontal status on PD, BOP and marginal bone loss (MBL) of the implant at the last follow-up examination by univariate analysis and multivariate analysis. Results: Fifty-three patients were followed up for (44.5±14.1) months in average, with longest interval of (8.3±2.7) months. The PD of adjacent natural teeth in the edentulous area improved from 4.3 (3.6, 4.6) mm before implantation to 3.6 (3.2, 4.0) mm in the last review (P<0.01), while the proportion of BOP (+) improved from 69.6% (94/135) before implantation to 46.7% (63/135) in the last review (P<0.01). The proportion of teeth with mobility≥Ⅱ decreased from 15.6% (21/135) to 5.9% (8/135) (P<0.01). The percentage of natural teeth with PD≥4 mm in the same segment improved from 21.0% (13.3%, 26.0%) before implantation to 18.0% (12.0%, 25.0%) in the last review (P<0.05). The BOP (+)% improved from 29.0% (24.0%, 35.0%) before implantation to 23.0% (18.0%, 31.0%) in the last review (P<0.05), and the number of teeth with mobility≥Ⅱ decreased from 0.0 (0.0, 1.0) to 0.0 (0.0, 0.8) (P<0.05). The functional tooth unit score of full natural teeth increased from 8.0 (6.0, 10.0) points before implantation to 12.0 (12.0, 12.0) points in the last review (P<0.01). PD≥4 mm % increased from 11.0% (6.0%, 25.0%) before implantation to 13.0% (3.0%, 21.0%) in the last review (P<0.05) and there was no significant differences in BOP (+)% [(17.0±9.7) % vs (14.6±7.2) %, P>0.05]. The number of teeth with mobility≥Ⅱ decreased from 1.0 (0.0, 1.8) to 0.0 (0.0, 0.8) (P<0.05). Conclusions: Under the premise of regular supportive care, implant restorative treatment in the posterior region of severe periodontitis patients is helpful to improve the PD, BOP and TM of remaining natural teeth. Besides, the stages and grades of periodontitis at initial diagnosis can affect the PD and BOP of implants.

Subverting the Canon: Novel Cancer-Promoting Functions and Mechanisms for snoRNAs

Small nucleolar RNAs (snoRNAs) constitute a class of intron-derived non-coding RNAs ranging from 60 to 300 nucleotides. Canonically localized in the nucleolus, snoRNAs play a pivotal role in RNA modifications and pre-ribosomal RNA processing. Based on the types of modifications they involve, such as methylation and pseudouridylation, they are classified into two main families-box C/D and H/ACA snoRNAs. Recent investigations have revealed the unconventional synthesis and biogenesis strategies of snoRNAs, indicating their more profound roles in pathogenesis than previously envisioned. This review consolidates recent discoveries surrounding snoRNAs and provides insights into their mechanistic roles in cancer. It explores the intricate interactions of snoRNAs within signaling pathways and speculates on potential therapeutic solutions emerging from snoRNA research. In addition, it presents recent findings on the long non-coding small nucleolar RNA host gene (lncSNHG), a subset of long non-coding RNAs (lncRNAs), which are the transcripts of parental SNHGs that generate snoRNA. The nucleolus, the functional epicenter of snoRNAs, is also discussed. Through a deconstruction of the pathways driving snoRNA-induced oncogenesis, this review aims to serve as a roadmap to guide future research in the nuanced field of snoRNA-cancer interactions and inspire potential snoRNA-related cancer therapies.

Quenched lattice fluctuations in optically driven SrTiO3

Crystal lattice fluctuations, which are known to influence phase transitions of quantum materials in equilibrium, are also expected to determine the dynamics of light-induced phase changes. However, they have only rarely been explored in these dynamical settings. Here we study the time evolution of lattice fluctuations in the quantum paraelectric SrTiO3, in which mid-infrared drives have been shown to induce a metastable ferroelectric state. Crucial in these physics is the competition between polar instabilities and antiferrodistortive rotations, which in equilibrium frustrate the formation of long-range ferroelectricity. We make use of high-intensity mid-infrared optical pulses to resonantly drive the Ti-O-stretching mode at 17 THz, and we measure the resulting change in lattice fluctuations using time-resolved X-ray diffuse scattering at a free-electron laser. After a prompt increase, we observe a long-lived quench in R-point antiferrodistortive lattice fluctuations. Their enhancement and reduction are theoretically explained by considering the fourth-order nonlinear phononic interactions to the driven optical phonon and third-order coupling to lattice strain, respectively. These observations provide a number of testable hypotheses for the physics of light-induced ferroelectricity.

Gli1+ Periodontal Mesenchymal Stem Cells in Periodontitis

Periodontal mesenchymal stem cells (MSCs) play a crucial role in maintaining periodontium homeostasis and in tissue repair. However, little is known about how periodontal MSCs in vivo respond under periodontal disease conditions, posing a challenge for periodontium tissue regeneration. In this study, Gli1 was used as a periodontal MSC marker and combined with a Gli1-cre ERT2 mouse model for lineage tracing to investigate periodontal MSC fate in an induced periodontitis model. Our findings show significant changes in the number and contribution of Gli1+ MSCs within the inflamed periodontium. The number of Gli1+ MSCs that contributed to periodontal ligament homeostasis decreased in the periodontitis-induced teeth. While the proliferation of Gli1+ MSCs had no significant difference between the periodontitis and the control groups, more Gli1+ MSCs underwent apoptosis in diseased teeth. In addition, the number of Gli1+ MSCs for osteogenic differentiation decreased during the progression of periodontitis. Following tooth extraction, the contribution of Gli1+ MSCs to the tooth socket repair was significantly reduced in the periodontitis-induced teeth. Collectively, these findings indicate that the function of Gli1+ MSCs in periodontitis was compromised, including reduced contribution to periodontium homeostasis and impaired injury response.

Regulome-wide association study identifies genetically driven accessible regions associated with pancreatic cancer risk

Genome-wide association studies (GWAS) have identified two dozen genetic variants that are associated with the risk of pancreatic ductal adenocarcinoma (PDAC), a deadly malignancy. However, a majority of these variants are located in noncoding regions of the genome, which limits the translation of GWAS findings into clinical applications. The regulome-wide association study (RWAS) is a recently developed method for identifying TF binding-induced accessibility regions for diseases. However, their potential connection to PDAC has yet to be fully explored. We evaluated the associations between genetically predicted levels of chromatin accessibility and risk of PDAC by using pan-cancer chromatin accessibility genetic prediction models. Our analysis included 8275 cases and 6723 controls from the PanScan (I, II, and III) and PanC4 consortia. To further refine our results, we also integrated genes associated to allele-specific accessibility quantitative trait loci (as-aQTL) and TF motifs located in the as-aQTL. We found that 50 chromatin accessibility features were associated with PDAC risk at a false discovery rate (FDR) of less than 0.05. A total of 28 RWAS peaks were identified as conditionally significant. By integrating the results from as-aQTL, motif analysis, and RWAS, we identified candidate causal regulatory elements for two potential chromatin accessibility regions (THCA_89956 and ESCA_89167) that are associated with PDAC risk. Our study identified chromatin accessibility features in noncoding genomic regions that are associated with PDAC risk. We also predicted the associated genes and disrupt motifs. Our findings provide new insights into the regulatory mechanisms of noncoding regions for pancreatic tumorigenesis.

Pan-cancer analyses of bromodomain containing 9 as a novel therapeutic target reveals its diagnostic, prognostic potential and biological mechanism in human tumours

BACKGROUND

Mutations in one or more genes responsible for encoding subunits within the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodelling complexes are found in approximately 25% of cancer patients. Bromodomain containing 9 (BRD9) is a more recently identified protein coding gene, which can encode SWI/SNF chromatin-remodelling complexes subunits. Although initial evaluations of the potential of BRD9-based targeted therapy have been explored in the clinical application of a small number of cancer types, more detailed study of the diagnostic and prognostic potential, as well as the detailed biological mechanism of BRD9 remains unreported.

METHODS

We used various bioinformatics tools to generate a comprehensive, pan-cancer analyses of BRD9 expression in multiple disease types described in The Cancer Genome Atlas (TCGA). Experimental validation was conducted in tissue microarrays and cell lines derived from lung and colon cancers.

RESULTS

Our study revealed that BRD9 exhibited elevated expression in a wide range of tumours. Analysis of survival data and DNA methylation for BRD9 indicated distinct conclusions for multiple tumours. mRNA splicing and molecular binding were involved in the functional mechanism of BRD9. BRD9 may affect cancer progression through different phosphorylation sites or N6 -methyladenosine site modifications. BRD9 could potentially serve as a novel biomarker for diagnosing different cancer types, especially could accurately forecast the prognosis of melanoma patients receiving anti-programmed cell death 1 immunotherapy. BRD9 has the potential to serve as a therapeutic target, when pairing with etoposide in patients with melanoma. The BRD9/SMARCD1 axis exhibited promising discriminative performance in forecasting the prognosis of patients afflicted with liver hepatocellular carcinoma (LIHC) and mesothelioma. Additionally, this axis appears to potentially influence the immune response in LIHC by regulating the programmed death-ligand 1 immune checkpoint. For experimental validation, high expression levels of BRD9 were observed in tumour tissue samples from both lung and colon cancer patients. Knocking down BRD9 led to the inhibition of lung and colon cancer development, likely via the Wnt/β-catenin signalling pathway.

CONCLUSIONS

These pan-cancer study revealed the diagnostic and prognostic potential, along with the biological mechanism of BRD9 as a novel therapeutic target in human tumours.

Single-cell RNA sequencing reveals characteristics of myeloid cells in post-acute sequelae of SARS-CoV-2 patients with persistent respiratory symptoms

Background

Although our understanding of the immunopathology and subsequent risk and severity of COVID-19 disease is evolving, a detailed account of immune responses that contribute to the long-term consequences of pulmonary complications in COVID-19 infection remains unclear. Few studies have detailed the immune and cytokine profiles associated with post-acute sequelae of SARS-CoV-2 infection (PASC) with persistent pulmonary symptoms. The dysregulation of the immune system that drives pulmonary sequelae in COVID-19 survivors and PASC sufferers remains largely unknown.

Results

To characterize the immunological features of pulmonary PASC (PPASC), we performed droplet-based single-cell RNA sequencing (scRNA-seq) to study the transcriptomic profiles of peripheral blood mononuclear cells (PBMCs) from a participant naïve to SARS-CoV-2 (Control) (n=1) and infected with SARS-CoV-2 with chronic pulmonary symptoms (PPASC) (n=2). After integrating scRNA-seq data with a naïve participant from a published dataset, 11 distinct cell populations were identified based on the expression of canonical markers. The proportion of myeloid-lineage cells ([MLCs]; CD14+/CD16+monocytes, and dendritic cells) was increased in PPASC (n=2) compared to controls (n=2). MLCs from PPASC displayed up-regulation of genes associated with pulmonary symptoms/fibrosis, while glycolysis metabolism-related genes were downregulated. Similarly, pathway analysis showed that fibrosis-related (VEGF, WNT, and SMAD) and cell death pathways were up-regulated, but immune pathways were down-regulated in PPASC. Further comparison of PPASC with scRNA-seq data with Severe COVID-19 (n=4) data demonstrated enrichment of fibrotic transcriptional signatures. In PPASC, we observed interactive VEGF ligand-receptor pairs among MLCs, and network modules in CD14+ (cluster 4) and CD16+ (Cluster 5) monocytes displayed a significant enrichment for biological pathways linked to adverse COVID-19 outcomes, fibrosis, and angiogenesis. Further analysis revealed a distinct metabolic alteration in MLCs with a down-regulation of glycolysis/gluconeogenesis in PPASC compared to SARS-CoV-2 naïve samples.

Conclusion

Analysis of a small scRNA-seq dataset demonstrated alterations in the immune response and cellular landscape in PPASC. The presence of elevated MLC levels and their corresponding gene signatures associated with fibrosis, immune response suppression, and altered metabolic states suggests a potential role in PPASC development.

Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Leveraging genome and plasma proteome data from the INTERVAL study, we established and validated models to predict protein levels using genetic variants. By examining 8,275 PDAC cases and 6,723 controls, we identified 40 associated proteins, of which 16 are novel. Functionally validating these candidates by focusing on 2 selected novel protein-encoding genes, GOLM1 and B4GALT1, we demonstrated their pivotal roles in driving PDAC cell proliferation, migration, and invasion. Furthermore, we also identified potential drug repurposing opportunities for treating PDAC.

SIGNIFICANCE

PDAC is a notoriously difficult-to-treat malignancy, and our limited understanding of causal protein markers hampers progress in developing effective early detection strategies and treatments. Our study identifies novel causal proteins using genetic instruments and subsequently functionally validates selected novel proteins. This dual approach enhances our understanding of PDAC etiology and potentially opens new avenues for therapeutic interventions.

Exploring Optimal Biomarker Sources: A Comparative Analysis of Exosomes and Whole Plasma in Fasting and Non-Fasting Conditions for Liquid Biopsy Applications

The study of liquid biopsy with plasma samples is being conducted to identify biomarkers for clinical use. Exosomes, containing nucleic acids and metabolites, have emerged as possible sources for biomarkers. To evaluate the effectiveness of exosomes over plasma, we analyzed the small non-coding RNAs (sncRNAs) and metabolites extracted from exosomes in comparison to those directly extracted from whole plasma under both fasting and non-fasting conditions. We found that sncRNA profiles were not affected by fasting in either exosome or plasma samples. Our results showed that exosomal sncRNAs were found to have more consistent profiles. The plasma miRNA profiles contained high concentrations of cell-derived miRNAs that were likely due to hemolysis. We determined that certain metabolites in whole plasma exhibited noteworthy concentration shifts in relation to fasting status, while others did not. Here, we propose that (1) fasting is not required for a liquid biopsy study that involves both sncRNA and metabolomic profiling, as long as metabolites that are not influenced by fasting status are selected, and (2) the utilization of exosomal RNAs promotes robust and consistent findings in plasma samples, mitigating the impact of batch effects derived from hemolysis. These findings advance the optimization of liquid biopsy methodologies for clinical applications.

Splicing transcriptome-wide association study to identify splicing events for pancreatic cancer risk

A large proportion of the heritability of pancreatic cancer risk remains elusive, and the contribution of specific mRNA splicing events to pancreatic cancer susceptibility has not been systematically evaluated. In this study, we performed a large splicing transcriptome-wide association study (spTWAS) using three modeling strategies (Enet, LASSO and MCP) to develop alternative splicing genetic prediction models for identifying novel susceptibility loci and splicing introns for pancreatic cancer risk by assessing 8275 pancreatic cancer cases and 6723 controls of European ancestry. Data from 305 subjects of whom the majority are of European descent in the Genotype-Tissue Expression Project (GTEx) were used and both cis-acting and promoter-enhancer interaction regions were considered to build these models. We identified nine splicing events of seven genes (ABO, UQCRC1, STARD3, ETAA1, CELA3B, LGR4 and SFT2D1) that showed an association of genetically predicted expression with pancreatic cancer risk at a false discovery rate ≤0.05. Of these genes, UQCRC1 and LGR4 have not yet been reported to be associated with pancreatic cancer risk. Fine-mapping analyses supported likely causal associations corresponding to six splicing events of three genes (P4HTM, ABO and PGAP3). Our study identified novel genes and splicing events associated with pancreatic cancer risk, which can improve our understanding of the etiology of this deadly malignancy.

[Sequence analysis of Paragonimus internal transcribed spacer 2 and cyclooxygenase 1 genes in freshwater crabs in Henan Province]

OBJECTIVE

To investigate the sequences of internal transcribed spacer 2 (ITS2) and cyclooxygenase 1 (COX1) genes of Paragonimus metacercariae in freshwater crabs in Henan Province, identify the species of Paragonimus and evaluate its genetic relationships with Paragonimus isolates from other provinces in China.

METHODS

Freshwater crabs were collected from 8 survey sites in Zhengzhou, Luoyang, Pingdingshan, Nanyang and Jiyuan cities of Henan Province from 2016 to 2021, and Paragonimus metacercariae were detected in freshwater crabs. Genomic DNA was extracted from Paragonimus metacercariae, and the ITS2 and COX1 genes were amplified using PCR assay, followed by sequencing of PCR amplification products. The gene sequences were spliced and aligned using the software DNASTAR, and aligned with the sequences of Paragonimus genes in the GenBank. Phylogenetic trees were created using the MEGA6 software with the Neighbor-Joining method based on ITS2 and COX1 gene sequences, with Fasciola hepatica as the outgroup.

RESULTS

The detection rates of Paragonimus metacercariae were 6.83% (11/161), 50.82% (31/61), 18.52% (5/26), 8.76% (12/137), 14.29% (9/63), 17.76% (19/105), 18.50% (32/173) and 42.71% (41/96) in freshwater crabs from 8 survey sites in Zhengzhou, Luoyang, Pingdingshan, Nanyang and Jiyuan cities of Henan Province, with a mean detection rate of 19.46% (160/822), and a mean infection intensity of 0.57 metacercariae/g. The amplified ITS2 and COX1 gene fragments of Paragonimus were approximately 500 bp and 450 bp in lengths, respectively. The ITS2 gene sequences of Paragonimus metacercariae from 8 survey sites of Henan Province showed the highest homology (99.8% to 100.0%) with the gene sequence of P. skrjabini (GenBank accession number: MW960209.1), and phylogenetic analysis showed that the Paragonimus in this study was clustered into the same clade with P. skrjabini from Sichuan Province (GenBank accession number: AY618747.1), Guangxi Zhuang Autonomous Region (GenBank accession number: AY618729.1) and Hubei Province (GenBank accession number: AY618751.1), and P. miyazaki from Fujian Province (GenBank accession number: AY618741.1) and Japan (GenBank accession number: AB713405.1). The COX1 gene sequences of Paragonimus metacercariae from 8 survey sites of Henan Province showed the highest homology (90.0% to 100.0%) with the gene sequence of P. skrjabini (GenBank accession number: AY618798.1), and phylogenetic analysis showed that the Paragonimus in this study was clustered into the same clade with all P. skrjabini and clustered into the same sub-clade with P. skrjabini from Hubei Province (GenBank accession numbers: AY618782.1 and AY618764.1).

CONCLUSIONS

Paragonimus species from freshwater crabs in Henan Province were all characterized as P. skrjabini, and the ITS2 and COX1 gene sequences had the highest homology to those of P. skrjabini from Hubei Province. The results provide insights into study of Paragonimus in Henan Province and China.

sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

Fragments derived from small RNAs such as small nucleolar RNAs are biologically relevant but remain poorly understood. To address this gap, we developed sRNAfrag, a modular and interoperable tool designed to standardize the quantification and analysis of small RNA fragmentation across various biotypes. The tool outputs a set of tables forming a relational database, allowing for an in-depth exploration of biologically complex events such as multi-mapping and RNA fragment stability across different cell types. In a benchmark test, sRNAfrag was able to identify established loci of mature microRNAs solely based on sequencing data. Furthermore, the 5' seed sequence could be rediscovered by utilizing a visualization approach primarily applied in multi-sequence-alignments. Utilizing the relational database outputs, we detected 1411 snoRNA fragment conservation events between two out of four eukaryotic species, providing an opportunity to explore motifs through evolutionary time and conserved fragmentation patterns. Additionally, the tool's interoperability with other bioinformatics tools like ViennaRNA amplifies its utility for customized analyses. We also introduce a novel loci-level variance-score which provides insights into the noise around peaks and demonstrates biological relevance by distinctly separating breast cancer and neuroblastoma cell lines after dimension reduction when applied to small nucleolar RNAs. Overall, sRNAfrag serves as a versatile foundation for advancing our understanding of small RNA fragments and offers a functional foundation to further small RNA research. Availability: https://github.com/kenminsoo/sRNAfrag.

[Acute macular neuroretinopathy: a case report]

A 16-year-old female patient experienced a rapid decline in bilateral visual acuity accompanied by central scotomas for 5 days following coronavirus disease 2019 infection. Ocular examination revealed findings consistent with acute macular neuroretinopathy. Structural en face imaging using optical coherence tomography demonstrated a wedge-shaped lesion with low reflectivity directed towards the fovea in both eyes. B-scan images revealed localized hyperreflective bands involving the outer nuclear layer and photoreceptor layer, with discontinuity of the ellipsoid zone. Based on clinical presentation and examination findings, a diagnosis of bilateral acute macular neuroretinopathy was established.

Effectiveness of various COVID-19 vaccine regimens among 10.4 million patients from the National COVID Cohort Collaborative during Pre-Delta to Omicron periods - United States, 11 December 2020 to 30 June 2022

OBJECTIVE

This study reports the vaccine effectiveness (VE) of COVID-19 vaccine regimens in the United States, based on the National COVID Cohort Collaborative (N3C) database.

METHODS

Data from 10.4 million adults, enrolled in the N3C from 11 December 2020 to 30 June 2022, were analyzed. VE against infection and death outcomes were evaluated across 13 vaccine regimens in recipient cohorts during the Pre-Delta, Delta, and Omicron periods. VE was estimated as (1-odds ratio) × 100% by multivariate logistic regression, using the unvaccinated cohort as reference.

RESULTS

Natural immunity showed a highly protective effect (70.33%) against re-infection, but the mortality risk among the unvaccinated population was increased after re-infection; vaccination following infection reduced the risk of re-infection and death. mRNA-1273 full vaccination plus mRNA-1273 booster showed the highest anti-infection effectiveness (47.59%) (95% CI, 46.72-48.45) in the overall cohort. In the type 2 diabetes cohort, VE against infection was highest with BNT162b2 full vaccination plus mRNA-1273 booster (61.19%) (95% CI, 53.73-67.75). VE against death was also highest with BNT162b2 full vaccination plus mRNA-1273 booster (89.56%) (95% CI, 85.75-92.61). During the Pre-Delta period, all vaccination regimens showed an anti-infection effect; during the Delta period, only boosters, mixed vaccines, and Ad26.COV2.S vaccination exhibited an anti-infection effect; during the Omicron period, none of the vaccine regimens demonstrated an anti-infection effect. Irrespective of the variant period, even a single dose of mRNA vaccine offered protection against death, thus demonstrating survival benefit, even in the presence of infection or re-infection. Similar patterns were observed in patients with type 2 diabetes.

CONCLUSIONS

Although the anti-infection effect declined as SARS-CoV-2 variants evolved, all COVID-19 mRNA vaccines had sustained effectiveness against death. Vaccination was crucial for preventing re-infection and reducing the risk of death following SARS-CoV-2 infection.

Long-Term Anorectal Function in Rectal Cancer Patients Managed by a Watch-and-Wait Strategy after Neoadjuvant Therapy: A Cross-Sectional Study

PURPOSE/OBJECTIVE(S)

Rectal cancer patients reaching complete clinical response (cCR) after neoadjuvant chemoradiotherapy can be offered a nonoperative watch-and-wait (W&W) strategy. As evidence of good oncological outcomes accumulates, the functional outcomes remain less explored. The aim of this study is to comprehensively assess the long-term rectal toxicity and anorectal function in patients managed by a W&W strategy and to investigate the clinical risk factors for anorectal dysfunction.

MATERIALS/METHODS

Seventy W&W patients who were disease-free at the moment of recruitment were included. A minimum 2-year follow-up was considered. We graded late rectal toxicity according to the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer (RTOG/EORTC) scale and the Late Effects of Normal Tissue/Subjective Objective Management Analytic (LENT/SOMA) system. Long-term anorectal function was assessed with the Wexner score, the Low Anterior Resection Syndrome score (LARS score), and the Memorial Sloan Kettering Bowel Function Instrument (MSK BFI).

RESULTS

All patients received standard chemoradiotherapy consisting of a total dose of 5000 cGy in 25 fractions. The median tumor distance from the anal verge was 3 (IQR 2-4) cm. After a median follow-up of 43 (IQR 28-66) months, less than half of patients developed Grade 1 (40.0%) or Grade 2 (1.4%) late rectal toxicity, and no patients complained of higher grades. LENT/SOMA criteria also identified more patients with mild symptoms. The most frequent symptoms were sphincter control problems, mainly manifested as fecal urgency, reported by 60.0% of patients. For long-term anorectal function, the median LARS score was 16 (IQR 4-25). 17.1% of patients reported minor LARS and 15.7% reported major LARS. The median Wexner score was 2 (IQR 0-3). The median MSK BFI total score was 82 (IQR 77-86). Smoking history was an independent risk factor for anorectal dysfunction in multivariate analyses (OR = 6.491, 95% CI 1.536-27.432).

CONCLUSION

Rectal cancer patients managed by a watch-and-wait strategy after neoadjuvant chemoradiotherapy have retained satisfactory anorectal function. However, fecal urgency might be a common problem. Smoking history was an independent risk factor for long-term anorectal dysfunction. Prospective studies with emphasis on bowel function outcomes containing a larger number of patients are needed.

Analysis of Institutional DIBH Coaching Program for Surface Guided-DIBH Patients

PURPOSE/OBJECTIVE(S)

Our institute has implemented a surface guided-DIBH (SG-DIBH) coaching program which involves consultation, pre-treatment (CT-sim) and treatment. We would like to analyze the effectiveness of the program.

MATERIALS/METHODS

A total of 72 left breast cancer patients between 1st Apr 2022 to 9th Dec 2022 were registered for radiation treatment. During consultation, oncologist selected suitable patients based on the following criteria: a) age of 18-70; b) left breast cancer, right breast cancer with internal mammary nodes irradiation or dextrocardia; c) no lung/cardiac disease history & d) volunteer for SG-DIBH technique. The eligible patients were then trained by the coaching therapist using a teaching video and practiced at home. During CT simulation, patients were assessed according to the DIBH evaluation form. The evaluation components included patient's compliancy and understanding, the differences of lateral skin marking (free breathing, FB vs DIBH), duration of breath hold and reproducibility. Patients who passed the evaluation were scanned under both FB and DIBH for SG-DIBH treatment. IMRT-FFF 6 to 7 fields were planned. During SG-DIBH treatment, first 3 fractions and weekly CBCT were taken. Patients were encouraged to continue DIBH practice at home throughout whole course of the treatment and they were given 3 identical survey forms (5 questions) at the beginning, middle and end of treatment. The measure for the success of this coaching program would be number of breath-holds, duration of treatment time, treatment accuracy (CBCT matching) and survey results.

RESULTS

There were 48 patients who were eligible for DIBH coaching program, however, only 24 patients had passed the coaching evaluation and 20 patients were treated with SG-DIBH technique successfully. The mean of number of breath-hold and treatment time was 7 times and 7.9 minutes. Total of 123 CBCT images were studied. The setup errors were (0.242±0.180) cm, (0.152±0.137) cm, (0.202±0.165) cm, (0.684±0.640) degrees, (0.816±0.767) degrees, (0.912±0.707) degrees in lateral, longitudinal, vertical, pitch, roll and yaw directions. According to the survey analysis, the number of times to practice at home decreased as the treatment went by. An improvement was seen in patients' self-evaluation in mastering DIBH technique with proper coaching program (from 60% to 90%). Patients' anxiety in performing DIBH were alleviated greatly towards the end of the treatment (from 47% to 15%). 100% of the patients were willing to go for DIBH treatment if given a second chance and additional suggestions claimed that professional clinical teams and coaching program were important for their DIBH treatment journey.

CONCLUSION

A comprehensive DIBH coaching program can effectively identify SG-DIBH patient's suitability. Patient compliancy, treatment accuracy and treatment experience can be enhanced with good coaching program. The involvement of clinical team from consultation to pre-treatment and treatment stage is essential for a successful SG-DIBH treatment.

Vanishing RKKY interactions in Ce-based cage compounds

We report the results of thermodynamic measurements in external magnetic field of the cubic Ce-based cage compounds CeT2Cd20(T= Ni,Pd). Our analysis of the heat-capacity data shows that the Γ7doublet is the ground state multiplet of the Ce3+ions. Consequently, for the Γ7doublet it can be theoretically shown that the Ruderman-Kittel-Kasuya-Yosida interaction between the localized Ce moments mediated by the conduction electrons, must vanish at temperatures much lower than the energy separating the ground state doublet from the first excited Γ8quartet. Our findings provide an insight as to why no long range order has been observed in these compounds down to temperatures in the milliKelvin range.

sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

Fragments derived from small RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood, calling for more comprehensive methods for analysis. We developed sRNAfrag, a standardized workflow and set of scripts to quantify and analyze sRNA fragmentation of any biotype. In a benchmark, it is able to detect loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5' seed sequence of miRNAs which we believe may extraoplate to other small RNA fragments. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.

Pediatric infection with the Omicron variant increases the risks of febrile seizures among COVID-19 infected children

Background

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is less likely to cause severe disease in children than the other variants but has become an increasing cause of febrile seizures (FS) among children. In this case-control study, we aimed to examine the risk factors associated with FS in children infected with the COVID-19 Omicron variant and related treatment modalities.

Methods

This retrospective case-control study includes 113 subjects infected with the COVID-19 Omicron variant, grouped into 45 cases (those with FS) and 68 controls (those without FS). Data on clinical features, laboratory parameters, and treatment modalities were collected and analyzed.

Results

Approximately 5.74% of COVID-19 infected children developed COVID-19-associated FS. Children with COVID-19 and high body temperatures [RR 1.474; (95% CI: 1.196-1.818), p < 0.001], previous history of FS [RR 1.421; (95% CI: 1.088-1.855), p = 0.010], high procalcitonin levels [RR 1.140; (95% CI: 1.043-1.246), p = 0.048] and high neutrophil counts [RR 1.015; (95% CI: 1.000-1.029), p = 0.048] were more likely to experience FS than the controls. In contrast, children with COVID-19 and low eosinophil counts, low hemoglobin levels, and cough had a lower risk of developing FS [RR 0.494; (95% CI: 0.311-0.783), p = 0.003], [RR 0.979; (95% CI: 0.959-0.999), p = 0.044]; and [RR 0.473 (95% CI 0.252-0.890), p = 0.020]; respectively. Children with FS received more anti-flu medications than those without.

Conclusion

A significant increase in FS was observed in children with Omicron SARS-CoV-2 infection. A higher body temperature, a history of FS, a higher procalcitonin level, and a high neutrophil count were all associated with an increased risk of FS in children with COVID-19. The risk of developing FS was lower in children with COVID-19 and low eosinophil counts and hemoglobin levels than in those without.

[Clinical characteristics and risk factors for bronchoscopic airway mucus hypersecretion in childhood pneumonia infected by different pathogens]

Objective: To investigate the risk factors for airway mucus hypersecretion in childhood pneumonia infected by different pathogens. Method: A retrospective cohort included 968 children who were hospitalized for Mycoplasma pneumoniae pneumonia (MPP), respiratory syncytial virus (RSV) pneumonia, adenovirus pneumonia and underwent bronchoscopy in Respiratory Department of Children's Hospital of Chongqing Medical University from January 2019 to December 2021 was conducted. The children were divided into two groups distinguished by airway mucus secretion according to the airway mucus hypersecretion score which were scored according to the mucus secretion under the bronchoscope. The demographic characteristics, clinical characteristics, laboratory tests and disease severity of the two groups were compared. And the risk factors for the development of airway mucus hypersecretion in two groups were analyzed. Chi square test, Mann-Whithey U test and Fisher exact test were used to analyze the differences between the two groups, and multivariate Logistic regression was used to analyze the influencing factors. Result: There were 559 males and 409 females in the 968 children, with an age of 4.0 (1.4, 6.0) years. Among the 642 children with MPP, 185 cases were in the hypersecretion group and 457 cases were in the non-hypersecretion group. There were 41 cases in the hypersecretion group and 160 cases in the non-hypersecretion group of 201 children with RSV pneumonia. In the 125 children with adenovirus pneumonia, there were 39 cases in the hypersecretion group and 86 cases in the non-hypersecretion group. In these children, the age of children in the hypersecretion group was older than that in the non-hypersecretion group (6.0 (4.0, 7.0) vs. 5.0 (3.0, 7.0) years old, 1.5 (0.5, 3.6) vs. 0.8 (0.4, 1.6) years old, 2.0 (1.2, 4.5) vs. 1.3 (0.8, 2.0) years old, U=35 295.00, 2 492.00, 1 101.00, all P<0.05). Through multivariate Logistic regression analysis it found that increased risk of airway mucus hypersecretion was present in childhood MPP with increase in peripheral blood white blood cell count (OR=3.30, 95%CI 1.51-7.93, P=0.004) or increase in neutrophil ratio (OR=2.24, 95%CI 1.16-4.33, P=0.016) or decrease in lymphocyte count (OR=3.22, 95%CI 1.66-6.31, P<0.001) or decrease in serum albumin (OR=2.00, 95%CI 1.01-3.98, P=0.047). The risk of airway mucus hypersecretion was increased in children with RSV pneumonia combined with elevated peripheral blood eosinophils (OR=3.04, 95%CI 1.02-8.93, P=0.043). Meanwhile, airway mucus hypersecretion was associated with severe pneumonia (OR=2.46, 95%CI 1.03-6.15, P=0.047) in children with RSV pneumonia. Older age was associated with increased risk of airway mucus hypersecretion in children with adenovirus pneumonia (OR=1.02, 95%CI 1.00-1.04, P=0.026). In these children with occurrence of pulmonary rales, wheezes or sputum sounds (OR=3.65, 95%CI 1.22-12.64, P=0.028) had an increased risk of airway mucus hypersecretion. Neutrophils in bronchoalveolar lavage fluid (BALF) demonstrated higher ratio in hypersecretion group from children with MPP (0.65 (0.43, 0.81) vs. 0.59 (0.34, 0.76), U=24 507.00, P<0.01), while the proportion of macrophages in BALF was lower (0.10 (0.05, 0.20) vs. 0.12 (0.06, 0.24), U=33 043.00, P<0.05). Nucleated cell count and neutrophil ratio in BALF were higher in hypersecretion group of children with RSV pneumonia (1 210 (442, 2 100)×10⁶ vs. 490 (210, 1 510)×10⁶/L, 0.43 (0.26, 0.62) vs. 0.30 (0.13, 0.52), U=2 043.00, 2 064.00, all P<0.05). Conclusions: The increase in peripheral blood white blood cell count, neutrophil ratio and decrease in lymphocyte count, serum albumin in children with MPP is related to the development of airway mucus hypersecretion. In children with RSV pneumonia, the abnormal increase of eosinophils in peripheral blood has relationship with hypersecretion. The appearance of lung rale, wheezing, and sputum rale are associated with airway mucus hypersecretion in children with adenovirus pneumonia. In addition, local neutrophil infiltration in the respiratory tract is closely related to the occurrence of airway mucus hypersecretion caused by Mycoplasma pneumoniae and RSV infection.

Single-cell RNA sequencing reveals characteristics of myeloid cells in pulmonary post-acute sequelae of SARS-CoV-2

Background

Although our understanding of the immunopathology and subsequent risk and severity of COVID-19 disease is evolving, a detailed account of immune responses that contribute to the long-term consequences of pulmonary complication in COVID-19 infection remain unclear. Few studies have detailed the immune and cytokine profiles associated with post-acute sequalae of SARS-CoV-2 infection with persistent pulmonary symptoms (PPASC). However, the dysregulation of the immune system that drives pulmonary sequelae in COVID-19 survivors and PASC sufferers remains largely unknown.

Results

To characterize the immunological features of pulmonary PASC (PPASC), we performed droplet-based single-cell RNA sequencing to study the transcriptomic profiles of peripheral blood mononuclear cells (PBMCs) from participants naïve to SARS-CoV-2 (Control) and infected with SARS-CoV-2 with chronic pulmonary symptoms (PPASC). We analyzed more than 34,139 PBMCs by integrating our dataset with previously reported control datasets (GSM4509024) cell distribution. In total, 11 distinct cell populations were identified based on the expression of canonical markers. The proportion of myeloid-lineage cells ([MLCs]; CD14 + /CD16 + monocytes and dendritic cells) was increased in PPASC compared to controls. MLCs from PPASC displayed up-regulation of genes associated with pulmonary symptoms/fibrosis, while glycolysis metabolism-related genes were downregulated. Similarly, pathway analysis showed that fibrosis- related ( VEGF , WNT , and SMAD ) and cell death pathways were up-regulated, but immune pathways were down-regulated in PPASC. In PPASC, we observed interactive VEGF ligand- receptor pairs among MLCs, and network modules in CD14 + (cluster 4) and CD16 + (Cluster 5) monocytes displayed a significant enrichment for biological pathways linked to adverse COVID- 19 outcomes, fibrosis, and angiogenesis. Further analysis revealed a distinct metabolic alteration in MLCs with a down-regulation of glycolysis/gluconeogenesis in PPASC compared to SARS- CoV-2 naïve samples.

Conclusion

This study offers valuable insights into the immune response and cellular landscape in PPASC. The presence of elevated MLC levels and their corresponding gene signatures associated with fibrosis, immune response suppression, and altered metabolic states suggests their potential role as a driver of PPASC.

A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk

Prostate cancer (PCa) represents a huge public health burden among men. Many susceptibility genetic factors for PCa still remain unknown. In this study, we performed a large splicing transcriptome-wide association study (spTWAS) using three modeling strategies to develop alternative splicing genetic prediction models for identifying novel susceptibility loci and splicing introns for PCa risk by assessing 79,194 cases and 61,112 controls of European ancestry in the PRACTICAL, CRUK, CAPS, BPC3, and PEGASUS consortia. We identified 120 splicing introns of 97 genes showing an association with PCa risk at false discovery rate (FDR)-corrected threshold (FDR <0.05). Of them, 33 genes were enriched in PCa-related diseases and function categories. Fine-mapping analysis suggested that 21 splicing introns of 19 genes were likely causally associated with PCa risk. Thirty-five splicing introns of 34 novel genes were identified to be related to PCa susceptibility for the first time, and 11 of the genes were enriched in a cancer-related network. Our study identified novel loci and splicing introns associated with PCa risk, which can improve our understanding of the etiology of this common malignancy.

[Uniportal thoracoscopic thorough debridement for tubercular empyema with abscess of the chest wall]

Objective: To examine the feasibility and technical considerations of thorough debridement using uniportal thoracoscopic surgery for tuberculous empyema complicated by chest wall tuberculosis. Methods: A retrospective analysis was conducted on 38 patients who underwent comprehensive uniportal thoracoscopy debridement for empyema complicated by chest wall tuberculosis in the Department of Thoracic Surgery, Shanghai Pulmonary Hospital, from March 2019 to August 2021. There were 23 males and 15 females, aged (M(IQR)) 30 (25) years (range: 18 to 78 years). The patients were cleared of chest wall tuberculosis under general anesthesia and underwent an incision through the intercostal sinus, followed by the whole fiberboard decortication method. Chest tube drainage was used for pleural cavity disease and negative pressure drainage for chest wall tuberculosis with SB tube, and without muscle flap filling and pressure bandaging. If there was no air leakage, the chest tube was removed first, followed by the removal of the SB tube after 2 to 7 days if there was no obvious residual cavity on the CT scan. The patients were followed up in outpatient clinics and by telephone until October 2022. Results: The operation time was 2.0 (1.5) h (range: 1 to 5 h), and blood loss during the operation was 100 (175) ml (range: 100 to 1 200 ml). The most common postoperative complication was prolonged air leak, with an incidence rate of 81.6% (31/38). The postoperative drainage time of the chest tube was 14 (12) days (range: 2 to 31 days) and the postoperative drainage time of the SB tube was 21 (14) days (range: 4 to 40 days). The follow-up time was 25 (11) months (range: 13 to 42 months). All patients had primary healing of their incisions and there was no tuberculosis recurrence during the follow-up period. Conclusion: Uniportal thoracoscopic thorough debridement combined with postoperative standardized antituberculosis treatment is safe and feasible for the treatment of tuberculous empyema with chest wall tuberculosis, which could achieve a good long-term recovery effect.

[Recompensation of complications in patients with hepatitis B virus-related decompensated cirrhosis treated with entecavir antiviral therapy]

Objective: To analyze the occurrence of recompensation conditions in patients with chronic hepatitis B virus-related decompensated cirrhosis after entecavir antiviral therapy. Methods: Patients with hepatitis B virus-related decompensated cirrhosis with ascites as the initial manifestation were prospectively enrolled. Patients who received entecavir treatment for 120 weeks and were followed up every 24 weeks (including clinical endpoint events, hematological and imaging indicators, and others) were calculated for recompensation rates according to the Baveno VII criteria. Measurement data were compared using the Student t-test or Mann-Whitney U test between groups. Categorical data were compared by the χ (2) test or Fisher's exact probability method between groups. Results: 283 of the 320 enrolled cases completed the 120-week follow-up, and 92.2% (261/283) achieved a virological response (HBV DNA 20 IU/ml). Child-Pugh and MELD scores were significantly improved after treatment (8.33 ± 1.90 vs. 5.77 ± 1.37, t = 12.70, P < 0.001; 13.37 ± 4.44 vs. 10.45 ± 4.58, t = 5.963, P < 0.001). During the 120-week follow-up period, 14 cases died, two received liver transplants, 19 developed hepatocellular cancer, 11 developed gastroesophageal variceal bleeding, and four developed hepatic encephalopathy. 60.4% (171/283) (no decompensation events occurred for 12 months) and 56.2% (159/283) (no decompensation events occurred for 12 months and improved liver function) of the patients had achieved clinical recompensation within 120 weeks. Patients with baseline MELD scores > 15 after active antiviral therapy achieved higher recompensation than patients with baseline MELD scores ≤15 [50/74 (67.6%) vs. 109/209 (52.2%), χ (2) = 5.275, P = 0.029]. Conclusion: Antiviral therapy can significantly improve the prognosis of patients with hepatitis B virus-related decompensated cirrhosis. The majority of patients (56.2%) had achieved recompensation. Patients with severe disease did not have a lower probability of recompensation at baseline than other patients.

Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease

Functional heterogeneity of healthy human tissues complicates interpretation of molecular studies, impeding precision therapeutic target identification and treatment. Considering this, we generated a graph neural network with Reactome-based architecture and trained it using 9,115 samples from Genotype-Tissue Expression (GTEx). Our graph neural network (GNN) achieves adjusted Rand index (ARI) = 0.7909, while a Resnet18 control model achieves ARI = 0.7781, on 370 held-out healthy human tissue samples from The Cancer Genome Atlas (TCGA), despite the Resnet18 using over 600 times the parameters. Our GNN also succeeds in separating 83 healthy skin samples from 95 lesional psoriasis samples, revealing that upregulation of 26S- and NUB1-mediated degradation of NEDD8, UBD, and their conjugates is central to the largest perturbed reaction network component in psoriasis. We show that our results are not discoverable using traditional differential expression and hypergeometric pathway enrichment analyses yet are supported by separate human multi-omics and small-molecule mouse studies, suggesting future molecular disease studies may benefit from similar GNN analytical approaches.

[Interpretation of Detection and identification standard of hookworm-Hook-worm larvae coproculture techniques (WS/T 791-2021)]

Detection and identification standard of hookworm-Hookworm larvae coproculture techniques (WS/T 791-2021) is the first recommended technical standard for hookworm detection and species identification using the hookworm larvae coproculture technique in China. This standard was issued on November 23, 2021, and had been in effect since May 1, 2022. This article provides a detailed interpretation pertaining to the background, drafting process, main contents, and dos and don'ts for better understanding and application of this standard among professionals working in disease control and prevention institutions and medical institutions.

[Anatomical and histological investigation of the area anterior to the anorectum passing through the levator hiatus]

Objective: To document the anatomical structure of the area anterior to the anorectum passing through the levator hiatus between the levator ani slings bilaterally. Methods: Three male hemipelvises were examined at the Laboratory of Clinical Applied Anatomy, Fujian Medical University. (1) The anatomical assessment was performed in three ways; namely, by abdominal followed by perineal dissection, by examining serial cross-sections, and by examining median sagittal sections. (2) The series was stained with hematoxylin and eosin to enable identification of nerves, vessels, and smooth and striated muscles. Results: (1) It was found that the rectourethralis muscle is closest to the deep transverse perineal muscle where the longitudinal muscle of the rectum extends into the posteroinferior area of the membranous urethra. The communicating branches of the neurovascular bundle (NVB) were identified at the posterior edge of the rectourethralis muscle on both sides. The rectum was found to be fixed to the membranous urethra through the rectourethral muscle, contributing to the anorectal angle of the anterior rectal wall. (2) Serial cross-sections from the anal to the oral side were examined. At the level of the external anal sphincter, the longitudinal muscle of the rectum was found to extend caudally and divide into two muscle bundles on the oral side of the external anal sphincter. One of these muscle bundles angled dorsally and caudally, forming the conjoined longitudinal muscle, which was found to insert into the intersphincteric space (between the internal and external anal sphincters). The other muscle bundle angled ventrally and caudally, filling the gap between the external anal sphincter and the bulbocavernosus muscle, forming the perineal body. At the level of the superficial transverse perineal muscle, this small muscle bundle headed laterally and intertwined with the longitudinal muscle in the region of the perineal body. At the level of the rectourethralis and deep transverse perineal muscle, the external urethral sphincter was found to occupy an almost completely circular space along the membranous part of the urethra. The dorsal part of the external urethral sphincter was found to be thin at the point of attachment of the rectourethralis muscle, the ventral part of the longitudinal muscle of the rectum. We identified a venous plexus from the NVB located close to the oral and ventral side of the deep transverse perineal muscle. Many vascular branches from the NVB were found to be penetrating the longitudinal muscle and the ventral part of rectourethralis muscle at the level of the apex of the prostate. The rectourethral muscle was wrapped ventrally around the membranous urethra and apex of the prostate. The boundary between the longitudinal muscle and prostate gradually became more distinct, being located at the anterior end of the transabdominal dissection plane. (3) Histological examination showed that the dorsal part of the external urethral sphincter (striated muscle) is thin adjacent to the striated muscle fibers from the deep transverse perineal muscle and the NVB dorsally and close by. The rectourethral muscle was found to fill the space created by the internal anal sphincter, deep transverse perineal muscle, and both levator ani muscles. Many tortuous vessels and tiny nerve fibers from the NVB were identified penetrating the muscle fibers of the deep transverse perineal and rectourethral muscles. The structure of the superficial transverse perineal muscle was typical of striated muscle. These findings were reconstructed three-dimensionally. Conclusions: In intersphincteric resection or abdominoperineal resection for very low rectal cancer, the anterior dissection plane behind Denonvilliers' fascia disappears at the level of the apex of the prostate. The prostate and both NVBs should be used as landmarks during transanal dissection of the non-surgical plane. The rectourethralis muscle should be divided near the rectum side unless tumor involvement is suspected. The superficial and deep transverse perineal muscles, as well as their supplied vessels and nerve fibers from the NVB. In addition, the cutting direction should be adjusted according to the anorectal angle to minimize urethral injury.

[Therapeutic mechanism of Shenbing Decoction Ⅲ for renal fibrosis in chronic kidney disease: a study with network pharmacology, molecular docking and validation in rats]

OBJECTIVE

To observe the effect of Shenbing Decoction Ⅲ for improving renal function and pathology in rats with 5/6 nephrectomy and analyze its therapeutic mechanism for renal fibrosis in chronic kidney disease using network pharmacology combined with molecular docking.

METHODS

Forty male SD rats were randomized into two groups to receive two-staged 5/6 nephrectomy (n=30) or sham operation (n=10), and 2 weeks after the final operation, serum creatinine level of the rats was measured. The rats with nephrectomy were further randomized into Shenbing Decoction Ⅲ group, losartan group and model group for daily treatment with the corresponding drugs via gavage starting at 1 week after 5/6 nephrectomy. After 16 weeks of treatment, serum creatinine and urea nitrogen levels of the rats were measured, and HE staining and Western blotting were used to examine the changes in renal pathology and fibrosis-related factors. Network pharmacology combined with molecular docking study was performed to explore the therapeutic mechanism Shenbing Decoction Ⅲ against renal fibrosis in chronic kidney disease, and Western blotting was used to verify the expressions of the core targets.

RESULTS

Compared with those in the model group, the rats receiving 5/6 nephrectomy and Shenbing Decoction Ⅲ treatment showed significantly reduced serum creatinine and urea nitrogen levels, lessened renal pathologies, and improvement of the changes in epithelial mesenchymal transition-related proteins. Network pharmacological analysis showed that the main active ingredients of Shenbing Decoction Ⅲ were acacetin, apigenin, eupatilin, quercetin, kaempferol and luteolin, and the key targets included STAT3, SRC, CTNNB1, PIK3R1 and AKT1. Molecular docking study revealed that the active ingredients of Shenbing Decoction Ⅲ had good binding activity to the key targets. Western blotting showed that in rats with 5/6 nephrectomy, treatment with Shenbing Decoction Ⅲ obviously restored the protein expression of STAT3, PI3K, and AKT in renal tissue.

CONCLUSION

Shenbing Decoction Ⅲ can reduce renal injury induced by 5/6 nephrectomy in rats, and its therapeutic effects are mediated possibly by its main pharmacologically active ingredients that alleviate renal fibrosis via modulating multiple targets including STAT3, PIK3R1, and AKT1.

SARS-CoV-2 and the host-immune response

The SARS-CoV-2 pandemic and the COVID-19 disease have affected everyone globally, leading to one of recorded history's most significant research surges. As our knowledge evolves, our approaches to the virus and treatments must also evolve. The evaluation of future research approaches to SARS-CoV-2 will necessitate reviewing the host immune response and viral antagonism of that response. This review provides an overview of the current knowledge on SARS-CoV-2 by summarizing the virus and human response. The focuses are on the viral genome, replication cycle, host immune activation, response, signaling, and antagonism. To effectively fight the pandemic, efforts must focus on the current state of research to help develop treatments and prepare for future outbreaks.

Regulation of epidermal growth factor receptor tyrosine kinase inhibitor resistance via Ambra1-mediated autophagy in non-small cell lung cancer

To explore the molecular mechanisms related to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI) resistance, along with potential therapeutic targets and strategies. The autophagy and Beclin 1 regulator 1 (Ambra1) short hairpin ribonucleic acid (shRNA) lentivirus vector and Ambra1 overexpression plasmid, constructed with a plasmid cloning deoxyribonucleic acid (pcDNA) 3.1 vector, were used to down-regulate and up-regulate Ambra1 expression in the human lung adenocarcinoma erlotinib-resistant cell line (PC9/ER), respectively, as well as to screen stable transgenic cell lines. The IC50 of Erlotinib in these cell lines were measured to determine their resistance status. The real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to measure messenger ribonucleic acid (mRNA) expression of resistance-related genes like multidrug resistance protein 1 (MDR1), multidrug resistance-associated protein 1 (MRP1), and lung drug-resistant-related protein (LRP). Western blot was performed to analyze the protein expressions of the autophagy-related genes Beclin 1, LC3II/I, and p62. Each stable transgenic line formed a tumor under the skin in nude mice; the mice with subcutaneous tumorigenesis of PC9/ER cells and shAmbra1-PC9/ER cells were subsequently treated with rapamycin (RAPA) and chloroquine (CQ), respectively. The mRNA expressions of MDR1, MRP1, and LRP in each tumor tissue sample were detected by qRT-PCR. The protein expressions of adenosine monophosphate-activated protein kinase (AMPK), phosphorylated-AMPK (p-AMPK), forkhead box O3 (FoxO3a), and phosphorylated forkhead box O3 (p-FoxO3a) in the AMPK/FoxO3a signaling pathway were analyzed via Western blot. The qRT-PCR result revealed that the level of Ambra1 in EGFR-TKI-resistant cells had increased. This was further exacerbated by the overexpression of Ambra1 and was reduced after its inhibition. Additionally, Ambra1 upregulated the mRNA expression of drug-resistant genes and the expression of autophagy-related proteins. Subcutaneous tumorigenesis of RAPA-treated shAmbra1-PC9/ER cells resulted in increased expression of drug resistance-related genes and a concomitant decrease in p-AMPK and increase in p-FoxO3a. The results revealed that Beclin-1/β-actin, p62/β-actin, and LC3II/I in the model group were all significantly increased compared to the control group, with P<0.05. Compared to the model group, Beclin-1/β-actin, p62/β-actin, and LC3II/I were all significantly higher in the pcDNA-Ambra1 group, with P<0.05. Compared to the model group, Beclin-1/β-actin, p62/β-actin, and LC3II/I were all significantly decreased in the shAmbra1 group, with P<0.05. Thus, these data suggest that Ambra1 promotes cellular autophagy. In addition, subcutaneous tumorigenesis of CQ-treated shAmbra1-PC9/ER cells resulted in reduced expression of drug resistance-related genes, and a concomitant increase in p-AMPK and decrease in p-FoxO3a. The results of this study revealed that Ambra1-mediated autophagy regulated EGFR-TKI resistance in NSCLC, most probably through the AMPK/FoxO3a signaling pathway.

SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database

The coronavirus disease 19 (COVID-19) is a highly pathogenic viral infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in the global pandemic of 2020. A lack of therapeutic and preventive strategies has quickly posed significant threats to world health. A comprehensive understanding of SARS-CoV-2 evolution and natural selection, how it impacts host interaction, and phenotype symptoms is vital to develop effective strategies against the virus. The SARS2Mutant database (http://sars2mutant.com/) was developed to provide valuable insights based on millions of high-quality, high-coverage SARS-CoV-2 complete protein sequences. Users of this database have the ability to search for information on three amino acid substitution mutation strategies based on gene name, geographical zone, or comparative analysis. Each strategy is presented in five distinct formats which includes: (i) mutated sample frequencies, (ii) heat maps of mutated amino acid positions, (iii) mutation survivals, (iv) natural selections and (v) details of substituted amino acids, including their names, positions, and frequencies. GISAID is a primary database of genomics sequencies of influenza viruses updated daily. SARS2Mutant is a secondary database developed to discover mutation and conserved regions from the primary data to assist with design for targeted vaccine, primer, and drug discoveries.

[The correlations between influenza and meteorological factors in 15 cities of northern China, 2008-2020]

Objective: To understand the influence of meteorological factors on the morbidity of influenza in northern cities of China and explore the differences in the influence of meteorological factors on the morbidity of influenza in 15 cities. Methods: The monthly reported morbidity of influenza and monthly meteorological data from 2008 to 2020 were collected in 15 provincial capital cities, including Xi 'an, Lanzhou, Xining, Yinchuan and Urumqi (5 northwestern cities), Beijing, Tianjin, Shijiazhuang, Taiyuan, Hohhot, Ji'nan, Zhengzhou (7 northern cities), Shenyang, Changchun and Harbin (3 northeastern cities). The panel data regression model was applied to conduct quantitative analyze on the influence of meteorological factors on influenza morbidity. Results: The univariate and multivariate panel regression analysis showed that after controlling the population density and other meteorological factors, for each 5 ℃ drop of monthly average temperature, the morbidity change percentage (MCP) of influenza was 11.35%, 34.04% and 25.04% in the 3 northeastern cities, 7 northern cities and 5 northwestern cities, respectively, and the best lag period months was 1, 0 and 1 month; When the monthly average relative humidity decreased by 10%, the MCP was 15.84% in 3 cities in northeastern China and 14.80% in 7 cities in northern China respectively, and the best lag period months was 2 and 1 months respectively; The MCP of 5 cities in northwestern China was 4.50% for each 10 mm reduction of monthly accumulated precipitation, and the best lag period months was 1 month; The MCPs of 3 cities in northeastern China and 5 cities in northwestern China were 4.19% and 5.97% respectively when the accumulated sunshine duration of each month decreased by 10 hours, the best lag period months was 1 month. Conclusions: In northern cities of China from 2008 to 2020, the temperature, relative humidity, precipitation and sunshine duration all had negatively impact on the morbidity of influenza, and temperature and relative humidity were the main sensitive meteorological factors. Temperature had a strong direct impact on the morbidity of influenza in 7 cities in northern China, and relative humidity had a strong lag effect on the morbidity of influenza in 3 cities in northeastern China. The duration of sunshine in 5 cities in northwestern China had a greater impact on the morbidity of influenza compared with 3 cities in northeastern China.

Large-Scale Surveys of Blackleg of Oilseed Rape (Leptosphaeria biglobosa) Revealed New Insights into Epidemics of This Disease in China

Blackleg of oilseed rape caused by Leptosphaeria maculans/L. biglobosa is a worldwide important disease. L. maculans is more virulent than L. biglobosa, so it causes a great concern for oilseed rape production. In China, blackleg (L. biglobosa) of oilseed rape was reported in the 2000s, but epidemiological features of blackleg have not been well elucidated. Moreover, whether L. maculans exists in China is still an open question. Therefore, a 5-year survey was done in China to collect blackleg-occurrence data for characterizing the features of blackleg epidemics and to identify the blackleg pathogens for assessing the risk of L. maculans invasion. The results showed that all the 19 surveyed provinces had blackleg on oilseed rape, and the most frequently occurring provinces are Gansu, Qinghai, Shaanxi, and Hubei. Phoma stem canker was the most common symptom, which was associated with stem cracks on winter oilseed rape and with stem-weevil activities on spring oilseed rape. Temperature and rainfall were the main factors for blackleg epidemics on winter oilseed rape, whereas rainfall was the main factor for blackleg epidemics on spring oilseed rape. Brassica campestris and B. juncea oilseed rapes were more susceptible than B. napus to blackleg. Oilseed rapes cultivated under the continuous dry land-cropping pattern were more prone to blackleg than those cultivated under the paddy land/dry land-cropping pattern. All 6,015 fungal isolates from blackleg plant tissues belonged to L. biglobosa. These results are helpful for understanding the blackleg epidemics of oilseed rapes and for management of this disease in China.

Mitochondria-derived small RNAs as diagnostic biomarkers in lung cancer patients through a novel ratio-based expression analysis methodology

Small non-coding RNAs are potential diagnostic biomarkers for lung cancer. Mitochondria-derived small RNA (mtRNA) is a novel regulatory small non-coding RNA that only recently has been identified and cataloged. Currently, there are no reports of studies of mtRNA in human lung cancer. Currently, normalization methods are unstable, and they often fail to identify differentially expressed small non-coding RNAs (sncRNAs). In order to identify reliable biomarkers for lung cancer screening, we used a ratio-based method using mtRNAs newly discovered in human peripheral blood mononuclear cells. In the discovery cohort (AUC = 0.981) and independent validation cohort (AUC = 0.916) the prediction model of eight mtRNA ratios distinguished lung cancer patients from controls. The prediction model will provide reliable biomarkers that will allow blood-based screening to become more feasible and will help make lung cancer diagnosis more accurate in clinical practice.

Circulating microRNA Biomarker for Detecting Breast Cancer in High-Risk Benign Breast Tumors

High-risk benign breast tumors are known to develop breast cancer at high rates. However, it is still controversial whether they should be removed during diagnosis or followed up until cancer development becomes evident. Therefore, this study sought to identify circulating microRNAs (miRNAs) that could serve as detection markers of cancers arising from high-risk benign tumors. Small RNA-seq was performed using plasma samples collected from patients with early-stage breast cancer (CA) and high-risk (HB), moderate-risk (MB), and no-risk (Be) benign breast tumors. Proteomic profiling of CA and HB plasma was performed to investigate the underlying functions of the identified miRNAs. Our findings revealed that four miRNAs, hsa-mir-128-3p, hsa-mir-421, hsa-mir-130b-5p, and hsa-mir-28-5p, were differentially expressed in CA vs. HB and had diagnostic power to discriminate CA from HB with AUC scores greater than 0.7. Enriched pathways based on the target genes of these miRNAs indicated their association with IGF-1. Furthermore, the Ingenuity Pathway Analysis performed on the proteomic data revealed that the IGF-1 signaling pathway was significantly enriched in CA vs. HB. In conclusion, these findings suggest that these miRNAs could potentially serve as biomarkers for detecting early-stage breast cancer from high-risk benign tumors by monitoring IGF signaling-induced malignant transformation.

[Quality of psychomotility recovery after propofol sedation for painless gastroscopy and colonoscopy]

OBJECTIVE

To study the effect of propofol used for painless gastroscopy and colonoscopy on psychomotility recovery.

METHODS

One hundred adult patients undergoing painless gastroscopy and colonoscopy were recruited, aged 18-72 years, with American Society of Anesthesiologist (ASA) physical status Ⅰ-Ⅱ. According to age, the patients were divided into youth group (20-39 years old, 27 cases), middle age group (40-54 years old, 37 cases), and elder group (55-64 years old, 36 cases). Propofol was continuously infused according to the patients' condition to mantain the bispectal index (BIS) score 55-64. All the patients received psychomotility assesment 30 min before the operations when the discharge criteria were met including number cancellation test, number connection test and board test. The heart rate, blood pressure, saturation of pulse oximetry, electrocardiograph and BIS were monitored during the operation. The operating time, recovery time, total volume of propofol and discharge time were recorded. If the results obtained were inferior to those before operation, a third assessment was taken 30 minutes later until the results recovered or being superior to the baseline levels.

RESULTS

All the patients completed the first and second assessments, and 25 patients had taken the third assessment. There was no statistically significant difference in the results of psychomotility assessment when the patients met the discharge standard. Furthermore, the results were analyzed by grouping with age, and there was no statistical difference in the test results of the youth and middle age groups compared with the preoperative group, among which, the efficiency of the number cancellation test was significantly better than that before operation in the youth group (P < 0.05). However, in the elderly patients the number cancellation efficiency, number connection test and board test were significantly inferior to that before operation (P < 0.05). There was no significant difference in the accuracy of number cancellation compared with that before operation. The patients who needed the third test in the elder group were significantly more than in the other groups (P < 0.05). Compared with the preoperative results, there was no statistical difference in the test results of those who completed the third test.

CONCLUSION

The psychomotility function of the patients who underwent painless gastroscopy and colonoscopy was recovered when they met discharge criteria. The elderly patients had a prolonged recovery period.

[Assessment of intensity of seasonal influenza activity in Beijing-Tianjin-Hebei region, 2019-2021]

Objective: To explore the feasibility of moving epidemic method (MEM) in the assessment of seasonal influenza (influenza) activity intensity from the perspective of urban agglomeration, assess influenza activity intensity in the Beijing-Tianjin-Hebei region from 2019 to 2021 and evaluate the reliability of surveillance data and the effectiveness of the MEM model application. Methods: The weekly reported incidence rate (IR) of influenza and the percentage of influenza-like illness (ILI%) from 2011-2021 in Beijing-Tianjin-Hebei region were collected to establish MEM models respectively. The model fitting effect and the reliability of the two data were evaluated for the purpose of establishing an optimal model to assess the influenza activity intensity in Beijing-Tianjin-Hebei region from 2019-2021. A cross-validation procedure was used to evaluate the performance of the models by calculating the Youden's index, sensitivity and specificity. Results: The MEM model fitted with weekly ILI% had a higher Youden's index compared with the model fitted with weekly IR at both Beijing-Tianjin-Hebei region level and provincial level. The MEM model based on ILI% showed that the epidemic threshold in Beijing-Tianjin-Hebei region during 2019-2020 was 4.42%, the post-epidemic threshold was 4.66%, with medium, high and very high intensity thresholds as 5.38%, 7.22% and 7.84%, respectively. The influenza season during 2019-2020 had 10 weeks (week 50 of 2019 to week 7 of 2020). The influenza season started in week 50 of 2019, and the intensity fluctuated above and below medium epidemic level for six consecutive weeks. The high intensity was observed in week 4 of 2020, the threshold of very high intensity was excessed in week 5, and the intensity gradually declined and became lower than the threshold at the end of the influenza season in week 8. The epidemic threshold was 4.29% and the post-epidemic threshold was 4.35% during 2020-2021. Influenza activity level never excessed the epidemic threshold throughout the year, and no epidemic period emerged. Conclusions: The MEM model could be applied in the assessment of influenza activity intensity in Beijing-Tianjin-Hebei region, and the use of ILI% to assess influenza activity intensity in this region was more reliable than IR data. Influenza activity intensity in Beijing-Tianjin-Hebei region was higher during 2019-2020 but significantly lower in 2020-2021.

Medium Roasting and Brewing Methods Differentially Modulate Global Metabolites, Lipids, Biogenic Amines, Minerals, and Antioxidant Capacity of Hawai'i-Grown Coffee (Coffea arabica)

In the United States, besides the US territory Puerto Rico, Hawai'i is the only state that grows commercial coffee. In Hawai'i, coffee is the second most valuable agricultural commodity. Health benefits associated with moderate coffee consumption, including its antioxidant capacity, have been correlated to its bioactive components. Post-harvest techniques, coffee variety, degree of roasting, and brewing methods significantly impact the metabolites, lipids, minerals, and/or antioxidant capacity of brewed coffees. The goal of our study was to understand the impact of roasting and brewing methods on metabolites, lipids, biogenic amines, minerals, and antioxidant capacity of two Hawai'i-grown coffee (Coffea arabica) varieties, "Kona Typica" and "Yellow Catuai". Our results indicated that both roasting and coffee variety significantly modulated several metabolites, lipids, and biogenic amines of the coffee brews. Furthermore, regardless of coffee variety, the antioxidant capacity of roasted coffee brews was higher in cold brews. Similarly, total minerals were higher in "Kona Typica" cold brews followed by "Yellow Catuai" cold brews. Hawai'i-grown coffees are considered "specialty coffees" since they are grown in unique volcanic soils and tropical microclimates with unique flavors. Our studies indicate that both Hawai'i-grown coffees contain several health-promoting components. However, future studies are warranted to compare Hawai'i-grown coffees with other popular brand coffees and their health benefits in vivo.

Global landscape of SARS-CoV-2 mutations and conserved regions

BACKGROUND

At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management.

METHODS

10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence.

RESULTS

Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively.

CONCLUSION

Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.

[Publication and citation analyses of Chinese Journal of Schistosomiasis Control from 2011 to 2020]

OBJECTIVE

To investigate the publications and citations of Chinese Journal of Schistosomiasis Control from 2011 to 2020, so as to provide insights into improving the journal quality and impact.

METHODS

All publications were retrieved from 60 issues of 10 volumes of Chinese Journal of Schistosomiasis Control from 2011 to 2020, and publication and citation analyses were performed using a bibliometric method.

RESULTS

A total of 1 867 articles were published in Chinese Journal of Schistosomiasis Control from 2011 to 2020, with the largest number in 2012 (220 publications) and the lowest in 2020 (135 publications), and original article (36.48%), control experience (17.14%) and control study (10.34%) were the three most common article type. The overall proportion of grant-supported articles was 59.08% (1 103/1 867), and the number of grant per article was (2.34±1.58) grants. The mean duration from submission to publication was (173.48±105.84) days per article, and there was a significant difference in the mean duration from submission to publication among years (F = 30.883, P < 0.01). Jiangsu Province (492 publications, 26.35%), Shanghai Municipality (264 publications, 14.14%) and Hubei Province (230 publications, 12.32%) were the three most productive provinces where the first author lived, and disease control and prevention institutions were the predominant affiliations of the first author (67.22%), with Jiangsu Institute of Schistosomiasis Control, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, and Wannan Medical College as the three most productive affiliations. The number of authors was 5.94 authors per publication, and the proportion of co-authored publications was 95.45% in Chinese Journal of Schistosomiasis Control from 2011 to 2020. Journal article was the predominant type of cited (89.97%), and the mean number of citations was (15.70±11.56) citations per publication, with a significant difference in the mean number of citations per publication among years (F = 2.205, P < 0.05). The impact factors of Chinese Journal of Schistosomiasis Control ranged from 0.877 to 1.676 during the period from 2011 to 2020, and the overall Price index was 47.59%.

CONCLUSIONS

Both the academic impact and national transmissibility of Chinese Journal of Schistosomiasis Control appeared a tendency towards a rise from 2011 to 2020. Seeking high-quality contributions, increasing interdisciplinary integration, shortening the duration from submission to publication, expanding the coverage of publication services and enhancing impact are the future priorities of the journal.

Exploration of 68Ga-labelled prostate-specific membrane antigen-11 PET/CT parameters for identifying PBRM1 status in primary clear cell renal cell carcinoma

AIM

To investigate the predictive value of ⁶⁸Ga-labelled prostate-specific membrane antigen-11 (⁶⁸Ga-PSMA-11) integrated positron-emission tomography (PET)/computed tomography (CT) in PBRM1-deficient clear cell renal cell carcinoma (ccRCC).

MATERIALS AND METHODS

A total of 41 patients with ccRCC, were enrolled retrospectively and underwent ⁶⁸Ga-PSMA-11 PET/CT preoperatively. Radiological parameters, including CT attenuation value and maximum standard uptake value (SUVmax), were derived. Immunohistochemical and multiple immunofluorescences staining were performed to evaluate the PBRM1 status and immune response. The predictive value of imaging factors was analysed using a receiver operator characteristic curve analysis. Univariate and multivariate logistic regression analyses were used to investigate the relationship between clinical and radiological variables and PBRM1 status.

RESULTS

A total of 41 patients were included in this study, with 14 patients having PBRM1-deficient status. The tumour diameter on imaging and SUVmax differed significantly in patients with different PBRM1 expression statuses and no difference in CT attenuation was identified. Univariate and multivariate logistic regression analyses showed SUVmax was an obvious predictor for identification of PBRM1-deficient tumours. In addition, PBRM1-deficient tumours tended to be accompanied by greater cytotoxic T-cell infiltration, although most of them were in an exhausted state.

CONCLUSIONS

⁶⁸Ga-PSMA-11 PET/CT could be used to discriminate invasive PBRM1-deficient ccRCC.

[Epidemiological features of echinococcosis cases reported in the National Notifiable Disease Report System in Henan Province from 2010 to 2021]

OBJECTIVE

To analyze the epidemiological characteristics of echinococcosis cases reported in the National Notifiable Disease Report System in Henan Province from 2010 to 2011, so as to provide insights into for echinococcosis control and surveillance.

METHODS

The data pertaining to reported echinococcosis cases in Henan Province from 2010 to 2021 were retrieved from the National Notifiable Disease Report System, and a descriptive epidemiological analysis was performed using the software SPSS 22.0.

RESULTS

A total of 150 echinococcosis cases were reported in Henan Province from 2010 to 2021, including 88 confirmed cases (58.67%) and 62 clinically diagnosed cases (41.33%), 77 cases reported by Henan Province (51.33%) and 73 cases reported by other provinces (48.67%). Echinococcosis cases were reported in each month, with 8 to 21 cases reported in each month, and the number of reported echinococcosis cases appeared no remarkable temporal changes. The echinococcosis cases were reported across 18 cities of Henan Province, with the highest number of cases reported in Zhoukou (17.33%) and Nanyang cities (17.33%) and the lowest number reported in Sanmenxia City (0.67%). The reported echinococcosis cases had a male to female ratio of 1.17:1, and the cases were found at each age group, with the the highest number of cases seen at ages of 20 to 59 years (73.33%). Farmer was the predominant occupation (63.33%), followed by housekeepers and the unemployed (12.67%). Of all reported echinococcosis cases, there were 25 local cases (16.67%) and 125 imported cases (83.33%), 144 cases reported by medical institutions (96.00%) and 6 cases reported by centers for disease control and prevention (4.00%).

CONCLUSIONS

Although imported echinococcosis cases were the predominant source of echinococcosis cases reported in the National Notifiable Disease Report System in Henan Province from 2010 to 2021, there were still sporadic local cases, and the emergence of local sources of infection cannot be excluded. Further expanded field surveys and surveillance of echinococcosis are required.

RSK1 and RSK2 serine/threonine kinases regulate different transcription programs in cancer

The 90 kDa ribosomal S6 kinases (RSKs) are serine threonine kinases comprising four isoforms. The isoforms can have overlapping functions in regulation of migration, invasion, proliferation, survival, and transcription in various cancer types. However, isoform specific differences in RSK1 versus RSK2 functions in gene regulation are not yet defined. Here, we delineate ribosomal S6 kinases isoform-specific transcriptional gene regulation by comparing transcription programs in RSK1 and RSK2 knockout cells using microarray analysis. Microarray analysis revealed significantly different mRNA expression patterns between RSK1 knockout and RSK2 knockout cell lines. Importantly some of these functions have not been previously recognized. Our analysis revealed RSK1 has specific roles in cell adhesion, cell cycle regulation and DNA replication and repair pathways, while RSK2 has specific roles in the immune response and interferon signaling pathways. We further validated that the identified gene sets significantly correlated with mRNA datasets from cancer patients. We examined the functional significance of the identified transcriptional programs using cell assays. In alignment with the microarray analysis, we found that RSK1 modulates the mRNA and protein expression of Fibronectin1, affecting cell adhesion and CDK2, affecting S-phase arrest in the cell cycle, and impairing DNA replication and repair. Under similar conditions, RSK2 showed increased ISG15 transcriptional expression, affecting the immune response pathway and cytokine expression. Collectively, our findings revealed the occurrence of RSK1 and RSK2 specific transcriptional regulation, defining separate functions of these closely related isoforms.

Harshening stem cell research and precision medicine: The states of human pluripotent cells stem cell repository diversity, and racial and sex differences in transcriptomes

In vitro investigation on human development, disease modeling, and drug discovery has been empowered by human induced pluripotent stem cell (hiPSC) technologies that form the foundation of precision medicine. Race and sex genetic backgrounds have become a major focus of many diseases modeling and drug response evaluation in the pharmaceutical industry. Here, we gathered data from major stem cell repositories to analyze the diversity with respect to ethnicity, sex, and disease types; and we also analyzed public datasets to unravel transcriptomics differences between samples of different ethnicities and sexes. We found a lack of diversity despite the large sample size of human induced pluripotent stem cells. In the ethnic comparison, the White group made up the majority of the banked hiPSCs. Similarly, for the organ/disease type and sex comparisons, the neural and male hiPSCs accounted for the majority of currently available hiPSCs. Bulk RNA-seq and single-cell transcriptomic analysis coupled with Machine Learning and Network Analysis revealed panels of gene features differently expressed in healthy hiPSCs and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) of different races and sexes. The data highlights the current ethnic and sex inequality in stem cell research and demonstrates the molecular biological diversity of hiPSCs and cardiomyocytes from different races and genders. We postulate that future efforts in stem cell biology, regenerative and precision medicine should be guided towards an inclusive, diverse repository reflecting the prevalence of diseases across racial and ethnic groups and the sexes, important for both common and rare disease modeling, drug screening, and cell therapeutics.

SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents

OBJECTIVE

Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it.

METHODS

In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different.

RESULTS

Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively.

CONCLUSION

According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.

Summary of Year-One Effort of the RCMI Consortium to Enhance Research Capacity and Diversity with Data Science

Despite being disproportionately impacted by health disparities, Black, Hispanic, Indigenous, and other underrepresented populations account for a significant minority of graduates in biomedical data science-related disciplines. Given their commitment to educating underrepresented students and trainees, minority serving institutions (MSIs) can play a significant role in enhancing diversity in the biomedical data science workforce. Little has been published about the reach, curricular breadth, and best practices for delivering these data science training programs. The purpose of this paper is to summarize six Research Centers in Minority Institutions (RCMIs) awarded funding from the National Institute of Minority Health Disparities (NIMHD) to develop new data science training programs. A cross-sectional survey was conducted to better understand the demographics of learners served, curricular topics covered, methods of instruction and assessment, challenges, and recommendations by program directors. Programs demonstrated overall success in reach and curricular diversity, serving a broad range of students and faculty, while also covering a broad range of topics. The main challenges highlighted were a lack of resources and infrastructure and teaching learners with varying levels of experience and knowledge. Further investments in MSIs are needed to sustain training efforts and develop pathways for diversifying the biomedical data science workforce.

[Role of Dipeptidyl peptidase inhibitors in lung ischemia-reperfusion injury]

Lung ischemia-reperfusion injury (LIRI)is a common complication after lung transplantation and cardiopulmonary bypass. It is an important factor affecting the success rate of transplantation. Its specific pathogenesis has not yet been fully elucidated. It is very significant to find the targets and drugs for the prevention and treatment of LIRI in order to improving the utilization rate of "marginal donor lung" and the long-term survival rate of lung transplant patients. Dipeptidyl peptidase 4(DPP4) inhibitors are a class of oral hypoglycemic agents. Previous studies have shown that DPP4 inhibitors have a variety of pharmacological activities, including anti-inflammatory, anti-fibrotic, immunomodulatory and other extrapancreatic functions. Recent studies have shown that DPP4 inhibitors may alleviate LIRI through various mechanisms, including inhibiting inflammatory responses, reducing oxidative stress, regulating blood glucose levels, and activating autophagy. This article reviewed the clinical and preclinical applications and mechanisms of DPP4 inhibitors in LIRI.

Integrated Analysis of Bulk RNA-Seq and Single-Cell RNA-Seq Unravels the Influences of SARS-CoV-2 Infections to Cancer Patients

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious and pathogenic coronavirus that emerged in late 2019 and caused a pandemic of respiratory illness termed as coronavirus disease 2019 (COVID-19). Cancer patients are more susceptible to SARS-CoV-2 infection. The treatment of cancer patients infected with SARS-CoV-2 is more complicated, and the patients are at risk of poor prognosis compared to other populations. Patients infected with SARS-CoV-2 are prone to rapid development of acute respiratory distress syndrome (ARDS) of which pulmonary fibrosis (PF) is considered a sequelae. Both ARDS and PF are factors that contribute to poor prognosis in COVID-19 patients. However, the molecular mechanisms among COVID-19, ARDS and PF in COVID-19 patients with cancer are not well-understood. In this study, the common differentially expressed genes (DEGs) between COVID-19 patients with and without cancer were identified. Based on the common DEGs, a series of analyses were performed, including Gene Ontology (GO) and pathway analysis, protein-protein interaction (PPI) network construction and hub gene extraction, transcription factor (TF)-DEG regulatory network construction, TF-DEG-miRNA coregulatory network construction and drug molecule identification. The candidate drug molecules (e.g., Tamibarotene CTD 00002527) obtained by this study might be helpful for effective therapeutic targets in COVID-19 patients with cancer. In addition, the common DEGs among ARDS, PF and COVID-19 patients with and without cancer are TNFSF10 and IFITM2. These two genes may serve as potential therapeutic targets in the treatment of COVID-19 patients with cancer. Changes in the expression levels of TNFSF10 and IFITM2 in CD14+/CD16+ monocytes may affect the immune response of COVID-19 patients. Specifically, changes in the expression level of TNFSF10 in monocytes can be considered as an immune signature in COVID-19 patients with hematologic cancer. Targeting N⁶-methyladenosine (m6A) pathways (e.g., METTL3/SERPINA1 axis) to restrict SARS-CoV-2 reproduction has therapeutic potential for COVID-19 patients.