Chronological changes of viral shedding in adult inpatients with Omicron infection in Shanghai, China.

Background: Coronavirus disease 2019 (COVID-19) caused by the Omicron variant occurred in Shanghai, China, but its clinical characteristics and virology have not been comprehensively described. Methods: This retrospective cohort study included adult inpatients (≥18 years) diagnosed with COVID-19 at Changhai Hospital. Laboratory and clinical data were obtained from electronic medical records to investigate the clinical characteristics of COVID-19 and the variations in the patients' laboratory indexes were examined. Results: The symptoms of COVID-19 caused by the Omicron variant were relatively mild. Upper respiratory tract specimens yielded higher positive detection rates than lower respiratory tract and intestinal specimens. Peak COVID-19 viral load was reached at the time of admission; quantification cycle (Cq) values increased to approximately 35 after 8.54 days. In vivo viral shedding duration correlated with age and disease severity (p<0.05). The older the patient and the more severe the disease, the longer the duration of viral shedding was. Portion parameters of blood routine, coagulative function, clinical chemistry, and inflammatory factor showed a certain correlation with the SARS-CoV-2 viral load. Conclusions: Virus replication and shedding are rapid in Omicron-positive patients; COVID-19 in these patients is characterized by acute onset, mild symptoms, and fast recovery. Older patients and those with more severe disease demonstrate prolonged virus shedding. Routine hematological indexes can reveal disease severity and help clinically evaluate the patient's condition.

A Pyramid Architecture-Based Deep Learning Framework for Breast Cancer Detection.

Breast cancer diagnosis is a critical step in clinical decision making, and this is achieved by making a pathological slide and gives a decision by the doctors, which is the method of final decision making for cancer diagnosis. Traditionally, the doctors usually check the pathological images by visual inspection under the microscope. Whole-slide images (WSIs) have supported the state-of-the-art diagnosis results and have been admitted as the gold standard clinically. However, this task is time-consuming and labour-intensive, and all of these limitations make low efficiency in decision making. Medical image processing protocols have been used for this task during the last decades and have obtained satisfactory results under some conditions; especially in the deep learning era, it has exhibited the advantages than those in the shallow learning period. In this paper, we proposed a novel breast cancer region mining framework based on deep pyramid architecture from multilevel and multiscale breast pathological WSIs. We incorporate the tissue- and cell-level information together and integrate these into a LSTM model for the final sequence modelling, which successfully keeps the WSIs' integration and is not mentioned by the prevalence frameworks. The experiment results demonstrated that our proposed framework greatly improved the detection accuracy than that only using tissue-level information.

CST: A Multitask Learning Framework for Colorectal Cancer Region Mining Based on Transformer.

Colorectal cancer is a high death rate cancer until now; from the clinical view, the diagnosis of the tumour region is critical for the doctors. But with data accumulation, this task takes lots of time and labor with large variances between different doctors. With the development of computer vision, detection and segmentation of the colorectal cancer region from CT or MRI image series are a great challenge in the past decades, and there still have great demands on automatic diagnosis. In this paper, we proposed a novel transfer learning protocol, called CST, that is, a union framework for colorectal cancer region detection and segmentation task based on the transformer model, which effectively constructs the cancer region detection and its segmentation jointly. To make a higher detection accuracy, we incorporate an autoencoder-based image-level decision approach that leverages the image-level decision of a cancer slice. We also compared our framework with one-stage and two-stage object detection methods; the results show that our proposed method achieves better results on detection and segmentation tasks. And this proposed framework will give another pathway for colorectal cancer screen by way of artificial intelligence.

Regulatory B Cells Dysregulated T Cell Function in an IL-35-Dependent Way in Patients With Chronic Hepatitis B.

Interleukin (IL)-35-secreting B (IL-35+B) cells are critical regulators in autoimmune and infectious diseases and exert suppressive functions in parallel with IL-10-producing B (B10) cells. However, the role of IL-35+B cells in persistent hepatitis B virus (HBV) infection remains unclear. To elucidate the role of IL-35+B cells in the progress of chronic HBV infection, we determined the frequency of IL-35+B cells and their relationship with the classical human regulatory B cell (Breg) subsets, namely, CD19+CD24hiCD38hi and CD19+CD24hiCD27+. Then, the regulatory effect and mechanism of Bregs on effector T cells were investigated in vitro. Here, we found that compared with healthy controls, the frequency of IL-35+B cells was increased in patients with chronic HBV infection and was enriched in human classical Breg subset CD19+CD24hiCD38hi B cells. Moderate correlation was observed between the frequency of IL-35+B cells and alanine aminotransferase levels (Spearman r = 0.401), but only mild correlation was noted between the frequency of IL-35+B cells and HBV DNA level (Spearman r = 0.314). The frequency of IL-35+B cells was negatively correlated with interferon-γ (IFN-γ)-producing CD4+ and CD8+ cells but positively correlated with IL-4-producing T cells. Bregs dysregulated T cell function through an IL-35-dependent mechanism and depended on cell-to-cell contact. In conclusion, IL-35+ B cell was enriched in CD19+CD24hiCD38hi B cell subset during persistent HBV infection and Breg cells exerted dysregulation in T cell function through IL-35 dependent mechanism and depend on cell-to-cell contact. Clinical Trial Registration: www.ClinicalTrials.gov, identifier NCT03734783.

Single-cell RNA sequencing of immune cells in gastric cancer patients.

Cancer immunotherapy has achieved positive clinical responses in the treatment of various cancers, including gastric cancer (GC). In this study, we characterized the heterogeneity of T cells isolated from GC patients at the single-cell level using single-cell RNA sequencing. We identified different immune cell subtypes and their heterogeneous transcription factors and depicted their developmental trajectories. In particular, we focused on exhausted CD8+ cells and Tregs and discovered that, as compared to control, the IRF8 transcription factor was downregulated in CD8+ tumour-infiltrating lymphocytes (TILs) from GC tissues, and that GC patients with lower IRF8 levels in blood CD8+ T cells tended to be a at a more advanced disease stage. These findings provide a theoretical basis for targeted immune therapy in GC.

Comparative Genomic and Regulatory Analyses of Natamycin Production of Streptomyces lydicus A02.

Streptomyces lydicus A02 is used by industry because it has a higher natamycin-producing capacity than the reference strain S. natalensis ATCC 27448. We sequenced the complete genome of A02 using next-generation sequencing platforms, and to achieve better sequence coverage and genome assembly, we utilized single-molecule real-time (SMRT) sequencing. The assembled genome comprises a 9,307,519-bp linear chromosome with a GC content of 70.67%, and contained 8,888 predicted genes. Comparative genomics and natamycin biosynthetic gene cluster (BGC) analysis showed that BGC are highly conserved among evolutionarily diverse strains, and they also shared closer genome evolution compared with other Streptomyces species. Forty gene clusters were predicted to involve in the secondary metabolism of A02, and it was richly displayed in two-component signal transduction systems (TCS) in the genome, indicating a complex regulatory systems and high diversity of metabolites. Disruption of the phoP gene of the phoR-phoP TCS and nsdA gene confirmed phosphate sensitivity and global negative regulation of natamycin production. The genome sequence and analyses presented in this study provide an important molecular basis for research on natamycin production in Streptomyces, which could facilitate rational genome modification to improve the industrial use of A02.

γ-Aminobutyric acid inhibits the proliferation and increases oxaliplatin sensitivity in human colon cancer cells.

γ-Aminobutyric acid (GABA) is a natural non-protein amino acid, which broadly exists in many plant parts and is widely used as an ingredient in the food industry. In mammals, it is widely distributed in central nervous system and non-neural tissues. In addition to a primary inhibitory neurotransmitter in the central nervous system, endogenous GABA content has been found to be elevated in neoplastic tissues in colon cancer. However, the effect of extraneous GABA on colon cancer has rarely been reported. In this study, we found the inhibitory effects of GABA on the proliferation of colon cancer cells (CCCs). The amino acid also suppressed metastasis of SW480 and SW620 cells. To further study the correlated mechanism, we analyzed the changes in cell cycle distribution and found that GABA suppressed cell cycle progression through G2/M or G1/S phase. Furthermore, RNA sequencing analysis revealed GABA-induced changes in the mRNA expression of 30 genes, including EGR1, MAPK4, NR4A1, Fos, and FosB, in all the three types of CCC. Importantly, GABA enhanced the anti-tumor efficacy of oxaliplatin (OXA) in subcutaneous xenograft tumor model in nude mice. The data suggest that GABA inhibits colon cancer cell proliferation perhaps by attenuating EGR1-NR4A1 axis, EGR1-Fos axis, and by disrupting MEK-EGR1 signaling pathway. This work reveals the pharmacological value of GABA derived from food and suggests that exogenous GABA might play an auxiliary role in polychemotherapy of colon cancer.

Adenylate kinase: a novel antigen for immunodiagnosis and subunit vaccine against tuberculosis.

UNLABELLED: Mycobacterium tuberculosis (M.tb)-derived antigens capable of inducing strong cellular and/or humoral responses are potential targets for both immunodiagnosis and vaccine development against tuberculosis (TB). In the present study, we identified adenylate kinase (ADK, Rv0733) as an antigen that induces high cellular and antibody responses in active TB patients. We consequently tested the use of ADK-specific T cells and antibodies as biomarkers for TB diagnosis. The ADK-specific IFN-γ-producing cells detected by ELISPOT assay showed a sensitivity of 85.0 % and specificity of 94.15 % for TB diagnosis while ADK-specific IgG antibody showed a sensitivity of 40.35 % and specificity of 96.43 %. Combining ADK-specific cellular and antibody responses increased the sensitivity to 91.59 % and the specificity to 96.15 %. Immunogenicity and protection against M.tb infection were further tested in a murine model. Immunization with ADK protein elicited strong specific T- and B-cell responses, and provided protection against the virulent H37Rv stain of M.tb resulting in lower bacilli load in the spleens and lungs. More ADK-specific polyfunctional Th1 cells were observed in the lungs when compared to adjuvant-immunized mice. ADK thus may serve as a novel M.tb antigen for TB immunodiagnosis and development of subunit vaccines. KEY MESSAGES: ADK induces strong immune responses both in humans and mice. ADK-specific IFN-γ production and B-cell responses have high potential for TB diagnosis. ADK immunization provides protection against M.tb infection.

A novel, alkali-tolerant thermostable xylanase from Saccharomonospora viridis: direct gene cloning, expression and enzyme characterization.

A xylanase gene, designated Svixyn10A, was cloned from actinomycetes Saccharomonospora viridis and the gene product was characterized. Gene Svixyn10A contains 1,374 bp and encodes a polypeptide of 457 amino acids composed of a glycoside hydrolase family 10 catalytic domain with a putative signal peptide, a short Gly-rich linker and a family 2 carbohydrate-binding module (CBM). The deduced amino acid sequence of SviXyn10A shared the highest identity (57 %) with a hypothetical xylanase from Streptomyces lividans TK24 (ZP_05528201). A recombinant His-tagged xylanase, SviXyn10A was expressed in Escherichia coli BL21 and purified. The optimum pH and temperature for SviXyn10A is 8.0 and 60 °C. Compared with thermophilic and mesophilic counterparts, SviXyn10A was more active at high temperatures, retaining >63 % of its maximum activity at 65-70 °C and ~40 % even at 80 °C. It had broad pH adaptability (>35 % activity at pH 5.0-11.0) and alkali-tolerance (>70 % activity after incubation at pH 8.0-11.0 for 1 h at 37 °C), and was highly thermostable (>75 % activity after incubation at 70 °C for 3 h at pH 8.0). It may be the first alkali-tolerant thermostable xylanase reported from Saccharomonospora. These favorable properties make SviXyn10A a good candidate for application in pulp and paper industries.

Distribution of mosquitoes and mosquito-borne arboviruses in Inner Mongolia, China.

During summers in 2007 and 2008, an investigation was conducted to identify the distribution of mosquitoes and circulation of mosquito-borne arboviruses in Inner Mongolia, China. A total of 10,542 mosquitoes consisting of seven species from the Aedes, Culex, and Anopheles genera were trapped by UV-light traps, and they were sorted into 211 pools according to species, location, and date of collection. The result showed that Aedes dorsalis was the most common species, accounting for 41.0% (4327/10,542) of the total. Culex modestus (17.1%, 1801/10,542) made up the second largest species, followed by Aedes flavidorsalis (16.3%, 1714/10,542). Six virus isolates were obtained from pooled mosquitoes using cell culture and were identified as Tahyna virus (two isolates from Ae. dorsalis and C. modestus), Banna virus (one isolate from C. modestus), and Culex Pipiens pallens Densovirus (three isolates from Aedes caspius) by serological and molecular methods.

[Isolation and identification of Banna virus from mosquito for the first time in Inner Mongolia].

OBJECTIVE: To identify the virus isolated from a mosquito Culex modestus collected from Tongliao city of Inner Mongolia Autonomous Region. METHODS: A strain of virus isolated from mosquito in Tongliao city was identified by serological and molecular biological methods. The nucleotides of the virus isolate were amplified by RT-PCR, and the products were purified and sequenced. Multiple alignment, phylogenetic and amino acid (AA) analysis were carried out by software Clustal X, MEGA4 and MegAlign (DNAStar). RESULTS: The new isolate was identified to be Banna virus by serological and molecular biological methods. Phylogenetic analysis showed that the Chinese isolates were distributed within one cluster. The homologue of nucleotide and amino acid of 12 segments between the new isolate and other strains isolated from China were 89.6%-98.4% and 90.4%-98.6%. CONCLUSION: The virus isolated from Culex modestus in Inner Mongolia belonged to Banna virus, and it is the first time that Banna virus was isolated in this region.

Wheat yellow mosaic virus Widely Occurring in Wheat (Triticum aestivum) in China.

Wheat yellow mosaic virus (WYMV) was identified in 25 of 27 wheat (Triticum aestivum) samples from six provinces in China using reverse-transcription polymerase chain reaction. Wheat spindle streak mosaic virus was not detected. Thus, contrary to previous reports, WYMV was the only bymovirus detected in wheat in China. The cDNA fragments corresponding to coat protein coding regions of five WYMV isolates from China were cloned and sequenced. Deduced amino acid comparison of coat proteins among these five isolates, another Chinese WYMV isolate HC, and one isolate from Japan showed very high sequence conservation, particularly in both the N- and C- termini. However, a highly virulent isolate HC from Henan Province showed four amino acid substitutions in highly conserved amino acid positions which might play a role in its pathogenic variation.