A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

BACKGROUND

Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species.

RESULTS

We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea.

CONCLUSIONS

The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

Bifidobacterium longum promotes postoperative liver function recovery in patients with hepatocellular carcinoma

Timely liver function recovery (LFR) is crucial for postoperative hepatocellular carcinoma (HCC) patients. Here, we established the significance of LFR on patient long-term survival through retrospective and prospective cohorts and identified a key gut microbe, Bifidobacterium longum, depleted in patients with delayed recovery. Fecal microbiota transfer from HCC patients with delayed recovery to mice similarly impacted recovery time post hepatectomy. However, oral gavage of B. longum improved liver function and repair in these mice. In a clinical trial of HCC patients, orally administering a probiotic bacteria cocktail containing B. longum reduced the rates of delayed recovery, shortened hospital stays, and improved overall 1-year survival. These benefits, attributed to diminished liver inflammation, reduced liver fibrosis, and hepatocyte proliferation, were associated with changes in key metabolic pathways, including 5-hydroxytryptamine, secondary bile acids, and short-chain fatty acids. Our findings propose that gut microbiota modulation can enhance LFR, thereby improving postoperative outcomes for HCC patients.

[Expression and clinical significance of NEK2 and EMT related molecules in oral squamous cell carcinoma]

PURPOSE

To investigate the expression and significance of NEK2 and EMT-related molecules in oral squamous cell carcinoma (OSCC).

METHODS

The expression levels of NEK2 and EMT-related molecules (E-Cadherin, N-Cadherin, Vimentin) in 60 cases of primary OSCC tissues and normal oral mucosa tissues were detected by immunohistochemistry(IHC). NEK2 mRNA expression in 25 OSCC tissues and 10 normal oral mucosa tissues was detected by qRT-PCR. Statistical analysis was performed using SPSS 26.0 software package.

RESULTS

The expression of NEK2, N-Cadherin, and Vimentin increased in OSCC tissues, while the expression of E-Cadherin decreased(P＜0.05). The worse the differentiation, the higher the expression of NEK2 and the lower the expression of E-Cadherin(P＜0.05).

CONCLUSIONS

NEK2 can be used as a prognostic marker for OSCC. The up-regulation of NEK2 and the changes in the expression levels of EMT related molecules can promote the occurrence and development of OSCC.

[BRAF V600E expression in ameloblastomas, ameloblastic carcinomas and cysts]

PURPOSE

To investigate protein and genetic status of BRAF V600E in ameloblastomas, ameloblastic carcinomas and cysts, and to explore if recurrence and malignant transformation of ameloblastomas depends on BRAF status.

METHODS

Twenty cysts, 25 primary ameloblastomas, 25 recurrent ameloblastomas and 8 ameloblastic carcinomas were analysed by immunohistochemistry, and 2 cysts, 5 primary ameloblatomas, 5 recurrent ameloblastomas, 3 atypical ameloblastomas and 6 ameloblastic carcinomas were analysed by quantitative real-time PCR(qPCR). SPSS 26.0 software package was used for data analysis.

RESULTS

There was no correlation between BRAF V600E expression and recurrence. Cysts and carcinomas had lower frequencies of BRAF V600E mutations than ameloblastomas. There was a concordance between positive staining of BRAF V600E protein and BRAF V600E mutation.

CONCLUSIONS

BRAF V600E mutation may be useful in the differential diagnosis of ameloblastomas with cysts and ameloblastic carcinomas. Immunohistochemistry may be a beneficial method to screen for BRAF V600E mutation in ameloblastoma.

[Efficacy analysis of laparoscopic sleeve gastrectomy in morbidly obese patients aged 10-21 years]

Objective: To investigate the efficacy of laparoscopic sleeve gastrectomy (LSG) in morbidly obese patients aged 10 to 21 years. Methods: We conducted a retrospective analysis of clinical data from 89 out of 200 patients who underwent LSG at the Gastrointestinal Surgery/Weight Loss Center of the First Affiliated Hospital of Jinan University between January 2015 and December 2020. The primary outcome measures were the completion rate of LSG, the incidence of perioperative complications, and weight-related indicators 3, 6, 12, and ≥24 months postoperatively. Additionally, we compared glucose metabolism, lipid metabolism, vitamin levels, liver function, and other relevant biochemical variables before and after surgery. Normally distributed continuous data are presented as x±s. Because the numbers of patients at each follow-up time point were not identical with the number of patients in the study cohort preoperatively, independent sample t-tests were used for intergroup comparisons. Non-normally distributed continuous data are presented as M(Q1, Q3), and Mann-Whitney U tests were used for intergroup comparisons. Results: Among the 89 patients, 35 were male (39.3%), the mean age was (18±2) years, and mean body mass index (BMI) 38.5±4.8 kg/m²; 37 of the patients having a BMI greater than 40 kg/m². Additionally, 63 patients (70.8%) had fatty livers, 34 (38.2%) hyperuricemia, 31(34.8%) sleep apnea syndrome, 20 (22.4%) gastroesophageal reflux, eight (8.9%) type 2 diabetes, and two (2.2%) hypertension. All 89 patients underwent LSG surgery successfully, with no conversions to open surgery. During the perioperative period, there were no cases of major bleeding, gastric leakage, or infections. Notable postoperative symptoms included nausea, vomiting, and pain, most of which improved by the second postoperative day. BMI values 3, 6, and 12 months postoperatively had decreased to 31.5±5.8 kg/m², 28.6±4.3 kg/m², and 26.3±4.4 kg/m², respectively. All of these BMI values differed significantly from preoperative values (all P<0.05). At 12 and ≥24 months postoperatively, the percentages of total weight loss were (31.3±9.3)% and (33.1±10.5)%, respectively, both differing significantly from 3 months postoperatively (20.5±5.1)% (all P<0.05). The percentages of excess weight loss at 12 and ≥24 months postoperatively were 91% (70%, 113%) and 95% (74%, 118%) , respectively, both differing significantly from the percentage of total weight loss 3 months postoperatively (56% [45%, 72%]) (both P<0.05). Alanine transaminase and aspartate transaminase serum concentrations decreased from preoperative values of 44.4 (25.5, 100.5) U/L and 29.0 (9.5, 48.0) U/L to 14.0 (10.8, 18.3) U/L and 13.0 (10.5, 17.3) U/L, respectively, ≥24 months postoperatively. Hemoglobin A1c decreased from 5.6 (5.3, 5.8)% preoperatively to ≥24 months postoperatively 5.3 (5.0, 5.4)%. High-density lipoprotein increased from 1.0 (0.9, 1.2) mmol/L preoperatively to 1.4 (1.1, 1.6) mmol/L ≥24 months postoperatively. Vitamin B12 decreased from 350.0 (256.8, 441.3) μg/L preoperative to 230.3(195.4, 263.9) μg/L ≥24 months postoperatively. All differed significantly from preoperative values (all P<0.05). Conclusion: LSG has favorable efficacy in morbidly obese patients aged 10 to 21 years. However, further confirmation is required through long-term, multicenter, randomized, controlled trials.

[Dilemma and breakthrough in the advancement of bariatric and metabolic surgery in China]

China currently has the largest population of overweight and obese individuals globally. Bariatric surgery is by far the most effective approach to address obesity and associated metabolic conditions. To manage the significant growth of obesity, China's bariatric and metabolic surgery has assumed a pivotal role. Despite a delayed start compared to other nations, China has made significant progress in bariatric metabolic surgery over the past two decades. Presently, the annual number of surgeries ranks ahead worldwide. However, the proportion of eligible obese patients undergoing bariatric surgery in China remains lower than global averages. Looking ahead, China's bariatric metabolic surgery field offers ample room for growth and improvement. This paper aims to highlight the achievements in bariatric and metabolic surgery within China while also addressing challenges, such as the high proportion of laparoscopic sleeve gastrectomy, adherence to operation standards and guidelines, postoperative management and loss of follow-up, and quality control of database. By analyzing the current landscape and challenges, it is anticipated that China's bariatric metabolic surgery will continue to make remarkable progress in the future, bolstered by the collective dedication of the medical community.

Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial

OBJECTIVE

We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis.

DESIGN

Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups.

RESULTS

Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users.

CONCLUSION

Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use.

TRIAL REGISTRATION NUMBER

ChiCTR2300072310.

The multi-kingdom microbiome of the goat gastrointestinal tract

BACKGROUND

Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT.

RESULTS

We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network.

CONCLUSIONS

Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.

[Advances in endoscopic sleeve gastroplasty for the treatment of obesity and metabolic disease]

Obesity poses a serious threat to human health, and although bariatric surgery has been proven effective treatment for morbidly obese patients, its surgical risks and high medical costs limit its clinical application and popularity. Endoscopic sleeve gastroplasty (ESG), as a relatively new endoscopic surgery technique for weight loss, has satisfactory weight loss effects compared to laparoscopic sleeve gastrectomy and lifestyle interventions, while preserving the normal structure of the stomach. Its weight loss effects and safety have been validated in multicenter studies abroad. Although, ESG has not yet been widely performed in China, with the gradual maturity of this technique, its prospects are worth attention in the field of weight loss. In the future, large-scale, long-term, multi-center studies are urgently needed in China to clarify the long-term effects, remission of comorbidities, and occurrence of complications of ESG surgery in obese and metabolic disease patients.

Enterotypes of the human gut mycobiome

BACKGROUND

The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.

RESULTS

We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.

CONCLUSIONS

We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.

Integrated single-cell and spatial transcriptomic profiling reveals higher intratumour heterogeneity and epithelial-fibroblast interactions in recurrent bladder cancer

BACKGROUND

Recurrent bladder cancer is the most common type of urinary tract malignancy; nevertheless, the mechanistic basis for its recurrence is uncertain. Innovative technologies such as single-cell transcriptomics and spatial transcriptomics (ST) offer new avenues for studying recurrent tumour progression at the single-cell level while preserving spatial data.

METHOD

This study integrated single-cell RNA (scRNA) sequencing and ST profiling to examine the tumour microenvironment (TME) of six bladder cancer tissues (three from primary tumours and three from recurrent tumours).

FINDINGS

scRNA data-based ST deconvolution analysis revealed a much higher tumour heterogeneity along with TME in recurrent tumours than in primary tumours. High-resolution ST analysis further identified that while the overall natural killer/T cell and malignant cell count or the ratio of total cells was similar or even lower in the recurrent tumours, a higher interaction between epithelial and immune cells was detected. Moreover, the analysis of spatial communication reveals a marked increase in activity between cancer-associated fibroblasts (CAFs) and malignant cells, as well as other immune cells in recurrent tumours.

INTERPRETATION

We observed an enhanced interplay between CAFs and malignant cells in bladder recurrent tumours. These findings were first observed at the spatial level.

Cross-Platform Transcriptomic Data Integration, Profiling, and Mining in Vibrio cholerae

A large number of transcriptome studies generate important data and information for the study of pathogenic mechanisms of pathogens, including Vibrio cholerae. V. cholerae transcriptome data include RNA-seq and microarray: microarray data mainly include clinical human and environmental samples, and RNA-seq data mainly focus on laboratory processing conditions, including different stresses and experimental animals in vivo. In this study, we integrated the data sets of both platforms using Rank-in and the Limma R package normalized Between Arrays function, achieving the first cross-platform transcriptome data integration of V. cholerae. By integrating the entire transcriptome data, we obtained the profiles of the most active or silent genes. By transferring the integrated expression profiles into the weighted correlation network analysis (WGCNA) pipeline, we identified the important functional modules of V. cholerae in vitro stress treatment, gene manipulation, and in vitro culture as DNA transposon, chemotaxis and signaling, signal transduction, and secondary metabolic pathways, respectively. The analysis of functional module hub genes revealed the uniqueness of clinical human samples; however, under specific expression patterning, the Δhns, ΔoxyR1 strains, and tobramycin treatment group showed high expression profile similarity with human samples. By constructing a protein-protein interaction (PPI) interaction network, we discovered several unreported novel protein interactions within transposon functional modules. IMPORTANCE We used two techniques to integrate RNA-seq data for laboratory studies with clinical microarray data for the first time. The interactions between V. cholerae genes were obtained from a global perspective, as well as comparing the similarity between clinical human samples and the current experimental conditions, and uncovering the functional modules that play a major role under different conditions. We believe that this data integration can provide us with some insight and basis for elucidating the pathogenesis and clinical control of V. cholerae.

Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces

Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.

scBrainMap: a landscape for cell types and associated genetic markers in the brain

The great variety of brain cell types is a fundamental element for neuronal circuits. One major goal of modern neuroscience is to decipher the various types of cellular composition and characterize their properties. Due to the high heterogeneity of neuronal cells, until recently, it was not possible to group brain cell types at high resolution. Thanks to the single-cell transcriptome technology, a dedicated database of brain cell types across species has been established. Here, we developed scBrainMap, a database for brain cell types and associated genetic markers for several species. The current scBrainMap database contains 4881 cell types with 26 044 genetic markers identified from 6 577 222 single cells, which link to 14 species, 124 brain regions and 20 different disease states. scBrainMap enables users to perform customized, cross-linked, biologically relevant queries for different cell types of interest. This quantitative information facilitates exploratory research on the role of cell types with regard to brain function in health and disease. Database URL https://scbrainmap.sysneuro.net/.

[Progress in research of deaths and disease burden of major chronic diseases caused by indoor and outdoor air pollution in China]

Health damage including chronic disease caused by air pollution have attracted increasing attention. With the acceleration of industrialization and urbanization, the emission of air pollutants has increased, and its association with chronic diseases has become a research trending topic. Cardiovascular disease, cancer, diabetes, and chronic respiratory disease are the major chronic diseases, causing about 86.6% of the total deaths in China. The prevention and control of chronic diseases, especially the etiologic prevention, is a major public health issue related to national health. This article summarizes the recent progress in research of association of indoor and outdoor air pollution with all-cause mortality, the deaths and disease burden of four major chronic diseases, i.e. cardiovascular disease, cancer, diabetes, and chronic respiratory disease, and puts forward suggestions for the reduction of the burden caused by chronic diseases due to air pollution to provide a theoretical foundation to revise air quality standards in China.

[Progress in research of relationship between metal or metalloid and persistent organic pollutants exposures and cardiovascular disease]

Cardiovascular disease (CVD) is the leading cause of mortality and healthy life expectancy loss, ranking first in causing the global burden of disease. In addition to the traditional CVD risk factors, such as hypertension and diabetes, environmental chemical pollutants may also play a role in the development of CVD. This paper summarizes the evidence regarding the relation of exposures to metal or metalloid and persistent organic pollutants with risk for CVD and introduces the research progress in the relation between the exposures to two environmental chemical pollutants and CVD risk. The study aims to provide scientific evidence for the effective prevention of CVD through the management of chemical pollutants in environment.

A survey on computational strategies for genome-resolved gut metagenomics

Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe-phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.

Risk factors for venous thromboembolism following surgical treatment of fractures: A systematic review and meta-analysis

This study aimed to determine the risk factors for postoperative venous thromboembolism (VTE) in patients treated surgically for fractures using a meta-analytic approach. Electronic searches were performed in PubMed, Embase, and the Cochrane library from inception until February 2022. The odds ratio (OR) and 95% confidence interval (CI) were applied to calculate the pooled effect estimate using the random-effects model. Sensitivity, subgroup, and publication bias tests were also performed. Forty-four studies involving 3 239 291 patients and reporting 11 768 VTE cases were selected for the meta-analysis. We found that elderly (OR: 1.72; 95% CI: 1.38-2.15; P < .001), American Society of Anesthesiologists (ASA) ≥ 3 (OR: 1.82; 95% CI: 1.46-2.29; P < .001), blood transfusion (OR: 1.82; 95% CI: 1.14-2.92; P = .013), cardiovascular disease (CVD) (OR: 1.40; 95% CI: 1.22-1.61; P < .001), elevated D-dimer (OR: 4.55; 95% CI: 2.08-9.98; P < .001), diabetes mellitus (DM) (OR: 1.36; 95% CI: 1.19-1.54; P < .001), hypertension (OR: 1.31; 95% CI: 1.09-1.56; P = .003), immobility (OR: 3.45; 95% CI: 2.23-5.32; P < .001), lung disease (LD) (OR: 2.40; 95% CI: 1.29-4.47; P = .006), obesity (OR: 1.52; 95% CI: 1.27-1.82; P < .001), peripheral artery disease (PAD) (OR: 2.13; 95% CI: 1.21-3.73; P = .008), prior thromboembolic event (PTE) (OR: 5.17; 95% CI: 3.14-8.50; P < .001), and steroid use (OR: 2.37; 95% CI: 1.73-3.24; P < .001) were associated with an increased risk of VTE. Additionally, regional anaesthesia (OR: 0.66; 95% CI: 0.45-0.96; P = .029) was associated with a reduced risk of VTE following surgical treatment of fractures. However, alcohol intake, cancer, current smoking, deep surgical site infection, fusion surgery, heart failure, hypercholesterolemia, liver and kidney disease, sex, open fracture, operative time, preoperative anticoagulant use, rheumatoid arthritis, and stroke were not associated with the risk of VTE. Post-surgical risk factors for VTE include elderly, ASA ≥ 3, blood transfusion, CVD, elevated D-dimer, DM, hypertension, immobility, LD, obesity, PAD, PTE, and steroid use.

[Application of transbronchial cryobiopsy in the diagnosis of postoperative complications after lung transplantation: a report of 6 cases]

Objective: To investigate the efficacy and safety of transbronchial cryobiopsy (TBCB) after lung transplantation. Methods: The clinical characteristics, TBCB procedure, diagnosis and treatment, and outcomes of lung transplant recipients of 6 patients (all male, aged 33-67 years) with TBCB in China-Japan Friendship Hospital from May to November 2021 were retrospectively analyzed. Results: Among the 6 patients diagnosed by TBCB, there were 2 cases of organizing pneumonia, 1 acute cellular rejection, 1 antibody-mediated rejection, and 1 bronchiolitis obliterans, and 1 diffuse alveolar damage. After the clinical diagnosis was confirmed, the condition improved after adjustment of the treatments followed. There were no serious complications related to the TBCB procedure. Conclusion: TBCB is valuable and relatively safe in the diagnosis of complications after lung transplantation, but the indications need to be strictly controlled.

Technological advances in the production of carotenoids and their applications- A critical review

Carotenoids are naturally occurring pigments that are widely distributed in algae, fungi, bacteria, and plants. Carotenoids play a significant role in the food, feed, cosmetic, nutraceutical, and pharmaceutical industries. These pigments are effectively considered as a health-promoting compounds, which are widely used in our daily diet to reduce the risk of chronic diseases such as cardiovascular diseases, cancer, acute lung injury, cataracts, neural disorders, etc. In this context, this review paper demonstrates the synthesis of carotenoids and their potential application in the food and pharmaceutical industries. However, the demand for carotenoid production is increasing overtime, and the extraction and production are expensive and technically challenging. The recent developments in carotenoid biosynthesis, and key challenges, bottlenecks, and future perspectives were also discussed to enhance the circular bioeconomy.

Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers

Cross-cohort validation is essential for gut-microbiome-based disease stratification but was only performed for limited diseases. Here, we systematically evaluated the cross-cohort performance of gut microbiome-based machine-learning classifiers for 20 diseases. Using single-cohort classifiers, we obtained high predictive accuracies in intra-cohort validation (~0.77 AUC), but low accuracies in cross-cohort validation, except the intestinal diseases (~0.73 AUC). We then built combined-cohort classifiers trained on samples combined from multiple cohorts to improve the validation of non-intestinal diseases, and estimated the required sample size to achieve validation accuracies of >0.7. In addition, we observed higher validation performance for classifiers using metagenomic data than 16S amplicon data in intestinal diseases. We further quantified the cross-cohort marker consistency using a Marker Similarity Index and observed similar trends. Together, our results supported the gut microbiome as an independent diagnostic tool for intestinal diseases and revealed strategies to improve cross-cohort performance based on identified determinants of consistent cross-cohort gut microbiome alterations.

metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies

Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC ( https://github.com/ZhaoXM-Lab/metaMIC ), a machine learning-based tool for identifying and correcting misassemblies in metagenomic assemblies. Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.

Fructobacillus apis sp. nov., isolated from the gut of honeybee (Apis mellifera)

A Gram-positive, facultatively anaerobic, catalase-negative, fructose-dependent strain (W13^T) was isolated from the gut of honeybee (Apis mellifera). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain W13^T represents a distinct line of descent within the genus Fructobacillus, with the closest neighbours being Fructobacillus broussonetiae BCRC 81240^T (98.9 % sequence similarity) and Fructobacillus durionis DSM 19113^T (96.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers rpoC and recA confirmed the 16S rRNA gene tree topology. The complete genome of strain W13^T consisted of 1 292 712 bp with a G+C content of 48.3 mol%. Pairwise comparisons of the average nucleotide identity values and digital DNA-DNA hybridization values between the genomes of W13^T and its close phylogenetic neighbours, F. broussonetiae BCRC 81240^T and F. durionis DSM 19113^T, resulted in 76.2-84.1 % and 20.2-27.6 %, respectively. The main cellular fatty acids of strain W13^T were C_16 : 0, C_18 : 1  ω9c and C_18 : 1  ω7c. Thus, we propose a novel species within the genus Fructobacillus, with the name Fructobacillus apis sp. nov. and the type strain is W13^T (= NBRC 115637^T=BCRC 81365^T).

[Application of the concept of precision obesity metabolic surgery in laparoscopic Roux-en-Y gastric bypass]

Due to the complexity and heterogeneity of obesity, the diagnosis and treatment of obesity vary greatly. Five to 10 percent of body weight can be lost through lifestyle modifications, nutritional and behavioral counseling, and the use of approved weight reduction medicines for obesity and diabetes; however, these non-surgical treatments are not effective for all patients. Compared to medical therapy, bariatric surgery is associated with higher rates of type 2 diabetes remission, lower mortality from vascular complications, and long-term, sustained weight loss. With the advent of precision medicine in surgical therapy, bariatric surgeons' fundamental understanding of laparoscopic Roux-en-Y gastric bypass surgery has evolved in recent years. The objective of surgery has shifted from short-term weight loss to the safe and successful long-term management of patient weight and comorbidities. In laparoscopic Roux-en-Y gastric bypass surgery, the concept of precision bariatric and metabolic surgery is mainly reflected in three aspects: accurate preoperative assessment, precise intraoperative operation, and comprehensive postoperative management. A new direction for the future development of precision laparoscopic Roux-en-Y gastric bypass surgery and obesity metabolic surgery is to formulate precise and individualized surgical treatment plans for patients and to use artificial intelligence and big data technology to improve the standardization of specialist data.

EXPERT: transfer learning-enabled context-aware microbial community classification

Microbial community classification enables identification of putative type and source of the microbial community, thus facilitating a better understanding of how the taxonomic and functional structure were developed and maintained. However, previous classification models required a trade-off between speed and accuracy, and faced difficulties to be customized for a variety of contexts, especially less studied contexts. Here, we introduced EXPERT based on transfer learning that enabled the classification model to be adaptable in multiple contexts, with both high efficiency and accuracy. More importantly, we demonstrated that transfer learning can facilitate microbial community classification in diverse contexts, such as classification of microbial communities for multiple diseases with limited number of samples, as well as prediction of the changes in gut microbiome across successive stages of colorectal cancer. Broadly, EXPERT enables accurate and context-aware customized microbial community classification, and potentiates novel microbial knowledge discovery.

Integrated multi-omics reveal important roles of gut contents in intestinal ischemia–reperfusion induced injuries in rats

Intestinal ischemia–reperfusion (IIR) is a life-threatening clinical event with damaging signals whose origin and contents are unclear. Here we observe that IIR significantly affect the metabolic profiles of most organs by unbiased organ-wide metabolic analysis of gut contents, blood, and fifteen organs in rats (n = 29). Remarkably, correlations between gut content metabolic profiles and those of other organs are the most significant. Gut contents are also the only ones to show dynamic correlations during IIR. Additionally, according to targeted metabolomics analysis, several neurotransmitters are considerably altered in the gut during IIR, and displayed noteworthy correlations with remote organs. Likewise, metagenomics analysis (n = 35) confirm the effects of IIR on gut microbiota, and identify key species fundamental to the changes in gut metabolites, particularly neurotransmitters. Our multi-omics results establish key roles of gut contents in IIR induced remote injury and provide clues for future exploration.

Die Dai et al. evaluate changes in the metabolomic and gut microbiome in response to experimental intestinal ischemia reperfusion (IIR) injury in rats. Their results provide further insight into how gut contents contribute to widespread injury in IIR patients.

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli

Bacteriophages (phages) are ideal alternatives to traditional antimicrobial agents in a world where antimicrobial resistance (AMR) is emerging and spreading at an unprecedented speed. In addition, due to their narrow host ranges, phages are also ideal tools to modulate the gut microbiota in which alterations of specific bacterial strains underlie human diseases, while dysbiosis caused by broad-spectrum antibiotics can be harmful. Here, we engineered a lambda phage (Eλ) to target enterohemorrhagic Escherichia coli (EHEC) that causes a severe, sometimes lethal intestinal infection in humans. We enhanced the killing ability of the Eλ phage by incorporating a CRISPR-Cas3 system into the wild-type λ (wtλ) and the specificity by introducing multiple EHEC-targeting CRISPR spacers while knocking out the lytic gene cro. In vitro experiments showed that the Eλ suppressed the growth of EHEC up to 18 h compared with only 6 h with the wtλ; at the multiplicity of infection (MOI) of 10, the Eλ killed the EHEC cells with ~100% efficiency and did not affect the growth of other laboratory- and human-gut isolated E. coli strains. In addition, the EHEC cells did not develop resistance to the Eλ. Mouse experiments further confirmed the enhanced and strain-specific killing of the Eλ to EHEC, while the overall mouse gut microbiota was not disturbed. Our methods can be used to target other genes that are responsible for antibiotic resistance genes and/or human toxins, engineer other phages, and support in vivo application of the engineered phages. IMPORTANCE Pathogenic strains of Escherichia coli are responsible for 0.8 million deaths per year and together ranked the first among all pathogenic species. Here, we obtained, for the first time, an engineered phage, Eλ, that could specifically and efficiently eliminate EHEC, one of the most common and often lethal pathogens that can spread from person to person. We verified the superior performance of the Eλ over the wild-type phage with in vitro and in vivo experiments and showed that the Eλ could suppress EHEC growth to nondetectable levels, fully rescue the EHEC-infected mice, and rescore disturbed mouse gut microbiota. Our results also indicated that the EHEC did not develop resistance to the Eλ, which has been the biggest challenge in phage therapy. We believe our methods can be used to target other pathogenic strains of E. coli and support in vivo application of the engineered phages.

[Pneumatosis cystoides intestinalis in lung transplant recipients: three cases report and literature review]

Objective: To report the clinical characteristics and treatment courses of pneumatosis cystoides intestinalis(PCI) after lung transplantation(LT). Methods: We included all cases of PCI after LT from March 2017 to June 2021 in China-Japan Friendship Hospital. In addition to our cases, we searched literatures published in Chinese and English languages using China National Knowledge Infrastructure (CNKI), Wanfang Data and PubMed/MEDLINE with the search terms"pneumatosis intestinalis"and"lung transplantation". The clinical characteristics and treatment courses of all cases were summarized and analyzed. Results: Three cases of PCI occurred after LT in this study, with an incidence of 0.804% (3/373). Thirteen related literatures were retrieved, with 51 cases enrolled. The median age of the 54 patients was 55.4 years (22-79 years), with 33 males and 21 females. 64.81% (35/54) of the 54 patients underwent LT for interstitial lung disease and 90.74% (49/54) underwent bilateral LT. Twenty-two cases(40.7%) were asymptomatic when PCI occurred. Thirty-eight cases (38/54,70.37%)had involvement of ascending colon, and 35 cases(35/54,64.81%)had involvement of transverse colon. Forty-three cases(43/54, 79.63%) were treated conservatively. The average interval between transplantation and PCI was 210 (5-2 495) days. Conclusion: PCI is a rare complication after lung transplantation, most often occurring in the colon. Most patients were asymptomatic and could improve by conservative treatments.

[Progress in the epidemiological studies on coal mine dust exposure with workers' health damage]

Coal is one of the major fuels, which brings huge energy and economic benefits to global industry and daily life. large amounts of coal dust produced in the process of coal mining and transportation, which seriously threatens the health of related workers. Productive coal dust exposure not only directly leads to respiratory diseases, but also may cause health damage to various systems throughout the body. Numerous studies have shown that coal dust exposure is closely associated with decreased lung function, coal worker's pneumoconiosis, chronic obstructive pulmonary disease, lung cancer, and cardiovascular diseases, and the severity of diseases is affected by coal rank, coal dust concentration, cumulative dust exposure, coal dust composition, and individual lifestyle, etc. The article comprehensively summarized the progress of the epidemiological studies on the health hazards of coal miners from coal dust exposure, in order to provide clues for further researches on health damage and protect the health of the occupational population.

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice

Fecal microbiota transplantation (FMT) of human fecal samples into germ-free (GF) mice is useful for establishing causal relationships between the gut microbiota and human phenotypes. However, due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms, it may not be possible to replicate human phenotypes in mice through FMT; similarly, treatments that are effective in mouse models may not be effective in humans. In this study, we aimed to identify human gut microbes that undergo significant and consistent changes (i.e., in relative abundances) after transplantation into GF mice in multiple experimental settings. We collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human-mouse pairs. Strikingly, on average, we found that only 47% of the human gut microbes could be re-established in mice at the species level, among which more than 1/3 underwent significant changes (referred to as "variable taxa"). Most of the human gut microbes that underwent significant changes were consistent across multiple human-mouse pairs and experimental settings. Consequently, about 1/3 of human samples changed their enterotypes, i.e., significant changes in their leading species after FMT. Mice fed with a controlled diet showed a lower enterotype change rate (23.5%) than those fed with a noncontrolled diet (49.0%), suggesting a possible solution for rescue. Most of the variable taxa have been reported to be implicated in human diseases, with some recognized as the causative species. Our results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes, provide useful information for researchers using mice in gut microbiota studies, and call for additional validations after FMT. An online database named FMT-DB is publicly available at http://fmt2mice.humangut.info/#/.

[Association between occupational noise exposure and the risk of cardiovascular diseases]

Objective: To explore the association between occupational noise exposure and cardiovascular disease (CVD) risk in a large Chinese population. Methods: In December 2019, the study included 21412 retired participants from the Dongfeng-Tongji Cohort Study at baseline from September 2008 to June 2010, occupational noise exposure was evaluated through workplace noise level and/or the job titles. In a subsample of 8931 subjects, bilateral hearing loss was defined as a pure-tone mean of 25 dB or higher at 0.5, 1 , 2, and 4 kHz in both ears. Logistic regression models were used to explore the association of occupational noise exposure, bilateral hearing loss with 10-year CVD risk. Results: Compared with participants without occupational noise exposure, the 10-year CVD risk was significantly higher for noise exposure duration ≥20 years (OR=1.20, 95%CI:1.01-1.41 , P=0.001) after adjusting for potential confounders. In the sex-specific analysis, the association was only statistically significant in males (OR=2.34, 95%CI: 1.18-4.66, P<0.001) , but not in females (OR=1.15, 95%CI:0.97-1.37, P=0.153). In the subsample analyses, bilateral hearing loss, which was an indicator for exposure to loud noise, was also associated with a higher risk of 10-year CVD (OR= 1.17, 95% CI:1.05-1.44, P <0.001) , especially for participants who were males (OR =1.24, 95% CI:1.07-2.30, P<0.001) , aged equal and over 60 years old (OR=2.30, 95%CI: 1.84-2.88, P<0.001) , and exposed to occupational noise (OR=1.66, 95%CI: 1.02-2.70, P=0.001). Conclusion: Occupational noise exposure may be a risk factor for CVD.

[Early onset Epstein-Barr virus-negative diffuse large B cell lymphoma after bilateral lung transplantation: a case report]

Lymphoma after solid organ transplantation is one of the manifestations of post-transplant lymphoproliferative disorders(PTLD). Here we reported a 39-year-old male patient presented with intermittent fever, markedly elevated level of peripheral blood lymphocytes and lactate dehydrogenase(LDH), rapid decrease in hemoglobin and platelet count ten months after bilateral lung transplantation. After systematic evaluation, the patient excluded infectious diseases. Positron emission tomography-computed tomography (PET/CT) revealed diffuse increasing of standard uptake value in bones throughout the body. The bone marrow aspiration, flow cytometric analysis and histopathology confirmed the diagnosis of diffuse large B-cell lymphoma (DLBCL) with negative Epstein-Barr virus-encoded small RNA (EBER) hybridization in situ. Meanwhile, complicated hemophagocytic lymphohistiocytosis was also diagnosed in the patient based on hypertriglyceridemia, abnormally elevated level of serum ferritin and solvable CD25 (sCD25). Treatment regimen included reduction of immunosuppression, anti-CD20 antibody (CD20⁺ B cell inhibitor, rituximab) and etoposide. Repeated PET/CT and bone marrow biopsy showed complete remission of lymphoma after 4 months of therapy.

Efficient conversion of sewage sludge into hydrochar by microwave-assisted hydrothermal carbonization

The treatment of sewage sludge (SS) is an environmental problem worldwide. In recent years, hydrothermal carbonization (HTC) of SS for hydrochar (HC) has attracted extensive attention. This study preliminarily explored the microwave-assisted HTC of SS for the first time. Increasing the reaction temperature (150-250 °C) and reaction time (0-120 min) resulted in a decrease in the HC yield, and it gradually increased with the rising solid-liquid ratio (0.03-0.25 g/mL). Compared with raw SS, the HC products possessed higher aromaticity, carbonization degree, porosity, and polarity, and lower content of soluble nutrients (N/P/K) and leachable heavy metals (Cu, Zn, Pb, Cd, Cr, and Ni), indicating a lower risk of nutrient and heavy metal loss. Attention should be paid to the total contents of Zn and Cd in HC exceeded the permitted value for use in cultivated land with edible crops. The use of CaO as a catalyst improved the yield of HC, made the HC and process water (PW) weakly alkaline, and further passivated the heavy metals in the HC. In the case of H₃PO₄, although the conversion of SS was enhanced (lower content of volatile organic matter in HC), the contents of soluble nutrients (N/P/K) in HC/PW increased, and the migration of Zn and Cd into process water was enhanced. The HCs obtained in this study had poor combustion properties, but higher ignition temperatures than raw SS. PW must be properly treated or recycled because it still contained high contents of organic matter and nutrients. This fundamental study provides basic insights into the microwave-assisted HTC of SS.

[Nonlinear Response Relationship Between Ozone and Precursor Emissions in the Pearl River Delta Region Under Different Transmission Channels]

With the rapid development of urbanization, ozone (O₃) pollution is an ongoing occurrence in the Pearl River Delta (PRD) region in China. The effective control of O₃ pollution is a great challenge owing to the nonlinear relationship between O₃ and precursor emissions and the effect of meteorological conditions. Based on the regional air quality model CAMx-OSAT (ozone source apportionment technology), O₃ formation regimes were determined, and inter-city transportation across PRD was quantified under different transmission channels. The results showed that spatial differences were observed for the O₃ formation regimes under different transmission channels. The VOCs-sensitive regime was mainly located in the central areas of the PRD region, and the NO_x-sensitive regime was distributed in the suburban areas of the PRD regions under calm wind conditions. When the northeast wind was prevailing, the polluted air mass of the urban agglomeration was transmitted southwesterly downward, resulting in the downwind areas being transformed to VOCs-sensitive; the upwind areas were still NO_x-sensitive. Under the southeast wind, the VOCs-sensitive regime had a banding distribution along the southeast-northwest direction, and the remaining areas were NO_x-sensitive. With the influence of transmission channels, downwind cities were significantly affected by the transmission of upwind urban agglomerations (41%-87%), whereas the local formation was the main contributor under the calm wind conditions (60%-87%). To explore the relationship between O₃ and precursor emissions, a series of sensitivity tests were designed. The results showed that maximized areas (20%-36%) with reductions in O₃ can be achieved by reducing VOCs and NO_x in the corresponding sensitive regimes, and the maximized level with the reduction in O₃ can be fulfilled by reducing VOCs in the VOCs-sensitive regime. For the typical city Jiangmen, the area that met the standard increased the most under the calm wind (11%) and southeast wind (8%) conditions when VOCs and NO_x were reduced in the corresponding sensitive regimes. Additionally, under northeast wind conditions, reducing VOCs in the VOCs-sensitive regime can more effectively control O₃, as the area up to the standard increased by 140%.

Alterations of the Human Lung and Gut Microbiomes in Non-Small Cell Lung Carcinomas and Distant Metastasis

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Although dysbiosis of the lung and gut microbiota have been associated with NSCLC, their relative contributions are unclear; in addition, their roles in distant metastasis (DM) are still illusive. We recruited in total 121 participants, including 87 newly diagnosed treatment-naive NSCLC patients of various stages and 34 healthy volunteers, and surveyed their fecal and sputum microbiota. We compared the microbial profiles between groups, identified microbial biomarkers, and generated machine learning models for distinguishing healthy individuals from patients with NSCLC and patients of various stages. We found significant perturbations of gut and sputum microbiota in patients with NSCLC and DM. A machine learning model combining both microbiota (combined model) performed better than an individual data set in patient stratification, with the highest area under the curve (AUC) value of 0.896. Sputum and gut microbiota both contributed to the combined model; in most cases, sputum-only models performed similar to the combined models. Several microbial biomarkers were shared by both microbiotas, indicating their similar roles at distinct body sites. Microbial biomarkers of distinct disease stages were mostly shared, suggesting biomarkers for DM could be acquired early. Furthermore, Pseudomonas aeruginosa, a species previously associated with wound infections, was significantly more abundant in brain metastasis, indicating that distinct types of DMs could have different microbes. Our results indicate that alterations of the sputum microbiota have stronger relationships with NSCLC and DM than the gut and strongly support the feasibility of metagenome-based noninvasive disease diagnosis and risk evaluation. (This study has been registered at ClinicalTrials.gov under registration no. NCT03454685). IMPORTANCE Our survey on gut and sputum microbiota revealed that both were significantly disturbed in non-small cell lung cancer (NSCLC) and associated with distant metastasis (DM) while only the sputum microbiota was associated with non-DM NSCLC. The lung microbiota could therefore have a stronger association with (and thus may contribute more to) disease development than the gut microbiota. Mathematic models using both microbiotas performed better in patient stratification than using individual microbiota. Sputum models, however, performed similar to the combined models, suggesting a convenient, noninvasive diagnostic for NSCLC. Microbial biomarkers of distinct disease stages were mostly shared, suggesting that the same set of microbes were underlying disease progression, and the signals for distant metastasis could be acquired at early stages of the disease. Our results strongly support the feasibility of noninvasive diagnosis of NSCLC, including distant metastasis, are of clinical importance, and should warrant further research on the underlying molecular mechanisms.

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison

GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.

mBodyMap: a curated database for microbes across human body and their associations with health and diseases

mBodyMap is a curated database for microbes across the human body and their associations with health and diseases. Its primary aim is to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes by consistently annotating the microbial contents of collected samples using state-of-the-art toolsets and manually curating the meta-data of corresponding human hosts. mBodyMap organizes collected samples based on their association with human diseases and body sites to enable cross-dataset integration and comparison. To help users find microbes of interest and visualize and compare their distributions and abundances/prevalence within different body sites and various diseases, the mBodyMap database is equipped with an intuitive interface and extensive graphical representations of the collected data. So far, it contains a total of 63 148 runs, including 14 401 metagenomes and 48 747 amplicons related to health and 56 human diseases, from within 22 human body sites across 136 projects. Also available in the database are pre-computed abundances and prevalence of 6247 species (belonging to 1645 genera) stratified by body sites and diseases. mBodyMap can be accessed at: https://mbodymap.microbiome.cloud.

The association between international normalized-ratio and long-term mortality in patients with coronary artery disease: a large cohort study

Background

The association between international normalized-ratio (INR) and long-term prognosis among patients with coronary artery disease (CAD) without atrial fibrillation (AF) or anticoagulant therapy was still unclear. We analyzed the association of INR levels and long-term mortality in a large cohort of CAD patients without atrial fibrillation or using of anticoagulant drugs.

Method

We obtained data from 44,662 patients who were diagnosed with CAD and had follow-up information from January 2008 to December 2018. The patients were divided into 4 groups (Quartile 1: INR ≤0.96; Quartile2: 0.961.06). The main endpoint was long-term all-cause death. Kaplan-Meier curve analysis and Cox proportional hazards models were used to investigate the association between quartiles of INR levels and long-term all-cause mortality.

Result

During a median follow-up of 5.25 years, 5,613 (12.57%) patients died. We observed a non-linear shaped association between INR levels and long-term all-cause mortality. Patients in high INR level (Quartile4: INR &gt;1.06) showed a significantly higher long-term mortality than other groups (Quartile2 or 3 or 4), (Compared with Quartile 1, Quartile 2 [0.961.06], aHR=1.33, 95% CI: 1.22–1.45, P&lt;0.05).

Conclusion

Our study demonstrates high levels of INR were associated with an increased risk of all-cause mortality.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): This study was supported by Guangdong Provincial People's Hospital Dengfeng Project Fund (DFJH201919) and The National Science Foundation for Young Scientist of China (grant no.8197021596, 81500520). Survival curves for mortalitySubgroup analysis

Association between recovered acute kidney injury within 48hours and mortality in patients following coronary angiography: a cohort study

Background

The association of recovered acute kidney injury (AKI) with mortality was controversial. Our study aims to investigate the impact of recovered AKI on mortality in patients following coronary angiography (CAG).

Methods

Our study retrospectively enrolled 3,970 patients with pre-operative serum p creatinine (Scr) and twice measurements within 48hours after procedure. Recovered AKI defined as the diagnosis of AKI (Scr &gt;0.3 mg/dL or &gt;50% from the baseline level) on day 1 when Scr failed to meet the criteria for AKI on the day 2. Maintained AKI was defined as AKI not meeting the definition for recovered AKI. The primary outcome was 1-year all-cause mortality. Multivariable logistic regression was used to assess the association between recovered AKI and 1-year mortality.

Results

Among 3,970 participants, 861 (21.7%) occurred AKI, of whom 128 (14.9%) was recovered AKI and 733 (85.1%) was maintained AKI. 312 (7.9%) patients died within 1-year after admission. After multivariable analysis, recovered AKI was not associated with higher 1-year mortality (adjusted odds ratio [aOR], 1.37; CI, 0.68–2.51) compared without AKI. Among AKI patients, Recovered AKI was associated with a 52% lower 1-year mortality compared with maintained AKI. Additionally, maintained AKI was significantly associated with higher 1-year mortality (aOR, 2.67; CI, 2.05–3.47).

Conclusions

Our data suggested that recovered AKI within 48h was a common subtype of AKI following CAG, without increasing mortality. More attention need to be paid to the patients suffering from maintained AKI following CAG.

Funding Acknowledgement

Type of funding sources: None. Association of AKI and mortalitySubgroups analysis

[Pulmonary mucormycosis after lung transplantation:3 cases report with literature review]

Objective: To report the risk factors, clinical characteristics and treatment courses of pulmonary mucormycosis after lung transplantation(LT). Methods: We included 3 cases with pulmonary mucormycosis after LT from March 2017 to July 2020 in the centre for lung transplantation of China-Japan Friendship Hospital. Twelve cases from Chinese and English literature from China National Knowledge Infrastructure (CNKI), China Biomedical Literature Service System and Pubmed Database from March 1980 to July 2020 were added. The risk factors, clinical characteristics and treatment courses of all cases were summarized and analyzed. Results: Pulmonary mucormycosis occurred in 1.06% (3/284) in our centre. A total of 15 cases with 12 cases from literature included 10 males and 5 females with a mean age of(47±20)years. Thirteen cases occurred after LT, and 2 cases occurred after heart-lung transplantation (HLT). Nine probable cases were diagnosed by positive isolation of the pathogen from bronchoalveolar lavage fluid or sputum. Three proven cases were diagnosed by transbronchial lung biopsy. Meanwhile, the other 3 proven cases diagnosed by CT-guided percutaneous lung biopsy, autopsy and surgical operation respectively. Ten cases (66.7%) were diagnosed with pulmonary mucormycosis within 90 days after lung transplantation. The mortality was as high as 46.67% (7/15), but if it occurred within 90 days, the mortality reached 70% (7/10). The average interval between transplantation and positive isolation of the pathogen was 112.3 (5-378) days. Conclusions: The clinical and radiographic features of pulmonary mucormycosis after LT were nonspecific. It had a high mortality, especially in those occurred within 90 days after LT. The combination of antifungal therapy and surgical resection may contribute to a better outcome of the disease.

[Analysis of the effect of modified cervical cerclage in the treatment of cervical insufficiency]

Objective: To discuss the surgical effect of modified cervical cerclage for the treatment of pregnant women with cervical insufficiency. Methods: The clinical data of 225 pregnant women who underwent modified cervical cerclage in Qilu Hospital (Qingdao) were selected for retrospective analysis from April 2014 to June 2020. Surgical success rate, full-term birth rate, preterm birth rate, prolonged pregnancy weeks and newborn birth weight were compared between singleton and twin pregnancies, preventive cerclage and emergency cerclage, surgery before and after 18 weeks, naturally and in vitro fertilization and embryo transfer (IVF-ET) conceived pregnant women respectively. Results: Among the 225 pregnant women, the gestational weeks of surgery were 14-24⁺⁵ weeks, mean gestational weeks of delivery were 38⁺² weeks (35⁺⁵-39⁺³ weeks), the number of prolonged gestation were (20.3±5.2) weeks, and the newborn birth weight was (3 065±735) g; the overall surgical success rate was 92.9% (209/225), and the miscarriage rate was 7.1% (16/225); among the surviving newborns, the full-term birth rate was 73.7% (154/209), and the preterm birth rate was 26.3% (55/209). All cases had no intraoperative complications. Among the 225 pregnant women, 202 (89.8%, 202/225) cases were singleton pregnancies, and 23 (10.2%, 23/225) cases were twin pregnancies; 201 (89.3%, 201/225) cases underwent preventive cervical cerclage, and 24 (10.7%, 24/225) cases underwent emergency cervical cerclage; 190 (84.4%, 190/225) cases underwent the surgery before 18 weeks, and 35 (15.6%, 35/225) cases underwent the surgery after 18 weeks; 49 (21.8%, 49/225) cases were conceived by IVF-ET. There was no statistically significant difference in the overall surgical success rate of single and twin group (P>0.05). The full-term birth rate, newborn birth weight and prolonged pregnancy weeks of single group were higher than those of twin group (P<0.05). There were no statistical differences between preventive and emergency cerclage in overall surgical success rate, full-term birth rate, preterm birth rate, and newborn birth weight (all P>0.05). The pregnancy prolonged weeks of preventive cerclage was higher than that of emergency cerclage (P<0.05). There were no statistically significant differences in the overall surgical success rate, full-term birth rate, preterm birth rate and birth weight of newborns at different surgical timings (all P>0.05). The pregnancy prolonged week for those who underwent surgery before 18 weeks was higher than that of surgery after 18 weeks (P<0.05). The premature birth rate of IVF-ET was higher than that of naturally conceived pregnant women (P<0.05). Conclusion: The modified cervical cerclage could effectively prolong the gestational weeks of delivery, reduce the rate of preterm birth, and the operation is simple and easy to promote. It could be used as a surgical option for patients with cervical insufficiency.

[Study on the association between occupational noise exposure and cardiovascular diseases]

Occupational noise is one of the most common occupational hazards in the workplace. Long-term exposure to occupational noise could not only lead to the damage of the hearing system, but also may cause a certain impact on the cardiovascular system. Studies have shown that occupational noise exposure was positively associated with cardiovascular diseases, including hypertension, coronary heart disease and myocardial infarction. However, the results of studies on occupational noise exposure and stroke are still controversial. This paper reviews the relationship between occupational noise exposure and hypertension, coronary heart disease, stroke, myocardial infarction by summarizing the epidemiological data of domestic and foreign population in recent years. Our study could provide evidence for the design and implementation of well-designed epidemiological and mechanism studies, and the recognition of the role of occupational noise exposure in the occurrence and development of cardiovascular diseases, so as to better protect workers' health.

[Using rotation cross-advancement flap for repairing complete unilateral cleft lip and nasolabial deformity]

To evaluate the efficacy of rotation cross-advancement flap method in repairing the nasolabial deformity of complete unilateral cleft lip. A retrospective study was performed to analyze the children who were treated by using the rotating cross-advancement flap for repairing the complete unilateral cleft lip at the Fujian Medical University Union Hospital from October 2018 to July 2019. The clinical data such as patient's lip height, lip length, nostril height, nostril width, nostril area and so on were collected at the pre-operation, post-operation and following-up visits respectively and used to evaluate the efficacy of the treatment. Six children were included in the present study. The ratios of lip height on noncleft side to cleft side were 2∶1 at the pre-operation time. The ratios of nostril height on the noncleft side to the cleft side were about 2∶1. The ratios of the width and the area of the nostril were 1∶2 to 1∶3. At the post-operation time, the ratios of length and height of the lip at the cleft side to the noncleft side were around 1∶1. The shape of the nostrils and nasolabial fold were almost symmetrical between the cleft side and noncleft side. The shapes of the nasal sill were acceptable and the postoperative scars were not obvious. There were no obvious incision healing complications and the treatment effects were satisfactory. Rotation cross-advancement flap method was safe and reliable for repairing the nasolabial deformities in children with complete unilateral cleft lip.

Identification of Blood-Based Glycolysis Gene Associated with Alzheimer's Disease by Integrated Bioinformatics Analysis

BACKGROUND

Alzheimer's disease (AD) is one of many common neurodegenerative diseases without ideal treatment, but early detection and intervention can prevent the disease progression.

OBJECTIVE

This study aimed to identify AD-related glycolysis gene for AD diagnosis and further investigation by integrated bioinformatics analysis.

METHODS

122 subjects were recruited from the affiliated hospitals of Ningbo University between 1 October 2015 and 31 December 2016. Their clinical information and methylation levels of 8 glycolysis genes were assessed. Machine learning algorithms were used to establish an AD prediction model. Receiver operating characteristic curve (AUC) and decision curve analysis (DCA) were used to assess the model. An AD risk factor model was developed by SHapley Additive exPlanations (SHAP) to extract features that had important impacts on AD. Finally, gene expression of AD-related glycolysis genes were validated by AlzData.

RESULTS

An AD prediction model was developed using random forest algorithm with the best average ROC_AUC (0.969544). The threshold probability of the model was positive in the range of 0∼0.9875 by DCA. Eight glycolysis genes (GAPDHS, PKLR, PFKFB3, LDHC, DLD, ALDOC, LDHB, HK3) were identified by SHAP. Five of these genes (PFKFB3, DLD, ALDOC, LDHB, LDHC) have significant differences in gene expression between AD and control groups by Alzdata, while three of the genes (HK3, ALDOC, PKLR) are related to the pathogenesis of AD. GAPDHS is involved in the regulatory network of AD risk genes.

CONCLUSION

We identified 8 AD-related glycolysis genes (GAPDHS, PFKFB3, LDHC, HK3, ALDOC, LDHB, PKLR, DLD) as promising candidate biomarkers for early diagnosis of AD by integrated bioinformatics analysis. Machine learning has the advantage in identifying genes.

Improving Cooling Performance of Injection Molding Tool with Conformal Cooling Channel by Adding Hybrid Fillers

Silicone rubber mold (SRM) is capable of reducing the cost and time in a new product development phase and has many applications for the pilot runs. Unfortunately, the SRM after injection molding has a poor cooling efficiency due to its low thermal conductivity. To improve the cooling efficiency, the thermal conductivity of the SRM was improved by adding fillers into the SRM. An optimal recipe for fabricating a high cooling efficiency low-pressure injection mold with conformal cooling channel fabricated by fused deposition modeling technology was proposed and implemented. This study proposes a recipe combining 52.6 wt.% aluminum powder, 5.3 wt.% graphite powder, and 42.1 wt.% liquid silicon rubber can be used to make SRM with excellent cooling efficiency. The price-performance ratio of this SRM made by the proposed recipe is around 55. The thermal conductivity of the SRM made by the proposed recipe can be increased by up to 77.6% compared with convention SRM. In addition, the actual cooling time of the injection molded product can be shortened up to 69.1% compared with the conventional SRM. The actual cooling time obtained by the experiment is in good agreement with the simulation results with the relative error rate about 20%.