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: Observational studies have found associations between inflammatory bowel disease (IBD) and the risk of dementia, including Alzheimer's dementia (AD) and vascular dementia (VD); however, these findings are inconsistent. It remains unclear whether these associations are causal. METHODS: We conducted a meta-analysis by systematically searching for observational studies on the association between IBD and dementia. Mendelian randomization (MR) analysis based on summary genome-wide association studies (GWASs) was performed. Genetic correlation and Bayesian co-localization analyses were used to provide robust genetic evidence. RESULTS: Ten observational studies involving 80,565,688 participants were included in this meta-analysis. IBD was significantly associated with dementia (risk ratio [ RR] =1.36, 95% CI = 1.04-1.78; I ² = 84.8%) and VD ( RR = 2.60, 95% CI = 1.18-5.70; only one study), but not with AD ( RR = 2.00, 95% CI = 0.96-4.13; I ² = 99.8%). MR analyses did not supported significant causal associations of IBD with dementia (dementia: odds ratio [ OR] = 1.01, 95% CI = 0.98-1.03; AD: OR = 0.98, 95% CI = 0.95-1.01; VD: OR = 1.02, 95% CI = 0.97-1.07). In addition, genetic correlation and co-localization analyses did not reveal any genetic associations between IBD and dementia. CONCLUSION Our study did not provide genetic evidence for a causal association between IBD and dementia risk. The increased risk of dementia observed in observational studies may be attributed to unobserved confounding factors or detection bias.
Humans ; Mendelian Randomization Analysis ; Inflammatory Bowel Diseases/complications* ; Dementia/etiology* ; Observational Studies as Topic ; Genome-Wide Association Study

With the increasing demand for dynamic,real-time and rapid qualitative analysis of chemical composition in areas such as emergency response and space exploration,chip-scale mass spectrometers have attracted significant attention.These devices are expected to drive the integration of mass spectrometry with micro/nano-fabrication and intelligent sensing technologies,fostering profound innovation and breakthroughs in analytical chemistry.As an excellent mass analyzer,the ion trap exhibits numerous advantages,and its miniaturization creates favorable conditions for the high-density integration of miniature mass spectrometers.However,the reduction in ion storage capacity may compromise its sensitivity and dynamic range,rendering the study of ion unidirectional ejection in highly miniaturized ion traps of significant practical importance.In this work,a research was conducted on achieving efficient ion unidirectional ejection while maintaining high mass resolution in the extremely miniature hyperbolic linear ion trap(M-HLIT)with a field radius of 1 mm,and an electric field compensation method was proposed,which combined asymmetric electrode stretching and unbalanced RF voltage to achieve high-precision optimization of the electric field composition.Simulations showed that in an ideal structure,this method achieved 100％unidirectional ejection efficiency with the mass resolution of 518,significantly outperforming traditional asymmetric structure method(365)and unbalanced voltage method(321).Following the introduction of ion ejection slots,further optimization through bidirectional stretching and electrical parameters improved the resolution to 790 while maintaining a unidirectional ejection efficiency of 93％.This method eliminated the requirement for additional excitation voltage,offering an ideal solution for the miniature mass analyzer with high detection performance of chip-level mass spectrometers.

Objective To explore the clinical value of anti-Müllerian hormone(AMH)to optimize endocrine therapy for peri-menopausal early breast cancer.Methods Two hundred and four patients of pre-menopausal breast cancer aged 45-55 years old between 2020 and 2023 were enrolled,and AMH≤0.1 ng/mL was considered as cut-off value for menopause.Switching from selective estrogen receptor modulator(SERM)to aromatase inhibitor aromatase inhibitor(AI)and initial endocrine therapy regimens were based on AMH,follicle-stimulating hormone(FSH)and estradiol(E2).Results Pre-chemotherapy AMH level was significantly negatively correlated with FSH level(P<0.001).Among 100 cases who were amenorrhea for one year during SERM treatment,42 cases did not have AMH testing.Fourteen out of the 42 cases switched to AI within one year,and ovarian function recovery(OFR)occurred in 2 cases after AI switching.Fifteen cases with AMH>0.1 ng/mL did not switch to AI within one year.Forty among 43 cases with AMH≤0.1 ng/mL switched to AI,after a significantly shorter median SERM treatment duration(3.15 months vs.8.14 months,P<0.001)and a significantly lower OFR rate(0 vs.12.5%,P=0.023)compared with those who did not test AMH but switched to AI.AMH≤0.1 ng/mL was an independent risk factor of transition to menopause shortly in peri-menopausal patients(OR=35.857,P<0.001).Among 104 cases with AMH tested before adjuvant chemotherapy,69 cases had AMH>0.1 ng/mL.Thirty-one out of the 69 cases were treated with ovarian function suppression(OFS)initially and 38 with SERM initially.Thirty-five cases with AMH≤0.1 ng/mL were all treated with SERM initially,with a higher rate of switching to AI(71.4%vs.23.7%,P<0.001)and a shorter SERM treatment duration(6.52 months vs.13.56 months,P=0.016)compared with the 38 cases(AMH>0.1 ng/mL)treated initially with SERM.After a median 30-month follow-up,no recurrence was observed in these thirty-five cases treated with SERM initially and AMH≤0.1 ng/mL,just like in OFS group.And they had a tendency of improved survival outcome compared with those treated with SERM initially and AMH>0.1 ng/mL(Log Rank P=0.076).Conclusion AMH could evaluate and predict menopause accurately,resulting in optimizing endocrine therapy for peri-menopausal patients effectively and safely.

Objective:To identify the key genes involved in the development and progression of prostate cancer(PCa)and those associated with the prognosis of the malignancy.Methods:We obtained the single-cell sequencing data on 4 cases of PCa from the GSE156632 database.Using R language and the Seurat package,we performed cell clustering and annotation,selected the subpop-ulations of epithelial cells for differential analysis after quality control and cell type identification,and conducted enrichment analysis of the identified differential genes using the Hiplot website.Then we downloaded the single nucleotide polymorphism(SNP)loci corre-sponding to the expression quantitative trait loci(eQTL)of these genes from the UK Biobank(UKB)database,and the clinical data and corresponding gene expression data on PCa patients from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO),followed by univariate COX regression analysis of the impact of the genes on the prognosis of the patients after Mendelian ran-domization.Results:A total of 1 566 genes were identified and subjected to enrichment analysis,which indicated that the differenti-al genes might be enriched in the Ras,apoptosis and oxidative phosphorylation signaling pathways.Subsequent Mendelian randomiza-tion revealed 74 potential causal genes among the 1 566 genes,and univariate COX regression analysis of the 74 genes identified 4 pos-sibly related genes FAM3B,JUNB,TMEM59,and KRT5.Comparison of the results of Mendelian randomization and univariate COX regression showed that KRT5 might be the most important gene influencing PCa.Conclusion:FAM3B,JUNB,TMEM59 and KRT5 may play a role in the progression of PCa,and KRT5 may potentially serve as a prognostic predictor and therapeutic target for the malig-nancy.

AIM To investigate the clinical effects of Yiqi Shengjin Prescription on patients with primary Sj?gren's syndrome due to Dual Deficiency of Qi and Yin.METHODS Ninety-two patients were randomly assigned into control group(46 cases)for 8-week intervention of conventional treatment,and observation group(46 cases)for 8-week intervention of both Yiqi Shengjin Prescription and conventional treatment.The changes in clinical effects,TCM syndrome scores,ESSDAI score,ESSPRI score,salivary flow rate,immunoinflammatory indices(ESR,hs-CRP,IgG,C3,C4),SAS score,SDS score,T lymphocytes(CD4+,CD8+,Treg,Th17)and safety indices were detected.RESULTS The observation group demonstrated higher total effective rate than the control group(P＜0.05).After the treatment,the observation group exhibited decreased TCM syndrome scores(P＜0.05),which was lower than those in the control group(P＜0.05);the two groups displayed decreased ESSDAI score,ESSPRI score,ESR,hs-CRP,IgG,SAS score,SDS score,CD8+,Th17(P＜0.05),and increased salivary flow rate,C3,C4,Treg(P＜0.05),especially for the observation group(except for CD4+)(P＜0.05).No obvious adverse reactions were observable in the two groups.CONCLUSION For the patients with primary Sjogren's syndrome due to Deficiency of Qi and Yin,Yiqi Shengjin Prescription can safely and effectively improve dry mouth and eye symptoms,and reduce inflammatory indices,whose mechanism may contribute to the regulation of T lymphocyte balance in vivo.

Objective:To investigate the risk factors of cognitive dysfunction and its relationship with poor prognosis in elderly hypertensive patients with frailty.Methods:A total of 150 elderly hypertensive patients with frailty trea-ted in Eighth People's Hospital of Hebei Province from July 2019 to March 2021 were selected.According to pres-ence of cognitive dysfunction,they were divided into normal cognition group(n=92)and cognitive dysfunction group(n=58),and general data and prognosis condition were collected in two groups.Multivariate Logistic regres-sion analysis was used to analyze the risk factors of cognitive dysfunction in elderly hypertensive patients with frail-ty;Spearman correlation analysis was used to analyze the correlation between cognitive dysfunction degree and prog-nosis.Results:Compared with normal cognition group,cognitive dysfunction group was significantly older and pos-sessed significant higher proportions of diabetes,coronary heart disease,stroke,hyponatremia,multiple medication and malnutrition(P＜0.05 or＜0.01).Multivariate Logistic regression analysis indicated that age ≥75 years,stroke,multiple medication and malnutrition were independent risk factors for cognitive dysfunction in elderly hy-pertensive patients with frailty(OR=2.804～6.434,P＜0.05 or＜0.01).Incidence rate of poor prognosis events in cognitive dysfunction group was significantly higher than that of normal cognition group(51.72％vs.11.96％,P＜0.001).Spearman correlation analysis showed that cognitive dysfunction was significant positively correlated with poor prognosis in these patients(r=0.435,P＜0.001).Conclusion:Age,stroke,multiple medication and malnu-trition are independent risk factors for cognitive dysfunction in elderly hypertensive patients with frailty.Cognitive dysfunction is closely related to poor prognosis in these patients.

The concept and harms of hypothermia were introduced.The research progress of the intelligent warning equipment and model for hypothermia was reviewed,and the advantages and problems in practical application were analyzed.It's pointed out the intelligent warning equipment had to be improved in environmental adaptability,operational convenience and functio-nal stability and the model be enhanced in robustness,large-scale clinical validation and warning parameter accessibility.[Chinese Medical Equipment Journal,2024,45(5):86-94]

Objective:To integrate and systematically evaluate the self-disclosure experience and feelings of cancer patients.Methods:Qualitative studies on self-disclosure of cancer patients in PubMed, Web of Science, Cochrane Library, Embase, EBSCO, SinoMed, China National Knowledge Infrastructure, Wanfang Data, and VIP searched by computer from the establishment of the databases to March 8, 2023. The literature was evaluated using the authenticity evaluation tool of qualitative studies by the Joanna Briggs Institute Evidence-based Health Care, and the results were summarized in an aggregative integration approach.Results:A total of eight literatures were included, 30 main results were extracted, and similar results were summarized into ten new categories. Finally, two integrated results were composed, which were the promoting factors and the hindering factors of self-disclosure.Conclusions:Self-disclosure can enhance the intimate relationship between cancer patients and others, thereby improving the self-acceptance and mental health of cancer patients.