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 correlations of fibrinogen-to-albumin ratio(Fib/Alb),soluble myeloid cell triggering receptor-like transcript factor-1(sTLT-1)and neutrophil gelatinase-as-sociated lipocalin(NGAL)in peripheral blood at admission with the risk of poor prognosis in patients with acute thoracoabdominal trauma and their early warning values.Methods A prospective study was conducted in 152 patients with acute thoracoabdominal trauma in the hospital from January 2022 to May 2024.The patients were divided into good prognosis group(n=120)and poor prognosis group(n=32)according to their prognosis.Baseline data and the levels of Fib/Alb,sTLT-1 and NGAL in peripheral blood at admission were compared between the two groups.The relationships between the levels of Fib/Alb,sTLT-1,and NGAL in peripheral blood at admission and the severity of trauma[the Circulation,Respiration,Abdomen,Movement,and Speech(CRAMS)score]and the risk of poor prognosis were analyzed.The early warning values of the levels of Fib/Alb,sTLT-1 and NGAL in peripheral blood at admission for the risk of poor prognosis were evaluated.Results The time from injury to admission in the poor prognosis group was longer than that in the good prognosis group,the CRAMS score,the Glasgow Coma Scale(GCS)score,and the levels of Fib,Alb and Fib/Alb in peripheral blood at admission in the poor prognosis group were lower than those in the good prognosis group,while the Sequential Organ Failure Assessment(SOFA)score and the levels of sTLT-1 and NGAL in peripheral blood at admission were higher than those in the good prognosis group,with statistically significant between-group differences(P＜0.05).The levels of Fib,Alb and Fib/Alb in peripheral blood at admission showed a decreasing trend,while the levels of sTLT-1 and NGAL showed an increasing trend in patients with mild,severe,and extremely severe trauma,with statistically significant differences(P＜0.05).Pearson correlation analysis showed that the level of Fib/Alb in peripheral blood at admission(r=0.839)was positively correlated with the CRAMS score,while the levels of sTLT-1 and NGAL(r=-0.832,-0.808)were negatively cor-related with the CRAMS score(P＜0.05).Logistic regression analysis showed that after adjusting for confounding factors,the levels of Fib/Alb(OR=0.769),sTLT-1(OR=1.562)and NGAL(OR=1.575)in peripheral blood at admission were still independently correlated with the risk of poor prognosis(P＜0.05).The receiver operating characteristic(ROC)curve showed that the area under the curve(AUC)for the combined early warning of the risk of poor prognosis by the levels of Fib/Alb,sTLT-1,and NGAL in peripheral blood at admission was 0.918,which was superior to the early warning value of individual indicators(Z=2.992,2.291,2.082,P＜0.05).Conclusion The levels of Fib/Alb,sTLT-1 and NGAL in peripheral blood are closely related to the severity of trauma and prognosis in patients with acute thoracoabdominal trauma.Combined detection has a certain ear-ly warning value for the risk of poor prognosis and can be used as potential factors for clinical assess-ment of trauma condition and early warning of the risk of poor prognosis.

Objective: To investigate the value of metagene next⁃generation sequencing ( mNGS) in the detection of pathogens in patients with pulmonary infection. Methods: A retrospective analysis was performed on clinical data from 434 patients with pulmonary infections admitted over the past four years. Based on the presence of underlying comorbidities , patients were divided into underlying disease group (n = 262) and non⁃underlying disease group (n = 172) . Pathogen detection was conducted using both mNGS and conventional tests. Clinical and laboratory parameters , radiographic findings , and pathogen detection results were systematically analyzed. The diagnostic performance of the two methods in identifying causative pathogens of pulmonary infections was compared. Results: The positive rate of mNGS in 434 patients was higher than that of conventional tests , and the difference was statisti⁃cally significant (P < 0. 05) . The efficacy of mNGS in detecting bacteria and viruses was significantly higher than that of conventional tests , and the difference was statistically significant (P < 0. 05) . Although the fungal detection rate of mNGS was higher than that of conventional tests , the difference was not statistically significant. Among them , the detection rates of Mycobacterium tuberculosis , Mycoplasma pneumoniae , Haemophilus influenzae , Strepto⁃ coccus pneumoniae , Streptococcus constellation , Staphylococcus aureus and Aspergillus fumigatus were significantly higher than those of conventional tests , and the difference was statistically significant (P < 0. 05) . Subgroup analy- sis showed that the proportion of males , hospital stay , smoking prevalence and average age in the underlying dis- ease group were higher than those in the non-underlying disease group , and the difference was statistically signifi- cant (P < 0. 05) , while there were no significant differences in antibiotic use and endotracheal intubation rate be- tween the two groups. The most common pathogens detected by mNGS in the underlying disease group were Myco⁃ bacterium tuberculosis , Haemophilus influenzae , Streptococcus pneumoniae , Pseudomonas aeruginosa , human herpes⁃ virus type 4 and Aspergillus fumigatus , while the most common pathogens in the non-underlying disease group were Mycobacterium tuberculosis , Haemophilus influenzae , Streptococcus pneumoniae , Mycoplasma pneumoniae and Kleb⁃ siella pneumoniae. The positive rate of mNGS in the two groups was significantly higher than that of conventional tests , and the difference was statistically significant (P < 0. 05) , while the difference in the positive rate of mNGS between the two groups was not statistically significant. Conclusion mNGS has significant advantages over con- ventional tests of pathogen in lung infection , and is less affected by underlying diseases , which can provide an etio- logical basis for lung infection.

In the past few decades, microbubbles were widely used as ultrasound contrast agents in the field of tumor imaging. With the development of research, ultrasound targeted microbubble destruction technology combined with drug-loaded microbubbles can achieve precise drug release and play a therapeutic role. As a micron-scale carrier, microbubbles are difficult to penetrate the endothelial cell space of tumors, and nano-scale drug delivery system—nanobubbles came into being. The structure of the two is similar, but the difference in size highlights the unique advantages of nanobubbles in drug delivery. Based on the classification principle of shell materials, this review summarized micro/nanobubbles used for ultrasound diagnosis or treatment and discussed the possible development directions, providing references for the subsequent development.

Taking the Ligustrum lucidum extract as an example, this study investigated the influence of external mechanical forces under different processing conditions on the crystallographic solid form and the key parameter of drug dissolution rate, so as to provide guidance for the preparation and quality control of traditional Chinese medicine preparations. Under different pulverization and tableting conditions, the change of crystallographic solid form of L. lucidum extract was observed by polarizing light microscope. Meanwhile, the effect of this change on the dissolution rate was investigated, and the mathematical relationship between crystal content and dissolution rate was analyzed. The results showed that the process of ball milling and tableting had a significant impact on the crystallographic solid form of L. lucidum extract. The amorphous extract displayed crystal transformation, which induced a significant decline in dissolution rate. Further studies revealed that there was a negative linear relationship between crystal content and dissolution rate. The results of this study indicated that the crystallographic solid form transformation of traditional Chinese medicine extracts might occur during the preparation process, which may cause potential risks to the quality of traditional Chinese medicine preparations. It is suggested that we should pay attention to and strengthen the investigation of the crystallographic solid form during the preparation process, so as to guarantee the safety, effectiveness, and quality controllability of traditional Chinese medicine preparations.

Ion concentration polarization (ICP) is an electrical transport phenomenon that occurs at the micro-nano interface under the action of an applied electric field, and the ICP phenomenon can be used to enrich charged particles with high efficiency. The microfluidic chip has the advantages of high precision, high efficiency, easy integration and miniaturization in biochemical analysis, which provides a new solution and technical way for biochemical analysis. In response to the demand for the detection of trace charged target analytes in sample solution, the advantages of high enrichment multiplicity, convenient operation and easy integration of ICP are utilized to provide an effective way for microfluidic biochemical detection. The combination of ICP phenomenon and microfluidic analysis technology has been widely used in the fields of pre-enrichment of charged particles, separation of targets, and detection of target analytes in biochemical analysis. In this paper, the principle of ICP and the microfluidic ICP chip are briefly introduced. Under the action of external electric field, the co-ions pass through the ion-selective nanochannel, the counterions are rejected at the boundary of nanochannel to form a depletion zone, and the charged samples will be enriched at the boundary of the depletion zone. Then the preparation techniques and methods of ICP chips are summarized. Among them, the design of microfluidic channel structure and the preparation and design of nanostructures are emphasized. The basic single-channel structure is analyzed, and the parallel-channel structure as well as the integrated multi-functional microfluidic ICP chip are sorted out and summarized. The preparation methods of nanostructures in ICP chips and their respective advantages and disadvantages are listed, and it is summarized that the current mainstream means are the embedding method and the self-assembly method, and attention is paid to the design of nanostructures preparation methods by both of them. In addition, this paper also discusses how to optimize the enrichment efficiency of ICP chip, through the introduction of multi-field coupling, valve control and other means to achieve the optimization of the enrichment efficiency of target substances. Meanwhile, this paper provides a classified overview of the progress of application of ICP chips in biochemical analysis and detection. ICP chips have been widely used in the research and development of biosensors, which can be used for the enrichment and separation of a variety of analytes including small molecules, nucleic acids, proteins, and cells, etc. By changing the design of microfluidic structures, integrating detection methods and modifying specific antibodies, ICP chips have shown great potential in the fields of rapid enrichment and pre-processing of targets, separation of targets and highly sensitive detection. Finally, it is pointed out that ICP chips are facing challenges in improving enrichment efficiency and selectivity, and solving the problems of fluid control, mixing and transport to match the biological properties of target assay, and that microfluidic ICP chips have been continuously promoting the development of ICP chips through the improvement of materials, chip design and integration of multifunctional units, opening up new possibilities in the field of biochemical analysis methods and applications. It can be seen that microfluidic ICP chips have the advantages of low sample flow rate, good separation and enrichment, high detection efficiency, and easy integration and miniaturization, which have shown good research significance and practical prospects in the field of biochemical detection.

Objective:To investigate the incidence characteristics and influencing factors of non-alcoholic fatty liver disease (NAFLD) in rural Uyghur ethnic group residents in Xinjiang Production and Construction Corps and to provide scientific evidence for early identification and prevention of NAFLD for residents.Methods:A total of 10 158 participants were included from the Xinjiang Uygur ethnic group population cohort. A prospective cohort study and Cox proportional hazards regression model analysis were used to explore the influencing factors and clustering of NAFLD, and the dose-response relationship between related biochemical indicators and the risk of NAFLD was studied using a restricted cubic spline.Results:The cumulative incidence rate of NAFLD was 6.9%, and the incidence density of NAFLD was 12.06/1 000 person-years. The incidence density of NAFLD in females was higher than in males (14.72/1 000 person-years vs. 9.17/1 000 person-years, P<0.001). The incidence density of NAFLD gradually increased with age in the total population, both men and women (all P<0.001). In the general population, an education level of junior high school or above was a protective factor for NAFLD, while older age, divorce, widowhood, overweight, obesity, hypertension, increased glomerular filtration rate, decreased HDL-C, increased LDL-C, and increased ALT were risk factors for NAFLD. Estimated glomerular filtration rate (eGFR), HDL-C, LDL-C, and ALT were non-linearly correlated with the incidence of NAFLD, and there was a significant dose-response relationship between them. Only 19.1% of residents had no NAFLD risk factors; over 80.9% had ≥1 NAFLD risk factors. The risk of NAFLD increased with the number of risk factors. Conclusions:The incidence of NAFLD in rural Uygur ethnic group residents in Xinjiang Production and Construction Corps was relatively low, but most residents had one or more risk factors for NAFLD. Prevention and control of NAFLD in this population cannot be ignored. In addition, people of older age, divorced or widowed, low education level, overweight or obese, hypertension, and abnormal eGFR, HDL-C, LDL-C, and ALT were the high-risk groups of NAFLD that need to be paid attention to in this population.

Purpose::Traumatic brain injury (TBI), currently a major global public health problem, imposes a significant economic burden on society and families. We aimed to quantify and predict the incidence and severity of TBI by analyzing its incidence, prevalence, and years lived with disability (YLDs). The epidemiological changes in TBI from 1990 to 2019 were described and updated to provide a reference for developing prevention, treatment, and incidence-reducing measures for TBI.Methods::A secondary analysis was performed on the incidence, prevalence, and YLDs of TBI by sex, age group, and region ( n =21,204 countries and territories) between 1990 and 2019 using the Global Burden of Diseases, Injuries, and Risk Factors Study 2019. Proportions in the age-standardized incidence rate due to underlying causes of TBI and proportions of minor and moderate or severe TBI were also reported. Results::In 2019, there were 27.16 million (95% uncertainty intervals ( UI): 23.36 -31.42) new cases of TBI worldwide, with age-standardized incidence and prevalence rates of 346 per 100,000 population (95% UI: 298 -401) and 599 per 100,000 population (95% UI: 573 -627), respectively. From 1990 to 2019, there were no significant trends in global age-standardized incidence (estimated annual percentage changes: -0.11%, 95% UI: -0.18% --0.04%) or prevalence (estimated annual percentage changes: 0.01%, 95% UI: -0.04% -0.06%). TBI caused 7.08 million (95% UI: 5.00 -9.59) YLDs in 2019, with age-standardized rates of 86.5 per 100,000 population (95% UI: 61.1 -117.2). In 2019, the countries with higher incidence rates were mainly distributed in Central Europe, Eastern Europe, and Australia. The 2019 global age-standardized incidence rate was higher in males than in females. The 2019 global incidence of moderate and severe TBI was 182.7 per 100,000 population, accounting for 52.8% of all TBI, with falls and road traffic injuries being the main causes in most regions. Conclusions::The incidence of moderate and severe TBI was slightly higher in 2019, and TBI still accounts for a significant portion of the global injury burden. The likelihood of moderate to severe TBI and the trend of major injury under each injury cause from 1990 to 2019 and the characteristics of injury mechanisms in each age group are presented, providing a basis for further research on injury causes in each age group and the future establishment of corresponding policies and protective measures.

Objective To investigate the value of wrist MRI in bone age estimation for male adoles-cents in Shanghai,Zhejiang and Jiangsu.Methods A total of 124 Han male adolescents aged 6.0 to 18.0 years from Shanghai,Zhejiang and Jiangsu were selected as subjects.Their weight and height were measured,and T1WI and T2WI sequences of the wrist were scanned.The distal ends of the ra-dius and ulna,and the first to five metacarpal epiphyses and corresponding metaphyses were selected as observational indexes after MRI images of the wrist were obtained.The development of each index was classified(0-2 grades)by a deputy senior imaging expert,then the maximum width of each in-dex was measured by another deputy senior expert.Height,weight,classification and maximum width of indexes were used as input variables,and age was used as the target variable.Support vector ma-chine,random forest,current reality tree,and linear regression models were established to estimate the bone age,and the model with the highest accuracy was selected.Results The height,weight,classifica-tion of wrist bone epiphysis development,maximum width of each bone metaphysis and epiphysis were all correlated with age(P<0.05).The accuracies of the support vector machine were the highest when the differences between bone age and actual chronological age were within 1.0 and 1.5 years(88.7%and 96.0%,respectively).Conclusion It is feasible to estimate bone age by using MRI images.Quantifying the maximum width of the epiphysis and corresponding metaphysis of bone and combining it with MRI image classification can effectively reduce the estimation error.