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 investigate the clinical characteristics of patients with high-myopia macular hole retinal detachment (MHRD) combined with choroidal detachment and to preliminarily analyze factors associated with postoperative hole closure.Methods:A retrospective clinical case series study. A total of 68 patients with high myopia (68 eyes) with MHRD diagnosed by Department of Ophthalmology, Peking University People’s Hospital from January 2019 to April 2024 were included in this study. Among them, there were 14 males (14 eyes) and 54 females (54 eyes). The mean age was (61.10±9.66) years. All eyes were treated with pars plana vitrectomy (PPV) combined with silicone oil or gas filling. Best corrected visual acuity (BCVA), intraocular pressure, and B-mode ultrasonography were performed. The BCVA test was performed using the Snellen visual acuity chart, which was statistically converted to logarithm of the minimum angle of resolution (logMAR) visual acuity. The range of choroidal detachment was defined according to the number of involved quadrants observed in B-mode ultrasound or surgery, which was divided into 1 to 4 quadrants. Axial length (AL) was measured under retinal reattachment. In 68 eyes, there were 17 eyes with choroidal detachment and 51 eyes without choroidal detachment, respectively. There were 17 eyes with choroidal detachment, and the detachment range involved 1, 2, 2 and 12 eyes in 1, 2, 3 and 4 quadrants, respectively. During operation, 13% C 3F 8 was filled in 2 eyes, all of which were not complicated with choroidal detachment. 66 eyes were filled with silicone oil. According to whether the patients were complicated with choroidal detachment, the patients were divided into the group without choroidal detachment and the group with choroidal detachment. Independent sample t test, Welch two-sample t test or Mann-Whitney U test were used for comparison between groups. Generalized linear regression and logistic regression were used to analyze the relationship between the aperture size of postoperative unclosed holes and the closed hole after surgery and clinical factors. Results:At 3 months after surgery, the logMAR BCVA of the affected eye was 1.29±0.43, with a preoperative to postoperative difference ranging from -1.60 to 0.70 (-0.51±0.51) logMAR units. The AL ranged from 26.6 to 34.3 (29.60±2.12) mm. Among 68 eyes, macular hole of 37 (54.4%, 37/68) eyes were open and 31 (45.6%, 31/68) eyes were closed, respectively. The hole diameter of the open eye was (753±424) μm. There was no significant difference in age, course of disease and AL between the two groups ( W=412.0, 477.5, 427.0; P>0.05). Before operation, BCVA in patients with choroidal detachment was worse ( W=257.5) and intraocular pressure was lower ( t=4.051) in patients with choroidal detachment compared with those without choroidal detachment, with statistical significance ( P<0.05). At 3 months after surgery, BCVA in patients with choroidal detachment was significantly worse than that in patients without choroidal detachment, with statistical significance ( W=284.0, P<0.05). There were no significant differences in logMAR BCVA difference ( t=0.616) and macular hole closure rate ( χ 2=0.000) before and after surgery ( P>0.05). The reoperation rate of retinal detachment due to persistent or recurrent retinal detachment was significantly higher in the group with choroid detachment than in the group without choroid detachment, and the difference was statistically significant (odds ratio=6.424, P<0.05). Logistic regression analysis showed that young age was significantly correlated with macular hole closure failure after surgery ( β=0.077, P=0.015). There was no correlation between AL, duration of disease, BCVA before surgery, intraocular pressure, wether combined with choroid detachment range and postoperative hole closure ( β=-0.072, 0.000, 0.672, -0.085, -0.391; P>0.05). Conclusions:Concomitant choroidal detachment adversely affected on both pre-operative and post-operative visual acuity in high myopia MHRD. It is closely associated with the risk of recurrent retinal detachment and the needs of multiple operations, but has no significant effect on hole closure rate. Lower age of onset may be a risk factor for macular hole closure.

Objective:To observe and analyze the correlation between ectopic foveal inner layer (EIFL) and the EIFL-based idiopathic epiretinal membrane (ERM) staging system and the anatomic and functional prognosis of ERM eyes post pars plana vitrectomy (PPV).Methods:A retrospective study. From January 1, 2020 to October 30, 2023, 345 eyes of 330 patients diagnosed with idiopathic ERM in Department of Ophthalmology of Peking University People's Hospital and treated with standard transciliary flat three-channel 25G PPV combined with ERM and internal limiting membrane exfoliation were included in the study. Among them, 96 were males (111 eyes) and 234 were females (234 eyes). The mean age was (66.8±7.7) years. All study eyes received standard three-port 25G PPV combined with ERM and internal limiting membrane peeling. All study eyes underwent best corrected visual acuity (BCVA) and optical coherence tomography (OCT) examinations. BCVA was performed using a standard logarithmic visual acuity chart and converted to logarithm of the minimum angle of resolution visual acuity for statistical analysis. EIFL thickness and central foveal thickness (CFT) on OCT were measured. ERM eyes were grouped into stage Ⅰ, Ⅱ, Ⅲ and Ⅳ according to ERM staging scheme based on EIFL; disorganization of the retinal inner layers (DRIL) of study eyes were assessed and grouped into no, mild and severe groups. The correlation between ERM staging as well as EIFL thickness and the anatomical and functional prognosis 6 months post-PPV were analyzed.Results:Among 345 study eyes, 12, 87, 174 and 72 eyes were stage Ⅰ-Ⅳ ERM respectively, 63 with no DRIL, 216 with mild DRIL and 66 with severe DRIL. Among the 153 eyes with macular edema, the edema subsided in 66 eyes (43.1%, 66/153) 6 months after the operation. Eighty-seven eyes (56.9%, 87/153) did not regress. The edema subsided 6 months after the operation was not significantly correlated with the ERM stage before the operation ( χ2=3.331, R=?0.145, P=0.304) or the degree of DRIL ( χ2=0.655, R=?0.108, P=0.445). The results of the correlation analysis showed that logMAR BCVA 6 months after the surgery was positively correlated with the degree of DRIL before the surgery ( Tau-b=0.236), ERM stage ( Tau-b=0.194), CFT ( r=0.383), and EIFL thickness ( r=0.317) ( P<0.05). There was no significant correlation with the thickness of the outer nuclear layer before the operation ( r=0.004, P>0.05). Preoperative ERM stage ( Tau-b=0.303, P<0.001) and DRIL severity ( Tau-b= 0.238, P=0.001) were positively correlated with CFT at 6 months after surgery. Conclusion:The ERM stage and EIFL thickness before the operation are positively correlated with logMAR BCVA and CFT 6 months after the operation.

Objective:To investigate the clinical characteristics of patients with high-myopia macular hole retinal detachment (MHRD) combined with choroidal detachment and to preliminarily analyze factors associated with postoperative hole closure.Methods:A retrospective clinical case series study. A total of 68 patients with high myopia (68 eyes) with MHRD diagnosed by Department of Ophthalmology, Peking University People’s Hospital from January 2019 to April 2024 were included in this study. Among them, there were 14 males (14 eyes) and 54 females (54 eyes). The mean age was (61.10±9.66) years. All eyes were treated with pars plana vitrectomy (PPV) combined with silicone oil or gas filling. Best corrected visual acuity (BCVA), intraocular pressure, and B-mode ultrasonography were performed. The BCVA test was performed using the Snellen visual acuity chart, which was statistically converted to logarithm of the minimum angle of resolution (logMAR) visual acuity. The range of choroidal detachment was defined according to the number of involved quadrants observed in B-mode ultrasound or surgery, which was divided into 1 to 4 quadrants. Axial length (AL) was measured under retinal reattachment. In 68 eyes, there were 17 eyes with choroidal detachment and 51 eyes without choroidal detachment, respectively. There were 17 eyes with choroidal detachment, and the detachment range involved 1, 2, 2 and 12 eyes in 1, 2, 3 and 4 quadrants, respectively. During operation, 13% C 3F 8 was filled in 2 eyes, all of which were not complicated with choroidal detachment. 66 eyes were filled with silicone oil. According to whether the patients were complicated with choroidal detachment, the patients were divided into the group without choroidal detachment and the group with choroidal detachment. Independent sample t test, Welch two-sample t test or Mann-Whitney U test were used for comparison between groups. Generalized linear regression and logistic regression were used to analyze the relationship between the aperture size of postoperative unclosed holes and the closed hole after surgery and clinical factors. Results:At 3 months after surgery, the logMAR BCVA of the affected eye was 1.29±0.43, with a preoperative to postoperative difference ranging from -1.60 to 0.70 (-0.51±0.51) logMAR units. The AL ranged from 26.6 to 34.3 (29.60±2.12) mm. Among 68 eyes, macular hole of 37 (54.4%, 37/68) eyes were open and 31 (45.6%, 31/68) eyes were closed, respectively. The hole diameter of the open eye was (753±424) μm. There was no significant difference in age, course of disease and AL between the two groups ( W=412.0, 477.5, 427.0; P>0.05). Before operation, BCVA in patients with choroidal detachment was worse ( W=257.5) and intraocular pressure was lower ( t=4.051) in patients with choroidal detachment compared with those without choroidal detachment, with statistical significance ( P<0.05). At 3 months after surgery, BCVA in patients with choroidal detachment was significantly worse than that in patients without choroidal detachment, with statistical significance ( W=284.0, P<0.05). There were no significant differences in logMAR BCVA difference ( t=0.616) and macular hole closure rate ( χ 2=0.000) before and after surgery ( P>0.05). The reoperation rate of retinal detachment due to persistent or recurrent retinal detachment was significantly higher in the group with choroid detachment than in the group without choroid detachment, and the difference was statistically significant (odds ratio=6.424, P<0.05). Logistic regression analysis showed that young age was significantly correlated with macular hole closure failure after surgery ( β=0.077, P=0.015). There was no correlation between AL, duration of disease, BCVA before surgery, intraocular pressure, wether combined with choroid detachment range and postoperative hole closure ( β=-0.072, 0.000, 0.672, -0.085, -0.391; P>0.05). Conclusions:Concomitant choroidal detachment adversely affected on both pre-operative and post-operative visual acuity in high myopia MHRD. It is closely associated with the risk of recurrent retinal detachment and the needs of multiple operations, but has no significant effect on hole closure rate. Lower age of onset may be a risk factor for macular hole closure.

Objective:To observe and analyze the correlation between ectopic foveal inner layer (EIFL) and the EIFL-based idiopathic epiretinal membrane (ERM) staging system and the anatomic and functional prognosis of ERM eyes post pars plana vitrectomy (PPV).Methods:A retrospective study. From January 1, 2020 to October 30, 2023, 345 eyes of 330 patients diagnosed with idiopathic ERM in Department of Ophthalmology of Peking University People's Hospital and treated with standard transciliary flat three-channel 25G PPV combined with ERM and internal limiting membrane exfoliation were included in the study. Among them, 96 were males (111 eyes) and 234 were females (234 eyes). The mean age was (66.8±7.7) years. All study eyes received standard three-port 25G PPV combined with ERM and internal limiting membrane peeling. All study eyes underwent best corrected visual acuity (BCVA) and optical coherence tomography (OCT) examinations. BCVA was performed using a standard logarithmic visual acuity chart and converted to logarithm of the minimum angle of resolution visual acuity for statistical analysis. EIFL thickness and central foveal thickness (CFT) on OCT were measured. ERM eyes were grouped into stage Ⅰ, Ⅱ, Ⅲ and Ⅳ according to ERM staging scheme based on EIFL; disorganization of the retinal inner layers (DRIL) of study eyes were assessed and grouped into no, mild and severe groups. The correlation between ERM staging as well as EIFL thickness and the anatomical and functional prognosis 6 months post-PPV were analyzed.Results:Among 345 study eyes, 12, 87, 174 and 72 eyes were stage Ⅰ-Ⅳ ERM respectively, 63 with no DRIL, 216 with mild DRIL and 66 with severe DRIL. Among the 153 eyes with macular edema, the edema subsided in 66 eyes (43.1%, 66/153) 6 months after the operation. Eighty-seven eyes (56.9%, 87/153) did not regress. The edema subsided 6 months after the operation was not significantly correlated with the ERM stage before the operation ( χ2=3.331, R=?0.145, P=0.304) or the degree of DRIL ( χ2=0.655, R=?0.108, P=0.445). The results of the correlation analysis showed that logMAR BCVA 6 months after the surgery was positively correlated with the degree of DRIL before the surgery ( Tau-b=0.236), ERM stage ( Tau-b=0.194), CFT ( r=0.383), and EIFL thickness ( r=0.317) ( P<0.05). There was no significant correlation with the thickness of the outer nuclear layer before the operation ( r=0.004, P>0.05). Preoperative ERM stage ( Tau-b=0.303, P<0.001) and DRIL severity ( Tau-b= 0.238, P=0.001) were positively correlated with CFT at 6 months after surgery. Conclusion:The ERM stage and EIFL thickness before the operation are positively correlated with logMAR BCVA and CFT 6 months after the operation.

Diabetes, hypertension, and dyslipidemia, collectively referred to the " Three Highs, " represent increasingly prevalent metabolic risk factors in China. Many individuals experience all three conditions concurrently, significantly heightening the risk of cardiovascular disease and mortality. Although the National Metabolic Management Center(MMC) has been established for over eight years and has its unique features, the awareness, treatment, and control rates of these diseases in China remain low, and the efficiency of community management is insufficient. According to the previous two editions of management guidelines and the most recent domestic and international diagnostic and treatment guidelines, this paper conducts an in-depth analysis of the operational experience and management strategies of the MMC. Its aim is to improve the efficiency of grassroots MMC mode management for " Three Highs" patients and ensure that patients receive more standardized management.

Objective:To prepare mesenchymal stem cells with antioxidant capacity (AO-MSC ) from human umbilical cords and evaluate its cell biological properties.Methods:In control group,mesenchymal stem cells (MSC) were isolated by digesting human umbilical cord Wharton's Jelly tissues with 0.2％ collagenase Ⅱ,and the released cells were collected and cultured in an animal serum-free culture medium.In AO-MSC group,incompletely collagenase Ⅱ-digested tissue debris were allowed to adhere to flusk flat bottoms and the AO-MSC was harvested by adherent culture. The conventional digestion and culture method was used as control.MSC colony forming ability was evaluated by fibroblast colony forming assay (CFU-F).MSC proliferative capacity was evaluated by CCK-8 assay.The MSC surface markers were detected by using flow cytometry and immunofluorescence staining.The adipogenic and osteogenic capacity of MSC was evaluated by multi-differentiation in vitro,and the mRNA expression of genes that control adipogenic and osteogenic differentiation was detected by real-time fluorescence quantitative PCR (RT-qPCR );Moreover,the mRNA expression of antioxidant substances such as SOD-1,GSH,GAT,and NQO1 in MSC was also evaluated by RT-qPCR.Results:The AO-MSC isolated by this strategy reached a confluence of 80％-90％ at around 18 days and grew in a swirling pattern.Flow cytometry and immunofluorescence staining assays showed that CD73,CD29,CD105,CD90 were highly expressed and CD31,CD45,HLA-DR were scarcely expressed in AO-MSC.AO-MSC exhibited stronger self-renewal and differentiation ability compared to MSC.However,the in vitro adipogenic-osteogenic capacity of MSC in the control group was stronger than that of AO-MSC.RT-qPCR assay showed that AO-MSC expressed higher mRNA levels of antioxidant substances compared to MSC.Conclusion:Human AO-MSC is successfully prepared from human umbilical cord without animal serum.

Acute liver injury (ALI) is one of the common severe diseases in clinic, which is characterized by redox imbalance and inflammatory storm. Untimely treatment can easily lead to liver failure and even death. Rosmarinic acid (RA) has been proved to have anti-inflammatory and antioxidant activity, but it is not clear how to protect ALI through antioxidation and inhibition of inflammation. Therefore, this study explored the therapeutic effect and molecular mechanism of RA on ALI through in vitro and in vivo experiments. In the mouse ALI model, the effects of RA on liver function and inflammatory indexes were studied, the pathological changes of liver were observed by HE, the effect of RA on reactive oxygen species in liver was detected by fluorescence method, and the level of F4/80 in liver tissue was detected by immunohistochemical method. The levels of thioredoxin interacting protein (TXNIP), NOD-like receptor protein 3 (NLRP3) and cysteinyl aspartate specific proteinase-1 (CASPASE-1) in liver tissue were measured by Western blot. All animal welfare and experimental procedures follow the rules of the Animal Ethics Committee of Southwest Minzu University. In vitro, human hepatoma cell line HepG2 was used to establish the model of oxidative damage induced by H₂O₂. The cell viability was detected by CCK-8 method. The level of interleukin-1β (IL-1β) in the supernatant was detected by enzyme linked immunosorbent assay (ELISA), the activity of lactatede hydrogenase (LDH) was detected by LDH kit, and the level of ROS was detected by fluorescence probe DCFH-DA labeling. The mRNA expression of Txnip, Nlrp3, Caspase 1, Il1β was detected by real-time fluorescence quantitative PCR (qPCR), and the protein levels of nuclear factor erythroid-2 related factor 2 (NRF2), TXNIP, NLRP3 and CASPASE-1 were measured by Western blot. The results showed that compared with the model group, the degree of liver swelling, tissue injury, liver function index in RA group were significantly lower than those in model group. And RA significantly attenuated the increases of ROS in liver tissue. The expression levels of TXNIP, NLRP3 and CASPASE-1 in liver tissue were significantly lower than those in model group. Additionally, RA inhibited the expressions of F4/80 and IL-1β. In vitro experiment, compared with model group, RA effectively inhibited the secretion of IL-1β and LDH. The level of ROS also decreased significantly. RA inhibited the mRNA expressions of Txnip, Caspase 1, Il1β. Furthermore, RA significantly increased the expression level of NRF2 protein in nucleus, and decreased the expression level of TXNIP and NLRP3 protein. Specifically, with the addition of ML385, the effect of RA on NRF2, TXNIP, NLRP3, CASPASE-1 protein expression was reversed. Collectively, these findings suggested that RA may inhibit the production of ROS by promoting NRF2 nuclear transfer, and then reduce the activation of NLRP3 inflammatory bodies by TXNIP, reduce cell death and inflammatory response to prevent the liver injury.

Objective:To construct the quality evaluation scale of specification of management for humanistic caring in outpatients and test its reliability and validity.Methods:Referring to the group standards in Specification of Management for Humanistic Caring in Outpatients released by the China Association for Life Care,as well as relevant guidelines and literature,a pool of items for the quality evaluation scale of specification of management for humanistic caring in outpatients was formed.After expert consultation and expert argumentation,a quality evaluation scale of specification of management for humanistic caring in outpatients was constructed.From January to February 2024,243 hospital managers from 5 hospitals in Zhengzhou were selected as survey subjects to conduct item analysis,and reliability and validity testing on the scale.Results:Two rounds of expert inquiry and two rounds of expert argumentation were conducted,with questionnaire response rates of 92.00%and 100.00%,respectively,and expert authority coefficients of 0.952.In the second round of the expert inquiry scale,the mean importance score of the first-level indicators was 4.80 to 5.00,the full score ratio was 88.00%to 100.00%,the coefficient of variation was 0.04 to 0.17,and Kendall's coefficient of concordance was 0.857(P＜0.001);the mean importance score of the second-level indicators was 4.60 to 5.00,the full score ratio was 80.00%to 100.00%,the coefficient of variation was 0.00 to 0.21,and Kendall's coefficient of concordance was 0.775(P＜0.001);the mean importance score of the third-level indicators was 4.60 to 5.00,the full score ratio was 76.00%to 100.00%,the coefficient of variation was 0.00 to 0.21,and Kendall's coefficient of concordance was 0.830(P＜0.001).Finally,a quality evaluation scale of specification of management for humanistic caring in outpatients was formed,including 5 first-level indicators,25 second-level indicators,and 58 third-level indicators.Exploratory factor analysis produced 5 common factors with a cumulative variance contribution rate of 74.628%.The Pearson correlation coefficients between the five-factor scores ranged from 0.648 to 0.798,and the correlation coefficients between the factor scores and the total score of the scale ranged from 0.784 to 0.938.The scale-level content validity index(S-CVI)of the scale was 0.945,the item-content validity index(I-CVI)was 0.725 to 1.000,the Cronbach's alpha coefficient of the total scale was 0.973,and the retest reliability coefficient was 0.934.Conclusion:The constructed quality evaluation scale of specification of management for humanistic caring in outpatients has good scientific validity and reliability,and can be used as an evaluation tool for specification of management for humanistic caring in outpatients.

Currently,human health due to corona virus disease 2019(COVID-19)pandemic has been seriously threatened.The coronavirus severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)spike(S)protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of COVID-19.However,the efficacy is compromised by the SARS-CoV-2 evolvement and mutation.Here we report the SARS-CoV-2 S protein receptor-binding domain(RBD)inhibitor licorice-saponin A3(A3)could widely inhibit RBD of SARS-CoV-2 variants,including Beta,Delta,and Omicron BA.1,XBB and BQ1.1.Furthermore,A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells,with EC50 of 1.016 pM.The mechanism was related to binding with Y453 of RBD deter-mined by hydrogen-deuterium exchange mass spectrometry(HDX-MS)analysis combined with quan-tum mechanics/molecular mechanics(QM/MM)simulations.Interestingly,phosphoproteomics analysis and multi fluorescent immunohistochemistry(mIHC)respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 mitogen-activated protein kinase(MAPK)path-ways and rebalancing the corresponding immune dysregulation.This work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.