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 explore the value of blood lactic acid (BLA), procalcitonin (PCT), and total bilirubin (TBil) in the diagnosis and prognosis evaluation of patients with trauma complicated with sepsis.Methods:The clinical data of 151 patients with severe trauma admitted to the Department of Emergency Medicine, Nanxishan Hospital of Guangxi Zhuang Autonomous Region from July 2019 to August 2023 were analyzed retrospectively. The patients were divided into the sepsis group (72 cases) and non-sepsis group (79 cases) according to the diagnosis. They were further divided into the death group (37 cases) and non-death group (114 cases) based on clinical outcomes. Clinical data were compared between groups. Receiver operating characteristic (ROC) curve was used to analyze the predictive efficacy of the above indicators, and Spearman correlation analysis was applied to evaluate the correlation between the indicators.Results:The levels of BLA, PCT, TBil, and Sequential Organ Failure Assessment (SOFA) score in the sepsis group were higher than those in the non-sepsis group (all P<0.05). The mortality rate of the sepsis group was significantly higher than that of the non-sepsis group, with a statistically significant difference [26/72(36.11%) vs 11/79(13.92%), χ 2=10.024, P=0.002]. The levels of BLA, PCT, TBil, and SOFA score in the death group were higher than those in the non-death group (all P<0.05). ROC curve analysis showed that the areas under the curve (AUC) of BLA, PCT, TBil, and their combination for diagnosing sepsis were 0.745, 0.826, 0.753, and 0.889 respectively; the sensitivity and specificity of the combined diagnosis of sepsis were 87.5% and 72.2%. The AUCs of BLA, PCT, TBil, and their combination for predicting the prognosis of sepsis were 0.644, 0.697, 0.614, and 0.713 respectively; the sensitivity and specificity of the combined prediction of sepsis prognosis were 64.9% and 71.1%. Among the 151 patients, the levels of BLA, PCT, TBil were positively correlated with SOFA score, with statistically significant differences ( r=0.3871, 0.4399, 0.4851, all P<0.001). Conclusions:BLA, PCT, and TBil levels have certain value in the early diagnosis and prognosis evaluation of patients with sepsis. The combined evaluation has the best efficacy and high guiding value in clinical practice.

Objective:To investigate the clinicopathological features, diagnosis, and prognosis of renal solitary fibrous tumor (SFT).Methods:Five cases of renal SFT with unequivocal diagnoses at the Affiliated Hospital of Qingdao University between January 2011 and July 2025 were subject to analyses of their clinical, morphological, immunophenotypic, and molecular characteristics, accompanied by a literature review.Results:Two males and three females aged between 45 and 62 years were included, all of whom presented with the discovery of a renal mass during routine physical examinations. Gross examination showed that the five tumors were all confined in the kidney. The tumors were nodular with maximum diameters ranging from 2.5 cm to 11.0 cm (mean, 5.8 cm). Upon cross-sectioning, they exhibited gray-white or gray-yellow cut surface. Histologically, the tumor cells exhibited oval or short spindle shapes in four cases, presenting with varying densities and arranged in short bundles, woven patterns, and irregular formation. Various amounts of coarse collagen and scattered staghorn blood-vessels were found in the stroma. In one case (case 5), the tumor cells were long spindle-shaped, densely organized in bundles, and interwoven, exhibiting inconspicuous boundaries, moderate nuclear atypia, and at least 4 mitotic figures per 10 high-power fields. Irregular patchy collagen deposition was particularly prominent at the edges of the tumor tissue. In two cases (cases 3 and 5), scattered and various amounts of renal tubules were observed in the tumor. Two cases (cases 4 and 5) demonstrated focal invasion of the renal parenchyma, although no necrosis was noted. Immunohistochemical staining showed that the tumor cells were diffusely and strongly positive for vimentin and STAT6 in all 5 cases, and positive for CD34. Bcl-2 positivity was present in 4 of the 5 cases. All cases were negative for CKpan, EMA, PAX8, HMB45, Melan A, SMA, and S-100 protein. The p53 status was wild type, and the Ki-67 index ranged from 1% to 8%. Next-generation sequencing was conducted on one case (case 4), revealing the NAB2 (exon 3)::STAT6 (exon 18) gene fusion. The 5 patients were followed up for 1 to 158 months (mean, 56 months), and all were alive with no recurrence or metastasis.Conclusions:SFT of the kidney are rare and morphologically similar to extrarenal SFT. Key morphological features include short spindle-shaped tumor cells arranged in bundles, interwoven patterns or irregularly, accompanied by staghorn blood-vessels and scattered coarse hyaline collagen fibers. SFT with epithelial inclusions may represent a relatively common histological subtype in the kidney. Immunohistochemical staining that demonstrates diffuse and strong positivity for STAT6 and CD34 is instrumental in diagnosing this tumor. The pathogenesis is linked to the centromeric inversion of chromosome 12q, resulting in the fusion of the NAB2 and STAT6 genes. Most of these tumors exhibit favorable prognosis.

Objective:To investigate the relationship between thoracic aortic calcification (TAC) and autonomic nervous system (ANS) function in patients receiving continuous ambulatory peritoneal dialysis (CAPD).Methods:It was a cross-sectional study. The CAPD patients with dialysis duration >6 months between January and December 2022 were retrospectively enrolled. The baseline clinical data, heart rate variability (HRV) data such as standard deviation of all normal to normal intervals (SDNN), root mean square of successive differences between adjacent normal-to-normal intervals (RMSSD), high frequency (HF), very low frequency (VLF), low frequency (LF), LF/HF, acceleration capacity (AC) and deceleration capacity (DC), and skin sympathetic nerve activity (SKNA) were collected. TAC was defined as TAC score (TACS) >100 AU. The patients were divided into TACS >100 AU group and TACS≤100 AU group based on whether the thoracic aorta was calcified. The differences of those data between the two groups were compared. Logistic regression model was used to analyze the related factors of TAC. Spearman correlation analysis method was used to analyze the correlation between peripheral blood neuropeptide Y, ANS parameters, average amplitude SKNA (aSKNA) and TACS.　Cox regression model was used to analyze the risk factors of all-cause mortality in patients with CAPD.Results:The study included 106 CAPD patients with 50 males (47.2%), age of (46.04±11.10) years and dialysis duration of (41.55±30.52) months. TACS>100 AU group exhibited significantly lower heart rate ( t=2.015, P=0.046), DC ( t=2.131, P=0.035), LF/HF ( Z=3.332, P<0.001) and ln(LF/HF) ( t=3.326, P=0.001), and higher AC ( t=-2.392, P=0.019) than TACS≤100 AU group. Multivariate logistic regression analysis results showed that after adjusting for age and eosinophil count, lnVLF ( OR=0.66, 95% CI 0.45-0.98, P=0.038), lnLF ( OR=0.69, 95% CI 0.49-0.97, P=0.032), DC ( OR=0.79, 95% CI 0.64-0.99, P=0.039) and AC ( OR=1.32, 95% CI 1.04-1.68, P=0.021) were independently correlated with the risk of TAC. Spearman correlation analysis showed that neuropeptide Y level in peripheral blood was correlated with aSKNA ( r=0.23, P=0.017), lnSDNN ( r=-0.20, P=0.036) and TACS ( r=0.19, P=0.048). During the follow-up period of (25.8±4.2) months, 5 patients (4.72%) died, including 1 patient in the TACS≤100 AU group and 4 patients in the TACS>100 AU group. Compared with the survival group, the death group had higher TACS ( Z=-2.262, P=0.024) and lower LF/HF ( Z=-2.750, P=0.006). Cox regression analysis results showed that increased ln(LF/HF) was an independent influencing factor for all-cause mortality in CAPD patients ( HR=0.22, 95% CI 0.05-0.83, P=0.026). Conclusions:HRV parameters (lnVLF, lnLF, AC and DC) of CAPD patients are independently associated with TAC. The dysfunction of ANS in CAPD patients (especially the decreased vagus nerve activity) may promote TAC.

Objective To explore the efficacy of endoscopic therapy for esophageal and gastric variceal bleeding(EGVB),investigate the risk factors for rebleeding within 1 year,and establish a predictive model accordingly.Methods A retrospective study was conducted using the clinical and follow-up data of 120 EGVB patients who underwent endoscopy at our hospital between January 2021 and December 2022.The efficacy of endoscopic therapy was analyzed,and the patients were divided into a bleeding group and a non-bleeding group based on whether rebleeding occurred within 1 year after treatment.The factors influencing rebleeding within 1 year after treatment were analyzed,and a predictive model was established using logistic regression analysis.The model's goodness of fit was evaluated using the Hosmer-Lemeshow test,and its clinical value was analyzed using the receiver operating characteristic(ROC)curve.Results The hemostasis success rate within 72 hours after endoscopic therapy was 100％in all 120 patients.Four weeks after endoscopic treatment,endoscopic reexamination showed that the complete and partial disappearance rate of varices was 75.83％(91/120),with rebleeding occurring in 10 cases(8.33％).There were 34 cases(28.33％)of cumulative rebleeding at 6 months and 63 cases(52.50％)at 1 year after endoscopic therapy.Nine patients(7.50％)died within 1 year after endoscopic therapy,all of whom were rebleeding cases.A total of 63 patients with rebleeding were included in the bleeding group,and 57 patients without rebleeding were included in the non-bleeding group.Serum sodium＜135 mmol/L(odds ratio[OR]=3.837,95％confidence interval[CI]:1.095-13.445),Child-Pugh grade C(OR=3.835,95％CI:1.137-12.935),esophageal varices degree G3(OR=5.113,95％CI:1.565-16.707),and main portal vein diameter＞12 mm(OR=5.964,95％CI:2.295-15.497)were identified as risk factors of rebleeding within 1 year after endoscopic therapy in EGVB patients(P＜0.05).The risk prediction model for rebleeding within 1 year after endoscopic therapy in EGVB patients was shown as P=1/{1+e[-(-3.815+1.345×serum sodium+1.344×Child-Pugh grade+1.786×main portal vein diameter+1.632×esophageal varices degree)]}.The Hosmer-Lemeshow x2 was 3.158(P=0.856).The area under the curve(AUC)for predicting rebleeding within 1 year after endoscopic therapy in EGVB patients was 0.815,indicating good predictive performance.Clinical validation showed that the model had an accuracy of 82.30％,with sensitivity and specificity being 81.03％and 83.63％,respectively.Conclusion Endoscopic therapy for EGVB achieves a high rate of acute bleeding control,but patients remain at risk of rebleeding.Rebleeding is associated with serum sodium＜135 mmol/L,Child-Pugh grade C,main portal vein diameter＞12 mm,and esophageal varices degree G3.The logistic regression model can effectively predict the probability of rebleeding within 1 year after endoscopic therapy.

Objective:To investigate the potential characteristic manifestations and application value of the Dynamic Visual Acuity Test（DVAT） in vestibular migraine（VM）. Methods:A total of 50 VM patients（case group） and 50 healthy subjects（control group） diagnosed at the Department of Otorhinolaryngology Head and Neck Surgery, First Hospital of Shanxi Medical University between November 1, 2023, and December 31, 2024, were enrolled. The case group underwent DVAT, video head impulse test（vHIT）, caloric test, and Dizziness Handicap Inventory（DHI） assessment, whereas the control group only received DVAT. Group-based analyses were conducted to examine the effect of age on Dynamic Visual Acuity Loss（DVALoss）, as well as the correlations of DVALoss with vestibular function tests and DHI scores. Results:DVALoss in the case group was significantly higher than that in the control group（P<0.001）. In both groups, age was significantly and positively correlated with DVALoss（P<0.001）. Within the case group, DVALoss was strongly and positively correlated with DHI scores（r=0.807, P<0.001）; it was negatively correlated with the vestibulo-ocular reflex（VOR） gain in vHIT, though without clinical significance, and showed no significant association with the caloric test. Age and DVALoss collectively accounted for 71.3% of the variance in DHI scores（R²=0.713）, with age exerting a relatively minor actual impact. Conclusion:DVAT can sensitively identify the core functional impairments of VM. DVALoss, as a direct functional reflection of the pathological mechanism of VM, is strongly correlated with DHI scores. Incorporating DVALoss into standardized assessments may provide an objective basis for the diagnosis and management of VM.
Humans ; Migraine Disorders/diagnosis* ; Visual Acuity ; Case-Control Studies ; Head Impulse Test ; Vestibular Function Tests ; Female ; Male ; Adult ; Vestibular Diseases/physiopathology* ; Middle Aged ; Caloric Tests

[This corrects the article DOI: 10.1016/j.apsb.2022.05.019.].

Osteoarthritis (OA) causes chronic pain that significantly impairs quality of life, with current treatments often proving insufficient and accompanied by adverse effects. Recent research has identified the dorsal root ganglion (DRG) and its resident macrophages as crucial mediators of chronic OA pain through neuroinflammation driven by macrophage polarization. We present a novel injectable thermo-sensitive hydrogel system, KAF@PLEL, designed to deliver an anti-inflammatory peptide (KAF) specifically to the DRG. This biodegradable hydrogel enables sustained KAF release, promoting the reprogramming of DRG macrophages from pro-inflammatory to anti-inflammatory phenotypes. Through comprehensive in vitro and in vivo studies, we evaluated the hydrogel's biocompatibility, effects on macrophage polarization, and therapeutic efficacy in chronic OA pain management. The system demonstrated significant capabilities in preserving macrophage mitochondrial function, suppressing neuroinflammation, alleviating chronic OA pain, reducing cartilage degradation, and improving motor function in OA rat models. The sustained-release properties of KAF@PLEL enabled prolonged therapeutic effects while minimizing systemic exposure and side effects. These findings suggest that KAF@PLEL represents a promising therapeutic approach for improving outcomes in OA patients through targeted, sustained treatment.