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Article ; Online: Prognostic implication of a ferroptosis-related gene signature associates with immunity in Ewing’s sarcoma

Xiejia Jiao / Qingbo Li / Xiao Xu

Electronic Journal of Biotechnology, Vol 64, Iss , Pp 42-

2023 Volume 58

Abstract: Background: Ewing's sarcoma is an extremely aggressive bone sarcoma in teenagers and adolescents. We managed to identify the potential role of ferroptosis-related genes (FRGs) in Ewing's sarcoma and its clinical prognostic value. Results: A total of 59 ... ...

Abstract	Background: Ewing's sarcoma is an extremely aggressive bone sarcoma in teenagers and adolescents. We managed to identify the potential role of ferroptosis-related genes (FRGs) in Ewing's sarcoma and its clinical prognostic value. Results: A total of 59 common differentially expressed FRGs were screened out. GO/KEGG enrichment and PPI network were executed. Based on 16 prognostic-related FRGs identified by univariate Cox regression in GSE17674, 2 molecular clusters were screened out via NMF consensus. Survival rate and immune infiltration were totally different in two clusters. Subsequently, multivariate/step Cox regression was conducted to identify 7 risk signatures (SLC2A1, PCK2, CHAC1, ATG13, PRKAA2, ARNT, and SIRT1). K-M survival (p = 1.785e-06) and ROC curves (with AUC value 0.816, 0877, 0.919 in 1, 3, 5 years) were plotted to assess the good predictive ability of risk model. ICGC dataset with K-M survival (p = 1.558e-02) and AUC value (0.886, 0.750, 0.709 in 1, 3, 5 years) was used to validate the risk model. Risk score and clinical features (gender, age stage status) were incorporated into a nomogram model. Immune microenvironment (IME) ingredients (ESTIMATE score, immune cells, immune-related pathways, and checkpoint genes) between two risk groups were also explored. High-risk group possessed an activated immune status compared to low-risk group. Finally, prognostic signatures exhibited perfect diagnostic ability in ES occurrence, and several drugs showed IC50 sensitivity to different risk groups. Conclusions: Our study identified 7 prognostic signatures of FRGs and explored related immune infiltration which provided new aspects for future research in Ewing's sarcoma.How to cite: Jiao X, Li Q, Xu X. Prognostic implication of a ferroptosis related gene signature associates with immunity in Ewing’s sarcoma. Electron J Biotechnol 2023;64. https://doi.org/10.1016/j.ejbt.2023.01.004.
Keywords	Bone sarcoma ; Cancer ; Ewing's sarcoma ; Ferroptosis ; FRGs ; Immune ; Biotechnology ; TP248.13-248.65 ; Biology (General) ; QH301-705.5
Subject code	616
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Raman spectral pattern recognition of breast cancer

Qingbo Li / Zhixiang Zhang / Zhenhe Ma

Heliyon, Vol 9, Iss 7, Pp e18148- (2023)

A machine learning strategy based on feature fusion and adaptive hyperparameter optimization

2023

Abstract: Raman spectroscopy, as a kind of molecular vibration spectroscopy, provides abundant information for measuring components and molecular structure in the early detection and diagnosis of breast cancer. Currently, portable Raman spectrometers have ... ...

Abstract	Raman spectroscopy, as a kind of molecular vibration spectroscopy, provides abundant information for measuring components and molecular structure in the early detection and diagnosis of breast cancer. Currently, portable Raman spectrometers have simplified and made equipment application more affordable, albeit at the cost of sacrificing the signal-to-noise ratio (SNR). Consequently, this necessitates a higher recognition rate from pattern recognition algorithms. Our study employs a feature fusion strategy to reduce the dimensionality of high-dimensional Raman spectra and enhance the discriminative information between normal tissues and tumors. In the conducted random experiment, the classifier achieved a performance of over 96% for all three average metrics: accuracy, sensitivity, and specificity. Additionally, we propose a multi-parameter serial encoding evolutionary algorithm (MSEA) and integrate it into the Adaptive Local Hyperplane K-nearest Neighbor classification algorithm (ALHK) for adaptive hyperparameter optimization. The implementation of serial encoding tackles the predicament of parallel optimization in multi-hyperparameter vector problems. To bolster the convergence of the optimization algorithm towards a global optimal solution, an exponential viability function is devised for nonlinear processing. Moreover, an improved elitist strategy is employed for individual selection, effectively eliminating the influence of probability factors on the robustness of the optimization algorithm. This study further optimizes the hyperparameter space through sensitivity analysis of hyperparameters and cross-validation experiments, leading to superior performance compared to the ALHK algorithm with manual hyperparameter configuration.
Keywords	Raman spectroscopy ; Breast cancer ; Feature fusion ; MSEA ; Hyperparameter optimization ; Pattern recognition ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	006
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Aging and diabetic retinopathy

Qingbo Li / Mengqi Wang / Xiaorong Li / Yan Shao

Experimental Gerontology, Vol 175, Iss , Pp 112138- (2023)

Inherently intertwined pathophysiological processes

2023

Abstract: Diabetic retinopathy (DR) is a leading cause of blindness worldwide and a costly complication of diabetes mellitus (DM). DR severity is associated with DM duration; thus, DR has become more devastating to individuals and healthcare systems owing to the ... ...

Abstract	Diabetic retinopathy (DR) is a leading cause of blindness worldwide and a costly complication of diabetes mellitus (DM). DR severity is associated with DM duration; thus, DR has become more devastating to individuals and healthcare systems owing to the aging population and the significantly increased human lifespan.Aging is an irreversible cellular state characterized by long-term stagnation of the cell cycle from excessive stress or damage. Furthermore, aging plays a critical role in developing age-related diseases, but its effects (direct or indirect) on DR development remain considerably understudied. Nonetheless, some studies have demonstrated that aging-related degeneration and DR development share common risk factors, which helps explain the increased prevalence of DR and visual impairment in the elderly population.This review aims to provide some conceptual insight into aging and DR development, two intertwined pathophysiological processes, and discusses potential therapeutic strategies for DR, including prevention and treatment, during this era of longevity.
Keywords	Diabetic retinopathy ; Aging ; Advanced glycation end products ; Cytokine ; Oxidative stress ; Metabolism ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Identification of enterotype and its predictive value for patients with colorectal cancer.

Qingbo, Li / Jing, Zhuang / Zhanbo, Qu / Jian, Chu / Yifei, Song / Yinhang, Wu / Shuwen, Han

Gut pathogens

2024 Volume 16, Issue 1, Page(s) 12

Abstract: Background: Gut microbiota dysbiosis involved in the pathogenesis of colorectal cancer (CRC). The characteristics of enterotypes in CRC development have not been determined.: Objective: To characterize the gut microbiota of healthy, adenoma, and CRC ... ...

Abstract	Background: Gut microbiota dysbiosis involved in the pathogenesis of colorectal cancer (CRC). The characteristics of enterotypes in CRC development have not been determined. Objective: To characterize the gut microbiota of healthy, adenoma, and CRC subjects based on enterotype. Methods: The 16 S rRNA sequencing data from 315 newly sequenced individuals and three previously published datasets were collected, providing total data for 367 healthy, 320 adenomas, and 415 CRC subjects. Enterotypes were analyzed for all samples, and differences in microbiota composition across subjects with different disease states in each enterotype were determined. The predictive values of a random forest classifier based on enterotype in distinguishing healthy, adenoma, and CRC subjects were evaluated and validated. Results: Subjects were classified into one of three enterotypes, namely, Bacteroide- (BA_E), Blautia- (BL_E), and Streptococcus- (S_E) dominated clusters. The taxonomic profiles of these three enterotypes differed among the healthy, adenoma, and CRC cohorts. BA_E group was enriched with Bacteroides and Blautia; BL_E group was enriched by Blautia and Coprococcus; S_E was enriched by Streptococcus and Ruminococcus. Relative abundances of these genera varying among the three human cohorts. In training and validation sets, the S_E cluster showed better performance in distinguishing among CRC patients, adenoma patients, and healthy controls, as well as between CRC and non-CRC individuals, than the other two clusters. Conclusion: This study provides the first evidence to indicate that changes in the microbial composition of enterotypes are associated with disease status, thereby highlighting the diagnostic potential of enterotypes in the treatment of adenoma and CRC.
Language	English
Publishing date	2024-02-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2478277-4
ISSN	1757-4749
ISSN	1757-4749
DOI	10.1186/s13099-024-00606-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The expression level of chicken telomerase reverse transcriptase in tumors induced by ALV-J is positively correlated with methylation and mutation of its promoter region

Yong Xiang / Qinxi Chen / Qingbo Li / Canxin Liang / Weisheng Cao

Veterinary Research, Vol 53, Iss 1, Pp 1-

2022 Volume 13

Abstract: Abstract Avian leukosis virus subgroup J (ALV-J) can cause neoplastic diseases in poultry and is still widely prevalent in China. Chicken telomerase reverse transcriptase (chTERT) is the core component of telomerase, which is closely related to the ... ...

Abstract	Abstract Avian leukosis virus subgroup J (ALV-J) can cause neoplastic diseases in poultry and is still widely prevalent in China. Chicken telomerase reverse transcriptase (chTERT) is the core component of telomerase, which is closely related to the occurrence and development of tumors. Our previous studies showed that chTERT is overexpressed in ALV-J tumors, but the mechanism is still not completely clear. Therefore, this study aims to analyze the possible molecular mechanism of chTERT overexpression in ALV-J tumors from the perspective of DNA methylation and promoter mutation. Methylation sequencing of the chTERT amplicon showed that ALV-J replication promoted the methylation level of the chTERT promoter. And the methylation level of the chTERT promoter in ALV-J tumors was significantly higher than that in tumor-adjacent and normal tissues. Compared with the tumor-adjacent and normal tissues, the chTERT promoter in each ALV-J tumors tested had a mutation of −183 bp C > T, and 36.0% (9/25) of the tumors also had mutations of −184 bp T > C, −73 bp::GGCCC and −56 bp A > T in the chTERT promoter, which formed the binding sites for the transcription factors NFAT5, TFAP2A and ZEB1, respectively. The results of RT–qPCR and Western blotting showed that the occurrence of these mutations significantly increased the expression level of chTERT. In conclusion, this study demonstrated that the high expression of chTERT in ALV-J tumors is positively correlated with the level of hypermethylation and mutation in its promoter, which provides a new perspective for further research on the molecular mechanism of chTERT in ALV-J tumorigenesis.
Keywords	Avian leukosis virus subgroup J ; tumorigenicity ; chicken telomerase reverse transcriptase ; DNA methylation ; promoter mutation ; Veterinary medicine ; SF600-1100
Subject code	570
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: HSV

Sheng Li / Qingbo Li / Yi Ren / Jia Yi / Jinhe Guo / Xianbin Kong

Frontiers in Molecular Biosciences, Vol

The scout and assault for digestive system tumors

2023 Volume 10

Abstract: More than 25% of all malignant tumors are digestive system tumors (DSTs), which mostly include esophageal cancer, gastric cancer, pancreatic cancer, liver cancer, gallbladder cancer and cholangiocarcinoma, and colorectal cancer. DSTs have emerged as one ... ...

Abstract	More than 25% of all malignant tumors are digestive system tumors (DSTs), which mostly include esophageal cancer, gastric cancer, pancreatic cancer, liver cancer, gallbladder cancer and cholangiocarcinoma, and colorectal cancer. DSTs have emerged as one of the prominent reasons of morbidity and death in many nations and areas around the world, posing a serious threat to human life and health. General treatments such as radiotherapy, chemotherapy, and surgical resection can poorly cure the patients and have a bad prognosis. A type of immunotherapy known as oncolytic virus therapy, have recently shown extraordinary anti-tumor effectiveness. One of the viruses that has been the subject of the greatest research in this field, the herpes simplex virus (HSV), has shown excellent potential in DSTs. With a discussion of HSV-1 based on recent studies, we outline the therapeutic effects of HSV on a number of DSTs in this review. Additionally, the critical function of HSV in the detection of cancers is discussed, and some HSV future possibilities are shown.
Keywords	HSV ; digestive system tumors ; oncolytic virus ; immunology ; cancer ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The efficacy and safety of ultrasonic bone scalpel for removing retrovertebral osteophytes in anterior cervical discectomy and fusion

Zhi Yao / Shishuang Zhang / Weijun Liu / Mengcheng Wei / Weizhi Fang / Qingbo Li / Lei Cai / Zhengkun Wang / Chuankun Zhou / Yichi Zhou

Scientific Reports, Vol 14, Iss 1, Pp 1-

A retrospective study

2024 Volume 7

Abstract: Abstract In this study, we present a novel surgical method that utilizes the ultrasonic bone scalpel (UBS) for the removal of large retrovertebral osteophytes in anterior cervical discectomy and fusion (ACDF) and evaluate its safety and efficacy in ... ...

Abstract	Abstract In this study, we present a novel surgical method that utilizes the ultrasonic bone scalpel (UBS) for the removal of large retrovertebral osteophytes in anterior cervical discectomy and fusion (ACDF) and evaluate its safety and efficacy in comparison to the traditional approach of using high-speed drill (HSD). A total of 56 patients who underwent ACDF for retrovertebral osteophytes were selected. We recorded patients' baseline information, operation time, intraoperative blood loss, complications, JOA and VAS scores, and other relevant data. The mean operation time and the mean intraoperative blood loss in the UBS group were less than those in the HSD group (P < 0.05). Although both groups exhibited considerable improvements in JOA and VAS scores following surgery, there was no statistically significant difference between the two groups (P > 0.05). Additionally, no significant disparities were found in bone graft fusion between the two groups at 6- and 12-months postsurgery. Notably, neither group exhibited complications such as dura tear or spinal cord injury. Our study found that the use of UBS reduced operative time, minimized surgical bleeding, and led to clinical outcomes comparable to HSD in ACDF. This technique offers an effective and safe method of removing large retrovertebral osteophytes.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates

Qingbo Li

International Journal of Proteomics, Vol

2010 Volume 2010

Keywords	Biochemistry ; QD415-436 ; Organic chemistry ; QD241-441 ; Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Biochemistry ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences
Language	English
Publishing date	2010-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Surface Modification of Catalysts via Atomic Layer Deposition for Pollutants Elimination

Xiaofeng Wang / Zhe Zhao / Chengcheng Zhang / Qingbo Li / Xinhua Liang

Catalysts, Vol 10, Iss 1298, p

2020 Volume 1298

Abstract: In recent years, atomic layer deposition (ALD) is widely used for surface modification of materials to improve the catalytic performance for removing pollutants, e.g., CO, hydrocarbons, heavy metal ions, and organic pollutants, and much progress has been ...

Abstract	In recent years, atomic layer deposition (ALD) is widely used for surface modification of materials to improve the catalytic performance for removing pollutants, e.g., CO, hydrocarbons, heavy metal ions, and organic pollutants, and much progress has been achieved. In this review, we summarize the recent development of ALD applications in environmental remediation from the perspective of surface modification approaches, including conformal coating, uniform particle deposition, and area-selective deposition. Through the ALD conformal coating, the activity of photocatalysts improved. Uniform particle deposition is used to prepare nanostructured catalysts via ALD for removal of air pollutions and dyes. Area-selective deposition is adopted to cover the specific defects on the surface of materials and synthesize bimetallic catalysts to remove CO and other contaminations. In addition, the design strategy of catalysts and shortcomings of current studies are discussed in each section. At last, this review points out some potential research trends and comes up with a few routes to further improve the performance of catalysts via ALD surface modification and deeper investigate the ALD reaction mechanisms.
Keywords	atomic layer deposition (ALD) ; conformal coating ; uniform particle deposition ; area-selective deposition ; pollutants removal ; Chemical technology ; TP1-1185 ; Chemistry ; QD1-999
Subject code	620
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chicken telomerase reverse transcriptase promotes the tumorigenicity of avian leukosis virus subgroup J by regulating the Wnt/β-catenin signaling pathway

Yong Xiang / Canxin Liang / Qingbo Li / Qinxi Chen / Yang Zhou / Xiaoxue Zheng / Di Zhou / Zepeng Wang / Guyao Wang / Weisheng Cao

Veterinary Research, Vol 53, Iss 1, Pp 1-

2022 Volume 19

Abstract: Abstract This research aimed to analyze the regulatory effect of chicken telomerase reverse transcriptase (chTERT) on the Wnt/β-catenin signaling pathway and its effect on the tumorigenicity of avian leukosis virus subgroup J (ALV-J) through in vivo ... ...

Abstract	Abstract This research aimed to analyze the regulatory effect of chicken telomerase reverse transcriptase (chTERT) on the Wnt/β-catenin signaling pathway and its effect on the tumorigenicity of avian leukosis virus subgroup J (ALV-J) through in vivo experiments. The chTERT eukaryotic expression plasmid and its recombinant lentivirus particles were constructed for in vivo transfection of chTERT to analyze the effect of chTERT continuously overexpressed in chickens on the tumorigenicity of ALV-J. During 156 days of the artificial ALV-J tumor-inducing process, 7 solid tumors developed in 3 chickens in the chTERT-overexpression group (n = 262) and no tumors developed in the control group (n = 262). Another 18 tumors induced by ALV-J were confirmed and collected from breeding poultry farms. And we confirmed that chTERT was significantly highly expressed in ALV-J tumors. The ELISA data suggested that the protein levels of β-catenin and c-Myc in the chicken plasma of the chTERT-overexpressing group with ALV-J infected were consistently and significantly higher than those of the control group. Compared with that of the tumor-adjacent tissues, the activity of the Wnt/β-catenin signaling pathway and expression of the c-Myc was significantly increased in ALV-J tumors. And the percentage of apoptosis in ALV-J tumors significantly lower than that in tumor-adjacent tissues. Immunohistochemistry, Western blot and RT-qPCR suggested that the replication level of ALV-J in tumors was significantly higher than that in tumor-adjacent tissues. This study suggests that chTERT plays a critical role in the tumorigenicity of ALV-J by enhancing the Wnt/β-catenin signaling pathway, which will contribute to further elucidating the tumor-inducing mechanism of ALV-J.
Keywords	Avian leukosis virus subgroup J ; chicken telomerase reverse transcriptase ; Wnt/β-catenin signaling pathway ; tumorigenicity ; in vivo ; Veterinary medicine ; SF600-1100
Subject code	570
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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