Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications for health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.
Humans ; Gastrointestinal Microbiome/genetics* ; Bacteriophages/physiology* ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA/methods* ; Bacteria/virology*

Objective:To explore the application of COVID-19-specific IgG antibody in identifying epidemic Omicron BA.5 strain infection.Method:Omicron BF.7/BA.5 naturally infected population, healthy population vaccinated with the COVID-19 vaccine, and Omicron BF.7/BA.5 breakthrough cases were enrolled into this study. The serum WT-S-IgG and BA.5-S-IgG were detected by indirect ELISA, and the serum-specific IgG antibody levels of different populations were compared. The application value of the two antibody titers and the ratio of the two antibodies in identifying Omicron BA.5 epidemic strain infection were explored by the ROC curve, aiming to provide technical support for pathogen diagnosis.Results:The antibody titers of WT-S-IgG and BA.5-S-IgG in the breakthrough cases were higher than those in the naturally infected population and the healthy population ( P<0.05). The area under the curve (AUC) of WT-S-IgG and BA.5-S-IgG in identifying epidemic Omicron BA.5 strain infection was 0.947 and 0.961, respectively. The AUC of BA.5-S-IgG and WT-S-IgG antibody titer ratio was 0.873. When the antibody titer ratio was 0.855, the sensitivity and specificity were 80.00% and 90.00%, respectively. According to the interval since the last infection, the AUC of the ratio of BA.5-S-IgG to WT-S-IgG antibody titer to identify the infection of epidemic strains less than 30 days and more than 30 days was 0.887 and 0.863, respectively, and the sensitivity and specificity were both above 80%. Conclusion:Both BA.5-S-IgG and WT-S-IgG, as well as the combination of these two antibodies, are of high value in the identification of epidemic strains.

Objective:To analyze the effects of SARS-CoV-2 infection and vaccination on virus mutation.Methods:The whole genome sequencing sequences of 2 659 local SARS-CoV-2 specimens from Jiangsu Province in 2023 were selected for analysis, and relevant information such as demographic and clinical characteristics were collected, and the effects of infection and vaccination on the genome-wide mutation rate and S gene′s selective pressure of the virus were analyzed by univariate and multivariate linear regression models.Results:The average age of these infected patients was 55.0 (31.0, 74.0) years, 1 150 cases (43.2%) in the age group of ≥60 years, 1 367 cases (51.4%) were males, 2 044 cases (76.9%) had a history of COVID-19 vaccination, and 1 629 cases (61.3%) had the first-time infection. The clinical symptoms of the infected patients were mainly mild, with a total of 2434 cases (91.5%), and 29 cases (1.1%) with severe symptoms or more. The average substitution rate of SARS-CoV-2 was 9.69 (9.38, 9.98)×10 -4 subs/site/year, and the dN/dS value of the S gene was 6.08 (5.56, 8.66), which was significantly greater than that of 1 ( P<0.001), indicating positive selection. The result of univariate and multivariate linear regression model analysis showed that the SARS-CoV-2 substitution rate was higher in those with vaccination history and reinfection, aged 20-30 years, ≥60 years, and the SARS-CoV-2 substitution rate was lower in males with moderate clinical symptoms and severe disease and above. Those with a history of vaccination and reinfection, aged 50-60 years old, ≥60 years old have smaller S gene dN/dS. Conclusions:Under the immune pressure exerted by vaccination and infection, the genome-wide mutation of SARS-COV-2 accelerated, but the non-synonymous mutation rate of the S gene decreased. The mechanism causing these phenomena needs further study.

Objective:To explore the application of COVID-19-specific IgG antibody in identifying epidemic Omicron BA.5 strain infection.Method:Omicron BF.7/BA.5 naturally infected population, healthy population vaccinated with the COVID-19 vaccine, and Omicron BF.7/BA.5 breakthrough cases were enrolled into this study. The serum WT-S-IgG and BA.5-S-IgG were detected by indirect ELISA, and the serum-specific IgG antibody levels of different populations were compared. The application value of the two antibody titers and the ratio of the two antibodies in identifying Omicron BA.5 epidemic strain infection were explored by the ROC curve, aiming to provide technical support for pathogen diagnosis.Results:The antibody titers of WT-S-IgG and BA.5-S-IgG in the breakthrough cases were higher than those in the naturally infected population and the healthy population ( P<0.05). The area under the curve (AUC) of WT-S-IgG and BA.5-S-IgG in identifying epidemic Omicron BA.5 strain infection was 0.947 and 0.961, respectively. The AUC of BA.5-S-IgG and WT-S-IgG antibody titer ratio was 0.873. When the antibody titer ratio was 0.855, the sensitivity and specificity were 80.00% and 90.00%, respectively. According to the interval since the last infection, the AUC of the ratio of BA.5-S-IgG to WT-S-IgG antibody titer to identify the infection of epidemic strains less than 30 days and more than 30 days was 0.887 and 0.863, respectively, and the sensitivity and specificity were both above 80%. Conclusion:Both BA.5-S-IgG and WT-S-IgG, as well as the combination of these two antibodies, are of high value in the identification of epidemic strains.

Autism spectrum disorder (ASD) is a multifactorial disease, with social difficulties and repetitive behaviors as its core symptoms. With the improvement of diagnostic methods, the detection rate of ASD is increasing year by year.Cognitive flexibility impairment is very obvious in most autistic patients.More and more studies have shown that cognitive flexibility impairment is related to the occurrence and development of core symptoms. However, the mechanism of cognitive flexibility impairment in autism remains unclear. The frontal lobe plays an important role in advanced cognition, and its complete development is related to cognitive function. Recent studies have shown that frontal lobe dysfunction is closely related to cognitive flexibility deficits in autistic patients, and the abnormal changes in the frontal lobe, the associated default mode network dysfunction and frontal striatal circuit defects may be the important mechanisms of cognitive flexibility impairment. Based on the recent clinical and basic studies on cognitive flexibility in autism, this article reviews the mechanisms of frontal lobe and related circuits involved in the impairment of cognitive flexibility in autism.

A significant proportion of patients with chorea-acanthocytosis (ChAc) fail to respond to standard therapies. Recent evidence suggests that globus pallidus internus (GPi) deep brain stimulation (DBS) is a promising treatment option; however, reports are few and limited by sample sizes. We conducted a systematic literature review to evaluate the clinical outcome of GPi-DBS for ChAc. PubMed, Embase, and Cochrane Library databases were searched for relevant articles published before August 2021. The improvement of multiple motor and nonmotor symptoms was qualitatively presented. Improvements in the Unified Huntington’s Disease Rating Scale motor score (UHDRS-MS) were also analyzed during different follow-up periods. A multivariate linear regression analysis was conducted to identify potential predictors of clinical outcomes. Twenty articles, including 27 patients, were eligible. Ninety-six percent of patients with oromandibular dystonia reported significant improvement. GPi-DBS significantly improved the UHDRS-motor score at < 6 months (p < 0.001) and ≥ 6 months (p < 0.001). The UHDRS-motor score improvement rate was over 25% in 75% (15/20 cases) of patients at long-term follow-up (≥ 6 months). The multiple linear regression analysis showed that sex, age at onset, course of disease, and preoperative movement score had no linear relationship with motor improvement at long-term follow-up (p > 0.05). GPi-DBS is an effective and safe treatment in most patients with ChAc, but no reliable predictor of efficacy has been found. Oromandibular dystonia-dominant patients might be the best candidates for GPi-DBS.

Objective: Analyze the clinical application rule of Chinese patent medicine in cervical radiculopathy (CR) .Method: The clinical real-world data of CR were extracted by using information sharing system of traditional Chinese medicine and clinical research. Six hundred and twenty-eight inpatients and out patients with CR were enrolled from December 2012 to July 2014 in the information system database of Wangjing Hospital. The correlation analyses and mutual information value were recorded for Chinese patent medicine therapy application of all patients by using liquorice software. Complex network diagrams were generated. Result: Yuxuebi capsule and Jingshu granule is the highest frequency in application of Chinese patent medicine. Jingshu granule and Cobamamide for injection were the highest frequency in combined application of Chinese patent medicine and western medicine. Association frequency was 822, mutual information value was 268.07. Biqi capsule and Daiwenjiu cream were the highest frequency in combined application of Chinese patent medicine and topical drugs. Association frequency was 384, mutual information value was1754.76. Conclusion: The basic treating principle for CR was promoting blood circulation and removing blood stasis. The efficacy and safety of combined Chinese patent medicine with other medicine need further research

OBJECTIVE:To investigate influential factors of standardization of clinical research on therapeutic efficacy of Yao-tongning capsules,and to provide direction for reasonable and standard development of clinical research. METHODS:Retrieved from CJFD,VIP and Wanfang database,RCTs about Yaotongning capsules in the treatment of related disease were collected. After data extraction and quality evaluation,Meta-analysis was conducted by using Rev Man 5.3 statistical software. The effects of the di-alectical situation,treatment course and route of administration on the evaluation of therapeutic efficacy of Yaotongning capsules were compared;based on this,the concepts of index evidence-based value which reflected clinical standardization were put for-ward,and its effects on Yaotongning capsules were investigated. RESULTS:A total of 71 RCTs were included,involving 11009 patients. Results of Meta-analysis showed therapeutic efficacy of Yaotongning capsules was better than that of other drugs in dialecti-cal case(P=0.02),while therapeutic efficacy of Yaotongning capsules was inferior to that of other drugs in non-dialectical case(P<0.01);therapeutic efficacy of Yaotongning capsules was inferior to that of other drugs when treatment course was shorter than 30 days(P<0.05),while treatment course was longer than 30 days,there was no difference in therapeutic efficacy between Yaotongn-ing capsules and other drugs(P=0.99). When did not take medicine according to the instruction,therapeutic efficacy of Yaotongn-ing capsule was inferior to that of other drugs(P<0.05);when taking medicine according to the instruction,there was no differ-ence in therapeutic efficacy between Yaotongning capsules and other drugs(P=0.94). When evidence-based value was ≥5,thera-peutic efficacy of Yaotongning capsules was better than that of other drugs(P=0.03);when evidence-based value was equal to 4, there was no difference in therapeutic efficacy between Yaotongning capsules and other drugs(P=0.56);when evidence-based val-ue was ≤3,therapeutic efficacy of Yaotongning capsules was inferior to that of other drugs(P<0.05),with statistical significance. CONCLUSIONS:It is an important guarantee of playing therapeutic efficacy of Yaotongning capsules to regularly use drugs strictly according to the principle of dialectical treatment,and take drugs according to treatment course and instructions. Clinical trials should be standardized strictly in accordance with the instructions,so as to provide objective and fair clinical findings.

This study was aimed to analyze the application of non-pharmacotherapy in treating cervical radiculopathy (CR) in real-world,and to provide clinical reference for CR non-pharmacotherapy.The clinical real-world data of CR was extracted by using information sharing system of traditional Chinese medicine (TCM) and clinical research.Six hundred and twenty-eight inpatients and outpatients with CR were enrolled from December 2012 to July 2014 in the information system database of Wangjing Hospital.Basic characteristics of the non-pharmacotherapy groups were analyzed by statistical description method.The node degree and mutual information value were recorded for non-pharmacotherapy application of all patients by using liquorice software.Complex network diagrams were generated.The results showed that 47％ of CR patients received non-pharmacotherapy (294/628),including 67 males and 227 females.The average age of patients was 49 years old,and the prevalence of the disease was the highest from 45 to 65 years old.In all patients,the usage of manipulation and cervical traction was higher,and the combination of manipulation and acupuncture was the most.Within outpatients,the proportion of cervical traction was higher,and the combination of manipulation and acupuncture was the most frequently.Within inpatients,the proportion of manipulation and cervical traction was higher,and the combination of comprehensive physical therapy and exercise therapy was the most frequently.It was concluded that non-pharmacotherapy has been commonly used in clinical treatment of CR.Cervical traction and manipulation was the widest applications.The combination treatment was in wide application.Future studies should increase the sample size of CR patients from different regions,and enhance gradually the level of evidence of clinical research for non-pharmacotherapy treating CR.

Objective The localization of pulmonary nodules in surgery remains a clinical challenge .In this study we dis-cussed the diagnostic and treatment value of CT-guided coil localization followed by real-time digital subtraction angiography ( DSA)-guided accurate resection of solitary pulmonary nodules (SPN) with video-assisted thracoscopic surgery (VATS). Methods This study involved 82 cases of SPN treated in the Department of Cardiothoracic Surgery of Jinling Hospital from September 2011 to May 2014 .The SPNs were preoperatively positioned by placing a metal coil close to the lesion under CT guidance on the same day of surger -y.Then VATS wedge resection of the SPNs was performed under the guidance of real -time DSA and further procedures followed in ac-cordance with the results of intraoperative pathology . Results The success rate of coil localization was 100%, the mean time of po-sitioning was (15.3 ±3.2) min, and the mean time of VATS wedge resection was (24.2 ±12.1) min.Pathological results revealed 45 cases of malignancy and 37 cases of benign lesions . Conclusion Preoperative CT-guided coil localization of SPNs showed a high accuracy and no serious complications , and by real-time DSA-guided VATS that immediately followed , the nodules could be precisely removed with the cutting edge 2 cm above the lesion , which achieved both the purposes of diagnosis and treatment of SPNs .