Increased Soluble PD-1 Predicts Response to Nivolumab plus Ipilimumab in Melanoma by Jesper Geert Pedersen, Mateo Sokac, Boe Sandahl Sørensen, Adam Andrzej Luczak, Ninna Aggerholm-Pedersen, Nicolai Juul Birkbak, Trine Heide Øllegaard, Martin Roelsgaard Jakobsen

“…Baseline and on-treatment plasma samples were tested for levels of PD-1, PD-L1, IFNγ, IFNβ, CCL20, CXCL5, CXCL10, IL6, IL8, IL10, MCP1, and TNFα and analyzed by Uniform Manifold Approximation and Projection (UMAP) dimension reduction method and k-means clustering analysis. Results: Interestingly, using UMAP analysis, we found that treatment-induced cytokine changes measured as a ratio between baseline and on-treatment samples correlated significantly to progression-free survival (PFS). …”
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Comparison of alive and dead benthic foraminiferal fauna off the Changjiang Estuary: Understanding water-mass properties and taphonomic processes by Feng Jiang, Daidu Fan, Daidu Fan, Quanhong Zhao, Yijing Wu, Fahui Ren, Yan Liu, Ang Li

“…Q-mode Hierarchical clustering analysis was used to differentiate foraminiferal assemblages based on the relative abundance of common species. …”
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An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis by Hongjin Wang, Nian Wang, Ze Tang, Qiuyu Liu, Shiyu Nie, Wu Tao

“…Methods We downloaded gene expression data and clinical information of HCC patients from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO). The clustering analysis and cox regression with LASSO were used for constructing an 8 PCmRNAs survival model. …”
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Immune depletion of the methylated phenotype of colon cancer is closely related to resistance to immune checkpoint inhibitors by Chengqian Zhong, Tingjiang Xie, Long Chen, Xuejing Zhong, Xinjing Li, Xiumei Cai, Kaihong Chen, Shiqian Lan

“…After pre-processing and calculating the clustering prediction index (CPI) with gap statistics, integrative clustering analysis was conducted via MOVICS. The tumor microenvironment (TME) was deconvolved using several algorithms such as GSVA, MCPcounter, ESTIMATE, and PCA. …”
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Multi-omics analysis elucidates the relationship between intratumor microbiome and host immune heterogeneity in breast cancer by Jia Li, Yu Zhang, Yifan Cai, Peizhuo Yao, Yiwei Jia, Xinyu Wei, Chong Du, Shuqun Zhang

“…Based on consensus clustering analysis, BC patients were categorized into two immune subtypes, referred to as immune-enriched and immune-deficient subtypes. …”
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Unveiling the key genes, environmental toxins, and drug exposures in modulating the severity of ulcerative colitis: a comprehensive analysis by Yao Wang, Hao Zhuang, Xiao-han Jiang, Rui-han Zou, Hai-yang Wang, Zhi-ning Fan

“…The “randomForest” packages in R was used to construct the random forest model. Unsupervised clustering analysis performed by “ConsensusClusterPlus”R package was utilized to identify different subtypes of UC patients. …”
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Comparative proteomic analysis of wall-forming bodies and oocyst wall reveals the molecular basis underlying oocyst wall formation in Eimeria necatrix by Lele Wang, Dandan Liu, Yu Zhu, Feiyan Wang, Weimin Cai, Qianqian Feng, Shijie Su, Zhaofeng Hou, Jinjun Xu, Junjie Hu, Jianping Tao

“…After functional clustering analysis of the identified proteins, three proteins, including E. necatrix disulfide isomerase (EnPDI), thioredoxin (EnTrx) and phosphoglycerate kinase (EnPGK), were selected for further study to confirm their potential roles in oocyst wall formation. …”
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Spatial analysis of human and livestock anthrax in Dien Bien province, Vietnam (2010–2019) and the significance of anthrax vaccination in livestock by Luong Minh Tan, Doan Ngoc Hung, Do Thai My, Morgan A. Walker, Hoang Thi Thu Ha, Pham Quang Thai, Tran Thi Mai Hung, Jason K. Blackburn

“…Spatial rate smoothing and spatial clustering analysis, using Local Moran’s I in GeoDa and space-time scan statistic in SaTScan, were employed to address these objectives. …”
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Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China by Jing Luo, Xudong Wei, Wenxian Liu, Shengmei Chen, Zulfiqar Ahmed, Wenping Sun, Chuzhao Lei, Zhijie Ma

“…The F ST values showed a moderate differentiation between Tianzhu and Menyuan (F ST  = 0.0763, P < 0.05) populations, but a weak differentiation between Huzhu and Tianzhu white yak breeds/populations (F ST  = 0.0186, P > 0.05) and Huzhu and Menyuan (F ST  = − 0.005, P > 0.05) populations. The clustering analysis revealed a close genetic relationship between Huzhu and Menyuan white yak, both were far from Tianzhu white yak breed. …”
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Harmine and 7,8-dihydroxyflavone synergistically suitable for amyotrophic lateral sclerosis management: An in silico study by Toluwase Fatoki, Stanley Chukwuejim, Omodele Ibraheem, Christiana Oke, Blessing Ejimadu, Isaiah Olaoye, Oluwabukola Oyegbenro, Taiwo Salami, Romilola Basorun, Oluwafisayomi Oluwadare, Yetunde Salawudeen

“…Materials and methods: Standard computational tools (webserver and software) were used, and the methods used are clustering analysis, pharmacokinetics and molecular target predictions, and molecular docking simulation. …”
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Dietary Supplementation with Fermented <i>Brassica rapa</i> L. Stimulates Defecation Accompanying Change in Colonic Bacterial Community Structure by Sachi Tanaka, Kana Yamamoto, Chisato Hamajima, Fuka Takahashi, Katsunori Endo, Yutaka Uyeno

“…The fecal bacterial community composition of the volunteers was characterized using terminal-restriction fragment length polymorphism patterning followed by clustering analysis. To evaluate the detailed changes in the immune responses and the gut bacterial composition, assessed by high-throughput sequencing, we fed healthy mice with freeze-dried, fermented <i>B. rapa</i> L. for 2 weeks. …”
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Expression profiles of m6A RNA methylation regulators, PD-L1 and immune infiltrates in gastric cancer by Zhiyuan Xu, Zhiyuan Xu, Qiuli Chen, Lilu Shu, Chunye Zhang, Wenjun Liu, Peter Wang

“…The changes in m6A regulator expression levels in gastric cancer tissues and normal tissues were studied. Consensus clustering analysis was used to separate gastric cancer samples into two categories. …”
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Measurement of the Reliability and Quality of Online Surgery Videos with Artificial Neural Networks by İdris Kurtuluş

“…Benefitting from the scores of the DISCERN questionnaire, a total of three groups were formed with K-means clustering analysis. The scores of the low-quality videos were between 0 and 26.50, of the medium quality videos between 26.50 and 34.9, and of the high-quality ones between 34.9 and 48. …”
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Model Analisis Aktivitas Tutor Dalam Learning Management System Berdasarkan Data Log Menggunakan K-Means Dan Deteksi Outlier by Agusriandi Agusriandi, Elihami Elihami, Irman Syarif, Ita Sarmita Samad

“…The stages of this research were 4 stages, namely collected log data of tutors' activities for one semester (n = 25), conducted descriptive analysis, clustered analysis with K-means, and outlier detection. …”
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Diagnostic potential of energy metabolism-related genes in heart failure with preserved ejection fraction by Qiling Gou, Qianqian Zhao, Mengya Dong, Lei Liang, Hongjun You

“…Additionally, consensus clustering analysis based on the expression of diagnostic biomarkers was utilized to identify differential HFpEF-related genes (HFpEF-RGs). …”
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Impact of Preharvest Ethephon Foliar Spray on the Postharvest Fatty Acid Profile and Dietary Indicators of Macadamia Nuts by Noluthando Noxolo Aruwajoye, Asanda Mditshwa, Lembe Samukelo Magwaza, Mjabuliseni Simon Cloapas Ngidi, Samson Zeray Tesfay

“…Additionally, unsaturated fatty acids (USFAs), such as eicosatrienoic acid + erucic acid (C20:3n³ + C22:1) and eicosatrienoic acid + alpha-linolenic acid (C20:1 + C18:3n³), were notably reduced. Hierarchical clustering analysis revealed positive correlations between ethylene treatment and saturated fatty acids (SFAs) in both ‘Beaumont’ (0.78) and ‘788’ (0.80) cultivars. …”
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Use of Heat-Shock and Edible Coating to Improve the Postharvest Preservation of Blueberries by Chunyan Liu, Jie Ding, Peng Huang, Hongying Li, Yan Liu, Yuwei Zhang, Xinjie Hu, Shanggui Deng, Yaowen Liu, Wen Qin

“…Gas chromatography–mass spectrometry hierarchical clustering analysis showed that this treatment also improved the aroma of the fruit, which maintained a certain similarity with that of fresh blueberries after 14 d. …”
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Establishment of Ferroptosis-Associated Molecular Subtypes and Hub Genes Related to the Immune Microenvironment of Heart Failure by Jiabin Zhou, Jiayu Shi, Peng Xu, Gujie Wu, Chen Wang, Jingyu Li, Hanrui Sun, Weiming Yan, Qi Lu

“…These FRGs were then leveraged to establish two different immune-related subtypes of HF based on clustering analysis results, after which these subtypes were characterized in further detail. …”
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Comparative efficacy of various CHIs combined with western medicine for non-small cell lung cancer: A bayesian network meta-analysis of randomized controlled trials by Ciyan Peng, Jing Chen, Wei Cui, Sini Li, Jianhe Li, Liubao Peng

“…Surface under the cumulative ranking curve (SUCRA) probability values were calculated to rank the treatments examined, and clustering analysis was used to compare the effects of CHIs on different outcomes.Results: A total of 389 studies involving 31,263 patients and 16 CHIs were included. …”
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Breathomics profiling of metabolic pathways affected by major depression: Possibilities and limitations by Laila Gbaoui, Melanie Fachet, Marian Lüno, Gabriele Meyer-Lotz, Thomas Frodl, Thomas Frodl, Christoph Hoeschen

“…The metabolomic pathway analysis and hierarchical clustering analysis (HCA) were performed to group the significant metabolites involved in the same metabolic pathways or networks. …”
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