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Total 122 results found since Jan 2013.
Machine learning for small interfering RNAs: a concise review of recent developments
The advent of machine learning and its subsequent integration into small interfering RNA (siRNA) research heralds a new epoch in the field of RNA interference (RNAi). This review emphasizes the urgency and relevance of assimilating the plethora of contributions and advancements in this domain, particularly focusing on the period of 2019–2023. Given the rapid progression of deep learning technologies, our synthesis of recent research is paramount to staying apprised of the state-of-the-art methods being utilized. It not only offers a comprehensive insight into the confluence of machine learning and siRNA but also serves a...
Source: Frontiers in Genetics - July 13, 2023 Category: Genetics & Stem Cells Source Type: research
Exploring the correlation of glycolysis-related chondroitin polymerizing factor ( < em > CHPF < /em > ) with clinical characteristics, immune infiltration, and cuproptosis in bladder cancer
Am J Cancer Res. 2023 Jun 15;13(6):2213-2233. eCollection 2023.ABSTRACTBladder cancer (BLCA) is a common malignant neoplasm of the urinary system. Glycolysis is an essential metabolic pathway regulated by various genes with implications for tumor progression and immune escape. Scoring the glycolysis for each sample in the TCGA-BLCA dataset was done using the ssGSEA algorithm for quantification. The results showed that the score in BLCA tissues was markedly greater than those in adjacent tissues. Additionally, the score was found to be correlated with metastasis and high pathological stage. Functional enrichment analyses of...
Source: Cell Research - July 10, 2023 Category: Cytology Authors: Quliang Zhong Kehua Jiang Facai Zhang Yuan Tian Jiang Gu Tao Li Xulong Chen Jianjun Yang Fa Sun Source Type: research
High-resolution visualization and assessment of basal and OXPHOS-induced mitophagy in H9c2 cardiomyoblasts
In this study, we visualized and assessed the level of mitophagy in H9c2 cardiomyoblasts at basal conditions and after OXPHOS induction by galactose adaptation. We used cells with a stable expression of a pH-sensitive fluorescent mitochondrial reporter and applied state-of-the-art imaging techniques and image analysis. Our data showed a significant increase in acidic mitochondria after galactose adaptation. Using a machine-learning approach we also demonstrated increased mitochondrial fragmentation by OXPHOS induction. Furthermore, super-resolution microscopy of live cells enabled capturing of mitochondrial fragments withi...
Source: Autophagy - July 5, 2023 Category: Cytology Authors: Gustav Godtliebsen Kenneth Bowitz Larsen Zambarlal Bhujabal Ida S Opstad Mireia Nager Abhinanda R Punnakkal Trine B Kalstad Randi Olsen Trine Lund Dilip K Prasad Krishna Agarwal Truls Myrmel Asa Birna Birgisdottir Source Type: research
Integrating machine learning and single-cell trajectories to analyze T-cell exhaustion to predict prognosis and immunotherapy in colon cancer patients
ConclusionIn this study, we systematically explored the T-cell exhaustion trajectory in COAD and developed a TES model to assess prognosis and provide guidelines for the treatment decision. This discovery gave rise to a fresh concept for novel therapeutic procedures for the clinical treatment of COAD.
Source: Frontiers in Immunology - May 3, 2023 Category: Allergy & Immunology Source Type: research
Upregulation of RasGRF1 ameliorates spatial cognitive dysfunction in mice after chronic cerebral hypoperfusion
In this study, we aimed to determine whether changes in the expression of RasGRF1, an important protein associated with cognition and synaptic plasticity, underlie the associated impairments in cognition after CCH. We found that RasGRF1 levels markedly decreased following CCH. Through prediction and validation studies, we observed that miRNA-323-3p was upregulated after CCH and could bind to the 3'-untranslated region of Rasgrf1 mRNA and regulate its expression in vitro. Moreover, the inhibition of miRNA-323-3p upregulated Rasgrf1 expression in the hippocampus after CCH, which was reversed by Rasgrf1 siRNA. This suggests t...
Source: Aging - April 13, 2023 Category: Biomedical Science Authors: Li-Jie Yang Wei Wu Wan-Rong Jiang Cheng-Liang Zhu Zhao-Hui Yao Source Type: research
Higher-order modular regulation of the human proteome
Mol Syst Biol. 2023 Mar 9:e9503. doi: 10.15252/msb.20209503. Online ahead of print.ABSTRACTOperons are transcriptional modules that allow bacteria to adapt to environmental changes by coordinately expressing the relevant set of genes. In humans, biological pathways and their regulation are more complex. If and how human cells coordinate the expression of entire biological processes is unclear. Here, we capture 31 higher-order co-regulation modules, which we term progulons, by help of supervised machine-learning on proteomics data. Progulons consist of dozens to hundreds of proteins that together mediate core cellular funct...
Source: Mol Biol Cell - March 9, 2023 Category: Molecular Biology Authors: Georg Kustatscher Martina H ödl Edward Rullmann Piotr Grabowski Emmanuel Fiagbedzi Anja Groth Juri Rappsilber Source Type: research
MicroRNA-128 suppresses tau phosphorylation and reduces amyloid-beta accumulation by inhibiting the expression of GSK3 β, APPBP2, and mTOR in Alzheimer's disease
CONCLUSION: Our findings suggest that miR-128 suppresses AD pathogenesis, and could be a promising therapeutic target for AD. We also find a possible mechanism underlying the dysregulation of miR-128 in AD, in which Aβ reduces miR-128 expression by inhibiting C/EBPα.PMID:36880288 | DOI:10.1111/cns.14143
Source: CNS Neuroscience and Therapeutics - March 7, 2023 Category: Neuroscience Authors: Siwen Li Chi Him Poon Zhigang Zhang Ming Yue Ruijun Chen Yalun Zhang Md Farhad Hossain Yining Pan Jun Zhao Lei Rong Leung Wing Chu Yat Fung Shea Ekaterina Rogaeva Jie Tu Peter St George-Hyslop Lee Wei Lim You-Qiang Song Source Type: research
Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL
Genomics Proteomics Bioinformatics. 2023 Feb 10:S1672-0229(23)00032-3. doi: 10.1016/j.gpb.2023.01.006. Online ahead of print.ABSTRACTPrediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized medicine. Here, we developed a deep learning framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical disc...
Source: Genomics Proteomics ... - February 12, 2023 Category: Genetics & Stem Cells Authors: David Earl Hostallero Lixuan Wei Liewei Wang Junmei Cairns Amin Emad Source Type: research
Cancers, Vol. 14, Pages 5367: The Histone Methyltransferase SETD8 Regulates the Expression of Tumor Suppressor Genes via H4K20 Methylation and the p53 Signaling Pathway in Endometrial Cancer Cells
We examined the expression profile of SETD8 and evaluated whether SETD8 plays a critical role in the proliferation of endometrial cancer cells using small interfering RNAs (siRNAs). We identified the prognostically important genes regulated by SETD8 via H4K20 methylation and p53 signaling using chromatin immunoprecipitation sequencing, RNA sequencing, and machine learning. We confirmed that SETD8 expression was elevated in endometrial cancer tissues. Our in vitro results suggest that the suppression of SETD8 using siRNA or a selective inhibitor attenuated cell proliferation and promoted the apoptosis of endometrial cancer ...
Source: Cancers - October 31, 2022 Category: Cancer & Oncology Authors: Asako Kukita Kenbun Sone Syuzo Kaneko Eiryo Kawakami Shinya Oki Machiko Kojima Miku Wada Yusuke Toyohara Yu Takahashi Futaba Inoue Saki Tanimoto Ayumi Taguchi Tomohiko Fukuda Yuichiro Miyamoto Michihiro Tanikawa Mayuyo Mori-Uchino Tetsushi Tsuruga Takayuk Tags: Article Source Type: research
Neuroprotection of Bone Marrow-Derived Mesenchymal Stem Cell-Derived Extracellular Vesicle-Enclosed miR-410 Correlates with HDAC4 Knockdown in Hypoxic-Ischemic Brain Damage
This study aimed to explore the mechanism by which miR-410 transferred by bone marrow-derived mesenchymal stem cell-derived extracellular vesicles (BMSC-EVs) may alleviate hypoxic-ischemic brain damage (HIBD) in newborn mice. BMSCs were isolated from total bone marrow cells of femur and tibia of newborn mice, and primary neurons were extracted from the cerebral cortex of newborn mice within 24 h of birth. EVs were extracted from BMSCs transfected with the mimic or inhibitor of miR-410. Primary neurons were subjected to hypoxia and treated with overexpression (oe)-HDAC4, small interfering RNA (siRNA)-β-catenin, or Wnt path...
Source: Cell Research - August 26, 2022 Category: Cytology Authors: Mingqi Shen Rongxiu Zheng Xuan Kan Source Type: research
