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Karperien AL, Jelinek HF. Box-Counting Fractal Analysis: A Primer for the Clinician. ADVANCES IN NEUROBIOLOGY 2024; 36:15-55. [PMID: 38468026 DOI: 10.1007/978-3-031-47606-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
This chapter lays out the elementary principles of fractal geometry underpinning much of the rest of this book. It assumes a minimal mathematical background, defines the key principles and terms in context, and outlines the basics of a fractal analysis method known as box counting and how it is used to perform fractal, lacunarity, and multifractal analyses. As a standalone reference, this chapter grounds the reader to be able to understand, evaluate, and apply essential methods to appreciate and heal the exquisitely detailed fractal geometry of the brain.
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Affiliation(s)
| | - Herbert F Jelinek
- Department of Medical Sciences and Biotechnology Center, Khalifa University, Abu Dhabi, UAE
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Wu L, Zhong Y, Yu X, Wu D, Xu P, Lv L, Ruan X, Liu Q, Feng Y, Liu J, Li X. Selective poly adenylation predicts the efficacy of immunotherapy in patients with lung adenocarcinoma by multiple omics research. Anticancer Drugs 2022; 33:943-959. [PMID: 35946526 PMCID: PMC9481295 DOI: 10.1097/cad.0000000000001319] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/14/2022] [Indexed: 02/05/2023]
Abstract
The aim of this study was to find the application value of selective polyadenylation in immune cell infiltration, biological transcription function and risk assessment of survival and prognosis in lung adenocarcinoma (LUAD). The processed original mRNA expression data of LUAD were downloaded, and the expression profiles of 594 patient samples were collected. The (APA) events in TCGA-NA-SEQ data were evaluated by polyadenylation site use Index (PDUI) values, and the invasion of stromal cells and immune cells and tumor purity were calculated to group and select the differential genes. Lasso regression and stratified analysis were used to examine the role of risk scores in predicting patient outcomes. The study also used the GDSC database to predict the chemotherapeutic sensitivity of each tumor sample and used a regression method to obtain an IC50 estimate for each specific chemotherapeutic drug treatment. Then CIBERSORT algorithm was used to conduct Spearman correlation analysis, immune regulatory factor analysis and TIDE immune system function analysis for gene expression level and immune cell content. Finally, the Kaplan-Meier curve was used to analyze the correlation between stromal score and the immune score of LUAD. In this study, APA's LUAD risk score prognostic model was constructed. KM survival analysis showed that immune score affected the prognosis of LUAD patients ( P = 0.027) but the matrix score was not statistically significant ( P = 0.1). We extracted 108 genes with APA events from 827 different genes and based on PUDI clustering and heat map, the survival rate of patients in the four groups was significantly different ( P = 0.05). Multiple omics studies showed that risk score was significantly positively correlated with Macrophages M0, T cells Follicular helper, B cells naive and NK cells resting. It is significantly negatively correlated with dendritic cells resting, mast cells resting, monocyte, T cells CD4 memory resting and B cells memory. We further explored the relationship between the expression of immunosuppressor genes and risk score and found that ADORA2A, BTLA, CD160, CD244, CD274, CD96, CSF1R and CTLA4 genes were highly correlated with the risk score. Selective poly adenylation plays an important role in the development and progression of LUAD, immune invasion, tumor cell invasion and metastasis and biological transcription, and affects the survival and prognosis of LUAD patients.
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Affiliation(s)
- Liusheng Wu
- Peking University Shenzhen Hospital, Clinical College of Anhui Medical University
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Yanfeng Zhong
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Xiaoya Yu
- First Clinical Medical College, Southern Medical University, Guangzhou
| | - Dingwang Wu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Pengcheng Xu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Le Lv
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Xin Ruan
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
- Shantou University Medical College, Shantou, Guangdong, China
| | - Qi Liu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Yu Feng
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Jixian Liu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Xiaoqiang Li
- Peking University Shenzhen Hospital, Clinical College of Anhui Medical University
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
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Inhibition of GSK-3β alleviates cerebral ischemia/reperfusion injury in rats by suppressing NLRP3 inflammasome activation through autophagy. Int Immunopharmacol 2019; 68:234-241. [DOI: 10.1016/j.intimp.2018.12.042] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022]
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DeGracia DJ. Regulation of mRNA following brain ischemia and reperfusion. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28097803 DOI: 10.1002/wrna.1415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/11/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022]
Abstract
There is growing appreciation that mRNA regulation plays important roles in disease and injury. mRNA regulation and ribonomics occur in brain ischemia and reperfusion (I/R) following stroke and cardiac arrest and resuscitation. It was recognized over 40 years ago that translation arrest (TA) accompanies brain I/R and is now recognized as part of the intrinsic stress responses triggered in neurons. However, neuron death correlates to a prolonged TA in cells fated to undergo delayed neuronal death (DND). Dysfunction of mRNA regulatory processes in cells fated to DND prevents them from translating stress-induced mRNAs such as heat shock proteins. The morphological and biochemical studies of mRNA regulation in postischemic neurons are discussed in the context of the large variety of molecular damage induced by ischemic injury. Open issues and areas of future investigation are highlighted. A sober look at the molecular complexity of ischemia-induced neuronal injury suggests that a network framework will assist in making sense of this complexity. The ribonomic network sits between the gene network and the various protein and metabolic networks. Thus, targeting the ribonomic network may prove more effective at neuroprotection than targeting specific molecular pathways, for which all efforts have failed to the present time to stop DND in stroke and after cardiac arrest. WIREs RNA 2017, 8:e1415. doi: 10.1002/wrna.1415 For further resources related to this article, please visit the WIREs website.
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Karperien AL, Jelinek HF. Box-Counting Fractal Analysis: A Primer for the Clinician. SPRINGER SERIES IN COMPUTATIONAL NEUROSCIENCE 2016. [DOI: 10.1007/978-1-4939-3995-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Fernandez-Lozano C, Seoane JA, Gestal M, Gaunt TR, Dorado J, Campbell C. Texture classification using feature selection and kernel-based techniques. Soft comput 2015. [DOI: 10.1007/s00500-014-1573-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Lin PL, Huang PY, Huang PW, Hsu HC, Chen CC. Teeth segmentation of dental periapical radiographs based on local singularity analysis. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014; 113:433-445. [PMID: 24252317 DOI: 10.1016/j.cmpb.2013.10.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 09/12/2013] [Accepted: 10/22/2013] [Indexed: 06/02/2023]
Abstract
Teeth segmentation for periapical raidographs is one of the most critical tasks for effective periapical lesion or periodontitis detection, as both types of anomalies usually occur around tooth boundaries and dental radiographs are often subject to noise, low contrast, and uneven illumination. In this paper, we propose an effective scheme to segment each tooth in periapical radiographs. The method consists of four stages: image enhancement using adaptive power law transformation, local singularity analysis using Hölder exponent, tooth recognition using Otsu's thresholding and connected component analysis, and tooth delineation using snake boundary tracking and morphological operations. Experimental results of 28 periapical radiographs containing 106 teeth in total and 75 useful for dental examination demonstrate that 105 teeth are successfully isolated and segmented, and the overall mean segmentation accuracy of all 75 useful teeth in terms of (TP, FP) is (0.8959, 0.0093) with standard deviation (0.0737, 0.0096), respectively.
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Affiliation(s)
- P L Lin
- Department of Computer Science and Information Engineering, Providence University, Shalu, Taichung 43301, Taiwan.
| | - P Y Huang
- Department of Computer Science and Engineering, National Chung Hsing University, Taichung 40227, Taiwan.
| | - P W Huang
- Department of Computer Science and Engineering, National Chung Hsing University, Taichung 40227, Taiwan.
| | - H C Hsu
- College of Oral Medicine, Chung Shan Medical University and Chung Shan Medical University Hospital, Taichung 40201, Taiwan.
| | - C C Chen
- College of Oral Medicine, Chung Shan Medical University and Chung Shan Medical University Hospital, Taichung 40201, Taiwan.
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Lewis MK, Jamison JT, Dunbar JC, DeGracia DJ. mRNA redistribution during permanent focal cerebral ischemia. Transl Stroke Res 2013; 4:604-17. [PMID: 24323415 PMCID: PMC3864703 DOI: 10.1007/s12975-013-0274-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 12/30/2022]
Abstract
Translation arrest occurs in neurons following focal cerebral ischemia and is irreversible in penumbral neurons destined to die. Following global cerebral ischemia, mRNA is sequestered away from 40S ribosomal subunits as mRNA granules, precluding translation. Here, we investigated mRNA granule formation using fluorescence in situ histochemistry out to 8 h permanent focal cerebral ischemia using middle cerebral artery occlusion in Long Evans rats with and without diabetes. Neuronal mRNA granules colocalized with PABP, HuR, and NeuN, but not 40S or 60S ribosomal subunits, or organelle markers. The volume of brain with mRNA granule-containing neurons decreased exponentially with ischemia duration, and was zero after 8 h permanent focal cerebral ischemia or any duration of ischemia in diabetic rats. These results show that neuronal mRNA granule response has a limited range of insult intensity over which it is expressed. Identifying the limits of effective neuronal stress response to ischemia will be important for developing effective stroke therapies.
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MESH Headings
- Animals
- Antigens, Nuclear/metabolism
- Brain Ischemia/complications
- Brain Ischemia/metabolism
- Diabetes Mellitus, Experimental/complications
- Diabetes Mellitus, Experimental/metabolism
- ELAV Proteins/metabolism
- In Situ Hybridization, Fluorescence
- Infarction, Middle Cerebral Artery/complications
- Male
- Nerve Tissue Proteins/metabolism
- Neurons/metabolism
- Poly(A)-Binding Proteins/metabolism
- RNA, Messenger/metabolism
- Rats
- Rats, Long-Evans
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Time Factors
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Affiliation(s)
- Monique K. Lewis
- Department of Physiology, Wayne State University School of Medicine, 4116 Scott Hall, 540 East Canfield Ave, Detroit, MI 48201, USA
| | - Jill T. Jamison
- Department of Physiology, Wayne State University School of Medicine, 4116 Scott Hall, 540 East Canfield Ave, Detroit, MI 48201, USA
| | - Joseph C. Dunbar
- Department of Physiology, Wayne State University School of Medicine, 4116 Scott Hall, 540 East Canfield Ave, Detroit, MI 48201, USA
| | - Donald J. DeGracia
- Department of Physiology, Wayne State University School of Medicine, 4116 Scott Hall, 540 East Canfield Ave, Detroit, MI 48201, USA. Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Fernandez-Lozano C, Seoane JA, Gestal M, Gaunt TR, Campbell C. Texture Classification Using Kernel-Based Techniques. ADVANCES IN COMPUTATIONAL INTELLIGENCE 2013. [DOI: 10.1007/978-3-642-38679-4_42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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