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Wollney EN, Bylund CL, Bedenfield N, Parker ND, Rosselli M, Curiel Cid RE, Kitaigorodsky M, Armstrong MJ. Persons living with dementia and caregivers' communication preferences for receiving a dementia diagnosis. PEC Innov 2024; 4:100253. [PMID: 38298558 PMCID: PMC10828581 DOI: 10.1016/j.pecinn.2024.100253] [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: 08/08/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
Objective As the number of individuals diagnosed with dementia increases, so does the need to understand the preferences of persons living with dementia (PLWD) and caregivers for how clinicians can deliver a dementia diagnosis effectively, which can be a difficult process. This study describes the diagnostic communication preferences of PLWD and caregivers. Methods We conducted semi-structured individual phone interviews with two groups: PLWD who were diagnosed in the past two years (n = 11) and family caregivers of PLWD (n = 19) living in Florida. PLWD and caregivers were not recruited/enrolled as dyads. Results The groups' communication preferences were largely similar. Data were analyzed thematically into five themes: communicate the diagnosis clearly, meet information needs, discuss PLWD/caregiver resources, prepare for continued care, and communicate to establish and maintain relationships. Conclusion Participants wanted clear communication, information, and support, but differed in some details (e.g. the language used to describe the diagnosis and the amount/type of desired information). Clinicians can apply general principles but will need to tailor them to individual preferences of PLWD and caregivers. Innovation Limited research has elicited PLWD and caregivers' communication preferences for receiving dementia diagnoses, particularly through an individualized data collection method allowing for richer descriptions and deeper understanding.
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Affiliation(s)
- Easton N. Wollney
- Department of Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America
| | - Carma L. Bylund
- Department of Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America
| | - Noheli Bedenfield
- Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, United States of America
| | - Naomi D. Parker
- College of Journalism & Communication, University of Florida, Gainesville, FL, United States of America
| | - Mónica Rosselli
- Department of Psychology, Florida Atlantic University, Boca Raton, FL, United States of America
| | - Rosie E. Curiel Cid
- Department of Psychiatry & Behavioral Sciences, Center for Cognitive Neuroscience and Aging, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | | | - Melissa J. Armstrong
- Department of Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America
- Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, United States of America
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Olivera A, Estevan I, Tassino B, Rossel C, Silva A. Epidemiology of sleep patterns and circadian typology in uruguayan children: The contribution of school shifts. Sleep Med X 2024; 7:100099. [PMID: 38234312 PMCID: PMC10792258 DOI: 10.1016/j.sleepx.2023.100099] [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: 10/06/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Healthy sleep is defined by the combination of adequate duration, good quality, and regular timing. In children, sleep thus depends on the interplay of individual, parental, organizational, community, and social variables, but only a few studies have addressed this issue in a comprehensive way nationwide. Using the Uruguayan nationally representative survey (Nutrition, Child Development, and Health Survey, Encuesta de Nutrición, Desarrollo Infantil y Salud, ENDIS), we present the first epidemiological characterization of chronobiological and sleep parameters in Latin American children. On average, Uruguayan urban children (n = 2437; 5-10-years old) showed quite late chronotypes (MSFsc = 03:53 ± 1:07), moderate misalignment (SJL = 1.0 ± 0.9 h), and adequate sleep duration (SDweek = 9.9 ± 1.0 h). Further, we show the substantial influence of school shift schedules on children's circadian typology and sleep patterns. Our results show that children attending the morning school shift have a higher risk of sleep problems than afternoon-school shift ones. The chronotype and sleep were earlier in morning-school shift children than in children attending the afternoon school shift. However, morning-school shift children had stronger misalignment, shorter sleep on school days, and a higher risk of chronic sleep deficit and non-healthy circadian misalignment (even worse in late chronotypes) than afternoon-shift children. This evidence points to the need of evaluating policies to reorganize school start times to prevent the negative effects that early schooling seems to have on children's sleep health, which has been neglected so far.
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Affiliation(s)
- Andrés Olivera
- Grupo Cronobiología, Comisión Sectorial de Investigación Científica, Universidad de la República, Jackson 1301, 11200, Montevideo, Uruguay
- Departamento de Ciencias Sociales, Universidad Católica del Uruguay, 8 de octubre 2768, 11600, Montevideo, Uruguay
| | - Ignacio Estevan
- Grupo Cronobiología, Comisión Sectorial de Investigación Científica, Universidad de la República, Jackson 1301, 11200, Montevideo, Uruguay
- Programa de Neuropsicología y Neurobiología, Facultad de Psicología, Universidad de la República, Tristán Narvaja 1674, 11200, Montevideo, Uruguay
| | - Bettina Tassino
- Grupo Cronobiología, Comisión Sectorial de Investigación Científica, Universidad de la República, Jackson 1301, 11200, Montevideo, Uruguay
- Sección Etología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Cecilia Rossel
- Departamento de Ciencias Sociales, Universidad Católica del Uruguay, 8 de octubre 2768, 11600, Montevideo, Uruguay
| | - Ana Silva
- Grupo Cronobiología, Comisión Sectorial de Investigación Científica, Universidad de la República, Jackson 1301, 11200, Montevideo, Uruguay
- Laboratorio de Neurociencias, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
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Babi A, Issa T, Gusmanov A, Akilzhanova A, Issanov A, Makhmetova N, Marat A, Iztleuov Y, Aimagambetova G. Prevalence of high-risk human papillomavirus infection and genotype distribution among Kazakhstani women with abnormal cervical cytology. Ann Med 2024; 56:2304649. [PMID: 38237138 PMCID: PMC10798292 DOI: 10.1080/07853890.2024.2304649] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024] Open
Abstract
AIM This study aimed to identify the prevalence and distribution of high-risk human papillomavirus (HR-HPV) types among Kazakhstani women with abnormal cervical cytology. METHODS A cross-sectional study was performed from May 2019 to June 2020. Cervical samples were collected from women in the different regions of Kazakhstan. RESULTS A total of 316 patients' samples were analysed for HR-HPV using real-time multiplex PCR. Cervical cytology abnormalities were reported according to the Bethesda classification. HPV detection by cytology showed a statistically significant association with HPV status and the number of HPV infection types (p < .05). Among women with abnormal cervical cytology, 62.4% were positive for HPV infection of those 79.4% had low-grade squamous intraepithelial lesions (LSIL), and 20.6% had high-grade squamous intraepithelial lesions (HSIL). Among patients with LSIL, 77.4% had HPV16 and 58.8% were infected with HPV18. Among patients with HSIL, 41.2% had HPV18 and 22.6% - HPV16. CONCLUSIONS There is a high prevalence of HR-HPV types among Kazakhstani women with abnormal cervical cytology. The most identified types were HPV16, 18, 31, 33 and 52. There is an emergency need to implement an HPV vaccination program to prevent cervical lesion development.
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Affiliation(s)
- Aisha Babi
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Torgyn Issa
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Arnur Gusmanov
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, National Laboratory of Astana, Center for Life Sciences, Nazarbayev University, Astana, Kazakhstan
| | - Alpamys Issanov
- Department of Medicine, School of Medicine, Nazarbayev University, Astana, Kazakhstan
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Aizada Marat
- Department of Obstetrics and Gynecology #1, NJSC "Astana Medical University", Astana, Kazakhstan
| | - Yerbolat Iztleuov
- Medical Center, Marat Ospanov West-Kazakhstan Medical University, Aktobe, Kazakhstan
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Chen S, Huang M, Zhang L, Huang Q, Wang Y, Liang Y. Inflammatory response signature score model for predicting immunotherapy response and pan-cancer prognosis. Comput Struct Biotechnol J 2024; 23:369-383. [PMID: 38226313 PMCID: PMC10788202 DOI: 10.1016/j.csbj.2023.12.001] [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: 06/09/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 01/17/2024] Open
Abstract
Background Inflammatory responses influence the outcome of immunotherapy and tumorigenesis by modulating host immunity. However, systematic inflammatory response assessment models for predicting cancer immunotherapy (CIT) responses and survival across human cancers remain unexplored. Here, we investigated an inflammatory response score model to predict CIT responses and patient survival in a pan-cancer analysis. Methods We retrieved 12 CIT response gene expression datasets from the Gene Expression Omnibus database (GSE78220, GSE19423, GSE100797, GSE126044, GSE35640, GSE67501, GSE115821 and GSE168204), Tumor Immune Dysfunction and Exclusion database (PRJEB23709, PRJEB25780 and phs000452.v2.p1), European Genome-phenome Archive database (EGAD00001005738), and IMvigor210 cohort. The tumor samples from six cancers types: metastatic urothelial cancer, metastatic melanoma, gastric cancer, primary bladder cancer, renal cell carcinoma, and non-small cell lung cancer.We further established a binary classification model to predict CIT responses using the least absolute shrinkage and selection operator (LASSO) computational algorithm. Findings The model had high predictive accuracy in both the training and validation cohorts. During sub-group analysis, area under the curve (AUC) values of 0.82, 0.80, 0.71, 0.7, 0.67, and 0.64 were obtained for the non-small cell lung cancer, gastric cancer, metastatic urothelial cancer, primary bladder cancer, metastatic melanoma, and renal cell carcinoma cohorts, respectively. CIT response rates were higher in the high-scoring training cohort subjects (51%) than the low-scoring subjects (27%). The five-year survival rates in the high- and low score groups of the training cohorts were 62% and 21%, respectively, while those of the validation cohorts were 54% and 22%, respectively (P < 0·001 in all cases). Inflammatory response signature score derived from on-treatment tumor specimens are highly predictive of response to CIT in patients with metastatic melanoma. A significant correlation was observed between the inflammatory response scores and tumor purity. Regardless of the tumor purity, patients in the low score group had a significantly poorer prognosis than those in the high score group. Immune cell infiltration analysis indicated that in the high score cohort, tumor-infiltrating lymphocytes were significantly enriched, particularly effector and natural killer cells. Inflammatory response scores were positively correlated with immune checkpoint genes, suggesting that immune checkpoint inhibitors may have benefited patients with high scores. Analysis of signature scores across different cancer types from The Cancer Genome Atlas revealed that the prognostic performance of inflammatory response scores for survival in patients who have not undergone immunotherapy can be affected by tumor purity. Interleukin 21 (IL21) had the highest weight in the inflammatory response model, suggesting its vital role in the prediction mode. Since the number of metastatic melanoma patients (n = 429) was relatively large among CIT cohorts, we further performed a co-culture experiment using a melanoma cell line and CD8 + T cell populations generated from peripheral blood monocytes. The results showed that IL21 therapy combined with anti-PD1 (programmed cell death 1) antibodies (trepril monoclonal antibodies) significantly enhanced the cytotoxic activity of CD8 + T cells against the melanoma cell line. Conclusion In this study, we developed an inflammatory response gene signature model that predicts patient survival and immunotherapy response in multiple malignancies. We further found that the predictive performance in the non-small cell lung cancer and gastric cancer group had the highest value among the six different malignancy subgroups. When compared with existing signatures, the inflammatory response gene signature scores for on-treatment samples were more robust predictors of the response to CIT in metastatic melanoma.
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Affiliation(s)
- Shuzhao Chen
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), Shantou, Guangdong, China
| | - Mayan Huang
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Limei Zhang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
| | - Qianqian Huang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
| | - Yun Wang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
| | - Yang Liang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
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Chen J, Lu RS, Diaz-Canestro C, Song E, Jia X, Liu Y, Wang C, Cheung CK, Panagiotou G, Xu A. Distinct changes in serum metabolites and lipid species in the onset and progression of NAFLD in Obese Chinese. Comput Struct Biotechnol J 2024; 23:791-800. [PMID: 38318437 PMCID: PMC10839226 DOI: 10.1016/j.csbj.2024.01.007] [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: 08/28/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Metabolic disturbances are major contributors to the onset and progression of non-alcoholic fatty liver disease (NAFLD), which includes a histological spectrum ranging from single steatosis (SS) to non-alcoholic steatohepatitis (NASH). This study aimed to identify serum metabolites and lipids enriched in different histological stages of NAFLD and to explore metabolites/lipids as non-invasive biomarkers in risk prediction of NAFLD and NASH in obese Chinese. Methods Serum samples and liver biopsies were obtained from 250 NAFLD subjects. Untargeted metabolomic and lipidomic profiling were performed using Liquid Chromatography-Mass Spectrometry. Significantly altered metabolites and lipids were identified by MaAsLin2. Pathway enrichment was conducted with MetaboAnalyst and LIPEA. WGCNA was implemented to construct the co-expression network. Logistic regression models were developed to classify different histological stages of NAFLD. Results A total of 263 metabolites and 550 lipid species were detected in serum samples. Differential analysis and pathway enrichment analysis revealed the progressive patterns in metabolic mechanisms during the transition from normal liver to SS and to NASH, including N-palmitoyltaurine, tridecylic acid, and branched-chain amino acid signaling pathways. The co-expression network showed a distinct correlation between different triglyceride and phosphatidylcholine species with disease severity. Multiple models classifying NAFLD versus normal liver and NASH versus SS identified important metabolic features associated with significant improvement in disease prediction compared to conventional clinical parameters. Conclusion Different histological stages of NAFLD are enriched with distinct sets of metabolites, lipids, and metabolic pathways. Integrated algorithms highlight the important metabolic and lipidomic features for diagnosis and staging of NAFLD in obese individuals.
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Affiliation(s)
- Jiarui Chen
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Leibniz Insitute for Natural Product Research and Infection Biology, Microbiome Dynamics, Hans Knöll Institute, Jena, Germany
| | - Ronald Siyi Lu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Candela Diaz-Canestro
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Erfei Song
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Metabolic and Bariatric Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xi Jia
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Yan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Cunchuan Wang
- Department of Metabolic and Bariatric Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Cynthia K.Y. Cheung
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Gianni Panagiotou
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Leibniz Insitute for Natural Product Research and Infection Biology, Microbiome Dynamics, Hans Knöll Institute, Jena, Germany
- Friedrich Schiller University, Faculty of Biological Sciences, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Department of Pharmacology and Pharmacy, the University of Hong Kong, Hong Kong Special Administrative Region
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106
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Liao C, Walters BW, DiStasio M, Lesch BJ. Human-specific epigenomic states in spermatogenesis. Comput Struct Biotechnol J 2024; 23:577-588. [PMID: 38274996 PMCID: PMC10809009 DOI: 10.1016/j.csbj.2023.12.037] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Infertility is becoming increasingly common, affecting one in six people globally. Half of these cases can be attributed to male factors, many driven by abnormalities in the process of sperm development. Emerging evidence from genome-wide association studies, genetic screening of patient cohorts, and animal models highlights an important genetic contribution to spermatogenic defects, but comprehensive identification and characterization of the genes critical for male fertility remain lacking. High divergence of gene regulation in spermatogenic cells across species poses challenges for delineating the genetic pathways required for human spermatogenesis using common model organisms. In this study, we leveraged post-translational histone modification and gene transcription data for 15,491 genes in four mammalian species (human, rhesus macaque, mouse, and opossum), to identify human-specific patterns of gene regulation during spermatogenesis. We combined H3K27me3 ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data to define epigenetic states for each gene at two stages of spermatogenesis, pachytene spermatocytes and round spermatids, in each species. We identified 239 genes that are uniquely active, poised, or dynamically regulated in human spermatogenic cells distinct from the other three species. While some of these genes have been implicated in reproductive functions, many more have not yet been associated with human infertility and may be candidates for further molecular and epidemiologic studies. Our analysis offers an example of the opportunities provided by evolutionary and epigenomic data for broadly screening candidate genes implicated in reproduction, which might lead to discoveries of novel genetic targets for diagnosis and management of male infertility and male contraception.
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Affiliation(s)
- Caiyun Liao
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| | | | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Department of Opthamology & Visual Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| | - Bluma J. Lesch
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Department of Genetics, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
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Wang Z, Chen H, Sun L, Wang X, Xu Y, Tian S, Liu X. Uncovering the potential of APOD as a biomarker in gastric cancer: A retrospective and multi-center study. Comput Struct Biotechnol J 2024; 23:1051-1064. [PMID: 38455068 PMCID: PMC10918487 DOI: 10.1016/j.csbj.2024.02.015] [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: 10/21/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Gastric cancer (GC) poses a significant health challenge worldwide, necessitating the identification of predictive biomarkers to improve prognosis. Dysregulated lipid metabolism is a well-recognized hallmark of tumorigenesis, prompting investigation into apolipoproteins (APOs). In this study, we focused on apolipoprotein D (APOD) following comprehensive analyses of APOs in pan-cancer. Utilizing data from the TCGA-STAD and GSE62254 cohorts, we elucidated associations between APOD expression and multiple facets of GC, including prognosis, tumor microenvironment (TME), cancer biomarkers, mutations, and immunotherapy response, and identified potential anti-GC drugs. Single-cell analyses and immunohistochemical staining confirmed APOD expression in fibroblasts within the GC microenvironment. Additionally, we independently validated the prognostic significance of APOD in the ZN-GC cohort. Our comprehensive analyses revealed that high APOD expression in GC patients was notably associated with unfavorable clinical outcomes, reduced microsatellite instability and tumor mutation burden, alterations in the TME, and diminished response to immunotherapy. These findings provide valuable insights into the potential prognostic and therapeutic implications of APOD in GC.
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Affiliation(s)
- Zisong Wang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Hongshan Chen
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Le Sun
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xuanyu Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Yihang Xu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Sufang Tian
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xiaoping Liu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
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Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [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: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
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Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
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Grützmann K, Kraft T, Meinhardt M, Meier F, Westphal D, Seifert M. Network-based analysis of heterogeneous patient-matched brain and extracranial melanoma metastasis pairs reveals three homogeneous subgroups. Comput Struct Biotechnol J 2024; 23:1036-1050. [PMID: 38464935 PMCID: PMC10920107 DOI: 10.1016/j.csbj.2024.02.013] [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: 11/06/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
Melanoma, the deadliest form of skin cancer, can metastasize to different organs. Molecular differences between brain and extracranial melanoma metastases are poorly understood. Here, promoter methylation and gene expression of 11 heterogeneous patient-matched pairs of brain and extracranial metastases were analyzed using melanoma-specific gene regulatory networks learned from public transcriptome and methylome data followed by network-based impact propagation of patient-specific alterations. This innovative data analysis strategy allowed to predict potential impacts of patient-specific driver candidate genes on other genes and pathways. The patient-matched metastasis pairs clustered into three robust subgroups with specific downstream targets with known roles in cancer, including melanoma (SG1: RBM38, BCL11B, SG2: GATA3, FES, SG3: SLAMF6, PYCARD). Patient subgroups and ranking of target gene candidates were confirmed in a validation cohort. Summarizing, computational network-based impact analyses of heterogeneous metastasis pairs predicted individual regulatory differences in melanoma brain metastases, cumulating into three consistent subgroups with specific downstream target genes.
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Affiliation(s)
- Konrad Grützmann
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Theresa Kraft
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Matthias Meinhardt
- Department of Pathology, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
| | - Dana Westphal
- Department of Dermatology, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
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Wang X, Wu L, Zhang W, Qiu S, Xu Z, Wan H, He J, Wang W, Wang M, Yin Q, Shi Y, Gao R, Xiang L, Yang W. Multi-omics analysis reveals promiscuous O-glycosyltransferases involved in the diversity of flavonoid glycosides in Periploca forrestii (Apocynaceae). Comput Struct Biotechnol J 2024; 23:1106-1116. [PMID: 38495554 PMCID: PMC10940802 DOI: 10.1016/j.csbj.2024.02.028] [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: 01/13/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Flavonoid glycosides are widespread in plants, and are of great interest owing to their diverse biological activities and effectiveness in preventing chronic diseases. Periploca forrestii, a renowned medicinal plant of the Apocynaceae family, contains diverse flavonoid glycosides and is clinically used to treat rheumatoid arthritis and traumatic injuries. However, the mechanisms underlying the biosynthesis of these flavonoid glycosides have not yet been elucidated. In this study, we used widely targeted metabolomics and full-length transcriptome sequencing to identify flavonoid diversity and biosynthetic genes in P. forrestii. A total of 120 flavonoid glycosides, including 21 C-, 96 O-, and 3 C/O-glycosides, were identified and annotated. Based on 24,123 full-length coding sequences, 99 uridine diphosphate sugar-utilizing glycosyltransferases (UGTs) were identified and classified into 14 groups. Biochemical assays revealed that four UGTs exhibited O-glycosyltransferase activity toward apigenin and luteolin. Among them, PfUGT74B4 and PfUGT92A8 were highly promiscuous and exhibited multisite O-glycosylation or consecutive glycosylation activities toward various flavonoid aglycones. These four glycosyltransferases may significantly contribute to the diversity of flavonoid glycosides in P. forrestii. Our findings provide a valuable genetic resource for further studies on P. forrestii and insights into the metabolic engineering of bioactive flavonoid glycosides.
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Affiliation(s)
- Xiaotong Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin 150006, China
| | - Lan Wu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wanran Zhang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin 150006, China
| | - Shi Qiu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhichao Xu
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin 150006, China
| | - Huihua Wan
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiang He
- Xinjiang Institute of Materia Medica/Key Laboratory of Xinjiang Uygur Medicine, Urumqi 830004, China
| | - Wenting Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mengyue Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qinggang Yin
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yuhua Shi
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ranran Gao
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Li Xiang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Xinjiang Institute of Materia Medica/Key Laboratory of Xinjiang Uygur Medicine, Urumqi 830004, China
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi 830000, China
| | - Weijun Yang
- Xinjiang Institute of Materia Medica/Key Laboratory of Xinjiang Uygur Medicine, Urumqi 830004, China
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Fleszar-Pavlović SE, Cameron LD. Developing a narrative communication intervention in the context of HPV vaccination. PEC Innov 2024; 4:100272. [PMID: 38525313 PMCID: PMC10957452 DOI: 10.1016/j.pecinn.2024.100272] [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: 09/07/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Objective We outline the development of a narrative intervention guided by the Common-Sense Model of Self-Regulation (CSM) to promote Human Papillomavirus (HPV) vaccination in a diverse college population. Methods We adapted the Obesity-Related Behavioral Intervention Trials (ORBIT) model to guide the development, evaluation, and refinement of a CSM-guided narrative video. First, content experts developed a video script containing information on HPV, HPV vaccines, and HPV-related cancers. The script and video contents were evaluated and refined, in succession, utilizing the think-aloud method, open-ended questions, and a brief survey during one-on-one interviews with university students. Results Script and video content analyses led to significant revisions that enhanced quality, informativeness, and relevance to the participants. We highlight the critical issues that were revealed and revised in the iterative process. Conclusions We developed and refined a CSM guided narrative video for diverse university students. This framework serves as a guide for developing health communication interventions for other populations and health behaviors. Innovation This project is the first to apply the ORBIT framework to HPV vaccination and describe a process to develop, evaluate, and refine comparable CSM guided narrative interventions that are tailored to specific audiences.
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Affiliation(s)
- Sara E. Fleszar-Pavlović
- Department of Psychological Sciences, University of California, Merced, CA, United States of America
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States of America
| | - Linda D. Cameron
- Department of Psychological Sciences, University of California, Merced, CA, United States of America
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112
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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [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: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Zanfardino M, Punzo B, Maffei E, Saba L, Bossone E, Nistri S, La Grutta L, Franzese M, Cavaliere C, Cademartiri F. Unsupervised machine learning for risk stratification and identification of relevant subgroups of ascending aorta dimensions using cardiac CT and clinical data. Comput Struct Biotechnol J 2024; 23:287-294. [PMID: 38173875 PMCID: PMC10762320 DOI: 10.1016/j.csbj.2023.11.021] [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: 09/14/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 01/05/2024] Open
Abstract
The potential of precision population health lies in its capacity to utilize robust patient data for customized prevention and care targeted at specific groups. Machine learning has the potential to automatically identify clinically relevant subgroups of individuals, considering heterogeneous data sources. This study aimed to assess whether unsupervised machine learning (UML) techniques could interpret different clinical data to uncover clinically significant subgroups of patients suspected of coronary artery disease and identify different ranges of aorta dimensions in the different identified subgroups. We employed a random forest-based cluster analysis, utilizing 14 variables from 1170 (717 men/453 women) participants. The unsupervised clustering approach successfully identified four distinct subgroups of individuals with specific clinical characteristics, and this allows us to interpret and assess different ranges of aorta dimensions for each cluster. By employing flexible UML algorithms, we can effectively process heterogeneous patient data and gain deeper insights into clinical interpretation and risk assessment.
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Affiliation(s)
| | | | - Erica Maffei
- Department of Imaging, Fondazione Monasterio/CNR, Pisa, 56124, Italy
| | - Luca Saba
- Department of Radiology, University Hospital of Cagliari, Cagliari, 09042, Italy
| | - Eduardo Bossone
- Department of Public Health, University of Naples Federico II, Naples, 80131, Italy
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Guo C, Wang X, Ren H. Databases and computational methods for the identification of piRNA-related molecules: A survey. Comput Struct Biotechnol J 2024; 23:813-833. [PMID: 38328006 PMCID: PMC10847878 DOI: 10.1016/j.csbj.2024.01.011] [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: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.
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Affiliation(s)
- Chang Guo
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Han Ren
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
- Laboratory of Language and Artificial Intelligence, Guangdong University of Foreign Studies, Guangzhou 510420, China
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Murase M, Fujita H, Oki M, Yoshioka F, Nishiyama Y, Ohyama T, Matsumoto C, Usui S, Sato Y, Sado T, Takahashi H, Sasaki K, Matsuyama M, Sumita Y. Time-study research on maxillofacial prosthetic treatment. Jpn Dent Sci Rev 2024; 60:73-80. [PMID: 38298267 PMCID: PMC10828541 DOI: 10.1016/j.jdsr.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: 09/16/2023] [Revised: 12/11/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
Unreasonable medical fees can cause problems such as increased medical costs, greater medical disparities, decreased medical standards, and physician shortages. To prevent such problems, it is important to set appropriate medical fees, ensure their proper use, and improve the efficiency of medical care. The treatment of patients with maxillofacial defects is generally more expensive compared with general prosthodontic treatment because it involves more materials and requires more frequently follow-ups for longer period. However, the actual time required for maxillofacial prosthetic treatment is unclear. Therefore, in this study, we aimed to clarify the amount of time spent treating maxillofacial prosthetic patients. We analyzed clinical data from patients undergoing routine maxillofacial prosthetic treatment, irrespective of difficulty level, at 8 university hospitals and 2 dental clinics. We also collected data from maxillofacial prosthodontists on the treatment time required for various Japanese health insurance items, including the fabrication of maxillofacial prostheses. The results revealed that some aspects of maxillofacial prosthetic treatment may take longer to perform and are more costly to perform than previously thought, suggesting the need for some adjustments to the health insurance reimbursement system. Maintaining an appropriate balance between expenditures and fees will greatly benefit patients and physicians, ensuring positive health outcomes and a healthy society.
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Affiliation(s)
- Mai Murase
- Department of Advanced Prosthodontics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Haruka Fujita
- Department of Advanced Prosthodontics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Meiko Oki
- Department of Basic Oral Health Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Fumi Yoshioka
- Department of Removable Prosthodontics, School of Dentistry, Aichi Gakuin University, Aichi, Japan
| | - Yuichiro Nishiyama
- Tsurumi University, School of Dental Medicine, Department of Oral Rehabilitation and Prosthodontics Yokohama, Japan
| | - Tetsuo Ohyama
- Department of Partial Denture Prosthodontics, Nihon University School of Dentistry, Tokyo, Japan
| | - Chihaya Matsumoto
- Department of Prosthetic Dentistry, School of Dentistry, Ohu University, Koriyama, Japan
| | | | - Yuji Sato
- Sato Dental Clinic, Hiroshima, Japan
| | | | - Hidekazu Takahashi
- Oral Biomedical Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | - Miwa Matsuyama
- Department of Oral Health Care and Rehabilitation, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yuka Sumita
- Division of General Dentistry 4, The Nippon Dental University Hospital, Tokyo, Japan
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Udatha DG. Introducing a New Article Type "Innovation Reports": Venue for Communication & Dissemination of Collaborative Projects. Comput Struct Biotechnol J 2024; 23:952-953. [PMID: 38379822 PMCID: PMC10877626 DOI: 10.1016/j.csbj.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Shariff A, Kumar TMP, Siddalingegowda SM, Wani SUD, Elsobky Y. PharmD students experiences on end year clerkship evaluation using objective structured clinical exam (OSCE) method at JSS College of Pharmacy, Mysuru, India. PEC Innov 2024; 4:100271. [PMID: 38495318 PMCID: PMC10940797 DOI: 10.1016/j.pecinn.2024.100271] [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: 08/28/2023] [Revised: 02/09/2024] [Accepted: 03/03/2024] [Indexed: 03/19/2024]
Abstract
Objectives To assess the PharmD student's experiences about end year clerkship evaluation conducted using Objective Structured Clinical Exam (OSCE) format at JSS College of Pharmacy, Mysuru, India. Methods The student's experiences were captured using a newly developed, 14-item, 5-point Likert's scale feedback form. The results were analyzed and presented descriptively. The Mann-Whitney U test was used to compare the Likert's scale responses between the sex, entry level for PharmD and performance in the end year exam, whereas the Spearman's rank correlation coefficient test was used to measure the strength of association between the Likert's' scale responses and these variables. A p value of <0.05 was considered statistically significant. Results Thirty-seven students of fifth year PharmD attended the end year clerkship evaluation and provided their feedback. Out of the 14-items, the most frequent response in eleven items was strongly agree and in three items it was agree. The Mann-Whitney U test revealed statistically significant differences between regular and postbaccalaureate students with respect to Likert's scale responses in all the domains (p < 0.02). The Spearman's rank correlation test revealed no association between the students' performance and their experiences with OSCE as an assessment tool for the end year clerkship exam. Conclusions The study results demonstrate that OSCE is an alternative and preferred method of evaluating the clinical skills and competencies of fifth year PharmD students in their end year clerkship exam in India. Innovation For the first time in India, the JSS College of Pharmacy, Mysuru, had successfully implemented the OSCE method for evaluating PharmD students' clerkship in their end year exam and had assessed their experiences about OSCE as an assessment tool.
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Affiliation(s)
- Atiqulla Shariff
- Research Scholar, Department of Pharmacy Practice, JSS College of Pharmacy, Mysuru, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India
| | - Teggina Math Pramod Kumar
- Dean, Faculty of Pharmacy, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India
| | - Srikanth Malavalli Siddalingegowda
- Lecturer, Department of Pharmacy Practice, JSS College of Pharmacy, Mysuru, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India
| | - Shahid Ud Din Wani
- Department of Pharmaceutical Sciences, School of Applied Science and Technology, University of Kashmir, Srinagar 190006, India
| | - Yasmin Elsobky
- Senior Research Specialist, ALNAS Hospital, Shubra El Kheima, Egypt 6210120
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Maheshwari V, Basu S. Sleep problems and their predictors in community-dwelling older adults with diabetes in India: Evidence from the Longitudinal Ageing Study in India. Sleep Med X 2024; 7:100108. [PMID: 38500780 PMCID: PMC10945249 DOI: 10.1016/j.sleepx.2024.100108] [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: 09/07/2023] [Revised: 12/04/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
Objectives To ascertain the prevalence and predictors of sleep disorders and poor sleep quality among older adults with Diabetes (DM) in India, and to assess the relationship between sleep quality and DM. Methods Data was utilized from the nationally representative Longitudinal Ageing Study in India (Wave-1, 2017-18), with a total sample of 66606 older adults (≥45 years) selected for the study. Sleep problems and sleep quality score were assessed using an adaptation based on the Jenkins Sleep Scale. Multivariate linear and logistic regressions were conducted to determine the effect of sociodemographic and clinical factors on sleep quality. Mediation analysis (Karlson-Holm-Breen) was done to assess the direct and indirect effects of independent variables on the sleep quality scores. Further, Propensity score matching (PSM) was done to assess the impact of diabetes on sleep problems. Results The prevalence of DM was 12.34% (n = 8564, 95% CI: 11.54, 13.20) among whom 24.38% (95% CI: 21.38, 27.65) reported sleep problems. On adjusted analysis, sleep problems were significantly associated with increasing education, higher wealth quintile, lack of physical activity, and multimorbidity. Mediation analysis showed adherence to anti-diabetes medication improved sleep quality (aB = -0.28 (95% CI: -0.54, -0.02)), while comorbidities worsened sleep quality (aB = 0.79 (95% CI: 0.67, 0.92)). Analysis from PSM indicated that DM was associated with a 6.2% higher chance of sleep problems. Conclusions Poor sleep quality is present in nearly one in four individuals diagnosed with DM in India and linked with certain adverse social determinants. Focused interventions to improve assessment and treatment of sleep problems in resource-limited primary care settings require prioritization.
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Affiliation(s)
- Vansh Maheshwari
- Indian Institute of Public Health – Delhi, Public Health Foundation of India, India
| | - Saurav Basu
- Indian Institute of Public Health – Delhi, Public Health Foundation of India, India
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Wang Y, Zuo J, Duan C, Peng H, Huang J, Zhao L, Zhang L, Dong Z. Large language models assisted multi-effect variants mining on cerebral cavernous malformation familial whole genome sequencing. Comput Struct Biotechnol J 2024; 23:843-858. [PMID: 38352937 PMCID: PMC10861960 DOI: 10.1016/j.csbj.2024.01.014] [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: 10/16/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Cerebral cavernous malformation (CCM) is a polygenic disease with intricate genetic interactions contributing to quantitative pathogenesis across multiple factors. The principal pathogenic genes of CCM, specifically KRIT1, CCM2, and PDCD10, have been reported, accompanied by a growing wealth of genetic data related to mutations. Furthermore, numerous other molecules associated with CCM have been unearthed. However, tackling such massive volumes of unstructured data remains challenging until the advent of advanced large language models. In this study, we developed an automated analytical pipeline specialized in single nucleotide variants (SNVs) related biomedical text analysis called BRLM. To facilitate this, BioBERT was employed to vectorize the rich information of SNVs, while a deep residue network was used to discriminate the classes of the SNVs. BRLM was initially constructed on mutations from 12 different types of TCGA cancers, achieving an accuracy exceeding 99%. It was further examined for CCM mutations in familial sequencing data analysis, highlighting an upstream master regulator gene fibroblast growth factor 1 (FGF1). With multi-omics characterization and validation in biological function, FGF1 demonstrated to play a significant role in the development of CCMs, which proved the effectiveness of our model. The BRLM web server is available at http://1.117.230.196.
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Affiliation(s)
- Yiqi Wang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Jinmei Zuo
- Physical Examination Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Chao Duan
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Hao Peng
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Jia Huang
- The Second Clinical Medical College, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730030, Gansu, China
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Li Zhang
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Zhiqiang Dong
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
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Fan S, Lü X, Wei X, Lü R, Feng C, Jin Y, Yan M, Yang Z. Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures. Comput Struct Biotechnol J 2024; 23:982-989. [PMID: 38404709 PMCID: PMC10883975 DOI: 10.1016/j.csbj.2024.02.005] [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: 09/12/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
The thermostable α-amylase derived from Bacillus licheniformis (BLA) has multiple advantages, including enhancing the mass transfer rate and by reducing microbial contamination in starch hydrolysis. Nonetheless, the application of BLA is constrained by the accessibility and stability of enzymes capable of achieving high conversion rates at elevated temperatures. Moreover, the thermotolerance of BLA requires further enhancement. Here, we developed a computational strategy for constructing small and smart mutant libraries to identify variants with enhanced thermostability. Initially, molecular dynamics (MD) simulations were employed to identify the regions with high flexibility. Subsequently, FoldX, a computational design predictor, was used to design mutants by rigidifying highly flexible residues, whereas the simultaneous decrease in folding free energy assisted in improving thermostability. Through the utilization of MD and FoldX, residues K251, T277, N278, K319, and E336, situated at a distance of 5 Å from the catalytic triad, were chosen for mutation. Seventeen mutants were identified and characterized by evaluating enzymatic characteristics and kinetic parameters. The catalytic efficiency of the E271L/N278K mutant reached 184.1 g L-1 s-1, which is 1.88-fold larger than the corresponding value determined for the WT. Furthermore, the most thermostable mutant, E336S, exhibited a 1.43-fold improvement in half-life at 95 ℃, compared with that of the WT. This study, by combining computational simulation with experimental verification, establishes that potential sites can be computationally predicted to increase the activity and stability of BLA and thus provide a possible strategy by which to guide protein design.
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Affiliation(s)
- Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xudong Lü
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiyu Wei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ruijie Lü
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Cuiyue Feng
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao 276800, Shandong, China
| | - Zhaoyong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Lau J, O G, Warnakulasuriya S, Balasubramaniam R, Frydrych A, Kujan O. Adjunctive aids for the detection of oral squamous cell carcinoma and oral potentially malignant disorders: A systematic review of systematic reviews. Jpn Dent Sci Rev 2024; 60:53-72. [PMID: 38283580 PMCID: PMC10821377 DOI: 10.1016/j.jdsr.2023.12.004] [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: 10/13/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024] Open
Abstract
This study presents the results of systematic reviews on adjunctive tools in screening and diagnosis of oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMD) and to determine if the current literature supports their use as either an adjunctive tool or replacement of gold standard techniques. Systemic reviews and meta-analysis that evaluated adjunctive tools including chemiluminescence, tissue autofluorescence, tissue fluorescence spectroscopy, vital staining and cytology techniques were systematically examined using AMSTAR II. Twenty-seven systematic reviews were included. Five studies had a low quality of evidence, and nine studies had a critically low quality of evidence. This review found limited evidence to recommend chemiluminescence, tissue autofluorescence tools and vital staining as diagnostic tools, but only serve as clinical adjuncts to conventional oral examination. Cytology techniques and narrow-band imaging may be utilised as a non-invasive diagnostic adjunctive tool for the detection of OSCC and the malignant transformation of OPMD. In conclusion, this paper provides evidence on several types of adjunctive tools and provides recommendations on their use in clinical practice. These tools are considered useful as clinical adjuncts but there is insufficient evidence for their use as a diagnostic tool to replace gold standard conventional oral examination and surgical biopsy.
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Affiliation(s)
- Jeremy Lau
- UWA Dental School, The University of Western Australia, Nedlands, WA, Australia
| | - Guru O
- UWA Dental School, The University of Western Australia, Nedlands, WA, Australia
| | | | | | - Agnieszka Frydrych
- UWA Dental School, The University of Western Australia, Nedlands, WA, Australia
| | - Omar Kujan
- UWA Dental School, The University of Western Australia, Nedlands, WA, Australia
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Li J, He L, Zhang X, Li X, Wang L, Zhu Z, Song K, Wang X. GCclassifier: An R package for the prediction of molecular subtypes of gastric cancer. Comput Struct Biotechnol J 2024; 23:752-758. [PMID: 38304548 PMCID: PMC10831507 DOI: 10.1016/j.csbj.2024.01.010] [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: 10/22/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Gastric cancer (GC) is one of the most commonly diagnosed malignancies, threatening millions of lives worldwide each year. Importantly, GC is a heterogeneous disease, posing a significant challenge to the selection of patients for more optimized therapy. Over the last decades, extensive community effort has been spent on dissecting the heterogeneity of GC, leading to the identification of distinct molecular subtypes that are clinically relevant. However, so far, no tool is publicly available for GC subtype prediction, hindering the research into GC subtype-specific biological mechanisms, the design of novel targeted agents, and potential clinical applications. To address the unmet need, we developed an R package GCclassifier for predicting GC molecular subtypes based on gene expression profiles. To facilitate the use by non-bioinformaticians, we also provide an interactive, user-friendly web server implementing the major functionalities of GCclassifier. The predictive performance of GCclassifier was demonstrated using case studies on multiple independent datasets.
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Affiliation(s)
- Jiang Li
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Lingli He
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Xianrui Zhang
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Xiang Li
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
| | - Lishi Wang
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
| | - Zhongxu Zhu
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Kai Song
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Region of China
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Region of China
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Sumitomo T, Kawabata S. Respiratory tract barrier dysfunction in viral-bacterial co-infection cases. Jpn Dent Sci Rev 2024; 60:44-52. [PMID: 38274948 PMCID: PMC10808858 DOI: 10.1016/j.jdsr.2023.12.006] [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: 10/02/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
A preceding viral infection of the respiratory tract predisposes the host to secondary bacterial pneumonia, known as a major cause of morbidity and mortality. However, the underlying mechanism of the viral-bacterial synergy that leads to disease progression has remained elusive, thus hampering the production of effective prophylactic and therapeutic intervention options. In addition to viral-induced airway epithelial damage, which allows dissemination of bacteria to the lower respiratory tract and increases their invasiveness, dysfunction of immune defense following a viral infection has been implicated as a factor for enhanced susceptibility to secondary bacterial infections. Given the proximity of the oral cavity to the respiratory tract, where viruses enter and replicate, it is also well-established that oral health status can significantly influence the initiation, progression, and pathology of respiratory viral infections. This review was conducted to focus on the dysfunction of the respiratory barrier, which plays a crucial role in providing physical and secretory barriers as well as immune defense in the context of viral-bacterial synergy. Greater understanding of barrier response to viral-bacterial co-infections, will ultimately lead to development of effective, broad-spectrum therapeutic approaches for prevention of enhanced susceptibility to these pathogens.
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Affiliation(s)
- Tomoko Sumitomo
- Department of Oral Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770–8504, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka 565–0871, Japan
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125
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Raj A, Aggarwal S, Singh P, Yadav AK, Dash D. PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects. Comput Struct Biotechnol J 2024; 23:711-722. [PMID: 38292474 PMCID: PMC10825656 DOI: 10.1016/j.csbj.2023.12.033] [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: 10/04/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Variant peptides resulting from single nucleotide polymorphisms (SNPs) can lead to aberrant protein functions and have translational potential for disease diagnosis and personalized therapy. Variant peptides detected by proteogenomics are fraught with high number of false positives, but there is no uniform and comprehensive approach to assess variant quality across analysis pipelines. Despite class-specific FDR along with ad-hoc filters, the problem is far from solved. These protocols are typically manual and tedious, and thus not uniform across labs. We demonstrate that variant peptide rescoring, integrated with intensity, variant event information and search result features, allows better discrimination of correct variant peptides. Implemented into PgxSAVy - a tool for quality control of variant peptides, this method can tackle the high rate of false positives. PgxSAVy provides a rigorous framework for quality control and annotations of variant peptides on the basis of (i) variant quality, (ii) isobaric masses, and (iii) disease annotation. PgxSAVy demonstrated high accuracy by identifying true variants with 98.43% accuracy on simulated data. Large-scale proteogenomic reanalysis of ∼2.8 million spectra (PXD004010 and PXD001468) resulted in 12,705 variant peptide spectrum matches (PSMs), of which PgxSAVy evaluated 3028 (23.8%), 1409 (11.1%) and 8268 (65.1%) as confident, semi-confident and doubtful respectively. PgxSAVy also annotates the variants based on their pathogenicity and provides support for assisted manual validation. The analysis of proteins carrying variants can provide fine granularity in discovering important pathways. PgxSAVy will advance personalized medicine by providing a comprehensive framework for quality control and prioritization of proteogenomics variants. PgxSAVy is freely available at https://pgxsavy.igib.res.in/ as a webserver and https://github.com/anuragraj/PgxSAVy as a stand-alone tool.
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Affiliation(s)
- Anurag Raj
- G. N. Ramachandran Knowledge Centre for Genomics Informatics, CSIR – Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suruchi Aggarwal
- Computational and Mathematical Biology Centre (CMBC), 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
- Centre for Drug Discovery (CDD), 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
- Centre for Microbial Research (CMR), Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Prateek Singh
- G. N. Ramachandran Knowledge Centre for Genomics Informatics, CSIR – Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amit Kumar Yadav
- Computational and Mathematical Biology Centre (CMBC), 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
- Centre for Drug Discovery (CDD), 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
- Centre for Microbial Research (CMR), Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Debasis Dash
- G. N. Ramachandran Knowledge Centre for Genomics Informatics, CSIR – Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Wen H, Ouyang H, Shang H, Da C, Zhang T. Helix-to-sheet transition of the Aβ42 peptide revealed using an enhanced sampling strategy and Markov state model. Comput Struct Biotechnol J 2024; 23:688-699. [PMID: 38292476 PMCID: PMC10825278 DOI: 10.1016/j.csbj.2023.12.015] [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: 09/11/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 02/01/2024] Open
Abstract
The self-assembly of Aβ peptides into toxic oligomers and fibrils is the primary cause of Alzheimer's disease. Moreover, the conformational transition from helix to sheet is considered a crucial step in the aggregation of Aβ peptides. However, the structural details of this process still remain unclear due to the heterogeneity and transient nature of the Aβ peptides. In this study, we developed an enhanced sampling strategy that combines artificial neural networks (ANN) with metadynamics to explore the conformational space of the Aβ42 peptides. The strategy consists of two parts: applying ANN to optimize CVs and conducting metadynamics based on the resulting CVs to sample conformations. The results showed that this strategy achieved better sampling performance in terms of the distribution of sampled conformations. The sampling efficiency is increased by 10-fold compared to our previous Hamiltonian Exchange Molecular Dynamics (MD) and by 1000-fold compared to ordinary MD. Based on the sampled conformations, we constructed a Markov state model to understand the detailed transition process. The intermediate states in this process are identified, and the connecting paths are analyzed. The conformational transitions in D23-K28 and M35-V40 are proven to be crucial for aggregation. These results are helpful in clarifying the mechanism and process of Aβ42 peptide aggregation. D23-K28 and M35-V40 can be identified as potential targets for screening and designing inhibitors of Aβ peptide aggregation.
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Affiliation(s)
- Huilin Wen
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, PR China
- The Third Hospital of Hebei Medical University, Shijiazhuang 050051, PR China
| | - Hao Ouyang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, PR China
| | - Hao Shang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, PR China
| | - Chaohong Da
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, PR China
| | - Tao Zhang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, PR China
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Zheng F, Jiang X, Wen Y, Yang Y, Li M. Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength. Comput Struct Biotechnol J 2024; 23:460-472. [PMID: 38235359 PMCID: PMC10792694 DOI: 10.1016/j.csbj.2023.12.018] [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: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/19/2024] Open
Abstract
The application of machine learning techniques in biological research, especially when dealing with limited data availability, poses significant challenges. In this study, we leveraged advancements in method development for predicting protein-protein binding strength to conduct a systematic investigation into the application of machine learning on limited data. The binding strength, quantitatively measured as binding affinity, is vital for understanding the processes of recognition, association, and dysfunction that occur within protein complexes. By incorporating transfer learning, integrating domain knowledge, and employing both deep learning and traditional machine learning algorithms, we mitigated the impact of data limitations and made significant advancements in predicting protein-protein binding affinity. In particular, we developed over 20 models, ultimately selecting three representative best-performing ones that belong to distinct categories. The first model is structure-based, consisting of a random forest regression and thirteen handcrafted features. The second model is sequence-based, employing an architecture that combines transferred embedding features with a multilayer perceptron. Finally, we created an ensemble model by averaging the predictions of the two aforementioned models. The comparison with other predictors on three independent datasets confirms the significant improvements achieved by our models in predicting protein-protein binding affinity. The programs for running these three models are available at https://github.com/minghuilab/BindPPI.
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Affiliation(s)
- Feifan Zheng
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Xin Jiang
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Yuhao Wen
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Yan Yang
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Minghui Li
- MOE Key Laboratory of Geriatric Diseases and Immunology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China
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128
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Mansbach P, Fadden JS, McGovern L. Registry and survey of circadian rhythm sleep-wake disorder patients. Sleep Med X 2024; 7:100100. [PMID: 38229915 PMCID: PMC10790090 DOI: 10.1016/j.sleepx.2023.100100] [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: 10/27/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
Objective Circadian Sleep Disorders Network has created a registry of circadian rhythm sleep-wake disorder (CRSWD) patients, and a survey of their experiences. The purpose of the registry is to provide volunteers willing to participate in research; the purpose of the survey is to fill some of the knowledge gaps on these disorders, including information on subjective patient experience and the efficacy and durability of treatments.Researchers are invited to contact Circadian Sleep Disorders Network for permission to use the registry to find potential research participants, and to further analyze the survey data. Patients Over 1627 patients have participated; 1298 have completed the entire survey. Here we present results based on the 479 clinically diagnosed CRSWD patients. Methods The survey covers a variety of topics relating to CRSWDs, including diagnosis, comorbidities, treatments, and work/educational accommodations. Conclusions Results of this survey diverged from much of the literature. More than half the participants reported tiredness even when sleeping on their preferred schedule. While depression may cause sleep problems, our data suggests that sleep/circadian problems often precede depression.There were more people suffering from sighted non-24-hour sleep-wake rhythm disorder than some of the literature would lead us to expect.Current treatments did not appear to be helpful to a large percentage of our participants. Most of them did not find light therapy helpful and nearly all participants who tried phase-delay chronotherapy reported at best only short-term improvement. A sizable proportion of people who tried phase-delay chronotherapy subsequently developed non-24-hour sleep-wake rhythm disorder.
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Affiliation(s)
- Peter Mansbach
- c/o Circadian Sleep Disorders Network, 4619 Woodfield Rd, Bethesda, MD, 20814, USA
| | - James S.P. Fadden
- c/o Circadian Sleep Disorders Network, 4619 Woodfield Rd, Bethesda, MD, 20814, USA
| | - Lynn McGovern
- c/o Circadian Sleep Disorders Network, 4619 Woodfield Rd, Bethesda, MD, 20814, USA
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Msaad S, Abid S, Wadhane I, Gargouri R, Kallel N, Triki F, Moussa N, Kammoun S. May home cardiorespiratory polygraphy be considered a realistic alternative to polysomnography for catathrenia screening? Sleep Med X 2024; 7:100097. [PMID: 38213881 PMCID: PMC10776971 DOI: 10.1016/j.sleepx.2023.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Affiliation(s)
- Sameh Msaad
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Sourour Abid
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Issraa Wadhane
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Rahma Gargouri
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Nesrine Kallel
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Fatma Triki
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Nadia Moussa
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Samy Kammoun
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
- Department of Respiratory and Sleep Medicine, University Hospital Hedi Chaker, Sfax, Tunisia
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Suárez A, Jiménez J, Llorente de Pedro M, Andreu-Vázquez C, Díaz-Flores García V, Gómez Sánchez M, Freire Y. Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery. Comput Struct Biotechnol J 2024; 24:46-52. [PMID: 38162955 PMCID: PMC10755495 DOI: 10.1016/j.csbj.2023.11.058] [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: 11/03/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
AI has revolutionized the way we interact with technology. Noteworthy advances in AI algorithms and large language models (LLM) have led to the development of natural generative language (NGL) systems such as ChatGPT. Although these LLM can simulate human conversations and generate content in real time, they face challenges related to the topicality and accuracy of the information they generate. This study aimed to assess whether ChatGPT-4 could provide accurate and reliable answers to general dentists in the field of oral surgery, and thus explore its potential as an intelligent virtual assistant in clinical decision making in oral surgery. Thirty questions related to oral surgery were posed to ChatGPT4, each question repeated 30 times. Subsequently, a total of 900 responses were obtained. Two surgeons graded the answers according to the guidelines of the Spanish Society of Oral Surgery, using a three-point Likert scale (correct, partially correct/incomplete, and incorrect). Disagreements were arbitrated by an experienced oral surgeon, who provided the final grade Accuracy was found to be 71.7%, and consistency of the experts' grading across iterations, ranged from moderate to almost perfect. ChatGPT-4, with its potential capabilities, will inevitably be integrated into dental disciplines, including oral surgery. In the future, it could be considered as an auxiliary intelligent virtual assistant, though it would never replace oral surgery experts. Proper training and verified information by experts will remain vital to the implementation of the technology. More comprehensive research is needed to ensure the safe and successful application of AI in oral surgery.
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Affiliation(s)
- Ana Suárez
- Department of Pre-Clinic Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
| | - Jaime Jiménez
- Department of Clinic Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
| | - María Llorente de Pedro
- Department of Pre-Clinic Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
| | - Cristina Andreu-Vázquez
- Department of Veterinary Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
| | - Víctor Díaz-Flores García
- Department of Pre-Clinic Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
| | - Margarita Gómez Sánchez
- Department of Pre-Clinic Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
| | - Yolanda Freire
- Department of Pre-Clinic Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Calle Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain
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131
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Sirugue L, Langenfeld F, Lagarde N, Montes M. PLO3S: Protein LOcal Surficial Similarity Screening. Comput Struct Biotechnol J 2024; 26:1-10. [PMID: 38189058 PMCID: PMC10770625 DOI: 10.1016/j.csbj.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: 11/14/2022] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
The study of protein molecular surfaces enables to better understand and predict protein interactions. Different methods have been developed in computer vision to compare surfaces that can be applied to protein molecular surfaces. The present work proposes a method using the Wave Kernel Signature: Protein LOcal Surficial Similarity Screening (PLO3S). The descriptor of the PLO3S method is a local surface shape descriptor projected on a unit sphere mapped onto a 2D plane and called Surface Wave Interpolated Maps (SWIM). PLO3S allows to rapidly compare protein surface shapes through local comparisons to filter large protein surfaces datasets in protein structures virtual screening protocols.
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Affiliation(s)
- Léa Sirugue
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
| | - Florent Langenfeld
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
| | - Nathalie Lagarde
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
| | - Matthieu Montes
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
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Filigheddu MT, Leonelli M, Varando G, Gómez-Bermejo MÁ, Ventura-Díaz S, Gorospe L, Fortún J. Using staged tree models for health data: Investigating invasive fungal infections by aspergillus and other filamentous fungi. Comput Struct Biotechnol J 2024; 24:12-22. [PMID: 38144574 PMCID: PMC10746417 DOI: 10.1016/j.csbj.2023.11.013] [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: 07/30/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/26/2023] Open
Abstract
Machine learning models are increasingly used in the medical domain to study the association between risk factors and diseases to support practitioners in understanding health outcomes. In this paper, we showcase the use of machine-learned staged tree models for investigating complex asymmetric dependence structures in health data. Staged trees are a specific class of generative, probabilistic graphical models that formally model asymmetric conditional independence and non-regular sample spaces. An investigation of the risk factors in invasive fungal infections demonstrates the insights staged trees provide to support medical decision-making.
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Affiliation(s)
- Maria Teresa Filigheddu
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS (Instituto Ramón y Cajal de Investigación Sanitaria); Universidad de Alcalá, Madrid, Spain
| | | | - Gherardo Varando
- Image Processing Laboratory (IPL), Universitat de València, Valencia, Spain
| | | | - Sofía Ventura-Díaz
- Radiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Luis Gorospe
- Radiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Jesús Fortún
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS (Instituto Ramón y Cajal de Investigación Sanitaria); Universidad de Alcalá, Madrid, Spain
- Microbiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
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133
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Xiong X, Gao C, Meng X, Liu A, Gong X, Sun Y. Research progress in stem cell therapy for Wilson disease. Regen Ther 2024; 27:73-82. [PMID: 38525238 PMCID: PMC10959646 DOI: 10.1016/j.reth.2024.03.005] [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: 12/25/2023] [Revised: 02/27/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024] Open
Abstract
Wilson disease (WD), also known as hepatolenticular degeneration, is an autosomal recessive disorder characterized by disorganized copper metabolism caused by mutations in the ATP7B gene. Currently, the main treatment options for WD involve medications such as d-penicillamine, trientine hydrochloride, zinc acetate, and liver transplantation. However, there are challenges that encompass issues of poor compliance, adverse effects, and limited availability of liver sources that persist. Stem cell therapy for WD is currently a promising area of research. Due to the advancement in stem cell directed differentiation technology in vitro and the availability of sufficient stem cell donors, it is expected to be a potential treatment option for the permanent correction of abnormal copper metabolism. This article discusses the research progress of stem cell therapy for WD from various sources, as well as the challenges and future prospects of the clinical application of stem cell therapy for WD.
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Affiliation(s)
- Xianlang Xiong
- Hospital of Hunan Guangxiu, Hunan Normal University, Changsha, 410205, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410205, China
| | - Ce Gao
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410205, China
| | - Xiangying Meng
- Hospital of Hunan Guangxiu, Hunan Normal University, Changsha, 410205, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410205, China
| | - Aihui Liu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410205, China
| | - Xin Gong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410205, China
| | - Yi Sun
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Hospital of Hunan Guangxiu, Hunan Normal University, Changsha, 410205, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410205, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, 410008, China
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134
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Bamba K, Ozawa M, Daitoku H, Kohara A. Diverting the food-freezing technology improves the cryopreservation efficiency of induced pluripotent stem cells and derived neurospheres. Regen Ther 2024; 27:83-91. [PMID: 38525239 PMCID: PMC10957518 DOI: 10.1016/j.reth.2024.03.007] [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: 09/10/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Recent advances in induced pluripotent stem (iPS) technology and regenerative medicine require effective cryopreservation of iPSC-derived differentiated cells and three-dimensional cell aggregates (eg. Spheroids and organoids). Moreover, innovative freezing technologies for keeping food fresh over the long-term rapidly developed in the food industry. Therefore, we examined whether one of such freezing technologies, called "Dynamic Effect Powerful Antioxidation Keeping (DEPAK)," could be effective for the cryopreservation of biological materials. Methods We evaluated the efficiency of cryopreservation using DEPAK and Proton freezers, both of which are used in the food industry, compared with conventional slow-freezing methods using a programmable freezer and a cell-freezing vessel. As they are highly susceptible cells to freeze-thaw damage, we selected two suspension cell lines (KHYG-1 derived from human natural killer cell leukemia and THP-1 derived from human acute monocyte leukemia) and two adherent cell lines (OVMANA derived from human ovarian tumors and HuH-7 derived from human hepatocarcinoma). We used two human iPS cell lines, 201B7-Ff and 1231A3, which were either undifferentiated or differentiated into neurospheres. After freezing using the above methods, the frozen cells and neurospheres were immediately transferred to liquid nitrogen. After thawing, we assessed the cryopreservation efficiency of cell viability, proliferation, neurosphere formation, and neurite outgrowth after thawing. Results Among the four cryopreservation methods, DEPAK freezing resulted in the highest cell proliferation in suspension and adherent cell lines. Similar results were obtained for the cryopreservation of undifferentiated human iPS cells. In addition, we demonstrated that the DEPAK freezing method sustained the neurosphere formation capacity of differentiated iPS cells to the same extent as unfrozen controls. In addition, we observed that DEPAK-frozen neurospheres exhibited higher viability after thawing and underwent neural differentiation more efficiently than slow-freezing methods. Conclusions Our results suggest that diversifying food-freezing technologies can overcome the difficulties associated with the cryopreservation of various biological materials, including three-dimensional cell aggregates.
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Affiliation(s)
- Kenzo Bamba
- JCRB Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Midori Ozawa
- JCRB Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Arihiro Kohara
- JCRB Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
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135
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Zhang R, Wu H. On secondary structure avoidance of codes for DNA storage. Comput Struct Biotechnol J 2024; 23:140-147. [PMID: 38146435 PMCID: PMC10749251 DOI: 10.1016/j.csbj.2023.11.035] [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: 09/23/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/27/2023] Open
Abstract
A secondary structure in single-stranded DNA refers to its propensity to undergo self-folding, leading to functional inactivity and irreparable failures within DNA storage systems. Consequently, the property of secondary structure avoidance (SSA) becomes a crucial criterion in the design of single-stranded DNA sequences for DNA storage, as it prohibits the inclusion of reverse-complement subsequences that contribute to such structures. This work is specifically focused on addressing the avoidance of secondary structures in single-stranded DNA sequences. We propose a novel sequence replacement approach, which successfully resolves the SSA problem under conditions where the stem exceeds a length of 2 log 2 n + 2 , and the loop is of length k ≥ 4 . These parameters have been carefully chosen to closely resemble the real-world scenarios encountered in biochemical processes, enhancing the practical relevance of our study.
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Affiliation(s)
- Rui Zhang
- Chern Institute of Mathematics, Nankai University, Tianjin, 300071, China
| | - Huaming Wu
- Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China
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136
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Dong X, Chen G, Zhu Y, Ma B, Ban X, Wu N, Ming Y. Artificial intelligence in skeletal metastasis imaging. Comput Struct Biotechnol J 2024; 23:157-164. [PMID: 38144945 PMCID: PMC10749216 DOI: 10.1016/j.csbj.2023.11.007] [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: 05/15/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023] Open
Abstract
In the field of metastatic skeletal oncology imaging, the role of artificial intelligence (AI) is becoming more prominent. Bone metastasis typically indicates the terminal stage of various malignant neoplasms. Once identified, it necessitates a comprehensive revision of the initial treatment regime, and palliative care is often the only resort. Given the gravity of the condition, the diagnosis of bone metastasis should be approached with utmost caution. AI techniques are being evaluated for their efficacy in a range of tasks within medical imaging, including object detection, disease classification, region segmentation, and prognosis prediction in medical imaging. These methods offer a standardized solution to the frequently subjective challenge of image interpretation.This subjectivity is most desirable in bone metastasis imaging. This review describes the basic imaging modalities of bone metastasis imaging, along with the recent developments and current applications of AI in the respective imaging studies. These concrete examples emphasize the importance of using computer-aided systems in the clinical setting. The review culminates with an examination of the current limitations and prospects of AI in the realm of bone metastasis imaging. To establish the credibility of AI in this domain, further research efforts are required to enhance the reproducibility and attain robust level of empirical support.
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Affiliation(s)
- Xiying Dong
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Guilin Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Yuanpeng Zhu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Boyuan Ma
- School of Intelligence Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Xiaojuan Ban
- School of Intelligence Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yue Ming
- Department of Nuclear Medicine (PET-CT Center), National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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137
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Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W. Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries. Comput Struct Biotechnol J 2024; 23:87-95. [PMID: 38116074 PMCID: PMC10730331 DOI: 10.1016/j.csbj.2023.11.047] [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: 07/04/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16 S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90 % of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.
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Affiliation(s)
- Yanghao Sheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jue Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yongchao Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Yilei Peng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Xiong Li
- Center for Clinical Precision Pharmacy, School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Center for Clinical Precision Pharmacy, School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
- The First Affifiliated Hospital of Shantou University Medical College, Shantou, China
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education, Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, China
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138
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Han L, Song T, Wang X, Luo Y, Gu C, Li X, Wen J, Wen Z, Shi X. miR-21 Responsive Nanocarrier Targeting Ovarian Cancer Cells. Comput Struct Biotechnol J 2024; 24:196-204. [PMID: 38495121 PMCID: PMC10940798 DOI: 10.1016/j.csbj.2024.02.021] [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: 11/10/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024] Open
Abstract
In recent years, DNA origami-based nanocarriers have been extensively utilized for efficient cancer therapy. However, developing a nanocarrier capable of effectively protecting cargos such as RNA remains a challenge. In this study, we designed a compact and controllable DNA tubular origami (DTO) measuring 120 nm in length and 18 nm in width. The DTO exhibited appropriate structural characteristics for encapsulating and safeguarding cargo. Inside the DTO, we incorporated 20 connecting points to facilitate the delivery of cargoes to various ovarian and normal epithelial cell lines. Specifically, fluorescent-labeled DNA strands were attached to these sites as cargoes. The DTO was engineered to open upon encountering miR-21 through RNA/DNA strand displacement. Significantly, for the first time, we inhibited fluorescence using the compact DNA nanotube and observed dynamic fluorescent signals, indicating the controllable opening of DTO through live-cell imaging. Our results demonstrated that the DTO remained properly closed, exhibited effective internalization in ovarian cancer cells in vitro, showcasing marked differential expression of miR-21, and efficiently opened with short-term exposure to miR-21. Leveraging its autonomous behavior and compact design, the DTO emerges as a promising nanocarrier for various clinically relevant materials. It holds significant application prospects in anti-cancer therapy and the development of flexible biosensors.
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Affiliation(s)
- Liting Han
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tao Song
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Xinyu Wang
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Luo
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuanqi Gu
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan, China
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Xin Li
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinda Wen
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Zhibin Wen
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Xiaolong Shi
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
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139
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Lim W. The test-induced warm-up effect on hamstring flexibility tests. Hong Kong Physiother J 2024; 44:119-125. [PMID: 38510156 PMCID: PMC10949106 DOI: 10.1142/s1013702524500094] [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: 03/12/2023] [Accepted: 10/30/2023] [Indexed: 03/22/2024] Open
Abstract
Background Although the effect of active warm-up (WU) on acute flexibility enhancement is well documented, the test-induced WU effect in muscle length test has not been widely studied. Objective This study aimed to verify the test-induced WU effect on hamstring flexibility tests. Methods The active knee extension (AKE) was performed using the right leg, whereas the straight leg raise (SLR) was performed using the left leg. Ten trials of AKE or SLR were performed: two as the pre-intervention trials (Pre); six as the WU intervention; and another two trials as the post-intervention (Post). During WU, subjects in the WO-Hold group performed six trials of the AKE or SLR without hold, and those in the W-Hold group performed six trials of the AKE or SLR with a 5 s hold. Results A significant difference was noted between Pre-AKE and Post-AKE, and between Pre-SLR and Post-SLR, respectively, in both the groups. The effect of WU is clear when performing consecutive AKE or SLR without any additional hold. Conclusion Practitioners should be cautious in interpreting the testing result to avoid overestimation of the treatment effect since the test itself may induce substantial WU effect to the target tissues.
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Affiliation(s)
- Wootaek Lim
- Department of Physical Therapy, College of Health and Welfare, Woosong University, Daejeon, Republic of Korea
- Department of Digital Bio-Health Convergence, College of Health and Welfare, Woosong University, Daejeon, Republic of Korea
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140
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Musilova J, Vafek Z, Puniya BL, Zimmer R, Helikar T, Sedlar K. Augusta: From RNA-Seq to gene regulatory networks and Boolean models. Comput Struct Biotechnol J 2024; 23:783-790. [PMID: 38312198 PMCID: PMC10837063 DOI: 10.1016/j.csbj.2024.01.013] [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: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of a GRN inferred from expression data is further refined by predicting transcription factor binding motifs in promoters of regulated genes and by incorporating verified interactions obtained from databases. Moreover, a refined GRN is transformed into a draft BN by searching in the curated model database and setting logical rules to incoming edges of target genes, which can be further manually edited as the model is provided in the SBML file format. The approach is applicable even if information about the organism under study is not available in the databases, which is typically the case for non-model organisms including most microbes. Augusta can be operated from the command line and, thus, is easy to use for automated prediction of models for various genomes. The Augusta package is freely available at github.com/JanaMus/Augusta. Documentation and tutorials are available at augusta.readthedocs.io.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno 61600, Czech Republic
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Zdenek Vafek
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
- Institute of Forensic Engineering, Brno University of Technology, Brno 61200, Czech Republic
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Ralf Zimmer
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Tomas Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno 61600, Czech Republic
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
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141
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Chandrashekar PB, Chen H, Lee M, Ahmadinejad N, Liu L. DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements. Comput Struct Biotechnol J 2024; 23:679-687. [PMID: 38292477 PMCID: PMC10825326 DOI: 10.1016/j.csbj.2023.12.044] [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: 08/29/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Gene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate the transcription levels of target genes. To decipher the complicated regulatory network, we present a novel multi-view attention-based deep neural network that models the relationship between genetic, epigenetic, and transcriptional patterns and identifies co-operative regulatory elements (COREs). We applied this new method, named DeepCORE, to predict transcriptomes in various tissues and cell lines, which outperformed the state-of-the-art algorithms. Furthermore, DeepCORE contains an interpreter that extracts the attention values embedded in the deep neural network, maps the attended regions to putative regulatory elements, and infers COREs based on correlated attentions. The identified COREs are significantly enriched with known promoters and enhancers. Novel regulatory elements discovered by DeepCORE showed epigenetic signatures consistent with the status of histone modification marks.
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Affiliation(s)
- Pramod Bharadwaj Chandrashekar
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53076, USA
| | - Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Matthew Lee
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | - Navid Ahmadinejad
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
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142
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Lindly OJ, Wahl TA, Stotts NM, Shui AM. Adaptation of a health literacy screener for computerized, self-administered use by U.S. adults. PEC Innov 2024; 4:100262. [PMID: 38375351 PMCID: PMC10875223 DOI: 10.1016/j.pecinn.2024.100262] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Objective Health literacy is a critical health determinant, for which few computerized, self-administered assessments exist. This study adapted and tested the reliability of the Newest Vital Sign© (NVS) as a computerized, self-administered health literacy screener. Methods Phase one involved 33 participants to create response options for a computerized, self-administered NVS (C-NVS). Phase two was a randomized crossover trial to test the consistency of C-NVS and original, interviewer-administered NVS (I-NVS) scores in 89 participants. Results Linear mixed-effects regression model results showed a significant carryover effect (p < .001). Crossover trial data from time 1 showed that participants who initially received the C-NVS had significantly higher average scores (M = 5.7, SD = 0.6) than participants who received the I-NVS (M = 4.5, SD = 1.5; t(87) = 5.25, p < .001). Exploratory analysis results showed that when the washout period was longer than 33 days (75th percentile) the carryover effect was not statistically significant (p = .077). Conclusion and innovation Findings suggest learning can occur when health literacy screeners are administered more than once in less than a month's time and computerized, self-administered health literacy screeners may produce ceiling effects. A universal precautions approach to health literacy therefore remains germane.
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Affiliation(s)
| | - Taylor A. Wahl
- Department of Health Sciences, Northern Arizona University, USA
| | - Noa M. Stotts
- Department of Biological Sciences, Northern Arizona University, USA
| | - Amy M. Shui
- Massachusetts General Hospital Biostatistics Center, USA
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143
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Brown SD, Garcia BL, Ritchie JL, Tsai AL, Millman A, Greenberg M, Quesenberry CP, Ferrara A. Digital health outreach to promote postpartum screening after gestational diabetes: A randomized factorial pilot study. PEC Innov 2024; 4:100256. [PMID: 38282680 PMCID: PMC10818066 DOI: 10.1016/j.pecinn.2024.100256] [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] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 12/18/2023] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
Objective We examined the acceptability and feasibility of a multi-component digital health outreach intervention to promote uptake of guideline-recommended postpartum screening for type 2 diabetes among patients with gestational diabetes (GDM). Methods We conducted a 24 randomized factorial experiment as part of the Multiphase Optimization Strategy (MOST) preparation phase for developing behavioral interventions. Participants with current or recent GDM in an integrated healthcare system were randomized to receive an outreach message with up to four intervention components, designed to be self-administered in about 10 min and efficiently delivered online via REDCap: a streamlined values affirmation, personalized information on diabetes risk, an interactive motivational interviewing-based component, and an interactive action planning component. Patient-reported acceptability and feasibility outcomes were assessed via survey. Results Among 162 participants, 72% self-identified with a racial/ethnic minority group. Across components, acceptability scores averaged 3.9/5; ≥91% of participants read most or all of the outreach message; ≥89% perceived the amount of information as "about right"; and ≥ 87% completed ≥1 interactive prompt. Conclusion Each intervention component was acceptable to diverse patients and feasible to deliver in a brief, self-directed, online format. Innovation These novel components target unaddressed barriers to patient engagement in guideline-recommended postpartum diabetes screening and adapt theory-based behavior change techniques for large-scale use.
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Affiliation(s)
- Susan D. Brown
- Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Brittany L. Garcia
- Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
| | - Jenna L. Ritchie
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Ai-Lin Tsai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Andrea Millman
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mara Greenberg
- Regional Perinatal Service Center, Kaiser Permanente Northern California, Oakland, CA, USA
| | | | - Assiamira Ferrara
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
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144
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Senger A, Venetis MK, Greene K, Catona D, Devine KA. Healthcare provider assessments of caregiver communication behaviors during gynecologic Cancer treatment appointments. PEC Innov 2024; 4:100259. [PMID: 38347863 PMCID: PMC10859277 DOI: 10.1016/j.pecinn.2024.100259] [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: 11/01/2023] [Revised: 12/28/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024]
Abstract
Objective Caregivers often accompany patients to cancer-related medical appointments. Limited research exists on healthcare providers' (HCPs) evaluation of how caregiver communication influences interactions between healthcare providers and patients, particularly during gynecologic treatment visits. HCPs may perceive caregiver communication as helpful or challenging, and these triadic interactions may influence patient outcomes. Methods Interviews with ten cancer specialist HCPs (medical assistants/technicians, nurse practitioners/registered nurses, oncologists) addressed experiences interacting with patients and caregivers. Results Analyses revealed two themes concerning helpful communication: caregivers managing information and managing patient emotions. Three challenging themes include caregiver communication unsettling healthcare interactions, caregiver presence limiting patient communication, and caregiver engagement challenges. Conclusion HCPs evaluate caregiver communication as helpful and challenging. Findings suggest benefits of communication training for gynecologic cancer patients such as requesting privacy when interacting with HCPs, for caregivers to promote awareness of effects of their behavior, and for HCPs to help manage triadic interactions while supporting patient needs. Innovation HCP assessment of caregiver communication during gynecologic treatment visits offers unique insights regarding helpful and challenging behaviors contributing to implications for patient care and well-being. Applications may extend to other triadic interactions and cancer settings.
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Affiliation(s)
- Angela Senger
- Rutgers, The State University of New Jersey, Department of Communication, 4 Huntington Street, New Brunswick, NJ 08901, USA
- Rutgers Cancer Institute of New Jersey, Department of Pediatric Population Science, Outcomes, and Disparities Research, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Maria K. Venetis
- Rutgers, The State University of New Jersey, Department of Communication, 4 Huntington Street, New Brunswick, NJ 08901, USA
| | - Kathryn Greene
- Rutgers, The State University of New Jersey, Department of Communication, 4 Huntington Street, New Brunswick, NJ 08901, USA
| | - Danielle Catona
- University of Maryland, School of Public Health, 4200 Valley Drive, Suite 2242, College Park, MD 20742-2611, USA
| | - Katie A. Devine
- Rutgers Cancer Institute of New Jersey, Department of Pediatric Population Science, Outcomes, and Disparities Research, 195 Little Albany Street, New Brunswick, NJ 08901, USA
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145
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Wang X, Song Z, Chen X, Zhou Y, Lou Y, Liu T, Zhang D. Rapid cycle deliberate practice: application in forceps simulation training for gynecology and obstetrics residents. Ann Med 2024; 56:2301596. [PMID: 38478750 PMCID: PMC10939101 DOI: 10.1080/07853890.2023.2301596] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 12/17/2023] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Rapid Cycle Deliberate Practice (RCDP) has gained prominence in recent years as an innovative teaching method in simulation-based training for adult and pediatric emergency medical skills. However, its application in the training of forceps delivery skills among obstetrics and gynecology residents remains unexplored. This study aimed to assess the impact of RCDP in this domain. METHODS Conducted in March 2021, this randomized controlled study involved 60 second-year obstetrics and gynecology residents undergoing standardized training. Participants were randomly assigned to the RCDP group or the traditional teaching method (TTM) group, each comprising 30 residents. The RCDP group followed the RCDP practice mode, while the TTM group adhered to conventional simulation teaching. Post-training assessment of operational proficiency was conducted immediately and after one year. Independent operational confidence and training satisfaction were evaluated through questionnaire surveys and the Satisfaction with Simulation Experience (SSE) scale. Data analysis utilized SPSS 23.0. RESULTS The RCDP group displayed significantly higher immediate post-training forceps operation scores compared to the TTM group (92.00 [range: 90.00-94.00] vs. 88.00 [range: 86.75-92.00]; z = 3.79; p < .001). However, no significant difference emerged in forceps operation scores after one year (86.00 [range: 85.00-88.00] vs. 85.50 [range: 84.00-88.25]; z = 0.54; p = .59). The RCDP group exhibited notable performance improvement over the TTM group (z = 3.49; p < .001). Independent operation confidence showed no significant discrepancy (p > .05). Importantly, the RCDP group reported higher satisfaction scores, particularly in the Debriefing and Reflection subscale (44.00 [range: 43.00-45.00] vs. 41.00 [range: 41.50-43.00]; z = 5.24; p < .001), contributing to an overall superior SSE score (z = 4.74; p < .001). CONCLUSIONS RCDP exhibits immediate efficacy in elevating forceps delivery skills among residents. However, sustained skill enhancement necessitates innovative approaches, while RCDP's value lies in tailored feedback and reflection for enriched medical education.
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Affiliation(s)
- Xiaoxue Wang
- Department of Health Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zixuan Song
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xueting Chen
- Department of Health Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yangzi Zhou
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yingze Lou
- Department of Health Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tong Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dandan Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
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Ruiz-Sánchez R, Arencibia-Jorge R, Tagüeña J, Jiménez-Andrade JL, Carrillo-Calvet H. Exploring research on ecotechnology through artificial intelligence and bibliometric maps. Environ Sci Ecotechnol 2024; 21:100386. [PMID: 38328508 PMCID: PMC10848037 DOI: 10.1016/j.ese.2023.100386] [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: 07/05/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 02/09/2024]
Abstract
Ecotechnology, quintessential for crafting sustainable socio-environmental strategies, remains tantalizingly uncharted. Our analysis, steered by the nuances of machine learning and augmented by bibliometric insights, delineates the expansive terrain of this domain, elucidates pivotal research themes and conundrums, and discerns the vanguard nations in this field. Furthermore, we deftly connect our discoveries to the United Nations' 2030 Sustainable Development Goals, thereby accentuating the profound societal ramifications of ecotechnology.
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Affiliation(s)
- Ricardo Ruiz-Sánchez
- Unidad Profesional Interdisciplinaria de Ingeniería Palenque (UPIIP), Instituto Politécnico Nacional, Palenque, Chiapas, CP 29960, Mexico
- Complexity Sciences Center, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
| | - Ricardo Arencibia-Jorge
- Complexity Sciences Center, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
| | - Julia Tagüeña
- Complexity Sciences Center, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
- Institute of Renewable Energies (IER), National Autonomous University of Mexico, Priv. Xochicalco s/n, Col. Centro, Temixco, Morelos, CP 62580, Mexico
| | - José Luis Jiménez-Andrade
- Complexity Sciences Center, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
- Faculty of Sciences, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
| | - Humberto Carrillo-Calvet
- Complexity Sciences Center, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
- Faculty of Sciences, National Autonomous University of Mexico, Circuito Centro Cultural s/n, Coyoacan, 04510, Mexico City, Mexico
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147
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Feng C, Bonetti L, Lu H, Zhou Z, Lotti T, Jia M, Rizzardi G, De Nardo L, Malpei F. Extracellular polymeric substances as paper coating biomaterials derived from anaerobic granular sludge. Environ Sci Ecotechnol 2024; 21:100397. [PMID: 38434491 PMCID: PMC10904903 DOI: 10.1016/j.ese.2024.100397] [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: 07/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 03/05/2024]
Abstract
Recovering extracellular polymeric substances (EPS) from waste granular sludge offers a cost-effective and sustainable approach for transforming wastewater resources into industrially valuable products. Yet, the application potential of these EPS in real-world scenarios, particularly in paper manufacturing, remains underexplored. Here we show the feasibility of EPS-based biomaterials, derived from anaerobic granular sludges, as novel coating agents in paper production. We systematically characterised the rheological properties of various EPS-based suspensions. When applied as surface sizing agents, these EPS-based biomaterials formed a distinct, ultra-thin layer on paper, as evidenced by scanning electron microscopy. A comprehensive evaluation of water and oil penetration, along with barrier properties, revealed that EPS-enhanced coatings markedly diminished water absorption while significantly bolstering oil and grease resistance. Optimal performance was observed in EPS variants with elevated protein and hydrophobic contents, correlating with their superior rheological characteristics. The enhanced water-barrier and grease resistance of EPS-coated paper can be attributed to its non-porous, fine surface structure and the functional groups in EPS, particularly the high protein content and hydrophobic humic-like substances. This research marks the first demonstration of utilizing EPS from anaerobic granular sludge as paper-coating biomaterials, bridging a critical knowledge gap in the sustainable use of biopolymers in industrial applications.
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Affiliation(s)
- Cuijie Feng
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133, Milan, Italy
- School of Civil Engineering, Sun Yat-sen University, 519082, Zhuhai, China
| | - Lorenzo Bonetti
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli, 7, 20131, Milan, Italy
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, 510275, Guangzhou, China
| | - Zhongbo Zhou
- Southwest University, College of Resources and Environment, Tiansheng Road 2, Beibei District, 400716, Chongqing, China
| | - Tommaso Lotti
- Civil and Environmental Engineering Department, University of Florence, Via di Santa Marta 3, 50139, Florence, Italy
| | - Mingsheng Jia
- Center for Microbial Ecological and Technology (CMET), Ghent University, Coupure Links 653, Gent, Belgium
| | - Giacomo Rizzardi
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133, Milan, Italy
| | - Luigi De Nardo
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli, 7, 20131, Milan, Italy
| | - Francesca Malpei
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133, Milan, Italy
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148
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Lv Q, Yang Z, Chen Z, Li M, Gao B, Yang J, Chen X, Xu B. Crop residue burning in China (2019-2021): Spatiotemporal patterns, environmental impact, and emission dynamics. Environ Sci Ecotechnol 2024; 21:100394. [PMID: 38357480 PMCID: PMC10864837 DOI: 10.1016/j.ese.2024.100394] [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: 07/03/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Crop residue burning (CRB) is a major contributor to air pollution in China. Current fire detection methods, however, are limited by either temporal resolution or accuracy, hindering the analysis of CRB's diurnal characteristics. Here we explore the diurnal spatiotemporal patterns and environmental impacts of CRB in China from 2019 to 2021 using the recently released NSMC-Himawari-8 hourly fire product. Our analysis identifies a decreasing directionality in CRB distribution in the Northeast and a notable southward shift of the CRB center, especially in winter, averaging an annual southward movement of 7.5°. Additionally, we observe a pronounced skewed distribution in daily CRB, predominantly between 17:00 and 20:00. Notably, nighttime CRB in China for the years 2019, 2020, and 2021 accounted for 51.9%, 48.5%, and 38.0% respectively, underscoring its significant environmental impact. The study further quantifies the hourly emissions from CRB in China over this period, with total emissions of CO, PM10, and PM2.5 amounting to 12,236, 2,530, and 2,258 Gg, respectively. Our findings also reveal variable lag effects of CRB on regional air quality and pollutants across different seasons, with the strongest impacts in spring and more immediate effects in late autumn. This research provides valuable insights for the regulation and control of diurnal CRB before and after large-scale agricultural activities in China, as well as the associated haze and other pollution weather conditions it causes.
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Affiliation(s)
- Qiancheng Lv
- Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Zeyu Yang
- Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Ziyue Chen
- Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Manchun Li
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Bingbo Gao
- College of Land Science and Technology, China Agriculture University, Beijing, 100083, China
| | - Jing Yang
- Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xiao Chen
- Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Bing Xu
- Department of Earth System Science, Tsinghua University, Beijing, 100084, China
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149
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Xue B, Tian L, Liu Y, Peng L, Iqbal W, Li L, Mao Y. Enhanced nitrate reduction in hypotrophic waters with integrated photocatalysis and biodegradation. Environ Sci Ecotechnol 2024; 21:100390. [PMID: 38328509 PMCID: PMC10847995 DOI: 10.1016/j.ese.2024.100390] [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: 05/28/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 02/09/2024]
Abstract
Addressing nitrate contamination in water bodies is a critical environmental challenge, and Intimately Coupling Photocatalysis and Biodegradation (ICPB) presents a promising solution. However, there is still debate about the effectiveness of ICPB in reducing nitrate under hypotrophic conditions. Further research is needed to understand its microbial metabolic mechanism and the functional changes in bacterial structure. Here we explored microbial metabolic mechanisms and changes in bacterial structure in ICPB reactors integrating a meticulously screened TiO2/g-C3N4 photocatalyst with biofilm. We achieved a 26.3% increase in nitrate reduction using 12.2% less organic carbon compared to traditional biodegradation methods. Metagenomic analysis of the microbial communities in ICPB reactors revealed evolving metabolic pathways conducive to nitrate reduction. This research not only elucidates the photocatalytic mechanism behind nitrate reduction in hypotrophic conditions but also provides genomic insights that pave the way for alternative approaches in water remediation technologies.
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Affiliation(s)
- Bingjie Xue
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, PR China
| | - Li Tian
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, PR China
| | - Yaqi Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, PR China
| | - Lingxiu Peng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, PR China
| | - Waheed Iqbal
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Liangzhong Li
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, PR China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, PR China
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150
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Yan Z, Feng C, Xu Y, Wang J, Huang N, Jin X, Wu F, Bai Y. Water temperature governs organophosphate ester dynamics in the aquatic food chain of Poyang Lake. Environ Sci Ecotechnol 2024; 21:100401. [PMID: 38487363 PMCID: PMC10937237 DOI: 10.1016/j.ese.2024.100401] [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: 07/14/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 03/17/2024]
Abstract
Organophosphate esters (OPEs) are increasingly recognized as pervasive environmental contaminants, primarily from their extensive application in flame retardants and plasticizers. Despite their widespread presence, the intricacies of OPE bioaccumulation within aquatic ecosystems remain poorly understood, particularly the environmental determinants influencing their distribution and the bioaccumulation dynamics across aquatic food chains. Here we show that water temperature plays a crucial role in modulating the dispersion of OPE in the aquatic environment of Poyang Lake. We quantified OPE concentrations across various matrices, uncovering levels ranging from 0.198 to 912.622 ng L-1 in water, 0.013-493.36 ng per g dry weight (dw) in sediment, 0.026-41.92 ng per g wet weight (ww) in plankton, 0.13-2100.72 ng per g dw in benthic invertebrates, and 0.31-3956.49 ng per g dw in wild fish, highlighting a pronounced bioaccumulation gradient. Notably, the intestines emerged as the principal site for OPE absorption, displaying the highest concentrations among the seven tissues examined. Among the various OPEs, tris(chloroethyl) phosphate was distinguished by its significant bioaccumulation potential within the aquatic food web, suggesting a need for heightened scrutiny. The propensity for OPE accumulation was markedly higher in benthic invertebrates than wild fish, indicating a differential vulnerability within aquatic biota. This study lays a foundational basis for the risk assessment of OPEs as emerging contaminants and underscores the imperative to prioritize the examination of bioaccumulation effects, particularly in benthic invertebrates, to inform future environmental safeguarding strategies.
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Affiliation(s)
- Zhenfei Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Chenglian Feng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yiping Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jindong Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Nannan Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiaowei Jin
- China National Environmental Monitoring Centre, Beijing, 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Yingchen Bai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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