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 observe the effects of probiotics and lactulose synergistic action on gastroin-testinal motility,mucosal function and disease progression in elderly patients with type 2 diabetes mellitus(T2DM)nephropathy constipation.Methods A total of 108 elderly patients with T2DM nephropathy consti-pation admitted and treated in this hospital from May 2021 to March 2023 were selected as the study subjects and divided into the observation group,control group 1 and control group 2 by the random number table meth-od,36 cases in each group.The control group 1 was treated with bifidobacterium tetrad tablet,the control group 2 adopted the lactulose treatment,and the observation group was treated with bifidobacterium tetrad tablet combined with lactulose.The clinical efficacy,constipation symptoms before treatment and in 1,4 weeks after treatment,gastrointestinal motility,serum cerebrointestinal peptide[substance P(SP),nitric oxide(NO),vasoactive intestinal peptide(VIP)],intestinal mucosal barrier function[D-lactic acid(DLC),diamine oxidase(DAO),lipopolysaccharide(LPS)],renal function[creatinine(Cr),urea nitrogen(BUN),estimated glomerular filtration rate(eGFR)]and Toll-like receptor 4(TLR4)/nuclear factor κB(NF-κB)mRNA ex-pression were compared between the groups.Results After 1-,4-week treatment,the total effective rate,bari-um discharge rate at different time points in the observation group were higher than those in the control group 1 and control group 2,and the scores of rectal,abdominal and fecal traits in the observation group were lower than those in the control group 1 and control group 2(P＜0.05),but there was no statistically significant difference between the control group 1 and control group 2(P＞0.05).The serum NO and VIP levels in the observation group were lower than those in the control group 1 and control group 2(P＜0.05),the SP level was higher than that in the control group 1 and control group 2(P＜0.05).After 4-week treatment,the levels of serum DLC,DAO and LPS in the observation group were lower than those in the control group 1 and con-trol group 2(P＜0.05);the Cr and BUN levels,TLR mRNA expression and NF-κB mRNA expression in the observation group and control group 1 were decreased compared with before treatment(P＜0.05),the eGFR level was increased compared with before treatment(P＜0.05),but the above indexes had no statistically sig-nificant difference between these two groups(P＞0.05).Conclusion Probiotics and lactulose in the treat-ment of elderly patients with T2DM nephropathy constipation could play a synergistic role,alleviate the con-stipation symptom,promote the gastrointestinal motility and restore the intestinal mucosal barrier function,which may be reach the anti-inflammation and anti-apoptosis goal by inhibiting TLR4/NF-κB,so as to inhibit the further development of diabetic nephropathy.

Objective:To explore the effect of bifidobacterium triple viable enteric coated capsule combined with pentoxifylline on renal function and prognosis in elderly patients with early diabetic nephropathy.Methods:The clinical data of 110 elderly patients with type 2 diabetes mellitus (T2DM) complicated with early diabetes nephropathy in Hebei Eighth People′s Hospital from May 2020 to May 2022 were retrospectively analyzed. All patients were given routine dietary control, exercise therapy and insulin therapy. On this basis, 55 patients were treated with pentoxifylline (control group), and 55 patients were treated with bifidobacterium triple viable enteric coated capsule combined with pentoxifylline (study group). The efficacy 3 months after treatment was evaluated, and the adverse reactions were record. Before treatment and after 1 and 3 months of treatment, the blood glucose indexes (including fasting blood glucose, FBG; 2 h postprandial blood glucose, 2 h PBG; insulin sensitivity index, Matsuda index), renal function indexes (including urea nitrogen; creatinine; urinary microalbumin excretion rate, UAER), intestinal flora amount (including bifidobacterium, lactobacillus, enterococcus and escherichia coli) and inflammatory response stress indexes (including interleukin-6, IL-6; transforming growth factor β 1, TGF-β 1; malondialdehyde; reactive oxygen species) were measured. Results:Three months after treatment, the total effective rate in study group was significantly higher than that in control group: 94.55% (52/55) vs. 81.82% (45/55), and there was statistical difference ( χ2 = 4.27, P<0.05). There was no statistical difference in the incidence of adverse reactions between study group and control group: 3.64% (2/55) vs. 10.91% (6/55), χ2 = 1.21, P>0.05. There were no statistical differences in all indexes before treatment between study group and control group ( P>0.05). The FBG and 2 h PBG after 1 and 3 months of treatment in study group were significantly lower than those in control group; while the Matsuda index was significantly higher than that in control group, with statistical differences ( P<0.01). The creatinine, urea nitrogen and UAER after 1 and 3 months of treatment in study group were significantly lower than those in control group, with statistical differences ( P<0.01). The amounts of bifidobacterium and lactobacillus after 1 and 3 months of treatment in study group were significantly higher than those in control group, while the amounts of enterococcus and escherichia coli were significantly lower than those in control group, with statistical differences ( P<0.01 or <0.05). The IL-6, TGF-β 1, malondialdehyde and reactive oxygen species after 1 and 3 months of treatment in study group were significantly lower than those in control group, with statistical differences ( P<0.01). Conclusions:Bifidobacterium triple viable enteric coated capsule combined with pentoxifylline is effective and safe in elderly patients with early diabetes nephropathy in the. It can effectively control blood sugar level and improve renal function, which may be related to regulating intestinal flora and inhibiting inflammatory reaction stress state.

Objective:To analyze the molecular epidemiological characteristics of the Corona virus disease 2019 (COVID-19) cases in Shijiazhuang, which can reveal the origin of the outbreak and provide a scientific basis for COVID-19 prevention and control.Methods:From January 2 to January 8, 2021, a total of 404 samples from 170 COVID-19 cases were collected from the Shijiazhuang Fifth Hospital. The consensus sequence of 2019 novel Coronavirus(2019-nCoV) was obtained through multiplex polymerase chain reaction-based sequencing. The sequences of 170 COVID-19 cases were analyzed by the PANGOLIN, and the data were statistically analyzed by T-test.Results:Among the 404 COVID-19 samples, a total of 356 samples obtained high quality genome sequences (>95%,100×sequencing depth). The whole genome sequences of 170 COVID-19 cases were obtained by eliminating repeated samples. All 170 sequences were recognized as lineage B1.1 using PANGOLIN. The number of single nucleotide polymorphism arrange from 18-22 and most of the single nucleotide polymorphism were synonymous variants. All of 170 genomes could be classified into 48 sub-groups and most of the genomes were classified into 2 sub-groups (66 and 31, respectively).Conclusions:All cases in this study are likely originated from one imported case. The viruses have spread in the community for a long time and have mutated during the community transmission.

BACKGROUND: Dabrafenib+Trametinib/Dabrafenib targeted therapy has been approved for V-RAF murine sarcoma viral oncogene homolog B1 with amino acid substitution for valine at position 600 (BRAF V600E) in lung cancer patients, however, the targeted therapy strategy for lung cancer patients with BRAF non-V600E mutations has not been determined yet. This study intends to explore the efficacy of targeted therapy for BRAF non-V600E mutant lung cancer, and provide a reference for clinical treatment. METHODS: Computer search of PubMed, Cochrane Library, Embase, Web of Science, Clinicaltrials.gov, CBM, CNKI, Wanfang database. Collect the relevant literature relevant on the targeted therapy of BRAF non-V600E mutant lung cancer, and conduct a descriptive analysis of the included literature. RESULTS: There were 10 articles that met the inclusion criteria, including 3 cohort studies and 7 case reports. 18 patients with BRAF non-V600E mutant lung cancer were ineffective to vermurafenib; 1 patient obtained partial response (PR) after applying vermurafenib, 5 patients did not respond to BRAF inhibitors; 9 patients showed a potential clinical benefit rate of 34% after monotherapy with trametinib; 7 patients have different degrees of benefit from dabrafenib and trametinib on progression-free survival (PFS); 1 patient is effective to sorafenib. CONCLUSIONS At present, there is no standard treatment specification for BRAF non-V600E mutation targeted therapy. The challenge lies in the heterogeneous mutation of BRAF gene. Different mutation types respond differently to targeted therapy. In addtion, real-world research evidence is scarce, so it is necessary to carry out further large-sample high-quality research to provide reference for clinical practice.
Animals ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use* ; Carcinoma, Non-Small-Cell Lung/drug therapy* ; Humans ; Lung Neoplasms/genetics* ; Mice ; Mutation ; Protein Kinase Inhibitors/therapeutic use* ; Proto-Oncogene Proteins B-raf/genetics*

Objective:To explore the survival status of rectal cancer patients with liver metastasis after receiving different treatments and its influencing factors.Methods:The clinicopathological characteristics, treatment methods and survival of 211 rectal cancer patients with liver metastasis who received different treatments in Shanxi Provincial Cancer Hospital from January 2012 to December 2016 were retrospectively analyzed. Cox proportional hazards regression model was used to analyze the related factors affecting the prognosis of patients.Results:The median overall survival (OS) time of 211 rectal cancer patients with liver metastasis was 19 months (1-115 months), and the 1-, 3- and 5-year OS rates were 66%, 22% and 10%. The OS of rectal cancer patients with metachronous liver metastasis was better than that of rectal cancer patients with simultaneous liver metastasis ( χ2 = 17.225, P < 0.01). The OS of patients with primary tumor resection was better than that of patients without primary tumor resection ( χ2 = 69.54, P < 0.01). Among patients with primary tumor resection, the OS of patients with untreated liver metastasis was worse than that of patients with interventional treatment of liver metastasis ( χ2 = 7.311, P = 0.007). Among the patients without primary tumor resection, the OS of patients with chemotherapy alone was better than that of untreated patients ( χ2 = 4.123, P = 0.042). The OS of patients with primary tumor resection and untreated liver metastasis and patients with primary tumor resection and liver metastasis intervention therapy was better than that of patients with chemotherapy alone (both P < 0.01). The results of Cox regression analysis showed that the differentiation degree of primary tumor, liver metastasis and carbohydrate antigen 199 level at diagnosis were independent factors influencing the survival of rectal cancer patients with liver metastasis (all P < 0.01). Conclusion:For patients with diagnosed rectal cancer, even if there is liver metastasis before surgery, active surgical resection of the primary tumor and local treatment of liver metastasis can still improve the survival.

OBJECTIVE：To provide reference for the R&D of TCM patents for treating gastric cancer and layout. METHODS：TCM patents for treating gastric cancer collected by the State Intellectual Property Office and the European Patent Office Espacenet were retrieved from the inception to Dec. 31st， 2019. After the initial examination ，a second search was conducted based on the keywords such as “Stomachache”“Fuliang” “Accumulation”“Cancer of stomach ”“Gastric”and their synonyms. Each literature was read one by one and screened manually. Excel 2007 software was used to input general information of included patents. SPSS modeler 15.0 software and SPSS 22.0 software were used for association rule analysis and hierarchical cluster analysis of TCM used more than 30 times and top 30 frequently used. Based on patent analysis ，internal strength （S），weakness（W），external opportunity （O）and threat （T）of TCM for treating gastric cancer were analyzed ；based on this ，four different types of combination strategies were formulated. RESULTS & CONCLUSIONS ：Finally，385 patents were obtained ，including 379 domestic patents （98.44％） and 6 foreign patents （1.56％）. The number of patent applications and applicants of TCM for treating gastric cancer in China was on the rise during 1994-2016. The commonly used TCM for treating gastric cancer were mainly tonifying deficiency drugs and heat clearing drugs ， and the meridian tropism were mostly the stomach meridian and spleen meridian. According to the efficacy ，the commonly used drug combinations include the combination of tonifying spleen and Qi ，the combination of anti-cancer and detoxification ，and the combination of drying dampness and resolving phlegm. The results of hierarchical cluster analysis showed that Poria cocos ， Atractylodes macrocephala ，Astragalus membranaceus ，Scutellaria barbata ，Hedyotis diffusa and Glycyrrhiza uralensis were clustered into one category and the common combination for treating gastric cancer. The remaining cluster distributions are also in line with the characteristics of TCM syndrome differentiation and treatment. Strength of domestic TCM patents for treating gastric cancer were that the number of patents in China was taking a leading position in the world ，the patent system of key applicants was mature，the combination of compound patents embodied the characteristics of disease and dialectical theory. Weakness included low patent authorization rate ，to-be-improved effectiveness and safety studies of TCM patents ，weak development of TCM extract patents，low degree of patent internationalization and hanging same-family patents. Opportunities were that the demand for drugs for gastric cancer was increasing with each passing day ，and natione actively support the development of the TCM industry. Threats were that competitors in the international market had the potential to seize the market. The development of TCM for treating gastric cancer in China should take market demand and national policy support as an opportunity ，learn from TCM patent characteristic system of key applicants ，continue to give full play to the advantages of TCM in prevention and syndrome differentiation of disease，pay more efforts to the development of weak links such as TCM extracts ，safety and effectiveness ，improve the international competitiveness in the field of patents ，while establish a warning and navigation analysis system for patents to effectively reduce the intellectual property threats and risks of invention patents of China in the international environment.

Objective:To explore the safety and therapeutic effect of programmed death 1 (PD-1) antibody combined with chemotherapy as a neoadjuvant therapy for patients with stage Ⅱ to Ⅲ non-small cell lung cancer (NSCLC).Methods:Thirteen patients, who had been diagnosed as stage Ⅱ-Ⅲ NSCLC and received PD-1 inhibitor plus chemotherapy as a neoadjuvant treatment in National Cancer Center/Cancer Hospital were recruited. The patients received consecutive neoadjuvant chemotherapy for 21 days as a cycle and the therapeutic efficacy was evaluated after two cycles.Results:At the last time of follow-up on December 2, 2019, the objective response rate (ORR) and disease control rate (DCR) of these patients were 61.5% (95% CI 30.9%-92.1%) and 100%, respectively. The downregulation rate of disease stage was 61.5% (8/13). The resectable rate was 38.5% (5/13), among them, the major pathologic response (MPR) was 60.0% (3/5) and the complete pathologic response (CPR) was 20.0% (1/5). The neoadjuvant chemotherapy displayed a low incidence of adverse reaction. The main grade 3 to 4 toxicities were neutropenia (38.5%) and leukopenia (23.1%). There was no significant immune-related toxicity. The safety and tolerability of perioperative period of patients underwent resection were promising. Conclusions:Immunotherapy combined with chemotherapy as a neoadjuvant treatment is an effective, low-toxicity treatment manner, which has perioperative safety and high rate of MPR for patients with resectable NSCLC. It is a promising treatment option for patients with stage Ⅱ to Ⅲ NSCLC.

Objective:To explore the safety and therapeutic effect of programmed death 1 (PD-1) antibody combined with chemotherapy as a neoadjuvant therapy for patients with stage Ⅱ to Ⅲ non-small cell lung cancer (NSCLC).Methods:Thirteen patients, who had been diagnosed as stage Ⅱ-Ⅲ NSCLC and received PD-1 inhibitor plus chemotherapy as a neoadjuvant treatment in National Cancer Center/Cancer Hospital were recruited. The patients received consecutive neoadjuvant chemotherapy for 21 days as a cycle and the therapeutic efficacy was evaluated after two cycles.Results:At the last time of follow-up on December 2, 2019, the objective response rate (ORR) and disease control rate (DCR) of these patients were 61.5% (95% CI 30.9%-92.1%) and 100%, respectively. The downregulation rate of disease stage was 61.5% (8/13). The resectable rate was 38.5% (5/13), among them, the major pathologic response (MPR) was 60.0% (3/5) and the complete pathologic response (CPR) was 20.0% (1/5). The neoadjuvant chemotherapy displayed a low incidence of adverse reaction. The main grade 3 to 4 toxicities were neutropenia (38.5%) and leukopenia (23.1%). There was no significant immune-related toxicity. The safety and tolerability of perioperative period of patients underwent resection were promising. Conclusions:Immunotherapy combined with chemotherapy as a neoadjuvant treatment is an effective, low-toxicity treatment manner, which has perioperative safety and high rate of MPR for patients with resectable NSCLC. It is a promising treatment option for patients with stage Ⅱ to Ⅲ NSCLC.

Objective To evaluate the application of a self-designed handy body position scaffold in the fluoroscopy for lower limb surgery.Methods We reviewed the intraoperative X-ray films of 161 patients with lower limb fracture who had undergone intraoperative fluoroscopy using our self-made handy body position scaffold during surgery from October 2013 to May 2017.They were 105 males and 56 females,aged from 10 to 91 years (mean,39.7 years).There were 42 femoral fractures of middle or lower shaft,12 fractures of medial or lateral condyle or tibial plateau,96 tibiofibular fractures,7 ankle fractures and 4 foot fractures.The operation time,intraoperative fluoroscopy time,intraoperative bleeding,rate and time of fracture union,and complications were recorded.Results All the 161 patients completed intraoperative fluoroscopy and radiography uneventfully,indicating that the handy body position scaffold effectively maintained the body position of the affected ipsilateral lower limb.The body position scaffold was slightly deviated due to one overweight (121 kg) patient when the knee joint was flexed 90°,but the fluoroscopy and radiography was completed after adjustment of the C-arm roentgenographic machine.The operation time averaged 71.5 minutes (from 28 to 119 minutes),the X-ray exposure time 9.8 seconds (from 6 to 31 seconds),and the intraoperative bleeding 157.2 mL (from 80 to 500 mL).The 161 patients obtained follow-up for 5 to 22 months (average,14.1 months).The rate of primary union was 97.5％ (157/161).The time for fracture union averaged 8.8 weeks (from 4 to 17 weeks).Fracture nonunion occurred in one case,and delayed union in 3 cases.The final follow-ups revealed normal functional recovery of the affected knees and ankles,but no limb shortening,or no rotational,lateral or anteroposterior angulation deformity.Conclusion In the lower limb surgery,the intraoperative fluoroscopy can be completed better with the aid of our self-designed handy body position scaffold that prevents movement of the affected lower limb and lowers the risk of radiation exposure.