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Tagawa K, Matsui K, Tsukamura A, Shibata M, Tsutsui H, Nagai S, Maruo Y. Use of a long-term continuous glucose monitor for predicting sulfonylurea dose in patients with neonatal diabetes mellitus: a case series. Clin Pediatr Endocrinol 2025; 33:131-138. [PMID: 38993723 PMCID: PMC11234181 DOI: 10.1297/cpe.2023-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/17/2024] [Indexed: 07/13/2024] Open
Abstract
Neonatal diabetes mellitus (NDM) is a monogenic form of diabetes that presents with uncontrolled hyperglycemia during the first 6 months of life. NDM is a rare disease in which gene variants mainly cause β-cell loss or dysfunction (6q24 duplication, KCNJ11, and ABCC8). Although NDM is primarily treated through insulin therapy, it is highly challenging to manage blood glucose levels using insulin therapy during infancy. In contrast, KCNJ11 and ABCC8 mutant patients received oral sulfonylureas (SU) instead of insulin injections; however, the dose and frequency differ among individuals. Continuous glucose monitoring (CGM) is useful in patients with type 1 diabetes; but reports on patients with NDM are lacking. Herein, we report two cases of NDM with the KCNJ11 variant. We used CGM not only during insulin injection therapy but also after switching to oral SU therapy. The CGM data can also be used to determine the dose and frequency of SU. Furthermore, long-term CGM may be useful for adjusting SU dose and frequency, and maintaining good glycemic control not only during insulin injection but also during oral SU therapy.
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Ellis R, Weiss A. Human vaccines and immunotherapeutics: News February 2024. Hum Vaccin Immunother 2024; 20:2327910. [PMID: 38478989 PMCID: PMC10939145 DOI: 10.1080/21645515.2024.2327910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
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Ibrahim K, Thwood D, ELgheriani H, Salem M, Elgadiym Z, Zaghdani A, Alhudiri I, Habibi A, Elfahem A, Belaid S, Ermithi O, Almaghrabi M, ELmaryul A, Almadah S, Rayes A, El Meshri SE, El Salabi A, Elzagheid A. Prevalence of multi-drug resistant bacteria in intensive care units at Tripoli University Hospital, Tripoli, Libya. Libyan J Med 2024; 19:2348235. [PMID: 38718270 PMCID: PMC11080667 DOI: 10.1080/19932820.2024.2348235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Among hospitalized patients worldwide, infections caused by multidrug-resistant (MDR) bacteria are a major cause of morbidity and mortality. This study aimed to isolate MDR bacteria from five intensive care units (ICUs) at Tripoli University Hospital (TUH). A prospective cross-sectional study was conducted over a seven-month period (September 2022 to March 2023) across five ICUs at TUH. A total of 197 swabs were collected from Patients', healthcare workers' and ICUs equipment. Samples collected from patients were nasal swabs, oral cavity swabs, hand swabs, sputum specimens, skin swabs, umbilical venous catheter swabs, and around cannula. Swabs collected from health care workers were nasal swabs, whereas ICUs equipment's samples were from endotracheal tubes, oxygen masks, and neonatal incubators. Identification and antimicrobial susceptibility test was confirmed by using MicroScan auto SCAN 4 (Beckman Coulter). The most frequent strains were Gram negative bacilli 113 (57.4%) with the predominance of Acinetobacter baumannii 50/113 (44%) followed by Klebsiella pneumoniae 44/113 (40%) and Pseudomonas aeruginosa 6/113 (5.3%). The total Gram positive bacterial strains isolated were 84 (42.6%), coagulase negative Staphylococci 55 (66%) with MDRs (89%) were the most common isolates followed by Staphylococcus aureus 15 (17.8%). Different antibiotics were used against these isolates; Gram- negative isolates showed high resistance rates to ceftazidime, gentamicin, amikacin and ertapenem. A. baumannii were the most frequent MDROs (94%), and the highest resistance rates in Gram-positive strains were observed toward ampicillin, oxacillin, ampicillin/sulbactam and Cefoxitin, representing 90% of total MDR Gram-positive isolates. ESBL and MRS were identified in most of strains. The prevalence of antibiotic resistance was high for both Gram negative and Gram positive isolates. This prevalence requires strict infection prevention and control intervention, continuous monitoring, implementation of effective antibiotic stewardship, immediate, concerted and collaborative action to monitor its prevalence and spread in the hospital.
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Lv Z, Hou J, Wang Y, Wang X, Wang Y, Wang K. Reply to "Knowledge-map analysis and bladder cancer immunotherapy: Comment". Hum Vaccin Immunother 2024; 20:2325756. [PMID: 38537105 PMCID: PMC10993802 DOI: 10.1080/21645515.2024.2325756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
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Oishi T, Hasegawa S, Nakano T, Sudo S, Kuwajima H, Tokuriki S, Tamura T. Changes in vaccine coverage and incidence of acute gastroenteritis and severe rotavirus gastroenteritis in children <5 years in Shibata City, Niigata Prefecture, Japan. Hum Vaccin Immunother 2024; 20:2322202. [PMID: 38478958 PMCID: PMC10939147 DOI: 10.1080/21645515.2024.2322202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
Rotavirus (RV) vaccines were first introduced in 2011 and adopted for universal vaccination in 2020 in Japan. However, the effectiveness of RV vaccines after being adopted for universal vaccination in 2020 has not been reported. Because of the easy accessibility of clinics in Japan, many children are not usually hospitalized for RV gastroenteritis (RVGE). Therefore, in order to evaluate the impact of the RV vaccine since 2008, we investigated the incidence of hospitalization for RVGE as well as the frequency of children aged < 5 years who received medical treatment for severe RVGE at clinics in Shibata City, Japan. The RV vaccine coverage rate was 94.0% (1,046/1,113) in Shibata City after universal vaccination in 2020; this was a significant increase from previous rates. The incidence per 1000 person - years for RVGE hospitalization and severe RVGE at clinics were significantly higher among children aged < 3 years than in previous time periods. The incidence in children with all acute gastroenteritis (AGE) decreased significantly after universal vaccination during the COVID-19 pandemic. The proportion of severe RVGE among all AGE cases also decreased significantly after universal vaccination among children aged < 3 years (0.0%) and those aged 3-4 years (0.6%). There were significant differences in the distribution of RV genotypes isolated from the feces of children with RVGE between different eras divided by RV vaccination rates, especially G1P[8], which was the major genotype before it recently almost disappeared. Further studies are warranted to assess the impact of the COVID-19 pandemic.
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Li K, Yu L, Gao L, Zhu L, Feng X, Deng S. Unveiling molecular mechanisms of pigment synthesis in gardenia ( Gardenia jasminoides) fruits through integrative transcriptomics and metabolomics analysis. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 9:100209. [PMID: 38973987 PMCID: PMC11225661 DOI: 10.1016/j.fochms.2024.100209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/23/2024] [Accepted: 06/02/2024] [Indexed: 07/09/2024]
Abstract
This study conducted a combined transcriptomics and metabolomics analysis in premature and mature developmental stages of Gardenia jasminoides Ellis fruits to identify the molecular mechanisms of pigment synthesis. The transcriptomics data produced high-quality clean data amounting to 46.98 gigabytes, exhibiting a mapping ratio of 86.36% to 91.43%. Transcriptomics analysis successfully identified about 3,914 differentially expressed genes which are associated with pivotal biological processes, including photosynthesis, chlorophyll, biosynthetic processes, and protein-chromophore linkage pathways. Functional diversity was clarified by the Clusters of Orthologous Groups (COG) classification, which focused mainly on pigment synthesis functions. Pathways analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) revealed critical pathways affecting pigment development. Metabolomics studies were carried out utilizing Ultra Performance Liquid Chromatography and mass spectrometry (UPLC-MS). About 480 metabolites were detected via metabolomics investigation, the majority of that were significantly involved in pigment synthesis. Cluster and pathway analyses revealed the importance of pathways such as plant secondary metabolite biosynthesis, biosynthesis of phenylpropanoids and plant hormone signal transduction in pigment synthesis. Current research advances our comprehension of the underlying mechanisms at the molecular level governing pigment synthesis in gardenia fruits, furnishing valuable insights for subsequent investigations.
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Bennett C, Beach S, Pacheco K, Hsu AT, Tanuseputro P, Manuel DG. Exploring perceptions of online calculators for identifying community-dwelling older people at risk of dying: A qualitative study. PEC INNOVATION 2024; 5:100313. [PMID: 39040661 PMCID: PMC11260570 DOI: 10.1016/j.pecinn.2024.100313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/31/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024]
Abstract
Objectives This study aimed to assess the acceptability, value, and perceived barriers of using electronic risk calculators for predicting and communicating the risk of death in community-dwelling older adults. Methods One focus group and eight interviews were conducted with 16 participants with experience caring for patients or family members at end of life. A prototype mortality risk tool was used to anchor discussions. Data were analysed using a qualitative content analysis approach. Results Five themes emerged: acceptability, communication, barriers to use, broadening the circle of care, and tool limitations. Participants found the tool helpful for preparation, planning, and providing care, but disagreed on its community availability. Personalized risk estimates were valued for facilitating early goals of care conversations and normalizing discussions about death. However, concerns were raised about the tool's interpretation for individuals with different language, cultural, or educational backgrounds. Conclusions While electronic risk calculators were found to be acceptable, balancing autonomy with varying preferences for receiving the information and potential need for support is crucial. Innovation Providing patient-oriented life-expectancy estimates can enhance decisional capacity and facilitate shared decision-making between patients, their families, and healthcare professionals. Further research is needed to explore effective communication of personalized risk tools and additional benefits, harms, and barriers to implementation.
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Dijkman BL, Luttik ML, Paans W, Driever EM, van der Wal-Huisman H, Brand PL, van Leeuwen B. Associations between physicians' SDM behaviour and participation of older patients and family members in triadic decision-making: An observational study. PEC INNOVATION 2024; 5:100306. [PMID: 39027230 PMCID: PMC11254731 DOI: 10.1016/j.pecinn.2024.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/26/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
Background Medical consultations with older patients often include triadic conversations and decision-making processes involving physicians, patients, and family members. The presence of family members may change the communication dynamics and therefore increase the complexity of the consultation and decision-making process. Objective This study explored associations between physicians' shared decision-making (SDM) behaviour and patients' and family members' participation in the decision-making process. Methods Using an observational design, we analysed 95 recorded consultations between medical specialists, patients aged ≥65 years, and accompanying family members at a Dutch hospital. The OPTIONMCC was used to assess the physicians' SDM behaviour and patients' and family members' levels of involvement in SDM. Results We found a strong positive correlation between physicians' behaviour and patients' and family members' participation in SDM (0.68 and 0.64, respectively, p < .01). Family members were more involved in SDM for patients aged 80 and older. Conclusion While not asserting causation, our study suggests physicians potentially play a facilitating role in shaping the SDM process together with proactive contributions from patients and family members. Innovation The results offer new insights into triadic SDM and provide suggestions for refining the OPTIONMCC. Further research is recommended into participants' mutual directional influences in triadic SDM.
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Li M, Devane D, Beecher C, Dowling M, Duffy AG, Duggan C, Grimes DR, Kennan A, Kilty C, Nsangi A, Oxman AD, Stewart DC, Toomey E, Tierney M. Prioritising Key Concepts for informed health choices in cancer: An evidence-based online educational programme. PEC INNOVATION 2024; 5:100311. [PMID: 39027229 PMCID: PMC11254741 DOI: 10.1016/j.pecinn.2024.100311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024]
Abstract
Objective The overabundance of health misinformation has undermined people's capacity to make evidence-based, informed choices about their health. Using the Informed Health Choices (IHC) Key Concepts (KCs), we are developing a two-stage education programme, Informed Health Choices-Cancer (IHC-C), to provide those impacted by cancer with the knowledge and skills necessary to think critically about the reliability of health information and claims and make well-informed choices. Stage 1 seeks to prioritise the most relevant Key Concepts. Methods A project group and a patient and carer participation group completed a two-round prioritisation process. The process involved disseminating pre-reading materials, training sessions, and a structured judgement form to evaluate concepts for inclusion. Data from each round were analysed to reach a consensus on the concepts to include. Results Fourteen participants were recruited and completed the first-round prioritisation. Fifteen participants undertook the second-round prioritisation. Nine Key Concepts were selected for the programme across five training sessions and two consensus meetings. Conclusion The prioritised concepts identified represent the most pertinent aspects of cancer-related information for those impacted by the disease. By incorporating these concepts into educational materials and communication strategies, healthcare providers and organisations can potentially help cancer patients, survivors, and their loved ones to recognise and combat cancer-related misinformation more effectively. Innovation This study introduces a participatory prioritisation process, which integrates the expertise of healthcare professionals with the insights of patients and carers, thereby enhancing the programme's relevance and applicability.
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Meyer R, Kotnis SR, Fog-Petersen CM, Tarnow L, Giraldi A, Jürgens G, Jacobsen CB. Steps to construct educational interventions on sexual dysfunction for healthcare professionals and patients. Experiences from the SECRET research study-group. PEC INNOVATION 2024; 5:100310. [PMID: 39035236 PMCID: PMC11259809 DOI: 10.1016/j.pecinn.2024.100310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/17/2024] [Accepted: 06/17/2024] [Indexed: 07/23/2024]
Abstract
Objectives To design an educational intervention on sexual dysfunction for patients suffering from schizophrenia and diabetes based on patients' and other relevant stakeholders' preferences, and to offer transparency into the basic decision-making process behind a final design. Methods We conducted a three-part investigation to explore theory, preferences, and feasibility based on literature searches and interviews with patients, healthcare professionals, heads of Assertive Community Treatment Centres and experts. Based on a content analysis of this material, a draft of the intervention was developed. The draft was quality-checked by involvement of stakeholder representatives and refined to its final design. Results The intervention evolved into having two components: One intervention for patients and one for healthcare professionals. In patient education, meeting peers and predictability were important factors. For healthcare professionals, daily clinical activities were prioritised. Conclusions We present a framework for an educational intervention about sexual dysfunction, schizophrenia and diabetes targeting both patients and healthcare professionals. Innovation The transparency of the design process underlying the interventions allows for reproduction and eases further refinement, extension, and adjustment if implemented in other contexts.
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Felber SJ, Zambrano SC, Guffi T, Schmitz FM, Brem BG, Schnabel KP, Guttormsen S, Eychmüller S. How to talk about dying? The development of an evidence-based model for communication with patients in their last days of life and their family caregivers. PEC INNOVATION 2024; 5:100309. [PMID: 39027227 PMCID: PMC11254737 DOI: 10.1016/j.pecinn.2024.100309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
Objective To help healthcare professionals (HCP) act with more confidence when communicating about approaching death, we sought to develop a communication model for HCP to facilitate conversations with dying patients and family caregivers (FC) in nonemergency situations. Methods We used a four-phase integrative approach: (1) creation of a preliminary model based on a systematic literature review and expert knowledge, (2) review of the model draft by international palliative care experts, (3) review by key stakeholders, and (4) final appraisal by communication experts. Results After the clinical recognition of dying, the communication model provides a structure and practical communication aids for navigating the conversation based on three phases. It describes the content and relational level as core dimensions of effective conversations about approaching death and highlights the importance of HCP self-awareness and self-care when caring for the dying. Conclusion Based on systematic involvement of key stakeholders, the model supports clinicians navigating challenging conversations about approaching death with dying patients and their FC successfully and with more confidence. Innovation This study expands the theoretical basis for communication about approaching death and offers a pragmatic model for educational interventions and clinical use.
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Tessaro I, Hooper SM, Watt D, Menestres D, Farrell D. Development of an online tool to support financial and legal planning in dementia. PEC INNOVATION 2024; 5:100312. [PMID: 39035235 PMCID: PMC11259804 DOI: 10.1016/j.pecinn.2024.100312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/16/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024]
Abstract
Objective To develop, assess, and refine an online educational tool, Plan for Clarity, to support financial and legal planning in dementia. Methods A Delphi mixed-method study with three rounds of anonymous review by lay and professional stakeholders was designed to reach consensus about the content of the online tool and explore the socio-cultural and behavioral factors that could affect access and use. Results Consensus showed that the online tool covered key information, knowledge, and communication skills for financial and legal planning. Study themes: 1) the online tool had to be easy to navigate with relevant, easily understood information; 2) people with early signs of memory difficulties would be able to use the tool; 3) a referral from a trusted source is a primary way to facilitate access and use of the tool; and 4) discussions about financial and legal issues should be held early, ahead of barriers that can block discussion. Conclusion These data suggest this online tool is relevant and feasible for dementia care and support as well as aging more generally. Innovation Plan for Clarity is innovative as an evidence and theory-driven online education tool to address financial and legal planning for dementia care, particularly among underserved older adults.
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Obilor HN, Veryha O, Weisz T, Botros M, Wilson R, Tranmer J, Woo K. The feasibility of a social media-based foot self-management education and support program for adults with diabetes: A partially randomized preference trial. PEC INNOVATION 2024; 5:100307. [PMID: 39027228 PMCID: PMC11254740 DOI: 10.1016/j.pecinn.2024.100307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/27/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
Aim To assess the feasibility of Diabetic Foot Care Group (DFCG), a social media-based self-management education and support intervention, for people with diabetes (PWD) empowerment in diabetes-related foot ulceration prevention. Methods A partially randomized preference trial was conducted among 32 PWD. DFCG was implemented through Facebook. Participants in the intervention group joined the DFCG in addition to their usual care, while the control group received usual care. Data were collected online using questionnaires on participants' DFCG acceptance, engagement and preliminary efficacy on nine diabetes foot care-related outcomes at baseline, one, and three months post-intervention. Results The participants' study intervention acceptability and engagement rates were 84.2% and 55.2%, respectively. DFCG efficacy rate compared to usual care was 88.9% to 22.2%. Three diabetes foot care-related outcomes increased significantly in the intervention group three-month post-intervention: foot self-care adherence (p = 0.001, ηp 2 = 0.35), preventive foot self-care practice (p = 0.002, ηp 2 = 0.33), and physical health status (p < 0.02, ηp 2 = 0.23). Conclusion DFCG is feasible and could effectively improve diabetes foot care-related outcomes. Innovation Social media is an innovative approach healthcare professionals could utilize to virtually support PWD in ongoing learning and engagement in optimal foot self-care activities. Trial registration ClinicalTrials.gov, Identifier: NCT04395521.
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Suire K, Hastert M, Herrmann SD, Donnelly JE. Feasibility of the flipped classroom approach for health education in a clinical weight loss program. PEC INNOVATION 2024; 5:100308. [PMID: 38988775 PMCID: PMC11231636 DOI: 10.1016/j.pecinn.2024.100308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/28/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Abstract
Aim To assess the feasibility of the flipped classroom pedagogy in a clinical weight loss program and its impact on 6-month weight change. Methods Adults with overweight/obesity enrolled in a 6-month program with a structured diet (portion-controlled meals and fruits/vegetables) and exercise plan (≥150mins/week), plus weekly, 1-h group education sessions. Sessions used a flipped classroom approach: educational content was delivered beforehand via podcast/video and book readings and session time involved application-based activities (e.g., case studies, games). Satisfaction surveys were completed at 3 months. Weight change was assessed using paired t-tests (SAS 9.4, significance 0.05). Results Eighteen participants completed 6 months (retention 94%). Participants maintained diet adherence and exercise at 3 months (∼84% diet adherence, ∼153mins exercise/week) and 6 months (∼83% diet adherence, ∼158mins exercise/week), as well as attendance to behavioral sessions (3 months: 77%; 6mo: 71%). Satisfaction surveys showed high program enjoyment (∼8.1/10). Mean weight change at 3 and 6 months was -6.5 ± 4.2% and - 9.3 ± 5.0% (both p < 0.01), respectively. Conclusion The flipped classroom pedagogy was feasible for delivery in a clinical weight loss program and supported significant 6-month weight loss. Innovation This is the first evaluation of the flipped classroom in a clinical setting and supports the investigation of this pedagogy in weight management.
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Chandranaik D, Goyal JP, Singh K, Kumar P. Association of digital media use with sleep habits in school children: A cross-sectional study. Sleep Med X 2024; 8:100117. [PMID: 38994446 PMCID: PMC11234148 DOI: 10.1016/j.sleepx.2024.100117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
Background The use of digital media (DM) is increasing among school-children, which can affect their sleep habits. The primary objective of this study was to evaluate the association of DM use with sleep habits in school-children. Methods It was a cross-sectional study of healthy school children. Sleep habits and DM use were assessed using the Children's Sleep Habits Questionnaire (CSHQ) and SCREENS-Q, respectively. The Pearson correlation coefficient was used to establish the correlation between the two variables. Logistic regression analysis was performed to quantify the extent of association between variables. A p-value <0.05 was considered statistically significant. Results A total of 205 children were enrolled with a mean (SD) age of 7.1 (2.1) years. The mean (SD) sleep duration was 7.58 (0.80) hours. The mean (SD) CSHQ score was 50.6 (5.1). Use of DM was observed in 204 (99.5 %) children. On multivariate logistic regression analysis, DM use ≥2 h/day was significantly associated with higher CSHQ score (OR 1.28, 95%CI 1.18-1.40; p = 0.001). Sleep domains significantly affected by DM use ≥2 h/day were bedtime resistance (OR 1.55, 95 % CI 1.24-1.94; p < 0.001), sleep duration (OR 0.40, 95 % CI 0.28-0.58:p < 0.001), sleep anxiety (OR 1.69, 95%CI 1.40-2.04:p < 0.001), night awakening (OR 4.81 95 % CI 2.98-7.78:p < 0.001), parasomnias (OR 1.86, 95 % CI 1.45-2.38:p < 0.001), and daytime sleepiness (OR1.89,95 % CI 1.52-2.36: p < 0.001). DM use 30 min before bedtime was significantly associated with a higher CSHQ score (OR 1.32, 95 % CI 1.20-1.45; p < 0.001). In bivariate regression analysis, DM use ≥2 h/day was associated with poor academic performance (OR 2.36 95 % CI 1.28-4.35; p 0.006). Conclusion This study has shown that the average sleep duration in children was shorter than the recommended duration. DM use was common in school children and it has a significant association with sleep habits especially with use of ≥2 h/day and 30 mints before bedtime. It was also associated with poor academic performance. Public awareness on effect of DM use in school children is the need of the hour.
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Qiao Y, Yang R, Liu Y, Chen J, Zhao L, Huo P, Wang Z, Bu D, Wu Y, Zhao Y. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures. Comput Struct Biotechnol J 2024; 23:617-625. [PMID: 38274994 PMCID: PMC10808905 DOI: 10.1016/j.csbj.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high-throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein-RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two sub-models to extract local motif-like information and long-term context information. We show that DeepFusion performs best compared with other cutting-edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBP-binding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
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Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
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Yao M, Zhang L, Teng X, Lei Y, Xing X, Ren T, Pan Y, Zhang L, Li Z, Lin J, Zheng Y, Xing L, Zhou J, Wu C. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Comput Struct Biotechnol J 2024; 23:700-710. [PMID: 38292475 PMCID: PMC10825174 DOI: 10.1016/j.csbj.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.
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Yadav S, Vora DS, Sundar D, Dhanjal JK. TCR-ESM: Employing protein language embeddings to predict TCR-peptide-MHC binding. Comput Struct Biotechnol J 2024; 23:165-173. [PMID: 38146434 PMCID: PMC10749252 DOI: 10.1016/j.csbj.2023.11.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023] Open
Abstract
Cognate target identification for T-cell receptors (TCRs) is a significant barrier in T-cell therapy development, which may be overcome by accurately predicting TCR interaction with peptide-bound major histocompatibility complex (pMHC). In this study, we have employed peptide embeddings learned from a large protein language model- Evolutionary Scale Modeling (ESM), to predict TCR-pMHC binding. The TCR-ESM model presented outperforms existing predictors. The complementarity-determining region 3 (CDR3) of the hypervariable TCR is located at the center of the paratope and plays a crucial role in peptide recognition. TCR-ESM trained on paired TCR data with both CDR3α and CDR3β chain information performs significantly better than those trained on data with only CDR3β, suggesting that both TCR chains contribute to specificity, the relative importance however depends on the specific peptide-MHC targeted. The study illuminates the importance of MHC information in TCR-peptide binding which remained inconclusive so far and was thought dependent on the dataset characteristics. TCR-ESM outperforms existing approaches on external datasets, suggesting generalizability. Overall, the potential of deep learning for predicting TCR-pMHC interactions and improving the understanding of factors driving TCR specificity are highlighted. The prediction model is available at http://tcresm.dhanjal-lab.iiitd.edu.in/ as an online tool.
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Rosati D, Palmieri M, Brunelli G, Morrione A, Iannelli F, Frullanti E, Giordano A. Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review. Comput Struct Biotechnol J 2024; 23:1154-1168. [PMID: 38510977 PMCID: PMC10951429 DOI: 10.1016/j.csbj.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.
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Guo H, Hu Z, Yang X, Yuan Z, Wang M, Chen C, Xie L, Gao Y, Li W, Bai Y, Lin C. Smad4 regulates TGF-β1-mediated hedgehog activation to promote epithelial-to-mesenchymal transition in pancreatic cancer cells by suppressing Gli1 activity. Comput Struct Biotechnol J 2024; 23:1189-1200. [PMID: 38525105 PMCID: PMC10957521 DOI: 10.1016/j.csbj.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/10/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024] Open
Abstract
Pancreatic cancer (PC) is an aggressive and metastatic gastrointestinal tumor with a poor prognosis. Persistent activation of the TGF-β/Smad signaling induces PC cell (PCC) invasion and infiltration via epithelial-to-mesenchymal transition (EMT). Hedgehog signaling is a crucial pathway for the development of PC via the transcription factors Gli1/2/3. This study aimed to investigate the underlying molecular mechanisms of action of hedgehog activation in TGF-β1-triggered EMT in PCCs (PANC-1 and BxPc-3). In addition, overexpression and shRNA techniques were used to evaluate the role of Smad4 in TGF-β1-treated PCCs. Our data showed that TGF-β1 promoted PCC invasion and infiltration via Smad2/3-dependent EMT. Hedgehog-Gli signaling axis in PCCs was activated upon TGF-β1 stimulation. Inhibition of hedgehog with cyclopamine effectively antagonized TGF-β1-induced EMT, thereby suggesting that the hedgehog signaling may act as a downstream cascade signaling of TGF-β1. As a key protein that assists the nuclear translocation of Smad2/3, Smad4 was highly expressed in PANC-1 cells, but not in BxPc-3 cells. Conversely, Gli1 expression was low in PANC-1 cells, but high in BxPc-3 cells. Furthermore, knockdown of Smad4 in PANC-1 cells by shRNA inhibited TGF-β1-mediated EMT and collagen deposition. Overexpression of Smad4 did not affect TGF-β1-mediated EMT due to the lack of significant increase in nuclear expression of Smad4. Importantly, Gli1 activity was upregulated by Smad4 knockdown in PANC-1 cells and downregulated by Smad4 overexpression in BxPc-3 cells, indicating that Gli1 may be a negative target protein downstream of Smad4. Thus, Smad4 regulates TGF-β1-mediated hedgehog activation to promote EMT in PCCs by suppressing Gli1 activity.
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Zeng M, He Y, Yang Y, Wang M, Chen Y, Wei X. Mesenchymal stem cell-derived extracellular vesicles relieve endothelial cell senescence via recovering CTRP9 upon repressing miR-674-5p in atherosclerosis. Regen Ther 2024; 27:354-364. [PMID: 38645280 PMCID: PMC11031720 DOI: 10.1016/j.reth.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 03/24/2024] [Indexed: 04/23/2024] Open
Abstract
Background The senescence of endothelial cells is of great importance involving in atherosclerosis (AS) development. Recent studies have proved the protective role of mesenchymal stem cell-derived extracellular vesicles in AS, herein, we further desired to unvei their potential regulatory mechanisms in endothelial cell senescence. Methods Senescence induced by H2O2 in primary mouse aortic endothelial cells (MAECs) was evaluated by SA-β-gal staining. Targeted molecule expression was detected by qRT-PCR and Western blotting. The biological functions of MAECs were determined by CCK-8, flow cytometry, transwell, and tube formation assays. Oxidative injury was assessed by LDH, total and lipid ROS, LPO and MDA levels. The proliferation of adipose-derived mesenchymal stem cell (ADSCs) was analyzed by EdU assay. Effect of ADSCs-derived extracellular vesicles (ADSC-EVs) on AS was investigated in HFD-fed ApoE-/- mice. Results miR-674-5p was up-regulated, while C1q/TNF-related protein 9 (CTRP9) was down-regulated in H2O2-induced senescent MAECs. CTRP9 was demonstrated as a target gene of miR-674-5p. miR-674-5p inhibition restrained senescence, oxidative stress, promoted proliferation, migration, and angiogenesis of H2O2-stimulated MAECs via enhancing CTRP9 expression. Moreover, treatment with ADSC-EVs inhibited H2O2-induced senescence and dysfunction of MAECs through regulating miR-674-5p/CTRP9 axis. In the in vivo AS mouse model, ADSC-EVs combination with miR-674-5p silencing slowed down AS progression via up-regulation of CTRP9. Conclusion ADSC-EVs repressed endothelial cell senescence and improved dysfunction via promotion of CTRP9 expression upon miR-674-5p deficiency during AS progression, which might provide vital evidence for ADSC-EVs as a promising therapy for AS.
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Yang Y, Wang Y, Huang Y, Song J, Ma X. Interceed combined with bone marrow mesenchymal stem cells improves endometrial receptivity of intrauterine adhesion. Regen Ther 2024; 27:445-454. [PMID: 38706569 PMCID: PMC11066143 DOI: 10.1016/j.reth.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
Background This study aimed to investigate the impact of intrauterine adhesions (IUA) therapy and endometrial receptivity by implanting autologous bone marrow mesenchymal stem cells (BMSCs) into the Interceed and subsequently placing them in the uterine cavity of rats. Methods Fifty rats were divided into 5 groups according to the random number table method (10 rats in each group). Following the development of the IUA model through mechanical injury, the animals were categorized into different treatment groups: the IUA model (intrauterine perfusion of saline), Interceed therapy (intrauterine placement of Interceed), BMSCs therapy (intrauterine perfusion of BMSCs), BMSCs + Interceed therapy (intrauterine placement of BMSCs + Interceed), and a control group (intrauterine perfusion of saline). The Hematoxylin-eosin (HE) staining technique was employed to identify and assess the pathological alterations in the endometrium. Additionally, it facilitated the quantification of endometrial glands and the determination of endometrial thickness. Masson staining was used to detect fibrosis in rat uterus. The number of microvascular density (MVD) was detected by immunohistochemistry (IHC). Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot were used to detect the levels of leukemia inhibitory factor (LIF), integrin ανβ3, and vascular endothelial growth factor (VEGF) in uterine tissue. Male and female rats were combined in cages for reproductive and conception evaluation. Results In comparison to the control, the number of endometrial glands in the IUA model was significantly reduced, and the degree of endometrial thinning and fibrosis was significantly increased (p < 0.05). Compared with the IUA model, the number of endometrial glands did not exhibit any significant alterations in endometrial thickness and MVD number. The expressions of LIF, integrin ανβ3, and VEGF in the uterine tissue were not significantly improved with Interceed therapy, resulting in no significant improvement in the pregnancy rate (p > 0.05). The number of endometrial glands, endometrial thickness, and MVD in the BMSCs therapy group were significantly increased. Moreover, the expressions of LIF, integrin ανβ3, and VEGF in uterine tissue exhibited a significant increase, leading to a comparatively higher pregnancy rate (p < 0.05). In the BMSCs + Interceed therapy group, the number of endometrial glands, endometrial thickness, and MVD were significantly increased, and the expressions of LIF, integrin ανβ3, and VEGF in uterine tissue were significantly increased as well, along with a corresponding rise in the pregnancy rate (p < 0.05). Conclusion The intrauterine placement of Interceed combined with BMSCs in IUA rats can thicken the damaged endometrium, increase the number of glands, promote endometrial angiogenesis, improve endometrial receptivity, and increase the rate of pregnancy in IUA rats.
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Sidky H, Hansen KA, Girvin AT, Hotaling N, Michael SG, Gersing K, Sahner DK. Assessing the effect of selective serotonin reuptake inhibitors in the prevention of post-acute sequelae of COVID-19. Comput Struct Biotechnol J 2024; 24:115-125. [PMID: 38318198 PMCID: PMC10839808 DOI: 10.1016/j.csbj.2023.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Background Post-acute sequelae of COVID-19 (PASC) produce significant morbidity, prompting evaluation of interventions that might lower risk. Selective serotonin reuptake inhibitors (SSRIs) potentially could modulate risk of PASC via their central, hypothesized immunomodulatory, and/or antiplatelet properties although clinical trial data are lacking. Materials and Methods This retrospective study was conducted leveraging real-world clinical data within the National COVID Cohort Collaborative (N3C) to evaluate whether SSRIs with agonist activity at the sigma-1 receptor (S1R) lower the risk of PASC, since agonism at this receptor may serve as a mechanism by which SSRIs attenuate an inflammatory response. Additionally, determine whether the potential benefit could be traced to S1R agonism. Presumed PASC was defined based on a computable PASC phenotype trained on the U09.9 ICD-10 diagnosis code. Results Of the 17,908 patients identified, 1521 were exposed at baseline to a S1R agonist SSRI, 1803 to a non-S1R agonist SSRI, and 14,584 to neither. Using inverse probability weighting and Poisson regression, relative risk (RR) of PASC was assessed.A 29% reduction in the RR of PASC (0.704 [95% CI, 0.58-0.85]; P = 4 ×10-4) was seen among patients who received an S1R agonist SSRI compared to SSRI unexposed patients and a 21% reduction in the RR of PASC was seen among those receiving an SSRI without S1R agonist activity (0.79 [95% CI, 0.67 - 0.93]; P = 0.005).Thus, SSRIs with and without reported agonist activity at the S1R were associated with a significant decrease in the risk of PASC.
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Kumah E, Asana Y, Agyei SK, Kokuro C, Ankomah SE, Fusheini A. Does health insurance status influence healthcare-seeking behavior in rural communities? evidence from rural Ghana. HEALTH POLICY OPEN 2024; 6:100119. [PMID: 38680189 PMCID: PMC11047188 DOI: 10.1016/j.hpopen.2024.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction National health insurance programs are considered important mechanisms for ensuring equity in access to and utilization of healthcare services by removing financial barriers associated with seeking treatment in healthcare facilities. Although studies on health insurance schemes in many low-and-middle-income countries (LMICs) have demonstrated a significant relationship between health insurance status and healthcare-seeking behavior, data on the influence of this health financing policy on the decision to seek formal healthcare among rural inhabitants remains limited. Underpinned by the Andersen-Newman behavioral model of healthcare use, this study examined the influence of health insurance status on healthcare-seeking behavior among rural dwellers in Ghana. Methods A community-based cross-sectional study was conducted among 460 rural residents in Ghana from 8th September to 5th December 2022. Chi-square tests were used to study the significance level and association between healthcare-seeking behavior and selected independent variables. A multiple logistic regression model was fitted to test the association between health insurance status and healthcare-seeking behavior, introducing other selected explanatory variables as controls. Results The mean age of the respondents was 29.6 ± 6.8 years. A little above half (53.1 %) disclosed having insurance, whereas 46.1 % stated they were without coverage. Regarding healthcare-seeking behavior, the most commonly chosen treatment source was traditional healers (37.2 %), followed by the public healthcare system (28.3 %) and self-treatment (18.2 %). The private healthcare system was the least preferred, with only 16.3 % opting for it. While the bivariate analysis demonstrated a significant relationship between health insurance status and healthcare-seeking behavior (p-0.001), the logistic regression model results showed that health insurance status was not an independent predictor of healthcare-seeking behavior (p = 0.069). Conclusion It could, therefore, not be concluded that the respondents with health insurance coverage were more likely than the uninsured to use formal healthcare providers as their most frequent source of treatment during illness. This study provides vital information for policymakers aiming at increasing access to and utilization of facility-based formal care in rural and remote settings.
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