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 risk factors and construct a nomogram prediction model for neonatal bacterial meningitis (BM).Methods:A retrospective cohort study was conducted on 1 228 neonates who underwent lumbar puncture for cerebrospinal fluid examination in the Department of Neonatology at Gansu Provincial Women and Child Healthcare Hospital from December 2019 to February 2024. The subjects were randomly divided into a training cohort and a validation cohort at a ratio of 7∶3 using a computer program. Rank sum test or Chi-square tests were used to compare differences between the two cohorts. The subjects were divided into BM and non-BM groups based on the presence or absence of BM. Multivariate logistic regression analysis (forward stepwise regression method) was used in the training cohort to identify risk factors for BM. The area under the receiver operating characteristic curve (AUC) and the Hosmer-Lemeshow goodness-of-fit test were used to assess the discrimination and calibration of the model, respectively. Calibration curves were used to evaluate the accuracy of the model and to construct the nomogram. Internal validation was performed using the Bootstrap resampling method. Decision curve analysis was used to assess the clinical utility of the model. Results:Among the 1 228 neonates, 151 (12.3%) had BM. The training cohort included 859 neonates, of whom 106 (12.3%) had BM and 753 (87.7%) did not. The validation cohort included 369 neonates, of whom 45 (12.2%) had BM and 324 (87.8%) did not. The results of the multivariate logistic regression analysis in the training cohort showed that sepsis ( OR=4.446, 95% CI:2.583-7.653), convulsions ( OR=3.749, 95% CI:1.930-7.280), high maximum body temperature ( OR=2.027, 95% CI:1.636-2.513), and elevated C-reactive protein ( OR=1.007, 95% CI:1.003-1.012) were independent risk factors for BM, while greater gestational age at birth ( OR=0.946, 95% CI: 0.898-0.995) and higher hemoglobin levels ( OR=0.990, 95% CI:0.981-0.998) were protective factors for BM (all P<0.05). Based on these findings, a nomogram prediction model for neonatal BM was constructed and validated for accuracy. The AUC values of the nomogram model in the training and validation cohorts were 0.796 (95% CI: 0.750-0.843) and 0.781 (95% CI: 0.700-0.862), respectively. The Hosmer-Lemeshow goodness-of-fit test showed P>0.05 in both cohorts. The clinical decision curve analysis demonstrated good net benefit across most threshold ranges. Conclusions:Sepsis, convulsions, high maximum body temperature, and elevated C-reactive protein increase the risk of neonatal BM. The nomogram model constructed based on these factors, combined with gestational age and hemoglobin levels, provides a reference value for predicting the risk of neonatal BM.

Aim To explore the therapeutic effect and mechanism of Qingjie Huagong decoction in modulating PI3K/AKT/NF-κB signaling pathway in inflammatory response of acute pancreatitis(AP)mice.Methods Twenty-four mice were randomly divided into Blank group,Model group,Ustekin group,and Qingjie Hua-gong decoction group,with six mice in each group.The AP model was prepared by using rain frogin.Serum α-AMS,PNLP,IL-1β,IL-6,IL-8,IL-18,and TNF-α lev-els were detected by ELISA;the pancreatic pathology was detected by HE staining;the expressions of PI3K,AKT,and NF-κB-related proteins and mRNAs were de-tected by immunohistochemistry,Western blot,and RT-qPCR.Results Compared with the blank group,the model group showed obvious pathological damage to the pancreas,with significantly higher serum α-AMS,PN-LP,IL-1β,IL-6,IL-8,IL-18,and TNF-α levels(P＜0.01),and significantly higher levels of PI3K,AKT,and NF-κB-related proteins and mRNA expression(P＜0.01).Compared with the model group,both the Qingjie Huagong decoction group and the ustekin group improved the histopathological changes in the pancreas of AP mice,decreased the serum α-AMS,PNLP,IL-1β,IL-6,IL-8,IL-18,and TNF-α levels,and down-reg-ulated the expression levels of pancreatic PI3K,AKT,NF-κB-related proteins and mRNA(P＜0.05 or P＜0.01).Conclusion Qingjie Huagong decoction may inhibit the inflammatory response and protect pancreat-ic tissues by regulating the expression of PI3K/AKT/NF-κB signaling pathway.

Postoperative infection of internal fixation of closed fractures the lower limbs in adults represents a devastating complication, characterized by diagnostic challenges, prolonged treatment duration and high disability rates. Current management of these infections faces multiple challenges, such as difficulties in early accurate diagnosis, and various controversies about the treatment plan, leading to poor overall diagnosis and treatment results. To address these issues, based on evidence-based medicine and principles with emphasis on scientific rigor, clinical applicability and innovation, the Trauma Branch of the Chinese Medical Association, Orthopedic Branch of the Chinese Medical Doctor Association, Orthopedics Branch of the Chinese Medical Association, and Trauma Orthopedics and Polytrauma Group of the Resuscitation and Emergency Committee of the Chinese Medical Doctor Association have collaboratively organized a panel of relevant experts to develop the Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults ( version 2025). The guideline proposed 10 recommendations, aiming to provide a foundation for standardized diagnosis and treatment of postoperative infection in adults with closed lower limb fractures.

[Purpose]To analyze the diagnostic yield of quantitative fecal immunochemical test(FIT)at different cut-offs in colorectal cancer(CRC)screening.[Methods]The sequential screening method was adapted in Jiashan CRC screening program for local residents aged 40～74 years old,which included a quantitative FIT and high-risk factor questionnaire for primary screening and subsequent colonoscopy for the diagnostic screening.Subjects who participated in quantitative FIT were included in this study between September,2021 and August,2023.The positive predictive values(PPVs)for colorectal neoplasms were calculated at the cut-offs of 100,120,140,160,180 and 200 ng/mL of FIT.The Cochran-Armitage trend test was performed to compare the trend of PPVs at different cut-offs.The effects of different starting age and FIT cut-offs on requirement of colonoscopy and advanced neoplasia detection were assessed.[Results]A total of 58 256 individuals completed the quantitative FIT,and 3 106 had fecal hemoglobin concentrations＞100 ng/mL,among whom 2 186 underwent colonoscopic examination with a compliance rate of 70.38％.The colonoscopy detected 588 cases of non-advanced adenomas and 355 cases of advanced neoplasms(AN),in-cluding 30 cases of CRC and 325 cases of advanced adenomas.Progressively increasing the cut-off showed a decrease in PPVs of non-advanced adenomas and an increase of AN.The ratio of the rate of reduced requirement of colonoscopy to the missed rate of the progressive lesions was the smallest when the screening start age was 45 years old and the positive FIT threshold was set at 100 ng/mL.[Conclusion]There were significant differences in the diagnostic yield at different cut-offs of FIT.Increasing the cut-offs of FIT will elevate PPVs for the advanced neoplasms.

Objective:To investigate the value of nomogram model based on CT features in differentiating ectopic pancreas (EP) from gastrointestinal stromal tumors (GIST) with a long diameter less than 3 cm.Methods:This study was a case-control study. The clinical and imaging data of 43 patients with EP and 90 patients with GIST confirmed by pathology in the Affiliated Hospital of Guizhou Medical University from August 2013 to March 2024 were retrospectively analyzed. Preoperative CT images were analyzed to obtain qualitative features (number of lesions, location, morphology, growth pattern, borders, cystic degeneration, calcification, ulceration, catheter sign, central umbilication) and quantitative features (lesion long diameter, short diameter, long/short diameter, lesion and normal pancreas arterial-phase and venous-phase CT values, and enhancement ratio). Statistical analyses, including independent sample t-tests, Mann-Whitney U tests, χ2 tests, and Fisher exact tests, were performed to compare CT characteristics between the two groups. Binary logistic regression analysis was used to obtain independent predictors to identify the two groups, to establish a joint model, and to draw a nomogram. The discriminative performance of the independent predictors and the combined model was assessed using receiver operating characteristic (ROC) curves, while calibration curves were used to evaluate model fit. Results:The differences in age, location, morphology, border, catheter sign, central umbilication, short diameter, long/short diameter, arteriovenous phase enhancement CT value and arteriovenous phase enhancement ratio were statistically significant between the EP group and the GIST group (all P<0.05). The logistic analysis showed that the differences in age ( OR=0.920, 95% CI 0.885-0.956, P<0.001), border ( OR=5.994, 95% CI 2.111-17.022, P=0.001), long/short diameter ( OR=7.820, 95% CI 1.841-33.224, P=0.005), and venous phase enhancement ratio ( OR=8.847, 95% CI 1.103-70.972, P=0.040) were the independent predictors for distinguishing EP from GIST, and the area under the ROC curve (AUC) were 0.782 (95% CI 0.698-0.866), 0.684 (95% CI 0.600-0.767), 0.705 (95% CI 0.607-0.803), and 0.693 (95% CI 0.605-0.781), respectively. Combined age, border, long diameter/short diameter and venous phase enhancement ratio were plotted in a nomogram with an AUC of 0.881 (95% CI 0.817-0.945), sensitivity and specificity of 74.4% and 93.3%, respectively. The calibration curve demonstrated a strong agreement between predicted and actual probabilities (Hosmer-Lemeschow test, P=0.267). Conclusions:CT imaging reveals significant differences between EP and small GISTs (<3 cm). EP is more likely when patients are younger and lesions exhibit indistinct borders, a higher long-to-short diameter ratio, and greater venous-phase enhancement. The nomogram derived from CT features provides a valuable tool for differentiating EP from GIST.

Hypoxic-ischemic brain damage (HIBD) is one of the main causes of disability in middle-aged and elderly people, as well as high mortality rates and long-term physical impairments in newborns. The pathological manifestations of HIBD include neuronal damage and loss of myelin sheaths. Tau protein is an important microtubule-associated protein in brain, exists in neurons and oligodendrocytes, and regulates various cellular activities such as cell differentiation and maturation, axonal transport, and maintenance of cellular cytoskeleton structure. Phosphorylation is a common chemical modification of Tau. In physiological condition, it maintains normal cell cytoskeleton and biological functions by regulating Tau structure and function. In pathological conditions, it leads to abnormal Tau phosphorylation and influences its structure and functions, resulting in Tauopathies. Studies have shown that brain hypoxia-ischemia could cause abnormal alteration in Tau phosphorylation, then participating in the pathological process of HIBD. Meanwhile, brain hypoxia-ischemia can induce oxidative stress and inflammation, and multiple Tau protein kinases are activated and involved in Tau abnormal phosphorylation. Therefore, exploring specific molecular mechanisms by which HIBD activates Tau protein kinases, and elucidating their relationship with abnormal Tau phosphorylation are crucial for future researches on HIBD related treatments. This review aims to focus on the mechanisms of the role of Tau phosphorylation in HIBD, and the potential relationships between Tau protein kinases and Tau phosphorylation, providing a basis for intervention and treatment of HIBD.
Humans ; tau Proteins/physiology* ; Phosphorylation ; Hypoxia-Ischemia, Brain/physiopathology* ; Animals ; Oxidative Stress

Objective To construction and investigate the application effect of auricular acupressure technology in patients with cough with different syndrome types.Methods From December 2022 to March 2023,the Delphi method was used to consult experts to form a technical scheme for auricular pressure in patients with cough with different syndrome types in the early and middle stages.122 patients with stage Ⅰ and stage Ⅱ lung cancer cough from the oncology department of 3 tertiary hospitals of Traditional Chinese Medicine in Beijing between July 2023 to January 2024 were randomly divided into an experimental group(61 cases)and a control group(61 cases).The experimental group referred to the constructed auricular acupressure technique program to identify and take acupoints,and the control group used the original auricular acupressure program for 7 d of continuous intervention.The changes in the scores of the Visual Analog Scale(VAS)and the scores of The MD Anderson Symptom Inventory for lung cancer(MDASI-LC)were observed in the 2 groups before and after the intervention.Results The final scheme included 3 first-level items,12 second-level items,and 14 third-level items.The 2 rounds of expert authority coefficients were 0.88,indicating a high degree of authority,and the Kendall harmony coefficients of the 2 rounds of correspondence were 0.170 and 0.130(P＜0.001),respectively,and the results tended to be consistent.A total of 122 patients completed the study.After intervention,the VAS score of cough severity in the experimental group was 3.0(2.0,3.0)points,which was lower than 3.0(3.0,4.0)points in the control group.The MDASI-LC score of the experimental group was 17.0(9.5,31.5)points,which was lower than 28.0(15.5,47.5)points in the control group,and the difference was statistically significant(P＜0.05).Conclusion The constructed auricular acupressure technique program has certain scientificity,and it can effectively relieve cough symptoms of stage Ⅰ～Ⅱ lung cancer patients,and the severity of symptom clusters has been improved,which provides the basis for TCM nursing intervention in cough symptoms of lung cancer patients.