Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

The contents recorded in the rotation registration manual is not only the quantitative indicators for evaluating the quality of residency training, but also the important basis for training assessment and issuance of training certificates. In order to solve the problems of data authenticity, information delay, and repeated entry in the rotation registration manual for residency training, Shanghai East Hospital, Tongji University, launched a project to dock the electronic rotation registration manual with the hospital information system. Through the establishment of the project team, the development of working mechanisms, and the implementation of the project, data analysis was used for process reformation and system optimization, so as to continuously improve management efficiency and medical safety while solving problems and form a set of implementation system with reference significance in practice.

【Objective】 To investigate the screen exposure status in 3- to 6-year-old children in Minhang district and to analyze its determinants, so as to provide a basis for scientific intervention of screen exposure in children. 【Methods】 A total of 1 035 children aged 3 to 6 years were selected from 30 classes in 10 kindergartens in Minhang district by multi-stage cluster sampling in October 2022. An online questionnaire survey was conducted by their parents. Screen exposure was difined as spending more than one hour on video products per day. Multivariate Logistic regression model was adopted to analyze the determinants of children screen exposure. 【Results】 Among 1 035 children, 730 experienced screen exposure (70.53%). The average time of daily screen exposure was (1.67±0.98)h. The daily screen exposure time of children aged 3, 4, 5 and 6 years at weekends was (1.77±1.13), (1.76±1.04), (1.98±1.10)h and(2.08±1.22)h, respectively, and the difference was statistically significant (F=3.98, P<0.01). Multivariate Logistic analysis showed that age group of 5 years old (OR=1.79, 95%CI:1.19 - 2.68), the caregivers using video products for 1 - 2hours/day (OR=2.61, 95%CI:1.90 - 3.60) and >2hours/day (OR=2.10, 95%CI:1.35 - 3.27) when accompanying children, parents supporting children using video products(OR=1.59, 95%CI:1.17 - 2.15), children using video products before bedtime(OR=1.94, 95%CI:1.32 - 2.86), and unsupervised use of video products for children(OR=1.94, 95%CI:1.36 - 2.77) were independent risk factors for children′s screen exposure(P<0.05). Father′s education level of bachelor(OR=0.61,95%CI:0.43 - 0.89), master and above(OR=0.49, 95%CI:0.34 - 0.73) was a protective factor for children′s screen exposure(P<0.05). 【Conclusions】 Attention should be paid to the problem of screen exposure of 3 -to 6 - year-old children. Targeted efforts should be made to popularize the knowledge of the harm of early screen exposure to children among caregivers, caregivers are advocated for the rule formulation of screen behavior, scientifically regulate children′s screen exposure behaviors, and increase parent-child communication, so as to reduce the adverse effects of screen exposure on children′s health.

ObjectiveTo investigate the detection rate and main influencing factors of growth retardation in infants aged 0-3 in Minhang District， and to provide relevant evidence for early intervention， nutrition promotion and health guidance in the future. MethodsFrom September 1， 2020 to August 31， 2021， the height， weight， basic information of parents， feeding methods， and lifestyle habits of infants who received systematic healthcare aged 0‒3 in community health service centers and Minhang maternal child health hospital were collected， and the current situation and influencing factors of infant growth retardation were analyzed. ResultsAmong the 68 637 infants who underwent a systematic physical examination in Minhang District， the total detection rate of growth retardation was 5.03% （3 453/68 637）. The detection rates in the 0-year-old， 1-year-old， 2-year-old， and 3-year-old groups were 6.57% （1 636/24 885）， 3.90% （664/17 031）， 4.62% （827/17 905）， and 3.72% （326/8 773）， respectively. There was no difference in the detection rate of growth retardation between boys and girls （P>0.05）， and a multinomial logistic regression analysis of 13 influencing factors （infant birth weight， birth length， parental weight， height， education level， mother’s childbearing age， delivery mode， household registration， feeding mode within 6 months， infant sleep， etc.） in univariate analysis showed that birth weight <2 500 g （OR=3.99， 95%CI： 2.809‒5.674） or ≥4 000 g （OR=12.78， 95%CI： 8.868‒18.443）， maternal height <150 cm （OR=7.10， 95%CI： 4.294‒11.753）， paternal height <160 cm （OR=5.65， 95%CI： 2.792‒11.422）， maternal education level of junior high school and below （OR=1.31， 95%CI： 1.087‒1.588）， paternal education level of junior high school and below （OR=1.02， 95%CI： 0.838‒1.236）， mixed feeding （OR=1.15， 95%CI： 1.031‒1.288）， and sleep duration exceeding the recommended time （OR=1.58， 95%CI： 1.466‒1.710） were risk factors for growth retardation in infants aged 0‒3. Infants with a birth length <50 cm or with household registration in Shanghai had a higher incidence of growth retardation. ConclusionGrowth retardation in infants aged 0‒3 is influenced by a combination of genetic， environmental， and sleep factors. It is essential for parents to realize the impact of growth retardation on the future of their children early on and actively participate in the early detection， screening， and intervention of growth retardation.

Objective This study aimed to comprehensively analyze and compare the clinicopathological features and prognosis of Chinese patients with human epidermal growth factor receptor 2(HER2)-low early breast cancer(BC)and HER2-IHC0 BC. Methods Patients diagnosed with HER2-negative BC(N=999)at our institution between January 2011 and December 2015 formed our study population.Clinicopathological characteristics,association between estrogen receptor(ER)expression and HER2-low,and evolution of HER2 immunohistochemical(IHC)score were assessed.Kaplan-Meier method and log-rank test were used to compare the long-term survival outcomes(5-year follow-up)between the HER2-IHC0 and HER2-low groups. Results HER2-low BC group tended to demonstrate high expression of ER and more progesterone receptor(PgR)positivity than HER2-IHC0 BC group(P<0.001).The rate of HER2-low status increased with increasing ER expression levels(Mantel-Haenszel χ2 test,P<0.001,Pearson's R=0.159,P<0.001).Survival analysis revealed a significantly longer overall survival(OS)in HER2-low BC group than in HER2-IHC0 group(P=0.007)in the whole cohort and the hormone receptor(HR)-negative group.There were no significant differences between the two groups in terms of disease-free survival(DFS).The discordance rate of HER2 IHC scores between primary and metastatic sites was 36.84%. Conclusion HER2-low BC may not be regarded as a unique BC group in this population-based study due to similar clinicopathological features and prognostic roles.

Background::Acute pulmonary embolism (APE) is a fatal cardiovascular disease, yet missed diagnosis and misdiagnosis often occur due to non-specific symptoms and signs. A simple, objective technique will help clinicians make a quick and precise diagnosis. In population studies, machine learning (ML) plays a critical role in characterizing cardiovascular risks, predicting outcomes, and identifying biomarkers. This work sought to develop an ML model for helping APE diagnosis and compare it against current clinical probability assessment models.Methods::This is a single-center retrospective study. Patients with suspected APE were continuously enrolled and randomly divided into two groups including training and testing sets. A total of 8 ML models, including random forest (RF), Na?ve Bayes, decision tree, K-nearest neighbors, logistic regression, multi-layer perceptron, support vector machine, and gradient boosting decision tree were developed based on the training set to diagnose APE. Thereafter, the model with the best diagnostic performance was selected and evaluated against the current clinical assessment strategies, including the Wells score, revised Geneva score, and Years algorithm. Eventually, the ML model was internally validated to assess the diagnostic performance using receiver operating characteristic (ROC) analysis.Results::The ML models were constructed using eight clinical features, including D-dimer, cardiac troponin T (cTNT), arterial oxygen saturation, heart rate, chest pain, lower limb pain, hemoptysis, and chronic heart failure. Among eight ML models, the RF model achieved the best performance with the highest area under the curve (AUC) (AUC = 0.774). Compared to the current clinical assessment strategies, the RF model outperformed the Wells score ( P = 0.030) and was not inferior to any other clinical probability assessment strategy. The AUC of the RF model for diagnosing APE onset in internal validation set was 0.726. Conclusions::Based on RF algorithm, a novel prediction model was finally constructed for APE diagnosis. When compared to the current clinical assessment strategies, the RF model achieved better diagnostic efficacy and accuracy. Therefore, the ML algorithm can be a useful tool in assisting with the diagnosis of APE.

This article describes the experience of implementing the informatization construction of teaching supervision for standardized residency training in Shanghai East Hospital, Tongji University, and discusses the means to improve teaching activity supervision, such as management informatization and internet technology. This study aims to ensure the efficiency and work quality of supervision, optimize the process and resource allocation of supervision, and lay a solid foundation for improving the quality of residency training and teaching in the hospital (especially the key indicators for residency training and teaching quality, including the supervision rate of teaching activities and the completion rate of teaching activities) and establishing a sound system and the assets of teaching data in residency training.

Objective To monitor the susceptibility of clinical isolates to antimicrobial agents in tertiary hospitals in major regions of China in 2022.Methods Clinical isolates from 58 hospitals in China were tested for antimicrobial susceptibility using a unified protocol based on disc diffusion method or automated testing systems.Results were interpreted using the 2022 Clinical &Laboratory Standards Institute(CLSI)breakpoints.Results A total of 318 013 clinical isolates were collected from January 1,2022 to December 31,2022,of which 29.5％were gram-positive and 70.5％were gram-negative.The prevalence of methicillin-resistant strains in Staphylococcus aureus,Staphylococcus epidermidis and other coagulase-negative Staphylococcus species(excluding Staphylococcus pseudintermedius and Staphylococcus schleiferi)was 28.3％,76.7％and 77.9％,respectively.Overall,94.0％of MRSA strains were susceptible to trimethoprim-sulfamethoxazole and 90.8％of MRSE strains were susceptible to rifampicin.No vancomycin-resistant strains were found.Enterococcus faecalis showed significantly lower resistance rates to most antimicrobial agents tested than Enterococcus faecium.A few vancomycin-resistant strains were identified in both E.faecalis and E.faecium.The prevalence of penicillin-susceptible Streptococcus pneumoniae was 94.2％in the isolates from children and 95.7％in the isolates from adults.The resistance rate to carbapenems was lower than 13.1％in most Enterobacterales species except for Klebsiella,21.7％-23.1％of which were resistant to carbapenems.Most Enterobacterales isolates were highly susceptible to tigecycline,colistin and polymyxin B,with resistance rates ranging from 0.1％to 13.3％.The prevalence of meropenem-resistant strains decreased from 23.5％in 2019 to 18.0％in 2022 in Pseudomonas aeruginosa,and decreased from 79.0％in 2019 to 72.5％in 2022 in Acinetobacter baumannii.Conclusions The resistance of clinical isolates to the commonly used antimicrobial agents is still increasing in tertiary hospitals.However,the prevalence of important carbapenem-resistant organisms such as carbapenem-resistant K.pneumoniae,P.aeruginosa,and A.baumannii showed a downward trend in recent years.This finding suggests that the strategy of combining antimicrobial resistance surveillance with multidisciplinary concerted action works well in curbing the spread of resistant bacteria.

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry(UPLC-Q-TOF-MS/MS) was used to rapidly identify the chemical components in Dracocephalum moldavica, and UPLC was employed to determine the content of its main components. MS analysis was performed using an electrospray ionization(ESI) source and data were collected in the negative ion mode. By comparing the retention time and mass spectra of reference compounds, and using a self-built compound database and the PubChem database, 68 compounds were identified from D. moldavica, including 36 flavonoids, 22 phenylpropanoids, 4 phenols, and 6 other compounds. On this basis, a UPLC quantitative method was established to simultaneously determine 8 main components, i.e., luteolin-7-O-glucuronide, apigenin-7-O-glucuronide, rosmarinic acid, diosmetin-7-O-glucuronide, tilianin, acacetin-7-O-glucuronide, acacetin-7-O-(6″-O-malonyl)-glucoside, and acacetin. A Waters ACQUITY BEH C_(18) column(2.1 mm × 100 mm, 1.7 μm) was used, with acetonitrile and a water solution containing 0.1% formic acid and 0.1% phosphoric acid as the mobile phase for gradient elution. The detection wavelength was set at 330 nm, with a flow rate of 0.4 mL·min~(-1), and the column temperature was maintained at 35 ℃. The 8 components demonstrated good linearity(r≥0.999 9) over a wide mass concentration range(50 or 100 times). The average recovery rate ranged from 97.5% to 105.1%, and the relative standard deviations(RSDs) were 0.90% to 3.4%(n= 6), indicating that the method was simple, accurate, and reliable. In 17 batches of D. moldavica samples, the content of these 8 components ranged from 0.405 to 2.10, 0.063 to 0.342, 0.446 to 2.43, 0.415 to 1.47, 1.57 to 4.34, 0.173 to 0.386, 1.00 to 5.40, and 0.069 to 0.207 mg·g~(-1), respectively. These results indicate significant differences in the internal quality of the samples, highlighting the need for strict quality control to ensure their pharmacodynamic efficacy. This study provides a scientific basis for the rapid discovery of pharmacodynamic substances, comprehensive quality control, and the formulation or revision of quality standards for D. moldavica.
Tandem Mass Spectrometry/methods* ; Chromatography, High Pressure Liquid/methods* ; Drugs, Chinese Herbal/chemistry* ; Lamiaceae/chemistry* ; Flavonoids/chemistry*

OBJECTIVE: To observe the effects of moxibustion on the ultrastructure of synovial cells of knee joint and serum cytokines in adjuvant arthritis (AA) rats, and to explore the potential mechanism of moxibustion in treatment of rheumatoid arthritis. METHODS: Forty-five Wistar male rats were randomly divided into a normal group, a model group and a moxibustion group, with 15 rats in each group. In the model group and the moxibustion group, the AA model was replicated under wind, cold and humid environment and by injection with complete freund's adjuvant. In the moxibustion group, moxibustion at "Zusanli" (ST 36) and "Shenshu" (BL 23) was used, 20 min each time, once daily, for consecutive 21 days. In the normal group and the model group, no intervention was processed. The scores of the knee joint swelling degree (JSD) and arthritis index (AI) were compared among groups. The ultrastructure of synovial cells of knee joint were observed under transmission electron microscope (TEM). The levels of serum cytokines such as tumor necrosis factor-α (TNF-α), interieukin (IL)-1β, IL-6 and IL-10 were detected using ELISA method. RESULTS: Compared with the normal group, JSD and AI scores, the levels of TNF-α, IL-1β and IL-6 were increased (P<0.01), while IL-10 was reduced (P<0.01) in the model group after intervention. JSD and AI scores, and the levels of TNF-α, IL-1β and IL-6 were lower (P<0.05, P<0.01), while the level of IL-10 was higher (P<0.01) in the moxibustion group compared with the model group. Compared with the normal group, the ultrastructure of synovial cell was obviously damaged in the model group, and the damage was attenuated in the moxibustion group compared with the model group. CONCLUSION Moxibustion can reduce the symptoms of arthritis in AA rats, which may be related to the improvement of the ultrastructure of synovial cells and the regulation of cytokines.
Male ; Rats ; Animals ; Cytokines ; Interleukin-10 ; Arthritis, Experimental ; Tumor Necrosis Factor-alpha ; Interleukin-6 ; Moxibustion ; Rats, Wistar ; Knee Joint