Effect of Layered Double Hydroxides on the Deterioration Process of Cement Paste under Sulfate Attack

This study investigated the effect of layered double hydroxides (LDHs) on the deterioration process of cement paste in the sulfate environment. Cement pastes with the addition of original and calcined LDHs at 2.5 wt.% and 5.0 wt.% of cement were exposed to Na₂SO₄ solution for 360 days. The macroscopic performance of the cement paste was assessed based on mass variation, porosity, compressive strength, and content of sulfate ions. Furthermore, the microhardness, microstructures, and composition of the degraded pastes were examined using Vickers hardness (HV), mercury intrusion porosimetry (MIP), scanning electron microscope (SEM), X-ray diffraction (XRD), and thermogravimetric analysis (TGA). The results indicate that cement paste incorporated with LDHs can mitigate the corrosion caused by sulfate effectively, especially in the case of calcined LDHs (C-LDHs), which primarily increase the adsorption of sulfate. Compared with the control specimen, the 180 d compressive strength loss ratio of specimens with 2.5 wt.% and 5.0 wt.% of C-LDHs decreased by 63.66% and 80.51%, respectively. Moreover, LDHs can reduce the amount of ettringite crystals, densify the microstructure, and refine the pore structure to mitigate the cement paste’s sulfate corrosion significantly. Compared with the control specimen, the 180 d harmful pore volume fraction of specimens laced with 2.5 wt.% and 5.0 wt.% C-LDHs decreased by 43.77% and 54.51%, respectively. In terms of the content of C-LDHs, an optimal content of C-LDHs could ensure the dominant effect of adsorption, while excessive C-LDHs could refine pores. In addition, Vickers hardness has an excellent correlation with compressive strength, which could precisely predict the compressive strength. Moreover, by combining the Vickers hardness distribution and content distribution of sulfate ions, the cross-section of the paste could be classified into four regions to evaluate the deterioration process accurately: the degraded zone, the strengthened zone, the invaded zone, and the intact zone.     

Modeling HPV-Associated Disease and Cancer Using the Cottontail Rabbit Papillomavirus

Approximately 5% of all human cancers are attributable to human papillomavirus (HPV) infections. HPV-associated diseases and cancers remain a substantial public health and economic burden worldwide despite the availability of prophylactic HPV vaccines. Current diagnosis and treatments for HPV-associated diseases and cancers are predominantly based on cell/tissue morphological examination and/or testing for the presence of high-risk HPV types. There is a lack of robust targets/markers to improve the accuracy of diagnosis and treatments. Several naturally occurring animal papillomavirus models have been established as surrogates to study HPV pathogenesis. Among them, the Cottontail rabbit papillomavirus (CRPV) model has become known as the gold standard. This model has played a pivotal role in the successful development of vaccines now available to prevent HPV infections. Over the past eighty years, the CRPV model has been widely applied to study HPV carcinogenesis. Taking advantage of a large panel of functional mutant CRPV genomes with distinct, reproducible, and predictable phenotypes, we have gained a deeper understanding of viral–host interaction during tumor progression. In recent years, the application of genome-wide RNA-seq analysis to the CRPV model has allowed us to learn and validate changes that parallel those reported in HPV-associated cancers. In addition, we have established a selection of gene-modified rabbit lines to facilitate mechanistic studies and the development of novel therapeutic strategies. In the current review, we summarize some significant findings that have advanced our understanding of HPV pathogenesis and highlight the implication of the development of novel gene-modified rabbits to future mechanistic studies.     

A Novel Single-Stranded RNA-Based Adjuvant Improves the Immunogenicity of the SARS-CoV-2 Recombinant Protein Vaccine

The research and development (R&D) of novel adjuvants is an effective measure for improving the immunogenicity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recombinant protein vaccine. Toward this end, we designed a novel single-stranded RNA-based adjuvant, L2, from the SARS-CoV-2 prototype genome. L2 could initiate retinoic acid-inducible gene-I signaling pathways to effectively activate the innate immunity. ZF2001, an aluminum hydroxide (Al) adjuvanted SARS-CoV-2 recombinant receptor binding domain (RBD) subunit vaccine with emergency use authorization in China, was used for comparison. L2, with adjuvant compatibility with RBD, elevated the antibody response to a level more than that achieved with Al, CpG 7909, or poly(I:C) as adjuvants in mice. L2 plus Al with composite adjuvant compatibility with RBD markedly improved the immunogenicity of ZF2001; in particular, neutralizing antibody titers increased by about 44-fold for Omicron, and the combination also induced higher levels of antibodies than CpG 7909/poly(I:C) plus Al in mice. Moreover, L2 and L2 plus Al effectively improved the Th1 immune response, rather than the Th2 immune response. Taken together, L2, used as an adjuvant, enhanced the immune response of the SARS-CoV-2 recombinant RBD protein vaccine in mice. These findings should provide a basis for the R&D of novel RNA-based adjuvants.     

Avian Reovirus σB Interacts with Caveolin-1 in Lipid Rafts during Dynamin-Dependent Caveolae-Mediated Endocytosis

Caveolin-1 (Cav-1) is the basic component of caveolae, a specialized form of lipid raft that plays an essential role in endocytic viral entry. However, the evidence of direct involvement of caveolae and Cav-1 in avian reovirus (ARV) entry remains insufficient. In this study, the membrane lipid rafts were isolated as detergent-resistant microdomains (DRMs) by sucrose gradient centrifugation, and the capsid protein σB of ARV was found to associate with Cav-1 in DRMs fractions. Additionally, the interaction between ARV σB protein and Cav-1 was demonstrated by immunofluorescence co-localization and co-immunoprecipitation assays. Furthermore, we found that the internalization of ARV is sensitive to caveolae and dynamin inhibitors, while it is insensitive to clathrin inhibitors. In conclusion, these results indicate that the ARV σB protein interacts with Cav-1 during dynamin-dependent caveolae-mediated endocytosis for the entry of ARV.     

Development and validation of a prognostic model related to pyroptosis-related genes for esophageal squamous cell carcinoma using bioinformatics analysis

BackgroundEsophageal squamous cell carcinoma (ESCC) is one of the most lethal malignant tumors worldwide, and a larger number of ESCC patients have unsatisfactory overall survival (OS) rates. While pyroptosis participates in the development of a variety of malignancies, the function of pyroptosis-related genes (PRGs) in ESCC is still obscure. The aim of this study was to construct the pyroptosis-related prognostic model for ESCC, which will be developed to stratify the risk hazards of ESCC patients and to provide theoretical evidence for individualized treatment.MethodsRNA-seq data of ESCC were download from the NCBI Gene Expression Omnibus (GEO) database. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to explore the potential biological functions or pathways. OS was considered as the primary prognosis outcome in this study. The riskscore was constructed by Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis. The pyroptosis-related prognostic model was constructed based on all independent prognostic factors and verified by C-index, Receiver operating characteristic (ROC) curves, and Calibration curves, and the role of the riskscore in ESCC immunotherapy was evaluated by the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm.ResultsThe current study found 31 differentially expressed PRGs (P<0.001), and functional enrichment analysis showed these PRGs were enriched in positive regulation of cytokine production, interleukin-1 beta production. Univariate and multivariate Cox regression analysis were applied to validate that the riskscore based on four prognostic PRGs (HMGB1, IL-18, NLRP7, and PLCG1) was an independent prognostic factor for ESCC, and the C-index of prognostic model related to the riskscore (C-index =0.705) was higher than that of tumor node metastasis (TNM) stage (0.620). The low-risk group showed a better efficacy of immune checkpoint inhibitors.ConclusionsThe riskscore related to PRGs was one of the independent prognostic factors for ESCC. Moreover, the prognostic model related to the riskscore could be used to predict the OS of ESCC patients effectively. However, there still were several limitations in this study, such as no external validation sample. In summary, our data provides a novel perspective in exploring the potential prognostic biomarkers of ESCC.     

A retrospective comparative cohort study on the efficacy and safety of bi-port robotic-assisted lobectomy and multi-port robotic-assisted lobectomy

BackgroundThe pursuit of less surgical incisions brings better postoperative experience of patients and earns extensive popularity recently. As the update to the da Vinci robotic surgical system has reduced the size of the robotic arm, a new surgical method with fewer ports has become feasible. We performed 20 cases of robotic surgery with only 2 ports and compared the efficacy and safety between bi-port robotic-assisted lobectomy and multi-port robotic-assisted lobectomy.MethodsTo compare the efficacy and safety of the different surgery strategies, we retrospectively reviewed 20 cases of bi-port robotic-assisted thoracic surgery (RATS) and 40 cases of multi-port RATS which were performed at the Shanghai Chest Hospital Between February 2021 and May 2021. The baseline characteristics and their perioperative data were collected and analyzed. Chest tube drainage, chest tube removal time, lymphadenectomy outcomes, operation duration were collected to compare the efficacy of the two groups and blood loss, perioperative complications were recorded to value the safety.ResultsA total of 60 surgeries in the 2 groups were successfully completed. The baseline characteristics in terms of sex, age, health statues were comparable (P≥0.05). The maximum diameter of the tumor in the bi-port surgery group was 0.5–3.6 cm (2.0±1.0) vs. 0.5–4.0 cm (1.9±0.9) cm in the control group. No significant difference was discovered in terms of tumor location, tumor maximum diameter, tumor histology. The intraoperative blood loss was 60.0±20.5 mL and the average operation time was 95.6±21.4 min in the bi-port surgery group compared to 65.0±30.4 mL and 101.4±25.0 min in the control group. An average of 6.0±1.4 lymph nodes were collected in the bi-port surgery group with a mean diameter of 1.2±0.4 cm, and in the control group, an average of 6.1±1.6 lymph nodes were collected with a mean diameter was 1.2±0.5 cm. The average time of chest drainage was 4.3±1 vs. 5.1±1.3 days in the bi-port surgery group and control group. No statistical significance was found between the two groups (P>0.05).ConclusionsCompared to multi-port RATS, Bi-port robotic-assisted lobectomy was safe and showed promising efficacy in patients with early staged operable lung cancer.     

Mushroom Polysaccharides as Potential Candidates for Alleviating Neurodegenerative Diseases

Neurodegenerative diseases (NDs) are a widespread and serious global public health burden, particularly among the older population. At present, effective therapies do not exist, despite the increasing understanding of the different mechanisms of NDs. In recent years, some drugs, such as galantamine, entacapone, riluzole, and edaravone, have been proposed for the treatment of different NDs; however, they mainly concentrate on symptom management and confer undesirable side effects and adverse reactions. Therefore, there is an urgent need to find novel drugs with fewer disadvantages and higher efficacy for the treatment of NDs. Mushroom polysaccharides are macromolecular complexes with multi-targeting bioactivities, low toxicity, and high safety. Some have been demonstrated to exhibit neuroprotective effects via their antioxidant, anti-amyloidogenic, anti-neuroinflammatory, anticholinesterase, anti-apoptotic, and anti-neurotoxicity activities, which have potential in the treatment of NDs. This review focuses on the different processes involved in ND development and progression, highlighting the neuroprotective activities and potential role of mushroom polysaccharides and summarizing the limitations and future perspectives of mushroom polysaccharides in the prevention and treatment of NDs.     

Local and systemic inflammation triggers different outcomes of tumor growth related to infiltration of anti-tumor or pro-tumor macrophages

Background:Previous evidence suggests inflammation may be a double-edged sword with cancer-promoting and cancer suppressing function. In this study, we explore the impact of local and systemic inflammation on cancer growth.Methods:Female BALB/C mice were subcutaneously implanted with foreign body (plastic plates) to build up a local inflammation and intraperitoneally injected with PolyIC or lipopolysaccharides (LPS) to build up a systemic inflammation, followed by subcutaneous injection of 5 × 10⁵ colon cancer cells. Immunohistochemistry and enzyme linked immunosorbent assay were utilized to detect the Ki67 and interleukin (IL) 6, IL-1β, and monocyte chemoattractant protein-1 expression in the tumor tissues and serum, respectively. The distributions of immune cells and expression of toll-like receptors (TLRs) were evaluated by flow cytometry (FCM) and quantitative real time-polymerase chain reaction.Results:The results showed that local inflammation induced by foreign body implantation suppressed tumor growth with decreased tumor weight (P = 0.001), volume (P = 0.004) and Ki67 index (P < 0.001). Compared with the control group, myeloid-derived suppressive cells sharply decreased (P = 0.040), while CD4⁺ T cells slightly increased in the tumor tissues of the group of foreign body-induced local inflammation (P = 0.035). Moreover, the number of M1 macrophages (P = 0.040) and expression of TLRs, especially TLR3 (P < 0.001) and TLR4 (P < 0.001), were significantly up-regulated in the foreign body group. Contrarily, tumor growth was significantly promoted in LPS or PolyIC-induced systemic inflammation (P = 0.009 and 0.006). FCM results showed M1 type macrophages (P = 0.017 and 0.006) and CD8⁺ T cells (P = 0.031 and 0.023) were decreased, while M2 type macrophages (P = 0.002 and 0.007) were significantly increased in tumor microenvironment of LPS or PolyIC-induced systemic inflammation group. In addition, the decreased expression of TLRs was detected in LPS or PolyIC group.Conclusions:The foreign body-induced local inflammation inhibited tumor growth, while LPS or PolyIC- induced systemic inflammation promoted tumor growth. The results suggested that the different outcomes of tumor growth might be attributed to the infiltration of anti-tumor or pro-tumor immune cells, especially M1 or M2 type macrophages into tumor microenvironment.     

Epigenetic analysis of cell-free DNA by fragmentomic profiling

Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5′ ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson’s absolute r > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.

Fragmentation patterns of cell-free DNA (cfDNA) molecules contain a wealth of molecular information related to their tissues of origin (1). For instance, compared with the background DNA molecules that are mainly derived from the hematopoietic system (2, 3), size shortening of fetal and tumoral DNA molecules occurs in the plasma DNA of pregnant women and cancer patients, respectively (4–6). In addition, a series of 10-bp periodicities were present in fetal and tumoral DNA molecules below 146 bp, with a relative reduction in the major peak at 166 bp (1). Such characteristic size profiles suggest that the fragmentation of cfDNA may be associated with nucleosome structures (5, 7). Many important characteristics pertaining to cfDNA fragmentation have been unveiled recently, such as nucleosome footprints (8, 9), fragment end motifs (10), preferred ends (7, 11), and jagged ends (12), which are examples of fragmentomic markers (1).cfDNA fragmentomics is an emergent and actively pursued area, with wide-ranging biological and clinical implications. It has been reported that the use of fragmentation patterns of cfDNA could inform the expression status of genes (13, 14). Using mouse models, DNA nucleases (e.g., DNASE1L3) were found to play important roles in the generation of plasma DNA molecules (15, 16). Fragmentomic features, such as cfDNA end motifs and jagged ends, were further demonstrated to be useful for monitoring DNA nuclease activities, providing biomarkers for autoimmune diseases (e.g., systemic lupus erythematosus) (17, 18). In addition, the deficiencies of nuclease activities in a mouse model resulted in altered DNA methylation profiles of plasma DNA molecules (19). However, how cfDNA fragmentation patterns interplay with DNA methylation in human individuals under different pathophysiological conditions, such as pregnancy and oncogenesis, and in healthy patients without nuclease deficiency, is unknown. It is also not known whether fragmentomic features can be used to deduce cfDNA methylation status.A widely employed way to assess DNA methylation is through bisulfite sequencing (20). A key limitation of this approach is the severe degradation of DNA molecules caused by the bisulfite treatment (21), which greatly increases the sampling variation when analyzing rare target molecules (e.g., tumoral cfDNA at early stages of cancer). Many efforts have been made toward overcoming this issue. For example, Vaisvila et al. developed enzymatic methyl sequencing for which DNA molecules were treated using tet methylcytosine dioxygenase 2 and T4 phage β-glucosyltransferase, followed by the apolipoprotein B mRNA editing enzyme catalytic subunit 3A (APOBEC3A) treatment. Cytosine conversion based on enzymatic processes was reported to be much less destructive (22). Recently, researchers developed approaches making use of third-generation sequencing technologies such as single-molecule real-time sequencing (Pacific Biosciences) (23) and nanopore sequencing (24) to analyze cytosine-phosphate-guanine (CpG) methylation patterns in native DNA molecules, theoretically overcoming the above-mentioned limitation. However, compared with second-generation sequencing (also called next-generation sequencing [NGS]) technologies, the throughput of third-generation sequencing technologies is generally lower and the sequencing cost per nucleotide (nt) is much higher, thus restricting its immediate application in clinical settings. Here, we explore the feasibility of enabling the assessment of DNA methylation using fragmentomic characteristics of cfDNA molecules deduced from NGS results without the use of bisulfite or enzymatic treatment. If successful, such an approach could leverage the high throughput of NGS while obviating the use of chemical/enzymatic conversion and could potentially be readily integrated into currently used NGS-based platforms for cfDNA analysis.In this study, we utilize the fragmentation patterns proximal to a CpG site for deducing its methylation status. The fragmentation pattern is depicted by the frequency of cfDNA fragment ends at each position within a certain nt range relative to a CpG of interest, termed a cleavage profile (Fig. 1). Such a cleavage profile varies according to the methylation status of the CpG site of interest, providing the basis for methylation analysis by using fragmentomic features. We further correlated two types of end motifs (CGN and NCG; N represents any nucleotide of A, C, G, or T) resulting from differential cutting in the measurement window related to DNA methylation, attempting to construct a simplified approach for methylation analysis. Modeling CpG methylation using cfDNA fragmentation may facilitate noninvasive prenatal testing, cancer detection, and tissue-of-origin analysis (Fig. 1). Furthermore, we explore the feasibility of using deep learning to deduce the methylation status at single CpG resolution through the cleavage profile (Fig. 1). We refer to this FRAGmentomics-based Methylation Analysis as FRAGMA in this study.Open in a separate windowFig. 1.Schematic for FRAGMA of cfDNA molecules. cfDNA molecules were sequenced by massively parallel sequencing and aligned to the human reference genome. The cleavage proportion within an 11-nt window (the cleavage measurement window) was used to measure the cutting preference of cfDNA molecules. The patterns of cleavage proportion within a window (the cleavage profile) depended on the methylation status of one or more CpG sites associated with that window. For example, a methylated CpG site might confer a higher probability of cfDNA cutting at the cytosine in the CpG context, but an unmethylated site might not. Such methylation-dependent differential fragmentation within a cleavage measurement window resulted in the change in CGN/NCG motif ratio. Thus, the CGN/NCG motif ratio provided a simplified version for reflecting CpG methylation, allowing cfDNA tissue-of-origin analysis of cfDNA and cancer detection. Furthermore, the great number of cleavage profiles derived from cfDNA molecules might provide an opportunity to train a deep learning model for methylation prediction at the single CpG resolution.