2.DeepCAGE:Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility
Liu QIAO ; Hua KUI ; Zhang XUEGONG ; Wong Hung WING ; Jiang RUI
Genomics, Proteomics & Bioinformatics 2022;20(3):496-507
Although computational approaches have been complementing high-throughput biolog-ical experiments for the identification of functional regions in the human genome,it remains a great challenge to systematically decipher interactions between transcription factors(TFs)and regulatory elements to achieve interpretable annotations of chromatin accessibility across diverse cellular con-texts.To solve this problem,we propose DeepCAGE,a deep learning framework that integrates sequence information and binding statuses of TFs,for the accurate prediction of chromatin acces-sible regions at a genome-wide scale in a variety of cell types.DeepCAGE takes advantage of a den-sely connected deep convolutional neural network architecture to automatically learn sequence signatures of known chromatin accessible regions and then incorporates such features with expres-sion levels and binding activities of human core TFs to predict novel chromatin accessible regions.In a series of systematic comparisons with existing methods,DeepCAGE exhibits superior perfor-mance in not only the classification but also the regression of chromatin accessibility signals.In a detailed analysis of TF activities,DeepCAGE successfully extracts novel binding motifs and mea-sures the contribution of a TF to the regulation with respect to a specific locus in a certain cell type.When applied to whole-genome sequencing data analysis,our method successfully prioritizes puta-tive deleterious variants underlying a human complex trait and thus provides insights into the understanding of disease-associated genetic variants.
3.Use of a linear stapler device in total laryngectomy
Xue-Kui LIU ; Hao LI ; Wei-Wei LIU ; Qiu-Li LI ; Quan LI ; Xin-Rui ZHANG ; Xing ZHANG ; Zhu-Ming GUO ; Zong-Yuan ZENG
Chinese Journal of Otorhinolaryngology Head and Neck Surgery 2012;47(7):587-590
Objective To evaluate the value of using a linear stapler device for the cloure of the pharynx during total laryngectomy.Methods Sixteen total laryngectomies were performed between August 2010 and December 2011,during the operation,the TA 60 linear stapler was used for pharyngeal closure.Among these patients,two patients had the history of pre-operative radiotherapy,four patients recurred after radiotherapy,ten patients were treated for the first time.100 ml methylene blue was injected into the newly closed laryngopharyngeal cavity through the nasopharyngeal breather pipe for checking up whether it was watertight or not.Results Amnong the sixteen patients,methylene blue leakage from the mucosal joint of the gular cavity closed by the stapler were not found in fifteen patients,it was only found in one patient.The transudatory places were sutured with absorbable Vicryl sutures. This patient healed well without pharyngocutaneous fistula.Negative surgical margins were achieved in all patients.No patient needed to be tranfered to open surgery.Using a linear stapler device in total laryngectomy,45 minutes could be saved as compaired to manual suture. One patient developed a light pharyngocutaneous fistula.The incidence of pharyngocutaneous fistula was 6.25% (1/16). Conclusions This stapled closed technique for pharyngoplasty is efficient,eliminates the risk of wound contamination,saves operation time and decreases the incidence of pharyngocutaneous fistula.This technique can be recommended as alternative for repairing the pharynx in patients undergoing total laryngectomy.
4.The clinical experience in transplantation of the anterolateral femoral skin flap.
Ya-jun XU ; Kui-shui SHOU ; Yong-jun RUI ; Quan-rong ZHANG ; Ming-yu XUE ; Zheng CHEN ; Qun YAO
Chinese Journal of Plastic Surgery 2005;21(6):418-420
OBJECTIVETo introduce the clinical experience in transplantation of the anterolateral femoral skin flap.
METHODSA total of 625 anterolateral femoral skin flaps in 600 patients were transplanted from 1988 to 2003. The retrospective analysis was carried out in all the cases as to the flap pedicle, the vascular variations, the surgical procedures and modifications, and the adaptation for a cutaneous-branch-absent flap.
RESULTSThe 625 flaps were transferred except 7 cancelled in the operation. Postoperatively, 17 cases encountered vascular complications, 10 of which survived completely with successful vessel exploration, 3 cases had partial necrosis, and 4 cases had complete necrosis. The survival rate was 97.8%. 545 flaps were pedicled with the descending branch or lateral branches; 45 flaps with the transverse branch or the high-site anterolateral cutaneous artery, 10 cases with the descending-transverse branch, 18 cases with other vessels. 7 cases were found cutaneous-branch-absent. The vessel variation rate of the flap was 4.06%.
CONCLUSIONSThe anterolateral femoral skin flap has less variation of its pedicle and high success rate of operation. It is an ideal choice for repair of soft tissue defects in the extremities.
Adolescent ; Adult ; Child ; Female ; Femur ; Humans ; Male ; Microsurgery ; Middle Aged ; Retrospective Studies ; Skin Transplantation ; Surgical Flaps ; Young Adult
5.Effect of occupational stress on mental health.
Shan-fa YU ; Rui ZHANG ; Liang-qing MA ; Gui-zhen GU ; Yan YANG ; Kui-rong LI
Chinese Journal of Industrial Hygiene and Occupational Diseases 2003;21(1):16-19
OBJECTIVETo study the effect of job psychological demands and job control on mental health and their interaction.
METHODS93 male freight train dispatchers were evaluated by using revised Job Demand-Control Scale and 7 strain scales. Stepwise regression analysis, Univariate ANOVA, Kruskal-Wallis H and Modian methods were used in statistic analysis.
RESULTSKruskal-Wallis H and Modian methods analysis revealed the difference in mental health scores among groups of decision latitude (mean rank 55.57, 47.95, 48.42, 33.50, P < 0.05), the differences in scores of mental health (37.45, 40.01, 58.35), job satisfaction (53.18, 46.91, 32.43), daily life strains (33.00, 44.96, 56.12) and depression (36.45, 42.25, 53.61) among groups of job time demands (P < 0.05) were all statistically significant. ANOVA showed that job time demands and decision latitude had interaction effects on physical complains (R(2) = 0.24), state-anxiety (R(2) = 0.26), and daytime fatigue (R(2) = 0.28) (P < 0.05). Regression analysis revealed a significant job time demands and job decision latitude interaction effect as well as significant main effects of the some independent variables on different job strains (R(2) > 0.05).
CONCLUSIONJob time demands and job decision latitude have direct and interactive effects on psychosomatic health, the more time demands, the more psychological strains, the effect of job time demands is greater than that of job decision latitude.
Humans ; Mental Health ; Occupational Diseases ; psychology ; Regression Analysis ; Stress, Psychological ; psychology
7.Influencing factors for duration of viral nucleic acid shedding in children with influenza A.
Gao-Feng ZHOU ; Hong-Mei WANG ; Rui-Mu ZHANG ; Ji-Kui DENG
Chinese Journal of Contemporary Pediatrics 2016;18(12):1269-1271
OBJECTIVETo investigate the features and duration of viral nucleic acid shedding in children with influenza A.
METHODSThe clinical data of 90 children with influenza A with positive influenza A virus nucleic acid in nasopharyngeal swab detected by PCR were collected, and these children were divided into simple influenza A group (n=10), influenza A-pneumonia group (n=61), influenza A-nervous system damage group (n=10), and influenza A-underlying disease group (n=9). A retrospective analysis was performed for clinical features, treatment process, duration of viral nucleic acid shedding, and prognosis.
RESULTSThe most common symptoms in these children were fever (89/90, 99%), cough (89/90, 99%), running nose (69/90, 77%), shortness of breath (26/90, 29%), and myalgia (23/90, 26%). The mean duration of viral nucleic acid shedding in 90 children was 9.4±2.9 days. The simple influenza A group had a significantly shorter duration of viral nucleic acid shedding than the influenza A-pneumonia, influenza A-nervous system damage, and influenza A-underlying disease groups (p<0.05), while there were no significant differences between the influenza A-pneumonia, influenza A-nervous system damage, and influenza A-underlying disease groups (p>0.05). The children who received antiviral therapy within 48 hours after disease onset had significantly shorter duration of viral nucleic acid shedding and time to body temperature recovery than those who received antiviral therapy more than 48 hours after disease onset (p<0.05). Of all the children with body temperature recovery, 83% still tested positive for viral nucleic acid.
CONCLUSIONSComplications, underlying diseases, and timing of antiviral therapy are influencing factors for the duration of influenza A virus nucleic acid shedding, and whether body temperature returns to normal cannot be used to decide whether to continue antiviral therapy.
Child ; Child, Preschool ; Female ; Fever ; etiology ; Humans ; Infant ; Influenza A virus ; isolation & purification ; Influenza, Human ; virology ; Male ; Nucleic Acids ; metabolism ; Retrospective Studies ; Time Factors ; Virus Shedding
8.Expression of E-cadherin and β-catenin in oral squamous cell carcinomas of tongue: correlation with the clinicopathologic features and patient prognosis
Rui ZHU ; Xiao-Yun JIANG ; Xiao-Ling SONG ; Wei ZHANG ; Sheng CHEN ; Lai-Kui LIU
Chinese Journal of Stomatology 2010;45(5):295-298
Objective To examine the E-cadherin and β-eatenin expression in oral squamous cell carcinoma of tongue (OSCCT) and investigate the relationship of these markers with clinicopathologic features and patient prognosis.Methods Quantitative immunohistochemistry analysis was used to examine E-cadherin and β-catenin expression in lesions of 30 OSCCT patients.The relationship between the expression of E-cadherin and β-catenin and clinicopathologicical features was analyzed.Results The decreased expression of E-cadherin was observed in 19 of 30 (63%) tumours from patients who eventually developed a recurrent tumour and was also associated with recurrence (P = 0.007).The expression of E-cadherin was associated with survival (P = 0.018) and an independent prognostic factor in univariate analysis.There was no correlation between the expression level of E-cadherin and sex, age, histological differentiation, tumour size, clinical stage, or lymph node metastasis.The high expression of β-catenin was observed in 18 of 30 (60%) tumours.No correlation between β-catenin expression and clinicopathological features was observed.Conclusions The absence or reduced expression of E-cadherin was closely associated with recurrence and survival in OSCCT patients.The aberrant expression of E-cadherin may provide a useful prognostic marker in OSCCT.
9.Value of Cuproptosis genes and characteristic genes in predicting prognosis,immunity and tumor microenvironment in acute myeloid leukemia
Yinzhen LI ; Weixia NONG ; Mei ZHANG ; Dongsheng RUI ; Wei LEI ; Wenli BAI ; Rui LI ; Yazhou ZHANG ; Kui WANG
Acta Universitatis Medicinalis Anhui 2024;59(6):1013-1022
Objective To screen Cuproptosis genes and characteristic genes for differential prognosis in acute mye-loid leukemia(AML)and explore their prognosis in AML as well as their biological roles and correlations in the immune and tumor microenvironment.Methods AML clinical,transcriptome,genomic,and copy number data were downloaded from three major databases,TCGA,GEO,and UCSC,and Cuproptosis genes were collected from published studies.From the perspective of multiomics,the effects of Cuproptosis gene and characteristic gene on survival,immunity,tumor microenvironment,stem cell correlation and drug sensitivity were studied by various bioinformatics methods,meta-analysis and secondary typing.Results One Cuproptosis gene was identified as a differential prognostic gene in AML and five characteristic genes were identified as influencing the prognosis of AML patients by influencing Cuproptosis,and a prognostic model was established.The differential genes were mainly concentrated in mitochondrial activity,REDOX enzyme and energy metabolism.In terms of immunity,macrophage M0,neutrophils,activated memory CD4 T cells and Tregs were positively correlated with risk score,while macro-phage M2,resting mast cells,immature CD4 T cells,helper follicular T cells and memory B cells were negatively correlated with risk score.In terms of tumor microenvironment,the immune cell score of the low-risk group was lower than that of the high-risk group,and in the total score,the tumor microenvironment score of the low-risk group was also lower than that of the high-risk group,indicating that the tumor purity of the high-risk group was lower than that of the low-risk group.However,there was no significant association between stem cells in the high-risk and low-risk groups,and a total of 14 drugs were found to be sensitive to treat AML.Conclusion Cuproptosis gene and characteristic gene are closely related to immune and tumor microenvironment in AML by constructing a prognostic model of AML.
10.Features and clinic values of normal lumbar nerve root anatomy with CT on multiple plane reconstruction techniques at the same slice
Jing-Fu LIN ; Yan-Ying LI ; Zhan-Yu WANG ; Hong-Jun YE ; Jan-He WANG ; Ying-Kui LIANG ; Li JIANG ; Xiao-Juan LI ; Chao ZHANG ; He-Quan GE ; Rui WANG ; Yan-qun ZHANG ;
Chinese Journal of Radiology 1994;0(06):-
Objective To explore features and clinic values of LNR anatomy with multiple planar reconstruction techniques with 16-slice spiral CT at the same slice.Methods The lumbar vertebrae with normal adults of 55 cases and 23 cases with abnormal ENR caused by 8 cases with protrusion of lumbar disc, 5 cases with spinal stenosis,4 cases with malignant tumor,5 cases with trauma and 1 case with lumbar TB confirmed by operation were scanned with 16-slice spiral CT made in American GE company in routine posture of the lumbar vertebrae,reconstructed LNR with UNIX system in workstation (ADW 4.1),and analyzed their normal and abnormal anatomic manifestations at the same slice.Results All of LNR can symmetrically showed on oblique and coronal planes according to different segments:one segment from L1 to L5(55,100% ),two segments: from L1 to L2,L2 to L3 and L3 to L4(55,100% ),three segments: from L1 to L3 (49,88%),from L2to L4(46,84% )and from L3 to L5(20,36% ),four segments: from L1 to L4 (15,27% )and five segments:(8,15% ),respectively.Each LNR,including their whole shapes of passage from starting to end,direction,size,shape,tension and peripheral relationship and so on can showed clearly on oblique and coronal planes and on other planes. However,the later planes can increase LNR but decreasing numbers of LNR and especially increase very long one LNR reconstruction.Primary manifestation of all diseases can be showed on oppressing along its walking line,meanwhile,20 cases with adhesion, 14 cases with displacement,13 cases atrophy and 9 cases with increasing diameter.Conclusions Image anatomy features of full LNR with 16-slice spiral CT with the multiple plane reconstruction techniques is very ideal ways at the same slice.It is a very valuable way to make diagnosis and treatment of LNR diseases.The concept of"road sing"and showing"at the same slice"of LNR are tried to rise from in order to make foundation for studying their image.