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*

Metastasis is the leading cause of death from cutaneous melanoma. Identifying metastasis-related targets and developing corresponding therapeutic strategies are major areas of focus. While functional genomics strategies provide powerful tools for target discovery, investigations at the protein level can directly decode the bioactive epitopes on functional proteins. Aptamers present a promising avenue as they can explore membrane proteomes and have the potential to interfere with cell function. Herein, we developed a target and epitope discovery platform, termed functional aptamer evolution-enabled target identification (FAETI), by integrating affinity aptamer acquisition with phenotype screening and target protein identification. Utilizing the aptamer XH3C, which was screened for its migration-inhibitory function, we identified the Chondroitin Sulfate Proteoglycan 4 (CSPG4), as a potential target involved in melanoma migration. Further evidence demonstrated that XH3C induces cytoskeletal rearrangement by blocking the interaction between the bioactive epitope of CSPG4 and integrin α4. Taken together, our study demonstrates the robustness of aptamer-based molecular tools for target and epitope discovery. Additionally, XH3C is an affinity and functional molecule that selectively binds to a unique epitope on CSPG4, enabling the development of innovative therapeutic strategies.

Objective To analyze chemical constituents of compound Maxing Shigan decoction by ultra-high perfor-mance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). Methods The separation was performed on a UPLC BEH C₁₈ column (2.1 mm×100 mm, 2.5 µm)，with a gradient elution applying 0.1% aqueous formic acid solution and 0.1% formic acid acetonitrile as a mobile phase. The column temperature was 40 °C. The flow rate was 0.4 ml/min and the analysis time was 15 min. Mass spectrometry (MS) data were collected in both positive and negative ESI ion modes. Results Through UPLC-QTOF/MS analysis and reference validation, a total of 59 chemical components in Maxing Shigan decoction were identified. Conclusion An ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) method was established to identify the chemical components of Maxing Shigan decoction. This method is simple, efficient, sensitive and accurate, and provides a basis for the elucidation of the pharmacodynamic material basis and mechanism of Maxing Shigan decoction. It can provide data reference for the optimization of the compatibility of traditional Chinese medicine in the treatment of COVID-19.

Objective To understand the application of skin disinfectant in neonatal intensive care units(NICUs)nationwide.Methods From April to May 2023,application of skin disinfectant in 93 NICUs nationwide was sur-veyed with convenience sampling method by a self-designed questionnaire.Questionnaire contents included types of disinfectant,disinfection tools,cleaning and disinfection frequency,disinfectant drying status,removal of disinfec-tant,and adverse reactions caused by disinfectant.Results A total of 93 nursing units in 71 medical institutions from 25 provinces/municipalities were included in this study.In NICUs,three most commonly used disinfectants were ethanol(79.57％),iodophor(74.19％),and anerdian(62.37％).In nursing units for neonates＜2 months of age,chlorhexidine was prohibited in 28 units(30.11％),used with caution in 23 units(24.73％),allowed in 9 units(9.68％),and there was no unified requirement in 33 units(35.48％).When using ethanol,staff only wiped once in 13(17.57％)nursing units.In some nursing units,there was no unified requirements on the wiping fre-quency of disinfectant.As for the removal of residual iodine,saline was used in 29(42.03％)nursing units,ethanol in 8(11.59％),and 19(27.54％)did not have unified requirements.The adverse reactions of disinfectant mainly included rash and contact dermatitis.Disinfectants that caused adverse reactions included ethanol,iodophor,aner-dian,and chlorhexidine.Conclusion In clinical practice,unified standards for the use of neonatal skin disinfectant remain absent.Selection and use of neonatal skin disinfectant vary considerably.Neonatal skin disinfectants have common adverse reactions.It is necessary to strengthen the training of health care workers on the standardized use of disinfectant,as well as carry out large-scale and rigorous randomized controlled trial designs to provide scientific basis for the correct selection of disinfectant.

BACKGROUND:Gastrodin has anti-inflammatory effects and is mainly used in clinical practice for the treatment of ischemic stroke,and its mechanism of action is still unclear. OBJECTIVE:To explore the mechanism of gastrodin intervention on inflammatory injury in ischemic stroke rats. METHODS:Fifty Sprague-Dawley rats were divided into sham-operated group,model group,positive control group,high-dose gastrodin group and low-dose gastrodin group by the randomized numerical method,with 10 rats in each group.Ischemic stroke models were established by the middle cerebral artery occlusion method in all groups of rats except for the sham operation group.Administration in each group started on the 3rd day after surgery,and the rats in the positive control group were intraperitoneally injected with edaravone injection(6 mg/kg),the rats in the high-and low-dose gastrodin groups were intraperitoneally injected with 50 and 10 mg/kg gastrodin injection respectively,and the rats in the sham-operated and model groups were intraperitoneally injected with the equal volume of physiological saline.After 14 days of continuous treatment in each group,the pathological changes in rat brain tissue were observed,and the positive expression of NLRP3 inflammasome and the expression of inflammatory response-related proteins and their mRNAs were detected. RESULTS AND CONCLUSION:Compared with the sham-operated group,the volume of cerebral infarction became larger in the model group;the structure of brain tissue was loose,irregular cavities could be observed,and the number of neurons was reduced and irregularly arranged;the positive expression of NLRP3 inflammasome increased(P<0.01);and the protein and mRNA expression levels of Toll-like receptor 4,myeloid differentiation factor 88,apoptosis-associated speck-like protein containing a caspase-recruitment domain,Caspase-1,and interleukin-1β increased(P<0.01).Compared with the model group,the volume of cerebral infarction became smaller in the high-and low-dose gastrodin groups;the neurons were regularly arranged,increased in number,and uniformly distributed;the positive expression of NLRP3 inflammasome was decreased(P<0.05);the protein and mRNA expression levels of Toll-like receptor 4,myeloid differentiation factor 88,apoptosis-associated speck-like protein containing a caspase-recruitment domain,Caspase-1,and interleukin-1β were decreased in the high-dose gastrodin group(P<0.01);Toll-like receptor 4 protein expression showed no significant changes in the low-dose gastrodin group,and the protein and mRNA expression of the other inflammatory response-associated factors decreased(P<0.05,P<0.01).To conclude,gastrodin attenuates inflammatory injury in ischemic stroke rats,and its mechanism of action may be related to the inhibition of inflammatory response-associate factor expression.

The use of tyrosine kinase inhibitors （TKI） has been an important advance in the systemic treatment of hepatocellular carcinoma， but their sustained anti-angiogenic therapy leads to increased tumor hypoxia， accelerates the development of a hypoxic microenvironment and promotes the expressions of hypoxia-inducible factors （HIF）， thereby inducing drug resistance of tumor patients to TKI. This paper summarizes the mechanism of action of HIF mediating TKI resistance in hepatocellular carcinoma in aspects of metabolic reprogramming， abnormal expressions of cancer and cancer-associated genes， and ferroptosis， and sorts resistance response strategies to provide reference for clinical solutions to TKI resistance issues. As results show， HIF/ glycolysis axis inhibitors （isoflavonoid genistein， simvastatin， etc.） can improve TKI resistance based on metabolic reprogramming mechanism； oncogene-targeted inhibitors combined with TKI （the combination of capsaicin and sorafenib） can improve TKI resistance based on abnormal expression of cancer and cancer-related genes； fatty acid synthase inhibitor （orlistat） can improve TKI resistance based on ferroptosis mechanism.

Objective:To establish high performance liquid chromatography (HPLC) wavelength switching method to simultaneously determine the contents of chlorogenic acid, hydroxysafflor yellow A, ferulic acid, Nicotiflorin, Osthole and columbianadin in Tongluo Zhibi Prescription.Methods:The column was XBridge C18 column (250 mm × 4.6 mm, 5 μm); the mobile phase was acetonitrile (A)-0.1% phosphate water (B); gradient eluted, with flow rate: 1 ml/min, column temperature: 30 °C, detection wavelength 330 nm (0-14 min detection of chlorogenic acid, 15-80 min detection of ferulic acid, Nicotiflorin, Osthole, and columbianadin), 403 nm (14-15 min detection of hydroxysafflower yellow pigment A).Results:Chlorogenic acid, hydroxyrhodopsin A, ferulic acid, kaempferol 3-O-rutinoside, serpentin, and dihydroeurobicarpus angelicus acid ester showed good linearity ( R2 ≥ 0.999 8) within 0.029 7-1.485 0, 0.030 0-1.500 0, 0.009 9-0.495 0, 0.017 5-0.875 0, 0.028 4-1.420 0, 0.013 7-0.685 0 μg, respectively. The precision, stability (24 h), repeatability relative standard deviation ( RSD) were all <2%. The average spiked recoveries were all in the range of 95%-105%, and the RSDs were all in the range of 0.32%-1.67%. In 10 batches of test samples of Tongluo Zhibi Prescription, the content of the above six components, including chlorogenic acid, was determined to be 0.221 60, 0.314 30, 0.085 10, 0.032 95, 0.043 87, 0.026 21 mg/g in the following order. Conclusion:The established HPLC wavelength switching method is fast, simple and accurate, which can be used for simultaneous determination of the content of the above six components in Tongluo Zhibi Prescription, which provides reference for quality monitoring and new dosage form research of Tongluo Zhibi Prescription.

Objective:To evaluate the efficacy of visualized precise lung expansion for determining the intersegmental plane in thoracoscopic segmentectomy.Methods:Sixty-four American Society of Anesthesiologists Physical Status classification Ⅰ or Ⅱ patients, regardless of gender, aged 33-77 yr, with body mass index of 16-34 kg/m 2, undergoing elective thoracoscopic segmentectomy under general anesthesia, were included. They were preoperatively reconstructed with 3D CT bronchovascularization to reconstruct the pulmonary vasculature, bronchus, and the virtual intersegmental planes of the lungs. The patients were divided into 2 groups ( n=32 each) using a random number table method: visualized precise lung expansion group (group V) and modified expansion and atrophy group (group E). Group V used visualized precision lung expansion to determine the intersegmental planes, and group E used the modified expansion and atrophy method to determine the intersegmental planes. The intraoperative intersegmental plane determination time, target segmental bronchus identification and treatment time, anesthesia time, operation time, postoperative air leakage, pulmonary atelectasis, fever, occurrence of lung infection, postoperative 24 h drainage volume, drain removal time and hospitalization time were recorded in the two groups. Results:Compared with group E, the intersegmental plane determination time, target segment bronchial identification and treatment time, anesthesia time and operation time were significantly shortened in group V( P<0.05).There were no significant differences between groups in the 24 h postoperative drainage volume, drain removal time, hospitalization time or incidence of postoperative pulmonary complications ( P>0.05). Conclusions:Compared with the modified expansion and atrophy method, visualized precise lung expansion can effectively shorten the intersegmental plane determination time in thoracoscopic segmentectomy.

Early identification and intervention of high-risk factors during pregnancy is important for the prevention of maternal mortality. A certain hospital has established a management system for pregnant women undergoing first visit in non-obstetric departments and started applying it in three campus of the hospital in July 2023. Through the information management module for pregnant women undergoing first visit in non-obstetric departments that embedded in the hospital information system, abnormal pregnancy situations could be screened in a timely, comprehensive, and standardized manner, and quality control management could be carried out. At the same time, the hospital established a graded management path based on the severity of the condition of pregnant women, and provided early intervention for critically ill pregnant women reported through standardized management and multidisciplinary collaboration. From July to December 2023, a total of 5 766 pregnant women were first diagnosed and reported in 41 non-obstetric departments. Telephone follow-up showed a true reporting rate of 93.0%, and a total of 11 critical illness case were reported, including 2 cases of misoperation, with an accuracy rate of 81.8%. There were no adverse outcomes caused by failure to detect critical illness cases in a timely manner. In contrast, the relevant statistical data from January to June 2023 showed that there were 257 cases of pregnant women reported by non-obstetric departments, including 0 cases of critical illness and 1 case of missed critical illness. In addition, the time for non-obstetricians to screen for critically illness pregnant women of childbearing age has been reduced from 5-10 min per person before the system application to 15 s-1 min per person. The application of this system has reduced the missed reporting of critical illnesses, effectively ensured the safety of pregnant women, and improved work efficiency. It can provide reference for safety management of pregnant women in other medical institutions.

Objective To study the relationship between the changes of sagittal spinopelvic parameters and facet joint-derived low back pain in patients with hip osteoarthritis after hip arthroplasty.Methods The clinical data of 30 patients with facet joint-derived low back pain induced by hip osteoarthritis who underwent unilateral hip arthroplasty(observation group)from June 2019 to November 2020 in our hospital were retrospectively analyzed,and 50 healthy subjects who underwent lumbar X-ray examination in the physical examination center of our hospital at the same time were randomly selected as the control group.The sagittal spinopelvic parameters were measured based on the X-ray,including pelvic incidence(PI),pelvic tilt(PT),sacral slope(SS),lumbar lordosis(LL),sacrum pubic incidence(SPI)and sacrum pubic posterior angle(SPPA).The correlation between the changes of sagittal spinopelvic parameters and facet joint-derived low back pain was analyzed by multiple linear regression,and its diagnostic efficacy to facet joint-derived low back pain was analyzed by receiver operating characteristic(ROC)curve.Results The PI,LL,SPI or SPA before and 1 year after surgery of the observation group had no significant difference combined with those of the control group(P>0.05).The PT before surgery of the observation group was smaller than that of the control group(P<0.05),and the SS before surgery was larger than that of the control group(P<0.05).Multiple linear regression analysis showed that PT and SS before surgery were correlated with facet joint-derived low back pain(P<0.05).The sensitivity of PT and SS before surgery in diagnosing facet joint-derived low back pain were 50.00%and 73.30%,with the specificity of 88.00%and 78.00%,respectively.ROC curve analysis showed that the area under the curve of PT and SS before surgery in diagnosing facet joint-derived low back pain were 0.708(95%CI:0.595 to 0.822)and 0.775(95%CI:0.673 to 0.877),respectively.Conclusion Patients with hip osteoarthritis pain have significantly larger SS and significantly smaller PT.Hip arthroplasty can alleviate the symptoms of low back pain without affecting the sagittal spinopelvic balance;the PT and SS before surgery are correlated with the facet joint-derived low back pain,and they are of high value in the diagnosing facet joint-derived low back pain.