Article
Oncology
Karolina Pilipow, Abbass Darwich, Agnese Losurdo
Summary: Cancer immunotherapy has shown promising results in various types of cancer, including breast cancer. Current research focuses on using T cells as markers for clinical practice and therapeutic options in breast cancer treatment to expand the application of immunotherapy.
SEMINARS IN CANCER BIOLOGY
(2021)
Article
Water Resources
Weigang Tang, Sean K. Carey
Summary: Flow regimes play a crucial role in understanding physical and biological processes in rivers. In this study, t-SNE was used to classify catchments in the mountainous Western North America based on their annual daily hydrograph (ADH). The results showed that t-SNE successfully clustered catchments with similar flow regimes on a 2D map, allowing for more accurate classification using KNN.
HYDROLOGICAL PROCESSES
(2022)
Article
Water Resources
Weigang Tang, Sean K. Carey
Summary: In this study, t-SNE was used to classify 17,110 ADHs for 304 reference catchments in mountainous Western North America, successfully clustering similar flow regimes on a 2D map and enhancing the capability to address 'unseen' samples with the help of Deep Learning encoder.
HYDROLOGICAL PROCESSES
(2022)
Article
Biology
Durga Khandekar, Debolanle O. Dahunsi, Isaac V. Manzanera Esteve, Sonya Reid, Jeffrey C. Rathmell, Jens Titze, Venkataswarup Tiriveedhi
Summary: A low salt diet reduces the development of immune-related adverse events (irAE) following immunotherapy, without affecting the anti-tumor efficacy.
Article
Computer Science, Artificial Intelligence
Sven Husmann, Antoniya Shivarova, Rick Steinert
Summary: The recent advancements in computational power and machine learning algorithms have led to vast improvements in manifold areas of research. In particular, in the field of finance, the application of machine learning algorithms such as t-SNE and spectral clustering has shown significant improvements in classification and visualization of financial data, as demonstrated in this paper. The authors present a general decision engine that utilizes these algorithms to improve benchmark models in portfolio optimization and company valuation.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Computer Science, Artificial Intelligence
Swati B. Bhonde, Sharmila K. Wagh, Jayashree R. Prasad
Summary: Cancer is caused by the transformation of a normal cell into an uncontrollable malignant tumor cell. Microarray analysis is used to classify and predict cancers. Although gene expression classifications remain a challenge, recent advances in microarray technologies have made it possible to discover tumor-specific biomarkers and improve accuracy.
Article
Immunology
Mauricio Campos-Mora, William Jacot, Genevieve Garcin, Marie-Lise Depondt, Michael Constantinides, Catherine Alexia, Martin Villalba
Summary: NK cells infiltrate tumor environment and eliminate tumor cells. They can perform trogocytosis by acquiring tumor antigens from solid cancer cells. The extent of trogocytosis depends on the target cell and the antigen.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Baibing Yang, Joy M. Davis, Thomas H. Gomez, Mamoun Younes, Xiurong Zhao, Qiang Shen, Run Wang, Tien C. Ko, Yanna Cao
Summary: This study investigated immune cell infiltration patterns in different experimental acute pancreatitis mouse models and found variations in immune responses based on different treatment methods. Computerized analysis proved to be more efficient and reproducible in analyzing immune cells compared to manual gating analysis.
CELL AND BIOSCIENCE
(2021)
Review
Oncology
Kuba Retecki, Milena Seweryn, Agnieszka Graczyk-Jarzynka, Malgorzata Bajor
Summary: Immunotherapy in breast cancer treatment faces challenges, with the tumor microenvironment as a key focus for research to enhance the immune system's efficacy and improve patient survival rates.
Review
Immunology
Anita K. Mehta, Sapana Kadel, Madeline G. Townsend, Madisson Oliwa, Jennifer L. Guerriero
Summary: Macrophages play a significant role in breast cancer progression, with their infiltration associated with poor prognosis. Tumor-associated macrophages impede productive tumor immunity by limiting antigen presentation and supporting tumor cell survival, angiogenesis, and metastasis, highlighting the urgent need to overcome their immune suppression for durable anti-tumor immunity in breast cancer.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chi Yan, Jinming Yang, Nabil Saleh, Sheau-Chiann Chen, Gregory D. Ayers, Vandana G. Abramson, Ingrid A. Mayer, Ann Richmond
Summary: The study identified that combining PI3K/mTOR inhibitors with paclitaxel can enhance response to immune checkpoint inhibitors, leading to a positive impact on breast cancer treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Julie Sammouri, Matthew C. Wong, Erica J. Lynn, Molly B. El Alam, David K. Lo, Daniel Lin, Timothy H. Harris, Tatiana V. Karpinets, Kyoko Court, Tatiana Cisneros Napravnik, Xiaogang Wu, Jianhua Zhang, Ann H. Klopp, Nadim J. Ajami, Lauren E. Colbert
Summary: This study aimed to investigate the relationship between intratumoral human papillomavirus (HPV) and treatment response in cervical cancer patients, and found that rare HPV types were associated with poor treatment response. This feasibility study provides a foundation for further predicting treatment outcomes in cervical cancer patients.
INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS
(2023)
Article
Automation & Control Systems
Chuanfang Zhang, Kaixiang Peng, Jie Dong
Summary: Hot rolling process (HRP) is a complex industrial process that requires monitoring of both loaded and idle conditions. This study proposes a novel nonlinear full condition process monitoring model combining dissimilarity index and support data vector description for condition identification. Utilizing t-SNE to extract NPC for SFA and CA analysis, the proposed model's monitoring performance is verified through real-world application.
Article
Biochemistry & Molecular Biology
Yufan Qiu, Yi Yang, Riyao Yang, Chunxiao Liu, Jung-Mao Hsu, Zhou Jiang, Linlin Sun, Yongkun Wei, Chia-Wei Li, Dihua Yu, Jin Zhang, Mien-Chie Hung
Summary: The study reveals that PD-1 can be secreted in an exosomal form by activated T cells and interact remotely with PD-L1. This interaction can attenuate the suppression of tumor-specific cytotoxic T cell activity by PD-L1, restoring tumor surveillance.
Article
Engineering, Biomedical
Wenwen Wu, Yanqi Huang, Xiaomei Wu
Summary: In this study, a 2D deep learning classification network SRT was proposed to improve automatic ECG analysis. The model structure was enhanced with the CNN and Transformer-encoder modules, and a novel attention module and Dilated Stem structure were introduced to improve feature extraction. Comparative experiments showed that the proposed model outperformed several advanced methods.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2024)
Article
Oncology
Defeng Kong, Guoliang Li, Zhenrong Yang, Shujun Cheng, Wen Zhang, Lin Feng, Kaitai Zhang
Summary: Activated ACK1 gene is associated with poor prognosis in colon cancer patients. Our constructed prognosis prediction model is significant for colon cancer patients. The expression of ACK1 gene may influence the infiltration level of immune cells and immunomodulators in the immune microenvironment.
Article
Oncology
Liyuan Yin, Wen Zhang, Dan Pu, Xiaoqian Zhai, Yiyun Lin, Qiang Wu, Tangel Chang, Jia Hu, Yan Li, Qinghua Zhou
Summary: This study investigated the tumor microenvironment of lung squamous carcinoma (LUSC) and found that the immune subtypes were associated with prognosis. A risk score model was constructed to predict overall survival rates. The findings provide important insights for the development of immunotherapy strategies.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Guoliang Li, Shuai Ma, Quanyou Wu, Defeng Kong, Zhenrong Yang, Zhaoru Gu, Lin Feng, Kaitai Zhang, Shujun Cheng, Yantao Tian, Wen Zhang
Summary: This study established gastric organoid models to test drugs for SRCC and non-SRCC tumors. The results showed that these organoid models were highly similar to the original tumors in phenotype and genotype, and could serve as living biomarkers for drug response testing.
CELL DEATH DISCOVERY
(2022)
Article
Cell Biology
Lulin Zhou, Zubiao Niu, Yuqi Wang, You Zheng, Yichao Zhu, Chenxi Wang, Xiaoyan Gao, Lihua Gao, Wen Zhang, Kaitai Zhang, Gerry Melino, Hongyan Huang, Xiaoning Wang, Qiang Sun
Summary: We uncover senescence as a hidden tumor feature in gastric cancer patients and identify two distinct senescence-associated subtypes. Patients with the senescence subtype have better prognosis and higher tumor mutation loads. We also develop a scoring system based on six signature genes that can predict patient survival and therapeutic efficacy.
CELL DEATH DISCOVERY
(2022)
Article
Oncology
Yi Zhang, Liping Guo, Qichen Dai, Bingqing Shang, Ting Xiao, Xuebing Di, Kaitai Zhang, Lin Feng, Jianzhong Shou, Yipeng Wang
Summary: The study reveals the crucial role of NETs in tumor progression, with a 19-gene NETs score showing predictive value for clinical outcomes of patients. NETs are significantly correlated to adverse biological processes and poor clinical outcomes across various types of tumors.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Andrology
Zhenrong Yang, Hongsong Bai, Quanyou Wu, Linjun Hu, Guoliang Li, Defeng Kong, Qi Zhang, Duo Wan, Zhaoru Gu, Changyun Zhao, Kaitai Zhang, Wen Zhang, Jianzhong Shou
Summary: This study explored the relationship between PSMA high expression in CTCs and the metastatic progress in prostate cancer using the TERT-based CTC detection method. The results showed that TERT-positive CTCs with high PSMA expression were associated with PCa metastatic progress.
TRANSLATIONAL ANDROLOGY AND UROLOGY
(2022)
Article
Chemistry, Analytical
Zihao Liu, Wen Zhang, Xin Zhang, Shijia Wang, Zhiwen Xia, Xiaoyan Guo, Yu Zhao, Pu Wang, Xiu-Hong Wang
Summary: This study presents a microstructured optical fiber sensor for rapid, sensitive, and accurate quantification of exosomes in blood samples of breast cancer patients. The sensor utilizes a AuNPs-dsDNA assembly containing gold nanoparticles, a recognizing DNA aptamer, and a fluorescent reporter DNA sequence, which is immobilized on the fiber wall to capture and quantify cancer-derived exosomes. The sensor exhibits enhanced sensitivity and specificity, enabling the detection of single digits of exosome particles at the nanoliter sample level. Additionally, the sensor can track exosome phenotypic changes for precise drug treatment monitoring. This work provides a robust platform for exosome-based biopsy for cancer diagnosis and prediction of therapeutic outcomes.
ANALYTICAL CHEMISTRY
(2023)
Review
Oncology
XiaoLi Zhang, PeiPei Xie, KaiTai Zhang, Wen Zhang
Summary: Circulating tumor cells (CTCs) are shed from solid tumors and circulate in the bloodstream, playing a significant role in early cancer diagnosis and treatment monitoring. However, their rarity and heterogeneity present challenges for isolation methods. Combined physical and biological enrichment methods may provide a solution to capture CTCs with higher specificity and sensitivity. Utilizing CTCs in combination with other liquid biopsy components could offer more clinically useful information and the circadian rhythm of CTC release may impact patient evaluation and treatment.
Article
Oncology
Wen-Yang Liu, Wen Zhang, Yuan Tang, Si-Lin Chen, Ning Li, Jun-Qin Lei, Jin-Ming Shi, Shu-Lian Wang, Ye-Xiong Li, Kai-Tai Zhang, Jing Jin
Summary: This study investigated the clinical relevance of viable circulating tumor cells (CTCs) in locally advanced rectal cancer (LARC), including distant metastasis and treatment response prediction. The presence of CTCs at baseline was found to be significantly associated with lower 3-year metastasis-free survival (MFS). Additionally, a decreased number of CTCs after radiotherapy was associated with higher rates of pathological complete response (pCR) and clinical complete response (cCR).
Article
Multidisciplinary Sciences
Caifeng Gong, Wen Zhang, Yongkun Sun, Jianzhong Shou, Zhichao Jiang, Tianyi Liu, Shengzhou Wang, Jun Liu, Ying Sun, Aiping Zhou
Summary: This study molecularly characterized cancer patients experiencing hyperprogressive disease (HPD) and non-HPD patients with solid tumors through genetic and tumor immune microenvironment (TiME) analyses. The genetic analysis showed that most tumor driver gene mutations were preserved between pre- and post-HPD tumors. HPD patients had higher frequencies of mutations in TP53 and CNN2, as well as significantly higher mutant-allele tumor heterogeneity. Furthermore, post-HPD samples showed upregulated IL-6 mRNA and a potential immune suppressive TiME. Salvage treatment with irinotecan plus bevacizumab was effective in one HPD patient, leading to prolonged survival. These genetic and TiME characteristics can help identify features of HPD after immunotherapy.
Article
Multidisciplinary Sciences
Wen Zhang, Defeng Kong, Guoliang Li, Zhenrong Yang, Shujun Cheng, Hong Li, Lin Feng, Kaitai Zhang
Summary: This study investigates the role of chemokines in predicting the prognosis of colon cancer. It suggests that the expression of chemokine genes in tumor tissue may be related to prognosis. Using a LASSO model based on chemokine gene families, the researchers construct a prediction model for colon cancer prognosis. They find that the high-risk group has less immune cell infiltration and the chemokine-related gene signature can predict patients' response to immunotherapy and chemotherapy.
Review
Immunology
Zhenzhen Zhou, Yuan Pang, Jingyuan Ji, Jianyu He, Tiankun Liu, Liliang Ouyang, Wen Zhang, Xue-Li Zhang, Zhi-Gang Zhang, Kaitai Zhang, Wei Sun
Summary: This Review highlights recent advances in 3D in vitro modelling technologies for studying immune cell and tumour cell interactions in the tumour microenvironment. It discusses the use of these models to evaluate the effectiveness of novel immunotherapies, including personalized immunotherapies, in cancer patients. The review also emphasizes the need for improved immunotherapy options for solid tumours and explores the establishment of 3D immuno-oncology models using various technologies and their applications in understanding the cancer-immunity cycle and improving immunotherapies for solid tumours.
NATURE REVIEWS IMMUNOLOGY
(2023)
Review
Medicine, Research & Experimental
Qi Zhang, Defeng Kong, Zhenrong Yang, Guoliang Li, Shujun Cheng, Lin Feng, Kaitai Zhang, Wen Zhang
Summary: This study conducted a meta-analysis to investigate the correlation between stem-like circulating tumor cells (CTCs) and prognosis in cancer patients. The results showed that patients with positive stem-like CTCs in peripheral blood had significantly shorter overall survival, progression-free survival, and disease-free survival. This study provides the first meta-analysis evidence for the prognostic value of stem-like CTCs, demonstrating their association with poor prognosis in cancer patients.
CLINICAL AND EXPERIMENTAL MEDICINE
(2023)
Article
Medicine, General & Internal
Zhenrong Yang, Hongsong Bai, Linjun Hu, Defeng Kong, Guoliang Li, Changyun Zhao, Lin Feng, Shujun Cheng, Jianzhong Shou, Wen Zhang, Kaitai Zhang
Summary: This study investigated the diagnostic capability of circulating tumor cells (CTCs) detected by telomerase-based CTC detection (TBCD) in men with a PSA level of 4 ng/ml or higher. The results showed that CTCs had better diagnostic ability than PSA, especially in the range of 4-10 ng/ml. Additionally, a CTC+PSA combined model further improved the diagnosis of PSA levels in the 4-10 ng/ml range.
Article
Medicine, Research & Experimental
Quanyou Wu, Xiao Hu, Xiaoli Zhang, Defeng Kong, Zhenrong Yang, Guoliang Li, Zhaoru Gu, Qi Zhang, Duo Wan, Shujun Cheng, Binlei Liu, Kaitai Zhang, Wen Zhang
Summary: This study comprehensively characterized the effects of OV therapy on systemic immunity, shedding new light on the anti-tumor mechanisms of OH2. It also contributes to the establishment of companion diagnostics for OH2 treatment and the improvement of oncolytic therapy strategies.