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 analyze the human immunodeficiency virus (HIV) screening status and the resulting residual risk (RR) among blood donors across 17 provincial blood centers in China.Methods:This study used a cross-sectional study. Data on HIV infection markers per 100 000 first-time donors (FD) and repeat donors (RD) from January 2015 to December 2024 were extracted from the National Blood Establishment Performance Comparison Information Management System. Questionnaires were used to collect each center′s HIV screening strategy, algorithm, serological test (ST) kit manufacturers, gray-zone setting for ST, and nucleic acid test (NAT) modality, method, and platform. The incidence-window-period model was used to calculate the residual risk for first-time donors (RR FD), repeat donors (RR RD), and total donors (RR TD) at each center. Horizontal and vertical analysis of RR FD, RR RD, and RR TD across centers and years were performed. Results:All 17 centers applied the same HIV screening strategy which was two rounds of ST followed by one round of NAT. Eight of them operated a single screening algorithm, six employed two algorithms and three used three. Eleven centers used both imported and domestic ST kits, five relied on domestic ST kits only, and one used imported ST kits only, while four centers never set a grey zone for ST throughout the decade. For NAT modalities, eight centers adopted both individual nucleic acid test (ID-NAT) and minipool nucleic acid test (MP-NAT), eight used MP-NAT only and one used ID-NAT only. Seven centers combined transcription mediated amplification (TMA) and polymerase chain reaction (PCR), nine used PCR only and one used TMA only, and fourteen centers ran both imported and domestic NAT systems, two used imported systems only and one used a domestic system only. Over the ten-year period, the mean RR FD across the centers ranged from 2.22 to 12.33 per 10 6 person-years, RR RD from 0.83 to 3.29 per 10 6 person-years and RR TD from 1.59 to 9.29 per 10 6 person-years, with center Z4 consistently showing the lowest values for all three metrics and center U4 recording the highest RR FD and RR TD, while center D2 had the highest RR RD. In 2024 compared with 2015, eleven centers achieved a lower RR FD and ten centers achieved lower RR RD and RR TD. The RR FD and RR TD of centers W2 and U4 displayed pronounced fluctuations and an upward trend in recent years. Conclusions:The 17 provincial blood centers maintain consistent HIV screening strategies, while demonstrating variations in screening algorithm, ST kit manufacturers, NAT modalities, methods, and platform. And the RR FD, RR RD, and RR TD differ across centers. Although most centers show declining trend in RR over the ten-year period, some centers exhibite data fluctuations with a rising trend, suggesting potential for further optimization of HIV screening protocols.

Objective:To analyze the human immunodeficiency virus (HIV) screening status and the resulting residual risk (RR) among blood donors across 17 provincial blood centers in China.Methods:This study used a cross-sectional study. Data on HIV infection markers per 100 000 first-time donors (FD) and repeat donors (RD) from January 2015 to December 2024 were extracted from the National Blood Establishment Performance Comparison Information Management System. Questionnaires were used to collect each center′s HIV screening strategy, algorithm, serological test (ST) kit manufacturers, gray-zone setting for ST, and nucleic acid test (NAT) modality, method, and platform. The incidence-window-period model was used to calculate the residual risk for first-time donors (RR FD), repeat donors (RR RD), and total donors (RR TD) at each center. Horizontal and vertical analysis of RR FD, RR RD, and RR TD across centers and years were performed. Results:All 17 centers applied the same HIV screening strategy which was two rounds of ST followed by one round of NAT. Eight of them operated a single screening algorithm, six employed two algorithms and three used three. Eleven centers used both imported and domestic ST kits, five relied on domestic ST kits only, and one used imported ST kits only, while four centers never set a grey zone for ST throughout the decade. For NAT modalities, eight centers adopted both individual nucleic acid test (ID-NAT) and minipool nucleic acid test (MP-NAT), eight used MP-NAT only and one used ID-NAT only. Seven centers combined transcription mediated amplification (TMA) and polymerase chain reaction (PCR), nine used PCR only and one used TMA only, and fourteen centers ran both imported and domestic NAT systems, two used imported systems only and one used a domestic system only. Over the ten-year period, the mean RR FD across the centers ranged from 2.22 to 12.33 per 10 6 person-years, RR RD from 0.83 to 3.29 per 10 6 person-years and RR TD from 1.59 to 9.29 per 10 6 person-years, with center Z4 consistently showing the lowest values for all three metrics and center U4 recording the highest RR FD and RR TD, while center D2 had the highest RR RD. In 2024 compared with 2015, eleven centers achieved a lower RR FD and ten centers achieved lower RR RD and RR TD. The RR FD and RR TD of centers W2 and U4 displayed pronounced fluctuations and an upward trend in recent years. Conclusions:The 17 provincial blood centers maintain consistent HIV screening strategies, while demonstrating variations in screening algorithm, ST kit manufacturers, NAT modalities, methods, and platform. And the RR FD, RR RD, and RR TD differ across centers. Although most centers show declining trend in RR over the ten-year period, some centers exhibite data fluctuations with a rising trend, suggesting potential for further optimization of HIV screening protocols.

Objective:To investigate the changes in adaptive phenotypes of Yersinia pestis ( Yp) during successive passages in macrophages. Methods:A Yp strain of 201-MI was induced by 50 successive passages of Yp 201 strain in Raw264.7 cells. Phenotypic characteristics of 201 and 201-MI strains were compared by analyzing their survival rates in macrophages, growth curves, biofilm formation abilities, acid and hydrogen peroxide-stress tolerance, and virulence to mammal cells (Raw264.7 and HeLa cells) and mice. Results:Comparing with 201 strain, 201-MI strain showed various phenotypic changes, including higher survival rate in Raw264.7 cells, faster growth in iron-deficient medium, higher tolerance to acid and hydrogen peroxide, decreased biofilm formation ability, and less damages to Raw264.7 and HeLa cells. More-over, 201-MI strain showed decreased virulence to mice in both subcutaneous and intraperitoneal challenges. Preliminary comparative genomics analysis revealed some indel and nonsense mutations in 201-MI strain, which might account for its phenotype changes.Conclusions:After successive passages in macrophages, Yp showed some phenotypic changes, which might reflect its adaptive evolution under the pressure of macrophages. Detailed multi-omics analysis would be of great help to understand the underlying genetic mechanisms of these changes, and the related Yp-macrophage interaction processes as well.

Objective: To discuss the effects of acupuncture plus Tuina (Chinese therapeutic massage) in intervening the mental development, motor function, cerebral hemodynamics, and muscle tone in kids with spastic cerebral palsy (CP). Methods: A retrospective analysis was conducted on 87 kids with spastic CP. They were divided into a control group and an observation group based on their original treatment plan. Kids in the control group received symptomatic treatment, motor development therapy, and Tuina treatment. The observation group was additionally given acupuncture treatment. One month was taken as a treatment course. After six courses, the efficacy, change in muscle tone, mental development, gross motor function, fine motor function, and the systolic velocity (Vs), mean velocity (Vm), and pulsatility index (PI) of the anterior cerebral artery (ACA), middle cerebral artery (MCA), and posterior cerebral artery (PCA) were compared between the two groups. Results: After treatment, the muscle tone score dropped in both groups (P<0.05) and was significantly lower in the observation group than in the control group (P<0.05). The observation group achieved more significant efficacy than the control group (P<0.05). After the intervention, the mental development index (MDI), psychomotor development index (PDI), gross motor function measure (GMFM) score, and fine motor function measure (FMFM) score all increased in both groups (P<0.05) and were notably higher in the observation group than in the control group (P<0.05). After treatment, the Vs and Vm of the ACA, MCA, and PCA were markedly higher in the observation group than in the control group (P<0.05), and the observation group was significantly lower than the control group comparing the PI of the ACA, MCA, and PCA (P<0.05). Conclusion: Based on the symptomatic treatment and motor development therapy, Tuina and acupuncture treatment can effectively treat spastic CP children, manifesting as reducing muscle tone, boosting mental development, and improving motor function and cerebral hemodynamics.

Objective:To investigate the clinicopathological characteristics of the T cell lymphomas with CD20 expression, and to better understand this rare entity.Methods:Two-hundred cases of T-cell lymphoma diagnosed in the Department of Pathology of the Affiliated Hospital of Qingdao University from November 2016 to February 2020 were examined, and 5 cases of CD20-positive T-cell lymphomas were identified and included. Combined with clinical data and review of the literature, the clinicopathological characteristics of the disease were analyzed.Results:The five patients were all male, and had an average age of 56 years (range, 47 to 64 years). There were 2 cases of monomorphic epitheliotropic intestinal T-cell lymphoma, 2 cases of mycosis fungoides (1 case was plaque stage and the other was tumor stage) and 1 case of indolent T-cell lymphoproliferative disorder of the gastrointestinal tract. Immunohistochemistry showed that all 5 cases expressed multiple T cell markers (CD3/CD4/CD5/CD7/CD8) and only one of B cell markers (CD20). Three of the 5 cases were negative for CD20 at the first diagnosis, while CD20 was diffusely positive on the second biopsy from the recurrence or progression of the disease, without expression of CD79a or PAX5. Epstein-Barr encoding region (EBER) in situ hybridization was negative in all 5 cases. T-cell receptor gene analysis showed monoclonal rearrangement of β or/and δ chains;Ig rearrangements were all polyclonal. None of the five patients were treated with rituximab, and 4 patients survived with disease and 1 patient survived without disease at the end of follow-up. Among them, the patient with mycosis fungoides at the cancerous stage has progressed rapidly and had poor quality of life.Conclusions:CD20-positive T-cell lymphoma is extremely rare. Its prognosis is closely related to the type of T-cell lymphoma, clinical stage and initial therapeutic effect. However, the expression of CD20 indicates the recurrence or progression of the disease, and the prognosis is relatively poor. When CD3 expression is absent in T-cell lymphoma, it is easy to be misdiagnosed as B-cell lymphoma. The combination of multiple immunohistochemical antibodies and molecular detection can improve the accuracy of diagnosis.

In this study, eight-month-old ectomycorrhizae of Tuber borchii with Corylus avellana were synthesized to explore the influence of T. borchii colonization on the soil properties and the microbial communities associated with C. avellana during the early symbiotic stage. The results showed that the bacterial richness and diversity in the ectomycorrhizae were significantly higher than those in the control roots, whereas the fungal diversity was not changed in response to T. borchii colonization. Tuber was the dominant taxon (82.97%) in ectomycorrhizae. Some pathogenic fungi, including Ilyonectria and Podospora, and other competitive mycorrhizal fungi, such as Hymenochaete, had significantly lower abundance in the T. borchii inoculation treatment. It was found that the ectomycorrhizae of C. avellana contained some more abundant bacterial genera (e.g., Rhizobium, Pedomicrobium, Ilumatobacter, Streptomyces, and Geobacillus) and fungal genera (e.g., Trechispora and Humicola) than the control roots. The properties of rhizosphere soils were also changed by T. borchii colonization, like available nitrogen, available phosphorus and exchangeable magnesium, which indicated a feedback effect of mycorrhizal synthesis on soil properties. Overall, this work highlighted the interactions between the symbionts and the microbes present in the host, which shed light on our understanding of the ecological functions of T. borchii and facilitate its commercial cultivation.
Colon ; Corylus ; Fungi ; Magnesium ; Mycorrhizae ; Nitrogen ; Phosphorus ; Podospora ; Rhizobium ; Rhizosphere ; Soil ; Streptomyces

Objective To evaluate the effect of case-PBL method and case-PBL method combined with SPSS software on the teaching of medical statistics for medical undergraduates. Methods Students from two classes major in experimental medicine from Nantong University Xingling College were selected as Experimental Class 1 ( using case-PBL teaching ) and Experimental Class 2 ( using case-PBL teaching combined with SPSS software). Each class attended lessons for five times. The teachers would send cases for each lesson one week in advance, and students would form into groups to access information, learn and discuss independently. Representatives from groups spoke in class, members would complement and discuss, while teachers offered guidance, review, analysis and summary. We shortened the discussion time in the class, and added instructions on the operation steps of SPSS software for case analysis and how to interpret the analysis result correctly in Experiment Class 2 . The Control Class received traditional teaching . Questionnaires, process assessment and final assessment were used to evaluate teaching effectiveness. SPSS 21.0 software was used to implement variance analysis and chi-square test for comparison between groups. Results The scores of the two experimental classes were higher than those of the control class in the five process assessments ( P<0 . 05 ) . Experimental Class 2 was the best in three section process assessments including those of t-test, the rank sum test and the straight-line correlation (P<0.05). However, there was no difference in the theoretical test scores among the three classes (P=0.670). 94％-100％of the students in the two experimental classes believed that the teaching effects of the case-PBL method and case-PBL method combined with SPSS software were better than the traditional teaching method (P<0.05) in such areas as stimulating interest in learning, improving learning efficiency, etc. Students in Experimental Class 2 were more prone to think these methods improved teaching effect. Conclusion The case-PBL teaching combined with the application of SPSS software will further help students to systematically grasp the statistical knowledge and cultivate statistical practice ability . However , neither methods will improve students' theoretical test scores.

Objective: To investigate the clinicopathologic characteristics, diagnostic features and prognosis of primary renal neuroendocrine carcinoma (NEC). Methods: The clinicopathologic data of eight cases of renal NEC was collected from January 2008 to December 2017 from Affiliated Hospital of Qingdao University. Immunohistochemical staining was performed, and follow-up information was analyzed, and the relevant literature reviewed. Results: The patients′ mean age at diagnosis was 45 years (range, 27-66 years); five were women, and three were men. The tumors located on the left side in five patients, and on the right side in three. Five cases were detected incidentally, and three patients presented with loin pain. Microscopically, these cases included five well-differentiated NECs (three carcinoids, two atypical carcinoids), two small cell NECs, and one large cell NEC according to the World Health Organization classification of 2016. The tumors infiltrated the renal capsule in six cases. Necrosis was found in five cases. Vascular invasion with tumor emboli was seen in three cases. Lymph node metastasis was identified in one case. Immunohistochemically, the expression rates of neuroendocrine markers CD56, chromogranin A (CgA) and synaptophysin (Syn) were 6/8, 4/8, and 8/8 respectively. Some of the NECs were positive for epithelial markers CKpan (6/8, with three cases showing focal positivity) and CAM5.2 (4/8) of variable degrees. The Ki-67 proliferation index was≤3% in the carcinoids; ≥50% in the small cell carcinoma and large cell carcinoma; and 5% and 8% for the two cases of atypical carcinoid, respectively. All cases were negative for EMA, CK7, CA9, CD10, CD117, PAX2, PAX8, WT1, p63, S-100 and TTF1. Three patients (two with small cell carcinoma and one with large cell carcinoma) died of extensive metastases at 3 months, 4 months and 9 months after operation, while five patients were well, without recurrence or distant metastasis for follow-up period of one to nine years. Conclusions Primary renal NEC is rare. Carcinoid is the most common histological type. The pathomorphological features and neuroendocrine markers (CD56, CgA, Syn), epithelial markers (CKpan, CAM5.2) and nephrogenic markers (PAX2, PAX8) are important for the diagnosis. Renal carcinoid tumors are indolent and prone to early metastasis, but are associated with prolonged survival. The small cell renal cell carcinoma and large cell carcinoma are highly malignant renal tumors with poor prognosis and short survival.

Objective To investigate the clinical pathological factors related to recurrence and metastasis of colorectal cancer patients treated with resection ,expect to improve the treatment effects .Methods The clinicopathologic and follow-up data of 212 patients with stage Ⅰ - Ⅲ colorectal cancer patients treated with resection from January 2009 to December 2013 were retrospec-tively analyzed by univariate and multivariate Logistic regression methods .Results Univariate analysis showed that T staging sys-tems ,gross type ,intestinal obstruction or perforation ,lymphatic and vascular invasion were correlated to recurrence of colorectal cancer after operation(P< 0 .05) ;age ,tumor size ,lymph node involvement ,T staging systems ,histological differentiation ,intestinal obstruction or perforation ,lymphatic and vascular invasion were correlated to metastasis of colorectal cancer after operation(P <0 .05) .Multivariate Logistic regression analysis showed that age ,tumor size and histological differentiation were independent factors for metastasis rate of colorectal cancer after operation(P< 0 .05) .There were no significant differences in Logistic regression analy-sis for recurrence(P> 0 .05) .Conclusion Age ,tumor size and histological differentiation are independent factors for metastasis rate of colorectal cancer after operation .