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Khijmatgar S, Yong J, Rübsamen N, Lorusso F, Rai P, Cenzato N, Gaffuri F, Del Fabbro M, Tartaglia GM. Salivary biomarkers for early detection of oral squamous cell carcinoma (OSCC) and head/neck squamous cell carcinoma (HNSCC): A systematic review and network meta-analysis. Jpn Dent Sci Rev 2024; 60:32-39. [PMID: 38204964 PMCID: PMC10776379 DOI: 10.1016/j.jdsr.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/21/2023] [Accepted: 10/26/2023] [Indexed: 01/12/2024] Open
Abstract
Oral cancer became a very common condition. WHO estimates that there are 4 cases of lip and oral cavity cancer for every 100,000 people worldwide. The early diagnosis of cancers is currently a top focus in the health sector. Recent systematic reviews and meta-analyses have identified promising biomarkers for early detection in several original research investigations. However, it is still unclear the quality of these evidence and which biomarker performs the best in terms of early detection. Therefore, the objective was, to map the methodological and reporting quality of available oral squamous cell carcinoma (OSCC) or head/neck squamous cell carcinoma (HNSCC) systematic reviews and meta-analysis. Secondly, to evaluate diagnostic accuracy of salivary biomarkers for common craniofacial cancers and to compare the diagnostic value of different salivary biomarkers. PubMed, Scopus, Web of Science, Embase and Cochrane Library electronic databases were used to map the methodological and reporting quality of the systematic reviews and meta-analysis conducted on the HNSCC, OSCC using the AMSTAR-2 checklist. The inclusion criteria were systematic reviews and meta-analysis published in the topic of HNSCC and OSCC biomarkers. Exclusion criteria were no animal studies; original primary studies, due to limitation of competency in other languages articles with language other than English were excluded. The sensitivity and specificity were calculated for salivary biomarkers and ranked according to network meta-analysis principles. A total of N = 5893 patients were included from four meta-analysis studies. All together, these included n = 37 primary studies. n = 94 biomarkers were pooled from these four meta-analyses and categorised into the stages at which they were detected (I-IV). In OSCC, Chemerin and MMP-9 displayed the highest sensitivity, registering 0.94 (95% CI 0.78, 1.00) and a balanced accuracy of 0.93. Phytosphingosine closely followed, with a sensitivity of 0.91 (95% CI 0.68, 0.99) and a balanced accuracy of 0.87. For HNSCC, the top three biomarkers are Actin, IL-1β Singleplex, and IL-8 ELISA. Actin leads with a sensitivity of 0.91 (95% CI 0.68-0.99), a specificity of 0.67, and an overall accuracy of 0.79. Subsequently, IL-1β Singleplex exhibits a sensitivity of 0.62 (95% CI 0.30-0.88), a specificity of 0.89, and an accuracy of 0.75, followed by IL-8 ELISA with a sensitivity of 0.81 (95% CI 0.54-0.97), a specificity of 0.59, and an accuracy of 0.70. In conclusion, there was highest sensitivity for MMP-9 and chemerin salivary biomarkers. There is need of further more studies to identify biomarkers for HNSCC and OSCC.
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Affiliation(s)
- Shahnawaz Khijmatgar
- SC Chirurgia Maxillo-Facciale e Odontostomatologia, Fondazione Ca’Granda IRCCS Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Josh Yong
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
- Harvard School of Dental Medicine, USA
| | - Nicole Rübsamen
- Institute of Epidemiology and Social Medicine, University of Münster, Germany
| | - Felice Lorusso
- Università degli Studi G. d'Annunzio Chieti - Pescara: Chieti, Abruzzi, Italy
| | - Pooja Rai
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Niccolo Cenzato
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Franscesca Gaffuri
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - Massimo Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
- SC Chirurgia Maxillo-Facciale e Odontostomatologia, Fondazione Ca’Granda IRCCS Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Gianluca Martino Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
- SC Chirurgia Maxillo-Facciale e Odontostomatologia, Fondazione Ca’Granda IRCCS Ospedale Maggiore Policlinico, Milan 20122, Italy
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Stokes SM, Haider M, Vadaparampil ST, Levitt C, Hardy O, Kim R, Castillo DL, Denbo J, Fleming JB, Anaya DA. Patient's informational needs and outreach preferences: A cross-sectional survey study in patients with hepatobiliary malignancies. PEC Innov 2024; 4:100248. [PMID: 38292078 PMCID: PMC10825679 DOI: 10.1016/j.pecinn.2023.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Objective Hepatobiliary tumors have evolving management guidelines. Patient educational needs and interest in community engagement are unknown. This study serves as a needs assessment. Methods A prospective, needs assessment, survey study of hepatobiliary patients was performed (2016-2019). Surveys (n = 169) were distributed covering three domains of interest: informational needs, interest in outreach, and engagement preferences. Results Seventy patients completed the survey (response rate = 41.4%). Most patients had completed surgical treatment (84.3%). Cancer treatment was ranked as their primary topic of interest (n = 39, 55.7bold%), followed by symptom management, nutrition, and survivorship. Most patients did not participate in screening (n = 57, 81.4%), though were interested in learning more about these programs. Thirty-nine patients (55.7%) stated they would want to receive more education. Only 17 (24.3%) were interested in attending in-person events. Patients preferred online methods for education (n = 49, 70%). While patients were aware of their case presentation at tumor board, only 38 (54.3%) felt well-informed about recommendations. Conclusion Multidisciplinary care is complex and difficult for patients to navigate. Most patients have interest in educational resources and prefer online modalities. Patients understand multidisciplinary tumor boards, but communication could be improved. Innovation These data inform a new, innovative, approach to outreach efforts in this population.
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Affiliation(s)
- Sean M. Stokes
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Mintallah Haider
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Susan T. Vadaparampil
- Office of Community Outreach Engagement & Equity, H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States
| | - Catherine Levitt
- Morsani College of Medicine, University of South Florida, 560 Channelside Drive, Tampa, FL 33602, United States
| | - Olivia Hardy
- Morsani College of Medicine, University of South Florida, 560 Channelside Drive, Tampa, FL 33602, United States
| | - Richard Kim
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Diana L. Castillo
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Jason Denbo
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Jason B. Fleming
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Daniel A. Anaya
- Department of GI Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
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Santos IS, Echevarria P, Tovo-Rodrigues L, Matijasevich A, Domingues MR, Hallal PC. Are nocturnal awakenings at age 1 predictive of sleep duration and efficiency at age 6: Results from two birth cohorts. Sleep Med X 2024; 7:100105. [PMID: 38312370 PMCID: PMC10837084 DOI: 10.1016/j.sleepx.2024.100105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024] Open
Abstract
Objective To investigate the association of nighttime awakenings at 12 months with the duration and efficiency of nighttime sleep at 6 years of age. Methods Data from two population-based prospective studies (The Pelotas 2004 and The Pelotas 2015 Birth Cohorts) were used. Information on nighttime awakenings was provided by mothers during the 12-month follow-up interview. Infants who awakened >3 times after sleep onset at 12 months were considered frequent wakeners. Sleep duration and sleep efficiency were obtained by actigraphy at the 6-year follow-up. Children wore the device at the wrist of the non-dominant arm continuously for 3-7 days, including at least one weekend day. Unadjusted and adjusted beta coefficients were obtained by linear regression for each cohort separately. Results 2500 children from the 2004 and 2793 from the 2015 cohort had full information on nighttime awakenings at 12 months and actigraphy at 6 years and were analyzed. Prevalence of frequent wakeners was 6.3 % and 5.9 % in the 2004 and 2015 cohort, respectively. Mean bedtime and wake-up time at 6 years were, respectively, 23:23 and 08:41 h in the 2004 cohort, and 00:10 and 09:00 h int the 2015 cohort. Nighttime sleep lasted on average 7.54 and 7.24 h respectively in the 2004 and the 2015 cohort, and the sleep efficiency was 81.1 and 82.5 % respectively. In adjusted analyses, no associations were found between awakening at 12 months and sleep duration or sleep efficiency at 6 years of age. Conclusion In both cohorts sleep duration and efficiency were below the recommendation for school-age children (respectively 9-11 h and 85 %). There was no relationship between the number of nighttime awakenings at 12 months and sleep duration or efficiency at 6 years.
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Affiliation(s)
- Ina S. Santos
- Post-graduate Program in Epidemiology, Federal University of Pelotas, Brazil
| | - Priscila Echevarria
- Post-graduate Program in Epidemiology, Federal University of Pelotas, Brazil
| | | | - Alicia Matijasevich
- Departamento de Medicina Preventiva, Faculdade de Medicina FMUSP, Universidade de São Paulo, SP, Brazil
| | - Marlos R. Domingues
- Post-graduate Program in Physical Education, Federal University of Pelotas, Brazil
| | - Pedro C. Hallal
- Post-graduate Program in Epidemiology, Federal University of Pelotas, Brazil
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Zhu Z, Cao H, Yan H, Liu H, Hong Z, Sun A, Liu T, Mao F. Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma. Comput Struct Biotechnol J 2024; 23:929-941. [PMID: 38375529 PMCID: PMC10875160 DOI: 10.1016/j.csbj.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Cancer immunotherapy has shown to be a promising method in treating hepatocellular carcinoma (HCC), but suboptimal responses in patients are attributed to cellular and molecular heterogeneity. Iron metabolism-related genes (IRGs) are important in maintaining immune system homeostasis and have the potential to help develop new strategies for HCC treatment. Herein, we constructed and validated the iron-metabolism gene prognostic index (IPX) using univariate Cox proportional hazards regression and LASSO Cox regression analysis, successfully categorizing HCC patients into two groups with distinct survival risks. Then, we performed single-sample gene set enrichment analysis, weighted correlation network analysis, gene ontology enrichment analysis, cellular lineage analysis, and SCENIC analysis to reveal the key determinants underlying the ability of this model based on bulk and single-cell transcriptomic data. We identified several driver transcription factors specifically activated in specific malignant cell sub-populations to contribute to the adverse survival outcomes in the IPX-high subgroup. Within the tumor microenvironment (TME), T cells displayed significant diversity in their cellular characteristics and experienced changes in their developmental paths within distinct clusters identified by IPX. Interestingly, the proportion of Treg cells was increased in the high-risk group compared with the low-risk group. These results suggest that iron-metabolism could be involved in reshaping the TME, thereby disrupting the cell cycle of immune cells. This study utilized IRGs to construct a novel and reliable model, which can be used to assess the prognosis of patients with HCC and further clarify the molecular mechanisms of IRGs in HCC at single-cell resolution.
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Affiliation(s)
- Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Huang Cao
- School of Medicine, Xiamen University, Xiamen, Fujian 361100, China
| | - Hongyu Yan
- School of Medicine, Xiamen University, Xiamen, Fujian 361100, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Hanzhi Liu
- The Third Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Zaifa Hong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361103, China
| | - Anran Sun
- Oncology Research Center, Foresea Life Insurance Guangzhou General Hospital, Guangzhou, Guangdong 511300, China
- Research Center for Translational Medicine, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, China
| | - Tong Liu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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Zelenski AB, Haug K, Bushaw KJ, Buffington A, Bradley T, Kwekkeboom KL, Stalter L, Hanlon BM, Wakeen MJ, Jhagroo RA, Maursetter LJ, Johnson SK, Campbell TC, Schwarze ML. Embedding an Education Intervention about Shared Decision Making into an RCT: Ensuring competency and fidelity. PEC Innov 2024; 4:100260. [PMID: 38347862 PMCID: PMC10859294 DOI: 10.1016/j.pecinn.2024.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/21/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024]
Abstract
Objective To describe the outcomes of training nephrology clinicians and clinical research participants, to use the Best Case/Worst Case Communication intervention, for discussions about dialysis initiation for patients with life-limiting illness, during a randomized clinical trial to ensure competency, fidelity to the intervention, and adherence to study protocols and the intervention throughout the trial. Methods We enrolled 68 nephrologists at ten study sites and randomized them to receive training or wait-list control. We collected copies of completed graphic aids (component of the intervention), used with study-enrolled patients, to measure fidelity and adherence. Results We trained 34 of 36 nephrologists to competence and 27 completed the entire program. We received 60 graphic aids for study-enrolled patients for a 73% return rate in the intervention arm. The intervention fidelity score for the graphic aid reflected completion of all elements throughout the study. Conclusion We successfully taught the Best Case/Worst Case Communication intervention to clinicians as research participants within a randomized clinical trial. Innovation Decisions about dialysis are an opportunity to discuss prognosis and uncertainty in relation to consideration of prolonged life supporting therapy. Our study reveals a strategy to evaluate adherence to a communication intervention in real time during a clinical study.
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Affiliation(s)
- Amy B. Zelenski
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Karlie Haug
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Kyle J. Bushaw
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Anne Buffington
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Taylor Bradley
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | | | - Lily Stalter
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - Bret M. Hanlon
- Department of Surgery, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI, USA
| | | | - Roy A. Jhagroo
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | | | - Sara K. Johnson
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Toby C. Campbell
- Department of Medicine, University of Wisconsin, Madison, WI, USA
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Zanwar R, Wani S. Reliability and validity of modified upper limb neurodynamic tests in patients with cervical radiculopathy. Hong Kong Physiother J 2024; 44:137-146. [PMID: 38510155 PMCID: PMC10949103 DOI: 10.1142/s1013702524500112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/23/2023] [Indexed: 03/22/2024] Open
Abstract
Background Neurodynamic Tests (NDTs) are used to assess neural mechanosensitivity in various conditions such as neural sliding, tension or inflammatory dysfunction. But in some upper quadrant dysfunctions, standard testing procedure of NDT cannot be assessed or tolerated by patient. Objective The purpose of the study was to determine the validity, intra-rater and inter-rater reliability of modified NDTs via median and ulnar nerve in patients with cervical radiculopathy. Methods Thirty-three patients (18 men and 15 women, mean age ± SD - 40 . 18 ± 9 . 01 ) with cervical radiculopathy having positive response to standard NDTs were included in the study. Modified neurodynamic tests for median & ulnar nerve were performed with modification in the sequencing of standard neurodynamic test at lower degrees of glenohumeral abduction and external rotation. Outcome measures used were angle of elbow extension for median nerve and angle elbow flexion for ulnar nerve at the point of pain onset indicated by "OP" (Onset of Pain). Results Reliability of OP was evaluated using measurement of Intra-class Correlation Coefficient (ICC), Standard Error of Measurement (SEM) and Minimal Detectable Change (MDC) values. Results indicated high ICC values and low SEM values for OP during modified median and modified ulnar NDTs (M-MNT1 and M-UNT) on symptomatic side of patients with cervical radiculopathy. Spearman correlation analysis for validity of test score showed strong correlation (r = 0 . 767 ) with standard NDT. Conclusion There was strong correlation between Modified NDTs and standard tests depicting good validity and substantial reliability of OP during M-MNT1 and M-UNT for positive NDT response in patients with cervical radiculopathy.
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Affiliation(s)
- Rupa Zanwar
- Department of Musculoskeletal Physiotherapy, MGM Institute of Physiotherapy, Aurangabad, Maharashtra, India
| | - Surendra Wani
- Department of Musculoskeletal Physiotherapy, MGM Institute of Physiotherapy, Aurangabad, Maharashtra, India
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Wang L, Zeng Z, Xue Z, Wang Y. DeepNeuropePred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model. Comput Struct Biotechnol J 2024; 23:309-315. [PMID: 38179071 PMCID: PMC10764246 DOI: 10.1016/j.csbj.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: 08/28/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024] Open
Abstract
Neuropeptides play critical roles in many biological processes such as growth, learning, memory, metabolism, and neuronal differentiation. A few approaches have been reported for predicting neuropeptides that are cleaved from precursor protein sequences. However, these models for cleavage site prediction of precursors were developed using a limited number of neuropeptide precursor datasets and simple precursors representation models. In addition, a universal method for predicting neuropeptide cleavage sites that can be applied to all species is still lacking. In this paper, we proposed a novel deep learning method called DeepNeuropePred, using a combination of pre-trained language model and Convolutional Neural Networks for feature extraction and predicting the neuropeptide cleavage sites from precursors. To demonstrate the model's effectiveness and robustness, we evaluated the performance of DeepNeuropePred and four models from the NeuroPred server in the independent dataset and our model achieved the highest AUC score (0.916), which are 6.9%, 7.8%, 8.8%, and 10.9% higher than Mammalian (0.857), insects (0.850), Mollusc (0.842) and Motif (0.826), respectively. For the convenience of researchers, we provide a web server (http://isyslab.info/NeuroPepV2/deepNeuropePred.jsp).
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Affiliation(s)
- Lei Wang
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zilu Zeng
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, China
| | - Zhidong Xue
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Wang
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong 264003, China
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Gao P, Kajiya M, Motoike S, Ikeya M, Yang J. Application of mesenchymal stem/stromal cells in periodontal regeneration: Opportunities and challenges. Jpn Dent Sci Rev 2024; 60:95-108. [PMID: 38314143 PMCID: PMC10837070 DOI: 10.1016/j.jdsr.2024.01.001] [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: 08/08/2023] [Revised: 12/06/2023] [Accepted: 01/15/2024] [Indexed: 02/06/2024] Open
Abstract
Guided tissue regeneration (GTR) has been widely used in the periodontal treatment of intrabony and furcation defects for nearly four decades. The treatment outcomes have shown effectiveness in reducing pocket depth, improving attachment gain and bone filling in periodontal tissue. Although applying GTR could reconstruct the periodontal tissue, the surgical indications are relatively narrow, and some complications and race ethic problems bring new challenges. Therefore, it is challenging to achieve a consensus concerning the clinical benefits of GTR. With the appearance of stem cell-based regenerative medicine, mesenchymal stem/stromal cells (MSCs) have been considered a promising cell resource for periodontal regeneration. In this review, we highlight preclinical and clinical periodontal regeneration using MSCs derived from distinct origins, including non-odontogenic and odontogenic tissues and induced pluripotent stem cells, and discuss the transplantation procedures, therapeutic mechanisms, and concerns to evaluate the effectiveness of MSCs.
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Affiliation(s)
- Pan Gao
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of General Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Mikihito Kajiya
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Souta Motoike
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Makoto Ikeya
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Jingmei Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
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Liang S, Lu M, Yu D, Xing G, Ji Z, Guo Z, Zhang Q, Huang W, Xie M, Hou S. Effects of age on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks by 16 S and transcriptomics. Comput Struct Biotechnol J 2024; 23:771-782. [PMID: 38304549 PMCID: PMC10832293 DOI: 10.1016/j.csbj.2024.01.005] [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: 09/24/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 02/03/2024] Open
Abstract
Duck hepatitis A virus genotype 3 (DHAV-3) is the major cause of viral hepatitis in ducks in Asia. Previous studies have shown that ducklings younger than 21 days are more susceptible to DHAV-3. To elucidate the mechanism by which age affects the differential susceptibility of Pekin ducks to DHAV-3, intestinal (n = 520), liver (n = 40) and blood (n = 260) samples were collected from control and DHAV-3-infected ducks at 7, 10, 14, and 21 days of age. Comparisons of plasma markers, mortality rates, and intestinal histopathological data showed that the resistance of Pekin ducks to DHAV-3 varied with age. 16 S sequencing revealed that the ileal microbial composition was influenced by age, and this correlation was greater than that recorded for caecal microbes. Candidatus Arthromitus, Bacteroides, Corynebacterium, Enterococcus, Romboutsia, and Streptococcus were the differntially abundant microbes in the ileum at the genus level after DHAV-3 infection and were significantly correlated with 7 differentially expressed genes (DEGs) in 7- and 21-day-old ducklings. 3 immunity-related pathways were significantly different between 7- and 21-day-old ducklings, especially for IFIH1-mediated induction of the interferon-alpha/beta pathway, which induces differential production of CD8(+) T cells and was influenced by a combination of differentially abundant microbiota and DEGs. We found that microbes in the ileum changed regularly with age. The intestinal microbiota was associated with the expression of genes in the liver through IFIH1-mediated induction of the interferon-alpha/beta pathway, which may partially explain why younger ducklings were more susceptible to DHAV-3 infection.
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Affiliation(s)
- Suyun Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Meixi Lu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Daxin Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guangnan Xing
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhanqing Ji
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhanbao Guo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Varilek BM, Mollman S. Healthcare professionals' perspectives of barriers to cancer care delivery for American Indian, rural, and frontier populations. PEC Innov 2024; 4:100247. [PMID: 38225930 PMCID: PMC10788248 DOI: 10.1016/j.pecinn.2023.100247] [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: 09/11/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
Objective This descriptive qualitative study sought to understand the barriers affecting cancer care delivery from the perspective of healthcare professionals (HCPs) serving American Indian (AI), rural, and frontier populations. Methods One-on-one, semi-structured interviews with multidisciplinary HCPs (N = 18) who provide cancer care to AI, rural, and frontier populations were conducted between January and April 2022. Interviews were conducted via Zoom. Data were analyzed following thematic content analysis methodologies. Results Thematic content analysis revealed three major themes: (a) Access, (b) Time, and (c) Isolation. The themes represent the HCP perspectives of the needs and barriers of persons with cancer to whom they provide cancer care. Furthermore, these themes also reflect the barriers HCPs experience while providing cancer care to AI, rural and frontier populations. Conclusions This study provides preliminary evidence for the need and strong multidisciplinary support for an early palliative care intervention in rural and frontier South Dakota (SD). This intervention could support the needs of persons with advanced cancer as well as the HCPs delivering cancer care in rural settings. Innovation This study is the initial step to develop the first culturally responsive, nurse-led, early palliative care intervention for AI, rural, and frontier persons with advanced cancer in SD.
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Affiliation(s)
- Brandon M. Varilek
- South Dakota State University, College of Nursing, 2300 North Career Ave, Suite 260, Sioux Falls, SD 57107, USA
| | - Sarah Mollman
- South Dakota State University, College of Nursing – Office of Nursing Research, 1011 11 St, Rapid City, SD 57701, USA
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Hatamikia S, George G, Schwarzhans F, Mahbod A, Woitek R. Breast MRI radiomics and machine learning-based predictions of response to neoadjuvant chemotherapy - How are they affected by variations in tumor delineation? Comput Struct Biotechnol J 2024; 23:52-63. [PMID: 38125296 PMCID: PMC10730996 DOI: 10.1016/j.csbj.2023.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023] Open
Abstract
Manual delineation of volumes of interest (VOIs) by experts is considered the gold-standard method in radiomics analysis. However, it suffers from inter- and intra-operator variability. A quantitative assessment of the impact of variations in these delineations on the performance of the radiomics predictors is required to develop robust radiomics based prediction models. In this study, we developed radiomics models for the prediction of pathological complete response to neoadjuvant chemotherapy in patients with two different breast cancer subtypes based on contrast-enhanced magnetic resonance imaging acquired prior to treatment (baseline MRI scans). Different mathematical operations such as erosion, smoothing, dilation, randomization, and ellipse fitting were applied to the original VOIs delineated by experts to simulate variations of segmentation masks. The effects of such VOI modifications on various steps of the radiomics workflow, including feature extraction, feature selection, and prediction performance, were evaluated. Using manual tumor VOIs and radiomics features extracted from baseline MRI scans, an AUC of up to 0.96 and 0.89 was achieved for human epidermal growth receptor 2 positive and triple-negative breast cancer, respectively. For smoothing and erosion, VOIs yielded the highest number of robust features and the best prediction performance, while ellipse fitting and dilation lead to the lowest robustness and prediction performance for both breast cancer subtypes. At most 28% of the selected features were similar to manual VOIs when different VOI delineation data were used. Differences in VOI delineation affect different steps of radiomics analysis, and their quantification is therefore important for development of standardized radiomics research.
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Affiliation(s)
- Sepideh Hatamikia
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
- Austrian Center for Medical Innovation and Technology (ACMIT), Viktor Kaplan-Straße 2/1, Wiener Neustadt 2700, Austria
| | - Geevarghese George
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
| | - Florian Schwarzhans
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
| | - Amirreza Mahbod
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
| | - Ramona Woitek
- Danube Private University, Krems, Rathausplatz 1, Krems-Stein, AT-3500, Austria
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63
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Shen C, Ding P, Wee J, Bi J, Luo J, Xia K. Curvature-enhanced graph convolutional network for biomolecular interaction prediction. Comput Struct Biotechnol J 2024; 23:1016-1025. [PMID: 38425487 PMCID: PMC10904164 DOI: 10.1016/j.csbj.2024.02.006] [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: 11/22/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Geometric deep learning has demonstrated a great potential in non-Euclidean data analysis. The incorporation of geometric insights into learning architecture is vital to its success. Here we propose a curvature-enhanced graph convolutional network (CGCN) for biomolecular interaction prediction. Our CGCN employs Ollivier-Ricci curvature (ORC) to characterize network local geometric properties and enhance the learning capability of GCNs. More specifically, ORCs are evaluated based on the local topology from node neighborhoods, and further incorporated into the weight function for the feature aggregation in message-passing procedure. Our CGCN model is extensively validated on fourteen real-world bimolecular interaction networks and analyzed in details using a series of well-designed simulated data. It has been found that our CGCN can achieve the state-of-the-art results. It outperforms all existing models, as far as we know, in thirteen out of the fourteen real-world datasets and ranks as the second in the rest one. The results from the simulated data show that our CGCN model is superior to the traditional GCN models regardless of the positive-to-negative-curvature ratios, network densities, and network sizes (when larger than 500).
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Affiliation(s)
- Cong Shen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Pingjian Ding
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Junjie Wee
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Jialin Bi
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China
| | - Kelin Xia
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
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Ammar N, Kühnisch J. Diagnostic performance of artificial intelligence-aided caries detection on bitewing radiographs: a systematic review and meta-analysis. Jpn Dent Sci Rev 2024; 60:128-136. [PMID: 38450159 PMCID: PMC10917640 DOI: 10.1016/j.jdsr.2024.02.001] [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: 11/18/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
The accuracy of artificial intelligence-aided (AI) caries diagnosis can vary considerably depending on numerous factors. This review aimed to assess the diagnostic accuracy of AI models for caries detection and classification on bitewing radiographs. Publications after 2010 were screened in five databases. A customized risk of bias (RoB) assessment tool was developed and applied to the 14 articles that met the inclusion criteria out of 935 references. Dataset sizes ranged from 112 to 3686 radiographs. While 86 % of the studies reported a model with an accuracy of ≥80 %, most exhibited unclear or high risk of bias. Three studies compared the model's diagnostic performance to dentists, in which the models consistently showed higher average sensitivity. Five studies were included in a bivariate diagnostic random-effects meta-analysis for overall caries detection. The diagnostic odds ratio was 55.8 (95 % CI= 28.8 - 108.3), and the summary sensitivity and specificity were 0.87 (0.76 - 0.94) and 0.89 (0.75 - 0.960), respectively. Independent meta-analyses for dentin and enamel caries detection were conducted and showed sensitivities of 0.84 (0.80 - 0.87) and 0.71 (0.66 - 0.75), respectively. Despite the promising diagnostic performance of AI models, the lack of high-quality, adequately reported, and externally validated studies highlight current challenges and future research needs.
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Affiliation(s)
- Nour Ammar
- Department of Conservative Dentistry and Periodontology, University Hospital, Ludwig-Maximilian University of Munich, Munich 80336, Germany
- Department of Pediatric Dentistry and Dental Public Health, Faculty of Dentistry, Alexandria University, Alexandria 21257, Egypt
| | - Jan Kühnisch
- Department of Conservative Dentistry and Periodontology, University Hospital, Ludwig-Maximilian University of Munich, Munich 80336, Germany
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D'souza CJ, Rajasekar S, Shetty RL. Comparing the immediate effects of different neural mobilization exercises on hamstring flexibility in recreational soccer players. Hong Kong Physiother J 2024; 44:147-155. [PMID: 38510157 PMCID: PMC10949107 DOI: 10.1142/s1013702524500124] [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: 05/02/2023] [Accepted: 12/27/2023] [Indexed: 03/22/2024] Open
Abstract
Background Hamstring strain injuries remain a challenge for both athletes and clinicians given the high incidence rate, slow healing, and persistent symptoms. Increased tension in the neural structures is a known causative factor for hamstring tightness for which neural mobilization has emerged as a significant adjunct to routine stretching techniques. Objective To compare the short-term effects of neural sliding and neural tensioning on hamstring length in male recreational soccer players with hamstring tightness. Methods Sixty-two participants between ages 18 and 30 years were randomly assigned to one of the two groups viz. neural sliding or neural tensioning. Participants in either group performed the given stretching protocol in three sets. The Active Knee Extension Test (AKET) and Sit and Reach Test (SRT) were recorded before intervention, immediately after intervention, and after 60 min. between- and within group-analysis was done using analysis of variance. Results Between-group analysis showed that neural tensioning was more effective than neural sliding in improving hamstring length on both measures, however this difference was negligible. Within-group analysis demonstrated that the mean post-test scores on the AKET test and SRT were significantly greater than the pre-test scores in both groups (p < 0 . 05 ). A reduction in the post-test scores was observed after 60 min, irrespective of the type of stretching (p < 0 . 05 ). Conclusion There was no difference in short-term effects of neural sliding or neural tensioning on hamstring flexibility in male recreational soccer players. Both groups showed improved flexibility immediately after the intervention with reduction in the effect after 60 min.
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Affiliation(s)
| | - Sannasi Rajasekar
- Institute of Physiotherapy, Srinivas University, Mangalore 575001, Karnataka, India
| | - Ruchit L Shetty
- Spine Clinic, Hiranandani Estate, Thane 400607, Maharashtra, India
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Wang YL, Gao S, Xiao Q, Li C, Grzegorzek M, Zhang YY, Li XH, Kang Y, Liu FH, Huang DH, Gong TT, Wu QJ. Role of artificial intelligence in digital pathology for gynecological cancers. Comput Struct Biotechnol J 2024; 24:205-212. [PMID: 38510535 PMCID: PMC10951449 DOI: 10.1016/j.csbj.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: 12/28/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024] Open
Abstract
The diagnosis of cancer is typically based on histopathological sections or biopsies on glass slides. Artificial intelligence (AI) approaches have greatly enhanced our ability to extract quantitative information from digital histopathology images as a rapid growth in oncology data. Gynecological cancers are major diseases affecting women's health worldwide. They are characterized by high mortality and poor prognosis, underscoring the critical importance of early detection, treatment, and identification of prognostic factors. This review highlights the various clinical applications of AI in gynecological cancers using digitized histopathology slides. Particularly, deep learning models have shown promise in accurately diagnosing, classifying histopathological subtypes, and predicting treatment response and prognosis. Furthermore, the integration with transcriptomics, proteomics, and other multi-omics techniques can provide valuable insights into the molecular features of diseases. Despite the considerable potential of AI, substantial challenges remain. Further improvements in data acquisition and model optimization are required, and the exploration of broader clinical applications, such as the biomarker discovery, need to be explored.
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Affiliation(s)
- Ya-Li Wang
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Information Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Song Gao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qian Xiao
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Li
- Microscopic Image and Medical Image Analysis Group, College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
| | - Marcin Grzegorzek
- Institute for Medical Informatics, University of Luebeck, Luebeck, Germany
| | - Ying-Ying Zhang
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao-Han Li
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ye Kang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fang-Hua Liu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dong-Hui Huang
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ting-Ting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qi-Jun Wu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China
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Cogan AM, Haltom TM, Shimada SL, Davila JA, McGinn BP, Fix GM. Understanding patients' experiences during transitions from one electronic health record to another: A scoping review. PEC Innov 2024; 4:100258. [PMID: 38327990 PMCID: PMC10847675 DOI: 10.1016/j.pecinn.2024.100258] [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: 06/12/2023] [Revised: 11/09/2023] [Accepted: 01/21/2024] [Indexed: 02/09/2024]
Abstract
Objectives Identify existing research on impacts of transitions between electronic health record (EHR) systems on patients' healthcare experiences. Methods Scoping review. We searched MedLine, OVID, Embase, CINAHL, and PsycInfo databases for articles on patient experiences with EHR-to-EHR transitions. Results Three studies met inclusion criteria. All three used validated surveys to compare patient satisfaction with care pre- and post-transition. The surveys did not include specific questions about the EHR transition; one study focused on patient perceptions of provider computer use. Satisfaction levels initially decreased following EHR implementation, then returned to baseline between six and 15 months later in two of three studies. Factors associated with changes in observed satisfaction are unknown. Conclusions Patient experience has been given limited attention in studies of EHR-to-EHR transitions. Future research should look beyond satisfaction, and examine how an EHR-to-EHR transition can impact the quality of patients' care, including safety, effectiveness, timeliness, efficiency, and equity. Innovation To our knowledge, this is the first literature review on EHR transitions that specifically focused on patient experiences. In preparation for a transition from one EHR to another, healthcare system leaders should consider the multiple ways patients' experiences with care may be impacted and develop strategies to minimize disruptions in care.
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Affiliation(s)
- Alison M. Cogan
- Mrs. T. H. Chan Division of Occupational Science and Occupational Therapy, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- Center for the Study of Health Innovation, Implementation and Policy, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Trenton M. Haltom
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E DeBakey VA Medical Center, Houston, TX, USA
- Department of Medicine-Health Services Research, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie L. Shimada
- Center for Healthcare Organization and Implementation Research (CHOIR) at the Bedford VA Medical Center, Bedford, MA, USA
- Department of Health Law, Policy and Management, Boston University School of Public Health, Boston, MA, USA
- Division of Health Informatics and Implementation Science, Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jessica A. Davila
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E DeBakey VA Medical Center, Houston, TX, USA
- Department of Medicine-Health Services Research, Baylor College of Medicine, Houston, TX, USA
| | - Bryan P. McGinn
- Department of Health Policy and Management, Providence College, Providence, RI, USA
| | - Gemmae M. Fix
- Center for Healthcare Organization and Implementation Research (CHOIR) at the Bedford VA Medical Center, Bedford, MA, USA
- Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Boston University School of Public Health, Boston, MA, USA
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Wang S, Li H, Zhang K, Wu H, Pang S, Wu W, Ye L, Su J, Zhang Y. scSID: A lightweight algorithm for identifying rare cell types by capturing differential expression from single-cell sequencing data. Comput Struct Biotechnol J 2024; 23:589-600. [PMID: 38274993 PMCID: PMC10809081 DOI: 10.1016/j.csbj.2023.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is currently an important technology for identifying cell types and studying diseases at the genetic level. Identifying rare cell types is biologically important as one of the downstream data analyses of single-cell RNA sequencing. Although rare cell identification methods have been developed, most of these suffer from insufficient mining of intercellular similarities, low scalability, and being time-consuming. In this paper, we propose a single-cell similarity division algorithm (scSID) for identifying rare cells. It takes cell-to-cell similarity into consideration by analyzing both inter-cluster and intra-cluster similarities, and discovers rare cell types based on the similarity differences. We show that scSID outperforms other existing methods by benchmarking it on different experimental datasets. Application of scSID to multiple datasets, including 68K PBMC and intestine, highlights its exceptional scalability and remarkable ability to identify rare cell populations.
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Affiliation(s)
- Shudong Wang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Hengxiao Li
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Kuijie Zhang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Hao Wu
- College of Information Engineering, Northwest A&F University, 712100, Yangling, China
- School of Software, Shandong University, 250100, Jinan, China
| | - Shanchen Pang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wenhao Wu
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Lan Ye
- Cancer Center, the Second Hospital of Shandong University, Jinan, 250033, China
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, China
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Ayele R, Macchi ZA, Jordan S, Jones J, Kluger B, Maley P, Hall K, Sumrall M, Lum HD. Holding back in communications with clinicians: Patient and care partner perspectives in Parkinson's disease. PEC Innov 2024; 4:100255. [PMID: 38304553 PMCID: PMC10832496 DOI: 10.1016/j.pecinn.2024.100255] [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: 08/09/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Objectives To describe how patients with Parkinson's disease (PD) and care partners choose to share or withhold information from clinicians. Methods This is a qualitative, descriptive study nested within a multisite, randomized clinical trial of outpatient palliative care compared to standard neurologic care for PD. Interviews with patients (n = 30) and care partners (n = 30) explored experiences communicating with neurology clinicians. Thematic analyses identified themes relevant to patient-care partner-clinician communication. Results There were four themes relevant to sharing and/or withholding information from clinicians: (1) Suppressing Concerns During Visits, (2) Care Partner Awareness of Patients' Communication Barriers due to Cognitive Impairment, (3) Limited Sharing of Sensitive or Intimate Issues by Patients and Care Partners, and (4) Patient and Care Partner Suggestions to Overcome 'Holding Back'. Conclusion Limitations to communication between patients, care partners, and clinicians should be acknowledged and recognized in routine Parkinson's disease care to foster accurate disclosure of unmet palliative care and other needs. Triadic communication strategies may help patients and care partners talk about unmet palliative care needs. Innovation By recognizing that cognitive impairment and sensitive topics can be barriers, clinicians can adjust or adopt targeted communication strategies for identifying and discussing care needs.
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Affiliation(s)
- Roman Ayele
- Division of Geriatric Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, 12631 E. 17th Ave, Aurora, CO 80045, United States of America
- College of Nursing, University of Colorado Anschutz Medical Campus, 12631 E. 17th Ave, Aurora, CO 80045, United States of America
- Denver-Seattle Center of Innovation, Rocky Mountain Regional Veterans Affairs Medical Center, 1800 N. Wheeling Street, Aurora, CO 80045, United States of America
| | - Zachary A. Macchi
- Department of Neurology, University of Colorado Anschutz Medical Campus, 12631 E. 17th Ave, Aurora, CO, 80045, United States of America
| | - Sarah Jordan
- Division of Geriatric Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, 12631 E. 17th Ave, Aurora, CO 80045, United States of America
| | - Jacqueline Jones
- College of Nursing, University of Colorado Anschutz Medical Campus, 12631 E. 17th Ave, Aurora, CO 80045, United States of America
| | - Benzi Kluger
- Departments of Neurology and Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, United States of America
| | - Patrick Maley
- Patient and Caregiver Advisory Council, University of Colorado Anschutz Medical Campus, 12631 E 17th Ave, Aurora, CO 80045, United States of America
| | - Kirk Hall
- Patient and Caregiver Advisory Council, University of Colorado Anschutz Medical Campus, 12631 E 17th Ave, Aurora, CO 80045, United States of America
| | - Malenna Sumrall
- Patient and Caregiver Advisory Council, University of Colorado Anschutz Medical Campus, 12631 E 17th Ave, Aurora, CO 80045, United States of America
| | - Hillary D. Lum
- Division of Geriatric Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, 12631 E. 17th Ave, Aurora, CO 80045, United States of America
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Tahir ul Qamar M, Noor F, Guo YX, Zhu XT, Chen LL. Deep-HPI-pred: An R-Shiny applet for network-based classification and prediction of Host-Pathogen protein-protein interactions. Comput Struct Biotechnol J 2024; 23:316-329. [PMID: 38192372 PMCID: PMC10772389 DOI: 10.1016/j.csbj.2023.12.010] [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: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
Host-pathogen interactions (HPIs) are vital in numerous biological activities and are intrinsically linked to the onset and progression of infectious diseases. HPIs are pivotal in the entire lifecycle of diseases: from the onset of pathogen introduction, navigating through the mechanisms that bypass host cellular defenses, to its subsequent proliferation inside the host. At the heart of these stages lies the synergy of proteins from both the host and the pathogen. By understanding these interlinking protein dynamics, we can gain crucial insights into how diseases progress and pave the way for stronger plant defenses and the swift formulation of countermeasures. In the framework of current study, we developed a web-based R/Shiny app, Deep-HPI-pred, that uses network-driven feature learning method to predict the yet unmapped interactions between pathogen and host proteins. Leveraging citrus and CLas bacteria training datasets as case study, we spotlight the effectiveness of Deep-HPI-pred in discerning Protein-protein interaction (PPIs) between them. Deep-HPI-pred use Multilayer Perceptron (MLP) models for HPI prediction, which is based on a comprehensive evaluation of topological features and neural network architectures. When subjected to independent validation datasets, the predicted models consistently surpassed a Matthews correlation coefficient (MCC) of 0.80 in host-pathogen interactions. Remarkably, the use of Eigenvector Centrality as the leading topological feature further enhanced this performance. Further, Deep-HPI-pred also offers relevant gene ontology (GO) term information for each pathogen and host protein within the system. This protein annotation data contributes an additional layer to our understanding of the intricate dynamics within host-pathogen interactions. In the additional benchmarking studies, the Deep-HPI-pred model has proven its robustness by consistently delivering reliable results across different host-pathogen systems, including plant-pathogens (accuracy of 98.4% and 97.9%), human-virus (accuracy of 94.3%), and animal-bacteria (accuracy of 96.6%) interactomes. These results not only demonstrate the model's versatility but also pave the way for gaining comprehensive insights into the molecular underpinnings of complex host-pathogen interactions. Taken together, the Deep-HPI-pred applet offers a unified web service for both identifying and illustrating interaction networks. Deep-HPI-pred applet is freely accessible at its homepage: https://cbi.gxu.edu.cn/shiny-apps/Deep-HPI-pred/ and at github: https://github.com/tahirulqamar/Deep-HPI-pred.
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Affiliation(s)
- Muhammad Tahir ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Fatima Noor
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Yi-Xiong Guo
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi-Tong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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González-Llera L, Santos-Durán GN, Sobrido-Cameán D, Núñez-González C, Pérez-Fernández J, Barreiro-Iglesias A. Spontaneous regeneration of cholecystokinergic reticulospinal axons after a complete spinal cord injury in sea lampreys. Comput Struct Biotechnol J 2024; 23:347-357. [PMID: 38205155 PMCID: PMC10776906 DOI: 10.1016/j.csbj.2023.12.014] [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: 10/26/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
In contrast to humans, lampreys spontaneously recover their swimming capacity after a complete spinal cord injury (SCI). This recovery process involves the regeneration of descending axons. Spontaneous axon regeneration in lampreys has been mainly studied in giant descending neurons. However, the regeneration of neurochemically distinct descending neuronal populations with small-caliber axons, as those found in mammals, has been less studied. Cholecystokinin (CCK) is a regulatory neuropeptide found in the brain and spinal cord that modulates several processes such as satiety, or locomotion. CCK shows high evolutionary conservation and is present in all vertebrate species. Work in lampreys has shown that all CCKergic spinal cord axons originate in a single neuronal population located in the caudal rhombencephalon. Here, we investigate the spontaneous regeneration of CCKergic descending axons in larval lampreys following a complete SCI. Using anti-CCK-8 immunofluorescence, confocal microscopy and lightning adaptive deconvolution, we demonstrate the partial regeneration of CCKergic axons (81% of the number of axonal profiles seen in controls) 10 weeks after the injury. Our data also revealed a preference for regeneration of CCKergic axons in lateral spinal cord regions. Regenerated CCKergic axons exhibit colocalization with synaptic vesicle marker SV2, indicative of functional synaptic connections. We also extracted swimming dynamics in injured animals by using DeepLabCut. Interestingly, the degree of CCKergic reinnervation correlated with improved swimming performance in injured animals, suggesting a potential role in locomotor recovery. These findings open avenues for further exploration into the role of specific neuropeptidergic systems in post-SCI spinal locomotor networks.
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Affiliation(s)
- Laura González-Llera
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Gabriel N. Santos-Durán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carmen Núñez-González
- CINBIO, Neurocircuits Group, Campus Universitario Lagoas, Marcosende, Universidade de Vigo, 36310 Vigo, Spain
| | - Juan Pérez-Fernández
- CINBIO, Neurocircuits Group, Campus Universitario Lagoas, Marcosende, Universidade de Vigo, 36310 Vigo, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Hiraba H, Takeuchi Y, Nishio K, Koizumi H, Yoneyama T, Matsumura H. Current status of dental journals published by Japanese organization. Jpn Dent Sci Rev 2024; 60:40-43. [PMID: 38204963 PMCID: PMC10776377 DOI: 10.1016/j.jdsr.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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/27/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024] Open
Abstract
The publication status of dental journals in Japan was examined, with a focus on metrics such as Journal Impact Factor (JIF), Eigenfactor, Article Influence Score, and percentage of open access. A total of 18 journals published by Japanese dental organizations were identified in the Journal Citation Reports (JCR), with JIF values ranging from 0.4 to 6.6. The highest JIF was observed in The Japanese Dental Science Review. Additionally, 16 journals were not listed on the JCR. The authors explored the implications of these findings on the visibility and impact of Japanese dental research, and discussed the potential benefits of embracing open-access publications for greater global dissemination. This study highlighted the opportunities for journals to enhance their international recognition by meeting the criteria for JIF inclusion and embracing open-access publications. By adopting effective publication strategies, the dental community in Japan will be able to contribute to the advancement of dentistry globally, ensuring broader accessibility and recognition of its research contributions.
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Affiliation(s)
- Haruto Hiraba
- Department of Dental Materials, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
- Division of Biomaterials Science, Dental Research Center, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101–8310, Japan
| | - Yoshimasa Takeuchi
- Department of Comprehensive Dentistry and Clinical Education, Nihon University School of Dentistry, Tokyo, Japan
| | - Kensuke Nishio
- Department of Complete Denture Prosthodontics, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Hiroyasu Koizumi
- Department of Dental Materials, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
- Division of Biomaterials Science, Dental Research Center, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101–8310, Japan
| | - Takayuki Yoneyama
- Department of Dental Materials, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
- Division of Biomaterials Science, Dental Research Center, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101–8310, Japan
| | - Hideo Matsumura
- Department of Fixed Prosthodontics, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
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Huang HY, Li FR, Zhang YF, Lau HC, Hsueh CY, Zhou L, Zhang M. Metagenomic shotgun sequencing reveals the enrichment of Salmonella and Mycobacterium in larynx due to prolonged ethanol exposure. Comput Struct Biotechnol J 2024; 23:396-405. [PMID: 38235358 PMCID: PMC10792199 DOI: 10.1016/j.csbj.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
The exposure of ethanol increases the risk of head and neck inflammation and tumor progression. However, limited studies have investigated the composition and functionality of laryngeal microbiota under ethanol exposure. We established an ethanol-exposed mouse model to investigate the changes in composition and function of laryngeal microbiota using Metagenomic shotgun sequencing. In the middle and late stages of the experiment, the laryngeal microbiota of mice exposed to ethanol exhibited obvious distinguished from that of the control group on principal-coordinate analysis (PCoA) plots. Among the highly abundant species, Salmonella enterica and Mycobacterium marinum were likely to be most impacted. Our findings indicated that the exposure to ethanol significantly increased their abundance in larynxes in mice of the same age, which has been confirmed through FISH experiments. Among the species-related functions and genes, metabolism is most severely affected by ethanol. The difference was most obvious in the second month of the experiment, which may be alleviated later because the animal established tolerance. Notable enrichments concerning energy, amino acid, and carbohydrate metabolic pathways occurred during the second month under ethanol exposure. Finally, based on the correlation between species and functional variations, a network was established to investigate relationships among microbiota, functional pathways, and related genes affected by ethanol. Our data first demonstrated the continuous changes of abundance, function and their interrelationship of laryngeal microbiota under ethanol exposure by Metagenomic shotgun sequencing. Importance Ethanol may participate in the inflammation and tumor progression by affecting the composition of the laryngeal microbiota. Here, we applied the metagenomic shotgun sequencing instead of 16 S rRNA sequencing method to identify the laryngeal microbiota under ethanol exposure. Salmonella enterica and Mycobacterium marinum are two dominant species that may play a role in the reconstruction of the laryngeal microenvironment, as their local abundance increases following exposure to ethanol. The metabolic function is most evidently impacted, and several potential metabolic pathways could be associated with alterations in microbiota composition. These findings could help us better understand the impact of prolonged ethanol exposure on the microbial composition and functionality in the larynx.
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Affiliation(s)
| | | | | | - Hui-Ching Lau
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Ming Zhang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
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Aoki A, Mizutani K, Taniguchi Y, Lin T, Ohsugi Y, Mikami R, Katagiri S, Meinzer W, Iwata T. Current status of Er:YAG laser in periodontal surgery. Jpn Dent Sci Rev 2024; 60:1-14. [PMID: 38148873 PMCID: PMC10750110 DOI: 10.1016/j.jdsr.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 12/28/2023] Open
Abstract
Lasers have numerous advantageous tissue interactions such as ablation or vaporization, hemostasis, bacterial killing, as well as biological effects, which induce various beneficial therapeutic effects and biological responses in the tissues. Thus, lasers are considered an effective and suitable device for treating a variety of inflammatory and infectious conditions of periodontal disease. Among various laser systems, the Er:YAG laser, which can be effectively and safely used in both soft and hard tissues with minimal thermal side effects, has been attracting much attention in periodontal therapy. This laser can effectively and precisely debride the diseased root surface including calculus removal, ablate diseased connective tissues within the bone defects, and stimulate the irradiated surrounding periodontal tissues during surgery, resulting in favorable wound healing as well as regeneration of periodontal tissues. The safe and effective performance of Er:YAG laser-assisted periodontal surgery has been reported with comparable and occasionally superior clinical outcomes compared to conventional surgery. This article explains the characteristics of the Er:YAG laser and introduces its applications in periodontal surgery including conventional flap surgery, regenerative surgery, and flapless surgery, based on scientific evidence from currently available basic and clinical studies as well as cases reports.
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Affiliation(s)
- Akira Aoki
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Koji Mizutani
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Yoichi Taniguchi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
- Taniguchi Dental Clinic, Kita 7−17, 18-chome, Nango-dori, Shiroishi-ku, Sapporo, Hokkaido, Japan
| | - Taichen Lin
- School of Dentistry, Chung Shan Medical University (CSMU), No.110, Section 1, Jianguo N. Rd., South Dist, Taichung 402, Taiwan
- Department of Dentistry, Chung Shan Medical University Hospital, No.110, Section 1, Jianguo N. Rd., South Dist, Taichung 402, Taiwan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Risako Mikami
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Walter Meinzer
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
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Dengsø KE, Berg A, Hansen CP, Burgdorf SK, Krohn PS, Sillesen M, Spiegelhauer N, Bach MT, Melton M, Nielsen B, Christensen BM, Finderup J, Hillingsø J. Have a vital end-user been overlooked? Developing a shared decision intervention for patients with potential pancreatic cancer regarding the choice of surgery. PEC Innov 2024; 4:100269. [PMID: 38435237 PMCID: PMC10907832 DOI: 10.1016/j.pecinn.2024.100269] [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: 05/01/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Objective To develop a patient decision aid facilitating shared decision making for patients with potential pancreatic cancer deciding about no treatment, surgical or medical treatment. Methods Based on a user-centred design by Wittemann et al., we developed a shared decision making intervention in three phases: 1) Understanding decision needs 2) Development of a patient decision aid (PtDA) based on a generic template 3) Assessment of the intervention from interviews with patients (n = 11), relatives (n = 11), nurses (n = 4) and surgeons (n = 2) analysed with thematic analysis, and measuring patients' perceptions of choice of options with the Decisional Conflict Scale. Results Results showed varying experiences with the use of the PtDA, with surgeons not finding PtDA useful as it was impractical and constraining with patients' conversations. There was no difference in patients' perceptions in choosing options for those being presented vs those patients not being presented for the PtDA. Conclusion The format and structure of the PtDA was not feasible for the surgeons as fundamental users in the present clinic. Innovation This study highlights the urgent need to consider clinical context before introducing a predefined tool and shows the importance of a multistakeholder approach. Research should focus on finding means to successful implement shared decision making.
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Affiliation(s)
- Kristine Elberg Dengsø
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Anne Berg
- Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Carsten Palnæs Hansen
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Stefan K. Burgdorf
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Paul S. Krohn
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Martin Sillesen
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Nina Spiegelhauer
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Mette Tholstrup Bach
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Marianne Melton
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Betina Nielsen
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Bo Marcel Christensen
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Jeanette Finderup
- Department of Renal Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
- Research Centre for Patient Involvement, Aarhus University & Central Region, Denmark
| | - Jens Hillingsø
- The Department of Surgical Gastroenterology and Transplantation, Center for Cancer and Organ and Disease, University Hospital Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
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Dunn Navarra AM, Gormley M, Liang E, Loughran C, Vorderstrasse A, Garcia DR, Rosenberg MG, Fletcher J, Goldsamt LA. Developing and testing a web-based platform for antiretroviral therapy (ART) adherence support among adolescents and young adults (AYA) living with HIV. PEC Innov 2024; 4:100263. [PMID: 38463238 PMCID: PMC10920727 DOI: 10.1016/j.pecinn.2024.100263] [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: 09/15/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 03/12/2024]
Abstract
Objective Describe the development and testing of a web-based platform for antiretroviral treatment (ART) adherence support among HIV+ adolescents and young adults (AYA) in a randomized controlled trial (RCT). Methods A seven-member multi-disciplinary team operationalized the flat, password protected, web-based platform. Manualized protocols guided the objectives and content for each of the eight web-based sessions. Team members evaluated usability and content validity. Client satisfaction and perceived ease of use was evaluated with the first ten HIV+ AYA participants. Results The web-based platform was developed, evaluated, refined, implemented and pilot tested between September 2020 to April 2022. Usability was rated as high; the evaluation of content validity showed an excellent fit between session content and objectives. HIV+ AYA participants (mean age = 24.2 years) were satisfied with the quality, type, and amount of support/education received, and found the platform easy to use, operate, and navigate. Average time spent per session was 6.5 min. Conclusion Findings support the usability, validity, acceptability, and feasibility of this web-based platform for ART adherence support among HIV+ AYA. Innovation Our research and findings are responsive to research gaps and the need for transparency in the methodological development and testing of web-based control arms for ART adherence support among HIV+ AYA.
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Affiliation(s)
- Ann-Margaret Dunn Navarra
- StonyBrook University, School of Nursing, 101 Nicolls Road, Health Sciences Center, Level 2, StonyBrook, NY 11794, USA
| | - Maurade Gormley
- University of Connecticut, School of Nursing, 231 Glenbrook Road, Storrs, CT 06269, USA
| | - Eva Liang
- New York University, Rory Meyers College of Nursing, 380 Second Avenue, New York, NY 10010, USA
| | - Claire Loughran
- New York University, Rory Meyers College of Nursing, 380 Second Avenue, New York, NY 10010, USA
| | - Allison Vorderstrasse
- University of Massachusetts Amherst, Elaine Marieb College of Nursing, 651 N Pleasant St., Amherst, MA 01003, USA
| | - David R. Garcia
- New York University, Rory Meyers College of Nursing, 433 First Avenue, New York, NY 10010, USA
| | - Michael G. Rosenberg
- Division of Infectious Diseases, Department of Pediatrics, Jacobi Medical Center, Bronx, NY, 10461, USA
| | - Jason Fletcher
- New York University, Rory Meyers College of Nursing, 433 First Avenue, New York, NY 10010, USA
| | - Lloyd A. Goldsamt
- New York University, Rory Meyers College of Nursing, 433 First Avenue, New York, NY 10010, USA
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Di J, Hickey C, Bumgardner C, Yousif M, Zapata M, Bocklage T, Balzer B, Bui MM, Gardner JM, Pantanowitz L, Qasem SA. Utility of artificial intelligence in a binary classification of soft tissue tumors. J Pathol Inform 2024; 15:100368. [PMID: 38496781 PMCID: PMC10940995 DOI: 10.1016/j.jpi.2024.100368] [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: 12/02/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 03/19/2024] Open
Abstract
Soft tissue tumors (STTs) pose diagnostic and therapeutic challenges due to their rarity, complexity, and morphological overlap. Accurate differentiation between benign and malignant STTs is important to set treatment directions, however, this task can be difficult. The integration of machine learning and artificial intelligence (AI) models can potentially be helpful in classifying these tumors. The aim of this study was to investigate AI and machine learning tools in the classification of STT into benign and malignant categories. This study consisted of three components: (1) Evaluation of whole-slide images (WSIs) to classify STT into benign and malignant entities. Five specialized soft tissue pathologists from different medical centers independently reviewed 100 WSIs, representing 100 different cases, with limited clinical information and no additional workup. The results showed an overall concordance rate of 70.4% compared to the reference diagnosis. (2) Identification of cell-specific parameters that can distinguish benign and malignant STT. Using an image analysis software (QuPath) and a cohort of 95 cases, several cell-specific parameters were found to be statistically significant, most notably cell count, nucleus/cell area ratio, nucleus hematoxylin density mean, and cell max caliper. (3) Evaluation of machine learning library (Scikit-learn) in differentiating benign and malignant STTs. A total of 195 STT cases (156 cases in the training group and 39 cases in the validation group) achieved approximately 70% sensitivity and specificity, and an AUC of 0.68. Our limited study suggests that the use of WSI and AI in soft tissue pathology has the potential to enhance diagnostic accuracy and identify parameters that can differentiate between benign and malignant STTs. We envision the integration of AI as a supportive tool to augment the pathologists' diagnostic capabilities.
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Affiliation(s)
- Jing Di
- University of Kentucky College of Medicine, Lexington, KY, United States
| | - Caylin Hickey
- University of Kentucky College of Medicine, Lexington, KY, United States
| | - Cody Bumgardner
- University of Kentucky College of Medicine, Lexington, KY, United States
| | | | | | - Therese Bocklage
- University of Kentucky College of Medicine, Lexington, KY, United States
| | - Bonnie Balzer
- Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Marilyn M. Bui
- Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | | | - Liron Pantanowitz
- University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Shadi A. Qasem
- University of Kentucky College of Medicine, Lexington, KY, United States
- Baptist Health Jacksonville, Jacksonville, FL, United States
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Aalders J, Léger L, Hassannia B, Goossens V, Vanden Berghe T, van Hengel J. Improving cardiac differentiation of human pluripotent stem cells by targeting ferroptosis. Regen Ther 2024; 27:21-31. [PMID: 38496011 PMCID: PMC10940893 DOI: 10.1016/j.reth.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)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/25/2024] [Indexed: 03/19/2024] Open
Abstract
Generation of cardiomyocytes from human pluripotent stem cells (hPSCs) is of high interest for disease modelling and regenerative medicine. hPSCs can provide an unlimited source of patient-specific cardiomyocytes that are otherwise difficult to obtain from individuals. Moreover, the low proliferation rate of adult cardiomyocytes and low viability ex vivo limits the quantity of study material. Most protocols for the differentiation of cardiomyocytes from hPSCs are based on the temporal modulation of the Wnt pathway. However, during the initial stage of GSK-3 inhibition, a substantial number of cells are lost due to detachment. In this study, we aimed to increase the efficiency of generating cardiomyocytes from hPSCs. We identified cell death as a detrimental factor during this initial stage of in vitro cardiomyocyte differentiation. Through pharmacological targeting of different types of cell death, we discovered that ferroptosis was the main cell death type during the first 48 h of the in vitro differentiation procedure. Inhibiting ferroptosis using ferrostatin-1 during cardiomyocyte differentiation resulted in increased robustness and cell yield.
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Affiliation(s)
- Jeffrey Aalders
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Entrance 37a, 2nd floor, 9000, Ghent, Belgium
| | - Laurens Léger
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Entrance 37a, 2nd floor, 9000, Ghent, Belgium
| | - Behrouz Hassannia
- Cell Death Signalling Lab, Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Tom Vanden Berghe
- Cell Death Signalling Lab, Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Entrance 37a, 2nd floor, 9000, Ghent, Belgium
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Kumi R, Quartey J, Kwakye SK, Oppong ED. Students' perceptions and experiences of remote learning amid covid-19 pandemic in Ghana. Hong Kong Physiother J 2024; 44:103-118. [PMID: 38510159 PMCID: PMC10949108 DOI: 10.1142/s1013702524500070] [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: 05/25/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 03/22/2024] Open
Abstract
Background The COVID-19 pandemic had a significant impact on students, instructors, and educational organisations all around the world. Remote learning was an emergency response by most universities in Ghana during this pandemic to ensure the continuation of their academic calendar. Conducting this study among Ghanaian undergraduate students is crucial because factors like socioeconomic status, technological resources, and individual learning preferences can significantly impact their experience and the perception of remote learning, which may differ from studies conducted elsewhere. Objective To determine the perceptions and experiences of remote learning among allied health sciences students during the COVID-19 pandemic. Methods This cross-sectional study involved 218 second, third, and final year Allied Health Sciences students in the University of Ghana. A questionnaire was used to obtain data concerning health professions students' perception and experience of remote learning. The readiness of students in respect to the emergency remote learning, attitudes towards remote learning, perception of remote learning, satisfaction, and the level of anxiety was calculated using mean and mean percentages. Kruskal-Wallis test was used to analyse differences between programmes of study and the perceptions and experiences of remote learning. Results One hundred and fifteen (53.1%) of the participants had moderate perceptions of independence and responsibility in their learning experiences while 80 (36.7%) students reported that their satisfaction levels regarding remote learning was high. Seventy-seven (38.4%) students reported that they had a burden of anxiety. There was no statistically significant difference between anxiety level and programme of study. Conclusion Ghana Allied Health Sciences students had positive perceptions and experiences towards remote learning. They could adapt to the new teaching method with appropriate technology integration. Despite a number of students who were anxious about using remote learning. Adequate support towards transitioning into the use of technology may be a good consideration.
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Affiliation(s)
- Rockson Kumi
- Physiotherapy Department, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Jonathan Quartey
- Department of Physiotherapy, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana
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80
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Safo-Kantanka NK, Quartey J, Kwakye SK. Physiotherapy students' rating on lecturers' and supervisors' clinical education attributes. Hong Kong Physiother J 2024; 44:79-90. [PMID: 38510158 PMCID: PMC10949104 DOI: 10.1142/s1013702524500045] [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: 05/24/2023] [Accepted: 08/30/2023] [Indexed: 03/22/2024] Open
Abstract
Background Clinical education is considered a vital aspect of education of health science students. Attributes of clinical educators play a crucial role in determining the outcome of clinical teaching and learning. A good clinical educator ensures that students get maximum benefits of the clinical learning experience. Objective To determine the ratings of physiotherapy students on clinical education attributes of lecturers and clinical supervisors. Methods The study was conducted with 81 clinical physiotherapy students from two universities in Ghana. Two copies of McGill clinical teachers' evaluation (CTE) tool were used to obtain students' ratings on their clinical supervisors' and lecturers' clinical education attributes. Independent t-test was used to compare the means of students' level of study and ratings regarding the clinical education attributes of clinical supervisors and lecturers. Results Students had a high rating on their clinical education attributes of supervisors and lecturers with a mean score of (121 . 22 ± 18 . 12 ) and (122 . 11 ± 16 . 71 ), respectively. Rating on clinical education attributes of supervisors (p = 0 . 111 ) and lecturers (p = 0 . 124 ) did not differ significantly between the different levels of study. Conclusion Clinical physiotherapy students rated the clinical education attributes of their lecturers and supervisors high.
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Affiliation(s)
| | - Jonathan Quartey
- Department of Physiotherapy, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana
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81
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Spector J, Kennedy A, Nedelcu E. BBDash: An Electron-based tool for analyzing blood product utilization. J Pathol Inform 2024; 15:100370. [PMID: 38524917 PMCID: PMC10959693 DOI: 10.1016/j.jpi.2024.100370] [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: 10/18/2023] [Revised: 02/02/2024] [Accepted: 02/17/2024] [Indexed: 03/26/2024] Open
Abstract
Blood transfusions can be associated with side effects ranging from occasional febrile reactions to extremely rare fatal reactions. Monitoring blood product orders and ensuring appropriate utilization is therefore an important strategy to ensure patient safety. However, data extracted from laboratory information systems can be difficult to interpret. We created BBDash, an Electron-based tool that reads Sunquest reports to create easy-to-interpret graphs related to blood product utilization.
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Affiliation(s)
- Jacob Spector
- Boston Children’s Hospital, Dept. of Clinical Informatics, Galleria Room 110, 300 Longwood Ave, Boston, MA 02130, United States
| | - Adrienne Kennedy
- University of California San Francisco, Dept. of Laboratory Medicine, 505 Parnassus Ave., San Francisco, CA 94143, United States
| | - Elena Nedelcu
- University of California San Francisco, Dept. of Laboratory Medicine, 505 Parnassus Ave., San Francisco, CA 94143, United States
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Lin X, Fang Y, Mi X, Fu J, Chen S, Wu M, Jin N. Intrauterine injection of bioengineered hydrogel loaded exosomes derived from HUCM stem cells and spermidine prominently augments the pregnancy rate in thin endometrium rats. Regen Ther 2024; 27:63-72. [PMID: 38525237 PMCID: PMC10959642 DOI: 10.1016/j.reth.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024] Open
Abstract
The endometrium is essential to the development of embryos and pregnancy. Human umbilical cord mesenchymal stem cells (HUCMSCs) are promising stem cell sources. HUCMSCs self-renew quickly and are painless to collect. Spermidine is an inherent polyamine needed for cellular and molecular processes that regulate physiology and function. HUCMSCs and spermidine (SN) may heal intrauterine adhesions. HUCMSCs were investigated for endometrial repair in rats. Composite hydrogels are used for medical exosome implantation, including their materials, properties, and embedding procedures. This study examined whether bioengineered hydrogel-loaded exosomes from HUCMSCs and spermidine prenatally improved conception rates in mice with poor endometrial lining. The data show that HUCMSC and SN provide a good experimental base for HUCMSC safety and intrauterine treatment in rats. Western blots, exosome structural analysis, pregnancy outcomes, flow cytometry, H&E staining, immunohistochemistry, and immunofluorescence labelling found and recovered the aberrant area. HUCM-derived stem cells and spermidine-derived exosomes biophysically match. These traits strengthen and prolong endometrial function. Pregnant rats with HUCMSC and SN had thinner endometrium. Hydrogel-incorporated HEHUCMSC and SN exosomes may improve IUI in rats with thin endometrium.
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Affiliation(s)
- Xiuying Lin
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Yanbian University, Yanbian 133002, China
- Center of Reproductive Medicine, Jilin Province People's Hospital, Changchun 130021, China
| | - Yanqiu Fang
- Center of Reproductive Medicine, Jilin Province People's Hospital, Changchun 130021, China
| | - Xuguang Mi
- Center of Reproductive Medicine, Jilin Province People's Hospital, Changchun 130021, China
| | - Jianhua Fu
- Center of Reproductive Medicine, Jilin Province People's Hospital, Changchun 130021, China
| | - Shiling Chen
- Center of Reproductive Medicine, Jilin Province People's Hospital, Changchun 130021, China
| | - Mengxue Wu
- Center of Reproductive Medicine, Jilin Province People's Hospital, Changchun 130021, China
| | - Ningyi Jin
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Yanbian University, Yanbian 133002, China
- Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun 130000, China
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83
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Zoehler B, de Aguiar AM, Silveira GF. SAEDC: Development of a technological solution for exploratory data analysis and statistics in cytotoxicity. Comput Struct Biotechnol J 2024; 23:483-490. [PMID: 38261941 PMCID: PMC10796974 DOI: 10.1016/j.csbj.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
INTRODUCTION The intergovernmental organizations Organisation for Economic Co-operation and Development (OECD) and Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) have developed guidelines for the use of in vitro models for toxicological evaluation of chemicals. However, the presence of manual steps and the requirement of multiple tools for data analysis, apart from being costly and time-consuming, can inadvertently introduce errors by researchers. OBJECTIVES We have developed the SAEDC platform (Technological Solution for Exploratory Data Analysis and Statistics for Cytotoxicity, in Portuguese), which enables analysis of cytotoxicity data from assays following OECD Guideline No. 129. METHODOLOGY In vitro experimental data were used to compare with the analysis methodology suggested in the Guideline. We analyzed 117 data sets covering chemicals from Category I to Unclassified according to GHS classification. RESULTS The four-parameters of non-linear regression (4PL) calculated by the SAEDC platform showed no significant differences compared to standard methodology in any of the data sets (p > 0.05). The coefficient of determination (R-squared) also demonstrated not only a good fit of the 4PL model to the data but also significant similarity to values obtained by the conventional methodology. Finally, the SAEDC platform predicted LD50 values for the chemicals from IC50, using the Registry of Cytotoxicity (RC) regression models. CONCLUSION The comparison with the standard data analysis methodology revealed that SAEDC platform fulfills the requirements for cytotoxicity data analysis, generating reliable and accurate results with fewer steps performed by researchers. The use of SAEDC platform for obtaining toxicity values can reduce analysis time compared to the standard methodology proposed by regulatory agencies. Thus, automation of the analysis using the SAEDC platform has the potential to save time and resources for cytotoxicity researchers and laboratories while generating reliable results.
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Affiliation(s)
- Bernardo Zoehler
- Instituto Carlos Chagas – ICC, Fundação Oswaldo Cruz – Fiocruz, Brazil
| | - Alessandra Melo de Aguiar
- Plataforma de Bioensaios com métodos alternativos em citotoxicidade, Instituto Carlos Chagas – ICC, Fundação Oswaldo Cruz – Fiocruz, Brazil
- Laboratório de Biologia Básica de Células-tronco, Instituto Carlos Chagas – ICC, Fundação Oswaldo Cruz – Fiocruz, Brazil
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84
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Kaldoudi E. Smart hospital: The future of healthcare. Comput Struct Biotechnol J 2024; 24:87-88. [PMID: 38222115 PMCID: PMC10787219 DOI: 10.1016/j.csbj.2023.12.011] [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: 01/16/2024] Open
Affiliation(s)
- Eleni Kaldoudi
- Professor of Medical Physics and Medical Informatics, Democritus University of Thrace, Greece
- ATHENA Research Center, Greece
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85
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Rodríguez JM, Jorge I, Martinez-Val A, Barrero-Rodríguez R, Magni R, Núñez E, Laguillo A, Devesa CA, López JA, Camafeita E, Vázquez J. iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data. Comput Struct Biotechnol J 2024; 23:452-459. [PMID: 38235360 PMCID: PMC10792623 DOI: 10.1016/j.csbj.2023.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
Many bioinformatics tools are available for the quantitative analysis of proteomics experiments. Most of these tools use a dedicated statistical model to derive absolute quantitative protein values from mass spectrometry (MS) data. Here, we present iSanXoT, a standalone application that processes relative abundances between MS signals and then integrates them sequentially to upper levels using the previously published Generic Integration Algorithm (GIA). iSanXoT offers unique capabilities that complement conventional quantitative software applications, including statistical weighting and independent modeling of error distributions in each integration, aggregation of technical or biological replicates, quantification of posttranslational modifications, and analysis of coordinated protein behavior. iSanXoT is a standalone, user-friendly application that accepts output from popular proteomics pipelines and enables unrestricted creation of quantification workflows and fully customizable reports that can be reused across projects or shared among users. Numerous publications attest the successful application of diverse integrative workflows constructed using the GIA for the analysis of high-throughput quantitative proteomics experiments. iSanXoT has been tested with the main operating systems. Download links for the corresponding distributions are available at https://github.com/CNIC-Proteomics/iSanXoT/releases.
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Affiliation(s)
- Jose Manuel Rodríguez
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Inmaculada Jorge
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ana Martinez-Val
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Rafael Barrero-Rodríguez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Ricardo Magni
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Estefanía Núñez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Andrea Laguillo
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Cristina A. Devesa
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Juan A. López
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Emilio Camafeita
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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86
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Zhao J, Wang Y, Feng C, Yin M, Gao Y, Wei L, Song C, Ai B, Wang Q, Zhang J, Zhu J, Li C. SCInter: A comprehensive single-cell transcriptome integration database for human and mouse. Comput Struct Biotechnol J 2024; 23:77-86. [PMID: 38125297 PMCID: PMC10731004 DOI: 10.1016/j.csbj.2023.11.024] [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: 09/27/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq), which profiles gene expression at the cellular level, has effectively explored cell heterogeneity and reconstructed developmental trajectories. With the increasing research on diseases and biological processes, scRNA-seq datasets are accumulating rapidly, highlighting the urgent need for collecting and processing these data to support comprehensive and effective annotation and analysis. Here, we have developed a comprehensive Single-Cell transcriptome integration database for human and mouse (SCInter, https://bio.liclab.net/SCInter/index.php), which aims to provide a manually curated database that supports the provision of gene expression profiles across various cell types at the sample level. The current version of SCInter includes 115 integrated datasets and 1016 samples, covering nearly 150 tissues/cell lines. It contains 8016,646 cell markers in 457 identified cell types. SCInter enabled comprehensive analysis of cataloged single-cell data encompassing quality control (QC), clustering, cell markers, multi-method cell type automatic annotation, predicting cell differentiation trajectories and so on. At the same time, SCInter provided a user-friendly interface to query, browse, analyze and visualize each integrated dataset and single cell sample, along with comprehensive QC reports and processing results. It will facilitate the identification of cell type in different cell subpopulations and explore developmental trajectories, enhancing the study of cell heterogeneity in the fields of immunology and oncology.
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Affiliation(s)
- Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Yuezhu Wang
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Chenchen Feng
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Mingxue Yin
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yu Gao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Chao Song
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Chunquan Li
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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Hennebelle A, Ismail L, Materwala H, Al Kaabi J, Ranjan P, Janardhanan R. Secure and privacy-preserving automated machine learning operations into end-to-end integrated IoT-edge-artificial intelligence-blockchain monitoring system for diabetes mellitus prediction. Comput Struct Biotechnol J 2024; 23:212-233. [PMID: 38169966 PMCID: PMC10758733 DOI: 10.1016/j.csbj.2023.11.038] [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: 07/11/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Diabetes Mellitus, one of the leading causes of death worldwide, has no cure to date and can lead to severe health complications, such as retinopathy, limb amputation, cardiovascular diseases, and neuronal disease, if left untreated. Consequently, it becomes crucial to be able to monitor and predict the incidence of diabetes. Machine learning approaches have been proposed and evaluated in the literature for diabetes prediction. This paper proposes an IoT-edge-Artificial Intelligence (AI)-blockchain system for diabetes prediction based on risk factors. The proposed system is underpinned by blockchain to obtain a cohesive view of the risk factors data from patients across different hospitals and ensure security and privacy of the user's data. We provide a comparative analysis of different medical sensors, devices, and methods to measure and collect the risk factors values in the system. Numerical experiments and comparative analysis were carried out within our proposed system, using the most accurate random forest (RF) model, and the two most used state-of-the-art machine learning approaches, Logistic Regression (LR) and Support Vector Machine (SVM), using three real-life diabetes datasets. The results show that the proposed system predicts diabetes using RF with 4.57% more accuracy on average in comparison with the other models LR and SVM, with 2.87 times more execution time. Data balancing without feature selection does not show significant improvement. When using feature selection, the performance is improved by 1.14% for PIMA Indian and 0.02% for Sylhet datasets, while it is reduced by 0.89% for MIMIC III.
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Affiliation(s)
- Alain Hennebelle
- School of Computing and Information Systems, The University of Melbourne, Australia
| | - Leila Ismail
- School of Computing and Information Systems, The University of Melbourne, Australia
- Intelligent Distributed Computing and Systems Lab, Department of Computer Science and Software Engineering, College of Information Technology, United Arab Emirates University, United Arab Emirates
- National Water and Energy Center, United Arab Emirates University, United Arab Emirates
| | - Huned Materwala
- Intelligent Distributed Computing and Systems Lab, Department of Computer Science and Software Engineering, College of Information Technology, United Arab Emirates University, United Arab Emirates
- National Water and Energy Center, United Arab Emirates University, United Arab Emirates
| | - Juma Al Kaabi
- College of Medicine and Health Sciences, Department of Internal Medicine, United Arab Emirates University, United Arab Emirates
- Tawam and Mediclinic Hospitals, Al Ain, Abu Dhabi, United Arab Emirates
| | - Priya Ranjan
- School of Computer Science, Internet of Things Center of Excellence, University of Petroleum and Energy Studies, India
| | - Rajiv Janardhanan
- Faculty of Medical & Health Sciences, SRM Institute of Science & Technology, India
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88
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Wang S, Sha P, Zhao X, Tao Z, Liu S. Peritendinous adhesion: Therapeutic targets and progress of drug therapy. Comput Struct Biotechnol J 2024; 23:251-263. [PMID: 38173878 PMCID: PMC10762322 DOI: 10.1016/j.csbj.2023.11.059] [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: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Peritendinous adhesion (PA) is one of the most common complications following hand surgery and characterized with abnormal hyperplasia of connective tissue and excessive deposition of extracellular matrix. Subsequently, various clinical symptoms such as chronic pain, limb dyskinesia and even joint stiffness occur and patients are always involved in the vicious cycle of "adhesion - release - re-adhesion", which seriously compromise the quality of life. Until present, the underlying mechanism remains controversial and lack of specific treatment, with symptomatic treatment being the only option to relieve symptoms, but not contributing no more to the fundamentally rehabilitation of basic structure and function. Recently, novel strategies have been proposed to inhibit the formation of adhesion tissues including implantation of anti-adhesion barriers, anti-inflammation, restraint of myofibroblast transformation and regulation of collagen overproduction. Furthermore, gene therapy has also been considered as a promising anti-adhesion treatment. In this review, we provide an overview of anti-adhesion targets and relevant drugs to summarize the potential pharmacological roles and present subsequent challenges and prospects of anti-adhesion drugs.
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Affiliation(s)
| | | | | | - Zaijin Tao
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Hanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Shen Liu
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Hanghai Jiao Tong University School of Medicine, Shanghai 200233, China
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Jarzynska K, Gajewicz-Skretna A, Ciura K, Puzyn T. Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations. Comput Struct Biotechnol J 2024; 25:3-8. [PMID: 38328349 PMCID: PMC10848030 DOI: 10.1016/j.csbj.2024.01.012] [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: 11/27/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
Liposomes, nanoscale spherical structures composed of amphiphilic lipids, hold great promise for various pharmaceutical applications, especially as nanocarriers in targeted drug delivery, due to their biocompatibility, biodegradability, and low immunogenicity. Understanding the factors influencing their physicochemical properties is crucial for designing and optimizing liposomes. In this study, we have presented the kernel-weighted local polynomial regression (KwLPR) nano-quantitative structure-property relationships (nano-QSPR) model to predict the zeta potential (ZP) based on the structure of 12 liposome formulations, including 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 3ß-[N-(N',N'-dimethylaminoethane)-carbamoyl]cholesterol (DC-Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), and L-α-phosphatidylcholine (EPC). The developed model is well-fitted (R 2 = 0.96, RMSE C = 5.76), flexible (Q CVloo 2 = 0.83, RMSE CVloo = 10.77), and reliable (Q Ext 2 = 0.89 RMSE Ext = 5.17). Furthermore, we have established the formula for computing molecular nanodescriptors for liposomes, based on constituent lipids' molar fractions. Through the correlation matrix and principal component analysis (PCA), we have identified two key structural features affecting liposomes' zeta potential: hydrophilic-lipophilic balance (HLB) and enthalpy of formation. Lower HLB values, indicating a more lipophilic nature, are associated with a higher zeta potential, and thus stability. Higher enthalpy of formation reflects reduced zeta potential and decreased stability of liposomes. We have demonstrated that the nano-QSPR approach allows for a better understanding of how the composition and molecular structure of liposomes affect their zeta potential, filling a gap in ZP nano-QSPR modeling methodologies for nanomaterials (NMs). The proposed proof-of-concept study is the first step in developing a comprehensive and computationally based system for predicting the physicochemical properties of liposomes as one of the most important drug nano-vehicles.
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Affiliation(s)
- Kamila Jarzynska
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Agnieszka Gajewicz-Skretna
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Krzesimir Ciura
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Tomasz Puzyn
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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90
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Shafiee A, Fili J, Ghafari S, Sattari MA, Borna N, Pourramzani A. The prevalence of sleep disturbance and its possible associated factors among iranian medical students: A cross-sectional study with a national meta-analysis. Sleep Med X 2024; 7:100107. [PMID: 38374870 PMCID: PMC10875233 DOI: 10.1016/j.sleepx.2024.100107] [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: 06/24/2023] [Revised: 11/25/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Background The aim of this cross-sectional study was to investigate the prevalence of sleep disturbance and its possible associated factors among Iranian medical students. Additionally, a national meta-analysis was conducted to provide a comprehensive overview of sleep disturbance in this population. Methods A sample of medical students from Guilan University of Medical Sciences, Iran was included in the study. The Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep disturbance. Demographic and lifestyle factors, as well as academic performance, were collected through a self-administered questionnaire. The data collected from this study were combined with existing studies through a meta-analysis to estimate the overall prevalence of sleep disturbance among Iranian medical students using the random effects model. Results A total of 249 medical students participated in the study. The prevalence of sleep disturbance among Guilan University of Medical Sciences medical students was found to be 71.1%. A significant difference was observed in total PSQI means regarding medical students' residency (p < 0.001) and their duration of sleep in the last 24 h (p = 0.006). The national prevalence of sleep disturbances was 59% (95% CI: [51%-66%], I2 = 97%). Conclusion Sleep disturbance is highly prevalent among Iranian medical students, with various factors contributing to its occurrence. The findings of this study highlight the need for interventions and strategies to improve sleep quality and overall well-being among this population. The national meta-analysis provides valuable insights into the overall burden of sleep disturbance among Iranian medical students and can serve as a reference for future studies and public health initiatives targeting this issue.
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Affiliation(s)
- Arman Shafiee
- Department of Psychiatry and Mental Health, Alborz University of Medical Sciences, Karaj, Iran
- Student Research Committee, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Jafar Fili
- Department of Psychiatry, Guilan University of Medical Sciences, Rasht, Iran
| | - Samane Ghafari
- Department of Psychiatry, Guilan University of Medical Sciences, Rasht, Iran
- Kavosh Behavioral, Cognitive and Addiction Research Center, Shafa Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Amin Sattari
- Department of Psychiatry and Mental Health, Alborz University of Medical Sciences, Karaj, Iran
| | - Nahid Borna
- Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Pourramzani
- Department of Psychiatry, Guilan University of Medical Sciences, Rasht, Iran
- Kavosh Behavioral, Cognitive and Addiction Research Center, Shafa Hospital, Guilan University of Medical Sciences, Rasht, Iran
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91
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Neely SR, Witkowski K. Belief in misinformation and acceptance of COVID-19 vaccine boosters: A survey analysis. PEC Innov 2024; 4:100261. [PMID: 38357380 PMCID: PMC10865392 DOI: 10.1016/j.pecinn.2024.100261] [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: 09/29/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Objective This study examines the impact of misinformation belief on the willingness of American adults to receive ongoing COVID-19 vaccine boosters. Methods A representative survey of 600 adults in the state of Florida was fielded in August of 2023. For this study, responses were analyzed for the 443 previously vaccinated respondents in that sample using both descriptive and inferential statistical methods. Results Among previously vaccinated individuals, belief in misinformation remained relatively high. 49% of respondents believe that COVID-19 vaccines contain a live strain of the virus, and roughly 40% believe that vaccines can cause you to "get sick" with COVID-19. Belief in misinformation was associated with a statistically significant decrease in the likelihood of receiving ongoing vaccine boosters, ceteris paribus. Conclusion While confidence in public health guidelines is the most compelling determinant of vaccine acceptance, misinformation continues to undermine vaccination efforts. Addressing common myths about COVID-19 vaccines may help to improve booster shot acceptance among previously vaccinated Americans. Innovation Throughout the COVID-19 pandemic, health professionals and public health agencies have been forced to innovate in real-time, as digital platforms have fueled the spread of viral misinformation. This study aims to inform these efforts by exploring and deepening our understanding of the impact that belief in misinformation has on vaccination behaviors.
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Affiliation(s)
- Stephen R. Neely
- School of Public Affairs, University of South Florida, 4202 E. Fowler Ave, SOC 107, Tampa, FL 33620, United States
| | - Kaila Witkowski
- School of Public Administrtion, Florida Atlantic University, 777 Glades Road, SO 202, Boca Raton, FL 33431, United States
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92
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Varner-Perez SE, Hoffman SM, Coleman-Phox K, Bhamidipalli S, Monahan PO, Kuppermann M, Tucker Edmonds B. Feasibility and acceptability of chaplain decision coaching on Periviable resuscitation decision quality: A pilot study. PEC Innov 2024; 4:100266. [PMID: 38440389 PMCID: PMC10909622 DOI: 10.1016/j.pecinn.2024.100266] [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: 09/22/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/06/2024]
Abstract
Objective To pilot test and assess the feasibility and acceptability of chaplain-led decision coaching alongside the GOALS (Getting Optimal Alignment around Life Support) decision support tool to enhance decision-making in threatened periviable delivery. Methods Pregnant people admitted for threatened periviable delivery and their 'important other' (IO) were enrolled. Decisional conflict, acceptability, and knowledge were measured before and after the intervention. Chaplains journaled their impressions of training and coaching encounters. Descriptive analysis and conventional content analysis were completed. Results Eight pregnant people and two IOs participated. Decisional conflict decreased by a mean of 6.7 (SD = 9.4) and knowledge increased by a mean of 1.4 (SD = 1.8). All rated their experience as "good" or "excellent," and the amount of information was "just right." Participants found it "helpful to have someone to talk to" and noted chaplains helped them reach a decision. Chaplains found the intervention a valuable use of their time and skillset. Conclusion This is the first small-scale pilot study to utilize chaplains as decision coaches. Our results suggest that chaplain coaching with a decision support tool is feasible and well-accepted by parents and chaplains. Innovations Our findings recognize chaplains as an underutilized, yet practical resource in value-laden clinical decision-making.
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Affiliation(s)
- Shelley E. Varner-Perez
- Department of Spiritual Care and Chaplaincy, Indiana University Health, Indianapolis, Indiana, USA
| | - Shelley M. Hoffman
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kimberly Coleman-Phox
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Sruthi Bhamidipalli
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Patrick O. Monahan
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Miriam Kuppermann
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Brownsyne Tucker Edmonds
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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93
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Zhai S, Zhang L, Li X, Yu Q, Liu C. Clustering human dental pulp fibroblasts spontaneously activate NLRP3 and AIM2 inflammasomes and induce IL-1β secretion. Regen Ther 2024; 27:12-20. [PMID: 38487102 PMCID: PMC10937208 DOI: 10.1016/j.reth.2024.02.010] [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: 01/19/2023] [Revised: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Objectives The objective of the present study was to investigate whether NOD-like receptor family pyrin domain-containing 3 (NLRP3) and absent in melanoma 2 (AIM2) inflammasomes pathways were involved in an experimental model of fibroblast activation named nemosis, which was used to mimic circumstances without bacteria stimulation. Methods Nemosis of human dental pulp fibroblast (DPFs) was induced by three-dimensional culture in U-shaped 96-well plates and investigated by scanning electron microscopy (SEM). DPFs monolayers were used as control. Annexin V-FITC/7-AAD apoptosis assay was performed on the DPFs spheroids by flowcytometry. Caspase-1 activity detection assay was conducted on the DPFs spheroids. Quantitative real-time polymerase chain reaction (qRT-PCR), cytokine measurements, Western blot and the effect of COX-2 inhibitor on spheroids was studied. Results SEM study observed human dental pulp fibroblast clusters and cell membranes damage on the surface of DPFs spheroids. The percentages of necrotic cells from DPFs spheroids gradually increased as the incubation time increased. A statistically significant increase in caspase-1 activity was observed after DPFs spheroids formation. DPFs spheroids displayed significant amounts of NLRP3, AIM2 mRNA and protein expression, caspase-1 mRNA expression and cleaved Caspase-1 protein expression and high IL-1β concentrations (P < 0.05) than DPFs monolayers. Specific COX-2 inhibitor (NS-398) decreased NLRP3 mRNA and protein expression, cleaved Caspase-1 protein expression, Caspase-1 activity and IL-1β mRNA expression and IL-1β concentrations (P < 0.05). However, Specific COX-2 inhibitor had no impact on AIM2 mRNA and protein expression, caspase-1 mRNA expression and pro-Caspase-1 protein expression. Conclusions In conclusion, clustering human DPFs spontaneously activated NLRP3 and AIM2 inflammasomes and induced IL-1β secretion which could be partially attenuated by COX-2 inhibitor. Thus, nemosis could become a powerful model for studying mechanisms underlying aseptic pulpitis.
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Affiliation(s)
- Shafei Zhai
- Department of Stomatology, Xi'an Medical University, Xi'an, 710075, Shaanxi Province, China
| | - Lihui Zhang
- Department of Stomatology, Xi'an Medical University, Xi'an, 710075, Shaanxi Province, China
| | - Xue Li
- Department of Stomatology, Xi'an Medical University, Xi'an, 710075, Shaanxi Province, China
| | - Qi Yu
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, 710021, Shaanxi Province, China
| | - Changkui Liu
- Department of Stomatology, Xi'an Medical University, Xi'an, 710075, Shaanxi Province, China
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94
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Wahid ARA, Taher SG, Mohamed AM, Atef D. Physical therapy exercises for improving intermittent exotropia control post-strabismus surgery: A randomized controlled study. Hong Kong Physiother J 2024; 44:127-135. [PMID: 38510153 PMCID: PMC10949105 DOI: 10.1142/s1013702524500100] [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: 07/14/2023] [Accepted: 10/26/2023] [Indexed: 03/22/2024] Open
Abstract
Background Exotropia control is deteriorated by post-strabismus surgery in many cases. Improving this control is considered as an important factor for success of the strabismus surgery like ocular motor alignment. Objective To determine the therapeutic effect of postoperative eye exercises on exodeviation eye control after the strabismus surgery. Methods Forty patients suffering from intermittent exotropia after strabismus surgery were randomly divided into experimental group and control groups. Both groups received the usual medical care, while the experimental group received different types of eye exercises using physiotherapy modalities in 24 sessions over three months (two sessions a week). The measurement of exotropia control for near target and far target using the office-based scale was done before and after the treatment. Results There was a significant improvement in near eye control post-treatment (0 . 45 ± 0 . 61 ) in the experimental group compared with control group (3 . 65 ± 0 . 88 ) as the mean difference was -3.20 and 95% CI of the difference between them was -3.645--2.755 with P < 0 . 01 . Also, far eye control improved post-treatment in the experimental group (0 . 75 ± 0 . 64 ) compared with control group (4 . 00 ± 0 . 86 ) with mean difference of -3.250 and 95% CI of the difference between them was -3.727--2.773 with P < 0 . 01 . Conclusions For patients with intermittent exotropia who had undergone strabismus surgery, the addition of physiotherapy exercises for the eye provided significant improvements in exotropia control for near target and far target.
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Affiliation(s)
- Amany R Abdel Wahid
- Department of Physical Therapy for Surgery, Faculty of Physical Therapy, Cairo University, Giza, Egypt
| | - Sameh G Taher
- Pediatric Ophthalmology and Strabismology Department, Research Institute of Ophthalmology, Cairo, Egypt
| | - Ayah Mohmoud Mohamed
- Department of Basic Science, Faculty of Physical Therapy, Cairo University, Giza, Egypt
| | - Doaa Atef
- Department of Physical Therapy for Surgery, Faculty of Physical Therapy, Cairo University, Giza, Egypt
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95
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Hu C, Li Q, Xiang L, Luo Y, Li S, An J, Yu X, Zhang G, Chen Y, Wang Y, Wang D. Comprehensive pan-cancer analysis unveils the significant prognostic value and potential role in immune microenvironment modulation of TRIB3. Comput Struct Biotechnol J 2024; 23:234-250. [PMID: 38161736 PMCID: PMC10757237 DOI: 10.1016/j.csbj.2023.11.043] [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: 07/09/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
TRIB3, a pseudokinase, was previously studied within only some specific cancer types, leaving its comprehensive functions in pan-cancer contexts largely unexplored. Here, we performed an integrated analysis of TRIB3 expression, prognosis, genetic alterations, functional enrichment and tumor immune-related characteristics in 33 cancer types. Our results showed that TRIB3 exhibits high expression levels across 24 different cancer types and correlates closely with unfavorable prognoses. Meanwhile, TRIB3 shows mutations in a wide spectrum of 22 distinct cancer types, with the predominant mutation types being missense mutations and gene amplifications, and significant changes in DNA methylation levels in 14 types of cancer. We further discovered that TRIB3 expression is significantly associated with cancer immune-related genome mutations, such as tumor mutational burden (TMB), microsatellite instability (MSI) and DNA mismatch repair (MMR), and infiltration of immunosuppressive cells, such as CD4+ Th2 cells and myeloid-derived suppressor cells (MDSCs), into the tumor microenvironment. These results indicated that the expression of TRIB3 might reshape the tumor immune microenvironment (TIME) and lead to immunosuppressive "cold" tumors. In addition, our results confirmed that the loss of function of TRIB3 inhibits cell proliferation, promotes apoptosis, and leads to significant enrichment of "hot" tumor-related immune pathways, at least in breast cancer cells, which further supports the important role of TRIB3 in cancer prognosis and TIME regulation. Together, this pan-cancer investigation provided a comprehensive understanding of the critical role of TRIB3 in human cancers, and suggested that TRIB3 might be a promising prognostic biomarker and a potential target for cancer immunotherapy.
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Affiliation(s)
- Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qingzhou Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lei Xiang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yan Luo
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shengrong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jun An
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiankuo Yu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Guochen Zhang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuhui Chen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yumei Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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96
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Ahmad M, Kelly J, Montano CB, Kumar D, Perdomo C, Malhotra M, Amchin J, Moline M. Transitioning insomnia patients from zolpidem to lemborexant: A multicenter, open-label study evaluating a next-dose transition approach to insomnia pharmacotherapy. Sleep Med X 2024; 7:100098. [PMID: 38312371 PMCID: PMC10835435 DOI: 10.1016/j.sleepx.2023.100098] [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: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 02/06/2024] Open
Abstract
Objective Few clinical studies have assessed real-world abrupt transitioning between insomnia medications. This study assessed strategies for directly transitioning patients from zolpidem tartrate (ZOL) immediate/extended release to the dual orexin receptor antagonist, lemborexant (LEM). Methods This randomized, open-label, multicenter study (Study 312; E2006-A001-312) enrolled 53 adults age ≥18 years with insomnia disorder and ≥1-month history of intermittent (3-4 nights/week) or frequent (≥5 nights/week) ZOL use. Subjects recorded their ZOL use in a 3-week Pretreatment Phase, followed by a 2-week Treatment Phase (TRT; Titration) during which ZOL was discontinued. Intermittent ZOL users transitioned to LEM 5 mg (LEM5), Cohort 1, and frequent ZOL users were randomized 1:1 to LEM5, Cohort 2A, or LEM 10 mg (LEM10), Cohort 2B. One dose adjustment was permitted during the TRT. Subjects completing the TRT could continue LEM in the 12-week Extension Phase (EXT). The primary outcome was proportion of subjects who successfully transitioned and remained on LEM at the end of the TRT. Results Most subjects (43 [81.1 %]) successfully transitioned to LEM (9 [90 %], 17 [81.0 %], and 17 [77.3 %] in Cohorts 1, 2A, and 2B, respectively). By the end of the EXT, 66.7 % in Cohort 1 and 60.0 % in Cohort 2A up-titrated to LEM10, whereas 41.2 % in Cohort 2B down-titrated to LEM5; 61.0 % were receiving LEM10 at study end. At the end of the TRT, more subjects taking LEM reported that it helped them return to sleep after waking, compared with those taking ZOL (71.7 % vs. 49.1 %). There were no important differences between treatments regarding how subjects reported feeling as they fell asleep. Most of the treatment-emergent adverse events with LEM were mild in severity. Conclusions Most subjects transitioned successfully to LEM from ZOL (intermittent or frequent use). LEM was well tolerated.
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Affiliation(s)
- Maha Ahmad
- Clinilabs Drug Development Corporation, New York, NY, USA
| | - James Kelly
- Clinilabs Drug Development Corporation, New York, NY, USA
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Hu Y, Wang Y, Hu X, Chao H, Li S, Ni Q, Zhu Y, Hu Y, Zhao Z, Chen M. T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors. Comput Struct Biotechnol J 2024; 23:801-812. [PMID: 38328004 PMCID: PMC10847861 DOI: 10.1016/j.csbj.2024.01.015] [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: 09/21/2023] [Revised: 01/20/2024] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.
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Affiliation(s)
- Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qinyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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Dai Z, Hu T, Wei J, Wang X, Cai C, Gu Y, Hu Y, Wang W, Wu Q, Fang J. Network-based identification and mechanism exploration of active ingredients against Alzheimer's disease via targeting endoplasmic reticulum stress from traditional chinese medicine. Comput Struct Biotechnol J 2024; 23:506-519. [PMID: 38261917 PMCID: PMC10796977 DOI: 10.1016/j.csbj.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/25/2024] Open
Abstract
Alzheimer's disease is a neurodegenerative disease that leads to dementia and poses a serious threat to the health of the elderly. Traditional Chinese medicine (TCM) presents as a promising novel therapeutic therapy for preventing and treating dementia. Studies have shown that natural products derived from kidney-tonifying herbs can effectively inhibit AD. Furthermore, endoplasmic reticulum (ER) stress is a critical factor in the pathology of AD. Regulation of ER stress is a crucial approach to prevent and treat AD. Thus, in this study, we first collected kidney-tonifying herbs, integrated chemical ingredients from multiple TCM databases, and constructed a comprehensive drug-target network. Subsequently, we employed the endophenotype network (network proximity) method to identify potential active ingredients in kidney-tonifying herbs that prevented AD via regulating ER stress. By combining the predicted outcomes, we discovered that 32 natural products could ameliorate AD pathology via regulating ER stress. After a comprehensive evaluation of the multi-network model and systematic pharmacological analyses, we further selected several promising compounds for in vitro testing in the APP-SH-SY5Y cell model. Experimental results showed that echinacoside and danthron were able to effectively reduce ER stress-mediated neuronal apoptosis by inhibiting the expression levels of BIP, p-PERK, ATF6, and CHOP in APP-SH-SY5Y cells. Overall, this study utilized the endophenotype network to preliminarily decipher the effective material basis and potential molecular mechanism of kidney-tonifying Chinese medicine for prevention and treatment of AD.
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Affiliation(s)
- Zhao Dai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Tian Hu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Junwen Wei
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Xue Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Chuipu Cai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yong Gu
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, Hainan Medical University, Haikou 570100, China
| | - Yunhui Hu
- Tasly Pharmaceutical Group Co., Ltd., Tianjin 300402, China
| | - Wenjia Wang
- Tasly Pharmaceutical Group Co., Ltd., Tianjin 300402, China
| | - Qihui Wu
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, Hainan Medical University, Haikou 570100, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
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99
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Chen B, Liu G, Chen Q, Wang H, Liu L, Tang K. Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes. Comput Struct Biotechnol J 2024; 23:406-416. [PMID: 38235362 PMCID: PMC10792170 DOI: 10.1016/j.csbj.2023.12.025] [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: 06/15/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Guohua Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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100
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Luo Y, Zhou T, Liu D, Wang F, Zhao Q. AIMER: A SNP-independent software for identifying imprinting-like allelic methylated regions from DNA methylome. Comput Struct Biotechnol J 2024; 23:566-576. [PMID: 38274999 PMCID: PMC10809074 DOI: 10.1016/j.csbj.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Genomic imprinting is essential for mammalian growth and embryogenesis. High-throughput bisulfite sequencing accompanied with parental haplotype-specific information allows analysis of imprinted genes and imprinting control regions (ICRs) on a large scale. Currently, although several allelic methylated regions (AMRs) detection software were developed, methods for detecting imprinted AMRs is still limited. Here, we developed a SNP-independent statistical approach, AIMER, to detect imprinting-like AMRs. By using the mouse frontal cortex methylome as input, we demonstrated that AIMER performs very well in detecting known germline ICRs compared with other methods. Furthermore, we found the putative parental AMRs AIMER detected could be distinguished from sequence-dependent AMRs. Finally, we found a novel germline imprinting-like AMR using WGBS data from 17 distinct mouse tissue samples. The results indicate that AIMER is a good choice for detecting imprinting-like (parent-of-origin-dependent) AMRs. We hope this method will be helpful for future genomic imprinting studies. The Python source code for our project is now publicly available on both GitHub (https://github.com/ZhaoLab-TMU/AIMER) and Gitee (https://gitee.com/zhaolab_tmu/AIMER).
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Affiliation(s)
| | | | - Deng Liu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Fan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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