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Lam WYS, Kwong E, Chan HWT, Zheng YP. Using Sequence Analyses to Quantitatively Measure Oropharyngeal Swallowing Temporality in Point-of-Care Ultrasound Examinations: A Pilot Study. J Clin Med 2024; 13:2288. [PMID: 38673561 PMCID: PMC11051012 DOI: 10.3390/jcm13082288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
(1) Background: Swallowing is a complex process that comprises well-timed control of oropharyngeal and laryngeal structures to achieve airway protection and swallowing efficiency. To understand its temporality, previous research adopted adherence measures and revealed obligatory pairs in healthy swallows and the effect of aging and bolus type on the variability of event timing and order. This study aimed to (i) propose a systemic conceptualization of swallowing physiology, (ii) apply sequence analyses, a set of information-theoretic and bioinformatic methods, to quantify and characterize swallowing temporality, and (iii) investigate the effect of aging and dysphagia on the quantified variables using sequence analyses measures. (2) Method: Forty-three participants (17 young adults, 15 older adults, and 11 dysphagic adults) underwent B-mode ultrasound swallowing examinations at the mid-sagittal plane of the submental region. The onset, maximum, and offset states of hyoid bone displacement, geniohyoid muscle contraction, and tongue base retraction were identified and sorted to form sequences which were analyzed using an inventory of sequence analytic techniques; namely, overlap coefficients, Shannon entropy, and longest common subsequence algorithms. (3) Results: The concurrency of movement sequence was found to be significantly impacted by aging and dysphagia. Swallowing sequence variability was also found to be reduced with age and the presence of dysphagia (H(2) = 52.253, p < 0.001, η2 = 0.260). Four obligatory sequences were identified, and high adherence was also indicated in two previously reported pairs. These results provided preliminary support for the validity of sequence analyses for quantifying swallowing sequence temporality. (4) Conclusions: A systemic conceptualization of human deglutition permits a multi-level quantitative analysis of swallowing physiology. Sequence analyses are a set of promising quantitative measurement techniques for point-of-care ultrasound (POCUS) swallowing examinations and outcome measures for swallowing rehabilitation and evaluation of associated physiological conditions, such as sarcopenia. Findings in the current study revealed physiological differences among healthy young, healthy older, and dysphagic adults. They also helped lay the groundwork for future AI-assisted dysphagia assessment and outcome measures using POCUSs. Arguably, the proposed conceptualization and analyses are also modality-independent measures that can potentially be generalized for other instrumental swallowing assessment modalities.
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Affiliation(s)
- Wilson Yiu Shun Lam
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong SAR, China (H.W.T.C.)
- Research Institute for Smart Ageing, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Elaine Kwong
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong SAR, China (H.W.T.C.)
- Research Institute for Smart Ageing, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Huberta Wai Tung Chan
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong SAR, China (H.W.T.C.)
| | - Yong-Ping Zheng
- Research Institute for Smart Ageing, The Hong Kong Polytechnic University, Hong Kong SAR, China;
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Mikolajewicz N, Gacesa R, Aguilera-Uribe M, Brown KR, Moffat J, Han H. Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline. Commun Biol 2022; 5:1142. [PMID: 36307536 PMCID: PMC9616830 DOI: 10.1038/s42003-022-04093-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) offers functional insight into complex biology, allowing for the interrogation of cellular populations and gene expression programs at single-cell resolution. Here, we introduce scPipeline, a single-cell data analysis toolbox that builds on existing methods and offers modular workflows for multi-level cellular annotation and user-friendly analysis reports. Advances to scRNA-seq annotation include: (i) co-dependency index (CDI)-based differential expression, (ii) cluster resolution optimization using a marker-specificity criterion, (iii) marker-based cell-type annotation with Miko scoring, and (iv) gene program discovery using scale-free shared nearest neighbor network (SSN) analysis. Both unsupervised and supervised procedures were validated using a diverse collection of scRNA-seq datasets and illustrative examples of cellular transcriptomic annotation of developmental and immunological scRNA-seq atlases are provided herein. Overall, scPipeline offers a flexible computational framework for in-depth scRNA-seq analysis.
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Affiliation(s)
- Nicholas Mikolajewicz
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rafael Gacesa
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Magali Aguilera-Uribe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
| | - Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
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Rodriguez SMB, Staicu GA, Sevastre AS, Baloi C, Ciubotaru V, Dricu A, Tataranu LG. Glioblastoma Stem Cells-Useful Tools in the Battle against Cancer. Int J Mol Sci 2022; 23:ijms23094602. [PMID: 35562993 PMCID: PMC9100635 DOI: 10.3390/ijms23094602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma stem cells (GSCs) are cells with a self-renewal ability and capacity to initiate tumors upon serial transplantation that have been linked to tumor cell heterogeneity. Most standard treatments fail to completely eradicate GSCs, causing the recurrence of the disease. GSCs could represent one reason for the low efficacy of cancer therapy and for the short relapse time. Nonetheless, experimental data suggest that the presence of therapy-resistant GSCs could explain tumor recurrence. Therefore, to effectively target GSCs, a comprehensive understanding of their biology and the survival and developing mechanisms during treatment is mandatory. This review provides an overview of the molecular features, microenvironment, detection, and targeting strategies of GSCs, an essential information required for an efficient therapy. Despite the outstanding results in oncology, researchers are still developing novel strategies, of which one could be targeting the GSCs present in the hypoxic regions and invasive edge of the glioblastoma.
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Affiliation(s)
- Silvia Mara Baez Rodriguez
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
| | - Georgiana-Adeline Staicu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
| | - Ani-Simona Sevastre
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Medicine and Pharmacy, 200349 Craiova, Romania;
| | - Carina Baloi
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
| | - Vasile Ciubotaru
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
| | - Anica Dricu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
- Correspondence:
| | - Ligia Gabriela Tataranu
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
- Department 6—Clinical Neurosciences, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
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Khouri-Farah N, Guo Q, Morgan K, Shin J, Li JYH. Integrated single-cell transcriptomic and epigenetic study of cell state transition and lineage commitment in embryonic mouse cerebellum. SCIENCE ADVANCES 2022; 8:eabl9156. [PMID: 35363520 PMCID: PMC10938588 DOI: 10.1126/sciadv.abl9156] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Recent studies using single-cell RNA-sequencing have revealed cellular heterogeneity in the developing mammalian cerebellum, yet the regulatory logic underlying this cellular diversity remains to be elucidated. Using integrated single-cell RNA and ATAC analyses, we resolved developmental trajectories of cerebellar progenitors and identified putative trans- and cis-elements that control cell state transition. We reverse engineered gene regulatory networks (GRNs) of each cerebellar cell type. Through in silico simulations and in vivo experiments, we validated the efficacy of GRN analyses and uncovered the molecular control of a posterior transitory zone (PTZ), a distinct progenitor zone residing immediately anterior to the morphologically defined rhombic lip (RL). We showed that perturbing cell fate specification in the PTZ and RL causes posterior cerebellar vermis hypoplasia, the most common cerebellar birth defect in humans. Our study provides a foundation for comprehensive studies of developmental programs of the mammalian cerebellum.
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Affiliation(s)
- Nagham Khouri-Farah
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Qiuxia Guo
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Kerry Morgan
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Jihye Shin
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - James Y. H. Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
- Institute for Systems Genomics, University of Connecticut, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
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