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*

ObjectiveThis study aimed to observe the impact of sinomenine hydrochloride on the proliferation of fibroblasts and the mRNA expression of related genes in knee joint adhesion and contracture in rabbits. Additionally, we sought to explore its potential mechanisms in combating knee joint adhesion and contracture. MethodsFibroblasts were cultured in vitro, and experimental groups with varying concentrations of sinomenine hydrochloride were established alongside a control group. Cell proliferation was assessed using the CCK-8 assay. Changes in the mRNA expression of fibroblast-related genes following sinomenine hydrochloride treatment were evaluated using RT-qPCR. The impact of the drug on serum levels of inflammatory cytokines was determined using the ELISA method, and the expression of related proteins was assessed using Western blot. ResultsSinomenine hydrochloride was found to inhibit fibroblast viability, with viability decreasing as the concentration of sinomenine hydrochloride increased. The effects of sinomenine hydrochloride in all experimental groups were highly significant (P<0.05). At the mRNA expression level, compared to the control group, sinomenine hydrochloride led to a significant downregulation of inflammatory cytokines in all groups (P<0.05). Additionally, the expression levels of apoptosis-related proteins significantly increased, while Bcl-2 mRNA expression decreased (P<0.05). The mRNA expression levels of the PI3K/mTOR/AKT3 signaling pathway also decreased (P<0.05). At the protein expression level, in comparison to the control group, the levels of inflammatory cytokines IL-6, IL-8, IL-1β, and TGF-β were significantly downregulated in the middle and high-dose sinomenine hydrochloride groups (P<0.05). The expression levels of cleaved-PARP, cleaved caspase-3/7, and Bax increased and were positively correlated with the dose, while the expression levels of the anti-apoptotic protein Bcl-2 and the PI3K/AKT3/mTOR signaling pathway were negatively correlated with the dose. Sinomenine hydrochloride exhibited a significant inhibitory effect on the viability of rabbit knee joint fibroblasts, which may be associated with the downregulation of inflammatory cytokines IL-6, IL-8, and IL-1β, promotion of apoptosis-related proteins cleaved-PARP, cleaved caspase-3/7, and Bax, suppression of Bcl-2 expression, and inhibition of gene expression in the downstream PI3K/AKT3/mTOR signaling pathway. ConclusionSinomenine hydrochloride can inhibit the inflammatory response of fibroblasts in adhesive knee joints and accelerate fibroblast apoptosis. This mechanism may offer a novel approach to improving and treating knee joint adhesion.

Objective To investigate the prognosis of childhood T-lymphoblastic lymphoma(T-LBL)treated with acute lymphoblastic leukemia(ALL)regimen and related influencing factors.Methods A retrospective analysis was performed for the prognostic characteristics of 29 children with T-LBL who were treated with ALL regimen(ALL-2009 or CCCG-ALL-2015 regimen)from May 2010 to May 2022.Results The 29 children with T-LBL had a 5-year overall survival(OS)rate of 84％±7％and an event-free survival(EFS)rate of 81％±8％.The children with B systemic symptoms(unexplained fever＞38° C for more than 3 days;night sweats;weight loss＞10％within 6 months)at initial diagnosis had a lower 5-year EFS rate compared to the children without B symptoms(P＜0.05).The children with platelet count＞400x109/L and involvement of both mediastinum and lymph nodes at initial diagnosis had lower 5-year OS rates(P＜0.05).There were no significant differences in 5-year OS and EFS rates between the children treated with CCCG-ALL-2015 regimen and those treated with ALL-2009 regimen(P＞0.05).Compared with the ALL-2009 regimen,the CCCG-ALL-2015 regimen reduced the frequency of high-dose methotrexate chemotherapy and the incidence rate of severe infections(P＜0.05).Conclusions The ALL regimen is safe and effective in children with T-LBL.Children with B systemic symptoms,platelet count＞400x109/L,and involvement of both mediastinum and lymph nodes at initial diagnosis tend to have a poor prognosis.Reduction in the frequency of high-dose methotrexate chemotherapy can reduce the incidence rate of severe infections,but it does not affect prognosis.

Metabolic dysfunction-associated fatty liver disease (MAFLD) is an increasingly common liver disease worldwide. MAFLD is diagnosed based on the presence of steatosis on images, histological findings, or serum marker levels as well as the presence of at least one of the three metabolic features: overweight/obesity, type 2 diabetes mellitus, and metabolic risk factors. MAFLD is not only a liver disease but also a factor contributing to or related to cardiovascular diseases (CVD), which is the major etiology responsible for morbidity and mortality in patients with MAFLD. Hence, understanding the association between MAFLD and CVD, surveillance and risk stratification of MAFLD in patients with CVD, and assessment of the current status of MAFLD management are urgent requirements for both hepatologists and cardiologists. This Taiwan position statement reviews the literature and provides suggestions regarding the epidemiology, etiology, risk factors, risk stratification, nonpharmacological interventions, and potential drug treatments of MAFLD, focusing on its association with CVD.

Patients with severe trauma require an extremely timely treatment and transfusion plays an irreplaceable role in the emergency treatment of such patients. An increasing number of evidence-based medicinal evidences and clinical practices suggest that patients with severe traumatic bleeding benefit from early transfusion of low-titer group O whole blood or hemostatic resuscitation with red blood cells, plasma and platelet of a balanced ratio. However, the current domestic mode of blood supply cannot fully meet the requirements of timely and effective blood transfusion for emergency treatment of patients with severe trauma in clinical practice. In order to solve the key problems in blood supply and blood transfusion strategies for emergency treatment of severe trauma, Branch of Clinical Transfusion Medicine of Chinese Medical Association, Group for Trauma Emergency Care and Multiple Injuries of Trauma Branch of Chinese Medical Association, Young Scholar Group of Disaster Medicine Branch of Chinese Medical Association organized domestic experts of blood transfusion medicine and trauma treatment to jointly formulate Chinese expert consensus on blood support mode and blood transfusion strategies for emergency treatment of severe trauma patients ( version 2024). Based on the evidence-based medical evidence and Delphi method of expert consultation and voting, 10 recommendations were put forward from two aspects of blood support mode and transfusion strategies, aiming to provide a reference for transfusion resuscitation in the emergency treatment of severe trauma and further improve the success rate of treatment of patients with severe trauma.

Objective:To explore the effects of frailty syndrome on activities of daily living and its associated risk for adverse outcomes among elderly residents in China.Methods:Using open data from "China Health and Retirement Longitudinal Survey", the 2011 baseline survey was conducted on general information, health risk factors, chronic disease, data obtained from various ability assessments and Fried frailty criteria assessments for community elderly aged 60 years and over.The follow-up data were used to analyze the adverse outcomes of frailty syndrome using a covariation-adjusted Logistic regression model.Results:Among the 5 630 people in the baseline population, 34.9%(1 963/5 630 cases)were non-frailty, 57.4%(3 236 cases)were pre-frailty, and 7.7%(431 cases)were frailty.The frailty group had higher rates of falls, hip fractures, hospitalizations, and death than the pre-frail and non-frail groups at the 3rd, 5th, and 8th years of follow-up.At follow up to 2015, the covariate-adjusted analysis of the study population showed that as compared with the non-frail group, the frail group had increased risks of falling( OR=1.738, 95% CI: 1.292-2.338, P<0.001), increased risks of hip fracture( OR=2.672, 95% CI: 1.365-5.233, P=0.004), increased risks of hospitalization( OR=1.670, 95% CI: 1.224-2.277, P=0.001), increased risk of death( OR=1.599, 95% CI: 1.256-2.035, P<0.001), increased risks of declined upper limb activity( OR=2.769, 95% CI: 2.101-3.650, P<0.001), of declined instrumental activity of daily living( OR=2.567, 95% CI: 1.941-3.395, P<0.001), and of declined basic activities of daily living( OR=2.790, 95% CI: 2.110-3.689, P<0.001). Conclusions:Frailty syndrome increases the risk of decreased ability to live, falls, hip fractures, hospitalization and death in older adults.Frailty screening is an effective tool for predicting the risk of adverse outcomes in elderly community populations.

Objective: We analyze the characteristics of Clostridioides difficile (C. difficile) infection among diarrhea patients in Kunming from 2018 to 2020 and provide evidence for follow-up surveillance and prevention. Methods: A total of 388 fecal samples of diarrhea patients from four sentinel hospitals in Yunnan Province from 2018 to 2020 were collected. Real-time quantitative PCR was used to detect the fecal toxin genes of C. difficile. The positive fecal samples isolated the bacteria, and isolates were identified by mass spectrometry. The genomic DNA of the strains was extracted for multi-locus sequence typing (MLST). The fecal toxin, strain isolation, and clinical patient characteristics, including co-infection with other pathogens, were analyzed. Results: Among the 388 fecal samples, 47 samples with positive reference genes of C. difficile were positive, with a total positive rate of 12.11%. There were 4 (8.51%) non-toxigenic and 43 (91.49%) toxigenic ones. A total of 18 strains C. difficile were isolated from 47 positive specimens, and the isolation rate of positive specimens was 38.30%. Among them, 14 strains were positive for tcdA, tcdB, tcdC, tcdR, and tcdE. All 18 strains of C. difficile were negative for binary toxins. The MLST results showed 10 sequence types (ST), including 5 strains of ST37, accounting for 27.78%; 2 strains of ST129, ST3, ST54, and ST2, respectively; and 1 strain of ST35, ST532, ST48, ST27, and ST39, respectively. Fecal toxin gene positive (tcdB+) results were statistically associated with the patient's age group and with or without fever before the visit; positive isolates were only statistically associated with the patient's age group. In addition, some C. difficile patients have co-infection with other diarrhea-related viruses. Conclusions: The infection of C. difficile in diarrhea patients in Kunming is mostly toxigenic strains, and the high diversity of strains was identified using the MLST method. Therefore, the surveillance and prevention of C. difficile should be strengthened.
Humans ; Bacterial Toxins/genetics* ; Enterotoxins/genetics* ; Clostridioides difficile/genetics* ; Multilocus Sequence Typing ; Coinfection ; Bacterial Proteins/genetics* ; China/epidemiology* ; Clostridium Infections/epidemiology* ; Diarrhea/microbiology*

Chinese Society of Hepatology and Chinese Society of Infectious Diseases, Chinese Medical Association update the guidelines for the prevention and treatment of chronic hepatitis B (version 2022) in 2022. The latest guidelines recommend more extensive screening and more active antiviral treating for hepatitis B virus infection. This article interprets the essential updates in the guidelines to help deepen understanding and better guide the clinical practice.
Humans ; Hepatitis B, Chronic/drug therapy* ; Hepatitis B/drug therapy* ; Hepatitis B virus ; Antiviral Agents/therapeutic use* ; Gastroenterology

Abstract: Objective　To analyze the epidemiological characteristics (season, age, gender, mixed infection and clinical manifestations, etc.) of Mycoplasma pneumoniae (MP) infection in children in Hainan Province, so as to provide epidemiological evidence-based medical basis for the prevention and control of MP infection in children in Hainan Province. Methods　The serum IgM antibodies of MP, Legionella pneumophila, Chlamydia pneumoniae, adenovirus, respiratory syncytial virus (RSV), Q fever Rickettsia, parainfluenza virus, influenza A virus and influenza B virus in children with respiratory tract infections (RTIs) who were hospitalized in pediatrics of many hospitals in Hainan Province from March 2012 to February 2020 were detected by indirect immunofluorescence method. The positive serum MP-IgM antibody was defined as MP infection. The epidemiological and clinical data of MP infected cases were analyzed retrospectively. Results　From March, 2012 to February, 2020, a total of 35 731 qualified pediatric inpatients with RTIs in many hospitals in Hainan Province were tested for serum MP-IgM with the total positive rate of 39.12% (13 978/35 731). The yearly positive rates of MP-IgM from 2012 to 2020 were 48.39%, 56.23%, 56.62%, 47.04%, 29.71%, 24.14%, 47.55%, 36.84% and 24.46% respectively. The positive rates of MP-IgM in 2013 and 2014 were significantly higher than those in other years (P<0.05). The positive rate of MP-IgM in summer in Hainan Province was the highest (41.34%) and the lowest in winter (35.77%) (P<0.05). MP infection occurred in all age groups, the positive rate of MP-IgM in children of preschool (51.80%) was significantly higher than that in other age groups (P<0.01), and the positive rate of MP IgM in children of infancy (15.36%) was lower than that in other age groups (P<0.01). The positive rate of MP-IgM in female was 44.77%, which was significantly higher than that in male (35.83%) (P<0.05). MP infection combined with positive IgM of another pathogen accounted for 32.63% (4 561 cases), positive IgM of another two pathogens accounted for 1.26% (176 cases). MP infection was mostly found in pneumonia (68.73%), and the main clinical symptoms were cough (84.72%), fever (51.01%) and wheezing (3.16%). Conclusions　MP is an important pathogen of respiratory tract infection in children in Hainan Province, and infection is more common in children in early school age and early childhood. Mp-specific tests should be performed to identify the pathogen in children suspected of MP infection. In the high incidence season, health education should be strengthened in kindergartens, schools and other places to prevent respiratory tract infection.

Objective:To investigate the feasibility and reliability of the frozen section during targeted prostate biopsy.Methods:The clinical and pathological information of patients who received cognitive fusion transperineal targeted plus systematic biopsy and frozen section of 1-2 core targeted biopsy were consecutively collected and retrospectively studied. The median age was 70 (ranging 64-78) years, with the median prostate-specific antigen (PSA) level of 11.00 (ranging 6.63-16.52) ng/ml and the median prostate volume of 35.72 (ranging 22.59-47.71) ml. All patients received bi-parametric magnetic resonance imaging (bp-MRI) and have Prostate Imaging Reporting and Data System (PI-RADS) 3 or higher lesions diagnosed on bp-MRI. The suspected lesions would be taken by targeted biopsy of which one or two cores would be sent to prepare for the frozen sections. Then a cognitive fusion targeted and systematic biopsy covering the above targeted zones would be routinely administered under a transperineal approach as a standard protocol. The total time used for diagnosis of the frozen sections, the pathological diagnosis and the International Society of Urological Pathology (ISUP) grade groups (GG) would be recorded. The sensitivity, the positive predictive value, and the accuracy on grade groups would be analyzed, using the pathological diagnosis based on standard sections from the same targeted lesion.Results:A total of 29 patients were included in this study. Accordingly, 29 suspected lesions were identified on bp-MRI. A total of 20 lesions were finally diagnosed of PCa on frozen section, with the detection rate of 69.0%. Of those, 9(45.0%) cases were ISUP GG 1 diseases, 5(25.0%) cases were GG 2 diseases, 1(5.0%) case was GG 3 disease, and 5(25.0%) cases were GG 4-5 diseases. A total of 22 lesions were diagnosed with PCa on standard sections of cores from the same targeted lesions, with the detection rate of 75.9%. Of those, 6(27.3%) cases were GG 1 disease, 11(50.0%) cases were GG 2 diseases, 1(4.5) case was GG 3 disease, and 4(18.2%) cases were GG 4-5 diseases. The sensitivity and the positive predictive value of frozen section were 90.9% and 100%, respectively. No false positive diagnosis was made by frozen section. Compared to diagnosis from frozen sections, the GG diagnosed from final standard sections were found to upgrade and downgrade in 2 and 2 cases, respectively. The accuracy rate on GG of frozen sections was 80%. The time used for the diagnosis of frozen sections was (11±2) minutes. The histology quality control of four specimens was dissatisfactory. Two were due to tissue loss and deformation during sampling, and the other two were due to cytoclasis during low-temperature transferring.Conclusion:It is feasible and reliable to make a pathological diagnosis from frozen section of prostate targeted biopsy.