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Ellis R, Weiss A. Human vaccines and immunotherapeutics: News February 2024. Hum Vaccin Immunother 2024; 20:2327910. [PMID: 38478989 PMCID: PMC10939145 DOI: 10.1080/21645515.2024.2327910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Affiliation(s)
| | - Adam Weiss
- Acquisitions Editor, Taylor & Francis Group
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Oishi T, Hasegawa S, Nakano T, Sudo S, Kuwajima H, Tokuriki S, Tamura T. Changes in vaccine coverage and incidence of acute gastroenteritis and severe rotavirus gastroenteritis in children <5 years in Shibata City, Niigata Prefecture, Japan. Hum Vaccin Immunother 2024; 20:2322202. [PMID: 38478958 PMCID: PMC10939147 DOI: 10.1080/21645515.2024.2322202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
Rotavirus (RV) vaccines were first introduced in 2011 and adopted for universal vaccination in 2020 in Japan. However, the effectiveness of RV vaccines after being adopted for universal vaccination in 2020 has not been reported. Because of the easy accessibility of clinics in Japan, many children are not usually hospitalized for RV gastroenteritis (RVGE). Therefore, in order to evaluate the impact of the RV vaccine since 2008, we investigated the incidence of hospitalization for RVGE as well as the frequency of children aged < 5 years who received medical treatment for severe RVGE at clinics in Shibata City, Japan. The RV vaccine coverage rate was 94.0% (1,046/1,113) in Shibata City after universal vaccination in 2020; this was a significant increase from previous rates. The incidence per 1000 person - years for RVGE hospitalization and severe RVGE at clinics were significantly higher among children aged < 3 years than in previous time periods. The incidence in children with all acute gastroenteritis (AGE) decreased significantly after universal vaccination during the COVID-19 pandemic. The proportion of severe RVGE among all AGE cases also decreased significantly after universal vaccination among children aged < 3 years (0.0%) and those aged 3-4 years (0.6%). There were significant differences in the distribution of RV genotypes isolated from the feces of children with RVGE between different eras divided by RV vaccination rates, especially G1P[8], which was the major genotype before it recently almost disappeared. Further studies are warranted to assess the impact of the COVID-19 pandemic.
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Affiliation(s)
- Tomohiro Oishi
- Department of Clinical Infectious Diseases, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Satoshi Hasegawa
- Pediatric Department, Niigata Prefectural Shibata Hospital, Shibata, Niigata, Japan
| | - Tokushi Nakano
- Pediatric Department, Nakano Children’s Clinic, Shibata, Niigata, Japan
| | - Shoji Sudo
- Pediatric Department, Sudo Pediatric Clinic, Shibata, Niigata, Japan
| | | | - Shuko Tokuriki
- Pediatric Department, Twin Smile Clinic, Shibata, Niigata, Japan
| | - Tsutomu Tamura
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Japan
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Qiao Y, Yang R, Liu Y, Chen J, Zhao L, Huo P, Wang Z, Bu D, Wu Y, Zhao Y. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures. Comput Struct Biotechnol J 2024; 23:617-625. [PMID: 38274994 PMCID: PMC10808905 DOI: 10.1016/j.csbj.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high-throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein-RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two sub-models to extract local motif-like information and long-term context information. We show that DeepFusion performs best compared with other cutting-edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBP-binding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
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Affiliation(s)
- Yixuan Qiao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Yang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Chen
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Peipei Huo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihao Wang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
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Affiliation(s)
- Xiaohong Liu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han Wang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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Yao M, Zhang L, Teng X, Lei Y, Xing X, Ren T, Pan Y, Zhang L, Li Z, Lin J, Zheng Y, Xing L, Zhou J, Wu C. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Comput Struct Biotechnol J 2024; 23:700-710. [PMID: 38292475 PMCID: PMC10825174 DOI: 10.1016/j.csbj.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.
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Affiliation(s)
- Mingze Yao
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
- Center of Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan 030006, China
| | - Xiaojuan Teng
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yu Lei
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Xiaoyu Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Tinglin Ren
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Yuanqing Pan
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Liwen Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhengfeng Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yaowu Zheng
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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Yadav S, Vora DS, Sundar D, Dhanjal JK. TCR-ESM: Employing protein language embeddings to predict TCR-peptide-MHC binding. Comput Struct Biotechnol J 2024; 23:165-173. [PMID: 38146434 PMCID: PMC10749252 DOI: 10.1016/j.csbj.2023.11.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023] Open
Abstract
Cognate target identification for T-cell receptors (TCRs) is a significant barrier in T-cell therapy development, which may be overcome by accurately predicting TCR interaction with peptide-bound major histocompatibility complex (pMHC). In this study, we have employed peptide embeddings learned from a large protein language model- Evolutionary Scale Modeling (ESM), to predict TCR-pMHC binding. The TCR-ESM model presented outperforms existing predictors. The complementarity-determining region 3 (CDR3) of the hypervariable TCR is located at the center of the paratope and plays a crucial role in peptide recognition. TCR-ESM trained on paired TCR data with both CDR3α and CDR3β chain information performs significantly better than those trained on data with only CDR3β, suggesting that both TCR chains contribute to specificity, the relative importance however depends on the specific peptide-MHC targeted. The study illuminates the importance of MHC information in TCR-peptide binding which remained inconclusive so far and was thought dependent on the dataset characteristics. TCR-ESM outperforms existing approaches on external datasets, suggesting generalizability. Overall, the potential of deep learning for predicting TCR-pMHC interactions and improving the understanding of factors driving TCR specificity are highlighted. The prediction model is available at http://tcresm.dhanjal-lab.iiitd.edu.in/ as an online tool.
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Affiliation(s)
- Shashank Yadav
- Department of Biomedical Engineering, University of Arizona, Tucson 85721, AZ, USA
| | - Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi 110020, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Jaspreet Kaur Dhanjal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi 110020, India
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Martino F, Ilardi G, Varricchio S, Russo D, Di Crescenzo RM, Staibano S, Merolla F. A deep learning model to predict Ki-67 positivity in oral squamous cell carcinoma. J Pathol Inform 2024; 15:100354. [PMID: 38148967 PMCID: PMC10750186 DOI: 10.1016/j.jpi.2023.100354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/14/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Anatomical pathology is undergoing its third revolution, transitioning from analogical to digital pathology and incorporating new artificial intelligence technologies into clinical practice. Aside from classification, detection, and segmentation models, predictive models are gaining traction since they can impact diagnostic processes and laboratory activity, lowering consumable usage and turnaround time. Our research aimed to create a deep-learning model to generate synthetic Ki-67 immunohistochemistry from Haematoxylin and Eosin (H&E) stained images. We used 175 oral squamous cell carcinoma (OSCC) from the University Federico II's Pathology Unit's archives to train our model to generate 4 Tissue Micro Arrays (TMAs). We sectioned one slide from each TMA, first stained with H&E and then re-stained with anti-Ki-67 immunohistochemistry (IHC). In digitised slides, cores were disarrayed, and the matching cores of the 2 stained were aligned to construct a dataset to train a Pix2Pix algorithm to convert H&E images to IHC. Pathologists could recognise the synthetic images in only half of the cases in a specially designed likelihood test. Hence, our model produced realistic synthetic images. We next used QuPath to quantify IHC positivity, achieving remarkable levels of agreement between genuine and synthetic IHC. Furthermore, a categorical analysis employing 3 Ki-67 positivity cut-offs (5%, 10%, and 15%) revealed high positive-predictive values. Our model is a promising tool for collecting Ki-67 positivity information directly on H&E slides, reducing laboratory demand and improving patient management. It is also a valuable option for smaller laboratories to easily and quickly screen bioptic samples and prioritise them in a digital pathology workflow.
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Affiliation(s)
- Francesco Martino
- Dedalus HealthCare, Division of Diagnostic Imaging IT, Gertrude-Frohlich-Sandner-Straße 1, Wien 1100, Austria
- Department of Advanced Biomedical Sciences, University of Naples, Via Pansini, 5, Naples 80131, Italy
| | - Gennaro Ilardi
- Department of Advanced Biomedical Sciences, University of Naples, Via Pansini, 5, Naples 80131, Italy
| | - Silvia Varricchio
- Department of Advanced Biomedical Sciences, University of Naples, Via Pansini, 5, Naples 80131, Italy
| | - Daniela Russo
- Department of Advanced Biomedical Sciences, University of Naples, Via Pansini, 5, Naples 80131, Italy
| | - Rosa Maria Di Crescenzo
- Department of Advanced Biomedical Sciences, University of Naples, Via Pansini, 5, Naples 80131, Italy
| | - Stefania Staibano
- Department of Advanced Biomedical Sciences, University of Naples, Via Pansini, 5, Naples 80131, Italy
| | - Francesco Merolla
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Via De Sanctis, Campobasso 86100, Italy
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Ross JL, Cagino SG, Denefrio CL. Examining technology use and mental health among parents with newborns in the intensive care unit during the COVID-19 pandemic: A cross-sectional study. PEC Innov 2024; 4:100252. [PMID: 38205429 PMCID: PMC10776774 DOI: 10.1016/j.pecinn.2023.100252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Objectives To investigate the relationship between pandemic-related stressors, mental health, and technology use among parents of hospitalized infants during the COVID-19 pandemic. Methods A cross-sectional study of 47 participants who had an infant in the Neonatal Intensive Care Unit (NICU) during the pandemic was completed. Participants ranked several statements on a Likert scale to assess mental health, technology use, and COVID-19-related stress during their infant's stay in the NICU. Results Mental health wellness scores were negatively associated with COVID-19-related stress (rs - 0.40, p = .015). The most prevalent stressor was hospital visitation restriction. Higher COVID-19-related stress was associated with greater use of text and video chat [(rs0.35, p = 0.016) and (rs0.33, p = .025)]. Enjoyment of technology use and access to technology were positively associated with higher mental health wellness scores [(rs0.42, p = .003) and (rs0.38, p = .009)]. Conclusions Social uses of technology were valuable in a cohort of parents with infants hospitalized during the COVID-19 pandemic. Innovation Technology is a tool that can help parents cope with the stress of having a hospitalized infant. Digital literacy and technology access should be promoted in the post-pandemic landscape to help parents of infants in the NICU attain more benefit from these resources.
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Affiliation(s)
| | - Sarah G. Cagino
- Department of Obstetrics & Gynecology, Albany Medical Center, Albany, NY, USA
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Belon AP, Yashadhana A, Kongats K, Atkey K, Glenn NM, Jaques K, Nieuwendyk L, Harris P, de Leeuw E, Nykiforuk CI. Australian and Canadian financial wellbeing policy landscape during COVID-19: An equity-informed policy scan. Health Policy Open 2024; 6:100114. [PMID: 38213762 PMCID: PMC10776654 DOI: 10.1016/j.hpopen.2023.100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/13/2024] Open
Abstract
Background This targeted and comprehensive policy scan examined how different levels of governments in Australia and Canada responded to the financial crisis brought on by the COVID-19 pandemic. We mapped the types of early policy responses addressing financial strain and promoting financial wellbeing. We also examined their equity considerations. Methods Through a systematic search, snowballing, and manual search, we identified Canadian and Australian policies at all government levels related to financial strain or financial wellbeing enacted or amended in 2019-2020. Using a deductive-inductive approach, policies were categorized by jurisdiction level, focal areas, and target population groups. Results In total, 213 and 97 policies in Canada and Australia, respectively, were included. Comparisons between Canadian and Australian policies indicated a more diversified and equity-targeted policy landscape in Canada. In both countries, most policies focused on individual and family finances, followed by housing and employment areas. Conclusions The policy scan identified gaps and missed opportunities in the early policies related to financial strain and financial wellbeing. While fast, temporary actions addressed individuals' immediate needs, we recommend governments develop a longer-term action plan to tackle the root causes of financial strain and poor financial wellbeing for better health and non-health crisis preparedness. Statement on Ethics and Informed Consent This research reported in this paper did not require ethical clearance or patient informed consent as the data sources were published policy documents. This study did not involve data collection with humans (or animals), nor any secondary datasets involving data provided by humans (or from animal studies).
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Affiliation(s)
- Ana Paula Belon
- Centre for Healthy Communities, School of Public Health, University of Alberta, 3-035 Edmonton Clinic Health Academy, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
| | - Aryati Yashadhana
- Centre for Primary Health Care & Equity, University of New South Wales, Sydney, Australia
- School of Social Sciences, University of New South Wales, Sydney, Australia
| | - Krystyna Kongats
- Centre for Healthy Communities, School of Public Health, University of Alberta, 3-035 Edmonton Clinic Health Academy, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
| | - Kayla Atkey
- Centre for Healthy Communities, School of Public Health, University of Alberta, 3-035 Edmonton Clinic Health Academy, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
| | - Nicole M. Glenn
- Centre for Healthy Communities, School of Public Health, University of Alberta, 3-035 Edmonton Clinic Health Academy, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
- PolicyWise for Children & Families, 1000 – 9925, 109 Street NW, Edmonton, AB T5K 2J8, Canada
| | - Karla Jaques
- Centre for Primary Health Care & Equity, University of New South Wales, Sydney, Australia
- Ingham Institute for Applied Medical Research, Sydney, Australia
| | - Laura Nieuwendyk
- Centre for Healthy Communities, School of Public Health, University of Alberta, 3-035 Edmonton Clinic Health Academy, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
| | - Patrick Harris
- Centre for Primary Health Care & Equity, University of New South Wales, Sydney, Australia
- Ingham Institute for Applied Medical Research, Sydney, Australia
| | - Evelyne de Leeuw
- Centre for Primary Health Care & Equity, University of New South Wales, Sydney, Australia
- Healthy Urban Environments Collaboratory, Maridulu Budyari Gumal SPHERE, Sydney, Australia
| | - Candace I.J. Nykiforuk
- Centre for Healthy Communities, School of Public Health, University of Alberta, 3-035 Edmonton Clinic Health Academy, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
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Sidky H, Hansen KA, Girvin AT, Hotaling N, Michael SG, Gersing K, Sahner DK. Assessing the effect of selective serotonin reuptake inhibitors in the prevention of post-acute sequelae of COVID-19. Comput Struct Biotechnol J 2024; 24:115-125. [PMID: 38318198 PMCID: PMC10839808 DOI: 10.1016/j.csbj.2023.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Background Post-acute sequelae of COVID-19 (PASC) produce significant morbidity, prompting evaluation of interventions that might lower risk. Selective serotonin reuptake inhibitors (SSRIs) potentially could modulate risk of PASC via their central, hypothesized immunomodulatory, and/or antiplatelet properties although clinical trial data are lacking. Materials and Methods This retrospective study was conducted leveraging real-world clinical data within the National COVID Cohort Collaborative (N3C) to evaluate whether SSRIs with agonist activity at the sigma-1 receptor (S1R) lower the risk of PASC, since agonism at this receptor may serve as a mechanism by which SSRIs attenuate an inflammatory response. Additionally, determine whether the potential benefit could be traced to S1R agonism. Presumed PASC was defined based on a computable PASC phenotype trained on the U09.9 ICD-10 diagnosis code. Results Of the 17,908 patients identified, 1521 were exposed at baseline to a S1R agonist SSRI, 1803 to a non-S1R agonist SSRI, and 14,584 to neither. Using inverse probability weighting and Poisson regression, relative risk (RR) of PASC was assessed.A 29% reduction in the RR of PASC (0.704 [95% CI, 0.58-0.85]; P = 4 ×10-4) was seen among patients who received an S1R agonist SSRI compared to SSRI unexposed patients and a 21% reduction in the RR of PASC was seen among those receiving an SSRI without S1R agonist activity (0.79 [95% CI, 0.67 - 0.93]; P = 0.005).Thus, SSRIs with and without reported agonist activity at the S1R were associated with a significant decrease in the risk of PASC.
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Affiliation(s)
- Hythem Sidky
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Kristen A. Hansen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
- Axle Research and Technologies, Rockville, MD, USA
| | | | - Nathan Hotaling
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
- Axle Research and Technologies, Rockville, MD, USA
| | - Sam G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
- Palantir Technologies, Denver, CO, USA
- Axle Research and Technologies, Rockville, MD, USA
| | - Ken Gersing
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - David K. Sahner
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
- Axle Research and Technologies, Rockville, MD, USA
| | - on behalf of the N3C consortium
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
- Palantir Technologies, Denver, CO, USA
- Axle Research and Technologies, Rockville, MD, USA
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Nisar H, Annamraju S, Deka SA, Horowitz A, Stipanović DM. Robotic mirror therapy for stroke rehabilitation through virtual activities of daily living. Comput Struct Biotechnol J 2024; 24:126-135. [PMID: 38352631 PMCID: PMC10862404 DOI: 10.1016/j.csbj.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Mirror therapy is a standard technique of rehabilitation for recovering motor and vision abilities of stroke patients, especially in the case of asymmetric limb function. To enhance traditional mirror therapy, robotic mirror therapy (RMT) has been proposed over the past decade, allowing for assisted bimanual coordination of paretic (affected) and contralateral (healthy) limbs. However, state-of-the-art RMT platforms predominantly target mirrored motions of trajectories, largely limited to 2-D motions. In this paper, an RMT platform is proposed, which can facilitate the patient to practice virtual activities of daily living (ADL) and thus enhance their independence. Two similar (but mirrored) 3D virtual environments are created in which the patients operate robots with both their limbs to complete ADL (such as writing and eating) with the assistance of the therapist. The recovery level of the patient is continuously assessed by monitoring their ability to track assigned trajectories. The patient's robots are programmed to assist the patient in following these trajectories based on this recovery level. In this paper, the framework to dynamically monitor recovery level and accordingly provide assistance is developed along with the nonlinear controller design to ensure position tracking, force control, and stability. Proof-of-concept studies are conducted with both 3D trajectory tracking and ADL. The results demonstrate the potential use of the proposed system to enhance the recovery of the patients.
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Affiliation(s)
- Harris Nisar
- Health Care Engineering Systems Center, University of Illinois Urbana Champaign, 1206 W Clark St, Urbana 61801, IL, USA
| | - Srikar Annamraju
- Coordinated Science Laboratory, University of Illinois Urbana Champaign, 1308 W Main St, Urbana 61801, IL, USA
| | - Shankar A. Deka
- Division of Decision and Control Systems at KTH Royal Institute of Technology, Brinellvägen 8, 114 28 Stockholm, Sweden
| | - Anne Horowitz
- Outpatient Rehabilitation, OSF Healthcare Saint Francis Medical Center, 6501 N Sheridan Rd, Peoria, IL, USA
| | - Dušan M. Stipanović
- Coordinated Science Laboratory, University of Illinois Urbana Champaign, 1308 W Main St, Urbana 61801, IL, USA
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Hashimoto N, Hanada H, Miyoshi H, Nagaishi M, Sato K, Hontani H, Ohshima K, Takeuchi I. Multimodal Gated Mixture of Experts Using Whole Slide Image and Flow Cytometry for Multiple Instance Learning Classification of Lymphoma. J Pathol Inform 2024; 15:100359. [PMID: 38322152 PMCID: PMC10844119 DOI: 10.1016/j.jpi.2023.100359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/07/2023] [Accepted: 12/23/2023] [Indexed: 02/08/2024] Open
Abstract
In this study, we present a deep-learning-based multimodal classification method for lymphoma diagnosis in digital pathology, which utilizes a whole slide image (WSI) as the primary image data and flow cytometry (FCM) data as auxiliary information. In pathological diagnosis of malignant lymphoma, FCM serves as valuable auxiliary information during the diagnosis process, offering useful insights into predicting the major class (superclass) of subtypes. By incorporating both images and FCM data into the classification process, we can develop a method that mimics the diagnostic process of pathologists, enhancing the explainability. In order to incorporate the hierarchical structure between superclasses and their subclasses, the proposed method utilizes a network structure that effectively combines the mixture of experts (MoE) and multiple instance learning (MIL) techniques, where MIL is widely recognized for its effectiveness in handling WSIs in digital pathology. The MoE network in the proposed method consists of a gating network for superclass classification and multiple expert networks for (sub)class classification, specialized for each superclass. To evaluate the effectiveness of our method, we conducted experiments involving a six-class classification task using 600 lymphoma cases. The proposed method achieved a classification accuracy of 72.3%, surpassing the 69.5% obtained through the straightforward combination of FCM and images, as well as the 70.2% achieved by the method using only images. Moreover, the combination of multiple weights in the MoE and MIL allows for the visualization of specific cellular and tumor regions, resulting in a highly explanatory model that cannot be attained with conventional methods. It is anticipated that by targeting a larger number of classes and increasing the number of expert networks, the proposed method could be effectively applied to the real problem of lymphoma diagnosis.
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Affiliation(s)
- Noriaki Hashimoto
- RIKEN Center for Advanced Intelligence Project, Furo-cho, Chikusa-ku, Nagoya, 4648603, Japan
| | - Hiroyuki Hanada
- RIKEN Center for Advanced Intelligence Project, Furo-cho, Chikusa-ku, Nagoya, 4648603, Japan
| | - Hiroaki Miyoshi
- Department of Pathology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 8300011, Japan
| | - Miharu Nagaishi
- Department of Pathology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 8300011, Japan
| | - Kensaku Sato
- Department of Pathology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 8300011, Japan
| | - Hidekata Hontani
- Department of Computer Science, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, 4668555, Japan
| | - Koichi Ohshima
- Department of Pathology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 8300011, Japan
| | - Ichiro Takeuchi
- RIKEN Center for Advanced Intelligence Project, Furo-cho, Chikusa-ku, Nagoya, 4648603, Japan
- Department of Mechanical Systems Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 4648603, Japan
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Mizoguchi T. In vivo dynamics of hard tissue-forming cell origins: Insights from Cre/loxP-based cell lineage tracing studies. Jpn Dent Sci Rev 2024; 60:109-119. [PMID: 38406212 PMCID: PMC10885318 DOI: 10.1016/j.jdsr.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Bone tissue provides structural support for our bodies, with the inner bone marrow (BM) acting as a hematopoietic organ. Within the BM tissue, two types of stem cells play crucial roles: mesenchymal stem cells (MSCs) (or skeletal stem cells) and hematopoietic stem cells (HSCs). These stem cells are intricately connected, where BM-MSCs give rise to bone-forming osteoblasts and serve as essential components in the BM microenvironment for sustaining HSCs. Despite the mid-20th century proposal of BM-MSCs, their in vivo identification remained elusive owing to a lack of tools for analyzing stemness, specifically self-renewal and multipotency. To address this challenge, Cre/loxP-based cell lineage tracing analyses are being employed. This technology facilitated the in vivo labeling of specific cells, enabling the tracking of their lineage, determining their stemness, and providing a deeper understanding of the in vivo dynamics governing stem cell populations responsible for maintaining hard tissues. This review delves into cell lineage tracing studies conducted using commonly employed genetically modified mice expressing Cre under the influence of LepR, Gli1, and Axin2 genes. These studies focus on research fields spanning long bones and oral/maxillofacial hard tissues, offering insights into the in vivo dynamics of stem cell populations crucial for hard tissue homeostasis.
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Thuangtong R, Suthakorn J. Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts. Comput Struct Biotechnol J 2024; 24:31-45. [PMID: 38162956 PMCID: PMC10755542 DOI: 10.1016/j.csbj.2023.11.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
The design and development of a prototype for a singular robotic hair transplant system capable of harvesting and implanting hair grafts were executed in this study. To establish a proof-of-concept for hair transplant procedures involving harvesting and implantation, a test system using a spherical phantom of the scalp was selected. The developed prototype of the robotic hair transplant system demonstrates the potential to reduce the duration that grafts remain without a blood supply, thereby minimizing hair graft damage. Additionally, the overall operation time for follicular unit extraction is comparatively shorter than that of conventional systems. Results from the robot vision tests indicate an 89.6% accuracy for hair graft detection with a 4 mm hair length phantom and 97.4% for a 2 mm hair length phantom. In the robot position control test, the root mean square error was found to be 1.268°, with a standard error of the mean of 0.203°. These outcomes suggest that the proposed system performs effectively under the conditions of a spherical phantom with a 2 mm hair length and a 5 mm distance between harvests.
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Affiliation(s)
- Rattapon Thuangtong
- Department of Biomedical Engineering, Center for Biomedical and Robotics Technology, Faculty of Engineering, Mahidol University, Salaya, Thailand
- Department of Dermatology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Jackrit Suthakorn
- Department of Biomedical Engineering, Center for Biomedical and Robotics Technology, Faculty of Engineering, Mahidol University, Salaya, Thailand
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Donovan EE, Shaffer A, Kaiser E, Quaack K, Mackert M, Shi W, De Luca D. Development and refinement of a communication guide to help young adults in Texas reconnect and reduce loneliness. PEC Innov 2024; 4:100246. [PMID: 38145251 PMCID: PMC10733666 DOI: 10.1016/j.pecinn.2023.100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/11/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023]
Abstract
Objective Loneliness among young people is a contemporary public health crisis exacerbated by the COVID-19 pandemic. The present research examined the development of a modest yet meaningful health communication intervention resource that would become an asset in a larger health campaign: a communication guide aimed at helping young people reach out and reconnect with others. Methods Study One established the need for a loneliness intervention in Texas with survey data (N = 795). A communication guide was developed based on research and theory. Study Two employed focus group interviews with potential audience members (N = 31) to critically assess and inform revisions to the communication guide. Results Study One results indicated that a substantial proportion of young adult Texans felt as though their social connection had decreased and their loneliness had increased since the onset of the pandemic. Themes in focus group responses from Study Two suggested several strengths of the communication guide and some opportunities for revision. Conclusion A communication guide with tips for reconnecting could be a valuable tool to empower young people and promote social connection. Innovation This study involved the development and refinement of a new communication resource that was informed by a priority audience of a major health communication campaign.
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Affiliation(s)
- Erin E. Donovan
- Department of Communication Studies, Moody College of Communication, The University of Texas at Austin, Austin, TX, USA
- Center for Health Communication, Moody College of Communication & Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Audrey Shaffer
- Department of Communication Studies, Moody College of Communication, The University of Texas at Austin, Austin, TX, USA
| | - Emily Kaiser
- Department of Communication Studies, Moody College of Communication, The University of Texas at Austin, Austin, TX, USA
| | - Karly Quaack
- Department of Communication Studies, Moody College of Communication, The University of Texas at Austin, Austin, TX, USA
| | - Michael Mackert
- Center for Health Communication, Moody College of Communication & Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Stan Richards School of Advertising & Public Relations, Moody College of Communication, The University of Texas at Austin, Austin, TX, USA
| | - Weijia Shi
- Center for Health Communication, Moody College of Communication & Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Daniela De Luca
- Stan Richards School of Advertising & Public Relations, Moody College of Communication, The University of Texas at Austin, Austin, TX, USA
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Hang JF, Ou YC, Yang WL, Tsao TY, Yeh CH, Li CB, Hsu EY, Hung PY, Hwang YT, Liu TJ, Tung MC. Comparative evaluation of slide scanners, scan settings, and cytopreparations for digital urine cytology. J Pathol Inform 2024; 15:100346. [PMID: 38125926 PMCID: PMC10730371 DOI: 10.1016/j.jpi.2023.100346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/22/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023] Open
Abstract
Background Acquiring well-focused digital images of cytology slides with scanners can be challenging due to the 3-dimensional nature of the slides. This study evaluates performances of whole-slide images (WSIs) obtained from 2 different cytopreparations by 2 distinct scanners with 3 focus modes. Methods Fourteen urine specimens were collected from patients with urothelial carcinoma. Each specimen was equally divided into 2 portions, prepared with Cytospin and ThinPrep methods and scanned for WSIs using Leica (Aperio AT2) and Hamamatsu (NanoZoomer S360) scanners, respectively. The scan settings included 3 focus modes (default, semi-auto, and manual) for single-layer scanning, along with a manual focus mode for 21 Z-layers scanning. Performance metrics were evaluated including scanning success rate, artificial intelligence (AI) algorithm-inferred atypical cell numbers and coverage rate (atypical cell numbers in single or multiple Z-layers divided by the total atypical cell numbers in 21 Z-layers), scanning time, and image file size. Results The default mode had scanning success rates of 85.7% or 92.9%, depending on the scanner used. The semi-auto mode increased success to 92.9% or 100%, and manual even further to 100%. However, these changes did not affect the standardized median atypical cell numbers and coverage rates. The selection of scanners, cytopreparations, and Z-stacking influenced standardized median atypical cell numbers and coverage rates, scanning times, and image file sizes. Discussion Both scanners showed satisfactory scanning. We recommend using semi-auto or manual focus modes to achieve a scanning success rate of up to 100%. Additionally, a minimum of 9-layer Z-stacking at 1 μm intervals is required to cover 80% of atypical cells. These advanced focus methods do not impact the number of atypical cells or their coverage rate. While Z-stacking enhances the AI algorithm's inferred quantity and coverage rates of atypical cells, it simultaneously results in longer scanning times and larger image file sizes.
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Affiliation(s)
- Jen-Fan Hang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine and Institution of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Chuan Ou
- Division of Urology, Department of Surgery, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan
| | | | - Tang-Yi Tsao
- Department of Pathology, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan
| | | | - Chi-Bin Li
- AIxMed, Inc., Santa Clara, CA, United States
| | - En-Yu Hsu
- AIxMed, Inc., Santa Clara, CA, United States
| | - Po-Yen Hung
- AIxMed, Inc., Santa Clara, CA, United States
| | - Yi-Ting Hwang
- Department of Statistics, National Taipei University, Taipei, Taiwan
| | | | - Min-Che Tung
- Division of Urology, Department of Surgery, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan
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Tan HQ, Cai J, Tay SH, Sim AY, Huang L, Chua ML, Tang Y. Cluster-based radiomics reveal spatial heterogeneity of bevacizumab response for treatment of radiotherapy-induced cerebral necrosis. Comput Struct Biotechnol J 2024; 23:43-51. [PMID: 38125298 PMCID: PMC10730953 DOI: 10.1016/j.csbj.2023.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Background Bevacizumab is used in the treatment of radiation necrosis (RN), which is a debilitating toxicity following head and neck radiotherapy. However, there is no biomarker to predict if a patient would respond to bevacizumab. Purpose We aimed to develop a cluster-based radiomics approach to characterize the spatial heterogeneity of RN and map their responses to bevacizumab. Methods 118 consecutive nasopharyngeal carcinoma patients diagnosed with RN were enrolled. We divided 152 lesions from the patients into 101 for training, and 51 for validation. We extracted voxel-level radiomics features from each lesion segmented on T1-weighted+contrast and T2 FLAIR sequences of pre- and post-bevacizumab magnetic resonance images, followed by a three-step analysis involving individual- and population-level clustering, before delta-radiomics to derive five radiomics clusters within the lesions. We tested the association of each cluster with response to bevacizumab and developed a clinico-radiomics model using clinical predictors and cluster-specific features. Results 71 (70.3%) and 34 (66.7%) lesions had responded to bevacizumab in the training and validation datasets, respectively. Two radiomics clusters were spatially mapped to the edema region, and the volume changes were significantly associated with bevacizumab response (OR:11.12 [95% CI: 2.54-73.47], P = 0.004; and 1.63[1.07-2.78], P = 0.042). The combined clinico-radiomics model based on textural features extracted from the most significant cluster improved the prediction of bevacizumab response, compared with a clinical-only model (AUC:0.755 [0.645-0.865] to 0.852 [0.764-0.940], training; 0.708 [0.554-0.861] to 0.816 [0.699-0.933], validation). Conclusion Our radiomics approach yielded intralesional resolution, enabling a more refined feature selection for predicting bevacizumab efficacy in the treatment of RN.
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Affiliation(s)
- Hong Qi Tan
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore
| | - Jinhua Cai
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shi Hui Tay
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Adelene Y.L. Sim
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Luo Huang
- Department of Radiation Oncology, Chongqing University Cancer Hospital, People's Republic of China
| | - Melvin L.K. Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore
| | - Yamei Tang
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China
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Eze C. Sleep health among medical students in Abakaliki Nigeria: A descriptive study. Sleep Med X 2024; 7:100103. [PMID: 38283143 PMCID: PMC10821605 DOI: 10.1016/j.sleepx.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/01/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Background Sleep health focuses on those measurable characteristics of sleep that are most clearly associated with physical, mental, and neurobehavioral well-being, and not necessarily the absence of sleep disorder. Sleep health is characterised by subjective satisfaction, appropriate timing, adequate duration, high efficiency, and sustained alertness during waking hours. Adequate and restful sleep is particularly crucial for medical students, who face unique challenges due to the demanding nature of their academic and clinical responsibilities. There is limited data on sleep health among medical students in Nigeria. Objectives This research study investigated the pattern of sleep health among medical students in Abakaliki Nigeria. Methods This cross-sectional observational study was undertaken among the medical students of 2 public institutions in Abakaliki Nigeria from 16th to 23rd June 2023. Results Out of the 288 medical students (males- 53.1 %, females- 46.9 %), good sleep health was recorded in 6.6 %. The mean SATED sleep score was 4.9 ± 1.7 (male- 4.9 ± 1.8, female- 4.9 ± 1.6) (p-value = 1) and it was significantly lower among the final-year students. Age difference, sex difference, and presence of chronic headache did not significantly affect the SATED sleep score. The mean sleep duration was 6.1 ± 1.5 hours (male- 6.1 ± 1.6, female- 6.0 ± 1.4). Sleep duration (54.5 %) had the best rating while sleep efficiency (44 %) had the lowest rating among the assessed sleep domains. Conclusion Sleep health is poor among medical students in Abakaliki Nigeria and significantly poorer among final-year medical students.
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Affiliation(s)
- Chukwuemeka Eze
- Neurology Unit, Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, (AEFUTHA), Ebonyi State, Nigeria
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Zhou S, Lin N, Yu L, Su X, Liu Z, Yu X, Gao H, Lin S, Zeng Y. Single-cell multi-omics in the study of digestive system cancers. Comput Struct Biotechnol J 2024; 23:431-445. [PMID: 38223343 PMCID: PMC10787224 DOI: 10.1016/j.csbj.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.
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Affiliation(s)
- Shuang Zhou
- The Second Clinical Medical School of Fujian Medical University, Quanzhou, Fujian Province, China
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Nanfei Lin
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiaoshan Su
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, & Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Xiaowan Yu
- Clinical Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Hongzhi Gao
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
- Fujian Provincial Key Laboratory of Lung Stem Cells, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, China
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Li J, Yu T, Sun J, Ma M, Zheng Z, Kang W, Ye X. Comprehensive integration of single-cell RNA and transcriptome RNA sequencing to establish a pyroptosis-related signature for improving prognostic prediction of gastric cancer. Comput Struct Biotechnol J 2024; 23:990-1004. [PMID: 38404710 PMCID: PMC10884435 DOI: 10.1016/j.csbj.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/04/2024] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
Cell pyroptosis, a Gasdermin-dependent programmed cell death characterized by inflammasome, plays a complex and dynamic role in Gastric cancer (GC), a serious threat to human health. Therefore, the value of pyroptosis-related genes (PRGs) as prognostic biomarkers and therapeutic indicators for patients needs to be exploited in GC. This study integrates single-cell RNA sequencing (scRNA-seq) dataset GSE183904 with GC transcriptome data from the TCGA database, focusing on the expression and distribution of PRGs in GC at the single-cell level. The prognostic signature of PRGs was established by using Cox and LASSO analyses. The differences in long-term prognosis, immune infiltration, mutation profile, CD274 and response to chemotherapeutic drugs between the two groups were analyzed and evaluated. A tissue array was used to verify the expression of six PRGs, CD274, CD163 and FoxP3. C12orf75, VCAN, RGS2, MKNK2, SOCS3 and TNFAIP2 were successfully screened out to establish a signature to potently predict the survival time of GC patients. A webserver (https://pumc.shinyapps.io/GastricCancer/) for prognostic prediction in GC patients was developed based on this signature. High-risk score patients typically had worse prognoses, resistance to classical chemotherapy, and a more immunosuppressive tumor microenvironment. VCAN, TNFAIP2 and SOCS3 were greatly elevated in the GC while RGS2 and MKNK2 were decreased in the tumor samples. Further, VCAN was positively related to the infiltrations of Tregs and M2 TAMs in GC TME and the CD274 in tumor cells. In summary, a potent pyroptosis-related signature was established to accurately forecast the survival time and treatment responsiveness of GC patients.
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Affiliation(s)
| | | | - Juan Sun
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Mingwei Ma
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Zicheng Zheng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
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Wittenberg E, Goldsmith JV, Chen C(K, Prince-Paul M. A conceptual model of the nurse's role as primary palliative care provider in goals of care communication. PEC Innov 2024; 4:100254. [PMID: 38298557 PMCID: PMC10828588 DOI: 10.1016/j.pecinn.2024.100254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/10/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Objective Nurses have opportunities to engage in goals of care conversations that can promote palliative care communication. The purpose of this study was to describe nurses' experiences in goals of care communication as summarized in the literature and to present a conceptual model of communication pathways for nurses. Methods An integrative review of the literature (2016-2022) addressing nurses' experiences in goals of care communication was conducted using PubMed, CINAHL, and PsychInfo databases. A total of 92 articles were retrieved. A total of 12 articles were included for this review after applying the inclusion and exclusion criteria. Results Of the 12 articles, the majority were qualitative studies (n = 8). Qualitative analysis of findings from all articles revealed three dominant themes: nurses' ambiguous role responsibilities, goals of care as end-of-life communication, and the need for nurse communication training. Conclusion This article suggests an innovative conceptual model for advancing nurse communication about goals of care to facilitate primary palliative care. Innovation The framework characterizes two communication pathways for Advanced Practice Nurses who direct goals of care discussions and Registered Nurses who support goals of care communication. The model informs future communication training aimed at supporting primary palliative care.
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Affiliation(s)
- Elaine Wittenberg
- From California State University Los Angeles, Department of Communication Studies, Los Angeles, CA, USA
| | - Joy V. Goldsmith
- From University of Memphis, Department of Communication and Film, Memphis, TN, USA
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Shinjo T, Nishimura F. The bidirectional association between diabetes and periodontitis, from basic to clinical. Jpn Dent Sci Rev 2024; 60:15-21. [PMID: 38098853 PMCID: PMC10716706 DOI: 10.1016/j.jdsr.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/02/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Abstract
The prevalence and severity of periodontitis are increased and advanced in diabetes. Severe periodontitis elicits adverse effects on diabetes by impairing insulin actions due to systemic microinflammation. Recent studies unveil the emerging findings and molecular basis of the bidirectional relationship between periodontitis and diabetes. In addition to conventional mechanisms such as hyperglycemia, hyperlipidemia, and chronic inflammation, deficient insulin action may play a pathogenic role in the progression of periodontitis under diabetes. Epidemiologically, from the viewpoint of the adverse effect of periodontitis on diabetes, recent studies have suggested that Asians including Japanese and Asian Americans with diabetes and mild obesity (BMI <25 kg/m2) should pay more attention to their increased risk for cardiovascular diseases. In this review, we summarize recent findings on the effect of diabetes on periodontitis from the viewpoint of abnormalities in metabolism and insulin resistance with novel mechanisms, and the influence of periodontitis on diabetes mainly focused on micro-inflammation related to mature adipose tissue and discuss future perspectives about novel approaches to interrupt the adverse interrelationship.
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Affiliation(s)
- Takanori Shinjo
- Section of Periodontology, Faculty of Dental Science, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Fusanori Nishimura
- Section of Periodontology, Faculty of Dental Science, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
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Walsh CA, Miller SJ, Smith CB, Prigerson HG, McFarland D, Yarborough S, Santos CDL, Thomas R, Czaja SJ, RoyChoudhury A, Chapman-Davis E, Lachs M, Shen MJ. Acceptability and usability of the Planning Advance Care Together (PACT) website for improving patients' engagement in advance care planning. PEC Innov 2024; 4:100245. [PMID: 38145252 PMCID: PMC10733677 DOI: 10.1016/j.pecinn.2023.100245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
Abstract
Objectives Most prior advance care planning (ACP) interventions lack integration of the social context of patients' ACP process, which patients indicate is critically important. The current study developed the Planning Advance Care Together (PACT) website to foster inclusion of loved ones in the ACP process. Methods To provide feedback about the PACT website, patients with advanced cancer (N = 11), their caregivers (N = 11), and experts (N = 10) participated in semi-structured interviews. Patients and caregivers also completed standardized ratings of acceptability and usability. Results Overall, patient (n = 11) and caregiver (n = 11) ratings of acceptability and usability of the website exceeded benchmark cut-offs (≥24 on the Acceptability E-Scale and ≥ 68 on the System Usability Scale). Patients, caregivers, and experts liked the topic of ACP but felt that it could be emotionally challenging. They recommended focusing more on planning and less on end of life. They appreciated being able to include loved ones and recommended adding resources for caregivers. Conclusions Study findings support the preliminary usability and acceptability of the PACT website. Findings will be used to inform a modified prototype of the PACT website that is interactive and ready for field testing with patients with advanced cancer and their loved ones. Innovation We utilized a novel application of the shared mind framework to support patients with advanced cancer in engaging their loved ones in the ACP process.
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Affiliation(s)
- Casey A. Walsh
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Sarah J. Miller
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Cardinale B. Smith
- Division of Hematology and Medical Oncology, Division of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Holly G. Prigerson
- Department of Medicine, Cornell Center for Research on End-of-Life Care, Weill Cornell Medical College, New York, NY, United States of America
| | - Daniel McFarland
- Department of Psychiatry, Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Sarah Yarborough
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Claudia De Los Santos
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Robert Thomas
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sara J. Czaja
- Division of Geriatrics and Palliative Medicine, Center on Aging and Behavioral Research, Weill Cornell Medicine, New York, NY, United States of America
| | - Arindam RoyChoudhury
- Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, United States of America
| | - Eloise Chapman-Davis
- Division of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, United States of America
| | - Mark Lachs
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Geriatrics and Palliative Medicine, New York Presbyterian Health Care System, United States of America
| | - Megan J. Shen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
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Kanarskii M, Nekrasova J, Kondratieva E, Borisov I, Simenel E, Sviryaev Y, Pradhan P, Gorshkov K, Shestopalov A, Petrova M. Are circadian rhythms in disarray in patients with chronic critical illness? Sleep Med X 2024; 7:100101. [PMID: 38234313 PMCID: PMC10792261 DOI: 10.1016/j.sleepx.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024] Open
Abstract
Aim The aim of our study is to assess circadian rhythms in patients with chronic critical illness due to severe brain injury in intensive care unit by establishing the relation between melatonin and cortisol secretion, considering astronomical time and the sleep-wake cycle in chronic critical illness. Materials and methods The study included 54 adult patients with chronic critical illness who resided in the intensive care unit for at least 30 days. The level of consciousness was determined using the CRS-R scale. We did the continuous electroencephalographic (EEG) monitoring with polygraphic leads for 24 h. Also, we determined the serum levels of cortisol and melatonin using the tandem mass spectrometry method with ultra-performance liquid chromatography. Results 90.74 % of patients had one acrophase in melatonin secretion curve, which suggests the preservation of the rhythmic secretion of melatonin. These acrophases of the melatonin rhythm occurred during the night time in 91.8 % of patients. Most of the patients (69.3 %) slept during the period from 2:00 to 4:00 a.m. The evening levels of cortisol and melatonin had an inverse relation (rs=0.61, p<0.05), i.e., a decrease in the level of cortisol secretion accompanies an increase in melatonin. Conclusions We concluded from our study that the rhythmic secretion of melatonin and cortisol is preserved in patients with chronic critical illness that resulted from severe brain injury. No statistically significant discrepancy between melatonin and cortisol secretion, day-and-night time and the sleep-wake cycle are found. We may focus our future work on finding more reliable methods to stabilize the preservation of circadian rhythms to protect vital organ functions.
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Affiliation(s)
- Mikhail Kanarskii
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
| | - Julia Nekrasova
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
| | - Ekaterina Kondratieva
- Federal State Budgetary Institution “Almazov National Medical Research Centre” of the Ministry of Health of the Russian Federation, St. Petersburg, Russia
| | - Ilya Borisov
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
| | - Elena Simenel
- Labaratory of Chromatography and Mass Spectrometry, Мedical Laboratory Archimed, Moscow, St. Vavilova, d. 68 bldg, Russia
| | - Yurii Sviryaev
- Federal State Budgetary Institution “Almazov National Medical Research Centre” of the Ministry of Health of the Russian Federation, St. Petersburg, Russia
| | - Pranil Pradhan
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
- Federal State Budgetary Educational Institution of Higher Education “Peoples' Friendship University of Russia”, Moscow, Russia
| | - Kirill Gorshkov
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
| | - Alexander Shestopalov
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
| | - Marina Petrova
- Federal State Budget Scientific Institution «Federal Reserach and Clinical Center of Intensive Care Medicine and Rehabilitology», Moscow, Russia
- Federal State Budgetary Educational Institution of Higher Education “Peoples' Friendship University of Russia”, Moscow, Russia
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Wei F, Kouro T, Nakamura Y, Ueda H, Iiizumi S, Hasegawa K, Asahina Y, Kishida T, Morinaga S, Himuro H, Horaguchi S, Tsuji K, Mano Y, Nakamura N, Kawamura T, Sasada T. Enhancing Mass spectrometry-based tumor immunopeptide identification: machine learning filter leveraging HLA binding affinity, aliphatic index and retention time deviation. Comput Struct Biotechnol J 2024; 23:859-869. [PMID: 38356658 PMCID: PMC10864759 DOI: 10.1016/j.csbj.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Accurately identifying neoantigens is crucial for developing effective cancer vaccines and improving tumor immunotherapy. Mass spectrometry-based immunopeptidomics has emerged as a promising approach to identifying human leukocyte antigen (HLA) peptides presented on the surface of cancer cells, but false-positive identifications remain a significant challenge. In this study, liquid chromatography-tandem mass spectrometry-based proteomics and next-generation sequencing were utilized to identify HLA-presenting neoantigenic peptides resulting from non-synonymous single nucleotide variations in tumor tissues from 18 patients with renal cell carcinoma or pancreatic cancer. Machine learning was utilized to evaluate Mascot identifications through the prediction of MS/MS spectral consistency, and four descriptors for each candidate sequence: the max Mascot ion score, predicted HLA binding affinity, aliphatic index and retention time deviation, were selected as important features in filtering out identifications with inadequate fragmentation consistency. This suggests that incorporating rescoring filters based on peptide physicochemical characteristics could enhance the identification rate of MS-based immunopeptidomics compared to the traditional Mascot approach predominantly used for proteomics, indicating the potential for optimizing neoantigen identification pipelines as well as clinical applications.
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Affiliation(s)
- Feifei Wei
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Taku Kouro
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Yuko Nakamura
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Hiroki Ueda
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Susumu Iiizumi
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Research & Early Development Division, BrightPath Biotherapeutics Co., Ltd., Kawasaki, Japan
| | - Kyoko Hasegawa
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Research & Early Development Division, BrightPath Biotherapeutics Co., Ltd., Kawasaki, Japan
| | - Yuki Asahina
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Takeshi Kishida
- Department of Urology, Kanagawa Cancer Center, Yokohama, Japan
| | - Soichiro Morinaga
- Department of Hepato-Biliary and Pancreatic Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Hidetomo Himuro
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Shun Horaguchi
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
- Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Kayoko Tsuji
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Yasunobu Mano
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Norihiro Nakamura
- Research & Early Development Division, BrightPath Biotherapeutics Co., Ltd., Kawasaki, Japan
| | | | - Tetsuro Sasada
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
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26
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Sinaci AA, Gencturk M, Alvarez-Romero C, Laleci Erturkmen GB, Martinez-Garcia A, Escalona-Cuaresma MJ, Parra-Calderon CL. Privacy-preserving federated machine learning on FAIR health data: A real-world application. Comput Struct Biotechnol J 2024; 24:136-145. [PMID: 38434250 PMCID: PMC10904920 DOI: 10.1016/j.csbj.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Objective This paper introduces a privacy-preserving federated machine learning (ML) architecture built upon Findable, Accessible, Interoperable, and Reusable (FAIR) health data. It aims to devise an architecture for executing classification algorithms in a federated manner, enabling collaborative model-building among health data owners without sharing their datasets. Materials and methods Utilizing an agent-based architecture, a privacy-preserving federated ML algorithm was developed to create a global predictive model from various local models. This involved formally defining the algorithm in two steps: data preparation and federated model training on FAIR health data and constructing the architecture with multiple components facilitating algorithm execution. The solution was validated by five healthcare organizations using their specific health datasets. Results Five organizations transformed their datasets into Health Level 7 Fast Healthcare Interoperability Resources via a common FAIRification workflow and software set, thereby generating FAIR datasets. Each organization deployed a Federated ML Agent within its secure network, connected to a cloud-based Federated ML Manager. System testing was conducted on a use case aiming to predict 30-day readmission risk for chronic obstructive pulmonary disease patients and the federated model achieved an accuracy rate of 87%. Discussion The paper demonstrated a practical application of privacy-preserving federated ML among five distinct healthcare entities, highlighting the value of FAIR health data in machine learning when utilized in a federated manner that ensures privacy protection without sharing data. Conclusion This solution effectively leverages FAIR datasets from multiple healthcare organizations for federated ML while safeguarding sensitive health datasets, meeting legislative privacy and security requirements.
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Affiliation(s)
- A. Anil Sinaci
- SRDC Software Research Development and Consultancy Corporation, Ankara, Turkey
| | - Mert Gencturk
- SRDC Software Research Development and Consultancy Corporation, Ankara, Turkey
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Celia Alvarez-Romero
- Group of Research and Innovation in Biomedical Informatics, Biomedical Engineering and Health Economy, Institute of Biomedicine of Seville, IBiS / Virgen del Rocío University Hospital / CSIC / University of Seville, Seville, Spain
| | | | - Alicia Martinez-Garcia
- Group of Research and Innovation in Biomedical Informatics, Biomedical Engineering and Health Economy, Institute of Biomedicine of Seville, IBiS / Virgen del Rocío University Hospital / CSIC / University of Seville, Seville, Spain
| | | | - Carlos Luis Parra-Calderon
- Group of Research and Innovation in Biomedical Informatics, Biomedical Engineering and Health Economy, Institute of Biomedicine of Seville, IBiS / Virgen del Rocío University Hospital / CSIC / University of Seville, Seville, Spain
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Qiu C, Li Z, Peng P. Human umbilical cord mesenchymal stem cells protect MC3T3-E1 osteoblasts from dexamethasone-induced apoptosis via induction of the Nrf2-ARE signaling pathway. Regen Ther 2024; 27:1-11. [PMID: 38476629 PMCID: PMC10926296 DOI: 10.1016/j.reth.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Objective To investigate the protective effect human umbilical cord mesenchymal stem cells (hUC-MSCs) have on Dexamethasone (Dex)-induced apoptosis in osteogenesis via the Nrf2-ARE signaling pathway. Methods Glucocorticoid-induced osteonecrosis of the femoral head (GC-ONFH) was developed in rats through the administration of lipopolysaccharide and methylprednisolone. The incidence of femoral head necrosis, cavity notch, apoptosis of osteoblasts, and bone density were observed by HE staining, TUNEL staining, and Micro-CT. HUC-MSCs were co-cultured with mouse pre-osteoblast MC3T3-E1. The survival rate of osteoblasts was determined by CCK8, and apoptosis and ROS levels of osteoblasts were determined by flow cytometer. The viability of antioxidant enzymes SOD, GSH-Px, and CAT was analyzed by biochemistry. Nrf2 expression levels and those of its downstream proteins and apoptosis-related proteins were analyzed by Western blotting. Results In rats, hUC-MSCs can reduce the rates of empty bone lacuna and osteoblast apoptosis that are induced by glucocorticoids (GCs), while reducing the incidence of GC-ONFH. hUC-MSCs can significantly improve the survival rate and antioxidant SOD, GSH-Px, and CAT activity of MC3T3-E1 cells caused by Dex, and inhibit apoptosis and oxidative stress levels. In addition, hUC-MSCs can up-regulate the expression of osteoblast antioxidant protein Nrf2 and its downstream protein HO-1, NQO-1, GCLC, GCLM, and apoptosis-related protein bcl-2, while also down-regulating the expression of apoptosis-related protein bax, cleaved caspase-3, cleaved caspase-9, and cytochrome C in MC3T3-E1 cells. hUC-MSCs improve the ability of MC3T3-E1 cells to mineralize to osteogenesis. However, the promoting effects of hUC-MSCs were abolished following the blocking of the Nrf2-ARE signaling pathway for osteoblasts. Conclusion The results reveal that hUC-MSCs can reduce Dex-induced apoptosis in osteoblasts via the Nrf2-ARE signaling pathway.
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Affiliation(s)
- Chen Qiu
- Department of Sports Medicine, The Affiliated Hospital of Wuhan Sports University, Wuhan, 430000, China
| | - Zhaowen Li
- Department of Sports Medicine, The Affiliated Hospital of Wuhan Sports University, Wuhan, 430000, China
| | - Puji Peng
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, 450003, China
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Xia YM, Guan YQ, Liang JF, Wu WD. TAK-242 improves sepsis-associated acute kidney injury in rats by inhibiting the TLR4/NF-κB signaling pathway. Ren Fail 2024; 46:2313176. [PMID: 38482886 PMCID: PMC10877656 DOI: 10.1080/0886022x.2024.2313176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/27/2024] [Indexed: 03/18/2024] Open
Abstract
OBJECTIVE This study was designed to observe the effect of toll-like receptor 4 (TLR4)/nuclear factor kappa-B (NF-κB) pathway activity on sepsis-associated acute kidney injury (SA-AKI), thereby providing new considerations for the prevention and treatment of SA-AKI. METHODS The rats were divided into Sham, cecal ligation and puncture (CLP), CLP + vehicle, and CLP + TAK-242 groups. Except the Sham group, a model of CLP-induced sepsis was established in other groups. After 24 h, the indicators related to kidney injury in blood samples were detected. The pathological changes in the kidneys were observed by hematoxylin-eosin staining, and tubular damage was scored. Oxidative stress-related factors, mitochondrial dysfunction-related indicators in each group were measured; the levels of inflammatory factors in serum and kidney tissue of rats were examined. Finally, the expression of proteins related to the TLR4/NF-κB signaling pathway was observed by western blot. RESULTS Compared with the CLP + vehicle and CLP + TAK-242 groups, the CLP + TAK-242 group reduced blood urea nitrogen (BUN), creatinine (Cr), cystatin-C (Cys-C), reactive oxygen species (ROS), malondialdehyde (MDA), and inflammatory factors levels (p < 0.01), as well as increased superoxide dismutase (SOD) activity of CLP rats (p < 0.01). Additionally, TAK-242 treatment improved the condition of CLP rats that had glomerular and tubular injuries and mitochondrial disorders (p < 0.01). Further mechanism research revealed that TAK-242 can inhibit the TLR4/NF-κB signaling pathway activated by CLP (p < 0.01). Above indicators after TAK-242 treatment were close to those of the Sham group. CONCLUSION TAK-242 can improve oxidative stress, mitochondrial dysfunction, and inflammatory response by inhibiting the activity of TLR4/NF-κB signaling pathway, thereby preventing rats from SA-AKI.
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Affiliation(s)
- Yan-mei Xia
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PRChina
| | - Yu-qian Guan
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
| | - Ji-fang Liang
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PRChina
| | - Wei-dong Wu
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PRChina
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29
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Li C, Luo Y, Xie Y, Zhang Z, Liu Y, Zou L, Xiao F. Structural and functional prediction, evaluation, and validation in the post-sequencing era. Comput Struct Biotechnol J 2024; 23:446-451. [PMID: 38223342 PMCID: PMC10787220 DOI: 10.1016/j.csbj.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024] Open
Abstract
The surge of genome sequencing data has underlined substantial genetic variants of uncertain significance (VUS). The decryption of VUS discovered by sequencing poses a major challenge in the post-sequencing era. Although experimental assays have progressed in classifying VUS, only a tiny fraction of the human genes have been explored experimentally. Thus, it is urgently needed to generate state-of-the-art functional predictors of VUS in silico. Artificial intelligence (AI) is an invaluable tool to assist in the identification of VUS with high efficiency and accuracy. An increasing number of studies indicate that AI has brought an exciting acceleration in the interpretation of VUS, and our group has already used AI to develop protein structure-based prediction models. In this review, we provide an overview of the previous research on AI-based prediction of missense variants, and elucidate the challenges and opportunities for protein structure-based variant prediction in the post-sequencing era.
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Affiliation(s)
- Chang Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yixuan Luo
- Beijing Normal University, Beijing, China
| | - Yibo Xie
- Information Center, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zaifeng Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lihui Zou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Normal University, Beijing, China
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30
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van Oort P, Maaskant J, Luttik ML, Eskes A. Impact of a patient and family participation education program on hospital nurses' attitudes and competencies: A controlled before-after study. PEC Innov 2024; 4:100249. [PMID: 38225931 PMCID: PMC10788253 DOI: 10.1016/j.pecinn.2023.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
Objective We designed a Patient and Family Participation Education Program (PFEP) with the aim of fostering a positive attitude and enhancing the competencies of hospital nurses required for effective patient and family participation in care. Methods In a Dutch university hospital, we conducted a before-after study. The PFEP comprising three courses: family conversation, supporting shared decision-making, and health literacy. We assessed nursing attitudes using the FINC-NA questionnaire and competencies with a separate questionnaire before and three months after the program. Changes in attitudes and competencies were analyzed using regression analysis. Results Twenty-two nurses participated in the education group, and 58 participated as controls.After three months, the change scores for the education group were statistically significantly higher on the total attitude score (FINC-NA) compared to the control group. Moreover, in six out of twelve competencies, the education group demonstrated significantly higher scores than the control group. Conclusion The educational program appeared effective in promoting nurses' attitudes and feelings of competencies towards patient and family-centered care. Innovation A blended education program focusing on patient and family has potential value for implementation in hospital care settings, especially for hospitals aiming to cultivate a more patient- and family-centered environment.
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Affiliation(s)
- Peter van Oort
- Amsterdam UMC Location University of Amsterdam, Emma Children's Hospital, Amsterdam, the Netherlands
- Amsterdam University of Applied Sciences, Faculty of Health, Center of Expertise Urban Vitality, Amsterdam, the Netherlands
| | - Jolanda Maaskant
- Amsterdam UMC Location University of Amsterdam, Emma Children's Hospital, Amsterdam, the Netherlands
- Amsterdam UMC Location University of Amsterdam, Internal Medicine, Amsterdam, the Netherlands
- Amsterdam UMC Location University of Amsterdam, Public Health, Amsterdam, the Netherlands
| | - Marie Louise Luttik
- Hanze University of Applied Sciences, Research Group Nursing Diagnostics, Professorship Family Care, Groningen, the Netherlands
| | - Anne Eskes
- Amsterdam University of Applied Sciences, Faculty of Health, Center of Expertise Urban Vitality, Amsterdam, the Netherlands
- Amsterdam UMC Location University of Amsterdam, Department of Surgery, Amsterdam, the Netherlands
- Amsterdam UMC Location University of Amsterdam, Public Health, Amsterdam, the Netherlands
- Menzies Health Institute Queensland and School of Nursing and Midwifery, Griffith University, Gold Coast, Australia
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Baris HE, Us MC, Boran P. Turkish adaptation of the maternal cognition about infant sleep questionnaire. Sleep Med X 2024; 7:100102. [PMID: 38268570 PMCID: PMC10805934 DOI: 10.1016/j.sleepx.2023.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/18/2023] [Accepted: 12/23/2023] [Indexed: 01/26/2024] Open
Abstract
Background Exploring early childhood sleep problems requires a detailed understanding of parental beliefs and cognitions related to infant sleep. There is a need for validated measures to investigate the cognitions of Turkish mothers about infant sleep however no scale measuring parental perceptions related to infant sleep behaviors in Turkish is available. We aimed to culturally adapt the Maternal Cognitions about Infant Sleep Questionnaire (MCISQ) in Turkish. Methods Subjects were recruited from an internet sample through social media. Internal consistency was evaluated by Cronbach's alpha, and test-retest reliability was determined by Pearson's correlation test and paired t-test. For factorial validity, the principal component factor analysis was performed for the components of MCISQ. Results A total of 417 mothers, most aged between 25 and 29 years (47.8 %), participated in the study. Infants' age ranged between 6 and 18 months, with a mean of 10.5 ± 3.9 months. Factor analysis revealed four factors after removal of item 11: Anger, doubt, safety, limit setting. Cronbach's alpha was 0.85. A subgroup of 32 mothers completed MCISQ three weeks after the initial administration. Total mean scores showed a significantly strong correlation (p:<0.01, r:0.82). Higher scores were noted in both total and subscale scores in infants with maternally reported sleep problems (p:<0.01). Conclusion Findings suggest a four-factor solution for MCISQ in Turkish mothers with infants aged 6-18 months. The adapted Turkish version is composed of 19 items with good reliability. Factor structure and items included in the subscales differed from the original study, highlighting the cultural factors related to maternal perceptions about infant sleep.
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Affiliation(s)
- Hatice Ezgi Baris
- Marmara University, School of Medicine, Department of Pediatrics, Division of Social Pediatrics, Istanbul, Turkey
- Marmara University, Institute of Health Sciences, Istanbul, Turkey
| | - Mahmut Caner Us
- Marmara University, School of Medicine, Department of Pediatrics, Division of Social Pediatrics, Istanbul, Turkey
- Marmara University, Institute of Health Sciences, Istanbul, Turkey
| | - Perran Boran
- Marmara University, School of Medicine, Department of Pediatrics, Division of Social Pediatrics, Istanbul, Turkey
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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Hiraba H, Nishio K, Takeuchi Y, Ito T, Yamamori T, Kamimoto A. Application of one-piece endodontic crowns fabricated with CAD-CAM system to molars. Jpn Dent Sci Rev 2024; 60:81-94. [PMID: 38303746 PMCID: PMC10830429 DOI: 10.1016/j.jdsr.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Computer-aided design-computer-aided manufacturing (CAD-CAM) systems have been widely used as a fabrication method for restorations because of their high efficiency and accuracy, which significantly reduces fabrication time. However, molars with insufficient clearance or short clinical crown lengths require retention holes or grooves on the preparation, making it difficult to replicate the shapes with the CAM milling system. In these cases, restorations using the lost-wax method are selected. This article focuses on one-piece endodontic crowns (endocrowns) fabricated with a CAD-CAM system (CAD-CAM endocrowns), in which their posts and crowns are integrated. Articles from July 2012 to August 2023 were searched in PubMed with the keyword "endocrown". This review discusses the application of CAD-CAM endocrowns to molars from the viewpoint of model experiment (fracture resistance, adaptation) and clinical research. This technique, which allows margins and internal gaps to be set within the clinically acceptable range, is reported to be an effective way of restoring molars with high survival rates in clinical research.
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Affiliation(s)
- Haruto Hiraba
- Department of Dental Materials, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
- Division of Biomaterials Science, Dental Research Center, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Kensuke Nishio
- Department of Complete Denture Prosthodontics, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Yoshimasa Takeuchi
- Department of Comprehensive Dentistry and Clinical Education, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Takashi Ito
- Center of Innovative Clinical Medicine, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8525, Japan
| | - Tetsuo Yamamori
- Department of Prosthetic Dentistry, School of Dentistry, Ohu University School of Dentistry, 31-1 Misumido, Tomita, Koriyama, Fukushima 963-8611, Japan
| | - Atsushi Kamimoto
- Department of Comprehensive Dentistry and Clinical Education, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
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Wang L, Yin N, Shi W, Xie Y, Yi J, Tang Z, Tang J, Xiang J. Splicing inhibition mediated by reduced splicing factors and helicases is associated with the cellular response of lung cancer cells to cisplatin. Comput Struct Biotechnol J 2024; 23:648-658. [PMID: 38283853 PMCID: PMC10819863 DOI: 10.1016/j.csbj.2023.12.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
Lung cancer's mortality is predominantly linked to post-chemotherapy recurrence, driven by the reactivation of dormant cancer cells. Despite the critical role of these reactivated cells in cancer recurrence and metastasis, the molecular mechanisms governing their therapeutic selection remain poorly understood. In this study, we conducted an integrative analysis by combining PacBio single molecule real-time (SMRT) sequencing with short reads Illumina RNA-seq. Our study revealed that cisplatin-induced dormant and reactivated cancer cells exhibited a noteworthy reduction in gene transcripts and alternative splicing events. Particularly, the differential alternative splicing events were found to be overlapping with the differentially expression genes and enriched in genes related to cell cycle and cell division. Utilizing ENCORI database and correlation analysis, we identified key splicing factors, including SRSF7, SRSF3, PRPF8, and HNRNPC, as well as RNA helicase such as EIF4A3, DDX39A, DDX11, and BRIP1, which were associated with the observed reduction in alternative splicing and subsequent decrease in gene expression. Our study demonstrated that lung cancer cells reduce gene transcripts through diminished alternative splicing events mediated by specific splicing factors and RNA helicase in response to the chemotherapeutic stress. These findings provide insights into the molecular mechanisms underlying the therapeutic selection and reactivation of dormant cancer cells. This discovery opens a potential avenue for the development of therapeutic strategies aimed at preventing cancer recurrence following chemotherapy.
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Affiliation(s)
- Lujuan Wang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Na Yin
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Wenhua Shi
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yaohuan Xie
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Junqi Yi
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ziying Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingqun Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Juanjuan Xiang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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Catalina-Hernández È, López-Martín M, Masnou-Sánchez D, Martins M, Lorenz-Fonfria VA, Jiménez-Altayó F, Hellmich UA, Inada H, Alcaraz A, Furutani Y, Nonell-Canals A, Vázquez-Ibar JL, Domene C, Gaudet R, Perálvarez-Marín A. Experimental and computational biophysics to identify vasodilator drugs targeted at TRPV2 using agonists based on the probenecid scaffold. Comput Struct Biotechnol J 2024; 23:473-482. [PMID: 38261868 PMCID: PMC10796807 DOI: 10.1016/j.csbj.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/25/2024] Open
Abstract
TRP channels are important pharmacological targets in physiopathology. TRPV2 plays distinct roles in cardiac and neuromuscular function, immunity, and metabolism, and is associated with pathologies like muscular dystrophy and cancer. However, TRPV2 pharmacology is unspecific and scarce at best. Using in silico similarity-based chemoinformatics we obtained a set of 270 potential hits for TRPV2 categorized into families based on chemical nature and similarity. Docking the compounds on available rat TRPV2 structures allowed the clustering of drug families in specific ligand binding sites. Starting from a probenecid docking pose in the piperlongumine binding site and using a Gaussian accelerated molecular dynamics approach we have assigned a putative probenecid binding site. In parallel, we measured the EC50 of 7 probenecid derivatives on TRPV2 expressed in Pichia pastoris using a novel medium-throughput Ca2+ influx assay in yeast membranes together with an unbiased and unsupervised data analysis method. We found that 4-(piperidine-1-sulfonyl)-benzoic acid had a better EC50 than probenecid, which is one of the most specific TRPV2 agonists to date. Exploring the TRPV2-dependent anti-hypertensive potential in vivo, we found that 4-(piperidine-1-sulfonyl)-benzoic acid shows a sex-biased vasodilator effect producing larger vascular relaxations in female mice. Overall, this study expands the pharmacological toolbox for TRPV2, a widely expressed membrane protein and orphan drug target.
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Affiliation(s)
- Èric Catalina-Hernández
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Mario López-Martín
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - David Masnou-Sánchez
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Marco Martins
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Victor A. Lorenz-Fonfria
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán-2, 46980 Paterna, Spain
| | - Francesc Jiménez-Altayó
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Department of Pharmacology, Toxicology and Therapeutics,Institute of Neurosciences, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Ute A. Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry & Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Hitoshi Inada
- Department of Biochemistry & Cellular Biology National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8551, Japan
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Dept. of Physics, Universitat Jaume I, 12071 Castellón, Spain
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
- Optobiotechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
| | | | - Jose Luis Vázquez-Ibar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Carmen Domene
- Dept. of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Rachelle Gaudet
- Dept of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alex Perálvarez-Marín
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
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Patridge E, Gorakshakar A, Molusky MM, Ogundijo O, Janevski A, Julian C, Hu L, Vuyisich M, Banavar G. Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness. Comput Struct Biotechnol J 2024; 23:834-842. [PMID: 38328005 PMCID: PMC10847690 DOI: 10.1016/j.csbj.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n = 9350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n = 14,129). Through this validation, we show that the relevant oral pathway scores are significantly worse in individuals with periodontal disease, acid reflux, and nicotine addiction, compared with controls. Given these associations, we make the case to use these oral pathway scores to provide molecular health insights from simple, non-invasive saliva samples, and as molecular endpoints for actionable interventions to address the associated conditions.
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Affiliation(s)
- Eric Patridge
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Anmol Gorakshakar
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | | | - Oyetunji Ogundijo
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Angel Janevski
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Cristina Julian
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Lan Hu
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | | | - Guruduth Banavar
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
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Sun J, Li J, He Y, Kang W, Ye X. Identification and validation of protein biomarkers for predicting gastrointestinal stromal tumor recurrence. Comput Struct Biotechnol J 2024; 23:1065-1075. [PMID: 38455069 PMCID: PMC10918489 DOI: 10.1016/j.csbj.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
We conducted a proteomic analysis using mass spectrometry to identify and validate protein biomarkers for accurately predicting recurrence risk in gastrointestinal stromal tumors (GIST) patients, focusing on differentially expressed proteins in metastatic versus primary GIST tissues. We selected five biomarkers-GPX4, RBM4, TPM3, PFKFB2, and PGAM5-and validated their expressions in primary tumors of recurrent and non-recurrent GIST patients via immunohistochemistry. Our analysis of the association between these biomarkers with recurrence-free survival (RFS) and overall survival (OS), along with their interrelationships, revealed that immunohistochemistry confirmed significantly higher expressions of these biomarkers in primary GIST tissues of recurrent patients. Kaplan-Meier survival analysis showed that high expressions of GPX4, RBM4, TPM3, PFKFB2, and PGAM5 correlated with lower RFS, and GPX4 and RBM4 with lower OS. All biomarker pairs showed positive associations, with high expressions correlating with increased recurrence rates, and GPX4 and RBM4 with higher mortality rates. In conclusion, the biomarkers GPX4, RBM4, TPM3, PFKFB2, and PGAM5 are clinically relevant for predicting GIST recurrence, with their high expressions in primary tumors linked to poorer RFS and OS. They serve as potential prognostic indicators, enabling early treatment and improved outcomes. The observed interrelationships among these biomarkers further validate their accuracy in predicting GIST recurrence.
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Affiliation(s)
| | | | - Yixuan He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Signorelli C, Kelada L, Wakefield CE, Alchin JE, Adam I, Hoffmann P. Pilot testing "Teach Ted": A digital application for children undergoing blood tests and their parents. PEC Innov 2024; 4:100251. [PMID: 38274175 PMCID: PMC10808896 DOI: 10.1016/j.pecinn.2023.100251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
Objective In this pilot study, we evaluated the acceptability and preliminary evidence of the impact of a new educational mobile application, "Teach Ted", for children undergoing blood tests. Methods Parents of children (4-10 years) completed questionnaires on anxiety and pain before their child had a blood test, and after using Teach Ted and receiving their blood test. Health professionals at each patient's blood test (e.g. technician/nurse) completed questionnaires on patient outcomes and procedure-related outcomes (e.g. time taken). Results Nine parents and eight health professionals participated. All but one parent (n = 8/9) reported Teach Ted was useful. Seventy-eight percent (n = 7/9) reported they would use Teach Ted again. All health professionals who completed the acceptability measure (n = 3/3) strongly agreed that Teach Ted was relevant/helpful. Many parents perceived Teach Ted helped reduce their/child's anxiety (n = 3/5, 60% and n = 4/6, 67% respectively), although child's pain and child's/parent's anxiety remained similar before and after using Teach Ted (all p > 0.05). The average blood test duration was 7.6 min (range ≤1 to 22), which health professionals (n = 3/3) reported was not elongated by offering Teach Ted. Conclusions Participants reported that Teach Ted was acceptable. Further evaluation of Teach Ted's impact on patient's outcomes are needed. Innovation Teach Ted is an innovative mobile application with potential to educate young children about their upcoming procedure and mitigate negative outcomes.
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Affiliation(s)
- Christina Signorelli
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, Discipline of Paediatrics, UNSW Sydney, NSW, Australia
| | - Lauren Kelada
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, Discipline of Paediatrics, UNSW Sydney, NSW, Australia
| | - Claire E. Wakefield
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, Discipline of Paediatrics, UNSW Sydney, NSW, Australia
| | - Joseph E. Alchin
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, Discipline of Paediatrics, UNSW Sydney, NSW, Australia
| | - Irene Adam
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Peta Hoffmann
- Acute Allied Health Services, Canberra Hospital, ACT, Australia
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Bardini R, Di Carlo S. Computational methods for biofabrication in tissue engineering and regenerative medicine - a literature review. Comput Struct Biotechnol J 2024; 23:601-616. [PMID: 38283852 PMCID: PMC10818159 DOI: 10.1016/j.csbj.2023.12.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/30/2024] Open
Abstract
This literature review rigorously examines the growing scientific interest in computational methods for Tissue Engineering and Regenerative Medicine biofabrication, a leading-edge area in biomedical innovation, emphasizing the need for accurate, multi-stage, and multi-component biofabrication process models. The paper presents a comprehensive bibliometric and contextual analysis, followed by a literature review, to shed light on the vast potential of computational methods in this domain. It reveals that most existing methods focus on single biofabrication process stages and components, and there is a significant gap in approaches that utilize accurate models encompassing both biological and technological aspects. This analysis underscores the indispensable role of these methods in understanding and effectively manipulating complex biological systems and the necessity for developing computational methods that span multiple stages and components. The review concludes that such comprehensive computational methods are essential for developing innovative and efficient Tissue Engineering and Regenerative Medicine biofabrication solutions, driving forward advancements in this dynamic and evolving field.
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Affiliation(s)
- Roberta Bardini
- Department of Control and Computer Engineering, Polytechnic University of Turin, Corso Duca Degli Abruzzi, 24, Turin, 10129, Italy
| | - Stefano Di Carlo
- Department of Control and Computer Engineering, Polytechnic University of Turin, Corso Duca Degli Abruzzi, 24, Turin, 10129, Italy
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Li W, Zhang Z, Xie B, He Y, He K, Qiu H, Lu Z, Jiang C, Pan X, He Y, Hu W, Liu W, Que T, Hu Y. HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data. Comput Struct Biotechnol J 2024; 23:659-668. [PMID: 38292471 PMCID: PMC10824657 DOI: 10.1016/j.csbj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Analyzing the vast amount of omics data generated comprehensively by high-throughput sequencing technology is of utmost importance for scientists. In this context, we propose HiOmics, a cloud-based platform equipped with nearly 300 plugins designed for the comprehensive analysis and visualization of omics data. HiOmics utilizes the Element Plus framework to craft a user-friendly interface and harnesses Docker container technology to ensure the reliability and reproducibility of data analysis results. Furthermore, HiOmics employs the Workflow Description Language and Cromwell engine to construct workflows, ensuring the portability of data analysis and simplifying the examination of intricate data. Additionally, HiOmics has developed DataCheck, a tool based on Golang, which verifies and converts data formats. Finally, by leveraging the object storage technology and batch computing capabilities of public cloud platforms, HiOmics enables the storage and processing of large-scale data while maintaining resource independence among users.
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Affiliation(s)
- Wen Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Zhining Zhang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Bo Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Yunlin He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Kangming He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Hong Qiu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Zhiwei Lu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Chunlan Jiang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Xuanyu Pan
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuxiao He
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Hu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Wenjian Liu
- Faculty of Data Science, City University of Macau, Macau, China
| | - Tengcheng Que
- Faculty of Data Science, City University of Macau, Macau, China
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Guangxi Zhuang Autonomous Terrestrial Wildlife Rescue Research and Epidemic Diseases Monitoring Center, Nanning, Guangxi, China
| | - Yanling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
- Faculty of Data Science, City University of Macau, Macau, China
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Hegde D, Suprabha BS, Rao A. Organic antibacterial modifications of high-viscosity glass ionomer cement for atraumatic restorative treatment: A review. Jpn Dent Sci Rev 2024; 60:22-31. [PMID: 38188639 PMCID: PMC10767272 DOI: 10.1016/j.jdsr.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
High viscosity glass ionomer cement (HVGIC) has been employed as a restorative material for Atraumatic Restorative Treatment (ART). As residual caries persist after caries removal in ART, the antibacterial activity of HVGIC gains importance. Organic and inorganic substances with antibacterial properties have been incorporated into HVGIC over the years, and their effects on the antibacterial and physical properties have been studied. The objective of this paper is to review the various alterations made to HVGIC using organic compounds, their effect on the antibacterial activity, and the physical properties of the cement. Various in vitro investigations have been conducted by adding antiseptics, antibiotics, and naturally occurring antibacterial substances. Most of these compounds render superior antibacterial properties to HVGIC, but higher concentrations affect physical properties in a dose-dependent manner. However, some naturally occurring antibacterial substances, such as chitosan, improve the physical properties of HVGIC, as they enhance cross-linking and polysalt bridging. There is potential for clinical benefits to be gained from the addition of organic antibacterial compounds to HVGIC. In-depth research is required to determine the optimum concentration at which the antibacterial effect is maximum without affecting the physical properties of the cement.
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Affiliation(s)
- Damodar Hegde
- Department of Pediatric and Preventive Dentistry, Manipal College of Dental Sciences Mangalore, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Baranya Shrikrishna Suprabha
- Department of Pediatric and Preventive Dentistry, Manipal College of Dental Sciences Mangalore, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Arathi Rao
- Department of Pediatric and Preventive Dentistry, Manipal College of Dental Sciences Mangalore, Manipal Academy of Higher Education (MAHE), Manipal, India
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Rajendran R, Beck RC, Waskasi MM, Kelly BD, Bauer DR. Digital analysis of the prostate tumor microenvironment with high-order chromogenic multiplexing. J Pathol Inform 2024; 15:100352. [PMID: 38186745 PMCID: PMC10770522 DOI: 10.1016/j.jpi.2023.100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/30/2023] [Accepted: 11/16/2023] [Indexed: 01/09/2024] Open
Abstract
As our understanding of the tumor microenvironment grows, the pathology field is increasingly utilizing multianalyte diagnostic assays to understand important characteristics of tumor growth. In clinical settings, brightfield chromogenic assays represent the gold-standard and have developed significant trust as the first-line diagnostic method. However, conventional brightfield tests have been limited to low-order assays that are visually interrogated. We have developed a hybrid method of brightfield chromogenic multiplexing that overcomes these limitations and enables high-order multiplex assays. However, how compatible high-order brightfield multiplexed images are with advanced analytical algorithms has not been extensively evaluated. In the present study, we address this gap by developing a novel 6-marker prostate cancer assay that targets diverse aspects of the tumor microenvironment such as prostate-specific biomarkers (PSMA and p504s), immune biomarkers (CD8 and PD-L1), a prognostic biomarker (Ki-67), as well as an adjunctive diagnostic biomarker (basal cell cocktail) and apply the assay to 143 differentially graded adenocarcinoma prostate tissues. The tissues were then imaged on our spectroscopic multiplexing imaging platform and mined for proteomic and spatial features that were correlated with cancer presence and disease grade. Extracted features were used to train a UMAP model that differentiated healthy from cancerous tissue with an accuracy of 89% and identified clusters of cells based on cancer grade. For spatial analysis, cell-to-cell distances were calculated for all biomarkers and differences between healthy and adenocarcinoma tissues were studied. We report that p504s positive cells were at least 2× closer to cells expressing PD-L1, CD8, Ki-67, and basal cell in adenocarcinoma tissues relative to the healthy control tissues. These findings offer a powerful insight to understand the fingerprint of the prostate tumor microenvironment and indicate that high-order chromogenic multiplexing is compatible with digital analysis. Thus, the presented chromogenic multiplexing system combines the clinical applicability of brightfield assays with the emerging diagnostic power of high-order multiplexing in a digital pathology friendly format that is well-suited for translational studies to better understand mechanisms of tumor development and growth.
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Affiliation(s)
- Rahul Rajendran
- Roche Diagnostics Solutions, (Ventana Medical Systems, Inc.), Tucson, AZ, USA
| | - Rachel C. Beck
- Roche Diagnostics Solutions, (Ventana Medical Systems, Inc.), Tucson, AZ, USA
| | - Morteza M. Waskasi
- Roche Diagnostics Solutions, (Ventana Medical Systems, Inc.), Tucson, AZ, USA
| | - Brian D. Kelly
- Roche Diagnostics Solutions, (Ventana Medical Systems, Inc.), Tucson, AZ, USA
| | - Daniel R. Bauer
- Roche Diagnostics Solutions, (Ventana Medical Systems, Inc.), Tucson, AZ, USA
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Yu J, Zhang H, Han P, Jiang X, Li J, Li B, Yang S, He C, Mao S, Dang Y, Xiang X. Circle-seq based method for eccDNA synthesis and its application as a canonical promoter independent vector for robust microRNA overexpression. Comput Struct Biotechnol J 2024; 23:358-368. [PMID: 38223344 PMCID: PMC10788182 DOI: 10.1016/j.csbj.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) has recently gained increasing attention due to its significant role in cancer and other pathophysiologic states. The majority of circular DNAs detected by Circle-seq are small-size eccDNAs with enigmatic functions. One major technical hurdle is to synthesize eccDNA for functional identification. Here, we describe CAES (Circle-seq based Artificial EccDNA Synthesis), a promising and reliable method for artificial eccDNA synthesis. Eight eccDNAs carrying different microRNA genes (eccMIR) found in gastric cancer tissues, ranging from 329 bp to 2189 bp in size, were created utilizing the CAES method. Exonuclease V and single restriction-endonuclease digestion identified the circular structure of synthetic eccDNAs. The DNA circularization efficiency afforded by CAES ranged from 15.6% to 31.1%, which was negatively correlated with the eccDNA length. In addition, we demonstrated that CAES-synthesized eccMIRs can express both miRNA-3p and - 5p molecules efficiently independent of a canonical promoter in human cell lines. Further assays proved that these eccMIRs were functional as they were able to repress the luciferase gene containing a miRNA-target sequence in the 3'UTR as well as the endogenous mRNA targets. Finally, kinetics study revealed that eccDNA exhibited a decay rate similar to the standard plasmids and linear DNA in cultured cells. Together, this study offers a rapid and convenient method for Circle-seq users to synthesize artificial eccDNAs. It also demonstrates the promising potential of eccMIR as a bacterial DNA-free vector for safe and robust miRNA overexpression in both basic research and therapeutic applications.
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Affiliation(s)
- Jiaying Yu
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Haoran Zhang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Peng Han
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Xianming Jiang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jing Li
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bo Li
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Shaohua Yang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Chunxiao He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Shuang Mao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yonghui Dang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xi Xiang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
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Khijmatgar S, Yong J, Rübsamen N, Lorusso F, Rai P, Cenzato N, Gaffuri F, Del Fabbro M, Tartaglia GM. Salivary biomarkers for early detection of oral squamous cell carcinoma (OSCC) and head/neck squamous cell carcinoma (HNSCC): A systematic review and network meta-analysis. Jpn Dent Sci Rev 2024; 60:32-39. [PMID: 38204964 PMCID: PMC10776379 DOI: 10.1016/j.jdsr.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/21/2023] [Accepted: 10/26/2023] [Indexed: 01/12/2024] Open
Abstract
Oral cancer became a very common condition. WHO estimates that there are 4 cases of lip and oral cavity cancer for every 100,000 people worldwide. The early diagnosis of cancers is currently a top focus in the health sector. Recent systematic reviews and meta-analyses have identified promising biomarkers for early detection in several original research investigations. However, it is still unclear the quality of these evidence and which biomarker performs the best in terms of early detection. Therefore, the objective was, to map the methodological and reporting quality of available oral squamous cell carcinoma (OSCC) or head/neck squamous cell carcinoma (HNSCC) systematic reviews and meta-analysis. Secondly, to evaluate diagnostic accuracy of salivary biomarkers for common craniofacial cancers and to compare the diagnostic value of different salivary biomarkers. PubMed, Scopus, Web of Science, Embase and Cochrane Library electronic databases were used to map the methodological and reporting quality of the systematic reviews and meta-analysis conducted on the HNSCC, OSCC using the AMSTAR-2 checklist. The inclusion criteria were systematic reviews and meta-analysis published in the topic of HNSCC and OSCC biomarkers. Exclusion criteria were no animal studies; original primary studies, due to limitation of competency in other languages articles with language other than English were excluded. The sensitivity and specificity were calculated for salivary biomarkers and ranked according to network meta-analysis principles. A total of N = 5893 patients were included from four meta-analysis studies. All together, these included n = 37 primary studies. n = 94 biomarkers were pooled from these four meta-analyses and categorised into the stages at which they were detected (I-IV). In OSCC, Chemerin and MMP-9 displayed the highest sensitivity, registering 0.94 (95% CI 0.78, 1.00) and a balanced accuracy of 0.93. Phytosphingosine closely followed, with a sensitivity of 0.91 (95% CI 0.68, 0.99) and a balanced accuracy of 0.87. For HNSCC, the top three biomarkers are Actin, IL-1β Singleplex, and IL-8 ELISA. Actin leads with a sensitivity of 0.91 (95% CI 0.68-0.99), a specificity of 0.67, and an overall accuracy of 0.79. Subsequently, IL-1β Singleplex exhibits a sensitivity of 0.62 (95% CI 0.30-0.88), a specificity of 0.89, and an accuracy of 0.75, followed by IL-8 ELISA with a sensitivity of 0.81 (95% CI 0.54-0.97), a specificity of 0.59, and an accuracy of 0.70. In conclusion, there was highest sensitivity for MMP-9 and chemerin salivary biomarkers. There is need of further more studies to identify biomarkers for HNSCC and OSCC.
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Affiliation(s)
- Shahnawaz Khijmatgar
- SC Chirurgia Maxillo-Facciale e Odontostomatologia, Fondazione Ca’Granda IRCCS Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Josh Yong
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
- Harvard School of Dental Medicine, USA
| | - Nicole Rübsamen
- Institute of Epidemiology and Social Medicine, University of Münster, Germany
| | - Felice Lorusso
- Università degli Studi G. d'Annunzio Chieti - Pescara: Chieti, Abruzzi, Italy
| | - Pooja Rai
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Niccolo Cenzato
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Franscesca Gaffuri
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Massimo Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
- SC Chirurgia Maxillo-Facciale e Odontostomatologia, Fondazione Ca’Granda IRCCS Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Gianluca Martino Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
- SC Chirurgia Maxillo-Facciale e Odontostomatologia, Fondazione Ca’Granda IRCCS Ospedale Maggiore Policlinico, Milan 20122, Italy
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Stokes SM, Haider M, Vadaparampil ST, Levitt C, Hardy O, Kim R, Castillo DL, Denbo J, Fleming JB, Anaya DA. Patient's informational needs and outreach preferences: A cross-sectional survey study in patients with hepatobiliary malignancies. PEC Innov 2024; 4:100248. [PMID: 38292078 PMCID: PMC10825679 DOI: 10.1016/j.pecinn.2023.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Objective Hepatobiliary tumors have evolving management guidelines. Patient educational needs and interest in community engagement are unknown. This study serves as a needs assessment. Methods A prospective, needs assessment, survey study of hepatobiliary patients was performed (2016-2019). Surveys (n = 169) were distributed covering three domains of interest: informational needs, interest in outreach, and engagement preferences. Results Seventy patients completed the survey (response rate = 41.4%). Most patients had completed surgical treatment (84.3%). Cancer treatment was ranked as their primary topic of interest (n = 39, 55.7bold%), followed by symptom management, nutrition, and survivorship. Most patients did not participate in screening (n = 57, 81.4%), though were interested in learning more about these programs. Thirty-nine patients (55.7%) stated they would want to receive more education. Only 17 (24.3%) were interested in attending in-person events. Patients preferred online methods for education (n = 49, 70%). While patients were aware of their case presentation at tumor board, only 38 (54.3%) felt well-informed about recommendations. Conclusion Multidisciplinary care is complex and difficult for patients to navigate. Most patients have interest in educational resources and prefer online modalities. Patients understand multidisciplinary tumor boards, but communication could be improved. Innovation These data inform a new, innovative, approach to outreach efforts in this population.
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Affiliation(s)
- Sean M. Stokes
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Mintallah Haider
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Susan T. Vadaparampil
- Office of Community Outreach Engagement & Equity, H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States
| | - Catherine Levitt
- Morsani College of Medicine, University of South Florida, 560 Channelside Drive, Tampa, FL 33602, United States
| | - Olivia Hardy
- Morsani College of Medicine, University of South Florida, 560 Channelside Drive, Tampa, FL 33602, United States
| | - Richard Kim
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Diana L. Castillo
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Jason Denbo
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Jason B. Fleming
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Daniel A. Anaya
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
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Santos IS, Echevarria P, Tovo-Rodrigues L, Matijasevich A, Domingues MR, Hallal PC. Are nocturnal awakenings at age 1 predictive of sleep duration and efficiency at age 6: Results from two birth cohorts. Sleep Med X 2024; 7:100105. [PMID: 38312370 PMCID: PMC10837084 DOI: 10.1016/j.sleepx.2024.100105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024] Open
Abstract
Objective To investigate the association of nighttime awakenings at 12 months with the duration and efficiency of nighttime sleep at 6 years of age. Methods Data from two population-based prospective studies (The Pelotas 2004 and The Pelotas 2015 Birth Cohorts) were used. Information on nighttime awakenings was provided by mothers during the 12-month follow-up interview. Infants who awakened >3 times after sleep onset at 12 months were considered frequent wakeners. Sleep duration and sleep efficiency were obtained by actigraphy at the 6-year follow-up. Children wore the device at the wrist of the non-dominant arm continuously for 3-7 days, including at least one weekend day. Unadjusted and adjusted beta coefficients were obtained by linear regression for each cohort separately. Results 2500 children from the 2004 and 2793 from the 2015 cohort had full information on nighttime awakenings at 12 months and actigraphy at 6 years and were analyzed. Prevalence of frequent wakeners was 6.3 % and 5.9 % in the 2004 and 2015 cohort, respectively. Mean bedtime and wake-up time at 6 years were, respectively, 23:23 and 08:41 h in the 2004 cohort, and 00:10 and 09:00 h int the 2015 cohort. Nighttime sleep lasted on average 7.54 and 7.24 h respectively in the 2004 and the 2015 cohort, and the sleep efficiency was 81.1 and 82.5 % respectively. In adjusted analyses, no associations were found between awakening at 12 months and sleep duration or sleep efficiency at 6 years of age. Conclusion In both cohorts sleep duration and efficiency were below the recommendation for school-age children (respectively 9-11 h and 85 %). There was no relationship between the number of nighttime awakenings at 12 months and sleep duration or efficiency at 6 years.
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Affiliation(s)
- Ina S. Santos
- Post-graduate Program in Epidemiology, Federal University of Pelotas, Brazil
| | - Priscila Echevarria
- Post-graduate Program in Epidemiology, Federal University of Pelotas, Brazil
| | | | - Alicia Matijasevich
- Departamento de Medicina Preventiva, Faculdade de Medicina FMUSP, Universidade de São Paulo, SP, Brazil
| | - Marlos R. Domingues
- Post-graduate Program in Physical Education, Federal University of Pelotas, Brazil
| | - Pedro C. Hallal
- Post-graduate Program in Epidemiology, Federal University of Pelotas, Brazil
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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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48
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Zelenski AB, Haug K, Bushaw KJ, Buffington A, Bradley T, Kwekkeboom KL, Stalter L, Hanlon BM, Wakeen MJ, Jhagroo RA, Maursetter LJ, Johnson SK, Campbell TC, Schwarze ML. Embedding an Education Intervention about Shared Decision Making into an RCT: Ensuring competency and fidelity. PEC Innov 2024; 4:100260. [PMID: 38347862 PMCID: PMC10859294 DOI: 10.1016/j.pecinn.2024.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/21/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024]
Abstract
Objective To describe the outcomes of training nephrology clinicians and clinical research participants, to use the Best Case/Worst Case Communication intervention, for discussions about dialysis initiation for patients with life-limiting illness, during a randomized clinical trial to ensure competency, fidelity to the intervention, and adherence to study protocols and the intervention throughout the trial. Methods We enrolled 68 nephrologists at ten study sites and randomized them to receive training or wait-list control. We collected copies of completed graphic aids (component of the intervention), used with study-enrolled patients, to measure fidelity and adherence. Results We trained 34 of 36 nephrologists to competence and 27 completed the entire program. We received 60 graphic aids for study-enrolled patients for a 73% return rate in the intervention arm. The intervention fidelity score for the graphic aid reflected completion of all elements throughout the study. Conclusion We successfully taught the Best Case/Worst Case Communication intervention to clinicians as research participants within a randomized clinical trial. Innovation Decisions about dialysis are an opportunity to discuss prognosis and uncertainty in relation to consideration of prolonged life supporting therapy. Our study reveals a strategy to evaluate adherence to a communication intervention in real time during a clinical study.
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Affiliation(s)
- Amy B. Zelenski
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Karlie Haug
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Kyle J. Bushaw
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Anne Buffington
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Taylor Bradley
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | | | - Lily Stalter
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Bret M. Hanlon
- Department of Surgery, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI, USA
| | | | - Roy A. Jhagroo
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | | | - Sara K. Johnson
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Toby C. Campbell
- Department of Medicine, University of Wisconsin, Madison, WI, USA
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49
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Zhu Z, Cao H, Yan H, Liu H, Hong Z, Sun A, Liu T, Mao F. Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma. Comput Struct Biotechnol J 2024; 23:929-941. [PMID: 38375529 PMCID: PMC10875160 DOI: 10.1016/j.csbj.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Cancer immunotherapy has shown to be a promising method in treating hepatocellular carcinoma (HCC), but suboptimal responses in patients are attributed to cellular and molecular heterogeneity. Iron metabolism-related genes (IRGs) are important in maintaining immune system homeostasis and have the potential to help develop new strategies for HCC treatment. Herein, we constructed and validated the iron-metabolism gene prognostic index (IPX) using univariate Cox proportional hazards regression and LASSO Cox regression analysis, successfully categorizing HCC patients into two groups with distinct survival risks. Then, we performed single-sample gene set enrichment analysis, weighted correlation network analysis, gene ontology enrichment analysis, cellular lineage analysis, and SCENIC analysis to reveal the key determinants underlying the ability of this model based on bulk and single-cell transcriptomic data. We identified several driver transcription factors specifically activated in specific malignant cell sub-populations to contribute to the adverse survival outcomes in the IPX-high subgroup. Within the tumor microenvironment (TME), T cells displayed significant diversity in their cellular characteristics and experienced changes in their developmental paths within distinct clusters identified by IPX. Interestingly, the proportion of Treg cells was increased in the high-risk group compared with the low-risk group. These results suggest that iron-metabolism could be involved in reshaping the TME, thereby disrupting the cell cycle of immune cells. This study utilized IRGs to construct a novel and reliable model, which can be used to assess the prognosis of patients with HCC and further clarify the molecular mechanisms of IRGs in HCC at single-cell resolution.
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Affiliation(s)
- Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Huang Cao
- School of Medicine, Xiamen University, Xiamen, Fujian 361100, China
| | - Hongyu Yan
- School of Medicine, Xiamen University, Xiamen, Fujian 361100, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Hanzhi Liu
- The Third Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Zaifa Hong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361103, China
| | - Anran Sun
- Oncology Research Center, Foresea Life Insurance Guangzhou General Hospital, Guangzhou, Guangdong 511300, China
- Research Center for Translational Medicine, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, China
| | - Tong Liu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
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50
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Hatamikia S, George G, Schwarzhans F, Mahbod A, Woitek R. Breast MRI radiomics and machine learning-based predictions of response to neoadjuvant chemotherapy - How are they affected by variations in tumor delineation? Comput Struct Biotechnol J 2024; 23:52-63. [PMID: 38125296 PMCID: PMC10730996 DOI: 10.1016/j.csbj.2023.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023] Open
Abstract
Manual delineation of volumes of interest (VOIs) by experts is considered the gold-standard method in radiomics analysis. However, it suffers from inter- and intra-operator variability. A quantitative assessment of the impact of variations in these delineations on the performance of the radiomics predictors is required to develop robust radiomics based prediction models. In this study, we developed radiomics models for the prediction of pathological complete response to neoadjuvant chemotherapy in patients with two different breast cancer subtypes based on contrast-enhanced magnetic resonance imaging acquired prior to treatment (baseline MRI scans). Different mathematical operations such as erosion, smoothing, dilation, randomization, and ellipse fitting were applied to the original VOIs delineated by experts to simulate variations of segmentation masks. The effects of such VOI modifications on various steps of the radiomics workflow, including feature extraction, feature selection, and prediction performance, were evaluated. Using manual tumor VOIs and radiomics features extracted from baseline MRI scans, an AUC of up to 0.96 and 0.89 was achieved for human epidermal growth receptor 2 positive and triple-negative breast cancer, respectively. For smoothing and erosion, VOIs yielded the highest number of robust features and the best prediction performance, while ellipse fitting and dilation lead to the lowest robustness and prediction performance for both breast cancer subtypes. At most 28% of the selected features were similar to manual VOIs when different VOI delineation data were used. Differences in VOI delineation affect different steps of radiomics analysis, and their quantification is therefore important for development of standardized radiomics research.
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Affiliation(s)
- Sepideh Hatamikia
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
- Austrian Center for Medical Innovation and Technology (ACMIT), Viktor Kaplan-Straße 2/1, Wiener Neustadt 2700, Austria
| | - Geevarghese George
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
| | - Florian Schwarzhans
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
| | - Amirreza Mahbod
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
| | - Ramona Woitek
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
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