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*

Objective To analyze the risk factors of permanent hypoparathyroidism(pHPP)after total thyroidectomy in patients with thyroid cancer and establish a nomogram prediction model.Methods A total of 245 patients with thyroid cancer who received total thyroidectomy in our hospital were enrolled between January 2020 and January 2024.According to presence or absence of postoperative pHPP,patients were divided into the pHPP group and the non-pHPP group.The influencing factors of postoperative pHPP in patients with thyroid cancer were analyzed by univariate and multivariate Logistic regression analysis.The nomogram prediction model for postoperative pHPP in patients with thyroid cancer was constructed and varified,and efficiency of the model was evaluated.Results In 245 patients with thyroid cancer,the incidence of pHPP within 6 months after surgery was 10.20%(25/245).Univariate analysis showed that there were significant differences in tumor size,surgical method,central lymph node dissection,use of nano carbon tracer,envelope invasion,parathyroid excision by mistake,Hashimoto thyroiditis,serum calcium and parathyroid hormone at 1 d after surgery between the two groups(P＜0.05),but there were no significant differences in gender,age,smoking,drinking,extraglandular invasion,parathyroid autologous transplantation,preoperative vitamin D or serum phosphorus at 1 d after surgery between the two groups(P＞0.05).Multivariate analysis showed that maximum tumor diameter≥4 cm,routine and open total thyroidectomy,central lymph node dissection,no use of nano carbon tracer and parathyroid excision by mistake were all independent risk factors for postoperative pHPP in patients with thyroid cancer(P＜0.05).Results of nomogram prediction model showed that C-index was 0.921,the corrected curve was close to ideal curve,and AUC of nomogram model for predicting postoperative pHPP was 0.926(95%CI:0.871-0.981).Conclusion The nomogram prediction model constructed based on independent risk factors of postoperative pHPP has good predictive efficiency in patients with thyroid cancer.

Objective:To explore the efficacy and prognosis of preoperative treatment based on arterial infusion chemotherapy (PTAC) in patients with advanced gastric cancer.Methods:Clinical and follow-up data of 821 patients with advanced gastric cancer who received PTAC treatment at the General Hospital of the Eastern Theater Command of the People's Liberation Army from January 2001 to January 2021 were collected. According to the treatment regimen, patients were divided into the FLEEOX group (89 cases), the XEEOX group (196 cases), the SEEOX group (406 cases), and the SEEOX+PD-1 group (130 cases). The primary endpoint was the 3-year progression-free survival rate. Secondary endpoints included the 3-year overall survival rate, objective response rate, radical resection rate, major pathological response rate, and incidence of treatment associated adverse events.Results:After PTAC treatment, the objective response rate was 74.9% (615/821). A total of 671 patients underwent radical surgery, with a radical resection rate of 81.7% and an R0 resection rate of 70.2% (576/821). The pathological complete response rate was 16.7% (112/671), and the major pathological response rate was 32.2% (216/671). With an average follow-up of 27.7 months, the 3-year progression-free survival rate was 52.2%, and the 3-year overall survival rate was 55.8%. The 3-year progression-free survival rate of patients in the SEEOX+PD-1 group was 66.9%, the objective response rate was 83.8% (109/130), the major pathological response rate was 45.3% (53/117), and the radical resection rate was 90.0% (117/130), all of which were better than those in the XEEOX and SEEOX groups (all P＜0.05). However, during the treatment period, three patients in the SEEOX+PD-1 group died from immune-related adverse events. Conclusion:PTAC treatment is an effective preoperative treatment method for advanced gastric cancer, and is expected to further improve the treatment effect when combined with immunotherapy such as PD-1 monoclonal antibodies.

Objective To analyze the risk factors of permanent hypoparathyroidism(pHPP)after total thyroidectomy in patients with thyroid cancer and establish a nomogram prediction model.Methods A total of 245 patients with thyroid cancer who received total thyroidectomy in our hospital were enrolled between January 2020 and January 2024.According to presence or absence of postoperative pHPP,patients were divided into the pHPP group and the non-pHPP group.The influencing factors of postoperative pHPP in patients with thyroid cancer were analyzed by univariate and multivariate Logistic regression analysis.The nomogram prediction model for postoperative pHPP in patients with thyroid cancer was constructed and varified,and efficiency of the model was evaluated.Results In 245 patients with thyroid cancer,the incidence of pHPP within 6 months after surgery was 10.20%(25/245).Univariate analysis showed that there were significant differences in tumor size,surgical method,central lymph node dissection,use of nano carbon tracer,envelope invasion,parathyroid excision by mistake,Hashimoto thyroiditis,serum calcium and parathyroid hormone at 1 d after surgery between the two groups(P＜0.05),but there were no significant differences in gender,age,smoking,drinking,extraglandular invasion,parathyroid autologous transplantation,preoperative vitamin D or serum phosphorus at 1 d after surgery between the two groups(P＞0.05).Multivariate analysis showed that maximum tumor diameter≥4 cm,routine and open total thyroidectomy,central lymph node dissection,no use of nano carbon tracer and parathyroid excision by mistake were all independent risk factors for postoperative pHPP in patients with thyroid cancer(P＜0.05).Results of nomogram prediction model showed that C-index was 0.921,the corrected curve was close to ideal curve,and AUC of nomogram model for predicting postoperative pHPP was 0.926(95%CI:0.871-0.981).Conclusion The nomogram prediction model constructed based on independent risk factors of postoperative pHPP has good predictive efficiency in patients with thyroid cancer.

Objective:To evaluate the immunogenicity and immune persistence of human rabies vaccine (Vero cell) in healthy people aged 10-17 years and compare it with a group of adults aged 18-60 years.Methods:This study was conducted between July 2021 and November 2022 with Shangyu district and Shengzhou city of Shaoxing city, Zhejiang Province selected as the research sites. Zagreb regimen (2-1-1 schedule) and Essen regimen (1-1-1-1-1 schedule) were used for rabies vaccine administration. Serum samples were collected at different time points before and after immunization to compare the differences in seropositivity rates and geometric mean concentrations (GMC) between the 10-17 age group and the 18-60 age group.Results:A total of 1 200 healthy participants aged 10-60 were included, with 157 individuals (13.1%) in the 10-17 age group and 1 043 individuals (86.9%) in the 18-60 age group. Both groups displayed a nearly 100% seropositivity rate at 3, 6 and 12 months, and the participants in the same age group had similar antibody levels. The GMC of antibodies gradually increased after vaccination and peaked on 14 d. The 10-17 age group showed higher GMC of antibodies than the 18-60 age group at 14 d after the first dose (Zagreb regimen: 81.85 IU/ml vs 63.15 IU/ml, t=2.411, P=0.018; Essen regimen: 86.61 IU/ml vs 69.24 IU/ml, t=3.906, P<0.001). Similar differences were observed in the GMC of antibodies at 14 d and 3 months after the full vaccination course, but these differences gradually decreased and disappeared at 6 and 12 months after vaccination. Conclusions:Human rabies vaccine (Vero cell) has lasting immune protection in all participants within one year after vaccination, with no significant differences between the two vaccination regimens. Participants aged 10-17 have higher antibody levels compared to adults aged 18-60, but there is no significant difference in immune persistence between the two age groups.

OBJECTIVE T o analyze the current situation and characteristics of hospital-associated infection in a psy-chiatric hospital,providing references for formulation of control measures for hospital-associated infection.METHODS A retrospective analysis was conducted on hospital-associated infection data from Shanghai Mental Health Center between Jan.1,2019,and Oct.31,2024.The infection rates and infection sites across different years,patient populations,and departments were analyzed.RESULTS A total of 47 051 inpatients were investiga-ted,with 1 798 cases of hospital-associated infections,resulting in an infection rate of 3.82％.The highest inci-dence rate was observed in 2020(4.13％).The top three departments with the highest incidence rates were the in-fectious disease department(12.13％),geriatric psychiatry(7.67％),and the Traditional Chinese Medicine De-partment department(4.90％).The primary infection sites were the lower respiratory tract(57.06％),urinary tract(18.24％),skin and soft tissue(14.29％).The incidence rate was higher in males(5.32％)than in females(2.72％)(P＜0.001).Statistically significant differences were found in the incidence rates among different age groups(P＜0.001),with the highest rate observed in patients aged over 90 years(17.11％).The lowest infection rate was found in patients hospitalized for less than 60 days(0.69％),while the highest was in those hospitalized for more than 1 000 days(49.94％).CONCLUSIONS The patients in psychiatric hospitals are susceptible to infec-tions in the respiratory tract,urinary tract,skin and soft tissue.Targeted prevention and control measures can be implemented based on high-risk factors such as age,length of stay,and gender to reduce the occurrence of in-fections.

OBJECTIVE T o analyze the current situation and characteristics of hospital-associated infection in a psy-chiatric hospital,providing references for formulation of control measures for hospital-associated infection.METHODS A retrospective analysis was conducted on hospital-associated infection data from Shanghai Mental Health Center between Jan.1,2019,and Oct.31,2024.The infection rates and infection sites across different years,patient populations,and departments were analyzed.RESULTS A total of 47 051 inpatients were investiga-ted,with 1 798 cases of hospital-associated infections,resulting in an infection rate of 3.82％.The highest inci-dence rate was observed in 2020(4.13％).The top three departments with the highest incidence rates were the in-fectious disease department(12.13％),geriatric psychiatry(7.67％),and the Traditional Chinese Medicine De-partment department(4.90％).The primary infection sites were the lower respiratory tract(57.06％),urinary tract(18.24％),skin and soft tissue(14.29％).The incidence rate was higher in males(5.32％)than in females(2.72％)(P＜0.001).Statistically significant differences were found in the incidence rates among different age groups(P＜0.001),with the highest rate observed in patients aged over 90 years(17.11％).The lowest infection rate was found in patients hospitalized for less than 60 days(0.69％),while the highest was in those hospitalized for more than 1 000 days(49.94％).CONCLUSIONS The patients in psychiatric hospitals are susceptible to infec-tions in the respiratory tract,urinary tract,skin and soft tissue.Targeted prevention and control measures can be implemented based on high-risk factors such as age,length of stay,and gender to reduce the occurrence of in-fections.

Objective:To evaluate the immunogenicity and immune persistence of human rabies vaccine (Vero cell) in healthy people aged 10-17 years and compare it with a group of adults aged 18-60 years.Methods:This study was conducted between July 2021 and November 2022 with Shangyu district and Shengzhou city of Shaoxing city, Zhejiang Province selected as the research sites. Zagreb regimen (2-1-1 schedule) and Essen regimen (1-1-1-1-1 schedule) were used for rabies vaccine administration. Serum samples were collected at different time points before and after immunization to compare the differences in seropositivity rates and geometric mean concentrations (GMC) between the 10-17 age group and the 18-60 age group.Results:A total of 1 200 healthy participants aged 10-60 were included, with 157 individuals (13.1%) in the 10-17 age group and 1 043 individuals (86.9%) in the 18-60 age group. Both groups displayed a nearly 100% seropositivity rate at 3, 6 and 12 months, and the participants in the same age group had similar antibody levels. The GMC of antibodies gradually increased after vaccination and peaked on 14 d. The 10-17 age group showed higher GMC of antibodies than the 18-60 age group at 14 d after the first dose (Zagreb regimen: 81.85 IU/ml vs 63.15 IU/ml, t=2.411, P=0.018; Essen regimen: 86.61 IU/ml vs 69.24 IU/ml, t=3.906, P<0.001). Similar differences were observed in the GMC of antibodies at 14 d and 3 months after the full vaccination course, but these differences gradually decreased and disappeared at 6 and 12 months after vaccination. Conclusions:Human rabies vaccine (Vero cell) has lasting immune protection in all participants within one year after vaccination, with no significant differences between the two vaccination regimens. Participants aged 10-17 have higher antibody levels compared to adults aged 18-60, but there is no significant difference in immune persistence between the two age groups.

Objective:To explore the efficacy and prognosis of preoperative treatment based on arterial infusion chemotherapy (PTAC) in patients with advanced gastric cancer.Methods:Clinical and follow-up data of 821 patients with advanced gastric cancer who received PTAC treatment at the General Hospital of the Eastern Theater Command of the People's Liberation Army from January 2001 to January 2021 were collected. According to the treatment regimen, patients were divided into the FLEEOX group (89 cases), the XEEOX group (196 cases), the SEEOX group (406 cases), and the SEEOX+PD-1 group (130 cases). The primary endpoint was the 3-year progression-free survival rate. Secondary endpoints included the 3-year overall survival rate, objective response rate, radical resection rate, major pathological response rate, and incidence of treatment associated adverse events.Results:After PTAC treatment, the objective response rate was 74.9% (615/821). A total of 671 patients underwent radical surgery, with a radical resection rate of 81.7% and an R0 resection rate of 70.2% (576/821). The pathological complete response rate was 16.7% (112/671), and the major pathological response rate was 32.2% (216/671). With an average follow-up of 27.7 months, the 3-year progression-free survival rate was 52.2%, and the 3-year overall survival rate was 55.8%. The 3-year progression-free survival rate of patients in the SEEOX+PD-1 group was 66.9%, the objective response rate was 83.8% (109/130), the major pathological response rate was 45.3% (53/117), and the radical resection rate was 90.0% (117/130), all of which were better than those in the XEEOX and SEEOX groups (all P＜0.05). However, during the treatment period, three patients in the SEEOX+PD-1 group died from immune-related adverse events. Conclusion:PTAC treatment is an effective preoperative treatment method for advanced gastric cancer, and is expected to further improve the treatment effect when combined with immunotherapy such as PD-1 monoclonal antibodies.

ObjectiveTo evaluate the effectiveness and safety of Qiaoqi Formula （翘芪组方） for mild influenza. MethodsA randomized controlled study was designed， recruiting 74 patients with mild influenza， who were randomly divided into trial group and control group. The trial group took Qiaoqi Formula orally， 40ml each time， twice a day； the control group took Lianhua Qingwen Capsules （连花清瘟胶囊） orally， 1.4 g each time， three times a day. Both groups were treated for 3 consecutive days and follow-up for 4 consecutive days after treatment. The time for fever reduction including onset of fever reduction， complete fever reduction time， fever reduction rates at 24， 48 and 72 hours， improvement of influenza symptoms， total traditional Chinese medicine （TCM） symptom score， and safety indicators in two groups after treatment were recorded. ResultsSixty-five patients were ultimately included， including 36 in the trial group and 29 in the control group. Onset time of fever reduction in the trial group was （15.49±23.47） h， the complete fever reduction time （21.37±30.06）h， and the 24 h， 48 h， 72 h， fever reduction rate was 77.14%， 88.57%， 91.42% respectively. The above indicators of the control group showed as （17.58±20.38）h， （24.30±21.87）h， 61.29%， 90.32%， 96.77% respectively， with no statistically significant differences （P＞0.05）. On the 7th day after treatment， the total score of TCM syndromes in trial group and control group decreased compared to those before treatment （P＜0.05）. There was no statistically significant difference in the cure rate， significant effective rate， effective rate， and total effective rate of TCM syndromes between groups （P＞0.05）. On the 4th day， the lymphocyte ratio of patients in the control group was higher than before treatment， while alanine aminotransferase （ALT）， aspartate aminotransferase （AST）， urea， and creatinine of both groups before and after treatment were within the normal range. The main adverse reactions in both groups were mild headache and dizziness， and no serious adverse reactions observed. ConclusionThe therapeutic effect of Qiaoqi Formula in treating mild influenza is equivalent to Lianhua Qingwen Capsules， which can shorten the fever reduction time， improve clinical symptoms， and no adverse events observed during the study.