STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization.

Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.

A high-resolution haplotype-resolved Reference panel constructed from the China Kadoorie Biobank Study.

Precision medicine depends on high-accuracy individual-level genotype data. However, the whole-genome sequencing (WGS) is still not suitable for gigantic studies due to budget constraints. It is particularly important to construct highly accurate haplotype reference panel for genotype imputation. In this study, we used 10 000 samples with medium-depth WGS to construct a reference panel that we named the CKB reference panel. By imputing microarray datasets, it showed that the CKB panel outperformed compared panels in terms of both the number of well-imputed variants and imputation accuracy. In addition, we have completed the imputation of 100 706 microarrays with the CKB panel, and the after-imputed data is the hitherto largest whole genome data of the Chinese population. Furthermore, in the GWAS analysis of real phenotype height, the number of tested SNPs tripled and the number of significant SNPs doubled after imputation. Finally, we developed an online server for offering free genotype imputation service based on the CKB reference panel (https://db.cngb.org/imputation/). We believe that the CKB panel is of great value for imputing microarray or low-coverage genotype data of Chinese population, and potentially mixed populations. The imputation-completed 100 706 microarray data are enormous and precious resources of population genetic studies for complex traits and diseases.

Interplay of chronic obstructive pulmonary disease and colorectal cancer development: unravelling the mediating role of fatty acids through a comprehensive multi-omics analysis.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) patients often exhibit gastrointestinal symptoms, A potential association between COPD and Colorectal Cancer (CRC) has been indicated, warranting further examination. METHODS: In this study, we collected COPD and CRC data from the National Health and Nutrition Examination Survey, genome-wide association studies, and RNA sequence for a comprehensive analysis. We used weighted logistic regression to explore the association between COPD and CRC incidence risk. Mendelian randomization analysis was performed to assess the causal relationship between COPD and CRC, and cross-phenotype meta-analysis was conducted to pinpoint crucial loci. Multivariable mendelian randomization was used to uncover mediating factors connecting the two diseases. Our results were validated using both NHANES and GEO databases. RESULTS: In our analysis of the NHANES dataset, we identified COPD as a significant contributing factor to CRC development. MR analysis revealed that COPD increased the risk of CRC onset and progression (OR: 1.16, 95% CI 1.01-1.36). Cross-phenotype meta-analysis identified four critical genes associated with both CRC and COPD. Multivariable Mendelian randomization suggested body fat percentage, omega-3, omega-6, and the omega-3 to omega-6 ratio as potential mediating factors for both diseases, a finding consistent with the NHANES dataset. Further, the interrelation between fatty acid-related modules in COPD and CRC was demonstrated via weighted gene co-expression network analysis and Kyoto Encyclopedia of Genes and Genomes enrichment results using RNA expression data. CONCLUSIONS: This study provides novel insights into the interplay between COPD and CRC, highlighting the potential impact of COPD on the development of CRC. The identification of shared genes and mediating factors related to fatty acid metabolism deepens our understanding of the underlying mechanisms connecting these two diseases.

Single-nucleus chromatin landscapes during zebrafish early embryogenesis.

Vertebrate embryogenesis is a remarkable process, during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis-regulatory elements (CREs) and gene expression within the hierarchy of cell fate decisions. Here, we employed single-nucleus ATAC-seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis, including 3.3 hpf, 5.25 hpf, 6 hpf, 10 hpf, 12 hpf, 18 hpf and 24 hpf, obtained 51,620 high-quality nuclei and 23 clusters. Furthermore, by integrating snATAC-seq data with single-cell RNA-seq data, we described the dynamics of chromatin accessibility and gene expression across developmental time points, which validates the accuracy of the chromatin landscape data. Together, our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.

Effect of evidence-based nursing management of protocol compliance in anticancer drug clinical trial.

Objective: This study aimed to construct evidence-based anticancer drug clinical trial nursing management norms to ensure the safety and quality of clinical trial nursing. Methods: This before-after study was carried out to complete the evidence implementation in a cancer hospital in Shanghai, China. Seven review indicators were developed and reviewed in one phase I clinical trial center and two oncology wards. The corresponding evidence-based intervention program was formulated, and the completion rate of good clinical practice certification, protocol training, delegation of duties, qualification rate of administration, sampling and document recording in anticancer drug clinical trials before and after implementation were compared. Results: After implementation, the completion rate of protocol training, delegation of duties, and the qualification rate of document recording were significantly higher than those of the baseline review, whereas the completion rate of good clinical practice certification and the qualification rate of sampling did not significantly differ from those observed at the baseline review. There was no administration or infusion device-related protocol deviation during the baseline and post reviews. Conclusions: Anticancer drug clinical trial nursing management norms and relevant standard operating procedures were constructed. The results showed that the implementation of this intervention improved the standardization of nurse qualification procedures and the nursing original document recording in anticancer drug clinical trials, and nursing-related protocol deviation could be reduced to a certain extent.

Screening of cell-virus, cell-cell, gene-gene crosstalk among animal kingdom at single cell resolution.

BACKGROUND: The exact animal origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains obscure and understanding its host range is vital for preventing interspecies transmission. METHODS: Herein, we applied single-cell sequencing to multiple tissues of 20 species (30 data sets) and integrated them with public resources (45 data sets covering 26 species) to expand the virus receptor distribution investigation. While the binding affinity between virus and receptor is essential for viral infectivity, understanding the receptor distribution could predict the permissive organs and tissues when infection occurs. RESULTS: Based on the transcriptomic data, the expression profiles of receptor or associated entry factors for viruses capable of causing respiratory, blood, and brain diseases were described in detail. Conserved cellular connectomes and regulomes were also identified, revealing fundamental cell-cell and gene-gene cross-talks from reptiles to humans. CONCLUSIONS: Overall, our study provides a resource of the single-cell atlas of the animal kingdom which could help to identify the potential host range and tissue tropism of viruses and reveal the host-virus co-evolution.

Cell transcriptomic atlas of the non-human primate Macaca fascicularis.

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.

Prechemotherapy nursing assessment among adult cancer patients in a university cancer center in Shanghai, China: a best practice implementation project.

OBJECTIVE: The current implementation project aimed to promote evidence-based practice with prechemotherapy nursing assessment among adult cancer patients in a large university cancer center in Shanghai, China, over a 6-month timeframe. INTRODUCTION: Prechemotherapy nursing assessment is an essential element of cancer patient care, aiming to prevent or minimize potential problems from chemotherapy treatment. Regular comprehensive prechemotherapy assessment is not part of routine care currently in many clinical settings within China. METHODS: The project utilized the JBI approach to implementation, incorporating audit and feedback tools. Twelve evidence-based audit criteria were developed for use in the program. A baseline audit was conducted of prechemotherapy nursing assessment among adult cancer patients, with a sample size of 68 patients and 36 nursing staff. Following implementation of systematic strategies based on the analysis of three main barriers, a follow-up audit involving a similar sample as the first audit was conducted using the same audit criteria. RESULTS: The baseline audit indicated that for nursing assessment among adult cancer patients undergoing chemotherapy, the criteria (1, 10, 11 and 12) which related to nurse education, weight measurement, premedication and access device assessment had very high compliance (from 93 to 100%). Compliance for criteria (2, 6, 7, 9) related to medical history, previous exposure to chemotherapy, patients' or caregivers' comprehension of treatment and psychosocial assessment was 0%, while compliance with the other five criteria (3, 4, 5, 8) was low, ranging from 16 to 61%. There was improvement in all 12 criteria in the follow-up audit. Criteria 1, 11 and 12 maintained high compliance (100%). Criterion 2 (patients' medical history), criterion 3 (presence or absence of allergies), criterion 7 (previous exposure to chemotherapy) and criterion 9 (psychosocial elements) demonstrated a significant improvement in compliance. Although progress has been made, there were still some criteria that require further improvement. These included assessment of patients' current diagnosis and cancer status (criterion 4, from 61 to 66%), recent laboratory results (criterion 5, from 31 to 62%), patients' and/or caregivers' comprehension of information regarding the disease and treatment (criterion 6, from 0 to 34%), any previous exposure to chemotherapy agents (criterion 7, from 0 to 57%), and physical assessment of the patient (criterion 8, from 46 to 72%). CONCLUSION: The project achieved increased compliance with evidence-based best practice in all assessed audit criteria improving the practice of prechemotherapy assessment. Involvement of informatics technology is a great strategy to help overcome barriers, simplify the change process and assist in sustaining evidence-based practice change. Future plans and ideas are in place and have been discussed. Further audits will need to be carried out to improve the validity and quality of nursing assessment.

CNSA: a data repository for archiving omics data.

With the application and development of high-throughput sequencing technology in life and health sciences, massive multi-omics data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly and Variation at present. Moreover, CNSA has created a correlation model of living samples, sample information and analytical data on some projects. Both living samples and analytical data are directly correlated with the sample information. From either one, information or data of the other two can be obtained, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for storing, managing and sharing of omics data. We will continue to improve the data standards and provide free access to open-data resources for worldwide scientific communities to support academic research and the bio-industry. Database URL: https://db.cngb.org/cnsa/.

TIGIT enhances CD4+ regulatory T-cell response and mediates immune suppression in a murine ovarian cancer model.

Ovarian cancer (OC) is the fifth-leading cause of cancer-related death in women with a pathogenesis involving activation of regulatory T cells (Tregs). The T-cell immunoglobulin and ITIM domain (TIGIT) is a well-known immune checkpoint molecule that inhibits T-cell responses. However, the role of TIGIT in OC is not comprehensively understood. In this study, we revealed crucial functions of TIGIT in the development and progression of OC. ID8 cells were used to establish a murine OC model. TIGIT expression was increased in immune cells of OC mice, particularly in CD4+ Tregs. Anti-TIGIT monoclonal antibodies (mAb) were used to block the function of TIGIT in OC mice, and we found that the anti-TIGIT treatment reduced the proportion of CD4+ Tregs, but did not affect CD4+ and CD8+ T cells or natural killer cells. Splenic CD4+ Tregs from OC mice were isolated after the anti-TIGIT treatment, and their functioning was examined. Inhibition of TIGIT lowered the degree of immunosuppression induced by CD4+ Tregs. A survival curve suggested that anti-TIGIT treatment can improve the survival rate of OC in mice. We conclude that TIGIT enhanced CD4+ Tregs response and mediated immunosuppression in the OC model. Our data suggest that inhibition of TIGIT is a potential therapeutic target in OC patients.

A study of the treatment of high-salt chromium-containing wastewater by the photocatalysis-constructed wetland combination method.

In this study, iron ore slag as the photocatalyst was introduced into a constructed wetland simulation system. A comparative experiment of the constructed wetland method and photocatalysis-constructed wetland combination method that treats the high-salt chromium-containing wastewater was carried out. The best hydraulic retention time (HRT) of the photocatalysis-constructed wetland combination system was studied. The effects of these two methods on biochemical oxygen demand (BOD5), chemical oxygen demand (COD) removal and Cr(VI) reduction rate of the high-salt chromium-containing wastewater were analysed after 14 periods. The results showed that under the optimal HRT of 4 hours, the COD and BOD5 of the wastewater reduced by 47% and 31%, and the reduction rate of Cr(VI) was 83% separately in the constructed wetland system. The COD and BOD5 of the wastewater reduced by 83% and 42%, and the reduction rate of Cr(VI) was 96% separately in the photocatalysis-constructed wetland combination method system. At the same time, the changes in plant parameters under these two systems were studied, and the results showed that the addition of photocatalyst and hydrogen peroxide to constructed wetlands did not affect the normal indicators of plant growth. The results showed that the photocatalysis-constructed wetland combination method not only reduced the treatment time greatly, but also improved the quality of the treated wastewater significantly.

[Povidone-iodine versus the benzethonium chloride wipe for penile skin disinfection before semen collection from sperm donors].

Objective: To study the influence of povidone-iodine (PI) versus that of the benzethonium chloride wipe (BCW) on semen collection and semen quality of sperm donors undergoing penile skin disinfection and provide some evidence for the selection of disinfection methods for semen collection. METHODS: We used PI from August to December 2015 and BCWs from January to July 2016 for penile skin disinfection before semen collection, with two samples from each donor, one collected with and the other without penis skin disinfection (the blank control group). After semen collection, we conducted a questionnaire investigation on the influence of the two disinfection methods on semen collection and compared the semen parameters between the two groups of sperm donors. RESULTS: Totally, 185 sperm donors were included in this study, of whom 63 underwent penile skin disinfection with PI and the other 122 with BCWs before semen collection. Statistically significant differences were found between the PI and BCW groups in the adaptability to the disinfectant and rigid disinfection procedures (P <0.05), but not in the other items of the questionnaire (P >0.05). Compared with the sperm donors of the blank control group, those of the PI group showed statistically significant difference in the percentage of progressively motile sperm (PMS) (ï¼»63.02 ± 3.18ï¼½% vs ï¼»61.45 ± 4.78ï¼½%, P<0.05), but not in the abstinence time (ï¼»4.97 ± 1.79ï¼½ vs ï¼»4.7 ± 0.94ï¼½ d, P >0.05), semen volume (ï¼»4.11 ± 1.54ï¼½ vs ï¼»4.15 ± 1.61ï¼½ ml, P >0.05), sperm concentration (ï¼»110 ± 29.6ï¼½ vs ï¼»107.5 ± 31.79ï¼½ ×106/ml, P >0.05), or total sperm count (ï¼»439.10 ± 170.13ï¼½ vs ï¼»434.02 ± 186.91ï¼½ ×106/ejaculate, P >0.05), while those of the BCW group exhibited no remarkable difference in any of the above parameters (P >0.05). Among the samples with abnormal semen quality, significantly fewer were found with abnormal PMS in the BCW than in the PI group (1.64% ï¼»2/122ï¼½ vs 9.68% ï¼»6/62ï¼½, P <0.05). However, there were no significant differences between the PI and BCW groups in the abnormal semen volume, abnormal sperm concentration, or the rate of semen bacterial contamination (P >0.05). CONCLUSIONS: Before semen collection from donors, penile skin disinfection with povidone-iodine may affect both the semen collection process and the quality of donor sperm, while the benzethonium chloride wipe can reduce the influence on the semen collection process and does not affect the semen parameters.

MiR-155-5p inhibits PDK1 and promotes autophagy via the mTOR pathway in cervical cancer.

Cervical cancer is one of the most common malignant tumors and the leading cause of cancer-related mortality in women. Persistent cervical infection by high-risk human papillomavirus (hrHPV) is related to cervical cancer. MicroRNAs could regulate autophagy caused by viral infection. The aim of the present study was to investigate the regulation of autophagy by miR-155-5p in cervical cancer. In HPV+ human cervical lesion tissues, miR-155-5p expression was found to be markedly decreased. Compared to C33A cancer cells (HPV-), the miR-155-5p expression was significantly lower in Siha and HeLa cells (HPV+), which are both hrHPV positive. The level of autophagy was higher in C33A cells than in Siha and HeLa cells. In addition, in C33A, Siha and HeLa cervical cancer cells, miR-155-5p overexpression promoted autophagy, whereas miR-155-5p downregulation had the opposite effects. Furthermore, miR-155-5p downregulation suppressed LC3 and promoted P62 protein expression in C33A cells through promoting the PDK1/mTOR pathway, whereas miR-155-5p overexpression recovered LC3 and suppressed P62 protein expression by suppressing PDK1/mTOR signaling. Taken together, our results indicate the importance of miR-155-5p in cervical cancer cells and suggest a novel mechanism of hrHPV in promoting cervical lesions.

High Pb concentration stress on Typha latifolia growth and Pb removal in microcosm wetlands.

When constructed wetlands are used to treat high-Pb wastewater, Pb may become a stress to wetland plants, which subsequently reduces treatment performance and the other ecosystem services. To facilitate the design and operation of constructed wetlands for treatment of Pb-rich wastewater, we investigated the irreversible inhibitory level of Pb for Typha latifolia through experiments in microcosm wetlands. Seven horizontal subsurface flow constructed wetlands were built with rectangular plastic tanks and packed with marble chips and sand. All wetlands were transplanted with nine stems of Typha latifolia each. The wetlands were batch operated in a greenhouse with artificial wastewater (10 L each) for 12 days. Influent to the seven wetlands had different concentrations of Pb: 0 mg/L, 10 mg/L, 25 mg/L, 50 mg/L, 100 mg/L, 200 mg/L, and 500 mg/L, respectively. The results suggested that leaf chlorophyll relative content, relative growth rate, photosynthetic characteristics, activities of superoxide dismutase, peroxidase, and content of malondialdehyde were not affected when initial Pb concentration was at 100 mg/L and below. But when initial Pb concentration was above 100 mg/L, all of them were seriously affected. We conclude that high Pb concentrations wastewater could inhibit the growth of Typha latifolia and decrease the removal rate of wetlands.

A new nervogenic acid glycoside with pro-coagulant activity from Liparis nervosa.

In an effort to identify hemostatic components from Liparis nervosa (Thunb.) Lindl. using a bioactivity-guided fractionation approach, the n-BuOH extract was found to promote ADP-induced platelet aggregation and two compounds were isolated from the active extract. Compound 1 was a new nervogenic acid glycoside and the structure was elucidated as 3,5-bis(3-methyl-but-2-enyl)-4-O-[beta-D-xylopyranosyl-(1 -->2)-beta-D-glucopyranosyl]-benzoic acid by extensive spectroscopic measurements. Adenosine (2) was isolated from this plant for the first time. Compound 1 also showed good pro-coagulant activity in vitro.

Studies of the thermal degradation of waste rubber.

One kind of Chinese waste tire's sample was pyrolyzed under an inert atmosphere by using thermo-gravimetric apparatus (TGA) and differential thermal analysis (DTA). Different pyrolysis temperature ranges were determined according to the reaction transition temperature obtained by TGA and DTA. Then, at each temperature range, the pyrolysis gaseous products were analyzed by gas chromatography (GC). The influence of the temperature range on the relative yields of the major decomposition products is studied, and a mechanism for the formation of the main components was also investigated. The results indicate that pyrolysis of waste rubber follows the radical mechanism, and the major products are not seriously affected by increasing the temperature from room temperature to 420 degrees C and from 421 to 600 degrees C, but the degradation of blend rubber is different for each of the compositional elastomer.