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https://f1000research.com/articles/13-636/v1
|
14 Jun 24
|
{
"type": "Study Protocol",
"title": "A cross sectional study on endemicity of VIM, NDM, KPC, IPM & OXA-48 genes in Carbapenemase producing Klebsiella pneumoniae and Escherichia coli from a tertiary hospital using mCIM, eCIM, and PCR in Central India",
"authors": [
"Radha Kunjalwar",
"Gargi Mudey",
"Gargi Mudey"
],
"abstract": "Background Carbapenem-resistant Enterobacteriaceae (CRE) represent a growing global health concern, necessitating comprehensive investigations into their prevalence and resistance mechanisms. This study protocol focuses on detecting carbapenemase genes, including blaVIM, blaNDM, blaKPC, blaIPM, and blaOXA-48, in clinical isolates of Klebsiella pneumoniae and Escherichia coli from a tertiary hospital in Eastern India. The rise of carbapenem resistance poses challenges to effective antimicrobial therapy and infection control strategies.\n\nMethods Conducted at the Department of Microbiology, Jawaharlal Nehru Medical College, the study employs a cross-sectional design from July 2022 to December 2023. The sample size calculation follows Daniel’s formula, considering a non-response rate of 10%. Modified Carbapenem Inactivation Method (mCIM) and EDTA-Modified Carbapenem Inactivation Method (eCIM) will be used for phenotypic detection, along with polymerase chain reaction (PCR) for genotypic confirmation. Antibiotic susceptibility testing using the Kirby-Bauer Disk Diffusion method will complement resistance profiling.\n\nExpected Outcome Anticipated outcomes include insights into the efficacy of mCIM and eCIM in detecting carbapenem resistance, the prevalence of carbapenemase genes in Klebsiella pneumoniae and Escherichia coli, and the antibiotic resistance pattern of carbapenemase-producing CRE. This study aims to provide valuable data for guiding empirical treatment strategies and reinforcing infection control measures in the region.",
"keywords": [
"Carbapenem resistance",
"Enterobacteriaceae",
"Klebsiella pneumoniae",
"Escherichia coli",
"Modified Carbapenem Inactivation Method (mCIM)",
"Antibiotic susceptibility testing"
],
"content": "Introduction\n\nAntibiotic resistance, particularly the emergence of Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE), poses a significant global health threat. Carbapenems are considered last-resort antibiotics, and the rise in resistance among critical pathogens such as Escherichia coli and Klebsiella pneumoniae undermines the efficacy of these vital drugs.1,2\n\nSeveral studies have reported an alarming increase in the prevalence of Carbapenemase-producing strains, highlighting the need for robust surveillance and detection methods.3,4 Carbapenemase enzymes, encoded by genes such as blaVIM, blaNDM, blaKPC, blaIPM, and blaOXA-48, contribute to resistance and are associated with difficult-to-treat infections.5,6\n\nIn India, where antimicrobial resistance is a growing concern, understanding the local epidemiology of CP-CRE becomes crucial for guiding effective treatment strategies.7 Previous research has underscored the importance of combining phenotypic and genotypic methods for accurately detecting and characterizing Carbapenemase production.8,9\n\nThe proposed study in the Department of Microbiology at Jawaharlal Nehru Medical College aims to address this gap by employing a comprehensive approach to identify CP-CRE in clinical isolates of E. coli and Klebsiella spp. The study will utilize modified Carbapenem Inactivation Methods (mCIM and eCIM), polymerase chain reaction (PCR), and antibiotic susceptibility testing to provide insights into the prevalence and antibiotic resistance patterns of CP-CRE in Eastern India.\n\nThis research study aims to detect Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE) among clinical isolates of Escherichia coli and Klebsiella pneumoniae in a tertiary hospital in Eastern India. The primary goal is to understand the prevalence of Carbapenemase genes and assess the antibiotic resistance patterns of CP-CRE in the specified region.\n\n\n\n1. Isolation and identification: To employ conventional microbiological methods for isolating and identifying Escherichia coli and Klebsiella pneumoniae from various clinical samples.\n\n2. Carbapenemase production testing: To determine Carbapenemase production in isolated strains using the Modified Carbapenem Inactivation Method (mCIM) and EDTA-Modified Carbapenem Inactivation Method (eCIM) based on CLSI Guidelines 2022.\n\n3. Genotypic identification: To identify Carbapenemase production through conventional PCR and gel electrophoresis for specific genes (blaVIM, blaNDM, blaKPC, blaIPM, & blaOXA-48).\n\n4. Antibiotic-sensitivity testing: To perform antibiotic-sensitivity testing using the Kirby-Bauer Disk Diffusion method according to CLSI Guidelines 2022 to understand the resistance patterns.\n\n\nMethod\n\nThe study design is a cross-sectional study. In a cross-sectional study, data is collected from a population at a specific time to understand the prevalence and distribution of a particular condition or characteristic. In this case, the researchers aim to assess the presence of Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE) in clinical isolates of Escherichia coli and Klebsiella pneumoniae. Microbial DNA kit - Hi purA Bacterial Genetic DNA purification (Code- MB505), Hi PCR Carbapenemase Gene (Multiplex) probe PCR kit (Code- MBPCR132)\n\nThe study population includes patients from the OPD (Outpatient Department) and IPD (Inpatient Department) at “Acharya Vinoba Bhave Rural Hospital,” Sawangi (M) Wardha, Eastern India. The inclusion criteria likely involve clinically relevant isolates of Escherichia coli, and Klebsiella pneumoniae recovered from various clinical samples.\n\nThe study is conducted at the Department of Microbiology, Jawaharlal Nehru Medical College, Sawangi (Meghe) Wardha, Eastern India. The specific setting within the department needs to be detailed. Still, it is mentioned that routine and conventional methods, as well as automated methods like VITEK-2, will be used to isolate and identify the bacterial strains.\n\nInclusion criteria:\n\n1. Clinical isolates: Isolates of Escherichia coli and Klebsiella pneumoniae obtained from clinical samples.\n\n2. Specimens: Isolates recovered from various clinical specimens indicate the presence of these bacteria.\n\n3. Timeframe: Isolates collected during the specified study duration from July 2022 to July 2023.\n\n4. Study location: Isolates obtained from patients under “Acharya Vinoba Bhave Rural Hospital,” Sawangi (M) Wardha.\n\nExclusion criteria:\n\n1. Non-clinical isolates: Isolates not obtained from clinical samples, excluding those recovered from routine environmental monitoring or non-human sources.\n\n2. Specimens from outside the specified timeframe: Isolates collected outside the defined study duration (before July 2022 or after July 2023).\n\n3. Isolates from locations outside the designated hospital: Not obtained from patients under “Acharya Vinoba Bhave Rural Hospital,” Sawangi (M) Wardha.\n\n4. Non-relevant isolates: Isolates lacking clinical relevance, such as those from healthy individuals or individuals without signs of infection.\n\n5. Duplicate isolates: Multiple isolates from the same patient for the same infection episode, considering only the first isolate.\n\n6. Unsuitable samples: Isolates with compromised sample quality or integrity that may affect the accuracy of test results.\n\n7. Non-consented isolates: Isolates obtained without proper ethical approval or without following ethical guidelines, particularly if written informed consent is required.\n\n\n\n1. Selection bias: The study may be vulnerable to selection bias if the samples collected do not represent the broader population of patients in the hospital with Escherichia coli and Klebsiella pneumoniae infections. For example, if only certain patient groups or specific types of infections are included, the results may not be generalizable.\n\n2. Sampling bias: If the samples are not collected randomly or there is a bias in the selection of samples, it could lead to sampling bias. For instance, if certain patients are more likely to be tested for CP-CRE, it may not reflect the actual prevalence in the overall population.\n\n3. Detection bias: The methods used for detection, such as PCR and phenotypic tests, may have inherent biases. If the tests are more sensitive or specific to certain strains or genes, it could affect the accuracy of the results.\n\nThe study aims to detect Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE), focusing on Escherichia coli and Klebsiella pneumoniae in a tertiary hospital in Eastern India. The enrollment process involves the collection and analysis of isolates from clinical samples. All clinically relevant isolates of Escherichia coli and Klebsiella spp. It will be obtained from specimens received at the Department of Microbiology, Jawaharlal Nehru Medical College, Sawangi (Meghe) Wardha. These isolates are expected to be recovered from OPD/IPD patients under “Acharya Vinoba Bhave Rural Hospital,” Sawangi (M) Wardha, during the enrollment period spanning from July 2022 to July 2023.\n\nThe study will commence after obtaining approval from the Institutional Ethics Committee, and written informed consent is deemed unnecessary as the focus is on isolates recovered from specimens. The sample size calculation is based on Daniel’s formula, considering the expected prevalence, precision, and confidence level. The study setting is the Department of Microbiology, Jawaharlal Nehru Medical College, Sawangi (Meghe) Wardha.\n\nQuality control strains, including Escherichia coli (ATCC 25922) and specific strains for mCIM and eCIM, will be utilized to ensure the reliability of phenotypic tests. The study incorporates a comprehensive approach involving phenotypic and genotypic methods to address the detection and characterization of Carbapenemase-Producing Enterobacteriaceae. The analysis will include Student’s t-test, Chi-square test, and Fisher’s exact test, if necessary, with a significance level set at P < 0.05.\n\nThe study’s expected outcomes include evaluating the utility of mCIM and eCIM in detecting Carbapenem resistance and determining the prevalence of Carbapenemase genes in the studied region. Additionally, understanding the antibiotic resistance pattern of CP-CRE in the area will contribute to instituting appropriate empirical treatment strategies. The study aims to provide valuable insights into the prevalence and antibiotic resistance patterns, enhancing treatment strategies in the specified region.\n\nThe study involves a comprehensive approach to collect and analyze data on Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE), with a focus on Escherichia coli and Klebsiella pneumoniae in a tertiary hospital in Eastern India. The enrollment process targets clinically relevant isolates, and the study duration spans from July 2022 to December 2023. Ethical approval from the Institutional Ethics Committee is a prerequisite, with written informed consent not required due to the use of isolates recovered in the Department of Microbiology.\n\nClinical isolates are obtained from OPD/IPD patients under “Acharya Vinoba Bhave Rural Hospital,” Sawangi (M) Wardha. Following Daniel’s formula, sample size calculation determines that 203 patients are needed for the study, considering a non-response rate of 10%. The study setting is the Department of Microbiology, Jawaharlal Nehru Medical College, Sawangi (Meghe) Wardha.\n\nData collection involves multiple steps. Conventional microbiological methods, including automated methods like VITEK-2,10 are employed for isolating and identifying Escherichia coli and Klebsiella spp. Antibiotic-susceptibility testing uses the Kirby-Bauer Disk Diffusion method, adhering to CLSI Guidelines 2022.11 Phenotypic methods, specifically the Modified Carbapenem Inactivation Method (mCIM) and EDTA-Modified Carbapenem Inactivation Method (eCIM) are used for Carbapenemase detection.12 Molecular methods, such as Real-Time PCR and Conventional PCR, are utilized for identifying specific Carbapenemase genes (blaNDM, blaIPM, blaVIM, blaKPC, and blaOXA-48).13 Control strains, like Escherichia coli ATCC 25922, ensure quality control in phenotypic tests.14\n\nStatistical analysis, including Student’s t-test, Chi-square test, and Fisher’s exact test, is applied to analyze the collected data. The expected outcomes include evaluating the utility of mCIM and eCIM in detecting Carbapenem resistance and determining the prevalence of Carbapenemase genes in the studied region. Additionally, the study aims to understand the antibiotic resistance pattern of CP-CRE in the area for informed empirical treatment decisions.\n\nThe sample size for the study was determined using a formula based on established statistical principles. With a level of confidence set at 95%, an expected prevalence (P) of 0.38 for OXA-48, like producing Enterobacteriaceae, and a desired precision (d) of 0.07, the formula yielded a sample size (n). To account for potential non-response, a 10% non-response rate was assumed. Consequently, the total sample size was adjusted to 203, ensuring robust statistical power for the investigation. This calculation, referencing the work of Daniel et al. (1977), was performed using R Studio Version 4.3.1, providing a solid foundation for the study’s research design and ensuring adequate representation of the population under investigation. The methodology follows established standards, as evidenced by the study reference to Renru Han et al., and emphasizes the importance of achieving statistical significance in understanding the prevalence and characteristics of Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae.\n\nThe study employs several essential statistical methods to analyze and interpret data gathered in the investigation of Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE), with a specific focus on Escherichia coli and Klebsiella pneumoniae. The statistical toolkit includes the student’s t-test, which compares means between two groups, aiding in identifying any statistically significant differences in measured variables. The Chi-square test is also applied to analyze categorical data, examining potential associations between variables. Fisher’s exact test, a valuable tool for situations with small sample sizes, ensures accurate assessments of associations between categorical variables.\n\nThese statistical analyses play a crucial role in evaluating data collected from various stages of the study, encompassing phenotypic methods (Modified Carbapenem Inactivation Method - mCIM and EDTA-Modified Carbapenem Inactivation Method - eCIM), molecular detection (Real-Time PCR and Conventional PCR), and antibiotic susceptibility testing. The overarching objective is to derive meaningful insights into the prevalence of Carbapenemase genes, assess the efficacy of different detection methods, and delineate the antibiotic resistance patterns of CP-CRE within the specified region.\n\nIn the context of these statistical analyses, the significance level, often represented by the p-value, holds paramount importance. A p-value less than 0.05 is conventionally considered statistically significant, indicating that observed results are unlikely to occur randomly.\n\nThe adoption of SPSS version 27.0 for statistical analysis underscores the study’s commitment to a robust and widely accepted platform for handling and interpreting the collected data. By leveraging these statistical methods, the study aims to draw informed conclusions regarding the prevalence, characteristics, and antibiotic resistance patterns of Carbapenemase-Producing Enterobacteriaceae in the targeted population.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nThe study protocol addresses the increasing concern of carbapenem-resistant Enterobacteriaceae (CRE) in a tertiary hospital in Eastern India. By employing a combination of phenotypic and genotypic methods, the study intends to shed light on the prevalence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the region. The choice of phenotypic methods, such as Modified Carbapenem Inactivation Method (mCIM) and EDTA-Modified Carbapenem Inactivation Method (eCIM), is based on their established utility in detecting carbapenemase production, particularly in distinguishing between metallo-beta-lactamases and serine carbapenemases.15 These methods align with the Clinical and Laboratory Standards Institute (CLSI) guidelines, providing a standardized approach to assess carbapenem resistance.16\n\nAdditionally, incorporating genotypic methods, including polymerase chain reaction (PCR) for specific carbapenemase genes, offers a molecular perspective on the genetic diversity and prevalence of resistance determinants.17 The utilization of real-time PCR and gel electrophoresis aims to enhance the accuracy and efficiency of gene identification. Antibiotic susceptibility testing using the Kirby-Bauer Disk Diffusion method complements the study by providing insights into the overall resistance patterns of carbapenemase-producing isolates. This information is crucial for understanding the challenges in treating infections caused by these strains and guiding empirical treatment strategies.18\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIMS (DU)/IEC/2022/1055. Date: 21-07-2022). Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nMeletis G: Carbapenem resistance: overview of the problem and future perspectives. Ther. Adv. Infect. Dis. 2016; 3: 15–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSuay-García B, Pérez-Gracia MT: Present and Future of Carbapenem-resistant Enterobacteriaceae (CRE) Infections. Antibiotics (Basel). 2019; 8: 122. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThomas GR, Corso A, Pasterán F, et al.: Increased Detection of Carbapenemase-Producing Enterobacterales Bacteria in Latin America and the Caribbean during the COVID-19 Pandemic. Emerg. Infect. Dis. 2022; 28: 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaji SH, Aka STH, Ali FA: Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilli. PLoS One. 2021; 16: e0259005. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGurung S, Kafle S, Dhungel B, et al.: Detection of OXA-48 Gene in Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae from Urine Samples. Infect. Drug Resist. 2020; 13: 2311–2321. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLoqman S, Soraa N, Diene SM, et al.: Dissemination of Carbapenemases (OXA-48, NDM and VIM) Producing Enterobacteriaceae Isolated from the Mohamed VI University Hospital in Marrakech, Morocco. Antibiotics (Basel). 2021; 10: 492. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKumar SG, Adithan C, Harish BN, et al.: Antimicrobial resistance in India: A review. J. Nat. Sci. Biol. Med. 2013; 4: 286–291. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVamsi SK, Moorthy RS, Hemiliamma MN, et al.: Phenotypic and genotypic detection of carbapenemase production among gram negative bacteria isolated from hospital acquired infections. Saudi Med. J. 2022; 43: 236–243. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaran I, Aksu N: Phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae in a tertiary-level reference hospital in Turkey. Ann. Clin. Microbiol. Antimicrob. 2016; 15: 20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBenkova M, Soukup O, Marek J: Antimicrobial susceptibility testing: currently used methods and devices and the near future in clinical practice. J. Appl. Microbiol. 2020; 129: 806–822. PubMed Abstract | Publisher Full Text\n\nMwansa TN, Kamvuma K, Mulemena JA, et al.: Antibiotic susceptibility patterns of pathogens isolated from laboratory specimens at Livingstone Central Hospital in Zambia. PLoS Glob. Public Health. 2022; 2: e0000623. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLasko MJ, Gill CM, Asempa TE, et al.: EDTA-modified carbapenem inactivation method (eCIM) for detecting IMP Metallo-β-lactamase–producing Pseudomonas aeruginosa: an assessment of increasing EDTA concentrations. BMC Microbiol. 2020; 20: 220. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSubirats J, Royo E, Balcázar JL, et al.: Real-time PCR assays for the detection and quantification of carbapenemase genes (bla KPC, bla NDM, and bla OXA-48) in environmental samples. Environ. Sci. Pollut. Res. Int. 2017; 24: 6710–6714. PubMed Abstract | Publisher Full Text\n\nJanezic KJ, Ferry B, Hendricks EW, et al.: Phenotypic and Genotypic Characterization of Escherichia coli Isolated from Untreated Surface Waters. Open Microbiol. J. 2013; 7: 9–19. PubMed Abstract | Publisher Full Text | Free Full Text\n\nM100Ed33|Performance Standards for Antimicrobial Susceptibility Testing. 33rd Edition.Clinical & Laboratory Standards Institute; Accessed: January 19, 2024. Reference Source\n\nPoirel L, Walsh TR, Cuvillier V, et al.: Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol. Infect. Dis. 2011; 70: 119–123. Publisher Full Text\n\nAntimicrobial resistance: global report on surveillance. Accessed: January 19, 2024. Reference Source\n\nCraig M: CDC’s Antibiotic Resistance Threats Report.2019."
}
|
[
{
"id": "357085",
"date": "27 Jan 2025",
"name": "Praveen Kumar",
"expertise": [
"Reviewer Expertise Antimicrobial Resistance",
"Anti-biofilm agents"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nEnsure that all scientific names are italicized throughout the manuscript. Polymerase Chain Reaction (PCR) should be written in full upon its first mention and abbreviated as PCR thereafter. Ensure such corrections are applied consistently throughout the text. Rewrite “expected outcomes” for the clarity. I suggest to include “designing better diagnostic, therapeutic, and preventive measures against carbapenem-resistant infections” Include “eCIM” in keywords. mCIM and eCIM expand the term on first usage in the text. In introduction “Carbapenems are considered last-resort antibiotics, and the rise in resistance among critical pathogens such as Escherichia coli and Klebsiella pneumoniae undermines the efficacy of these vital drugs” also add “colistin” which is also a last resort drug and give appropriate reference Rewrite the second objective as “Detection of major carbapenemase genes (blaVIM, blaNDM, blaKPC, blaIMP, and blaOXA-48) using PCR and analysis of their expression levels through RT-PCR” The study period mentioned in the abstract (July 2022 to December 2023) does not match the one provided in the methodology (July 2022 to July 2023). Please verify the correct timeframe and ensure consistency across the manuscript. Consider incorporating MIC (Minimum Inhibitory Concentration) testing of carbapenems into the study which is highly relevant.\n\nIn the study population “The inclusion criteria likely involve clinically relevant isolates of Escherichia coli, and Klebsiella pneumoniae recovered from various clinical samples” Authors must provide details of the clinical samples, such as urine, aspirates, and wound swabs, that will be used in the study In antibiotic sensitivity testing using the Kirby-Bauer Disk Diffusion method, authors should specify the carbapenem antibiotics used, such as meropenem and imipenem. Clearly provide the detailed methodology for the assays (mCIM and eCIM) to ensure reproducibility and transparency. Provide detailed protocols for PCR and RT-PCR, including reaction conditions, primer sequences, and the concentrations of PCR components In the discussion section, emphasize the recent reports of Carbapenem-Resistant Enterobacteriaceae (CRE) from India. In the discussion “The utilization of real-time PCR and gel electrophoresis aims to enhance the accuracy and efficiency of gene identification” replace gel electrophoresis with PCR\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-636
|
https://f1000research.com/articles/13-635/v1
|
14 Jun 24
|
{
"type": "Study Protocol",
"title": "Comparative observational study on diagnostic utility of impulse oscillometry vs spirometry in obstructive airway diseases",
"authors": [
"Souvik Sarkar",
"Ulhas Jadhav",
"Ulhas Jadhav"
],
"abstract": "Background Obstructive airway diseases, including chronic obstructive pulmonary disease (COPD) and asthma, pose significant global health challenges. Early and accurate diagnosis is crucial for effective management. Although Spirometry has traditionally been the cornerstone of diagnostics, Impulse Oscillometry (IOS) has emerged as a promising alternative. This study aims to compare the diagnostic performance of Spirometry and IOS in patients attending the Respiratory Medicine Department at the Acharya Vinoba Bhave Rural Hospital, Sawangi, India.\n\nMethods A Comparative Observational Study was conducted between August 2022 and August 2024, enrolling patients who met specific inclusion criteria. Data were collected through a comprehensive medical history, clinical examination, routine blood tests, chest radiography, High-resolution computed tomography (HRCT), spirometry, and IOS. Key parameters, including Forced expiratory volume in the first second FEV1, FEV1/FVC (Forced Expiratory Volume), (Forced Expiratory Volume) FVC, (Forced Expiratory Flow) FEF 25-75 for Spirometry, and R5, R20, fres, X5, and AX for IOS, were analyzed using the Chi-Square Test and Student’s t-test with SPSS 27.0 and GraphPad Prism 7.0.\n\nExpected outcome The study included 130 participants with the primary objective of evaluating IOS’s diagnostic advantages of IOS over spirometry. Our findings demonstrate that IOS offers enhanced sensitivity for diagnosing early small airway diseases, which is a crucial factor for early diagnosis in both pediatric and adult populations.",
"keywords": [
"Impulse Oscillometry",
"Spirometry",
"Obstructive Airway Diseases",
"COPD Diagnosis",
"Respiratory Medicine",
"Diagnostic Sensitivity"
],
"content": "Introduction\n\nAsthma and Chronic Obstructive Pulmonary Disease (COPD) are prominent constituents of obstructive airway diseases and are ranked as the fourth leading cause of death globally. In the context of obstructive airway diseases (OADs), pulmonary function measurement serves as a pivotal factor in diagnosing these conditions, gauging disease severity, predicting prognosis, and evaluating therapeutic response.1\n\nPatients exhibiting symptoms of dyspnea, cough, chronic expectoration, and exposure to harmful chemicals warrant suspicion of COPD. The diagnostic confirmation of COPD is achieved through spirometry, particularly when the FEV1/FVC ratio is less than 70% after bronchodilator administration. Notably, as the disease progressed, FEV1 demonstrated a decline.2\n\nIn the case of asthma, patients may present with recurrent chest wheezing, cough, chest tightness, or breathing difficulties, often accompanied by other allergic symptoms. The diagnosis of asthma, according to (Global Initiative for Asthma) guidelines, involves identifying airway reversibility after bronchodilator administration, specifically, a greater than 200 ml or 12% increase in FEV1 in spirometry. Asthma, a growing health concern, is diagnosed based on clinical history, physical examination, and pulmonary function testing following the GINA guidelines.3\n\nSpirometry is the gold standard diagnostic test for OADs and is routinely performed as a pulmonary function test (PFT). However, it requires active patient participation and physical dexterity, which may be challenging for young children, the elderly, and individuals with physical or cognitive impairment. Additionally, the forced expiratory maneuver in spirometry can trigger volume-dependent closure of the small airways.4 Impulse Oscillometry (IOS) was developed as a modernized approach to traditional pulmonary function testing. It employs pressure flow oscillations at the mouth, superimposing over the patient’s tidal breaths at various oscillation frequencies to assess the respiratory system’s resistance and reactance.5\n\nThe IOS represents a variant of the forced oscillation technique (FOT), which investigates the mechanical properties of the respiratory system, including resistance and elasticity, across a frequency range of 5–20 Hz. Unlike FOT, which employs sinusoidal waves, IOS assesses the respiratory machine’s response to a triangular strain pulse.6 The key advantage of FOT/IOS lies in its use of simpler tidal breathing, requiring less cooperation and effort compared to spirometry. Furthermore, because IOS is conducted without forceful respiratory movements, it is less likely to affect airway smooth muscle tone.7\n\nSeveral parameters were measured through IOS, including R5, representing the resistance at 5 Hz frequency, which reflects total airway resistance; R20, indicating resistance at a 20 Hz frequency, representing larger airway resistance; X5, denoting reactance at 5 Hz frequency, which reflects the elasticity of peripheral airways; and Ax, signifying the Area of Reactance, reflecting the degree of peripheral airway obstruction.8\n\nReversible blockage and bronchial hyperresponsiveness are key criteria for asthma diagnosis. The IOS exhibited sensitivity and accuracy in both aspects. A 30-35 percent decrease in R5 is considered a significant bronchodilator response. Asthmatic individuals typically present higher R5, fres, and AX values, whereas X5 values are lower. This pattern was also observed during bronchoprovocation testing, with an increase in R5, fres, and AX and a decrease in X5. Notably, a 20% reduction in FEV1 corresponds to a 50% decrease in X5, which is a more sensitive metric for detecting bronchial hyperreactivity.9\n\nGong et al. demonstrated that reactance parameters correlate more strongly with lung function than resistance parameters in COPD patients. They propose that changes in X5 over time could serve as an effective disease monitoring tool.5 For COPD diagnosis, even when spirometric values are within the normal range, patients with COPD-related complaints exhibit increased pulmonary resistance and decreased pulmonary reactance. Hence, IOS is highly sensitive in detecting subtle changes in pulmonary function, making it a more sensitive modality for this purpose.10\n\nTo study the utility of Impulse oscillometry vs Spirometry in obstructive airway diseases.\n\n\n\n1. To study the utility of Impulse oscillometry over Spirometry in OADs\n\n2. To compare diagnostic parameters of IOS vs Spirometry\n\n3. To study the parameters of OADs in the pediatric and adult age groups of patients\n\nThe study will be conducted at Acharya Vinoba Bhave Rural Hospital (AVBRH), located in Sawangi, Wardha, in the central part of India. AVBRH is a tertiary care hospital affiliated with Jawaharlal Nehru Medical College and serves as the primary site for this research. The study will be conducted over a two-year period, from August 2022 to August 2024.\n\nThis study was designed as a Comparative Observational Study, which means that no interventions or treatments will be administered to study participants. Data were collected through observation and diagnostic tests.\n\nThe study population will consist of patients attending the outpatient department (OPD) or admitted to the inpatient department (IPD) of the Respiratory Medicine Department at AVBRH, Sawangi, and Wardha. The inclusion and exclusion criteria for patient selection were as follows:\n\n\n\n• Clinically suspected cases of obstructive airway diseases.\n\n• Age above 6 years.\n\n• Patients capable of understanding and performing the investigations required.\n\n\n\n• Patients who are positive for tuberculosis.\n\n• History of recent abdominal, thoracic, eye, or ear surgery.\n\n• Patients with oral abnormalities.\n\n• Individuals who were suspected of having COVID-19 or tested positive for COVID-19 by RT-PCR.\n\n• Patients unwilling to provide informed consent.\n\n\nMethods\n\nBefore data collection began, all patients who met the inclusion criteria were approached, informed about the study, and provided with a detailed explanation of the study’s purpose, procedures, potential risks, and benefits. Written informed consent will be obtained from the patients who voluntarily agree to participate. Consent will be obtained from legal guardians of participants under the age of 18 years.\n\nA comprehensive medical history of each participant was obtained. This will include information on the patient’s past medical conditions, family history of respiratory diseases, exposure to risk factors (e.g., smoking and occupational exposure), and previous treatments for respiratory conditions.\n\nA complete clinical examination will be performed by qualified healthcare professionals. This examination will include the assessment of vital signs, general appearance, respiratory rate, lung sounds, and any physical signs or symptoms related to obstructive airway diseases.\n\nA set of routine blood tests, as specified in the annex, will be conducted to assess various hematological and biochemical parameters that may be relevant to the diagnosis of obstructive airway diseases.\n\n\n\n1. Chest X-ray: Standard posterior-anterior (PA) and lateral chest X-rays will be used to assess lung structure and identify any abnormalities.\n\n2. High-resolution computed tomography (HRCT) of the thorax: HRCT scans will be performed when needed to provide more detailed images of the lung anatomy and pathology.\n\n\n\n1. Spirometry Spirometry will be performed to measure key lung function parameters, including Forced Expiratory Volume in 1 s (FEV1), FEV1/FVC ratio, Forced Vital Capacity (FVC), and Forced Expiratory Flow (FEF) between 25% and 75% of FVC (FEF 25-75).\n\n2. Impulse Oscillometry (IOS): Impulse Oscillometry will be conducted to assess airway resistance and reactance. The parameters to be measured include R5 the Total Airway Resistance), R20 (Large Airway Resistance), Resonant Frequency (Fres), X5 (Reactance at 5 Hz), and area under reactance curve (AX).\n\n\n\n1. Data collected during these examinations and tests will be meticulously recorded to ensure accuracy and completeness.\n\n2. Electronic data capture tools or standardized forms may be used for data entry.\n\n3. Patient information will be anonymized and coded to maintain confidentiality and privacy.\n\n\n\n1. To ensure the quality and reliability of the data, all diagnostic tests were performed by trained and certified healthcare professionals.\n\n2. Calibration and maintenance of equipment (spirometers and IOS devices) will be performed regularly to ensure accurate measurements.\n\n3. Interobserver and intraobserver variability will be monitored and minimized.\n\nThe sample size for this study was calculated using Daniel’s formula, with a 95% confidence interval. The calculated sample size was 65 patients in each group, totaling 130 participants.\n\nThe collected data will be analyzed using statistical methods, including the Chi-Square Test for categorical variables and the student’s t-test for continuous variables. The analysis will be performed with the assistance of statistical software,\n\nThe Institutional Ethics Committee of the Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol on 18th July 2022. Prior to commencing the study, written informed consent was obtained from all participants, providing them with a comprehensive explanation of the study’s objectives. We prioritized interviewees’ privacy and comfort during the interview process. Reference Number: DMIHER (DU)/IEC/2022/74.\n\nThe study aims to enroll 130 participants and expects to demonstrate the advantages of Impulse Oscillometry over conventional spirometry in diagnosing obstructive airway diseases. It also seeks to identify the parameters that are sensitive to COPD and asthma. The primary hypothesis is that the IOS will show better sensitivity as a diagnostic tool for early small airway diseases in both children and adults.\n\nAfter completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has not yet started after the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nIn this study, we performed a comprehensive comparison of Impulse Oscillometry (IOS) and spirometry as diagnostic tools for the early detection of asthma and Chronic Obstructive Pulmonary Disease (COPD). In individuals with asthma and COPD, we expected to find elevated values of respiratory resistance indices R5 and R20, while reactance index X5 should exhibit a marked reduction.\n\nA study conducted by Al-Mutairi et al.11 in 2007 reported that the IOS demonstrated a sensitivity of 31.3% in diagnosing asthma, surpassing traditional pulmonary function tests, which had a sensitivity of 19.6%. Similarly, their research revealed that IOS had a sensitivity of 38.95% for diagnosing COPD compared to 47.4% sensitivity for conventional pulmonary function tests. Furthermore, the IOS exhibited a sensitivity of 45.8%, which was notably higher than that of pulmonary function tests (28.8%) for identifying individuals without any respiratory illnesses.11\n\nImportantly, reactance values have been used to gauge the progression of COPD. IOS resistance measurements have shown potential for identifying early stage COPD and subtle alterations in the small airways, particularly in response to bronchodilators and bronchogenic challenges.12\n\nBuilding on the findings of prior research,13 our study anticipated a higher sensitivity of reactance measurements in asthmatic patients and a heightened sensitivity of resistance measurements in individuals with COPD. Our study aimed to highlight the exceptional sensitivity of IOS in detecting obstructive pulmonary diseases. We examined the comparative utility of Spirometry and IOS measures, including R5, R20, and X5, in patients with asthma and COPD. Our findings have the potential to elucidate the correlation between R5 stage and COPD severity. Prior research has also indicated strong associations between R5, X5, and FEV1.14\n\nIt is noteworthy that patients with advanced COPD tend to exhibit greater within-breath variations in Xrs5, as indicated by Kanda et al.15 Furthermore, recent studies suggest that the ability to differentiate between COPD and asthma patients using inspiratory-expiratory X5 analysis is more effective than relying solely on total respiratory IOS.16 In the context of IOS, it is worth highlighting that inspiratory assessments tend to offer superior accuracy compared to expiratory assessments.17 These insights contribute to a better understanding of the diagnostic potential of IOS and the nuanced nuances of its measurements in different respiratory conditions.",
"appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nReferences\n\nChronic obstructive pulmonary disease (COPD): [cited 2023 Jul 21]. Reference Source\n\nGupta D, Agarwal R, Aggarwal AN, et al.: Guidelines for diagnosis and management of chronic obstructive pulmonary disease: Joint ICS/NCCP (I) recommendations. Lung India. 2013; 30(3): 228–267. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUkena D, Fishman L, Niebling WB: Bronchial Asthma: Diagnosis and Long-Term Treatment in Adults. Dtsch. Arztebl. Int. 2008 May; 105(21): 385–394. PubMed Abstract | Publisher Full Text\n\nPonce MC, Sankari A, Sharma S: Pulmonary Function Tests. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023 [cited 2023 Oct 15]. Reference Source\n\nDesiraju K, Agrawal A: Impulse oscillometry: The state-of-art for lung function testing. Lung India. 2016; 33(4): 410–416. PubMed Abstract | Publisher Full Text\n\nBhattarai P, Myers S, Chia C, et al.: Clinical Application of Forced Oscillation Technique (FOT) in Early Detection of Airway Changes in Smokers. J. Clin. Med. 2020 Aug 27; 9(9): 2778. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrashier B, Salvi S: Measuring lung function using sound waves: role of the forced oscillation technique and impulse oscillometry system. Breathe (Sheff.). 2015 Mar; 11(1): 57–65. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWei X, Shi Z, Cui Y, et al.: Impulse oscillometry system as an alternative diagnostic method for chronic obstructive pulmonary disease. Medicine (Baltimore). 2017 Nov 17; 96(46): e8543.\n\nCoverstone AM, Bacharier LB, Wilson BS, et al.: Clinical significance of the bronchodilator response in children with severe asthma. Pediatr. Pulmonol. 2019 Nov; 54(11): 1694–1703. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKakavas S, Kotsiou OS, Perlikos F, et al.: Pulmonary function testing in COPD: looking beyond the curtain of FEV1. NPJ Prim. Care Respir. Med. 2021 May 7; 31: 23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAl-Mutairi SS, Sharma PN, Al-Alawi A, et al.: Impulse oscillometry: an alternative modality to the conventional pulmonary function test to categorise obstructive pulmonary disorders. Clin. Exp. Med. 2007 Jun; 7(2): 56–64. PubMed Abstract | Publisher Full Text\n\nMcNulty W, Usmani OS: Techniques of assessing small airways dysfunction. Eur. Clin. Respir. J. 2014 Oct 17; 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKolsum U, Borrill Z, Roy K, et al.: Impulse oscillometry in COPD: identification of measurements related to airway obstruction, airway conductance and lung volumes. Respir. Med. 2009 Jan; 103(1): 136–143. PubMed Abstract | Publisher Full Text\n\nSong TW, Kim KW, Kim ES, et al.: Utility of impulse oscillometry in young children with asthma. Pediatr. Allergy Immunol. 2008 Dec; 19(8): 763–768. PubMed Abstract | Publisher Full Text\n\nKanda S, Fujimoto K, Komatsu Y, et al.: Evaluation of respiratory impedance in asthma and COPD by an impulse oscillation system. Intern. Med. 2010; 49(1): 23–30. PubMed Abstract | Publisher Full Text\n\nParedi P, Goldman M, Alamen A, et al.: Comparison of inspiratory and expiratory resistance and reactance in patients with asthma and chronic obstructive pulmonary disease. Thorax. 2010 Mar; 65(3): 263–267. PubMed Abstract | Publisher Full Text\n\nKubota M, Shirai G, Nakamori T, et al.: Low frequency oscillometry parameters in COPD patients are less variable during inspiration than during expiration. Respir. Physiol. Neurobiol. 2009 Apr 30; 166(2): 73–79. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "323770",
"date": "18 Sep 2024",
"name": "Warawut Chaiwong",
"expertise": [
"Reviewer Expertise Lung funtion",
"COPD",
"asthma",
"rehabilitation",
"air pollution"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read an interesting a study protocol by Sarkar et al. The authors aim to compare the diagnostic performance of spirometry and IOS in patients with obstructive airway diseases including asthma and COPD. However, this study protocol has some major issues that should be addressed. Major concerns\n\nThe reference standard is a key of diagnostic research. Nowadays, spirometry is the gold standard for diagnosing COPD. Which is reference standard that will be used for comparison between spirometry and IOS in diagnosis of COPD, as well as in asthma?\n\nIntroduction\n\nMore studies on the utility of IOS for diagnosing asthma and COPD must be provided. Moreover, the gap of knowledge in this area must be mentioned.\n\nMethods 1. The key parameter likes R5-R20 in IOS must be included in the analysis. 2. The trade name of spirometry and IOS devices must be mentioned. 3. The sample size calculation for diagnostic research must be calculated using the AUC from the ROC study. 4. The diagnostic study parameters including AUC, sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, positive predictive value, negative predictive value, diagnostic odds ratio must be provided. 5. Due to the objective of this study that focus on a comparison on the diagnostic performance of spirometry and IOS in patients with obstructive airway diseases. Thus, the comparison of ROC curve for parameters in spirometry and IOS must be provided.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
},
{
"id": "323777",
"date": "24 Sep 2024",
"name": "Alberto Vidal Grell",
"expertise": [
"Reviewer Expertise Pediatric Lung Function"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear editor:\nIntroduction is very long, it can be limited. The population to be studied is very heterogeneous, a pediatric patient with asthma of an adult patient with COPD is not the same. A child with obliterary bronchiolitis secondary to early infection by adenovirus is not the same as an adult with obliterant bronchiolitis post transplant. All of the above are example of obstructive diseases.\n\nIt is not detailed in the calculation of the sample size (n = 130) and that you want to compare. Does the diagnosis of asthma ? Do you want to compare the diagnosis of small airway disease? How would the diagnosis of asthma or small airway obstruction be made with iOS? What would the predictive values used in spirometry and IOS?\nIf the main hypothesis is that iOS will show better sensitivity as a diagnostic tool for the first diseases of small respiratory tract both in children and adults. What would be the standard Gold to discriminate between patients with or without small airway disease, since to calculate sensitivity it is necessary to have a Gold Standard, for example FEF 25-75 < lower limit of normality according to GLI 2012 in spirometry. I recommend that in order to measure the clinical utility of a test, the positive Likelihood ratio (LR+)\n\nshould be used. LR+ = sensitivity/1 − specificity, considering the sensitivity and specificity with the best cut‐off points for the prevalence of abnormal spirometry or small airway disease.\nThe R5-R20 difference (DR5-R20) is not included, which is one of the most important parameters to measure peripheral airway obstruction. See Postma et al. , Ref 1 The inclusion criteria should mention whether respiratory comorbidities are excluded (e.g., bronchopulmonary dysplasia, cystic fibrosis, post-viral lung damage, ciliary dyskinesia, congenital heart disease, or neuromuscular diseases), since all of these medical conditions can affect lung function to varying degrees in the medium or long term.\nIf study is carried out with children in addition to the informed consent to parents, an informed assent should be applied to those over 11 years.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-635
|
https://f1000research.com/articles/12-1506/v1
|
27 Nov 23
|
{
"type": "Research Article",
"title": "Sex difference in body image, exercise motivation and social comparison among Instagram users: a cross sectional study",
"authors": [
"Aysha Nimiya",
"Vasudha K.G",
"Sharanya B Shetty",
"Keshava Pai",
"Reshma N S",
"Radhika K",
"Mariella D'Souza",
"Priyanka D'Souza",
"Aysha Nimiya",
"Sharanya B Shetty",
"Keshava Pai",
"Reshma N S",
"Radhika K",
"Mariella D'Souza",
"Priyanka D'Souza"
],
"abstract": "In the 21st century, impact of social media, particularly Social Networking Sites (SNSs) has been linked to a wide range of human beliefs and expectations. Growing body of research has indicated that body image concerns along with exercise motivation and social comparison are on the rise among young adults. The present study aimed to examine the sex difference in body image, exercise motivation and social comparison among people who use Instagram in the age group 20-30. A total of 212 participants (men=106, women=106) aged 20-30 years, who are users of Instagram completed Body Self Image Questionnaire Short Form as a measure of Body image, Exercise Motivation Inventory – 2 as a measure of Exercise Motivation and Instagram as a Tool for Social Comparison as a measure of Social Comparison. Results showed that a significant difference in body image exist across gender with body image issues higher among females and significant difference in exercise motivation across gender with exercise motivation higher among males. No sex differences were seen in social comparison. It was concluded that body image concerns are higher among females and the drive for exercise is higher among males who used Instagram. It was found that body image concerns were higher among people who exercised regularly as well as among those who followed fitness related pages on Instagram as compared to those who did not. These results provide an insight into the sex differences between the variables and future directions can be aimed at conducting an in-depth analysis using body image, exercise motivation and social comparison.",
"keywords": [
"Instagram",
"Body Image",
"Exercise Motivation",
"Social Comparison"
],
"content": "Introduction\n\nIn this era of developing technology, many studies have been focusing on how social media and social networking sites (SNSs) relate to body image issues. Research indicates that peer contacts, the prevalence of sharing pictures, and the availability of cell phone automation all contribute to the possibility that people who use SNSs may internalize the “skinny” prototype and self-embody (Lewallen, Behm-Morawitz, 2016). The role of exercise in understanding body image distortions are undeniable in the contemporary world (Littrell, 2017). The harmful possible side effects of engagements in physical activities to enhance one’s body image has been intensified by the SNSs, especially via applications like Facebook, Instagram, Snapchat etc. Research has consistently shown that celebrities, fashion influencers, peer and media effects are particularly important in influencing social comparison among both men and women. Thus, the statistics imply that social comparisons of physical appearance and the internalization of notions of beauty remain more prominent in people who actively use social networking (Lewallen, Behm-Morawitz, 2016; Brown & Tiggemann, 2016).\n\nSocial media use refers to use of various kinds of artificial intelligence, such as social networking platforms and personal websites or online columns, through which users build online communities to share knowledge, concepts, beliefs, exclusive and intimate messages, and other contents such as photos & videos (Cohen, Newton-John & Slater, 2017). According to recent data, around 59% world’s population use social media, which in number approximates to 4.76 billion and about 137 million people have created online profiles/accounts within the last 12 months with an average daily time of 2h and 31 m spent in these social networking websites (Kemp S. Digital, 2023: Global Overview Report [Internet], 2023) The various motives for engaging in social media includes entertainment (25.51%),personal utility (12.34%), information seeking (7.53%), convenience (6.21%) and altruism (4.90%) (Al-Menayes, 2015). Recent studies have looked at how social media and social networking sites (SNS) are connected to body image issues (Eckler, Kalyango & Paasch, 2017). Instagram is a distinctive social network application which allows users to connect with friends and post photos and videos (Panjrath & Tiwari, 2021). As of October 2021, the number of Instagram users have boosted up to 1.38 billion. While 70% of Instagram users are under 35 years, the proportion of users over 35years has grown every year since 2018, similar to Facebook (Statista Research Department, 2022). The terms “body image disturbance,” “body dissatisfaction,” or “body image concern” are frequently used in the literature to describe an unfavorable, displeased impression of one’s body (Fardouly et al., 2015). In Western nations, both women and men accept the “thin ideal” conception of women portrayed by media and society. Women oftentimes feel a gap between their existing real bodies and the elusive ideal female body, which eventually paves the way for body dissatisfaction (Mills, Musto, Williams, & Tiggemann, 2018). However, in the past few decades, the concept of ‘perfect’ male body has gained popularity. According to research, media representations of the ideal man have evolved through time and are now highly exaggerated and promoted to men through publications and television (Singh, Parsekar, & Bhumika, 2016).\n\nExercise motivation refers to individuals’ reasons for exercising (participation motives) in determining long-term adherence to regular physical activity (Markland & Hardy, 1993). Exercise motivation is primarily predicted by the perception of one’s physical appearance as being favourable or unfavourable. One of the specific reasons people exercise is to preserve or improve their desired physical appearance. Weight management, looks, and body dissatisfaction have all repeatedly ranked highly as factors that motivate people to exercise, demonstrating the connection between body image and exercise participation (Halder & Mondal, 2020). Even though studies on body image with respect to social media usage have primarily focused on women, it has been discovered that male millennials are increasingly using SNSs such as Instagram and fitness hashtags to communicate and gain knowledge about fit bodies, raising the likelihood of body image concerns.\n\nLean and toned bodies are frequently portrayed in media, and diet and exercise are frequently promoted for their aesthetic rather than health benefits (Holland & Tiggemann, 2016). This evidence points to the fact that people are inclined to desire to change the dimensions of their bodies resulting from the media and societal influence to keep up with the idealized convention of a thin and toned body for women and a lean and muscular physique for men, with a desire for the rewards for looking good, and the health benefits of maintaining the prescribed body weight (Gültzow, Guidry & Schneider, 2020).\n\nAnother crucial element that has been identified to be a key component in understanding body image is social comparison. It refers to the cognitive judgments that people make about their own attributes compared to others (Yang, 2016). According to Festinger’s social comparison theory (1954), people frequently compare their lives and selves to those of others based on the information they learn about others (Hobza et al., 2007). Social comparison comes in two main forms. Comparison to those we believe to be less fortunate than ourselves in some way, or downward social comparison, tends to improve happiness and self-worth. Upward social comparison or comparing oneself to someone we believe to be socially superior to oneself, typically results in a bad mood and can jeopardise one’s ability to evaluate oneself. When there are differences between oneself and the comparison standard, people are motivated to modify themselves in order to resemble the comparison standard more closely, which serves to promote the self (Vogel, Rose & Okdie, 2015; Yang, 2016). There is evidence that various SNS information, including user profiles, “likes,” and comments, can cause social comparison (de Vries et al., 2018).\n\n\nCurrent study\n\nThe media and popular culture endorse a thin beauty standard for women, which women and men in Western cultures simply accept. However, in the past few decades, the concept of ‘perfect’ male body has gained popularity. As a result, men, these days are also forced to work towards building an ideal body that is challenging to achieve (Chatzopoulou, Filieri & Dogruyol, 2020). In line with these findings, research has shown that men, like women, feel discontented and distressed when they encounter same sex individuals with an ‘ideal body’ (Prichard et al., 2020). Although this preference towards bodily stimuli is well-documented in female populations, research on it in male populations is very scarce (Daniel Talbot & Daniella Saleme, 2022). However, the existence of enormous literature in the western countries on body image and exercise motivation across gender is not necessarily globally representative, stemming from the finite number of investigations conducted in the Indian context. Additionally, there are very few published studies on the role of social comparison in body image of males, because of which Sex differences in social comparison have not been deeply analyzed. With the existing literature, there is insufficient research on use of social media, body image, exercise motivation and social comparison in men as most of the studies have been focused on women. For instance a study titled “Attractive celebrity and peer images on Instagram: Effect on women’s mood and body image”(Brown & Tiggemann, 2016), another study titled “Facebook Use and Negative Body Image among U.S. College Women” (Eckler, Kalyango & Paasch, 2017) and similarly, another study also focused on women titled, “Why Them, Not Me?”: A Study Exploring The Impact Of Following Fashion Influencers on Instagram on Body Image Satisfaction of Adolescent Girls and Middle-aged Women (Panjrath & Tiwari, 2021). These are few among the studies that mostly focused on women and their body image disturbances. So, we believe a comparative study is required to throw light on how these variables operate in women as well as in men. We aimed to study the Sex difference in body image, exercise motivation and social comparison among people who use Instagram in the age group 20-30 years.\n\n\nMethods\n\nA cross-sectional study was conducted in India, where participants were recruited through various online platforms. Two Google forms were created, in which the first one consisted of the participant study information sheet, inclusion criteria and informed consent. The second one consisted of the three questionnaires used in the study. The first Google form was circulated through various online platforms such as Whatsapp, Instagram and Gmail. After a period of 15 days, a reminder was sent to the participants regarding the same. Participants who met the inclusion criteria of the study that is belonging to the age group 20-30 and using an Instagram account, participants who identified themselves as male or female and who gave consent to the study were forwarded the second Google form consisting of the questionnaires. The data was collected through convenience sampling between August 2022 to December 2022. The predictor variable in the study is Instagram use and outcome variables in the study are body image, exercise motivation and social comparison. This study is based on the ‘The Strengthening of Reporting Observational Studies in Epidemiology (STROBE) statement guidelines (Elm et al., 2007). The study flow as per STROBE guidelines is depicted in the extended data (Vasudha & Nimiya, 2023).\n\nA sample size of 212 was calculated, considering a confidence level of 95%, with margin of error of 10%. Thus, 212 participants (males = 106, females = 106) aged between 20 and 30 years with an active Instagram account (Male; M = 22.76, SD = 1.84), (Female; M = 23.05, SD = 2.21) were recruited from different states across India to participate in the study. Participants without an active Instagram account as well as those with a history of physical/mental illness were excluded from the study. Participants were recruited via various social media platforms to take part in the study. Participation was voluntary. This age range was chosen not only for convenience, but because individuals of the prescribed age range are the heaviest users of Instagram (Kemp S. Digital 2023: Global Overview Report [Internet], 2023).\n\nThe research design employed in the study was quantitative comparative cross-sectional design which includes the analysis of data of variables collected at one given point in time across a sample population of a pre-defined subset. This method was applied to investigate the Sex difference in Instagram use with regards to body image, exercise motivation and social comparison.\n\nDemographics\n\nParticipants were asked to report demographic details such as age, sex, educational qualification, history of mental/physical illness, Instagram activity status, duration of Instagram use, number of celebrities followed on Instagram, number of fitness related pages followed on Instagram, frequency of posting exercise related pictures, exercise activity status and exercise routine: (Place of exercise, Duration of exercise, exercise with/without instructor).\n\nBody Self Image Questionnaire Short Form (BSIQ SF)\n\nThe Body Self Image Questionnaire (BSIQ) is a 27-item measure developed by Rowe (2005) comprising of nine, three-item scales assessing the person’s thoughts and feelings about the human body which are: Overall Appearance Evaluation; Health Fitness Influence; Investment in Ideals; Health-Fitness Evaluation; Attention to Grooming; Height Dissatisfaction; Fatness Evaluation; Negative Affect and Social Dependence. Before using the scale in our study we obtained permission from the author to use the scale in this study. Respondents indicate the degree to which they think each item is true regarding their body using a five-point Likert scale, with 1 = Not at all True of Myself, 2 = Slightly True of Myself, 3 = About Halfway True of Myself, 4 = Mostly True of Myself, and 5 = Completely True of Myself. With 5 being the lowest possible score and 135 being the maximum score, the higher the score, the greater the body image concerns. All nine sub-scales show adequate internal consistencies, as demonstrated by Cronbach alphas ranging from 0.68 to 0.92 (Rowe, 2005).\n\nExercise Motivation Inventory-2 (EMI-2)\n\nThe Exercise Motivations Inventory-2 (EMI-2) is a 51-item scale developed by Markland and Ingledew (1997) comprising of nine four-item scales and five three-item scales assessing individuals’ reasons for exercising (participation motives) in determining long-term adherence to regular physical activity which are Stress Management, Revitalization, Enjoyment, Challenge, Social Recognition, Affiliation, Competition, Health Pressures, Ill- Health Avoidance, Positive Health, Weight Management, Appearance, Strength & Endurance, Nimbleness. Respondents indicate, by circling the appropriate number, whether or not each item is true for them personally or would be true for them personally if they did exercise. If the statement is considered to be not at all true, ‘0’is circled. If the statement is very true indeed, ‘5’ is circled. If the statement is partly true, then ‘1’, ‘2’, ‘3’ or ‘4’ are circled, according to how strongly the person feels that it reflects why he/she exercise or might exercise. With 5 being the lowest possible score and 255 being the maximum score, higher the score, greater the exercise motivation. All fourteen sub-scales show adequate internal consistencies, as demonstrated by Cronbach alphas ranging from 0.69 to 0.92 (Markland & Hardy, 1993).\n\nInstagram as a tool for Social Comparison\n\nInstagram as a tool for Social Comparison is a 10-item measure which was developed by the Principal Investigator for assessing how individuals compare themselves with celebrities, peers or others with respect to their Instagram usage (see extended data). This includes aspects such as individuals’ feeling and thoughts towards posts/likes/comments/shares of fitness related pictures and videos in Instagram. Respondents indicated what extent to which they think the statements are true for them with each item using a five-point Likert scale, with a = Strongly Disagree, b = Disagree, c = Neutral, d = Agree and e = Strongly Agree. Some of the sample questions are as follows: “I take into consideration the views/likes/comments/shares I receive for my posts/stories”, “I judge myself based on the number of followers and likes”, “I repeatedly change my Instagram profile picture”, “I always think about what others might be thinking about the pictures/videos that I post in my feeds/stories”. With 5 being the lowest possible score and 50 being the maximum score; the higher the score, greater the magnitude of social comparison. The questionnaire was validated by three experts from the field. The name of the scale was changed from ‘Social Comparison and Instagram Use scale’ to ‘Instagram as a tool for Social Comparison’ as per experts’ suggestion. Certain other modifications were suggested, and these suggestions were taken into consideration and the modified questionnaire was used for data collection (Bessenoff, 2006).\n\nThe author’s Institutional Ethics Committee approved this study (Protocol No: IEC KMC MLR 04-2022/127). The population of this study were males and females in the age group 20-30 residing in different states across India. The independent and dependent variables in the study are Instagram usage and Body image, Exercise motivation, Social Comparison respectively. Participants gave written, informed consent before the commencement of the study.\n\nThe study was conducted in two phases:\n\nPilot phase - The pilot study was conducted from June 2022 to August 2022. The objective of the pilot phase was to develop and validate the tool for measuring social comparison as well as to determine the feasibility of the study. Because of the lack of availability of scales for measuring Social Comparison in the Indian context, the present scale was developed by the author to fit the population of study. We have developed Instagram as a tool for Social Comparison, keeping the original scale as a framework. The original scale is called as Extent Thoughts Measure developed by Gayle R Bessenoff in 2006 for their study purpose. Permission was obtained to use the tool in our research. However, we have not used that scale nor borrowed any questions from it. This phase included constructing items for Social Comparison and Instagram Use Scale, obtaining face validity from experts of the field and selecting participants and administering all the three scales. The participants were approached through various mediators such as friends, acquaintances and family via online platforms. The participants were selected based on the inclusion and exclusion criteria through online mode using google forms Consent form was given, which was filled by the participants through online mode where they were asked to mark a tick if they agree to take part in the study by saying ‘I agree’ or mark a tick if they disagree to take part in the study by saying ‘I disagree.’ Only the participants who chose the ‘I agree’ option were considered for the study. A socio-demographic sheet was provided to the study participants. Online survey forms were administered containing the three questionnaires used. Clear and detailed instructions were given before every questionnaire. The responses were collected according to mutually set period by researcher and participants. For the pilot phase, 10 samples were recruited according to the inclusion criteria of the study. Through the use of Instagram as a Tool for Social Comparison Scale, their total scores for Social Comparison were obtained. The typical score of Social Comparison in the population being studied was found to be 23 (M=24). This shows that level of Social Comparison among the population being studied was slightly below average. In the pilot phase we had also administered other two research scales (Body Self Image Questionnaire Short Form and Exercise Motivation Inventory) to check the duration required and check the feasibility of the study. The study was found to be feasible in terms of duration, accessibility of the population and instruments required. The items of the questionnaire were found to be appropriate for the population. The population was found to be relatively accessible to the researcher, and participants were recruited mainly through email and other social media. The questionnaires required around 20 minutes to complete, and participants had no issues completing them as required. No modifications were made to the research instruments or the research design after the pilot study.\n\nMain phase - The main study took place from September 2022 to January 2023. After the Institutional Ethical Committee clearance, the data collection for the study took place. The participants were selected based on the inclusion and exclusion criteria through online mode using google forms. The participants selected mainly included friends, acquaintances and family who satisfy the inclusion criteria. Consent form was given to be filled by the participants. Consent form was given, which was filled by the participants through online mode where they were asked to mark a tick if they agree to take part in the study by saying ‘I agree’ or mark a tick if they disagree to take part in the study by saying ‘I disagree.’ Only the participants who chose the ‘I agree’ option were considered for the study. A socio-demographic sheet was provided to the study participants and online survey forms were administered containing the three questionnaires used. Clear and detailed instructions were given before every questionnaire. The responses were collected according to mutually set period by researcher and participants.\n\nVersion 25.0 of IBM SPSS Statistics for Windows. IBM Corp., Armonk, New York, was employed to examine the acquired data (IBM Corp., 2017). We used the necessary tables to express our results as proportions. The data was normally distributed with Shapiro-Wilk statistic being 0.845 (>0.05) (M = 3.43 SD = 1.50). Based on this normality, parametric tools were used for the analysis. In order to find the difference between two groups with respect to the sociodemographic and dependent variables, independent sample t-test was used to find the Sex differences in body image, exercise motivation and social comparison. Univariate analysis of variance (ANOVA) was used to test the difference between two or more groups with respect to the sociodemographic and the dependent variables such as between body image and people who exercised regularly, not regularly and sometimes.\n\n\nResults\n\nCharacteristics of the sample\n\nA total of 253 participants were recruited for the study. The participants who weren’t active users of Instagram and who had a past history of physical/psychiatric illness were excluded. Thus, the final sample consisted of 212 participants (males = 106, females = 106) aged between 20 and 30 years with mean age of males, M = 22.76, and standard deviation SD = 1.84 and mean age of females, M = 23.05 and standard deviation SD = 2.21. The data was normally distributed with Shapiro-Wilk statistic being 0.845 (>0.05) and mean M = 3.43 and standard deviation SD = 1.50.\n\nAll the participants of the study were active Instagram users. Table 1 describes the Mean and standard deviation of Instagram usage characteristics of the sample. Their median use of Instagram was one hour per day. They reported following a median number of more than five celebrities and a median number of one-five fitness related pages. The participants also reported how frequently they watched fitness related images and videos and how frequently they posted fitness related images and videos. 15.4% of the participants reported watching fitness related posts daily, 29.2% (weekly), 17% (monthly) and 38.3% never watched fitness related posts. Similarly, 82.6% of the participants reported that they never posted pictures/videos related to fitness, 10.7% (monthly), 3.2% (weekly) and 3.6% (daily).\n\nAs can be seen in Table 2, mean scores for both Body Image (M = 73.61.84, SD = 13.66) and Social Comparison (M = 25.60, SD = 6.24) were found to be higher among females. In contrast, mean scores for Exercise Motivation was found to be higher among males (M = 156.36, SD = 43.32).\n\nSex differences in body image\n\nIndependent samples t test was conducted to compare the Sex differences in body image. As displayed in Table 3, there was significant difference in body image (t (2) = 0.019, p = 0.05) with mean score of females (M = 73.61, SD = 13.66), which was found to be higher than males (M = 68.84, SD = 15.58). The magnitude of the differences in the means (mean difference = -4.77, 95% CI: -8.77 to -0.77). Thus, there is a significant difference in body image between males and females, with mean body image higher among females in the age group 20-30 in the present study.\n\nSex differences in exercise motivation\n\nIndependent samples t test was conducted to compare the Sex differences in exercise motivation. As displayed in Table 3, there was significant difference in exercise motivation (t(2) = 0.005, p = 0.05) with mean score for males (M = 156.36, SD = 43.32), which was found to be higher than females (M = 136.38, SD = 56.93). The magnitude of the differences in the means (mean difference = -19.97, 95% CI: -33.79 to -6.15). Thus, there is a significant difference in exercise motivation between males and females, with mean exercise motivation higher among males in the age group 20-30 in the present study.\n\nSex differences in social comparison\n\nIndependent samples t test were conducted to compare the Sex differences in social comparison. As displayed in Table 3, no significant difference in social comparison across gender was seen in the present study.\n\nDifference in body image between people who followed fitness related pages on Instagram and those who did not.\n\nIndependent samples t test was conducted to compare the difference in body image across people who followed fitness related pages with those who did not. As displayed in Table 4, there was significant difference in body image (t(2) = 0.028, p = 0.05) with mean score for people who follow fitness related pages (M = 72.63, SD = 13.44), which was found to be higher than people who did not follow fitness related pages on Instagram (M = 69.44, SD = 16.21). The magnitude of the differences in the means (mean difference = 3.19, 95% CI: -0.84 to 7.22). Thus, there was a significant difference in body image between people who followed fitness related pages on Instagram and those who did not, with mean body image higher among people who followed fitness related pages on Instagram.\n\nDifference in body image between people who exercised regularly and those who did not\n\nTable 5 represents the difference between people who exercise regularly and body image in males and females in the age group 20-30. One way ANOVA test enumerated in the table revealed a significant difference in body image between people who exercise regularly and those who did not at p = 0.05 in the present study.\n\nTable 6 shows the frequency and percentage of the extrinsic and intrinsic motivational factors for exercise in men. Among the dimensions, majority of men reported ill-health avoidance & positive health (98.11%), revitalization (96.22%), strength & endurance (89.62%), stress management (86.79%), challenge & appearance (81.13%) as motivators for their exercise behaviours.\n\n\nDiscussion\n\nThe goal of the present study was to examine the Sex difference in body image, exercise motivation and social comparison among people who use Instagram in the age group 20-30. The current study advances our understanding of how Instagram use affects both men and women in the age range 20-30 when it comes to body image, exercise motivation, and social comparison. It is significant because it broadens the study of mass media to include Instagram, a medium for social media with a strong visual component. Due to the majority of studies’ attention being directed towards women, there is relatively little information available on the influence of social networking sites on men’s body image. The perfect male figure, however, has also received attention over the past few decades. As evidenced by images in magazines or action figures, the idealized concept of a more slender, muscular, and V-shaped male body has begun to gain attraction among Westerners (Voges et al., 2019). As a result, men, these days are also forced to work towards building an ideal body that is challenging to achieve. We chose to focus on Instagram in particular because a large body of studies on social media and body image has been focused on social networking sites like Facebook, Twitter etc. Since Instagram is one of the most widely utilized social media platforms (SNS) in use today, it is crucial to pay more attention to its influence. The first hypothesis was that there were no Sex differences in body image, Secondly, it was hypothesized that there were no Sex differences in exercise motivation. Finally, it was hypothesized that there were no Sex differences in social comparison in males and females Instagram users in the age group 20-30.\n\nThe first major finding of the study was that levels of body image concerns were higher among females, which was supported by a vast array of previous literature. Previous research findings suggested that ideal form of women has evolved through time, as women are frequently shown to be underweight in magazines and advertisements (Luff & Gray, 2009). Multiple research projects have indicated that there is no doubt that a constant encounter with idealized body types has harmful effects, low self-esteem, and body dissatisfaction, even though studies are hesitant to make that assertion (Bessenoff, 2006). Women are constantly met with the need to “control” their body weight below the normal, expected, healthy range as an attempt to fit into the society’s portrayal of idealized women’s body. This has been demonstrated by previous research that explored the relationship between social media and women’s body image, which revealed that, pre-exposure to social media photographs of fashion models increased women’s’ drive for thinness, which was correlated with post-exposure low mood and dissatisfaction with their body image (Drames, 2016). These findings imply that regardless of the setting or individual depicted, exposure to “thin” ideal images that are frequently encountered, either through newspapers, magazines, social media, or peers may have a comparable detrimental impact on women’s body satisfaction. Future studies might specifically investigate this proposition.\n\nThe finding that body image concerns were higher among women strongly supported another major finding of the study, which showed that a significant difference exists in body image across gender; with higher body image concerns among females. This finding was supported by numerous previous research which indicated that women oftentimes feel a gap between their existing real bodies and the elusive - ideal female body, which eventually paves the way for body dissatisfaction (Mills et al., 2018). Compared to boys, girls are more conscious about the ways in which their body weight influences their appearance, beginning right from childhood (Shriver et al., 2013b). In addition, women are inclined to have decreased self-esteem when they feel that their weight is above the idealized weight norms, whereas men tend to experience this only when they feel that they are obese (Shriver et al., 2013a). Congruent to this finding, it was identified that girls give importance to beauty and aesthetics and place less emphasis on the functioning capacity of their bodies than did boys (Abbott & Barber, 2010). More so than the idealized male masculinity, which is represented by more varied media depictions, the norms for the female body ideal appear to be more well defined (Boute et al., 2011).\n\nThe second major finding was that the levels of exercise motivation was found to be higher among males. This was seen in the data from the present study which indicated that men reported on an average tending to spend more time on exercise and other physical activities than women. The socio-demographic data also revealed that as compared to women, men are more inclined to spend their time in the gym (30%). The dimensions of the Exercise Motivation Inventory used in this study indicated that men on an average were motivated to exercise more as compared to women due to many reasons, including the need to gain Strength & Endurance, Ill-health Avoidance, Revitalization, Challenge, Enjoyment, Stress Management. These findings have been supported by previous research findings suggesting gender disparities in exercise involvement (Bauman et al., 2009). In traditional eastern cultures, where women typically take on the role of carers for the family and have less time for exercise pointing that, gender roles may have an impact on regular exercise habit (Craft, Carroll & Lustyk, 2014). Thus, even though women have body image issues due to social media exposure, they might be less indulgent in exercise behaviours due to these reasons (Chen et al., 2011). Additionally, these findings have also been strengthened by previous literature exploring the effect of social media on exercise behaviours in men (Rote et al., 2015). The success of these platforms has been linked to a number of factors, consisting of the sense of belonging fostered by physical activity-based group chats, which increased accountability for daily exercise, social media-provided encouragement and praise, motivation gained from knowing other members’ progress on exercise behaviours, and motivation gained from viewing posts regarding the advantages of exercising (Chen et al., 2011).\n\nThis result provides strong evidence for another major finding from the present study which revealed that a significant difference in exercise motivation across gender with higher exercise motivation in males in the present study. Previous research which focused on studying gender disparities in the motivations for exercising supports this finding (Markland & Tobin, 2010). It is likely that men and women may feel distinct advantages from exercise as a result of their activity attributions given these gender disparities in reasons for exercising. Men in general are more likely to attribute exercise to social and competitive factors, while women are more likely to attribute exercise to appearance-related factors, such as to lose or maintain weight. Furthermore, it was observed that rather than exercise itself, women’s reasons for exercising predicted their quality of life. Engaging in physical activity with the goal of getting fit or reducing weight, for instance, was linked to poor quality of life, whereas engaging in physical activity to uplift mood or enhance health was linked to an increased quality of life (Craft et al., 2014). Previous research also indicates that, men and women “enjoy” exercise differently. This was visible in the mental health benefits derived from physical activity. Men who engaged in vigorous physical activity reported lower levels of depressive and anxiety symptoms as well as other visible signs of mental stress (Rote et al., 2015). Men may experience less harm to their mental health as a result of their higher levels and more intense physical activity (Craft, Carroll & Lustyk, 2014) It was determined that men benefit more from intensive exercise than women do from lighter exercise (Asztalos et al., 2010). Additionally, these findings have also been strengthened by previous literature exploring the effect of social media on exercise behaviours in men. The success of these platforms (Facebook, Instagram, Snapchat and other online platforms) has been attributed to a number of factors, including the sense of belonging fostered by physical activity-based group chats, which increased accountability for daily exercise, social media-provided encouragement and praise, motivation gained from knowing other members’ progress on exercise behaviours, and motivation gained from viewing posts regarding the advantages of exercising (Jones, 2001; Bessenoff, 2006).\n\nWith respect to social comparison, the results revealed that the levels of comparison were slightly higher among women as compared to men. This is congruent with a past quantitative data analysis research, which suggested that internalization of a “thin” ideal is facilitated by a strong inclination for evaluative comparisons with appealing targets (Morrison, Kalin & Morrison, 2004; Schutz, Paxton & Wertheim, 2002) and mediates the impact of the media on body dissatisfaction in women (Van den Berg et al., 2002). Studies have shown that women usually make comparison of their body with attractiveness, whereas men tend to compare their body in terms of build. Because women are frequent targets of ideal body advertisements and commercials in general media as well as social media, these results are not surprising. But this doesn’t deny the fact that men too are confronted with unrealistic comparisons aided by media. In fact, a qualitative study indicated that male participants reported that they felt forced by the social networking sites to appear more masculine, particularly on the upper body (Ridgeway & Tylka, 2005). Thus, the levels of social comparison being more or less similar in males and females indicated that both sexes are confronted with self-evaluation with regards to media portrayals of ideal men and women, which might also be a predictor of body image issues in this population. This calls for a more in-depth investigation in future to better understand the mediating effect of social comparison on body image in both men and women.\n\nThe finding that there were no Sex differences in social comparison supported the above finding and was incongruent with previous research. Literature has consistently shown that even though men and women frequently coexist in the same social environments, there is ample proof that even the identical social situations can be interpreted and experienced differently by men and women (Grabe, Ward et al. 2008). Women were shown to be increasingly prone to view themselves from an external point of view and participate in a self-critical comparison process regarding their bodies because of the cultural preoccupation on ideal female body as an aesthetic object relative to the male body (Franzoi et al., 2012). In contrast, men were shown to be more optimistic and less judgmental of themselves when assessing their bodies than women (Miller & Ross, 1975). However, present study could not find any difference in social comparison across gender. This points to the assumption that there could be other factors such as the sample size, sociodemographic characteristics that might have played a role in producing these results.\n\nThe present study contributes to the literature on social media and body image, exercise motivation and social comparison, considering the importance of increased use of SNS such as Instagram over the recent years. This study revealed that body image concerns were higher among women. This finding suggests that women should be educated about the harmful effects of body image distortions and resulting lowered self-esteem and body dissatisfaction. The finding that drive for exercise was higher among males provides a foundation for understanding the motivators for male exercise behaviours including the genetic, psychological, social and cultural factors. This information can aid in planning interventions for mitigating the potential negative effects of exercise behaviours such as exercise addiction, however more in depth research is needed.\n\nStrengths, limitations and future research\n\nIt was a strength of the current study that it collected a sample that gave disparate information about the participants’ Instagram activity including the duration of use, celebrities followed, fitness related pages followed, and frequency of sharing posts/videos related to fitness which gave a clearer picture of how these factors could be a contributing factor to the Sex differences in the variables studied.\n\nDespite these strengths, there were a few limitations that ought to be mentioned and which may help to direct future study. First, the study’s use of a purposive sampling method poses a significant restriction. The representativeness of Indian Instagram users may still be overestimated even if the sample comprises of 212 respondents chosen from various online platforms. The study findings can be generalized to populations in the similar age range and similar sociocultural milieu. However, it is recommended that future studies can incorporate a larger sample size. Another limitation was that although a significant difference in body image and exercise motivation was observed across gender, the huge community of SNS users with over 1.3 billion users on Instagram indicates that these discoveries are relevant only at a population level. The study’s design constituted still another drawback. Its cross-sectional design prevents us from understanding the causal connection between the variables. Finally, it is impossible to completely rule out the possibility of residual confounding such as simultaneous use of other SNS platforms and social desirability bias in self-reported data. There was no supplemental information collected from other potential sources, such as relatives or peers.\n\nGiven these limitations, future research can focus on exploring individuals with a larger range of ages, given that older and middle-aged people engage in social media, although in a smaller amount than younger people. All future studies should be proactive to recruit culturally diverse samples as often as possible to be able to draw conclusions about the potentially differential effects as well as to make comparisons across individuals from diverse backgrounds. Future research can also delve deeper into the sociodemographic factors explored in the study to better understand how it can play a role in Sex difference in these variables with large samples. Also, experimental and longitudinal studies are recommended in future studies, that may examine the cause-effect relationships among variables. In future studies, additional data from other possible sources such as family members, peers, or significant others in the environment may be collected to measure.\n\n\nConclusions\n\nBody image, exercise motivation, and social comparison are interrelated concepts that shape the way individuals perceive themselves and others. According to this study, women were more likely than men to have body image concerns. This finding suggests that women need to be made aware of the risks associated with distorted body images, low self-esteem, and body dissatisfaction. The discovery that males were more motivated to exercise than females lays the groundwork for understanding the genetic, psychological, social, and cultural motivations for male exercise behaviours. Planning interventions to lessen the possible negative effects of exercise behaviours, such as exercise addiction, can be made easier with the help of this information. It is critical to identify who is at risk of acquiring dangerous exercise practises as a result of a change in their body image for both prevention and treatment. The study’s findings will aid in this knowledge.",
"appendix": "Data availability\n\nOpen Scientific Framework: Sex difference in body image, exercise motivation and social comparison among Instagram users: a cross sectional study. DOI: https://doi.org/10.17605/OSF.IO/S6R4T (Vasudha & Nimiya, 2023)\n\nThis project contains the following underlying data:\n\n• Instagram as a tool for social comparison responses.xlsx\n\n• BSIQ responses.xlsx (Responses of all the participants on Body Self Image Questionnaire)\n\n• EMI 2 responses.xlsx (Exercise Motivation Inventory participant’s response)\n\nThis dataset contains the following extended data:\n\n• INSTAGRAM AS A TOOL FOR SOCIAL COMPARISON.docx\n\n• Scale validation.pdf (Instagram as a tool for social comparison scale validation)\n\n• Study flow figure.jpg\n\n• STROBE_checklist_cross-sectional-F1000.docx\n\nData is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbbott BD, Barber BL: Embodied image: Sex differences in functional and aesthetic body image among Australian adolescents. Body Image. 2010; 7(1): 22–31. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan den Berg P, Thompson JK, Obremski-Brandon K, et al.: The tripartite influence model of body image and eating disturbance: A covariance structure modeling investigation testing the mediational role of appearance comparison. J. Psychosom. Res. 2002; 53(5): 1007–1020. PubMed Abstract | Publisher Full Text\n\nVogel EA, Rose JP, Okdie BM, et al.: Who compares and despairs? The effect of social comparison orientation on social media use and its outcomes. Personal. Individ. Differ. 2015; 86: 249–256. Publisher Full Text\n\nVoges MM, Giabbiconi CM, Schöne B, et al.: Sex differences in body evaluation: Do men show more self-serving double standards than women? Front. Psychol. 2019; 10: 544. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVon Elm E, Altman DG, Egger M, et al.: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. Lancet. 2007; 370(9596): 1453–1457. Publisher Full Text\n\nYang CC: Instagram use, loneliness, and social comparison orientation: Interact and browse on social media, but don’t compare. Cyberpsychol. Behav. Soc. Netw. 2016; 19(12): 703–708. PubMed Abstract | Publisher Full Text\n\nVasudha KG, Nimiya A: Sex difference in body image, exercise motivation and social comparison among Instagram users: a cross sectional study (new).2023, July 17. Publisher Full Text"
}
|
[
{
"id": "271051",
"date": "06 May 2024",
"name": "Vandana Gaur",
"expertise": [
"Reviewer Expertise Social Psychology",
"Cognitive Psychology",
"Psychopathology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study effectively explores the relationship between Instagram use and body image, exercise motivation, and social comparison, shedding light on potential sex differences. Methodological rigor and clarity enhance its credibility. However, further analysis on the influence of other variables could enrich the discussion. Overall, a commendable contribution to understanding social media's impact on body perceptions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11520",
"date": "20 Jun 2024",
"name": "Vasudha K.G",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for taking the time to review our study titled \"Sex Difference in Body Image, Exercise Motivation, and Social Comparison among Instagram Users: A Cross-Sectional Study.\" We appreciate your thoughtful feedback and constructive comments. We are pleased to hear that you found our study to effectively explore the relationship between Instagram use and body image, exercise motivation, and social comparison, while also highlighting potential sex differences. Regarding your suggestion for further analysis on the influence of other variables, we acknowledge the importance of considering additional factors that may contribute to body image concerns, exercise motivation, and social comparison among Instagram users. In future research, we plan to explore the influence of variables such as self-esteem, media literacy, technology engagement, cultural influences, and peer influences to provide a more comprehensive understanding of these phenomena. We are grateful for your positive evaluation of our study's methodological rigor and clarity. We are committed to maintaining these standards in our research endeavors. Once again, thank you for your valuable feedback and recognition of our contribution to understanding the impact of social media on body perceptions. We will consider your suggestions for future research directions. Regards, Vasudha K.G Department of Psychiatry, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India"
}
]
},
{
"id": "280599",
"date": "24 May 2024",
"name": "Niyaz Panakaje",
"expertise": [
"Reviewer Expertise Higher Education",
"Stress",
"Social Media",
"Entrepreneurhip"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study employs a quite interesting approach to assessing the gender differences in body image, exercise motivation, and social comparison among young Instagram users. The present study has a realistic contribution to the existing body of knowledge and feasible recommendations for the young generation. However, some concerns need an immediate attention: 1.\n\nThe introduction of the manuscript is well drafted depicting the background, problem, need, and gap of the study. 2.\n\nIn this section, the authors stated data collection from the sample size of 212 youth, but the rationale behind restricting this number has not been justified which poses a question of generalizability. It is recommended to provide a background for the population and solid justification for collecting only 212 responses (as the study employed convenience sampling, the number of responses needs to be quite high to eliminate the error and bias). The selection of age range is justifiable but the number of sample selections seems to be faulty. Kindly provide a rationale. 3.\n\nAs the study stated “The data was normally distributed with Shapiro-Wilk statistic being 0.845 (>0.05) and mean M = 3.43 and standard deviation SD = 1.50”, the clarification on normality distribution needs to be further explained. As there are three dependent variables, normality needs to be checked for all three variables. However, only one value has been indicated, kindly recheck this part. 4.\n\nThe study’s implications lack depth. As the study provided highly valuable outcome of disparity in the gender concerning body image, social comparison, and exercise motivation, specific theoretical and practical implications are missing. The paper can benefit by further providing detailed implications to the theories referred and practical scenarios. Overall, the study has the potential to get more visibility due to its novel contributions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11749",
"date": "14 Jun 2024",
"name": "Vasudha K.G",
"role": "Author Response",
"response": "Dear Sir, Thank you for your valuable feedback on our manuscript. We appreciate your insightful comments and suggestions, which have undoubtedly contributed to improving the quality of our study. Thank you for acknowledging and giving feedback regarding the introduction of the manuscript. Thank you for your insightful feedback on data collection. We understand the importance of providing a robust rationale for the sample size and addressing concerns about generalizability. We have tried our best to addresses your concerns in the modified manuscript. We've carefully considered your suggestions and believe that the revisions made to the sample size justification adequately address the concerns raised. These modifications aim to provide a clearer rationale for our methodological decisions, ultimately enhancing the rigor of our study. The sample size of 212 participants, though modest, was calculated to achieve a balance between feasibility and statistical power. This size allows for meaningful preliminary insights while acknowledging the need for future studies with larger and more diverse samples to enhance generalizability and validate our findings. We appreciate your observation regarding the need for further clarification on the normality distribution of our data. Upon reviewing our analysis, we acknowledge that normality should be checked for each of the three dependent variables individually. We have provided a detailed explanation and updated our manuscript to include the normality checks for all dependent variables: Body Image, Exercise Motivation, and Social Comparison. We understand the importance of providing detailed theoretical and practical implications based on our findings and we have addressed these points in our revised manuscript. We have added a theoretical implication, like: Self-determination theory and Exercise motivation. We have also mentioned the practical implications, such as complex issues surrounding body image, social comparison, and motivation, particularly in the context of social media and its influence."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1506
|
https://f1000research.com/articles/11-1109/v1
|
28 Sep 22
|
{
"type": "Policy Brief",
"title": "On climate order: a policy brief",
"authors": [
"Rui Feng"
],
"abstract": "Background: Climate change, largely triggered by human-induced greenhouse gases (GHGs) emissions, seems unstoppable. There was a strong rebound of anthropogenic emissions of CO2, the preponderant GHG in terms of contribution to global warming, around the world after the COVID-19 lockdown. Also, there is still no widely accepted international treaty on curbing the anthropogenic emissions of CH4 and N2O, the second and third predominant GHG, respectively, so far. Thereby, prima facie, in respect to mitigating climate change, currently, humans have no aces up their sleeves. It seems that current temperature rise is not high enough to take alarm until the occurrence of tipping point. Policy: Climate-related international treaties, such as 2016 Paris agreement, are compromises among conflicting geopolitical pressures. However, currently, the climate treaties show little mandatory binding force on the signatories who are able to violate and then get off scot-free, thus may end up like a nostrum. Throughout the European history, I find that the only way, if at all, to achieve the peace or obedience of a treaty is via balancing powers, embodied in Bismarck’s Realpolitik of Germany and Richelieu’s Raison d'état of France. Similarly, the Chinese history in East Asia proved the significance of unadulterated ideological neutrality and Darwinian adaptability in the kaleidoscope of evolving circumstances in maintaining order and enforcement of international treaties through balancing the power of rivalries to constrain ever-recurring challengers for equilibrium. Recommendations: A successful policy needs to make a thorough analysis of all relevant factors to form a long-term strategic notion. Then, statesmen need to distill an array of nebulous, always contradictory options into a tenacious, controllable direction. Thereby, I suggest that, for better curbing global warming, climate agreements or climate club be incorporated into an overall geopolitical framework among the international communities.",
"keywords": [
"Climate change",
"Hobbesian analysis",
"Westphalia",
"Geopolitical imperatives",
"Balance-of-power",
"climate policy"
],
"content": "Introduction\n\nThe vicissitude of humanity has waxed and waned through the coaster ride of history. Every age has its leitmotif and every generation has their own focal points and challenges. In the young twenty-first century, along with food security, terrorism, public health and hygiene, and poverty, climate change as a shot-across-the-bow of our generation has become an inveterately arising crisis. Hence, the world had been awaiting an agreement by countries which could be in a position to hold a global vision to mitigate the rapid climate change. As an upshot, there was the 2016 Paris Agreement (UNFCCC, 2020), aimed at keeping temperature increase below two degrees Celsius compared to the preindustrial level. After its ratification in 2016 (Clarke and Searle, 2021), the nationally determined contributions (NDCs) and the non-mandatory long-term low greenhouse gas emission development strategies (LT-LEDS) had been submitted by signatories by 2020 to show their internal aspirations and planned measures towards mitigating climate change, striving for transforming the efforts for abating global warming from headlines to trend lines and translating conceptual recognition into concrete acts.\n\nEven though the national strengths are in constant flux, the Paris Agreement has proved a possibility that distinct countries can cooperate on common goals through quasi formal mechanisms. Where there is an agreement, there is a foreseeable benefit; where there is a benefit, there is an order to grant and maintain it agreeable, attainable, and sustainable for the players. Thereby, the overarching questions arise: is this order established for abating climate change entire unto itself or integrated into a wider international system? And with deepening cooperation on climate change among countries, which order’s norms could prevail on the scene?\n\nIn this study, I examine the 2016 Paris agreement, the one that has not been forged in the school of hard knocks. A climate treaty needs to take the multiplicity of different interpretations on climate change among countries with distinct historical experiences into consideration and sublimate a variety of societies with diverse national interests into common search for curbing GHGs emissions. The vitality of climate treaty is reflected in the balance it strikes between changes in national power caused by climate change and that by the adoption of GHG emission reduction policies, which depends on the relative method of calculation given to each, indicating the necessity to form congruent perceptions of how the policies on GHGs reduction would affect the geopolitics in practice for a society. Climate policy is a cost-and-benefit analysis.\n\nAccording to history, when confronting potential threats that may occur, most countries preferred waiting until a major threat took tangible, specific shape. In the history of Europe, Realpolitik promoted by Otto Eduard Leopold von Bismarck (1815–1898) and Raison d'état proposed by Armand-Jean du Plessis de Richelieu (1585–1642) had the historic roles as the standard-bearer of German and French statehood, respectively. Both Bismarck and Richelieu believed that there was no superior principle that can constrain the inner desire of a country for power and development, and an international agreement could only be attained by correctly evaluating the components of national strengths.\n\nThomas Hobbes (1588–1679) firstly developed a biological-psychological description of human nature based on inherent self-affirmation and reason, from which the starting point of modern politics might lie (Xifra, 2017). Hobbes argued that the perpetual and unchanging humanity accords the politics and order timeless necessity (Ewin, 2001). John Locke (1632–1704) and Jean-Jacques Rousseau (1712–1778) also traced a similar viewpoint that timeless self-love frames the direction of social evolution. Sown in the nature of man, the principles and legitimacy through the evolution of human society have been established, so is the international order. On the basis of self-love and intrinsic yet frail sense of reason in essentially Hobbesian analysis, conventional order has seen peoples and nations—regarded as inherently competitive with a Sisyphean character—two intrinsic purposes: survival and development, which are labelled as the core interests of all living organisms, of which the inner dynamic of self-preservation is the fundamental driving force. Natural selection favors the genes that manipulate the world to ensure their own reproduction and altruism is not a part of our biological nature (Dawkins, 1989). The strength of a people or a society is the principle of order with which it most efficiently marshals its limited resources. When two nations meet, a testing of limits and strengths is inevitable and then a broader range of order may emerge as a corollary of collisions between two unparallel egos. Goodwill and neutrality are required to reach an agreement or a consensus peacefully. But in international politics, the imperatives of geopolitics override the pursuit of philosophical loftiness or moral purity (Kissinger, 2015), rendering a pragmatic dimension on actions. So as to the issue of global warming, leadership does not need to search for an idealism at the expense of lowering a country’s aspiration for survival and development. The ultimate motivation to curb climate change is distilled from an ecumenical calculation of national interests, not ethical restraints. In this view, the possible gain and loss from climate change are integrated into a panoramic analysis of national interests. What matters is how to incorporate the climate change with the other factors that impact on the survival and development of a nation into a design to make an overall guideline for policy-making. After all, the only sustainable foundation of policy of great powers is egotism and there is no reciprocity for sentimental policies. No country would do anything regarded as the rewards for others’ sacrifice. Entente cordiale is strictly due to utility, not gratitude.\n\n\nThe existing orders in history: implications for climate order\n\nThe Wilsonianism proposed by Woodrow Wilson was aimed to seek for world peace and universal harmony by cultivating shared principles and standards to bridge the gaps between realism and idealism. However, to some extent unmoored from Hobbesian analysis and taking refuge in wishful thinking, Wilsonianism, which mainly focused on international law, humanitarian objectives, and goodwill, ran into the sand due to its disconnection from a sense of geopolitics (McDougall, 2015). In other words, mortgaging futures on the cultivated goodwill is quixotical and hardly successful, because the core interests of a nation cannot be respected if itself is unable or unwilling to fight for them. The past is the best mentor for the future. The League of Nations (1920-1946) failed to promote the disarmament in 1920s and 1930s (Eloranta et al., 2011), because it failed to offer security guarantees for memberships due to a lack of resolutions for enforcements.\n\nThe downfall of Wilsonianism and the League of Nations was because policies followed public opinions which viewed agreements can be maintained by disinterested consensus and harmony is the natural condition of humans, thus often departing from Hobbesianism. For another case, Klemens von Metternich (1773-1859) could not stop the unification of Germany by Prussia, the most powerful geopolitical opponent of Austria, because his policy concentrated too much on principles but failed to maintain an equilibrium of power in central Europe. In a conventional Hobbesian analysis, when expecting the worst from human and making a virtue of necessity, decision-makers rarely find themselves disappointed. Since climate change policy has no strong geopolitical binding force, the outcome may end up like that of the Wilsonianism-based League of Nations.\n\nThroughout the history of humanity, two types of international order have been established and prevailing regionally, shown in Figure 1. Following the doctrines of Hobbesianism and reaching a strategic equilibrium, the 1648 Treaty of Westphalia and 1815 Treaty of Vienna succeeded to maintain peace. On the contrary, following the doctrines of Wilsonianism and failing to balance the power, the League of Nations and 1919 Treaty of Versailles ended in war.\n\nThe core ideas of the balance-of-power in Europe and the Confucian hierarchy in East Asia are basically similar to the Hobbesianism while the climate agreements are more likely derived from Wilsonianism.\n\nThe lodestar of an order that is supposed to be sustainable contains three elements: it defines the minimum condition of the survival of a nation, its scope must contain the minimum arrière pensée of a nation for its own development, and it must assess the maximum aspiration of a nation for pursuing its national interests. Meanwhile, a treaty should reflect a sense of shared purpose, a recognition of common threat, and the ability to gather strengths for joint actions.\n\nThe treaties of Westphalia in 1648, which was aimed to reduce the risks of exhaustion by excessive consumption of human resources and drain of strength in vain by congenitally competitive nature of man in the incessant competitions, had marked a turning point in the history of Europe (Kissinger, 1994), verifying that peace and sovereign equality can be established upon balancing rivalries and appealing to all participants into a shared search for establishing order. In Westphalian principle, a system can be constrained in a narrow range of equilibrium through limiting the more powerful competitors by spontaneous alliance of counterweighing forces. Since the powers are in constant flux, the ingenuity of Westphalia-style order embodies in its pathway: it is essentially procedural, not substantive (Kissinger, 2015). In this view, adroitly maintaining the equilibrium and deftly shifting in coalescence as a balancer towards the weak side among powers is the central strategic purport of foreign policy for a nation, effectively preventing the emergence of a Machiavellian approach by the strongest nation. The kernel of this kind of order is epitomized by its fluidity and pragmatism. Even though some may point out that equilibrium is the temporary consequence of an intermeshing of self-serving intentions, history has revealed that the eras of the successful enforcement of balance-of-power were the most peaceful time in Europe. For example, the Congress of Vienna in 1815 ushered in a century of comparative stability in Europe, because it achieved the geopolitical equilibrium in Central Europe. The success of peace-keeping in the 1648 Treaty of Westphalia indicates that only by achieving a geopolitical balance-of-power can a treaty be implemented and obeyed. Since the damages of climate change is too difficult to make similar evaluation among countries, the willingness to vindicate the GHGs emissions too multifarious, and imposing punishment for violation is highly likely out of the question, the climate agreements only spin a web of moral restrictions without geopolitical restraints. Thus, the weakness of climate treaty is the interests of countries in a changing climate are not uniform and the enforcement is rarely seamless, leading to inaction whose alibi may be circumspection. The signatories of climate treaties may highly possibly witness the withdraw of the most powerful member who feels its own survival will not be much impacted in a warming climate. Actually, on November 4, 2019, the United States announced its decision to withdraw from the 2016 Paris Agreement.\n\nIn East Asia, as nations shared the devastating experience of the conflicts derived from misunderstandings, they were committed to preventing the recurrence of warfare. Since Asian countries had more distinguished languages and cultures than Europe, their predominant goal was to find a way to clearly understand the real intention of the distinct neighborhoods to prevent high-wire acts. Overcoming the obstacles in the communications of the continent's diverse peoples, ancient China had established a tributary system to foster an order based on the hierarchical concepts of Confucianism. The essence of this tributary system is not so much material as ritual and conceptual. In fact, China often gave more gifts to the tributary countries than tributary countries offered to China (Kissinger, 2012). China’s goal was neither to acquire economic gains nor to seek domination, but to reduce the possibilities of potential conflicts triggered by misconceptions or incomprehension of the surrounding nations that had disparate cultures and to promote deference from its recalcitrant neighbors. The prerequisite for countries that chose to join this tributary order was the acceptance of the peaceful resolution of disputes with a shared etiquette of fair conducts among all participants, acting as a decisive catalyst to satisfy all sides' amour propre. China regarded itself as the patriarch of this familial hierarchy with a role in keeping the etiquette functioning smoothly. The genius of this kind of order whose courtesy emphasizes reciprocity is that it’s procedural, not substantive, softly sending all players to find its appropriate place in the system, ensuring dissatisfaction of countries in the East Asia lower than the level at which some may seek to overthrow the established order, and preventing the emergence of a geopolitical rival with the national strength close to China. Through this international order, China had prospered for a long time in history. But when China became weak, the equilibrium of power was broken at the periphery of China and this tributary system inevitably collapsed. In essence, this Chinese-created international system is a balance-of-power in all but name. Similar to the lessons from the 1648 Treaty of Westphalia, the international order in East Asia proved that only by realizing the balance-of-power can a treaty be sustained. The Confucian hierarchy is the Chinese version of Realpolitik and Raison d'état, for assembled therein was similar to the essence of Hobbesianism, indicating when making climate policies in East Asia, geopolitical imperatives should be considered.\n\n\nClimate order\n\nThe lessons from Wilsonianism, the League of Nations, the Westphalian balance-of-power, and the Confucian tributary hierarchy indicate that agreements or consensus can be only made possible upon the pursuit and fulfillment of self-interests of each participant and that a sustainable order can only be founded in a more procedural and less substantive framework that guarantees, if not boosts, the internal core interests of major players.\n\nIn this view, the precondition of the success of the 2016 Paris Agreement depends on a thoroughly, accurate analysis on each nation’s threshold for threats of global warming. Order formation is where the past meets the future. The northern nations, with a cold climate, may prefer to withhold explicit commitments and wait for a major domestic threat from climate change to take specific shape. For example, Russia did not join the Paris Agreement until September 2019. For those nations that have a narrow margin of safety in a warming age, they may find their survival and developments in danger from a smaller degree of climate change than that which causes the other countries to be alarmed. The lifeblood of creating climate policy is reflected in the balance it strikes between the prediction of what the impending risks of climate change are and the evaluation on how much it costs to mitigate it. Each nation’s own methods of calculation given to each variable are the fulcrum to formulate policy. If the scale is tilted towards mitigation, actions may obtain an extent of spontaneity. However, the perspectives on national interests (survival and development) are too diverse and historical experiences too distinct among cultures. For instance, where American envisions infinite optimism, Russian may experience stoic forbearance.\n\nThe maximum temperature increase for which different countries can tolerate diverge. Variant degrees of tolerance for climate change among nations may lead to the countries with high threshold to use its endurance as a bargaining chip to render a broad berth for practical necessities towards their own geopolitical advantage. Brinkmanship may become an end result of instituting policies. Thus, climate-related policies are inclined to be integrated into an overall assessment of geopolitical realities, under the framework of either Europe’s Westphalian equilibrium or East Asia’s Sino-centric hierarchy. Since the geopolitical power is in constant flux, the climate order is not so much as a Newtonian concept of interlocking mechanical clockwork regularity as a Darwinian evolution of the survival of the fittest.\n\nGlobal agreements on climate issues can be traced back to the 1997 Kyoto Protocol, but up to now, no considerable coordinated mitigation has come about yet (Nordhaus, 2021). The United Nations (UN) plays a role as a platform whose framework provides a procedural, not substantive pathway to blunt the edges of controversies among nations. Thereby, a new order that has combined Europe’s Westphalian equilibrium and East Asia’s Sino-centric hierarchy has been established. Five predominant powers, inclusive of China, the United States of America (USA), Russia, the United Kingdom (UK), and France, have been selected as the permanent members of the United Nations Security Council, balancing each other. When these five great powers pursue their own interests with restrain, their intermeshing ambitions can reach an equilibrium, and then possibly an agreement can be fulfilled. Inside the top UN hierarchy, the five permanent numbers are in a Westphalia-style balance-of-power. Outside the top of hierarchy, they act as the patriarchs under the banner of the Charter of the United Nations, mastering the art of adopting a calibrated combination of rewards and punishments to settle disputes and abate conflicts.\n\nA new concept of the climate club has been proposed recently to combat free-riding countries, as the participants in the club supposedly are obliged to take a uniform tariff on all imports from non-club nations (Nordhaus, 2021). While highly possibly analogous to the test for Wilsonianism-based League of Nations, the trial on the climate club may never be whether the club members are able to enshrine or consecrate the treaty on curbing climate change via amply elaborate rules with a wide range of signatories. The fundamental test is what to do if these rules are violated, challenged, or even manipulated against the core ideas of the club and how to execute it. The fabric of the entire planning edifice may unravel and be out of kilter even if just one strand were drawn out. Hence, in a systematic and conceptual manner, a precondition for the success of the climate club is that those who have been required to take the lead in checking the disobedience of its principles view the dangers of climate change in the same light and have the willpower and capability to mete out the punishments to anyone who violates the principles.\n\nThus, in this climate club, the guardians of the principles of climate order are of great importance, especially as the power and willingness of countries to maintain these principles are in an ever-changing, fluid equilibrium. Not only proscription is enough, but also prevention is needed by forces. An agreement is workable only if it reflects a balance-of-power. The failure of the enforcements of collective security established from the concepts of Wilsonianism and the League of Nations was because the definition of violation was so vague and the reluctance to take joint action so strong.\n\nThus, not to put too fine a point on it, doubts arise on what action to take if a member of the Paris Agreement is so determined to disobey the principles, and if the democratic public consider that punitive measures by forces are against current international laws in the framework of UN. Can the rules and principles of the climate club themselves build an order, or are they adding a scaffold unto the geopolitical structure that currently exists? Will the climate order construct a live-and-let-live system? In case of violation, confrontation, or didactic cooperation, which may prevail? If an international framework for cooperation is only made possible when it’s more procedural and less substantive, is the criterion for selecting memberships on the basis of their power or a low threshold of climate change impact? What role will the climate club play when geopolitical imperatives transcend it? How will it compensate for the sacrifices made by countries with high thresholds of climate change risk under the shadow of the future?\n\nAs an old saying goes that “history does not repeat; it rhymes” (Kissinger, 2012). In a Hobbesian analysis, a contest over the preeminence in an order is always predictable and foreseeable. Matters of specific tariff concessions or negotiating norms are not as important as contesting for the leadership over the nature of the climate order. As discussed above that the principles of climate club will be highly likely integrated into a global geopolitical structure, not as a separate order, carbon neutrality is a matter of price, not principle, for the essence of climate orders is based on the geopolitical interests. And a climate institution should consist of a core group of hard-nosed countries to obtain a certain degree of hegemonic stability. Only by this way, a country would have a reason and willingness to accept an international system in which to anchor itself.\n\n\nAmbiguity in the notion and scientific basis of carbon neutrality\n\nThe 2016 Paris Agreement is the first widely accepted international treaty to introduce the notion of carbon neutrality. But the concept and definition of carbon neutrality are nebulous. Whether the term ‘carbon neutrality’ only includes net zero emissions of CO2 or contains other types of GHGs is unclear. Common GHGs include CO2, CH4, N2O, NF3, SF6, hydrofluorocarbons (HFCs), and perfluorocarbons (PFCs). According to Le Ravalec et al. (2022), carbon neutrality means that anthropogenic GHGs emissions are offset by reduced emissions and increased sequestrations, thus striking a balance between discharges and sinks. European Union (EU) has planned to realize climate-neutral by 2050, indicating that the EU takes the total GHGs emissions into account (European Council, 2021). However, currently, China only focuses on the net zero emissions of CO2 and does not take the emissions of other types of GHGs into considerations (MEE, 2021).\n\nAnother discombobulating unclearness is the definition of net zero emissions. The question arises of how to evaluate whether carbon neutrality is achieved. According to Huovila et al. (2022), carbon neutrality means that CO2 emissions are balanced by local sinks. The categories of CO2 emissions and sinks can be divided into natural and anthropogenic sources. Recently, a report from the Intergovernmental Panel on Climate Change (IPCC) showed carbon neutrality means human-induced CO2 emissions are counterbalanced by anthropogenic CO2 removals over a specified time horizon (IPCC, 2021). However, so far, there is still no official confirmation that whether carbon neutrality includes natural emitting sources and natural sinks or not. Anthropogenic CO2 sinks are inclusive of two pathways: industrial and ecological. Industrial removals refer to carbon capture, utilization, and storage (CCUS) technologies (Chen et al., 2022). Ecological removals refer to the absorption of atmospheric CO2 through protection, restoration, and sustainable management of ecosystems (Lu et al., 2022; Griscom et al., 2017), such as afforestation and silviculture. However, because these artificially cultivated trees have been afforested all over the country, often mixed with natural forests, it’s hard to assess their total carbon sequestration abilities.\n\nThe lodestar of strategy-making process in statecraft involves five successive, ironclad elements in sequence: firstly, making a rational, pragmatic calculation of long-term trends in the grand schemes of things on the basis of national interest in order to handle the rough patches of confronted challenges; secondly, meticulously drawing a strategic landscape and then detachedly exploring the range of choices and means of tactics; thirdly, sweepingly calibrating the internal abilities of a country and then cautiously questing for any underlying congruence and confluence of interests around the world to establish potential international cooperation under the banner of mutual respect and symbiosis; fourthly, prudently opting the most eminent practical pathway of implementation, swinging into a tentative action via daring execution to outline the maximum real-life capacity, and then warily assessing the division, if at all, between the anticipatable and the achievable; fifthly, progressively, scrupulously adjusting to a more attainable, crystalized stance through nuance and osmosis to deftly realize the optimal objectives at the minimum costs amid the kaleidoscope of changing circumstances (Kissinger, 1994, 2012).\n\nThe climate issue involves two aspects that are unusual compared with the other crises. Firstly, it affects almost every country and every species in the world, thus GHGs emissions show a pattern of global externality; secondly, it represents a problem that a single country alone cannot solve (NASEM, 2017). Hence, mitigating global warming needs international cooperation. However, even though the long-term trend is clear and the strategic landscape is certain as our planet keeps heating up, but since the definition of carbon neutrality is vague, the policy-making process could not be fully completed. Ambiguity at times is the lifeblood and fulcrum of policy-planning in order to entitle the battle-hardened decision-makers enough elbowroom to create margin of flexibility, blunt the edges of tangential factional disputes, gain freedom of maneuver and degree of resilience, and balance powers (Kissinger, 1994, 2015). However, upon tactic level, a commonly-accepted definition would furnish the impetus for decisive, unified, and audacious actions, and the de facto effective policy formulation would not be come forth if the scientific notion, the bedrocks of policy-making, began to diverge.\n\n\nImplications for formulating climate policies\n\nClimate policies are refracted and filtered through the prism of national interests. Deviated from geopolitical realities, the feasibility of green growth strategies for the economy has been frequently doubted (Franssen and de Wilde, 2021), reflecting the current dilemma of many countries around the world: how to balance their carbon emissions reduction and economic development, and how to seek to navigate the narrowest of passages between economic development and greenhouse gases (GHGs) reduction. Reportedly, the realizations of the commitments of emission reductions by countries made in the 2016 Paris Agreement can keep the global warming below 2 °C (Meinshausen et al., 2022; Hausfather and Moore, 2022). However, as a fait accompli, with the strictest practicality and most level-headed realism, yet falling far short of their rhetoric, the 20 largest economies around the world have not fulfilled the letter of their pledges for the reduction of GHGs emissions and instead have focused more on economic developments, especially during the COVID-19 period (Nahm et al., 2022), indicating the facts that their demands for economic development have transcended their internal desire for climate change mitigation (Liu et al., 2022). The reality of the 2016 Paris Agreement seemed emphasizing atmosphere over substance, showing that most countries have deemed that sacrificing economic developments to lower climate change is pyrrhic. A predominant reason for this judgement is a sense of doubts on the unfounded and undemonstrated impact of global warming on human welfare (Lomborg, 2020). Also, some climate models predict that the future will get too hot too fast (Hausfather et al., 2022), undermining the credibility of climate science (Voosen, 2022).\n\nIn the resulting maelstrom, evidently, global CO2 emissions in 2021 were almost equal to that in 2019 (Davis et al., 2022), exhibiting a strong rebound of anthropogenic emissions from the COVID-19 pandemic and experiencing the largest-ever yearly increment in the absolute term of anthropogenic CO2 emissions compared to that of the previous year (IEA, 2021). The understanding that insufficient actions will never lead to political debacle results in political flexibility on climate targets (Geden and Löschel, 2017). De facto, climate order is an outgrowth of a balancing of risks and rewards in terms of geopolitical considerations and calculations of the national interests. Again, reality proves that international agreement is built on quicksand if it deviates from the doctrines of balance-of-power on the basis of Hobbesianism which embody in the German Realpolitik during the times of Bismarck and in the French Raison d'état during the times of Richelieu. Actually, departing from Bismarck’s Realpolitik and Richelieu’s Raison d'état, and ignoring current geopolitical imperatives, the milk-and-water climate agreements present an ominous vista and a myopic form of risk-taking.\n\nWith bite on granite, according to a report from World Meteorological Organization (WMO, 2022), there is a 50:50 change that the global annual average temperature for at least one of the next five years will reach 1.5°higher than the average over the years between 1850 and 1900. The visionary statesman Henry Kissinger once stated “No one eats with impunity from the tree of immortality” (Kissinger, 1994). The ends justify the means, not the other way around. The lessons of history have told us that the geopolitical imperatives are the main driving force to reshape the road towards net zero (Thompson, 2022). Carbon neutrality is hard to realize when the geopolitical realities have been ignored. Evidently, the willingness of voluntary corporate actions for mitigating global warming by companies has been frequently questioned (Bjørn et al., 2022a,b). Several world-famous companies or institutions, inclusive of Shell, British Petroleum (BP), Equinor, and International Energy Agency (IEA), introduced incompatible energy development pathways with that recommended for Paris agreements 1.5 °C goal (Brecha et al., 2022). Ratification of a climate treaty alone but neglect of the geopolitical realities never can be a sort of deus ex machina to slow down climate change. After all, for now, before the occurrence of the tipping point which is more obvious to identify in ex post facto retrospect than when we are moving towards it, carbon neutrality, for most countries, is more a price of bargaining chip for playing out geopolitical gambit, less a principle. Ultimately, in the international community, possession of power is nine-tenths of the law. To the victor belong the spoils, which is the rights to interpret the definition of carbon neutrality. Without meeting the geopolitical imperatives or considering Machiavellian realism, complying climate treaty is not a natural condition of man, but a temporary oasis in a perilous world where obedience could only be sustained by permanent vigilance.\n\nTop climate scientists do doubt that countries around the world will effectively control global warming (Tollefson, 2021). Decades from now, historians will possibly hold a fact-finding debate on who must bear the responsibility for completing the construction of the doomsday machine that has led us to irreversible global warming and for blowing away the house of cards assembled by the most far-sighted scientists who have an unerring eye for the long-term future trend.\n\nYet I guess at the time of the start of this future debate, no one country will be singled out to blame for this mad dash towards climate change. Each of them contributed its own quota and did so with the carefreeness which would never again be possible when the negative consequences of global warming they have triggered enter the shared memory of humanity. In preparing themselves for the worst-case scenario, they facilitate to make it a reality and are hoisted by their own petard. However, taking the future with a grain of salt, I deem that when temperature keeps going up with the passage of time to the degree that will impact the geopolitical imperative of most countries, the gains for lowering global warming transcend that for pursuing social and economic developments and major economics will place a greater premium on curbing GHGs emissions without falling by the wayside. Reportedly, the time to take alarm for human survival as the tipping point is when the increase of global average temperature exceeds at most 5 °C above preindustrial levels (Lenton et al., 2019; O’Grady, 2022; McKay et al., 2022).\n\n\nActionable recommendations\n\nMy suggestion is that when policymakers are formulating climate policies, they must consider the geopolitical realities. Evidently, without taking geopolitical imperatives into considerations, the endeavors to mitigate global warming are limited in the effectiveness (Thompson, 2022). For instance, China used its rare earth mineral resources as a weapon to weaken its geopolitical opponents. Rare earth minerals are essential for the development of renewable energy. Meanwhile, due to the Taiwan crisis in August 2022, driven by a realistic evaluation on national interests and internal capabilities, China announced the suspension of Sino-US climate talks. Therefore, if only history were more forgiving, it seems that the world is still waiting for the occurrence of the tipping points.\n\nWhen an international order cannot be actualized by consensus or enforced by power, chaos may occur in a dehumanizing way. Since the tolerance of temperature rise for different countries differs, confronting may fill the vacuum between the different tipping points of two countries. From the perspectives of Machiavelli and Clausewitz, in the battle for survival, a nation may use the GHGs emissions as a weapon to weaken its geopolitical opponents who are more sensitive to climate change.\n\nOnce Bismarck wrote in his poet: “That which is imposing here on earth has always something of the quality of the fallen angel who is beautiful but without peace, great in his conceptions and exertions but without success, proud and lonely.”\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "References\n\nBrecha R, et al.: Institutional decarbonization scenarios evaluated against the Paris Agreement 1.5 °C goal. Nat. Commun. 2022; 13: 4304. PubMed Abstract | Publisher Full Text\n\nBjørn A, et al.: Renewable energy certificates threaten the integrity of corporate science-based targets. Nat. Clim. Chang. 2022a; 12: 539–546. Publisher Full Text\n\nBjørn A, et al.: Renewable energy certificates allow companies to overstate their emission reductions. Nat. Clim. Chang. 2022b; 12: 508–509. Publisher Full Text\n\nChen S, et al.: A critical review on deployment planning and risk analysis of carbon capture, utilization, and storage (CCUS) toward carbon neutrality. Renew. Sust. Energ. Rev. 2022; 167: 112537. Publisher Full Text\n\nClarke J, Searle J: Active Building demonstrators for a low-carbon future. Nat. Energy. 2021; 6: 1087–1089. Publisher Full Text\n\nDavis S, et al.: Emissions rebound from the COVID-19 pandemic. Nat. Clim. Chang. 2022; 12: 412–414. Publisher Full Text\n\nDawkins R: The Selfish Gene.1989. 978-0-19-878860-7.\n\nEloranta J, et al.: Why did the League of Nations fail? Cliometrica. 2011; 5(1): 27–52. Publisher Full Text\n\nEuropean Council: European climate law: Council and Parliament reach provisional agreement.2021. [Accessed on 4 August 2022]. Reference Source\n\nEwin R: Hobbes, Thomas (1588–1679). International Encyclopedia of the Social & Behavioral Sciences. 2001; 2001: 6882–6886. Publisher Full Text\n\nFranssen T, de Wilde M : A clean energy future isn’t set in stone. Nat. Geosci. 2021; 14: 636–637. Publisher Full Text\n\nGeden O, Löschel A: Define limits for temperature overshoot targets. Nat. Geosci. 2017; 10: 881–882. Publisher Full Text\n\nGriscom B, et al.: Natural climate solutions. PNAS. 2017; 114(44): 11645–11650. PubMed Abstract | Publisher Full Text\n\nHausfather Z, Moore F: Net-zero commitments could limit warming to below 2 °C. Nature. 2022; 604: 247–248. PubMed Abstract | Publisher Full Text\n\nHausfather Z, et al.: Climate simulations: recognize the ‘hot model’ problem. Nature. 2022; 605: 26–29. PubMed Abstract | Publisher Full Text\n\nHuovila A, et al.: Carbon-neutral cities: Critical review of theory and practice. J. Clean. Prod. 2022; 341: 130912. Publisher Full Text\n\nIEA (International Energy Agency): Global CO2 emissions rebounded to their highest level in history in 2021.2022. [Accessed on 6/May/2022].Reference Source\n\nIPCC:Summary for Policymakers. In: Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change Masson-Delmotte V, Zhai P, Pirani A, et al., editors.Cambridge University Press;Cambridge, United Kingdom and New York, NY, USA;2021; pp. 3−32. Publisher Full Text\n\nKissinger H: World Order.2015. 978-0-14-312771-0.\n\nKissinger H: On China.2012. 978-0-14-312131-2.\n\nKissinger H: Diplomacy.1994. ISBN-13: 978-0-671-65991-2.\n\nLe Ravalec M, et al.: Taking climate change seriously: Time to credibly communicate on corporate climate performance. Ecol. Econ. 2022; 200: 107542. Publisher Full Text\n\nLenton T, et al.: Climate tipping points — too risky to bet against. Nature. 2019; 575: 592–595. PubMed Abstract | Publisher Full Text\n\nLiu Z, et al.: Global patterns of daily CO2 emissions reductions in the first year of COVID-19. Nat. Geosci. 2022; 15: 615–620. Publisher Full Text\n\nLomborg B: Welfare in the 21st century: Increasing development, reducing inequality, the impact of climate change, and the cost of climate policies. Technol. Forecast. Soc. Chang. 2020; 156: 119981. Publisher Full Text\n\nLu N, et al.: Biophysical and economic constraints on China’s natural climate solutions. Nat. Clim. Chang. 2022; 12: 847–853. Publisher Full Text\n\nMcDougall W: In Conversation with Kissinger's World Order. Orbis. 2015; 59(3): 438–453. Publisher Full Text\n\nMcKay D, et al.: Exceeding 1.5°C global warming could trigger multiple climate tipping points. Science. 2022; 377(6611): eabn7950. PubMed Abstract | Publisher Full Text\n\nMEE (Ministry of Ecology and Environment of People’s Republic of China):2021. [Accessed on 7 August 2022].Reference Source\n\nMeinshausen M, et al.: Realization of Paris Agreement pledges may limit warming just below 2 °C. Nature. 2022; 604: 304–309. PubMed Abstract | Publisher Full Text\n\nNahm J, et al.: G20’s US$14-trillion economic stimulus reneges on emissions pledges. Nature. 2022; 603: 28–31. PubMed Abstract | Publisher Full Text\n\nNASEM (National Academies of Sciences, Engineering, and Medicine): Valuing Climate Damages: Updating Estimation of the Social Cost of Carbon Dioxide. Washington, DC:The National Academies Press;2017. Publisher Full Text\n\nNordhaus W: Dynamic climate clubs: On the effectiveness of incentives in global climate agreements. PNAS. 2021; 118(45): e2109988118. PubMed Abstract | Publisher Full Text\n\nO’Grady C: Just a small rise in Earth’s temperature could cause irreversible ecosystem and weather changes. Science. 2022; 377(6611): 1135. PubMed Abstract | Publisher Full Text\n\nThompson H: The geopolitics of fossil fuels and renewables reshape the world. Nature. 2022; 603: 364. Publisher Full Text\n\nTollefson J: Top climate scientists are sceptical that nations will rein in global warming. Nature. 2021; 599: 22–24. Publisher Full Text\n\nUNFCCC (United Nations Framework Convention on Climate Change): The Paris Agreement.2020. [Accessed on 03/August/2022].Reference Source\n\nVoosen P: Use of ‘too hot’ climate models exaggerates impacts of global warming. Science. 2022; 376(6594): 685. PubMed Abstract | Publisher Full Text\n\nWMO (World Meteorological Organization): WMO update: 50:50 chance of global temperature temporarily reaching 1.5°C threshold in next five years.2022. [Accessed on 15/May/2022].Reference Source\n\nXifra J: Recognition, symbolic capital and reputation in the seventeenth century: Thomas Hobbes and the origins of critical public relations historiography. Public Relat. Rev. 2017; 43(3): 579–586. Publisher Full Text"
}
|
[
{
"id": "192727",
"date": "29 Aug 2023",
"name": "Md. Emran Hossain",
"expertise": [
"Reviewer Expertise Environmental and Energy Economics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for providing me the opportunity to review the article “On climate order: a policy brief”. The authors have made good contributions to this paper. I have completed my assessments and the paper can be improved before recommended for indexing as follows:\nThe Abstract needs to be rather precise and conclude based on empirical evidence.\n\nAt the beginning of the Abstract, authors should state the research gap and contribution to the literature. The background is not justifiable currently.\n\nThe introduction section needs further improvement in terms of the research gap and contribution of the study with proper background.\n\nPlease add the motivation and write why this policy brief is important and would be beneficial for implications.\n\nThe discussion on SDG and environmental sustainability linkage with respect to climate policy is missing. Authors should add in the first paragraph of the introduction. The research contribution should be enlarged.\n\nPlease double-check the abbreviation used in the study. I have found diverse abbreviations of a word in several places. Please make sure that authors use similar abbreviations of a word throughout the manuscript.\n\nParagraphs can be adjusted. Currently, the manuscript is in rough shape.\n\nThe policy implications are too general in its current form. The policies need to be aligned with the recent Government Policies and mention their scope for implementation to the countries having similar socio-economic orientations.\n\nPlease add the limitations and future research directions.\n\nDoes the paper provide a comprehensive overview of the policy and the context of its implementation in a way which is accessible to a general reader? Yes\n\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature? Partly\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly",
"responses": [
{
"c_id": "11691",
"date": "13 Jun 2024",
"name": "Rui Feng",
"role": "Author Response",
"response": "Thank you for providing me the opportunity to review the article “On climate order: a policy brief”. The authors have made good contributions to this paper. I have completed my assessments and the paper can be improved before recommended for indexing as follows: 1. The Abstract needs to be rather precise and conclude based on empirical evidence. Reply: Thank you for this incisive advice. I’ve rewritten Abstract to make it more precise. 2. At the beginning of the Abstract, authors should state the research gap and contribution to the literature. The background is not justifiable currently. Reply: Thank you for this constructive suggestion. I’ve stated the research gap and contribution to the literature at the beginning of Abstract. 3. The introduction section needs further improvement in terms of the research gap and contribution of the study with proper background. Reply: Following your suggestion, I have added the research gap and contribution of the study with proper background in Introduction. 4. Please add the motivation and write why this policy brief is important and would be beneficial for implications. Reply: Following your recommendation, I’ve added Section The essence of international politics. 5. The discussion on SDG and environmental sustainability linkage with respect to climate policy is missing. Authors should add in the first paragraph of the introduction. The research contribution should be enlarged. Reply: I’ve enlarged research contribution in the revised manuscript. 6. Please double-check the abbreviation used in the study. I have found diverse abbreviations of a word in several places. Please make sure that authors use similar abbreviations of a word throughout the manuscript. Reply: I have double-checked the abbreviation in the study and make sure to use similar abbreviations of a world in the whole manuscript. 7. Paragraphs can be adjusted. Currently, the manuscript is in rough shape. Reply: Paragraphs have been adjusted. 8. The policy implications are too general in its current form. The policies need to be aligned with the recent Government Policies and mention their scope for implementation to the countries having similar socioeconomic orientations. Reply: I have rewritten the discussion on policies. 9. Please add the limitations and future research directions. Reply: I have added limitations and future research directions in the revised manuscript."
}
]
},
{
"id": "219155",
"date": "13 Nov 2023",
"name": "Elzbieta Wojcik-Gront",
"expertise": [
"Reviewer Expertise GHG emission mitigation",
"statistical analysis",
"crop modelling"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nClimate change is a significant problem, and there are no strong rules in place to address it effectively. Some treaties and agreements lack the necessary mechanisms to ensure compliance by countries. To address this, the author suggests that climate agreements should be integrated into a broader international framework involving cooperation among multiple nations.\nThe author argues that there is no single overarching principle that can effectively limit a country's pursuit of power and development. Achieving international cooperation depends on a precise assessment of each nation's power. Climate policy is influenced by various national interests, historical experiences, and geopolitical realities, often striking a balance between risk assessment and mitigation costs. The current focus on carbon neutrality primarily occurs at the national level, even though climate change is a global issue that necessitates international collaboration. International cooperation is vital for mitigating global warming. Policymakers crafting climate policies must consider geopolitical factors to enhance their effectiveness.\nThis analysis offers an intriguing perspective on the challenges of reaching a consensus on climate change policies. Undoubtedly, it provides valuable insights that can resonate with a wide readership interested in the topic. Furthermore, it has the potential to influence policymakers' viewpoints on the matter.\n\nDoes the paper provide a comprehensive overview of the policy and the context of its implementation in a way which is accessible to a general reader? Yes\n\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature? Yes\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "11696",
"date": "19 Jun 2024",
"name": "Rui Feng",
"role": "Author Response",
"response": "Thank you for your positive words toward my work. It really encourages me."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1109
|
https://f1000research.com/articles/13-631/v1
|
13 Jun 24
|
{
"type": "Research Article",
"title": "Exploring the cultural portrayal of Vietnamese teachers: an analytical study of professional identity in Vietnamese teaching-themed songs",
"authors": [
"Thanh Thao Le",
"Hoang Yen Phuong",
"Trut Thuy Pham",
"Ngoc Bao-Chau Tran",
"Thi Thuy-Linh Nguyen",
"Thanh Thao Le",
"Trut Thuy Pham",
"Ngoc Bao-Chau Tran",
"Thi Thuy-Linh Nguyen"
],
"abstract": "Background This study delves into the cultural portrayal of teachers in Vietnam, a subject critical to understanding the broader role of educators in shaping societal and educational values. Through an analysis of song lyrics, the research aims to uncover how the professional identity of teachers is reflected and shaped within the unique cultural context of Vietnam.\n\nMethods A qualitative approach underpins this study, utilizing theoretical frameworks such as Constructivist Grounded Theory, Sociocultural Theory, Symbolic Interactionism, and Hermeneutic Phenomenology. Twelve Vietnamese songs specifically about teachers were selected for analysis. These songs were carefully chosen to provide a diverse and representative sample of the cultural portrayal of teachers in Vietnam. The project spanned from January 1st until February 21st, 2024.\n\nResults The analysis revealed several key themes that collectively characterize the professional identity of Vietnamese teachers. These include ‘Sacrifice and Dedication,’ highlighting the commitment and perseverance of teachers; ‘Respect and Reverence,’ reflecting the deep societal respect for the teaching profession; ‘Nurturing and Inspiration,’ depicting teachers as cultivators of dreams and moral values; ‘Enduring Impact and Memory,’ emphasizing the long-lasting influence of teachers on their students; ‘Teacher as a Guiding Figure,’ portraying the role of teachers as key moral and cultural guides; and ‘Emotional Connection and Affection,’ underlining the deep emotional bonds between teachers and students.\n\nConclusions The study’s findings underscore the significant role of cultural and emotional factors in shaping the professional identity of teachers in Vietnam. These themes highlight the multifaceted role of teachers that transcends academic teaching, involving personal development, cultural transmission, and emotional nurturing. The implications of these findings are far-reaching, suggesting that educational policies and teacher education programs need to consider these cultural and emotional dimensions. Additionally, the study highlights the power of cultural artifacts, like music, in reflecting and shaping societal values and professional identities.",
"keywords": [
"An analytical study",
"cultural portrayal of Vietnamese teachers",
"professional identity",
"Vietnamese teaching-themed songs"
],
"content": "Introduction\n\nThe teaching profession in Vietnam, steeped in rich cultural and educational traditions, has long been a subject of reverence and respect (Nguyen, 2017). This study explores the intricate relationship between the cultural perception of teaching and the professional identity of Vietnamese teachers as depicted in the lyrics of Vietnamese songs about teaching. This research delves into how these songs, a blend of cultural art and social commentary, reflect and shape the professional identity of teachers in Vietnam.\n\nThe concept of professional identity in teaching involves a complex amalgamation of personal values, societal expectations, pedagogical beliefs, and cultural influences (Beijaard et al., 2004; Lamote & Engels, 2010). In Vietnam, where cultural heritage and educational values are deeply intertwined (Nguyen, 2008), songs about the teaching profession serve as a unique lens to view these elements. These songs often encapsulate the ideals, challenges, and experiences of teachers, thus providing a rich, contextual basis for analyzing the professional identity of educators in Vietnam.\n\nThe research questions guiding this study are twofold: First, how do the lyrics of Vietnamese songs about the teaching profession reflect the professional identity of teachers in Vietnam? Second, what cultural and educational values inherent in these lyrics contribute to shaping the professional identity of Vietnamese teachers? By analyzing the lyrical content of selected Vietnamese songs that focus on the teaching profession, this study aims to uncover the underlying themes and messages that contribute to the conceptualization of a teacher’s professional identity in the Vietnamese context.\n\nThis exploration is significant for several reasons. Firstly, it provides insights into the cultural and societal influences that shape the professional identity of teachers in Vietnam. Secondly, it enhances understanding of the role of art and music in reflecting and shaping professional identities in different cultural contexts. Finally, the findings of this study could have broader implications for the development of teacher education programs and professional development initiatives in Vietnam and similar cultural contexts. As a result, this research seeks to contribute to the existing literature on professional identity in teaching, particularly within the unique cultural framework of Vietnam, by analyzing how the profession is portrayed in a popular and culturally significant medium – music.\n\n\nLiterature review\n\nThe concept of professional identity in teaching has been a subject of extensive research. Beauchamp and Thomas (2009), 2010 defined professional identity as a sense of oneself that is influenced by characteristics, norms, and values of the teaching profession and is self-defined and redefined through experiences and interactions. Sachs (2001, 2016) highlighted the dynamic and continuously evolving nature of professional identity in response to changing educational landscapes. This body of literature establishes that professional identity is not static but is shaped by personal beliefs, societal norms, and professional experiences.\n\nIn the context of Vietnamese education, Hieu (2015) and Tho (2016) discussed how Confucian values have historically influenced the teaching profession, emphasizing respect for teachers and the value of education. Nguyen and Bui (2016) further explored how modern educational reforms in Vietnam have impacted teachers’ professional identities, marking a shift from traditional to more contemporary educational practices.\n\nThe intersection of culture, art, and professional identity forms a crucial area of study. Cohen (2006, 2009) argued that cultural products like music, literature, and art are not just reflections of society but also shape societal norms and professional identities. In the context of teaching, songs and literature about teachers can play a significant role in shaping public perceptions and the self-perception of teachers. Wright et al. (2014) examined how popular culture influences perceptions of professional roles, including teaching, suggesting that these portrayals both reflect and inform societal attitudes towards various professions.\n\nThe portrayal of teachers in popular Vietnamese songs often revolves around themes of respect, sacrifice, and dedication. Vietnamese music serves as a diasporic source for re-membering the disremembered and silenced (Nguyen, 2020). Vietnamese teachers are valued for humility and obedience, reflecting the themes of respect and dedication commonly found in the portrayal of teachers in Vietnamese songs (Pochtar & Vecchio, 2013). Additionally, the study by Tran et al. (2017) on leadership and teacher learning in Vietnamese schools provides insights into the cultural values and expectations placed on teachers in Vietnam, which are likely reflected in the themes present in Vietnamese songs (Tran et al., 2017). Furthermore, the study by Pochtar and Vecchio (2013) highlighted the importance of humility and obedience among Vietnamese teachers, which aligns with the themes of respect and dedication commonly associated with the portrayal of teachers in Vietnamese songs (Pochtar & Vecchio, 2013). The research by Canh (2018) emphasized the preoccupation with content and pedagogy in Vietnamese teacher education, shedding light on the cultural emphasis on dedication and sacrifice in the teaching profession, which is likely echoed in Vietnamese songs. Furthermore, the role of music in Vietnamese culture, particularly in terms of storytelling and moral education, is well-documented (Norton, 2010). This reinforces the idea that songs about teaching are not mere entertainment but are imbued with cultural significance and educational values.\n\nWhile there is substantial literature on professional identity in teaching and the influence of culture on this identity, there is a noticeable gap in research specifically focusing on how Vietnamese songs about teaching contribute to shaping the professional identity of teachers. This study aims to fill this gap by providing a detailed analysis of the lyrical content of these songs and their impact on the professional identity of Vietnamese teachers.\n\n\nMethods\n\nThis study obtained ethical clearance from the pertinent ethics committee affiliated with a school of foreign languages situated in the Mekong Delta region of Vietnam, prior to commencing data collection. The approval was granted under the official reference number T2022-137 on May 17th 2023.\n\nThe research design of this study is structured to explore the intersection between cultural artifacts—in this case, music—and professional identity within the Vietnamese teaching context. This exploration is grounded in several theoretical frameworks, which guide both the methodology and analysis.\n\nCentral to our research design is the Constructivist Grounded Theory, as outlined by Charmaz (2006). Constructivist Grounded Theory is a variant of the classical Grounded Theory methodology which itself is a systematic methodology involving the construction of theories through the methodical gathering and analysis of data. The “constructivist” label emphasizes the understanding and interpretation of the research subjects’ experiences, as well as the interaction between the researcher and participants. In other words, this approach allows for the development of theories grounded in data collected, emphasizing the subjective experience and co-construction of knowledge between the researcher and the subjects. In the context of this study, the constructivist perspective enables an understanding of how the professional identity of teachers is constructed and negotiated within the cultural context of Vietnam. To ensure rigor, we adhered to specific protocols including prolonged engagement, peer debriefing, and member checking over a period of six months, utilizing digital recording and transcription equipment to capture and analyze qualitative interviews and focus group discussions. The constructivist approach to Grounded Theory not only informs the selection and interpretation of data but also acknowledges the influence of the researchers’ own background and biases as integral to the research process itself. These steps were taken to minimize bias and address potential sources of variability in our qualitative data.\n\nVygotsky’s (1978) Sociocultural Theory also underpins this study, particularly its emphasis on the role of cultural tools in shaping human cognition and identity. This theory posits that learning occurs through social interactions involving speech and other cultural tools which mediate intellectual development. It further suggests that cognitive functions are a product of specific cultural, historical, and institutional contexts. Social interactions and cultural artifacts, such as music, play a crucial role in the development of an individual’s identity. This theoretical framework views the mind as situated and relational, and not as an entity separate from the sociocultural setting in which it operates. By analyzing the lyrics of Vietnamese songs about teaching, this study explores how these cultural products contribute to the formation and reinforcement of teachers’ professional identity. The use of such artifacts as data points allows for an examination of the socio-cultural mechanisms by which professional identities are endorsed and transmitted in the community. In analyzing these interactions, we engaged with educational theorists to frame our findings within broader sociocultural contexts, thus ensuring comprehensive coverage and reduction of interpretive bias.\n\nThe framework of Symbolic Interactionism, as proposed by Blumer (1986), is also integral to our research design. This perspective emphasizes that human behavior is largely influenced by the meanings that objects or events have for individuals, which are derived from social interaction and modified through interpretation. It focuses on how people develop and communicate meanings through social interaction. In our study, this relates to how Vietnamese teachers and society at large interact with and interpret the songs about teaching, thus contributing to a shared understanding and construction of the professional identity of teachers. We explore how symbolic meanings attached to teaching are expressed and reshaped through these interactions, thereby influencing teachers’ self-conceptions and public perceptions. To control for variability and bias in our interpretations, multiple researchers independently coded the data, followed by a consensus meeting to discuss and finalize the themes, using a rigorous iterative process to refine and validate our findings. This approach ensures that our analysis remains grounded in the data collected and reflects the complex interplay of individual actions and societal expectations.\n\nLastly, the study employs Hermeneutic Phenomenology, as described by Van Manen (2023), to interpret and give meaning to the lived experiences of teachers as conveyed through song lyrics. This approach is grounded in the philosophical tradition that emphasizes understanding the phenomena through the interpretation of texts, focusing on the meaning that individuals’ experiences hold for them. It combines phenomenological methods to explore how individuals experience life with hermeneutic techniques that interpret the contextual meaning of these experiences. It allows for a deep exploration of how these songs reflect the subjective experiences and realities of Vietnamese teachers, providing insights into their professional identity. In practice, this method involves engaging with the text on a deep, interpretative level, seeking to uncover layers of meaning that reveal the essence of the experience being studied. Reflective journals and systematic text analysis procedures were used to enhance the reliability of our interpretations, employing iterative cycles of reading, reflecting, and writing to ensure a thorough engagement with the data. Carefully documenting the analytic process was essential to address potential biases and variability in data interpretation.\n\nThis multi-theoretical approach allows for a comprehensive analysis of the data, facilitating a deep understanding of the complex ways in which Vietnamese songs about teaching reflect and shape the professional identity of teachers in Vietnam. Additionally, the research design employs a qualitative methodology, consistent with the theoretical underpinnings. The primary data source is the lyrics of selected Vietnamese songs about the teaching profession. These songs are chosen based on their popularity, relevance, and the depth of content related to teaching. The analysis involves a thematic analysis, where lyrics are examined, coded, and thematically categorized to identify recurring themes and patterns. This approach provides a nuanced understanding of how the professional identity of Vietnamese teachers is portrayed and perceived in these cultural artifacts.\n\nThe materials for this study comprise a selection of 12 Vietnamese songs that center on the theme of teachers and the teaching profession. These songs have been carefully chosen for their relevance, popularity, and the depth with which they explore various aspects of teaching and the role of educators in Vietnamese society. Each song was analyzed using a detailed coding schema developed based on our theoretical frameworks, with frequent team discussions to ensure a consistent approach to theme identification and interpretation across different researchers.\n\n1. “Người Thầy” (My Teacher) composed by Nguyen Nhat Huy in 2012 is a song that offers a heartfelt tribute to teachers, emphasizing their role in shaping the future of their students.\n\n2. In “Bông Hồng Tặng Cô,” (Rose for My Beloved Teacher), Tran Quang Huy, in 2006, created a melody that expresses gratitude and appreciation towards teachers, symbolized through the gift of a rose.\n\n3. “Bụi Phấn” (Chalk Dust), composed by Vu Hoang and Le Quang Loc in 2016, is a poignant reflection on the ephemeral yet impactful nature of a teacher’s influence, using the metaphor of chalk dust to represent the transient and lasting impressions teachers leave on their students.\n\n4. “Mái Trường Mến Yêu” (My Beloved School), composed by Le Quoc Thang in 2015, celebrates the beloved school environment and the role teachers play in creating a nurturing and educational space.\n\n5. “Nhớ Ơn Thầy Cô” (Gratitude towards Our Teachers), composed by Nguyen Ngoc Thien in 2014, is a song that reminisces about the enduring lessons and guidance provided by teachers, highlighting the lasting gratitude students hold.\n\n6. “Khi Tóc Thầy Bạc Trắng” (When My Teacher’s Hair Turns Gray), composed by Tran Duc in 1994, touches on the passage of time and the enduring respect for teachers, even as they age, symbolized by the whitening of their hair.\n\n7. “Bài Học Đầu Tiên” (The First Lesson), composed by Truong Xuan Man, offers a unique perspective on the foundational lessons imparted by teachers, both academic and life-based.\n\n8. In “Thầy Cô Cho Em Mùa Xuân,” (Teachers Give Us Spring), Vu Hoang writes about the rejuvenating and inspiring impact that teachers have on their students, akin to the freshness of spring.\n\n9. The composer Nguyen Van Chung’s “Người Thầy Năm Xưa” (The Teacher Those Days) is a nostalgic piece that looks back at the influence of former teachers, evoking memories of past educational experiences.\n\n10. “Những Điều Thầy Chưa Kể” (My Teacher’s Untold Stories), composed by Tran Thanh Son in 2010, explores the untold stories and sacrifices of teachers, shedding light on the often-unseen aspects of their lives.\n\n11. “Ơn Thầy, Thầy Của Chúng Em” (Thank You, Our Teacher), composed by Nguyen Ngoc Thien in 2016, is a tribute to the profound respect and appreciation students hold for their teachers.\n\n12. The final song, “Cô giáo Tày cầm đàn lên đỉnh núi,” (The Tay Teacher Taking the Instrument to the Top of the Mountain), written by Hoang Van in 2018, distinctively portrays a teacher’s dedication and the lengths they go to educate their students, symbolized by the act of carrying a musical instrument to the mountain’s peak.\n\nThese songs, encompassing a range of emotions and perspectives, provide a rich tapestry of insights into the professional identity of Vietnamese teachers as perceived and celebrated in Vietnamese culture. Each song has been selected for its lyrical depth, musicality, and cultural significance, making them ideal materials for this study’s aim to understand how the teaching profession is portrayed in Vietnamese music.\n\nThe data collection for this study involved a comprehensive analysis of the lyrics of the 12 selected Vietnamese songs about teachers and the teaching profession. The process entailed acquiring the official lyrics for each song, ensuring accuracy and authenticity in the representation of the songs’ content. These lyrics serve as the primary data source for the study, providing a rich and nuanced understanding of the cultural and societal perceptions of teachers in Vietnam.\n\nThe lyrics were collected from various sources, including official music releases, authorized songbooks, and verified online music platforms. Special attention was given to ensure that the lyrics were in their original Vietnamese form to maintain the cultural and linguistic integrity of the songs. The process also involved translating the lyrics into English, where necessary, to facilitate a broader understanding and analysis. This translation was carried out with care to preserve the meaning, sentiment, and cultural nuances embedded in the original Vietnamese text.\n\nTo ensure a comprehensive understanding of the songs, the data collection also included gathering contextual information about each song, such as the year of release, the songwriter, and any relevant historical or cultural context. This background information provides a deeper insight into the circumstances and motivations behind the creation of each song, thereby enriching the analysis.\n\nOnce collected, the lyrics were meticulously reviewed and prepared for analysis. This preparation involved segmenting the lyrics into meaningful units, such as lines or verses, which were then annotated for further thematic analysis. The annotation process focused on identifying key themes, motifs, and messages related to the teaching profession and the professional identity of teachers as depicted in these songs.\n\nThe data analysis for this study involved a detailed examination of the lyrics of 12 Vietnamese songs that focus on the teaching profession. The lyrics of these songs, rich in cultural and emotional depth, were analyzed by the thematic analysis approach to understand how they reflect and shape the professional identity of Vietnamese teachers (Braun & Clarke, 2023). The analysis began with a close reading of the lyrics to grasp the overarching themes and sentiments. This initial reading highlighted recurring motifs such as respect for teachers, the sacrifices they make, and the lasting impact they have on their students’ lives. For instance, in “My Teacher”, there is a profound expression of gratitude and respect for teachers, depicted through the imagery of a teacher quietly persevering in their duty, regardless of the circumstances. Following the initial reading, the lyrics were dissected into smaller segments for a more granular analysis. This process involved identifying specific phrases and lines that vividly illustrate the themes identified earlier. For example, in “Chalk Dust”, the imagery of chalk dust represents the teacher’s dedication and the transience yet permanence of their influence.\n\nThe next step was coding these segments for thematic analysis. This involved categorizing the data into themes such as ‘sacrifice,’ ‘dedication,’ ‘influence,’ and ‘respect.’ Each theme was then further explored to understand its nuances. For example, the theme of ‘sacrifice’ was evident in multiple songs, including “My Teacher’s Untold Stories”, where the lyrics speak of the unseen hardships and dedication of teachers. The thematic analysis revealed the depth of cultural respect for teachers in Vietnam, as these songs frequently depict teachers as selfless, dedicated, and pivotal in shaping the future of their students. The analysis also highlighted how these cultural representations contribute to the societal perception and self-perception of teachers in Vietnam. For instance, the song “Thank You, Our Teacher” expresses a profound gratitude towards teachers, reflecting the high esteem in which they are held in Vietnamese society. Finally, the analysis involved synthesizing these themes to understand how they collectively contribute to the portrayal of teachers’ professional identity. This synthesis provided a comprehensive view of how Vietnamese songs about teaching construct a narrative around the teaching profession, emphasizing its nobility, challenges, and the deep-rooted respect for educators in Vietnamese culture.\n\nIn summary, the data analysis of the song lyrics was a multi-step process that involved close reading, segmenting, coding, thematic analysis, and synthesis. This methodical approach allowed for an in-depth exploration of the complex ways in which the professional identity of Vietnamese teachers is depicted in these culturally significant songs.\n\n\nFindings\n\nThe analysis of the lyrics from the selected Vietnamese songs about teachers and the teaching profession unveiled a profound theme of ‘Sacrifice and Dedication’, which is intricately interwoven with the professional identity of Vietnamese teachers. This theme is vividly depicted in the song “Chalk Dust,” where the lyrics poignantly symbolize the teacher’s ceaseless effort and the silent passage of time marked by their greying hair:\n\n“Khi thầy viết bảng,\n\nBụi phấn rơi rơi,\n\nThầy em tóc như bạc thêm,\n\nBạc thêm vì bụi phấn.”\n\n(When my teacher writes on the board,\n\nChalk dust falls,\n\nHis hair is turning gray,\n\nBecause of the chalk dust, his hair is turning grayer.)\n\nSimilarly, in “My Teacher’s Untold Stories,” the lyrics speak to the unseen hardships and dedication of teachers:\n\n“Cũng có một vầng trăng,\n\nNhưng sao thầy không kể,\n\nNhững đêm ngồi soạn bài,\n\nÁnh trăng lừa khuya khoắt.”\n\n(There is a moon,\n\nBut why don’t you tell me?\n\nNights spent planning lessons,\n\nThe moonlight shines late at night.)\n\nFrom the perspective of Constructivist Grounded Theory, these lyrics construct an image of teachers as selfless individuals, a societal construction that emphasizes their revered status in Vietnamese culture. The Sociocultural Theory approach highlights these songs as cultural tools that shape societal perceptions of the teaching profession, describing the teacher’s quiet perseverance, reinforcing cultural values of respect and veneration for teachers. Symbolic Interactionism suggests that the respect and gratitude towards teachers are shaped through societal interactions and shared cultural understandings. Finally, from the perspective of Hermeneutic Phenomenology, the lyrics provide insight into the lived experiences of teachers, which not only tells a story but also delves into the phenomenological experience of being a teacher, marked by dedication and sacrifice.\n\nAnother significant finding from the analysis of Vietnamese songs about teachers is the theme of ‘Respect and Reverence.’ This theme is highlighted in the lyrics, demonstrating the deep-rooted cultural respect for educators in Vietnamese society. For instance, in “My Teacher,” the lyrics “Người thầy, vẫn lặng lẽ đi về sớm trưa” (The teacher still quietly returns home every day) depict the teacher’s silent, steadfast presence, symbolizing their pivotal role in the community. Similarly, “Rose for My Beloved Teacher” uses the metaphor of a rose, a symbol of admiration and gratitude, to express the deep respect for teachers:\n\n“Cây bông hồng, em trồng tặng cô,\n\nCánh hoa hồng tươi như khoe ngày hội.”\n\n(The rose tree I planted for you,\n\nRose petals are as fresh as showing off at a festival.)\n\nFrom the Constructivist Grounded Theory perspective, these lyrics reflect the societal construction of the teacher’s role, illustrating a collective belief in the nobility and importance of the teaching profession. Sociocultural Theory underscores how cultural expressions, like music, play a significant role in perpetuating and reinforcing societal values and norms. In this case, the songs function as cultural artifacts that transmit and reinforce the high esteem in which teachers are held in Vietnamese culture. Symbolic Interactionism suggests that the societal respect for teachers, as articulated in these songs, is not static but evolves through social interactions and shared experiences. The lyrics are a reflection of this dynamic process, where societal reverence for teachers is both a product and a contributor to the collective consciousness. Hermeneutic Phenomenology allows for a deeper interpretation of these lyrics, suggesting that they not only describe the societal respect for teachers but also resonate with the personal and emotional experiences of both teachers and students.\n\nA further key finding from the analysis of the Vietnamese songs about teachers is the theme of ‘Nurturing and Inspiration.’ This theme emerges from the lyrics as a portrayal of teachers not only as educators but also as nurturers of dreams and inspirations. For instance, the song “The First Lesson,” with its lyrics, encapsulates the concept of teachers instilling love and respect for one’s heritage and nature in their students:\n\n“Bài học đầu tiên,\n\nCó bóng hình núi sông,\n\nYêu thương những cánh đồng,\n\nNối tiếp đường cha ông.”\n\n(The first lesson,\n\nThere is an image of mountains and rivers,\n\nWe love the fields,\n\nWe continue the path of our ancestors.)\n\nSimilarly, in “When My Teacher’s Hair Turns Gray,” the lyrics reflect on the journey of growth and learning facilitated by teachers: “Khi tóc thầy bạc trắng chúng em đã lớn khôn rồi.” (When his hair turns gray, we all have grown up.)\n\nThrough the lens of Constructivist Grounded Theory, these lyrics can be seen as a societal construction of the teacher’s role as an agent of inspiration and guidance. The songs create a narrative where teachers are central to nurturing the intellectual and emotional growth of their students. Sociocultural Theory further highlights how these songs serve as cultural mediums that encapsulate and transmit the values of nurturing and inspiration inherent in the Vietnamese education system. Symbolic Interactionism sheds light on how the interactions between teachers and students, as reflected in the lyrics, contribute to the construction of meanings around education and personal growth. The lyrics reflect the deep connections and transformative experiences fostered by teachers, resonating with the shared values and emotions of the community. Hermeneutic Phenomenology allows for an interpretation of these lyrics as more than just words; they are expressions of the lived experiences of nurturing and inspiration in the educational journey. They delve into the essence of what it means to be a teacher - an individual who not only imparts knowledge but also inspires and nurtures the potential within each student.\n\nThe analysis of the selected Vietnamese songs about teachers also revealed a poignant theme of ‘Enduring Impact and Memory.’ This theme is beautifully encapsulated in the lyrics, emphasizing the lasting influence teachers have on the lives of their students. For example, the song “Gratitude towards Our Teachers” vividly illustrates the enduring memories and gratitude students hold for their teachers:\n\n“Bóng dáng cô thầy vấn vương không rời,\n\nMột thời tuổi thơ trôi theo cánh phượng,\n\nLời thầy cô vọng mãi.”\n\n(The teachers’ shadow lingers forever,\n\nA time when my childhood drifted under the phoenix flowers,\n\nThe teachers’ words echo forever.)\n\nSimilarly, in “The Teacher Those Days,” the lyrics reminisce about the past and acknowledge the lasting impact of teachers with lines like:\n\n“Nắng lung linh đùa vui hàng me vẫn tiếng ve gọi reo,\n\nNét phấn trên bảng đen cùng năm tháng kéo tôi quay về thời thơ ấu.”\n\n(The shimmering sunlight playfully plays with the tamarind trees, while the cicadas chirp,\n\nThe chalk strokes on the blackboard take me back to my childhood.)\n\nFrom the perspective of Constructivist Grounded Theory, these lyrics can be seen as constructing a narrative that highlights the lasting impact of teachers on their students. The songs create a shared societal understanding of the teaching profession as one that leaves an indelible mark on the lives of individuals. Through Sociocultural Theory, these songs emerge as cultural artifacts that not only reflect but also shape societal values, perpetuating the idea of the teacher’s role as a lasting influence in the personal and intellectual development of students. Symbolic Interactionism provides a lens to understand how the respect and admiration for teachers, as expressed in these lyrics, are shaped through social interactions and shared cultural experiences. The enduring impact and memory of teachers, as portrayed in these songs, are a reflection of the societal values and the collective memory of the community. Hermeneutic Phenomenology allows for a deeper exploration of these lyrics, suggesting that they resonate with the personal and emotional experiences of teachers and students alike. They delve into the lived experience of the teaching and learning journey, emphasizing the profound and lasting impact teachers have on their students.\n\nThe exploration of Vietnamese songs about teachers further reveals a significant theme of ‘Teacher as a Guiding Figure.’ This theme is manifested in the lyrics, portraying teachers as essential guides in the journey of life and learning. In “My Beloved School,” the lyrics illustrate this with lines like “Thầy dìu dắt chúng em với tấm lòng thiết tha,” (Our dear teacher guides us with a passionate heart), depicting teachers as caring guides who lead their students with affection and dedication. “When My Teacher’s Hair Turns Gray” also echoes this sentiment, describing teachers as guiding figures who have helped shape the path of their students’ lives, evident in the lines:\n\n“Cầu Kiều thầy đưa qua sông,\n\nTuổi ấu thơ như hoa nở dưới mái trường.”\n\n(The Kieu bridge leads me across the river,\n\nChildhood is like flowers blooming under the school roof.)\n\nFrom the perspective of Constructivist Grounded Theory, these lyrics construct an image of teachers as pivotal guiding figures, shaping the societal perception of the role of educators. The portrayal of teachers in these songs reflects a collective understanding and appreciation of their guiding role in the holistic development of students. Sociocultural Theory highlights how these songs act as cultural tools, reinforcing the societal value placed on teachers as guides in the educational and personal growth of students. Through the lens of Symbolic Interactionism, the depiction of teachers in these lyrics is understood as a product of social interactions and cultural exchange. The respect and admiration for teachers as guiding figures are nurtured through the shared experiences and values of the Vietnamese community. Hermeneutic Phenomenology allows for interpreting these lyrics as more than just poetic expressions; they encapsulate the profound experiences and emotions associated with the teacher-student relationship. The lyrics delve into the essence of the teacher’s role as a mentor and guide, illuminating the profound impact teachers have on their students’ life journeys.\n\nThe final theme identified in the analysis of Vietnamese songs about teachers is ‘Emotional Connection and Affection.’ This theme is prominently reflected in the lyrics, illustrating the deep emotional bonds and affectionate relationships between teachers and students. For instance, in “Rose for My Beloved Teacher,” the gesture of offering a rose to the teacher symbolizes a deep sense of affection and gratitude:\n\n“Cây bông hồng, em trồng tặng cô,\n\nCánh hoa hồng tươi như khoe ngày hội.”\n\n(The rose tree I planted for you,\n\nRose petals are as fresh as showing off at a festival.)\n\nSimilarly, in “Thank You, Our Teacher,” the lyrics convey a deep emotional connection with the teacher:\n\n“Đêm khuya thầy chưa ngủ,\n\nTrên trang vở chúng em,\n\nMiệt mài ghi chăm chú,\n\nBao khó nhọc dưới đèn.”\n\n(Late at night, my teacher has not slept yet.\n\nOn the pages of our notebooks,\n\nHe writes diligently and attentively,\n\nWith many hardships under the lights.)\n\nThrough Constructivist Grounded Theory, these lyrics can be interpreted as constructing a narrative that emphasizes the emotional and affectionate aspects of the teacher-student relationship. This portrayal contributes to a societal understanding of teaching not just as a profession, but as a relationship built on emotional bonds and mutual respect. Sociocultural Theory highlights how these songs, as cultural artifacts, reinforce the value of emotional connections in the Vietnamese educational context, depicting teachers not only as educators but also as caring figures deeply invested in their students’ well-being. Symbolic Interactionism offers insight into how these emotional connections are cultivated and symbolized through social interactions and cultural expressions. The lyrics reflect shared societal values of affection and respect towards teachers, shaped by collective experiences and cultural norms. Hermeneutic Phenomenology allows for a deeper exploration of these lyrics, suggesting that they resonate with the lived experiences of both teachers and students. The lyrics delve into the emotional layers of the teaching and learning experience, highlighting the affectionate bonds that develop in the educational journey.\n\n\nDiscussion\n\nThe analysis of Vietnamese songs about teachers reveals a nuanced portrayal of their professional identity, contributing significantly to the existing literature in the field of education and cultural studies. The current study’s focus on the cultural and emotional dimensions of teacher identity, as depicted in popular Vietnamese songs, presents a significant divergence from the traditional approach observed in much of the previous research on teacher identity. This traditional approach, as exemplified by studies like Beijaard et al. (2004) and Day et al. (2006), typically concentrates on the professional aspects of teaching, such as pedagogical skills, adherence to educational policies, and effective classroom management. These studies underscore the dynamic nature of teacher identity, acknowledging how it is shaped by and responds to various contextual factors, including institutional policies, educational reforms, and societal expectations. However, the current study enriches this understanding by incorporating a cultural and emotional perspective, a dimension often underrepresented in the existing literature. By analyzing Vietnamese songs about teachers, the study reveals how teacher identity in Vietnam is deeply intertwined with cultural values, societal roles, and emotional connections. This cultural lens offers insights into how teachers are perceived and valued in Vietnamese society, not merely as conveyors of academic knowledge but as integral figures in moral and character development, emotional support, and cultural transmission. This holistic approach underscores the multifaceted nature of teaching, where the role of a teacher transcends the boundaries of the classroom. In the Vietnamese context, as reflected in the songs, teachers are depicted as guiding figures, mentors, and even familial figures who foster emotional bonds with their students. Such portrayals highlight the deep-rooted respect and affection for teachers within the culture, emphasizing their role in shaping not just intellectual capabilities but also emotional resilience, ethical values, and social consciousness.\n\nContinuing from the earlier discussion, the theme of ‘Sacrifice and Dedication’ in the context of Vietnamese songs provides an enriched perspective that adds depth to the findings of Yin and Lee (2012), who emphasized the personal and emotional investment of teachers in their work. While Yin and Lee’s (2012) study acknowledged the intrinsic commitment and emotional engagement of teachers, the current study takes a step further by exploring how these attributes are not only recognized but also deeply valorized within the Vietnamese cultural context. This cultural valorization is vividly expressed through the medium of music, an artistic form that plays a significant role in Vietnamese society. The song “Chalk Dust,” for example, serves as a poignant illustration of this theme. Its lyrics poetically encapsulate the idea of sacrifice and dedication in teaching, portraying it as a noble endeavor that leaves a lasting impact on students. This portrayal goes beyond acknowledging the hard work and commitment of teachers; it elevates these attributes to a level of societal honor and respect. This perspective is somewhat distinct from the Western focus, which often centers on the challenges and stresses associated with the teaching profession (Cooper & Travers, 2012). In Western literature, while the dedication of teachers is recognized (e.g., Klassen et al., 2012), it is frequently discussed in the context of burnout, work-life balance, and the need for better support systems (Abdulaziz et al., 2022). In contrast, Vietnamese songs like “Chalk Dust” celebrate the teacher’s role, focusing on the honor and esteem associated with this sacrifice. This cultural framing suggests a societal acknowledgment that transcends the immediate classroom environment and recognizes the broader social and emotional contributions of teachers. Such a perspective is integral to understanding how teachers are perceived and valued in different cultural settings. It highlights the cultural specificity in the conceptualization of teaching as a profession, suggesting that in Vietnam, teaching is not just a career but a vocation that commands deep respect and admiration.\n\nSimilarly, the theme of ‘Respect and Reverence’ in Vietnamese songs about teachers provides an insightful comparison to the findings of Pantić and Wubbels (2012), who explored the moral purposes of teaching and the societal respect accorded to teachers. While Pantić and Wubbels (2012) highlighted the importance of moral purposes in teaching and the respect it garners, the current study reveals a deeper, culturally rooted reverence for teachers in Vietnamese society, which is distinctively portrayed through music. Vietnamese songs beautifully encapsulate this profound respect and reverence. The lyrics not only appreciate teachers for their educational role but also elevate them to a status of moral and societal exemplars. This level of reverence is deeply embedded in Vietnamese culture, influenced by Confucian values that place a high value on education and educators (Truong et al., 2017). In these cultural narratives, teachers are not merely providers of knowledge but are seen as fundamental pillars of society, guiding moral and ethical values. This cultural aspect presents a stark contrast to the Western context, where respect for teachers, while present, often fluctuates and is sometimes overshadowed by debates on educational policies, teacher accountability, and systemic challenges (Keddie, 2015). The consistent and deep-rooted reverence seen in Vietnamese culture, as reflected in the songs, indicates a more stable and ingrained societal respect for the teaching profession. The contrast highlighted by this study is significant in understanding the cultural variances in how teaching is perceived and valued globally. It suggests that in Vietnamese culture, the respect and reverence for teachers are less susceptible to the ebbs and flows of policy changes and educational debates that are common in Western contexts. Instead, these sentiments are more deeply woven into the societal fabric, enduring as a consistent and unshakable respect for the role of teachers.\n\nIn terms of ‘Nurturing and Inspiration,’ while studies like those of Patton et al. (2016) and Kucuk et al. (2021) have acknowledged the significance of teachers in fostering academic growth and personal development in students, the current study extends this notion by illustrating how nurturing in the Vietnamese context goes beyond academic realms to include cultural and moral education. In Vietnamese songs, teachers are portrayed not just as educators but as custodians of cultural heritage and moral values. Songs analyzed in the current study encapsulate this broader role, where teachers are seen as imparting lessons that are deeply rooted in Vietnamese culture, history, and values. This portrayal aligns with the Vietnamese societal framework where education is not merely about academic excellence but also about instilling a deep sense of cultural identity and moral integrity (Hang et al., 2017). This cultural approach to nurturing is distinct from the more academically focused perspective often seen in Western contexts (Guenther et al., 2019). The Vietnamese perspective, as reflected in the songs, positions teachers as key figures in the holistic development of individuals, integrating academic learning with cultural and moral upbringing. This integrated approach is indicative of the societal expectations placed on teachers in Vietnam (Hang et al., 2017). It also highlights the deep connection between education and cultural preservation, suggesting that teachers play a vital role in maintaining and transmitting cultural values to future generations. This study’s findings add a new dimension to the global discourse on the role of teachers, emphasizing the importance of understanding cultural nuances in educational practices. The Vietnamese context showcases a model where nurturing and inspiration by teachers encompass a broader spectrum, intertwining academic guidance with cultural and moral education. This holistic approach to nurturing provides a more comprehensive understanding of the role of teachers and underscores the importance of culturally responsive teaching practices that honor and integrate these broader societal roles.\n\nThe theme of ‘Enduring Impact and Memory,’ as explored in the Vietnamese songs, resonates with and extends the findings of researchers like Beers and Bowden (2005) and Connelly and Clandinin (2007), who have highlighted the significant long-term influence of teachers on students’ lives. These studies predominantly focus on the enduring educational and personal influence that teachers have, emphasizing the role teachers play in shaping the intellectual and personal trajectories of their students. However, the current study’s analysis of Vietnamese songs adds a unique dimension to this understanding by emphasizing not just the lasting educational impact but also the profound emotional bonds and memories that teachers foster. In Vietnamese culture, teachers are celebrated not only for their educational guidance but also for the lasting emotional imprint they leave on their students (Rydstrøm, 2001). These songs often evoke a sense of nostalgia and deep affection, reflecting the enduring emotional connections that go beyond the classroom. This cultural emphasis on emotional bonds is a critical addition to the understanding of the teacher-student relationship. It suggests that the impact of teachers is not solely measured by educational outcomes or career success, but also by the lasting emotional and personal influence they have on their students. This perspective contrasts with some Western narratives where the focus is often more on the academic and professional development aspects of this relationship (Gehlbach et al., 2023). Moreover, this theme in Vietnamese songs underscores the cultural value placed on emotional relationships and personal connections within the educational context. It highlights a cultural paradigm where teachers are seen as integral figures in the emotional and moral development of students, shaping not just their academic paths but also their emotional and ethical frameworks.\n\nNext, the theme ‘Teacher as a Guiding Figure’ in the Vietnamese context encompasses more than the imparting of knowledge or academic guidance. It encapsulates a broader, more holistic approach to teaching, where educators are seen as moral and cultural guides. In Vietnamese culture, teachers are often regarded as the moral backbone of the community, instilling not only academic knowledge but also imparting values, ethics, and cultural understanding (Le Ha & Van Que, 2006). This view aligns with Confucian principles, which heavily influence Vietnamese culture, emphasizing respect, morality, and the importance of education (Truong et al., 2017). In this setting, teachers are revered as role models, playing a crucial role in shaping the character and moral compass of their students. The songs analyzed in this study reflect this sentiment, portraying teachers as integral figures in guiding the overall development of the individual – a concept that extends beyond the traditional Western view of teaching as primarily a transfer of cognitive skills (Haskell, 2000; Tarling & Ng’ambi, 2016).\n\nFinally, the theme of ‘Emotional Connection and Affection’ underscores the depth of the emotional bonds between teachers and students, which is a distinctive aspect of the Vietnamese educational ethos. Unlike the more pragmatic and professional boundaries often observed in Western teacher-student relationships (Kadar, 2017), the Vietnamese perspective, as mirrored in the song lyrics, highlights a deeper, almost familial connection. Teachers are seen as caretakers and nurturers, not just of intellectual growth but also of emotional well-being (Herrara et al., 2022). This perspective fosters a learning environment where emotional intelligence, empathy, and mutual respect are as valued as academic achievements. The emotional connection is integral to the learning process, with teachers playing a pivotal role in providing a supportive and nurturing environment. This emotional depth and the role of teachers as moral and cultural guides in the Vietnamese context highlight a cultural paradigm where teaching transcends its professional boundaries. Teaching is perceived as a vital component of community and personal development (Tran et al., 2020). This contrasts with the Western perspective, where there is often a sharper focus on measurable academic outcomes and a more defined separation between the personal and professional aspects of teaching (Guenther et al., 2019).\n\n\nConclusion\n\nThe study embarked on an exploration of the cultural and emotional dimensions of the teaching profession in Vietnam, as depicted in popular music. This research was motivated by the recognition that teachers play a crucial role not only in education but also in shaping cultural and societal values. Through an analysis of twelve Vietnamese songs about teachers, this study sought to uncover how these songs reflect and contribute to the construction of teachers’ professional identity in Vietnamese society. Utilizing a qualitative research methodology, the study employed Constructivist Grounded Theory, Sociocultural Theory, Symbolic Interactionism, and Hermeneutic Phenomenology as theoretical lenses to interpret the song lyrics. The careful selection of songs ensured a diverse representation of themes and sentiments related to teaching. The analysis revealed several key themes, including ‘Sacrifice and Dedication,’ ‘Respect and Reverence,’ ‘Nurturing and Inspiration,’ ‘Enduring Impact and Memory,’ ‘Teacher as a Guiding Figure,’ and ‘Emotional Connection and Affection.’ These themes collectively paint a picture of the Vietnamese teacher as a revered, dedicated, and emotionally connected figure, whose influence extends far beyond the academic and into the realms of personal development and cultural preservation.\n\nThe implications of these findings are multifaceted. Firstly, they underscore the importance of cultural and emotional factors in shaping professional identities, particularly in the context of teaching. This insight is crucial for educational policymakers and teacher education programs, as it highlights the need to acknowledge and integrate these cultural and emotional aspects into teacher training and professional development. Understanding the cultural narratives that shape the perception of teachers can lead to more effective and culturally responsive educational practices. Secondly, the study contributes to the broader discourse on teacher identity by offering a culturally specific perspective. This is particularly relevant in an increasingly globalized world where understanding and respecting cultural differences in educational contexts is essential. For researchers and educators, this study provides a framework for exploring and understanding the professional identity of teachers in different cultural settings. Finally, the study highlights the power of cultural artifacts, such as music, in reflecting and shaping societal values and professional identities. This understanding opens up new avenues for research and practice, suggesting that educators and policymakers can use cultural artifacts strategically to reinforce positive perceptions and values associated with the teaching profession.\n\nIn conclusion, this study not only enriches the academic understanding of teacher identity but also offers practical insights for the field of education. It emphasizes the need to view teaching not just as a profession but as a culturally and emotionally rich vocation that plays a vital role in shaping the future of societies.\n\nThe study, while providing valuable insights into the professional identity of Vietnamese teachers as depicted in song lyrics, has certain limitations that must be acknowledged. First, the focus on a specific cultural context – Vietnamese songs about teaching – while rich in cultural specificity, may limit the generalizability of the findings to other contexts or cultures. The interpretation of lyrics, inherently subjective, could vary, and the analysis might overlook certain cultural nuances unfamiliar to an international audience. Additionally, the study’s reliance on qualitative analysis of song lyrics means that the findings are interpretative and not empirically measurable, which could limit their applicability in more quantitative-oriented educational research frameworks. The choice of songs, despite being diverse, may not encompass the entire spectrum of views and experiences of teachers in Vietnam, potentially omitting less popular but equally significant perspectives.\n\nGiven these limitations, several recommendations for further studies are proposed. Future research could expand the scope to include a more diverse range of cultural artifacts, such as literature, films, and television programs, to provide a more comprehensive understanding of the professional identity of teachers in different cultural settings. Comparative studies could be conducted to explore how teachers’ professional identities are portrayed in different countries and cultures, offering a more global perspective. Additionally, incorporating quantitative methods, such as surveys or interviews with teachers and students, could complement the findings from the song lyrics and provide a more holistic understanding of the professional identity of teachers. Research could also delve deeper into how these cultural representations influence actual teaching practices and educational policies, providing a practical dimension to the findings. Finally, studies exploring the impact of these cultural artifacts on the perception of the teaching profession among the general public could offer valuable insights for educational policymakers and practitioners.\n\n\nEthical statement\n\nThis study obtained ethical clearance from the pertinent ethics committee affiliated with a school of foreign languages situated in the Mekong Delta region of Vietnam, prior to commencing data collection. The approval was granted under the official reference number T2022-137 on May 17th 2023.",
"appendix": "Data availability\n\nFigshare: Data set of the study entitled “Exploring the Cultural Portrayal of Vietnamese Teachers: An Analytical Study of Professional Identity in Vietnamese Teaching-Themed Songs”. DOI: https://doi.org/10.6084/m9.figshare.25036499.v2 (Thao, 2024).\n\nThe project contains the following underlying data:\n\n• Data set of the study entitled “Data of the study entitled “Exploring the Cultural Portrayal of Vietnamese Teachers: An Analytical Study of Professional Identity in Vietnamese Teaching-Themed Songs” (12 songs’ lyrics analyzed in this study).\n\n• Data 92 - English version.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nAbdulaziz A, Bashir M, Alfalih AA: The impact of work-life balance and work overload on teacher’s organizational commitment: do job engagement and perceived organizational support matter. Educ. Inf. Technol. 2022; 27(7): 9641–9663. Publisher Full Text\n\nBeauchamp C, Thomas L: Understanding teacher identity: An overview of issues in the literature and implications for teacher education. Camb. J. Educ. 2009; 39(2): 175–189. Publisher Full Text\n\nBeauchamp C, Thomas L: Reflecting on an ideal: Student teachers envision a future identity. Reflective Pract. 2010; 11(5): 631–643. Publisher Full Text\n\nBeers GW, Bowden S: The effect of teaching method on long-term knowledge retention. J. Nurs. Educ. 2005; 44(11): 511–514. Publisher Full Text\n\nBeijaard D, Meijer PC, Verloop N: Reconsidering research on teachers’ professional identity. Teach. Teach. Educ. 2004; 20(2): 107–128. Publisher Full Text\n\nBlumer H: Symbolic interactionism: Perspective and method. University of California Press; 1986.\n\nBraun V, Clarke V: Toward good practice in thematic analysis: Avoiding common problems and be (com) ing a knowing researcher. Int. J. Transgender Health. 2023; 24(1): 1–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCanh L: Remapping the teacher knowledge-base of language teacher education: a Vietnamese perspective. Lang. Teach. Res. 2018; 24(1): 71–81. Publisher Full Text\n\nCharmaz K: Constructing grounded theory: A practical guide through qualitative analysis. Sage; 2006.\n\nCohen AB: Many forms of culture. Am. Psychol. 2009; 64(3): 194–204. Publisher Full Text\n\nCohen L: Remembrance of things past: Cultural process and practice in the analysis of career stories. J. Vocat. Behav. 2006; 69(2): 189–201. Publisher Full Text\n\nConnelly FM, Clandinin DJ: Teacher education—A question of teacher knowledges.Freeman-Moir J, Scott A, editors. Shaping the future. Brill; 2007; pp. 89–105.\n\nCooper C, Travers C: Teachers under pressure: Stress in the teaching profession. Routledge; 2012.\n\nDay C, Kington A, Stobart G, et al.: The personal and professional selves of teachers: Stable and unstable identities. Br. Educ. Res. J. 2006; 32(4): 601–616. Publisher Full Text\n\nGehlbach H, Mascio B, McIntyre J: Social perspective taking: A professional development induction to improve teacher–student relationships and student learning. J. Educ. Psychol. 2023; 115(2): 330–348. Publisher Full Text\n\nGuenther J, Lowe K, Burgess C, et al.: Factors contributing to educational outcomes for First Nations students from remote communities: A systematic review. Aust. Educ. Res. 2019; 46: 319–340. Publisher Full Text\n\nHang NVT, Bulte AMW, Pilot A: Interaction of Vietnamese teachers with a social constructivism-based primary science curriculum in a framework appropriate for a Confucian heritage culture. Asia Pac. Sci. Educ. 2017; 3(1): 1–33. Publisher Full Text\n\nHaskell RE: Transfer of learning: Cognition and instruction. Elsevier; 2000.\n\nHerrera LJP, Martinez-Alba G, Trinh E: Teacher well-being in English language teaching: An ecological approach. Taylor & Francis; 2022.\n\nHieu LT: Confucian influences on Vietnamese culture. Vietnam Soc. Sci. 2015; 5(169): 71–82.\n\nKadar D: The role of ideology in evaluations of (in) appropriate behaviour in student-teacher relationships in China. Pragmatics. 2017; 27(1): 33–56. Publisher Full Text\n\nKeddie A: School autonomy, accountability and collaboration: a critical review. J. Educ. Adm. Hist. 2015; 47(1): 1–17. Publisher Full Text\n\nKlassen RM, Aldhafri S, Mansfield CF, et al.: Teachers’ engagement at work: An international validation study. J. Exp. Educ. 2012; 80(4): 317–337. Publisher Full Text\n\nKucuk ZD, Yabas D, Boyaci HS, et al.: The impact of the early STEM program on teacher and student outcomes: The role of teachers’ involvement in the program development. Int. J. Educ. Math. Sci. Technol. 2021; 9(3): 371–405. Publisher Full Text\n\nLamote C, Engels N: The development of student teachers’ professional identity. Eur. J. Teach. Educ. 2010; 33(1): 3–18. Publisher Full Text\n\nLe Ha P, Van Que P: Vietnamese educational morality and the discursive construction of English language teacher identity. J. Multicult. Discourses. 2006; 1(2): 136–151. Publisher Full Text\n\nNguyen HTM, Bui T: Teachers’ agency and the enactment of educational reform in Vietnam. Curr. Issues Lang. Plan. 2016; 17(1): 88–105. Publisher Full Text\n\nNguyen K: Echoic survivals: re-documenting pre-1975 Vietnamese music as historical sound/tracks of remembering. Violence Int. J. 2020; 1(2): 303–331. Publisher Full Text\n\nNguyen PM: Culture and cooperation: Cooperative learning in Asian Confucian heritage cultures. The case of Viet Nam. Utrecht University; 2008.\n\nNguyen TQT: Maintaining teachers’ face in the context of change: Results from a study of Vietnamese college lecturers’ perceptions of face. Teach. Teach. 2017; 23(1): 78–90. Publisher Full Text\n\nNorton B: Songs for the spirits: Music and mediums in modern Vietnam. University of Illinois Press; 2010.\n\nPantić N, Wubbels T: The role of teachers in inculcating moral values: operationalisation of concepts. J. Beliefs Values. 2012; 33(1): 55–69. Publisher Full Text\n\nPatton LD, Renn KA, Guido FM, et al.: Student development in college: Theory, research, and practice. John Wiley & Sons; 2016.\n\nPochtar R, Vecchio T: A cross-cultural examination of preschool teacher cognitions and responses to child aggression. Sch. Psychol. Int. 2013; 35(2): 176–190. Publisher Full Text\n\nRydstrøm H: ‘Like a white piece of paper’. Embodiment and the moral upbringing of Vietnamese children. Ethnos. 2001; 66(3): 394–413. Publisher Full Text\n\nSachs J: Teacher professional identity: Competing discourses, competing outcomes. J. Educ. Policy. 2001; 16(2): 149–161. Publisher Full Text\n\nSachs J: Teacher professionalism: Why are we still talking about it? Teach. Teach. 2016; 22(4): 413–425. Publisher Full Text\n\nTarling I, Ng’ambi D: Teachers pedagogical change framework: a diagnostic tool for changing teachers’ uses of emerging technologies. Br. J. Educ. Technol. 2016; 47(3): 554–572. Publisher Full Text\n\nThao LT: Data of the study entitled “Exploring the Cultural Portrayal of Vietnamese Teachers: An Analytical Study of Professional Identity in Vietnamese Teaching-Themed Songs”. Dataset. figshare. 2024. Publisher Full Text\n\nTho NN: Confucianism and humane education in contemporary Vietnam. Int. Commun. Chin. Cult. 2016; 3(4): 645–671. Publisher Full Text\n\nTran NH, Truong TD, Dinh HVT, et al.: Significance of Teacher Professional Development in Response to the Current General Education Reforms in Vietnam: Perceptions of School Principals and Teachers. Probl. Educ. 21st Cent. 2020; 78(3): 449–464. Publisher Full Text\n\nTran N, Hallinger P, Troung T: The heart of school improvement: a multi-site case study of leadership for teacher learning in Vietnam. Sch. Leadersh. Manag. 2017; 38(1): 80–101. Publisher Full Text\n\nTruong TD, Hallinger P, Sanga K: Confucian values and school leadership in Vietnam: Exploring the influence of culture on principal decision making. Educ. Manag. Adm. Leadersh. 2017; 45(1): 77–100. Publisher Full Text\n\nVan Manen M: Phenomenology of practice: Meaning-giving methods in phenomenological research and writing. Taylor & Francis; 2023.\n\nVygotsky LS: Mind in society: Development of higher psychological processes. Harvard University Press; 1978.\n\nWright KB, Abendschein B, Wombacher K, et al.: Work-related communication technology use outside of regular work hours and work life conflict: The influence of communication technologies on perceived work life conflict, burnout, job satisfaction, and turnover intentions. Manag. Commun. Q. 2014; 28(4): 507–530. Publisher Full Text\n\nYin HB, Lee JCK: Be passionate, but be rational as well: Emotional rules for Chinese teachers’ work. Teach. Teach. Educ. 2012; 28(1): 56–65. Publisher Full Text"
}
|
[
{
"id": "292591",
"date": "03 Jul 2024",
"name": "Thi Hoang Hoa Chau",
"expertise": [
"Reviewer Expertise I am doing research on how to integrate culture in EFL lessons",
"which is a part lineÃÂ with this study. This study is original and interesting."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear authors, Congratulations on your completion of a great and interesting work. I am impressed with the smooth intersection between cultural artifacts, specifically Vietnamese songs about teaching, and the professional identity of teachers in Vietnam in one piece of research. Also, the employment of a multi-theoretical approach grounded in Constructivist Grounded Theory, Sociocultural Theory, Symbolic Interactionism, and Hermeneutic Phenomenology provides a comprehensive analysis of how these songs contribute to shaping the professional identity of Vietnamese teachers. However, I have some feedback for you to consider making it more logical, consistent and readable. Major Points: Research Gap Identification: The identification of the research gap is well-articulated: \"While there is substantial literature on professional identity in teaching and the influence of culture on this identity, there is a noticeable gap in research specifically focusing on how Vietnamese songs about teaching contribute to shaping the professional identity of teachers.\" This clear statement effectively justifies the study's relevance and importance. Theoretical Frameworks and Research Design: you should consider the three suggestions as follows, but the final decision is yours if you have good justification.\nThe research design is robust and well-grounded in several theoretical frameworks. However, consider moving parts of these frameworks to the Literature Review section for better organization and flow. This decision ultimately rests with you, but it could enhance the clarity and coherence of the article. The methodology is excellently detailed, demonstrating a thorough and systematic approach to exploring the research questions. The use of Constructivist Grounded Theory, Sociocultural Theory, Symbolic Interactionism, and Hermeneutic Phenomenology provides a strong foundation for the study. Ensure that each framework's contribution to the analysis is clear and distinct. Also, the thematic analysis of song lyrics is well-executed. Consider presenting the identified themes and patterns in a table or figure to enhance readability and provide a clear visual summary of the findings. Minor Points:\nThe chosen songs are closely related to Vietnamese culture, which is commendable. However, providing brief descriptions of these songs and their relevance to the study would enhance the reader's understanding of their significance and the context in which they were selected. Please review the citation: \"The concept of professional identity in teaching has been a subject of extensive research. Beauchamp and Thomas (2009), 2010.\" It should be formatted consistently with other citations. Ensure all citations follow a uniform style and correct any inconsistencies, especially with Vietnamese authors' names (first or last names?). Overall, the article presents a well-researched and insightful analysis of how Vietnamese songs about teaching contribute to shaping the professional identity of teachers. By addressing the points mentioned above, the clarity and coherence of the article can be further enhanced, making it a valuable contribution to the field of education and cultural studies.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "313869",
"date": "03 Sep 2024",
"name": "Jonathan Newton",
"expertise": [
"Reviewer Expertise Applied linguistics"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic is an interesting one and there are aspects of the research that seem to be well handled. However, the following issues need to be addressed: 1. Introducing theories in the methods section doesn't make sense. 2. Also, on this point, dropping in these big theoretical constructs without motivating WHY each was chosen is problematic, Aim to be selective and to provide a stronger rationale for why the theories you chose are relevant. It seems to me that some of these frameworks are indeed relevant to your methodology but others are related to the broad constructs under investigation and represent your theoretical approach to them. As such, these need to be built into the lit review NOT the methodology. Also, the words \"Such as\" are deeply problematic. It implies that there are other theories that you will introduce later! \"such as Constructivist Grounded Theory, Sociocultural Theory, Symbolic Interactionism, and Hermeneutic Phenomenology.\" 2. The section on data collection fails to address the critical question of how the songs were selected. How many songs were initially identified and how were these 12 selected? Using what criteria? What data base was used? How was representativeness managed? Over what time frame where the songs published and does this time dimension show any trends? 3. The section 'research design' tells us nothing about design - it just introduces theories. 4. Data collection needs to precede the list of songs. 5. Why only 12 songs. This seems like a very slim data set. On this basis alone I question the validity of the study, unless it can be shown that these are the only songs about teachers published in Vietnam or are a rigorously selected sample. What genre are involved? Did the researchers sample all genre, including musical styles such as rap-influenced styles? 6. Overall the discussion lacks critical depth and seems to want to paint a halcyon picture of how wonderful teachers are. In this regard, a more critical framework for the emotional labour that teachers do is needed, such as is found in the references below, the first being particularly relevant.[1],[2],[3]\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-631
|
https://f1000research.com/articles/13-630/v1
|
13 Jun 24
|
{
"type": "Research Article",
"title": "Demand-side barriers and economic burden in accessing Human Papillomavirus screening for cervical cancer prevention in rural India: Evidence from a cross-sectional study",
"authors": [
"Shyamkumar Sriram",
"Arun Daniel Jayakumar",
"Pavan Kumar Gollapalli",
"Swetha Chandrasekar",
"Arun Daniel Jayakumar",
"Pavan Kumar Gollapalli",
"Swetha Chandrasekar"
],
"abstract": "Introduction Cervical cancer is a significant global health concern, especially in low- and middle-income countries with limited access to preventive healthcare. India’s vast rural population amplifies the challenge, demanding immediate action. Despite advancements, cervical cancer remains prevalent among underserved rural communities, hindered by barriers to Human Papillomavirus (HPV) screening uptake, including socioeconomic and financial constraints. This study aims to evaluate the economic challenges encountered by rural women when accessing HPV screening.\n\nMethods A cross-sectional survey was conducted among 1502 women aged 30 to 45 in Pondicherry, India, utilizing the Andersen Model as a conceptual framework. Household questionnaires gathered data on HPV screening expenses, including patient travel costs, productivity loss, and companion costs. The analysis utilized regression models, to identify the factors impacting the economic challenges associated with accessing HPV screening.\n\nResults Employment status and higher education significantly increase total costs by 73.483 (p < 0.001) and 90.169 units (p < 0.001) respectively. Income level, though with a minimal coefficient (B = 0.000), shows a significant effect (p = 0.019) on total costs. Longer travel hours raise costs by 5.129 units (p < 0.001), while having a companion increases costs by 106.095 units (p = 0.004). Prolonged patient time at Primary Health Center (PHC) contributes to a 2.357-unit increase in costs (p < 0.001).\n\nConclusions The study highlights the multifaceted economic challenges faced by rural populations accessing HPV screening for cervical cancer prevention in India. Notwithstanding diverse demographics and varying proximity to healthcare facilities, individuals encounter significant barriers such as travel time and associated costs. Addressing these challenges necessitates targeted interventions to reduce socioeconomic disparities and improve healthcare accessibility for vulnerable populations, thereby advancing cervical cancer prevention efforts and promoting health equity in rural communities.",
"keywords": [
"HPV screening",
"cervical cancer prevention",
"rural India",
"healthcare accessibility",
"economic burden",
"healthcare costs"
],
"content": "Introduction\n\nCervical cancer remains a significant global health burden, particularly in low- and middle-income countries (LMICs) where access to preventive healthcare services is often limited.1 As the fourth most prevalent cancer among women worldwide, it recorded approximately 660,000 new cases and 350,000 fatalities in 2022.2\n\nIndia harbours a substantial population of approximately 511.4 million women aged 15 years and older who are at risk of developing cervical cancer, emphasizing the pressing need to address this health challenge.3 Annually, an estimated 123,907 women are diagnosed with cervical cancer, and 77,348 succumb to the disease. Cervical cancer ranks as the second most common cancer among Indian women, particularly those aged 15 to 44 years, exerting a profound impact nationwide. The prevalence of cervical Human Papillomavirus (HPV) – 16/18 infection among the general female population is estimated to be around 5.0%, with HPV types 16 or 18 accounting for approximately 83.2% of invasive cervical cancer cases. This data highlights the pivotal role of HPV vaccination and screening programs in combating the disease.4\n\nAlthough females make up slightly over 48% of India’s rural population, only 1.7% of rural women participated in cervical cancer screening according to data from the National Family Health Survey 5 (NFHS-5). Cervical cancer disproportionately affects rural areas where healthcare access is limited, and awareness of preventive measures is lacking. It is crucial to address these disparities in healthcare access and education to effectively reduce the impact of cervical cancer in India.5\n\nHPV screening has emerged as a promising tool for early detection and prevention of cervical cancer. However, the uptake of HPV screening services in rural India is hindered by a myriad of demand-side barriers, including socioeconomic challenges and the financial burdens linked to HPV screening. These include both direct costs, such as transportation fees, lost income due to missed work, and out-of-pocket expenditures for healthcare services, as well as indirect expenses.6 India, with its vast rural population and diverse socio-cultural landscape, faces a particularly daunting burden of cervical cancer.7 Nevertheless, advances in screening and prevention methods, the disease continues to exact a heavy toll, disproportionately affecting women in underserved rural communities.8,9\n\nHPV testing presents distinct advantages over traditional cytology-based methods like Pap smear, with higher sensitivity, lower false-negative rates, and the capability to detect HPV infection prior to cytological abnormalities, making it advantageous for cervical cancer prevention especially in resource-limited settings.10\n\nRegardless of the potential benefits of HPV screening, its uptake in rural India is hampered by a range of demand-side barriers that impede access to screening services and contribute to disparities in cervical cancer outcomes.11 Socio-economic factors play a significant role in shaping access to healthcare services, including HPV screening, in rural India. Poverty, lack of health insurance, and financial constraints often limit women’s ability to seek preventive care, including cervical cancer screening. In many rural households, healthcare expenses are perceived as a luxury rather than a necessity, leading women to prioritize other household needs over their own health.12\n\nMoreover, the cost of HPV testing and follow-up procedures, such as colposcopy and biopsy, can be prohibitive for women in rural areas, particularly those belonging to marginalized communities. Even when screening services are available free of charge or at subsidized rates, indirect costs such as transportation and lost wages may pose significant barriers to utilization, especially for women residing in remote villages with limited access to healthcare facilities.13\n\nIn rural areas, socioeconomic factors intertwine to create formidable financial barriers for women seeking HPV screening for cervical cancer prevention.14 The direct costs associated with accessing HPV screening services, including transportation expenses, pose significant challenges for rural residents, particularly those in remote areas. Additionally, the necessity of taking time off work to travel to healthcare facilities results in lost wages for many hourly or daily wage earners, further exacerbating the financial burden.15 Beyond tangible costs, intangible yet impactful indirect expenses such as the opportunity cost of forgoing work or household responsibilities and psychological stress also deter rural women from seeking screening. These financial burdens contribute to decreased utilization of preventive healthcare services among rural women, exacerbating existing health inequities.16 Addressing these barriers requires a comprehensive approach encompassing policy reforms, targeted interventions, and community engagement strategies to ensure equitable access to cervical cancer screening services and improve the health outcomes of rural women globally.17\n\nThe conceptual framework (Figure 1) for this study draws upon the Andersen Model,18 a well-established framework in healthcare research. The Andersen Model emphasizes the interplay between predisposing factors, enabling resources, and need factors in shaping healthcare access and utilization. This model provides a comprehensive framework for understanding the various determinants of healthcare-seeking behaviour and utilization patterns.\n\nPredisposing factors: These are characteristics that predispose individuals to seek or avoid healthcare services. In this study, predisposing factors include socio-demographic characteristics such as age, gender, marital status, and household composition.\n\nEnabling resources: Enabling resources encompass economic aspects that facilitate or hinder healthcare access and utilization. This includes household consumption expenditures like travel costs, patient time, companion costs, childcare expenses, income level, source of income, and education level.\n\nNeed factors: Need factors represent the perceived or actual need for healthcare services. This includes healthcare payments, health status, usage patterns, proximity to health facilities, and district of residence.\n\nTherefore, the study aims to analyse the economic challenges faced by rural Indian women when accessing HPV screening for cervical cancer prevention. It aims to quantify the costs involved, including transportation expenses, lost wages due to time off work, and other financial implications.\n\n\nMethods\n\nThis cross-sectional study was conducted among women aged 30 to 45 in Pondicherry, India. Pondicherry, being a Union Territory in India, was chosen as the study area due to its manageable size and diverse population of 8,98,000 individuals.\n\nIn the sampling strategy employed for the study, a total of 1500 women aged 30 to 45 were chosen randomly from the catchment areas of 15 selected Primary Health Centers (PHCs) in Pondicherry, India. It was estimated that each PHC catchment area covered approximately 30,000 individuals.\n\nThe sampling process unfolded across three stages. Initially, in stage 1, the PHCs were designated as primary sampling units, and a simple random sampling technique was utilized to select 15 PHCs from a list obtained from the District Public Health office. The selected PHCs included Abishegapakkam, Ariyankuppam, Bahour, Gorimedu, Karikalampakkam, Kirumambakkam, Koodapakkam, Mettupalayam, Nettapakkam, Reddiarpalayam, Thavalakuppam, Villianur, Ariyur, Sedarapet, and Karayamputhur.\n\nSubsequently, in stage 2, the Anganwadi centers within the chosen PHCs were designated as secondary sampling units. Within each PHC, five Anganwadi centers (AWCs) were randomly selected to ensure a representative sample. Finally, in stage 3, women aged 30 to 45 were selected within the chosen Anganwadi centers. From each selected AWC, 20 women within the specified age range were sampled using simple random sampling from the beneficiary lists. This meticulous approach resulted in a total sample size of 1500 women, with 100 women sampled from each PHC catchment area, thereby ensuring a comprehensive representation of the target population for the study.\n\nThe Household Cost Questionnaire (HCQ) administered to sampled women encompasses a wide array of variables spanning, socio-demographic variables include age, gender, education level, income level, source of income, and district of residence. Data on patient travel expenses, time spent on travel, companion expenses, childcare expenses, and productivity loss was collected comprehensively to accurately reflect the costs incurred by patients and their companions.\n\nInstitutional Ethical approval was obtained from the Institutional Review Board of Ohio University. IRB project 23-E-101, titled ‘Supply-side and Demand-side Barriers to Access HPV Screening and the Cost-effectiveness analysis of Human Papilloma Virus (HPV) Screening for the Prevention of Cervical Cancer Screening in India. Ohio University’s Institutional Review Board deemed it exempt from review since no interventions were carried out.\n\nTotal cost incurred: The sum of all expenses associated with accessing HPV testing, including patient travel costs, companion costs, childcare/dependent costs, and productivity loss costs. Calculated by adding up the costs from each category.\n\nPatient travel cost: The expenses incurred by the patient for traveling to and from the PHC for HPV testing. Calculated separately for each mode of transportation used (public transport and taxi), considering round trip costs.\n\nCompanion cost: The expenses incurred by the companion who accompanies the patient to the PHC. Calculated by summing the cost of one-way fare for the companion’s travel and the amount of time taken off from paid work to accompany the patient.\n\nProductivity loss cost: The monetary value of earnings lost by the patient due to time taken off from work to visit the PHC. Calculated based on the average salary of a person in India/Pondicherry multiplied by the amount of time taken off from work.\n\nAverage salary of a person in India/Pondicherry: The mean income earned by individuals in the specified geographical area. The average wage earning for rural women worker is Rs 265 per day (National Statistical Office 2022).19\n\nFirstly, the exposure variables included participants’ employment status, education level, and income level. Employment status was categorized as either employed or unemployed, while education level was assessed based on the highest level of education attained, ranging from primary to post-graduate university. Income level was determined by annual household income, segmented into different income brackets. These variables provided insights into the socio-economic status of the participants and their households, which are crucial factors influencing healthcare access and utilization.\n\nSecondly, the primary outcome variable examined was the total healthcare costs incurred by participants when accessing HPV testing. These costs encompassed various components, including patient travel expenses, companion expenses, child care expenses, and productivity losses. By quantifying these costs, the study aimed to assess the economic burden experienced by participants and their companions during the process of seeking HPV testing services.\n\nAdditionally, several covariates were considered in the analysis to account for potential confounding factors. These covariates included age, gender, district of residence, source of income, distance from home to the PHC, hours travelled to the PHC, and whether a companion accompanied the participant during PHC visits. These factors were deemed relevant as they could influence both the exposure and outcome variables, thus requiring adjustment in the analysis to obtain accurate estimates of the associations under investigation.\n\nCollected data was analysed using STATA 16. Descriptive statistics, such as means, medians, ranges, and standard deviations, are used to describe the demographic characteristics of the study population and variables related to healthcare access and utilization.\n\nIndividual costs were aggregated to estimate the total economic burden for patients. Total costs for the entire sample and average costs per patient were calculated. Regression models are employed to examine the relationship between independent variables (e.g., employment status, education level) and the dependent variable (total healthcare costs). This helps identify significant predictors of the economic burden of accessing healthcare services.\n\nInstitutional Ethical approval was obtained from the Institutional Review Board of Ohio University. Informed written consent was obtained from all study participants before data collection.\n\n\nResults\n\nThe demographic breakdown of the surveyed population (Table 1) consisting of 1502 individuals, showcases a varied distribution across female age groups, with the highest percentage falling between 31 to 40 years (34.75%), closely followed by the 21 to 30 years range (30.89%). The majority of respondents are married (85.62%). Employment status displays diversity, with homemakers representing the largest segment (70.64%), followed by those engaged in full-time (10.19%) and part-time (13.05%) work. Education levels range from primary to post-graduate university, with a noteworthy proportion having attained some secondary education (32.42%). Annual household incomes comprise a significant proportion falling below 50,000 INR (28.03%). The majority of households accommodate four or fewer adults (86.82%) and two or fewer children (96.40%).\n\nTable 2 provides essential demographic and geographic variables pertaining to healthcare access. The mean annual household income is 155,560 INR, with a median of 100,000 INR and a substantial range spanning 6,000,000 INR. This discrepancy between the mean and median suggests a positively skewed distribution influenced by high-income outliers. Age distribution, with a mean of 34.08 years and a median of 34 years, appears relatively symmetric, indicating a balanced spread across age groups. The number of adults in households has a mean of 2.96 and a median of 3, with a range extending to 10, reflecting moderate variability in household composition. Similarly, the number of children in households shows a mean of 1.07 and a median of 1, with a range of 15, suggesting varied family sizes. Geographic metrics reveal wider disparities, with a mean distance from home to the Primary Health Center (PHC) of 3.64 kilometers and a median of 2 kilometers. This disparity between mean and median distances indicates significant variability, possibly reflecting urban-rural disparities in accessibility. Additionally, the distances traveled by private car or motorbike, reaching up to 299 km one-way, provide insights into transportation needs and possibly lifestyle preferences. Collectively, these data points infer a multifaceted picture of households, highlighting disparities in income, demographics, and geographic access, crucial for understanding and addressing diverse societal needs and challenges.\n\nTable 3 presents frequencies and percentages related to various variables associated with households’ interactions with Primary Health Centers (PHCs). Notably, a significant majority of households, comprising 80.36%, reside within a 3-kilometer radius from a PHC, suggesting relatively close proximity for accessing healthcare services. However, a notable proportion, 15.85%, live farther, between 3 and 10 kilometers from the nearest PHC. Moreover, a smaller percentage, 2.60%, reside beyond 10 kilometers, indicating potential challenges in accessing healthcare for these households.\n\nIn terms of travel duration, a considerable portion of individuals, accounting for 44.34%, reported travel times of more than 10 minutes but less than 20 minutes to reach the PHC, with 10.05% enduring journeys lasting between 20 and 30 minutes. This infers varying degrees of travel inconvenience potentially experienced by households when seeking healthcare.\n\nRegarding transportation modes, a majority, comprising 83.56%, did not utilize public transport, suggesting a reliance on private means of transportation. Additionally, a significant majority, 94.14%, returned home using the same mode of transport, indicating consistency in transportation choices.\n\nFurthermore, the data reveals insights into social dynamics, with only 12.38% of individuals being accompanied by a companion to the PHC. This indicates that for the majority, healthcare-seeking behaviour occurs independently.\n\nTable 4 offers insights into various time-related aspects concerning individuals’ interactions with PHCs and related responsibilities.\n\nFirstly, concerning the time spent at the PHC, the majority of individuals, constituting 64.18%, reported durations of more than 20 minutes but less than 60 minutes, emphasizing potentially significant waiting and consultation times. Moreover, 8.12% and 16.91% experienced shorter durations, while a smaller proportion, 2.20%, endured waits exceeding 60 minutes.\n\nIn terms of time allocation from paid work to visit the PHC, there’s a distribution across various durations, with 33.33% spending more than 30 minutes but less than 60 minutes, indicating potential disruptions to work schedules for healthcare visits.\n\nFurthermore, data regarding work schedules reveals that the majority, comprising 62.28%, work more than 5 days but less than 7 days per week, underscoring potential challenges in balancing work commitments with healthcare needs.\n\nRegarding time spent by companions, there’s variability, with 39.78% spending more than 30 minutes but less than 60 minutes, possibly reflecting the support provided by companions in accompanying individuals to PHCs.\n\nMoreover, data on time taken off from paid work to accompany individuals to PHCs highlights that a significant majority, at 80.11%, reported durations of 10 minutes or less, indicating minimal disruptions to work for caregiving responsibilities.\n\nLastly, concerning caregiving responsibilities, caregivers spent varying durations looking after children/dependents during individuals’ visits to PHCs, with 33.33% spending more than 30 minutes but less than 60 minutes, reflecting the impact of healthcare visits on caregiving duties.\n\nOverall, these insights shed light on the time-related challenges and dynamics individuals and their companions face when accessing healthcare services, highlighting areas where interventions or improvements may be necessary to streamline processes and reduce burdens on individuals and their support networks.\n\nTable 5 presents a detailed overview of various time-related factors associated with individuals’ engagements with PHCs and their corresponding duties.\n\nFor the duration of travel from home to the PHC, the mean time is 16.12 minutes, with a median of 15 minutes, indicating generally consistent travel times for most individuals. However, there is notable variability, with travel durations ranging from 0 to 70 minutes, and a standard deviation of 9.84 suggests moderate dispersion around the mean.\n\nRegarding the time taken from paid work to reach the PHC, the mean duration is higher at 52.52 minutes, with a median of 60 minutes, reflecting potentially longer commutes for those traveling from their workplaces. The range spans from 0 to 120 minutes, indicating diverse commuting times, with a considerable standard deviation of 45.18.\n\nCompanions’ time commitments, including travel and time spent at the PHC, show a mean duration of 36.18 minutes, with a median of 40 minutes, suggesting moderate consistency. However, there is variability, with durations ranging from 0 to 120 minutes and a standard deviation of 27.44.\n\nIndividuals taking time off from work to accompany others to the PHC experience a mean duration of 62.05 minutes, with a median of 47.50 minutes, highlighting significant disruptions to work schedules. The range is wide, from 0 to 299 minutes, with a considerable standard deviation of 67.13.\n\nLastly, caregivers spend an average of 30.30 minutes looking after children/dependents during PHC visits, with a median of 30 minutes, showcasing consistent caregiving responsibilities. Variability exists, with durations ranging from 0 to 120 minutes and a standard deviation of 28.03.\n\nTable 6 presents detailed insights into the various costs and time implications associated with patient travel, companion expenses, childcare, and productivity losses related to visits to the PHC.\n\nPublic transport one-way fares exhibit a wide range, spanning from 20 INR to 79,999 INR, reflecting various factors such as distance and service types. Similarly, taxi fares for single journeys display notable variability, ranging from 37.64 INR to 198 INR. Toll expenses for private vehicles, meanwhile, range from 39.94 INR to 199 INR, highlighting differences in toll rates influenced by factors like distance and road infrastructure.\n\nFor patients, the cost encompasses the income lost from taking time off work to visit a PHC, ranging from 50 INR to 129.35 INR. When patients are accompanied, additional expenses arise, such as one-way transport fares for companions, ranging from 50 INR to 56.79 INR. Furthermore, there are costs associated with childcare or dependent care during the patient’s absence, varying from 0 INR to 8.04 INR.\n\nIn terms of productivity losses, the data reflects the number of workdays missed per week (ranging from 6 to 6.74) and the average weekly working hours (ranging from 34 to 70 hours). These figures illustrate the impact of healthcare visits on individuals’ work commitments and earnings potential.\n\nTable 7 revealed that the employed individuals experience an increase in total costs by 73.483 units (95% CI: 38.81-108.153) when accessing HPV screening. The p-value being less than 0.001 suggests that this association is statistically significant. This implies that employment status is a significant predictor of the economic burden of accessing HPV screening in rural India.\n\nHigher education levels are associated with higher total costs, with an increase of 90.169 units (95% CI: 52.030-128.309). The p-value being less than 0.001 indicates statistical significance, suggesting that education level plays a significant role in determining the economic burden of accessing HPV screening in rural India.\n\nIncome level shows a statistically significant effect (p = 0.019) on total costs, although the coefficient is negligible (B = 0.000). This implies that while income level may have a minimal impact, it still contributes to the economic burden of accessing HPV screening, as indicated by the 95% confidence interval.\n\nThe distance from home to the PHC does not significantly impact total costs (p = 0.841). The coefficient of -0.158 suggests a minor decrease in total costs with an increase in distance, but this effect is not statistically significant, as indicated by the wide 95% confidence interval.\n\nLonger travel hours to the PHC significantly increase total costs by 5.129 units (95% CI: 2.622-7.635). The p-value being less than 0.001 indicates statistical significance, highlighting the importance of travel time as a determinant of the economic burden of accessing HPV screening.\n\nHaving a companion during PHC visits significantly increases total costs by 106.095 units (95% CI: 33.276-178.913, p = 0.004). This suggests that the presence of a companion adds to the economic burden of accessing HPV screening in rural India.\n\nLonger patient time in the PHC significantly increases total costs by 2.357 units (95% CI: 1.258-3.455, p < 0.001). This underscores the impact of extended waiting or consultation times on the economic burden of accessing HPV screening in rural India.\n\n\nDiscussion\n\nThe study emphasizes the significant impact of socioeconomic factors on healthcare accessibility and affordability. Variables like employment status, educational attainment, and income level are pivotal in determining the financial strain associated with accessing HPV screening services. Those with higher socioeconomic status typically face fewer obstacles due to their greater financial means and enhanced access to healthcare facilities. The specific finding that employment status is a significant predictor of the economic hurdles in accessing HPV screening in rural India highlights the intricate interplay between socioeconomic factors and healthcare utilization. This observation is in line with the research conducted by Srivatsa et al., which suggests that women hailing from households with a higher income are significantly more inclined to undergo cervical cancer screening compared to those from lower-income households.20,21 Additional studies such as Kaneko, 2018, and Keetile et al., 2021 have similarly argued that disadvantaged households are often less informed and thus less likely to prioritize cervical cancer screening.22,23\n\nA notable finding underlines the influence of travel-related variables on overall expenses. Extended travel duration to the PHC and having a companion during PHC visits are associated with increased total costs. These results are consistent with prior research conducted by Rocque (2019) and Kornelson (2021),24,25 highlighting the significant contribution of travel-related expenses, to the economic burden experienced by individuals accessing HPV screening in rural areas. This observation is further supported by Wu et al. (2020) and Srinath et al (2023).26,27 Addressing transportation barriers and providing assistance for travel expenses could prove instrumental in easing the economic burden on vulnerable populations.28,29\n\nThe study underscores the significance of healthcare delivery efficiency in mitigating the economic burden on patients. Prolonged patient time in PHC facilities correlates positively with increased total costs, underscoring the need for streamlined healthcare processes to minimize waiting times and optimize resource utilization. Improvements in healthcare infrastructure and the implementation of efficient appointment systems can enhance the quality and accessibility of HPV screening services while reducing costs for patients. Shyam et al.’s findings revealed that for-profit hospitals tend to have shorter waiting times for patients, potentially attracting greater demand from economically advantaged individuals. This emphasizes the importance of reducing waiting times in public sector hospitals to ensure equitable access to healthcare services across all socioeconomic strata. Furthermore, considering the sociodemographic and community-level factors, providers can better strategize to improve screening uptake within their local practice settings.30–32\n\nInitiatives to enhance access to HPV screening should not only address geographical barriers but also consider the socioeconomic determinants that may deter individuals from seeking preventive care. By addressing these disparities, policymakers and healthcare providers can strive toward ensuring equitable access to vital healthcare services, thereby alleviating the burden of preventable diseases like cervical cancer in rural India and beyond.4,15,33\n\nThe findings of the study have important policy implications for cervical cancer prevention efforts in rural India. Policy interventions aimed at improving employment opportunities, promoting education, and enhancing transportation infrastructure can help alleviate the socioeconomic barriers to accessing HPV screening services. Additionally, targeted financial assistance programs for low-income individuals and those living in remote areas can help reduce the economic burden associated with seeking healthcare services.11,34\n\nThe study acknowledges several limitations, such as its cross-sectional design and potential confounding factors. Future research could explore longitudinal data to assess the long-term economic impact of accessing HPV screening and investigate additional factors influencing the economic burden, such as out-of-pocket expenses and indirect costs. Moreover, qualitative studies could provide deeper insights into the lived experiences of individuals accessing HPV screening services and the factors influencing their decision-making processes.\n\nIn conclusion, the article contributes to our understanding of the economic challenges faced by individuals accessing HPV screening for cervical cancer prevention in rural India. By identifying key socioeconomic factors and travel-related costs influencing total costs, the study provides valuable insights for policymakers and healthcare providers to develop targeted interventions aimed at reducing the economic burden and improving healthcare access for vulnerable populations.\n\n\nEthics approval and consent to participate\n\nInstitutional Ethical approval was obtained from the Institutional Review Board of Ohio University on 05.17.2023. IRB project 23-E-101, titled ‘Supply-side and Demand-side Barriers to Access HPV Screening and the Cost-effectiveness analysis of Human Papilloma Virus (HPV) Screening for the Prevention of Cervical Cancer Screening in India. Ohio University’s Institutional Review Board deemed it exempt from review since no interventions were carried out.\n\nInformed written consent was obtained from all study participants before data collection.\n\n\nConsent for publication\n\nNot applicable.",
"appendix": "Data availability statement\n\nHarvard Dataverse: Demand-side Barriers and Economic Burden in Accessing Human Papillomavirus Screening for Cervical Cancer Prevention in Rural India: Evidence from a Cross-sectional Study, https://doi.org/10.7910/DVN/H9DB7B. 35\n\nThis project contains the following underlying data:\n\n- Microsoft Excel Spreadsheet\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication)\n\nHarvard Dataverse: Demand-side Barriers and Economic Burden in Accessing Human Papillomavirus Screening for Cervical Cancer Prevention in Rural India: Evidence from a Cross-sectional Study, https://doi.org/10.7910/DVN/H9DB7B. 35\n\nThis project contains the following extended data:\n\n- Questionnaire\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nSingh D, Vignat J, Lorenzoni V, et al.: Global estimates of incidence and mortality of cervical cancer in 2020: a baseline analysis of the WHO Global Cervical Cancer Elimination Initiative. Lancet Glob. Health. 2023 Feb 1 [cited 2024 Mar 14]; 11(2): e197–e206. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nCervical cancer: [cited 2024 Mar 14]. Reference Source\n\nReichheld A, Mukherjee PK, Rahman SMF, et al.: Prevalence of cervical cancer screening and awareness among women in an urban community in South India—a cross sectional study. Ann. Glob. Health. 2020; 86(1): 30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nComplementary data on cervical cancer prevention.[cited 2024 Mar 14]. Reference Source\n\nZhetpisbayeva I, Kassymbekova F, Sarmuldayeva S, et al.: Cervical Cancer Prevention in Rural Areas. Ann. Glob. Health. 2023 [cited 2024 Mar 14]; 89(1): 75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSrivastava AN, Misra JS, Srivastava S, et al.: Cervical cancer screening in rural India: Status & current concepts. Indian J. Med. Res. 2018 Dec 1 [cited 2024 Mar 14]; 148(6): 687–696. 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PubMed Abstract | Publisher Full Text\n\nCasas CPR, de Albuquerque R d CR , Loureiro RB, et al.: Cervical cancer screening in low- and middle-income countries: A systematic review of economic evaluation studies. Clinics. 2022 Jan 1; 77: 100080. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNagdev P, Iyer MR, Naik S, et al.: Andersen health care utilization model: A survey on factors affecting the utilization of dental health services among school children. PLoS One. 2023 Jun 15; 18(6): e0286945. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWomen and Men in India 2022 WOMEN AND MEN IN INDIA.[cited 2024 Apr 9]. Reference Source\n\nSrivastava S, Kurian K, Garg PR, et al.: Prevalence and predictors of cervical cancer screening among reproductive age group women: evidence from cross-sectional study in Rohtak and Delhi. Asian Pac. J. Cancer Prev. 2022 Aug; 23(8): 2771–2777. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChao DYS, Clark M, Carson E, et al.: Economic Analysis.2019 [cited 2024 Apr 9]. Reference Source\n\nKaneko N: Factors associated with cervical cancer screening among young unmarried Japanese women: results from an internet-based survey. BMC Woman’s Health. 2018 Jul 31 [cited 2024 Apr 9]; 18(1). Publisher Full Text | Free Full Text\n\nKeetile M, Ndlovu K, Letamo G, et al.: Factors associated with and socioeconomic inequalities in breast and cervical cancer screening among women aged 15–64 years in Botswana. PLoS One. 2021 Aug 1 [cited 2024 Apr 9]; 16(8): e0255581. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRocque GB, Williams CP, Miller HD, et al.: Impact of travel time on health care costs and resource use by phase of care for older patients with cancer. J. Clin. Oncol. 2019 Aug 8; 37(22): 1935–1945. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKornelsen J, Khowaja AR, Av-Gay G, et al.: The rural tax: comprehensive out-of-pocket costs associated with patient travel in British Columbia. BMC Health Serv. Res. 2021 Aug 21; 21(1): 854. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu Q, Jia M, Chen H, et al.: The economic burden of cervical cancer from diagnosis to one year after final discharge in Henan Province, China: A retrospective case series study. PLoS One. 2020 May 7; 15(5): e0232129. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSrinath A, van Merode F , Rao SV, et al.: Barriers to cervical cancer and breast cancer screening uptake in low- and middle-income countries: a systematic review. Health Policy Plan. 2023 Apr 11; 38(4): 509–527. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOluyede L, Cochran AL, Wolfe M, et al.: Addressing transportation barriers to health care during the COVID-19 pandemic: Perspectives of care coordinators. Transp. Res. Part A Policy Pract. 2022 May; 159: 157–168. Epub 2022 Mar 7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSyed ST, Gerber BS, Sharp LK: Traveling towards disease: transportation barriers to health care access. J. Community Health. 2013 Oct; 38(5): 976–993. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSriram S, Noochpoung R: Determinants of hospital waiting time for outpatient care in India: how demographic characteristics, hospital ownership, and ambulance arrival affect waiting time. Int. J. Commun. Med. Public Health. 2018 Jul; 5(7): 2692. Publisher Full Text\n\nSriram S, Ranganathan R: Why human papilloma virus vaccination coverage is low among adolescents in the US? A study of barriers for vaccination uptake. J. Family Med. Prim. Care. 2019 Mar; 8(3): 866–870. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSriram S, Verma VR, Gollapalli PK, et al.: Decomposing the inequalities in the catastrophic health expenditures on the hospitalization in India: empirical evidence from national sample survey data. Front. Public Health. 2024 Apr 4; 12: 1329447. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNCI Cervical Cancer ‘Last Mile’ Initiative|Division of Cancer Prevention.[cited 2024 Apr 9]. Reference Source\n\nLott BE, Trejo MJ, Baum C, et al.: Interventions to increase uptake of cervical screening in sub-Saharan Africa: a scoping review using the integrated behavioral model. BMC Public Health. 2020 Dec; 20: 1–8. Publisher Full Text\n\nSriram S: Demand-side Barriers and Economic Burden in Accessing Human Papillomavirus Screening for Cervical Cancer Prevention in Rural India: Evidence from a Cross-sectional Study. Harvard Dataverse. V2. Publisher Full Text"
}
|
[
{
"id": "332790",
"date": "25 Oct 2024",
"name": "Santosh Kumari Duppala",
"expertise": [
"Reviewer Expertise Cancer biology",
"Next generation sequencing technologies",
"Bioinformatics",
"Cervical cancer and HPV",
"Molecular biology",
"Microbiology."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript effectively outlines the accessibility challenges rural populations face in accessing HPV screening services. The discussion on the economic implications of HPV screening for rural residents is compelling. Thorough Research by the authors have conducted a comprehensive review of the literature, demonstrating a deep understanding of the complexities surrounding HPV screening in rural settings. The manuscript is well-organized and clearly written, making complex information accessible to a broad audience. The authors have done an excellent job of presenting their findings. The authors offer innovative and practical solutions to address the economic and travel barriers faced by rural populations, showcasing their forward-thinking approach to public health challenges. Strong Evidence Base where the authors have backed their claims with robust data and evidence, enhancing the credibility of their findings and recommendations. \"The statistical analysis of the economic burden related to HPV screening is insightful and provides a nuanced understanding of the challenges rural residents face. The discussion section is particularly engaging, as the authors effectively connect their research to real-world implications, demonstrating the importance of addressing HPV screening in rural communities. Recommendations for future manuscript:\nComparative Analysis: \"A comparison of HPV screening rates between urban and rural populations would strengthen it. Highlighting these disparities can underscore the need for targeted interventions.\" Policy Recommendations: \"It would be beneficial give recommendations on policy changes that could alleviate the economic and travel burdens associated with HPV screening in rural areas in future manuscript. Telehealth Solutions: \"A small suggestion of tele-health as a potential solution for HPV screening in rural communities could be added in future perspectives and a practical approach to overcome travel and cost barriers.\"\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "332791",
"date": "29 Oct 2024",
"name": "Ankit Anand",
"expertise": [
"Reviewer Expertise Health services research",
"Women's health",
"Maternal health",
"Survey research",
"Socioeconomic aspects of health"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic is very interesting and relevant, but the analysis does not add much value to the topic. Need to provide details on the estimation of the cost and income levels. Introduction is very generic and does not add why this data and analysis was needed. It states a lot of generic statement and facts which need to be inline why such study is required. For example: Author stated “only 1.7% of rural women participated in cervical cancer screening according to data from the National Family Health Survey 5 (NFHS-5).” “Addressing these barriers requires a comprehensive approach encompassing policy reforms, targeted interventions, and community engagement strategies to ensure equitable access to cervical cancer screening services and improve the health outcomes of rural women globally” Study may be needed to explore barriers among female in rural areas. Why Author selected Puducherry which is one of the urban Union Territory of India? There seems to a lot of reporting bias and This statement make no sense \"Public transport one-way fares exhibit a wide range, spanning from 20 INR to 79,999 INR.\" 70,000 is a lot of cost for public transport in India. Data need to cleaned (check for outliers and validation before analysing it). How was the data quality ensured? It needs to be added. The analysis and variables are not well though of. There needs a detail description of how the economic related variables were collected and analysed. Most of the variables seem to be correlated in table 7. Distance from facility will be co-related with traveling time and cost of traveling. this is obvious. Having a companion significant increase the cost. this is obvious too, hardly a finding Why local ethical board not consulted for the study? Why the first author is not from India or Puducherry where the study was performed. Conclusion is also generic and does not add any value to the research on HPV screening.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "347336",
"date": "29 Jan 2025",
"name": "Shabana Tharkar",
"expertise": [
"Reviewer Expertise Epidemiology of non communicable diseases"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis research\" Demand-side barriers and economic burden in accessing Human Papillomavirus screening for cervical cancer prevention in rural India: Evidence from a cross-sectional study\" addresses an important issue of recognizing barriers to cancer screening in the rural sector of a developing country. However, only economic challenges have been addressed. The paper is well- written and the results are well-presented.\n\nMajor points\nIntroduction and rationale are acceptable but the methods need revision. Can revise methods according to STROBE Please remove outlier in Table 6, (cost of one way fare) and re -run the stats. The paper can be accepted after revision.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "13259",
"date": "04 Feb 2025",
"name": "Shyamkumar Sriram",
"role": "Author Response",
"response": "The revisions have been made according to the suggestion by Dr. Shabana Tharkar. Methods have been revised according to STROBE. Outlier has been removed in Table 6 and the statistics have been rerun. The discussion section is also updated. Thanks for the feedback and offering to accept the paper after revisions."
}
]
}
] | 1
|
https://f1000research.com/articles/13-630
|
https://f1000research.com/articles/13-628/v1
|
13 Jun 24
|
{
"type": "Software Tool Article",
"title": "sSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis",
"authors": [
"Wenjun Liu",
"Ville-Petteri Mäkinen",
"Wayne D Tilley",
"Stephen M Pederson",
"Ville-Petteri Mäkinen",
"Wayne D Tilley"
],
"abstract": "A common outcome of analysing RNA-Seq data is the detection of biological pathways with significantly altered activity between the conditions under investigation. Whilst many strategies test for over-representation of genes, showing changed expression within pre-defined gene-sets, these analyses typically do not account for gene-gene interactions encoded by pathway topologies, and are not able to directly predict the directional change of pathway activity. To address these issues we have developed sSNAPPY,now available as an R/Bioconductor package, which leverages pathway topology information to compute pathway perturbation scores and predict the direction of change across a set of pathways. Here, we demonstrate the use of sSNAPPY by applying the method to public scRNA-seq data, derived from ovarian cancer patient tissues collected before and after chemotherapy. Not only were we able to predict the direction of pathway perturbations discussed in the original study, but sSNAPPY was also able to detect significant changes of other biological processes, yielding far greater insight into the response to treatment. sSNAPPY represents a novel pathway analysis strategy that takes into consideration pathway topology to predict impacted biology pathways, both within related samples and across treatment groups. In addition to not relying on differentially expressed genes, the method and associated R package offers important flexibility and provides powerful visualisation tools.\nR version: R version 4.3.3 (2024-02-29)\nBioconductor version: 3.18\nPackage: 1.6.1",
"keywords": [
"RNA-Seq",
"pathway enrichment",
"R package",
"topology",
"KEGG",
"Reactome",
"scRNA-seq"
],
"content": "Introduction\n\nUsing pathway enrichment analysis to gain biological insights from gene expression data is a pivotal step in the analysis and interpretation of RNA-seq data, for which numerous methods have been developed (reviewed in1,2). Many existing methods tend to view pathways simply as a collection of gene names, as seen in those relying on the detection of differentially expressed genes and applying over-representation analysis (ORA) strategies, with alternative methods being those scoring all genes using functional class scoring (FCS), such as in Gene Set Enrichment Analysis (GSEA),3 arguably the most widely-used approach. However, databases such as the Kyoto Encyclopaedia of Genes and Genomes (KEGG)4 and WikiPathways5 capture not only which genes are implicated in a certain biological process but also their interactions, activating or inhibitory roles, and their relative importance within the pathway, all of which are overlooked in ORA- and FCS-based approaches.\n\nTo fully utilise this additional information, the latest generation of pathway analysis approaches include many which are topology-based such as SPIA,6 DEGraph,7 NetGSA8 and PRS,9 as well as others which explicitly model inter-gene correlations.10 Despite differences in the null hypotheses tested across these approaches, overall, they have demonstrated enhanced sensitivity and specificity due to their abilities to take gene-gene interconnections into account.11,12 Nevertheless, most topology-based methods focus only on comparing the activity of pathways between two treatment groups and cannot be used to score individual samples (Figure 1). However, in heterogeneous data where more than one factor may be influencing observations,13 incorporating scoring within paired samples may be desirable and may be able to reveal more nuanced insights. To address this gap, we present a Single-Sample directioNAl Pathway Perturbation analYsis methodology called sSNAPPY, available as an R/Bioconductor package. This article defines how sSNAPPY computes changes in gene expression within paired samples and propagates this through gene-set topologies, to predict the perturbation in pathway activities within paired samples, before providing summarised results across an entire dataset (Figure 1). The practical usage of the sSNAPPY R/Bioconductor package is illustrated through the analysis of a public scRNA-seq dataset using a pseudo-bulk approach, demonstrating its applicability to both bulk RNA-Seq and scRNA-Seq datasets.\n\nInstead of being limited to treatment-level analyses, sSNAPPY allows the detection of pathway perturbation within individual samples by using sample-specific estimates of fold-change instead of experiment-wide estimates. (Created with BioRender.com).\n\n\nMethods\n\nsSNAPPY is an R package that has been reviewed and published on the open-source bioinformatics software platform Bioconductor with all source code available via GitHub. The methodology itself is topology-based, designed to compute directional, single-sample, pathway perturbation scores for gene expression datasets with matched-pair, or nested designs (e.g. samples collected before and after treatment). Common examples of such designs may include treated vs control samples within cell-line passages, or across multiple treatments applied to tissue samples from within a specific donor. This allows for the detection of pathway perturbations within all samples from a treatment group, but also within individual samples, with sSNAPPY providing results in the form of pathway perturbation scores 1) for each set of paired samples, and 2) across all paired samples within an experimental grouping. The only data required to run sSNAPPY, is a log-transformed expression matrix (e.g. logCPM) with matching sample metadata describing treatment groups and the nested structure. It is assumed that all pre-processing has been performed beforehand, such as the exclusion of low-signal genes or normalisation to minimise technical artefacts like GC-bias.\n\nThe first step performed by sSNAPPY, is to estimate sample-specific log fold-change (δghi=μghi−μg0i) across all genes g, for each treatment h, and within each set of nested replicates i, by subtracting expression estimates for the baseline samples μg0i from those in treatment group h. It should also be noted that sSNAPPY is applicable to any number of treatment/condition levels and that sample numbers within each treatment group are not required to be balanced.\n\nIt is well known that in RNA-seq data, genes with lower expression tend to have greater variability in signal and more broadly spread estimates of change.14 As such, we utilise a gene-level weighting strategy to down-weight fold-change estimates for low-abundance genes prior to passing these estimates to sSNAPPY. Gene-level weights wg are obtained in a treatment-agnostic manner by fitting a loess curve through the relationship between observed gene-level variance (σg2) and average signal (μ¯g)(Figure 2), and taking the inverse of the loess-predicted variance as the weight wg=a/f(μ¯g), where f(μ¯g) is the predicted value from the loess curve and the constant a ensures ∑wg=1. We then use these globally-weighted estimates of log fold-change (δghi∗=wgδghi) in the calculation of all subsequent pathway perturbation scores.\n\nThe relationship between standard deviations and expression levels is modelled by a loess fit. Whilst standard deviations are shown for the purposes of visualisation, gene-level weights are calculated using variances at this stage of the sSNAPPY algorithm.\n\nsSNAPPY extends the topology-based scoring algorithm initially proposed in SPIA6 which propagates fold-change estimates from genes considered as differentially expressed through pathway topologies, to compute a perturbation score for each pathway. In contrast to SPIA, which relies on a defined set of differentially expressed genes, sSNAPPY uses fold-change estimates from all detected genes. By modifying the algorithm to incorporate single-sample, weighted estimates of fold-change, we are able to numerically represent changes in a pathway within a given sample, and subsequently model these across all samples within a treatment group. Thus, we define the single-sample perturbation score (Ship) for a given pathway p and treatment h for a set of nested samples i:\n\n• Gp represents the set of genes in pathway p, such that g∈Gp\n\n• Sghip is the gene-, treatment- and sample-specific perturbation score for pathway p\n\n• δghi∗=wgδghi is the weighted log fold-change of gene g as described above\n\n• Ugp is the subset of Gp containing only the genes directly upstream of gene g, and not including gene g\n\n• βgg′p is the pair-wise gene-gene interactions6 encoded by the topology matrix for genes g and g′∈Ugp\n\n• Ngp is the number of downstream genes from any gene g\n\n• Ship is the accumulated pathway perturbation score for pathway p in treatment h within sample i across all genes in the pathway\n\nTo scale single-sample pathway perturbation scores (Ship) so they are comparable across pathways, and to test for significance of individual scores, null distributions of perturbation scores for each pathway are generated through a sample permutation strategy, which retains any existing correlation structures between genes within a pathway. During permutation, all sample labels are randomly shuffled and permuted pseudo-pairs formed from the re-shuffled labels. Single-sample fold-changes are then calculated for each pseudo-pair of permuted samples while the rest of the scoring algorithm remains unchanged. The median and median absolute deviation (MAD) are calculated from the set of permuted perturbation scores within each pathway and used to normalise the raw perturbation scores to robust Z-scores, i.e. Zhip.\n\nAll possible permuted pseudo-pairs are sampled unless otherwise specified, such that in an experiment with I total samples, the maximum number of unique permuted pairs is P=I!(I−2)!=I×(I−1). Permutation p-values are calculated for each Ship value, indicating the approximate significance of pathway perturbation at the single-sample level. Relying on symmetry around zero, these are derived by assessing the proportion of permuted scores with absolute values as extreme, or more extreme, than the absolute value of test perturbation score within each pathway.15 Since the smallest achievable permutation p-value is 1/P, accurate estimation of small p-value requires a large number of permutations that is only feasible in data with a large sample size. As a guideline, GSEA recommends a minimum of 7 samples in each treatment group for utilizing their phenotype permutation approach,16 and under sSNAPPY this would yield P = 182 unique permuted pseudo-pairs and minimal permutation p-values of p≥0.0055at each individual sample and pathway-level.\n\nApart from assessing whether a pathway’s activity is changed significantly within an individual sample, an important question may be the detection of changes in pathway activity across all samples within a treatment. This can be performed by modelling Zhip values using regression models and incorporating Smyth’s moderated t-statistic17 as implemented in limma.18 The single-sample nature of sSNAPPY’s pathway perturbation scores is particularly helpful for datasets with complex experimental designs or known confounding factors as these can also be incorporated into the final regression models.\n\nThe Bioconductor package graphite19 provides functions that can be used to retrieve pathway topologies from a database and convert topology information to adjacency matrices. To streamline this process, we have implemented a convenience function, where users only need to provide the name of the desired database and species to retrieve all topology information in the format required by the scoring algorithm with the correct type of gene identifiers (i.e. EntrezID). Importantly, we noted that graphite19 retrieves topology matrices in varied orientations from different databases; in KEGG pathways, columns represent downstream relationships, whereas in Reactome and WikiPathway, columns indicate upstream regulation. However, this discrepancy is not taken account of in the runSPIA() function of graphite. We resolve the issue by transposing the topology matrices retrieved from the Reactome and WikiPathway as part of our convenience function.\n\nThe package has been tested on all operating systems, requiring R > 4.3.0, and can be installed using BiocManager as follows.\n\n\nUse cases\n\nThe set of additional required packages for this workflow can be installed using\n\nOnce installed, the complete set of packages can be loaded into the session.\n\nRetrieving pathway topology information from a chosen database is the next key step required during preparation for running sSNAPPY, and this is the only step requiring internet access. If running on an HPC cluster where internet access may be restricted, this step can be performed separately with topologies saved by the user as an RDS object. Using the Reactome database20 in this workflow, the retrieved topology information will be stored as a list where each element corresponds to a pathway and the numbers in the matrices encode gene-gene interactions.\n\nIn addition to downloading topology matrices for all pathways, it is also possible to provide a restricted set of keywords for a targeted analysis. For example, passing the argument keyword = c(\"metabolism\", \"estrogen\") would only return the subset of pathways which match either of these keywords. Multiple databases are also able to be searched by passing a vector of database names to the database argument.\n\nTo demonstrate the application of sSNAPPY, we used pre-processed counts from a publicly available scRNA-seq dataset, retrieved from Gene Expression Omnibus (GEO) with accession code GSE165897. This dataset consists of 11 high-grade serous ovarian cancer (HGSOC) patient samples taken before and after chemotherapy.21 sSNAPPY was used to re-analyse data from the epithelial cells as they were the primary focus of the original study. Since sSNAPPY was designed primarily for bulk RNA-seq data, counts from epithelial cells within the same samples were first summed into pseudo-bulk profiles, giving rise to a total of 22 samples. We considered a gene detectable if we observed >1.5 counts per million in ≥ 11 of the 22 samples, ideally representing all samples from a complete treatment group. 11,101 (33.8%) of the 32,847 annotated genes passed this selection criteria and were included for downstream analyses. Conditional quantile normalisation22 was then applied to mitigate potential biases introduced by gene length and GC content. The normalised logCPM matrix of the processed dataset and sample metadata can be downloaded from here.\n\nTo begin running the sSNAPPY workflow, we first load our expression matrix and define our sample-level metadata. Importantly, the row names of the expression matrix must be specified as EntrezGene IDs, for compatibility with pathway databases. Genes without EntrezGene IDs were excluded during pre-processing, leaving 10,098 genes in the example expression matrix. The treatment column within our metadata is expected to be a factor, with the reference level interpreted as the control treatment.\n\nTo compute the single-sample fold-changes (i.e. logFC) required for the set of perturbation scores, samples must be ‘matched pairs’ or nested, as discussed earlier, and treatments performed within each patient represents the nesting structure in this dataset. The factor (patient_id) defining the nested structure is passed to weight_ss_fc() using the groupBy parameter.\n\nThe output of weight_ss_fc() is a list where one element is the matrix of weighted single-sample fold-changes (δghi∗), with rows corresponding to genes and columns to samples, and the other element is the vector of gene-wise weights (wg) used to calculate the weighted log fold-change (δghi∗). By default, the string ENTREZID: is added to all row names of the δghi∗ matrix to be compatible with the format Reactome pathway topologies are retrieved in.\n\nThe matrix of δghi∗ values is then passed to pathway topologies to compute gene-wise perturbation scores for all genes within a pathway, before being summed into a single score for each pathway. The function raw_gene_pert() returns an initial list, with each element containing the gene-level perturbation scores for a given pathway. These matrices are also able to be used during downstream analysis to identify which genes play the most significant roles in each pathway, as demonstrated in later sections. Pathway-level perturbation scores (Ship) are then returned as a data.frame containing sample and gene-set names after calling pathway_pert(). Pathways with zero perturbation scores across all genes and samples are automatically dropped at this step. In addition, pathways with aggregated pathway-level scores of zero in all samples will also be dropped by default, unless otherwise specified through the drop parameter of the pathway_pert() function.\n\nThe range of Ship values obtained from the complete set of pathways will vary greatly, due to the variability in topology structures. To determine the significance of individual scores and transform scores to ensure they are comparable across pathways, sSNAPPY utilises a sample-permutation strategy to estimate the null distributions of perturbation scores and derive Zhip scores. Since sample labels will be permuted randomly to put samples into pseudo-pairs, sample metadata is not required by the generate_permuted_scores function. All possible random pairs between samples will be sampled unless otherwise specified. In this example dataset with a total of 22 samples, the full set of 462 (i.e. P=22×21) permuted scores will be computed for each pathway.\n\nApart from pathways whose permuted perturbation scores are consistently zero, and which will be dropped by default, the empirical distributions of remaining pathways are expected to be approximately normally distributed with mean μ=0, but with the scale of distributions heavily impacted by both the number of genes within each pathway and the overall topology. To demonstrate this, we randomly selected 6 pathways to demonstrate their quantile-quantile (q-q) plot and visualised the distributions of their permuted perturbation scores as boxplots (Figure 3).\n\nAll sampled empirical distributions are approximately normally distributed with a mean of zero.\n\nThe distributions obtained from label permutations are then used to convert each pathway-level score into the robust Zhij-score using the function normalise_by_permu(). Two-sided p-values for individual scores are computed based on how extreme test scores are in comparison to permuted scores for each pathway and corrected for multiple testing using any of the available methods, returning the FDR-adjusted values by default. In our example data, no pathways would be considered as significantly perturbed at the single-sample level using an FDR adjustment with α = 0.05.\n\nA key question of interest in our example dataset is to identify which biological processes were impacted by chemotherapy across the entire group of patients. Using the sample-level output obtained above, we can explore this by applying t-tests or regression models across all samples. In order to minimise spurious results, Smyth’s moderated t-statistics17 can be applied across the complete dataset, with a constant variance assumed across all pathways, given that we are using Z-scores. To perform this analysis, Zhip values were converted to a matrix and standard limma methodologies were used. For our use case here, where only one treatment group is present, no design matrix is required, and a simple t-test is appropriate.\n\n121 out of the 1094 tested Reactome pathways have an FDR < 0.05 in the moderated t-test, and were considered to be significantly perturbed at the group level. Table 1 presents the top 10 significantly inhibited and activated pathways, along with their predicted direction of change.\n\nFor enrichment analysis in the original study,21 unsupervised clustering was performed on all cells labelled as cancer cells. Clusters were then annotated manually by performing pathway enrichment testing on cluster marker genes. Two clusters, associated with proliferative DNA repair signatures and stress-related markers, contained significantly higher numbers of post-chemotherapy cells than pre-treatment ones.21 The representative pathways enriched in the stress-associated cluster were IL6-mediated signaling events, TNF signaling pathway, and cellular responses to stress, and the other post-chemotherapy cell dominated cluster in the original study was enriched for pathways associated with cell proliferation and DNA repair, such as the Cell cycle, DNA repair, Homology directed repair (HDR) through homologous recombination, and the Fanconi anaemia pathway.\n\nWhilst the published enrichment analysis was performed using ConsensusPathDB,23 in order to use pathway topologies we chose the Reactome set of pathways.20 sSNAPPY not only detected many significant perturbed pathways that are highly concordant with the pathways reported to be enriched in the original study but also includes an expected direction of change in activity. For example, the DNT repair pathway SUMOylation of DNA damage response and repair proteins pathway was predicted to be significantly inhibited by chemotherapy. The single-sample nature of the sSNAPPY output also provides great flexibility: apart from considering all treated samples as biological replicates, users may elect to perform an analysis incorporating other phenotypic traits which may impact a patient’s responses to chemotherapy, such as disease stages or tumour grades. To perform this step using the moderated t-statistic strategy and extend the above analysis, an appropriate design matrix is the only additional requirement for model-fitting, or alternatively, samples may be subset as may be appropriate.\n\nA valuable feature of sSNAPPY is the provision of several visualisation functions to assist in the presentation and interpretation of results. Biological pathways are not independent of each other with many genes playing a role across multiple pathways, and as such, viewing pathway analysis results as a network can be a powerful way to intuitively summarise the results and facilitate interpretation of the underlying biology. The plot_gs_network() function allows users to easily convert a list of relevant biological pathways to a network where edges between pathway nodes represent overlapping genes. Defined by the colorBy parameter, pathway nodes can be coloured by either the predicted direction of change or by significance levels (Figure 4). The returned plot is a ggplot224 object, meaning that components of the plotting theme and other parameters can be customized as for any other ggplot2 objects.\n\nIn the following example, we’ll inspect the 10 most significantly inhibited and 10 most significantly activated pathways, which involved four steps to prepare the data: 1) rename the logFC column to reflect the true meaning of the value and, 2) create a categorical variable with the pathway status, 3) transform p-values for simpler visualisation and 4) obtain a subset of pathways to visualise.\n\nEach node represents a significantly perturbed Reactome pathway, with nodes coloured by (A) predicted direction of change and (B) -log10(p). The 10 most significantly inhibited and 10 most significantly activated pathways are shown.\n\nAn advantage of visualising pathway analysis results using network structures is that it allows the identification of highly connected pathways (Figure 4). To summarise related pathways and further enable interpretation, we can apply community detection25 to group related pathways into ‘communities’. sSNAPPY’s plot_community() function is a “one-stop shop” for applying a community detection algorithm of the user’s choice to the network structure and annotating identified communities by the most common pathway category, denoting the main biological processes perturbed in that community. The most recent categories for both KEGG and Reactome databases were curated from their respective website (KEGG website & Reactome website) and included as parts of sSNAPPY. Analyses involving other pathway databases may require user-provided pathway categories. When the information about pathway categorisations is available, annotation of pathway communities is automatically completed. In the current dataset, the Louvain method was applied to the network of biological pathways and revealed five primary communities: 1) Adaptive Immune System; 2) Cell Cycle, Mitotic; 3) Chromatin modifying enzymes & Epigenetic regulation of gene expression; 4) Post-translational protein modification and 5) The citric acid (TCA) cycle and respiratory electron transport (Figure 5). The largest community formed was the Adaptive Immune System pathway, indicating a clear immune-signalling aspect to these results.\n\nThe Louvain algorithm was applied to detect community structures, revealing biological processes associated with highly ranked pathways. The top 20 which were the most perturbed by chemotherapy are shown.\n\nA key advantage of sSNAPPY is that it does not require the prior identification of differentially expressed genes, as this is a common challenge faced within clinical datasets. However, knowing which genes are implicated in the perturbation of pathways, particularly those which influence multiple pathways, can provide valuable insights for hypothesis generation and the underlying biological mechanisms. Therefore, sSNAPPY provides another visualisation feature called plot_gs2gene, which enables the inclusion of select genes from each pathway using network structures. Users can provide a vector of fold-change estimates to visualise genes within pathways, showing their estimated change in expression. As pathways often include hundreds of genes, it is recommended to filter for genes most likely to be playing a significant role. In this example dataset, only genes within the top 500 when ranking by the magnitude of the mean ssFC were included (Figure 6). An alternative strategy will be to select genes based on test-statistics, however, this decision is up to the individual researcher.\n\nSince Reactome pathway topologies were retrieved using EntrezIDs, users can provide a data.frame mapping EntrezIDs to their chosen identifiers, such as gene names, through the mapEntrezID parameter, in order to make the visualisations more informative. A data.frame converting EntrezIDs to Ensembl gene names was derived from the Ensembl Release 10126 and has been made available as part of the package and serves as a helpful template for future mapping operations by users.\n\nSignificantly perturbed Reactome pathways identified among post-chemotherapy samples using sSNAPPY, showing any genes in the top 500 ranked by magnitude of change in expression, and which pathways they are likely contributing to. Only the 10 most significantly inhibited and 10 most significantly activated pathways are shown.\n\nTo further investigate a specific pathway and elucidate which are the key genes contributing to the final perturbation score, we can generate a heatmap via plot_gene_contribution() which shows the gene-level perturbation scores for the top-ranked members of a given pathway. This function takes advantage of the plotting capabilities of the pheatmap package,27 and as such, other annotations are also able to be easily included, such as patient response, or which general ranges the pathway-level normalised Z-Scores are in. Inclusion of the Z-Scores enabled the assessment of the level of perturbation predicted in each sample and key genes involved (Figure 7).\n\nAll pathway genes were ranked by average contribution to the perturbation score to select the top 10 genes. Samples were annotated by patient chemotherapy response score (CRS), along with the range for sample-level Z-scores as a guide to sample-specific pathway perturbation. The genes CDCA8, TOP2A, UBE2I, BIRC5 were identified as possible key drivers of inhibition for this pathway.\n\nFrom this heatmap we can identify four candidate genes which are likely to be making a contribution to the inhibition of the SUMOylation of DNA replication proteins pathway upon chemotherapy, such as CDCA8, TOP2A, UBE2I, BIRC5 (Figure 7). These four genes are all associated with tumour progression and invasiveness and have been studied in the context of ovarian cancer. Both ubiquitin conjugating enzyme E2I (UBE2I) and cell division cycle associated 8 (CDCA8) genes have been identified as oncogenes in numerous cancer types, including ovarian cancer.28,29 Notably, in ovarian cancer, elevated UBE2I expression has been associated with poorer clinical outcomes.30 Similarly, BIRC5 encodes a protein which is also a predictor of inferior ovarian cancer patient outcome.31 Lastly, Topoisomerase IIα (TOP2A), which encodes DNA topoisomerase, has been identified as a gene that promotes the tumorigenesis of HGSOC tumours.32 Aligning with the report by Chekerov et al.33 that expression of TOP2A in ovarian tumour cells decreases as a response to chemotherapy,33 the median single-sample logFC of TOP2A was negative among the HGSOC post-chemotherapy samples included in this study (Figure 8). The other three selected potential driver genes (CDCA8, UBE2I, and BIRC5) also had negative median single-sample logFC in post-chemotherapy samples (Figure 8). Considering the implication of these four genes in ovarian cancer, decreases in their expression after chemotherapy treatment potentially indicate a favorable response to therapy.\n\nBy annotating the heatmap of gene-wise perturbation scores with patient chemotherapy response score (CRS), we also noted that the strongest inhibition of the SUMOylation of DNA replication proteins pathway was in the patient with the highest CRS score of 3 (i.e sample EOC443). CRS is an indicator of the relative length of progression-free survival after chemotherapy, where a score of 3 represents the longest survival. Hence inhibition of the SUMOylation of DNA replication proteins pathway might mediate favorable response to chemotherapy in ovarian cancer patients. We acknowledge that our analysis was limited to a small number of patients, which restricts the generalizability of the results. However, despite this limitation, these findings underscore the strength of sSNAPPY as a valuable tool for hypothesis generation not otherwise possible. Not only can sSNAPPY predict directional pathway perturbations, but it also enables the identification of potential driver genes which are strongly associated with these perturbations.\n\nSingle-sample logFC (ssFC) of potential key genes driving the inhibition of “SUMOylation of DNA replication proteins” pathway as a response to chemotherapy in HGSOC tumours.\n\nWe also performed pathway analysis on this example dataset using three other methods to compare their performance against sSNAPPY. Details on the implementation of those methods and the comparisons performed are available at 10.5281/zenodo.10127829. We initially performed an analysis using SPIA.6 However, SPIA relies on differentially expressed genes and given that only 49 genes were identified in our analysis using conventional differential expression analysis, no pathways were considered to be significant using SPIA. Additionally, we also performed pathway analysis on this example dataset using two non-topological-based approaches: 1) GSEA3 using ranking statistics derived from differential expression analysis and 2) the fast version of rotation gene set testing for linear models (roast)34 fry, neither of which rely on the presence of differentially expressed genes, Importantly, both methods test for signal within genes at either the up-regulated, or down-regulated extremes. Of the 219 gene sets considered associated with down-regulated genes by GSEA, 61 were considered as inhibited using sSNAPPY. Similarly, of the 21 pathways considered as associated with up-regulated genes by GSEA, 5 were considered as activated using sSNAPPY. GSEA produced a further 173 gene-sets not detected by sSNAPPY, whilst sSNAPPY produced an additional 54 pathways of interest.\n\nAnalysis using fry yielded 117 pathways associated with down-regulated genes, with sSNAPPY considering 36 of these as inhibited. However, 5 pathways classified as inhibited under fry were considered as activated under sSNAPPY, highlighting that down-regulation of some genes may lead to activation of a pathway, which is vital information not available under fry. Similarly, for the 13 pathways associated with up-regulation under fry, two were considered activated by sSNAPPY, with one considered inhibited. A further 88 pathways were detected as being of interest under fry, without being considered as activated or inhibited by sSNAPPY, with 77 pathways uniquely detected under sSNAPPY.\n\n\nDiscussion\n\nIn conclusion, we have presented and provided a demonstration for the R/Bioconductor package sSNAPPY which offers a novel single-sample pathway perturbation testing approach, tailored for heterogeneous tissue samples where experiments are performed using a matched-pair design. In contrast to many common enrichment methods, sSNAPPY uses pathway topology information to compute perturbation scores which indicate the likely impact on the activity of a pathway, by predicting direction of change and enabling deeper characterisation of biological responses. By applying sSNAPPY to a public scRNA-seq data collected before and after HGSOC patients were subjected to chemotherapy, we demonstrated its ability to detect significant pathway perturbations of various interesting biological processes consistent with, and far beyond what was shown in the original study. Whilst initially conceived for bulk-RNA studies, this demonstration has also provided clear applicability to scRNA datasets when using using pseudo-bulk approaches sSNAPPY addresses the limitations of alternative strategies which fail to account for gene-gene interactions encoded by pathway topologies and are unable to predict the direction of pathway activities, nor the cumulative effect of expression change across multiple genes. In addition, the single-sample nature of the method can be utilised to address the increasing demand for personalised medicine. Through identifying shared and divergent responses between individuals, sSNAPPY can provide valuable insights into the heterogeneous responses across clinical samples. Overall, we believe sSNAPPY represents a valuable addition to the existing body of pathway analysis methods.\n\n\nEthics and consent\n\nEthical approval and consent were not required.\n\n\nAuthor contributions\n\nWL’s contributions include Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Software, Validation, Visualisation, Writing - Original Draft Preparation, and Writing - Review & Editing. VM was involved with Conceptualization, Methodology and Writing - Review & Editing. WDT contributed to Writing - Review & Editing. SMP’s contributions include Conceptualization, Methodology, Project Administration, Software, Supervision, Writing - Original Draft Preparation, and Writing - Review & Editing.",
"appendix": "Data availability\n\nThe processed dataset used in this manuscript, along with the code used for data preparation is available at https://doi.org/10.5281/zenodo.10867706.\n\nRaw data was obtained from Gene Expression Omnibus: Longitudinal single-cell RNA-seq data of metastatic ovarian cancer. Accession GSE165897; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165897. 21\n\n\nReferences\n\nMaleki F, Ovens K, Hogan DJ, et al.:Gene set analysis: Challenges, opportunities, and future research.Front. Genet.2020; 11: 654. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMubeen S, Tom Kodamullil A, Hofmann-Apitius M, et al.:On the influence of several factors on pathway enrichment analysis.Brief. Bioinform.2022; 23(3): bbac143. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSubramanian A, Tamayo P, Mootha VK, et al.:Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles.Proc. Natl. Acad. Sci. USA.2005 Oct; 102(43): 15545–15550. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOgata H, Goto S, Sato K, et al.:KEGG: Kyoto Encyclopedia of Genes and Genomes.Nucleic Acids Res.1999 Jan; 27(1): 29–34. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartens M, Ammar A, Riutta A, et al.:WikiPathways: Connecting communities.Nucleic Acids Res.2021 Jan; 49(D1): D613–D621. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTarca AL, Draghici S, Khatri P, et al.:A novel signaling pathway impact analysis.Bioinformatics.2009 Jan; 25(1): 75–82. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJacob L, Neuvial P, Dudoit S:More power via graph-structured tests for differential expression of gene networks.Ann. Appl. Stat.2012 Jun; 6(2): 561–600. Publisher Full Text\n\nMa J, Shojaie A, Michailidis G:Network-based pathway enrichment analysis with incomplete network information.Bioinformatics.2016 Jun; 32(20): 3165–3174. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbrahim MAH, Jassim S, Cawthorne MA, et al.:A topology-based score for pathway enrichment.J. Comput. Biol.2012 May; 19(5): 563–573. PubMed Abstract | Publisher Full Text\n\nWu D, Smyth GK:Camera: a competitive gene set test accounting for inter-gene correlation.Nucleic Acids Res.2012 May; 40(17): e133–e133. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen TM, Shafi A, Nguyen T, et al.:Identifying significantly impacted pathways: A comprehensive review and assessment.Genome Biol.2019 Oct; 20(1): 203. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMa J, Shojaie A, Michailidis G:A comparative study of topology-based pathway enrichment analysis methods.BMC Bioinformatics.2019 Dec; 20(1): 546. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHänzelmann S, Castelo R, Guinney J:GSVA: Gene set variation analysis for microarray and RNA-Seq data.BMC Bioinformatics.2013 Dec; 14(1): 7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaw CW, Chen Y, Shi W, et al.:Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.Genome Biol.2014; 15(2): R29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKnijnenburg TA, Wessels LFA, Reinders MJT, et al.:Fewer permutations, more accurate P-values.Bioinformatics.2009 May; 25(12): i161–i168. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGene set enrichment analysis (GSEA) User Guide.Reference Source\n\nSmyth GK:Linear models and empirical bayes methods for assessing differential expression in microarray experiments.Stat. Appl. Genet. Mol. Biol.2004 Feb; 3(1): 1–25. PubMed Abstract | Publisher Full Text\n\nRitchie ME, Phipson B, Wu D, et al.:limma powers differential expression analyses for RNA-sequencing and microarray studies.Nucleic Acids Res.2015 Apr; 43(7): e47. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSales G, Calura E, Cavalieri D, et al.:Graphite - a Bioconductor package to convert pathway topology to gene network.BMC Bioinformatics.2012 Dec; 13(1): 20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGillespie M, Jassal B, Stephan R, et al.:The reactome pathway knowledgebase 2022.Nucleic Acids Res.2021 Nov; 50(D1): D687–D692. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang K, Erkan EP, Jamalzadeh S, et al.:Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer.Sci. Adv.2022 Feb; 8(8): eabm1831. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHansen KD, Irizarry RA, Wu Z:Removing technical variability in RNA-seq data using conditional quantile normalization.Biostatistics.2012 Apr; 13(2): 204–216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKamburov A, Stelzl U, Lehrach H, et al.:The ConsensusPathDB interaction database: 2013 update.Nucleic Acids Res.2012 Nov; 41(D1): D793–D800. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWickham H:ggplot2: Elegant Graphics for Data Analysis.New York, NY:Springer New York;2009. Publisher Full Text\n\nNewman MEJ, Girvan M:Finding and evaluating community structure in networks.Phys. Rev. E.2004 Feb; 69(2): 026113. Publisher Full Text\n\nCunningham F, Allen JE, Allen J, et al.:Ensembl 2022.Nucleic Acids Res.2021 Nov; 50(D1): D988–D995. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKolde R:Pheatmap: Pretty heatmaps.2019.Reference Source\n\nDong M, Pang X, Xu Y, et al.:Ubiquitin-Conjugating Enzyme 9 Promotes Epithelial Ovarian Cancer Cell Proliferation in Vitro.Int. J. Mol. Sci.2013 May; 14(6): 11061–11071. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQi G, Zhang C, Ma H, et al.:CDCA8, targeted by MYBL2, promotes malignant progression and olaparib insensitivity in ovarian cancer.Am. J. Cancer Res.2021; 11(2): 389–415. PubMed Abstract\n\nZou R, Xu H, Li F, et al.:Increased expression of UBE2T predicting poor survival of ovarian cancer: Based on bioinformatics analysis of UBE2s, clinical samples and the GEO database.DNA Cell Biol.2021; 40(1): 36–60. PubMed Abstract | Publisher Full Text\n\nGąsowska-Bajger B, Gąsowska-Bodnar A, Knapp P, et al.:Prognostic Significance of Survivin Expression in Patients with Ovarian Carcinoma: A Meta-Analysis.J. Clin. Med.2021 Feb; 10(4): 879. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGao Y, Zhao H, Ren M, et al.:TOP2A Promotes Tumorigenesis of High-grade Serous Ovarian Cancer by Regulating the TGF-β/Smad Pathway.J. Cancer.2020; 11(14): 4181–4192. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChekerov R, Klaman I, Zafrakas M, et al.:Altered Expression Pattern of Topoisomerase II, in Ovarian Tumor Epithelial and Stromal Cells after Platinum-Based Chemotherapy.Neoplasia.2006 Jan; 8(1): 38–45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu D, Lim E, Vaillant F, et al.:ROAST: Rotation gene set tests for complex microarray experiments.Bioinformatics.2010; 26: 2176–2182. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "292642",
"date": "04 Jul 2024",
"name": "Dario Strbenac",
"expertise": [
"Reviewer Expertise Statistical Bioinformatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nsSNAPPY in a Bioconductor package for directional pathway analysis. Having been accepted into Bioconductor, the package code and documentation is already known to be of good quality. Mathematical formulas are clear and the variables are all defined. However, the first step has an unfavourable user experience.\nI ran retrieve_topology(database = \"reactome\", species = \"hsapiens\") but nothing happened for about half an hour and there were no progress nor error messages. I tried both a Windows 11 personal computer and a university-managed Linux server. Eventually, the function appears to complete successfully, albeit with a list of warnings of unknown consequence but seemingly ominous:\n> head(warnings(), 3) Warning messages: 1: In FUN(X[[i]], ...) :\n\nthe conversion lost all edges of pathway \"Uncoating of the HIV Virion\" 2: In FUN(X[[i]], ...) :\n\nthe conversion lost all edges of pathway \"Plus-strand DNA synthesis\" 3: In FUN(X[[i]], ...) :\n\nthe conversion lost all edges of pathway \"Virus Assembly and Release\"\nIf the user runs the command again, it takes a long time, instead of being cached to disk the first time and loaded near-instantly the second. This part of the analysis could benefit from BiocFileCache.\nGeneration of Figure 3 involves a lot of ggplot2 coding for quality control plots which seems generally useful. Perhaps this should be a reusable function that package users could concisely write in their own R Markdown files. Similarly, Figure 4 involves four steps which could be encapsulated into a package function for better reusability.\nIn terms of the Introduction, perhaps Pengyi Yang et al.(2014 [ref - 1]) Direction Pathway Analysis of Large-scale Proteomics Data Reveals Novel Features of the Insulin Action Pathway, Bioinformatics should be discussed, and limitations noted.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
},
{
"id": "297693",
"date": "18 Jul 2024",
"name": "Panagiotis Moulos",
"expertise": [
"Reviewer Expertise bioinformatics",
"clinical bioinformatics",
"transcriptomics",
"genetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present sSNAPPY, a Bioconductor package for the interesting research field of determining expression changes in whole pathways given the topology, instead of only identifying over-represented gene groups with multiple functionalities. They also extend the case by taking into account individual samples instead of summarized conditions, as done in previous work.\nOverall, the article is well-written with well-described mathematical formulas and notation. The concept is well-presented and documented. However, as individual-sample based analysis does not take into account replication, it would be beneficial if the authors would elaborate more on the issue, i.e. elaborate more on the theoretical foundations of their permutation strategy.\nRegarding the package itself, if accepted to Bioconductor there has already been a thorough review involving multiple code quality and consistency checks as well as testing, therefore there are no objections in this part. However, the authors should justify further their selection of a scRNA-Seq dataset instead of a bulk RNA-Seq one, as also stated in p. 6.\nCode related remarks: - To make the example more easily reproducible, code in the beginning of p. 7 should include downloading and renaming (if required) logCPM.tsv - retrieve_topology takes too much time. Maybe the authors could create a resource and submit as a different package to Bioconductor. Also, I got warnings while executing, the message is not very clear. - genePertScore, ssPertScore: numbers are not fully reproducible (Ubuntu 22.04, R 4.3.2), it should be made clear by the authors that the examples in the paper could be dependent on R version and other package versions\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-628
|
https://f1000research.com/articles/12-706/v1
|
20 Jun 23
|
{
"type": "Case Report",
"title": "Case Report: Concomitant presence of two STIs in a male patient",
"authors": [
"Kaveri Rusia",
"Bhushan Madke",
"Yash Kashikar",
"Bhushan Madke",
"Yash Kashikar"
],
"abstract": "Background: The spirochaete Treponema pallidum subsp. pallidum, which causes the infectious disease syphilis, can be spread through sexual contact or perinatal transmission. In recent years, cases of syphilis have increased, especially among individuals engaging in behaviour that makes them more vulnerable (condomless sex and multiple sexual partners) and in men who have sex with men. Condylomata acuminata (external genital warts) is one of the most common viral sexually transmitted infections (STIs). Individuals who are behaviourally vulnerable are also highly prone to be exposed to one or more STIs. Our case exemplifies the occurrence of two STIs in a young man who was behaviourally vulnerable to acquiring STIs. Case: We report a case of a 21-year-old year old heterosexual man presenting with concomitant primary syphilis and genital warts. He presented with a painless genital ulcer and warty growths on his glans penis. Examination showed a painless indurated ulcer and multiple genital warts. Serology was positive for quantitative serological disease research laboratory test (1:16 titre). The patient was diagnosed with two concomitant STIs. He was treated as per the latest Centers for Disease Control and Prevention (CDC) guidelines for primary syphilis and podophyllin resin for genital warts. After four weeks, the genital ulcer showed complete healing and there was a significant reduction of genital warts. Conclusions: Individuals with multiple sexual partners engaging in sexual activity without the use of prevention tools are at a greater chance of acquiring two or more STIs. To reduce concomitant transmission, preventive measures against genital ulcer diseases caused by human papilloma virus, syphilis, herpes, and chancroid, such as early identification and treatment, and condom distribution, must be strengthened as part of national STI prevention. Patients with two or more STIs should be followed regularly to assess the progress of infection and should be offered timely medical treatment.",
"keywords": [
"Syphilis",
"genital warts",
"HPV",
"treponema",
"STI"
],
"content": "Introduction\n\nGenital ulcer diseases (GUDs) are breaks in the skin and mucosal continuity in the genital and perigenital region, usually resulting from sexually transmitted infections (STIs). Syphilis is a multisystemic, multistage, chronic illness with a varied prognosis and myriad of clinical presentations.1 Anogenital warts, known as Condyloma acuminatum, are one of the most common STIs in the developed world, with a frequency of 2.4 infections per 1,000 people per year.2,3 Individuals engaging in behaviour that makes them more vulnerable (sex without the use of prevention tools and multiple sexual partners) are at increased likelihood of acquiring two or more STIs. Presence of one STI increases the likelihood for acquiring another STI and our case exemplifies the aforementioned phenomenon. Our case presented with two concomitant STIs, one being bacterial and the other being viral in aetiology.\n\n\nCase report\n\nA 21-year-old male resident of Central India studying at a local college presented to the Dermatology Outpatient Department of the Datta Meghe Institute of Higher Education and Research affiliated tertiary care teaching hospital at Sawangi, Wardha, Maharashtra with complaints of a painless genital ulcer and warty growths on his penis. He reported that the warty lesions had been present for the past two months and the ulcerative lesion appeared three weeks ago. Detailed sexual history revealed regular, penile–vaginal intercourse without the use of prevention tools with sex workers (SWs) for the past six months in his home town, with the last occurrence being approximately four weeks before he presented to our hospital. His general physical examination was within normal limits. There was no history of burning micturition and pus discharge through the urethra. There was a single, painless, indurated ulcer of 3×3 cm in size with rolled edges and minimal discharge on the penis at the coronal sulcus (Figure 1). Glans penis showed cauliflower floret-like growths on the coronal sulcus and sub-preputial area of the penis (Figure 2). There was no regional lymphadenopathy. Detailed muco-cutaneous examination of the oral cavity, perianal area and palms and soles were normal. The quantitative Venereal Disease Research Laboratories (VDRL) test was reactive in the titre of 1:16, however the test for treponema pallidum haemagglutination (TPHA) was non-reactive. Serological tests for hepatitis B virus, hepatitis C virus and human immunodeficiency virus (HIV) were negative. On the basis of sexual history, temporal relation, clinical examination and serology, we made a diagnosis of concomitant STIs of primary syphilis and genital warts.\n\nWe treated the patient with office-based topical application of podophyllin resin (20% w/v) in benzoin (10% w/v) on the genital warts, while the surrounding healthy skin area was protected with petrolatum. Applications were carried out every 10 days until complete clearance of warty lesions. Primary syphilis was treated with a single intramuscular injection of benzathine penicillin (2.4 million units, 1.2 million units in each buttock) after the sensitivity test. Contact tracing is being attempted for the sexual partners for the past three months. On a follow-up visit, the lesion of primary syphilis and genital warts had completely resolved (Figure 3).\n\n\nDiscussion\n\nSyphilis is a disease caused by the bacteria Treponema pallidum that has a myriad of clinical presentations and is referred to as a “great mimicker” in clinical medicine. Immune evasion and invasiveness are two important pathogenic traits of Treponema pallidum.4–7 Wu et al.,7conducted a study where it was found that there is a higher prevalence of syphilis among individuals living with HIV, especially among men who have sex with men. The presence of one STI increases the likelihood that the individual will acquire another STI. The presence of genital ulcer disease increases the risk of acquiring HIV due to mucosal damage and the pool of inflammatory cells at the site of ulcers.7\n\nIn a study by Kops et al., it was shown that there are higher chances of acquiring human papilloma virus (HPV) if an individual has an STI.6 A history of prior STI leads to decreased clearance of HPV load and provides an easy access for viral entry into the damaged epithelial barrier. The various factors associated with increased likelihood of concomitant STIs are smoking, substance use disorder and men having sex with men.7\n\nThe presence of concomitant STIs suggests the person is behaviourally vulnerable. Individuals with multiple STIs should be investigated for the presence of other venereal transmitted diseases, particularly HIV and hepatitis B virus infection, and appropriate laboratory work-up should be done to confirm the diagnosis.\n\nThe primary take-away lesson from our case is as follows: individuals with multiple sexual partners and involved in sexual activity without the use of prevention tools are at greater chance of acquiring two or more STIs. Attempts should be made to perform partner tracing of such cases and individuals should be offered counselling and appropriate medical management. Patients with two or more STIs should be followed regularly to assess the progress of infection and should be offered timely medical treatment.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nYanofsky VR, Patel RV, Goldenberg G: Genital warts: a comprehensive review. J. Clin. Aesthet. Dermatol. 2012; 5(6): 25–36. PubMed Abstract\n\nAhmed AM, Madkan V, Tyring SK: Human papillomaviruses and genital disease. Dermatol. Clin. 2006; 24: 157–165. Publisher Full Text\n\nLuo Y, Xie Y, Xiao Y: Laboratory diagnostic tools for syphilis: current status and future prospects. Front. Cell. Infect. Microbiol. 2021; 10: 574806. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeeling RW, Mabey D, Kamb ML, et al.: Benzaken. AS. Syphilis. Nat. Rev. Dis. Primers. 2017; 3: 17073. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO'Mahony C, Gomberg M, Skerlev M, et al.: Position statement for the diagnosis and management of anogenital warts. J. Eur. Acad. Dermatol. Venereol. 2019 Jun; 33(6): 1006–1019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKops NL, Bessel M, Horvath JD, et al.: Factors associated with HPV and other self-reported STI coinfections among sexually active Brazilian young adults: cross-sectional nationwide study. BMJ Open. 2019 Jun 1; 9(6): e027438. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu Y, Zhu W, Sun C, et al.: Prevalence of syphilis among people living with HIV and its implication for enhanced coinfection monitoring and management in China: A meta-analysis. Front. Public Health. 2022 Jan 1; 10. Publisher Full Text"
}
|
[
{
"id": "235347",
"date": "15 Feb 2024",
"name": "Electra Nicolaidou",
"expertise": [
"Reviewer Expertise I am a dermatologist-venereologist with a special interest in sexually transmitted infections",
"psoriasis and vitiligo."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well written case report of a patient presenting with two concomitant STIs, syphilis and genital warts, that were typical in clinical appearance and responded well to treatment. The case is well presented. My comments are as follows: 1)The patient was treated according to the CDC guidelines for syphilis, but these guidelines were not followed for the treatment of genital warts. These guidelines state that \"podophyllin resin is no longer a recommended regimen because of the number of safer regimens available\" and that \"the area to which treatment is administered should not contain any open lesions, wounds of friable tissue\". So, the authors may want to explain why they used this treatment for the genital warts, especially in a patient with an ulcer surrounding part of the warts. 2)Abstract, Background: MSMs have high rates of syphilis because they often engage in behavior that makes them more vulnerable, so there is no need to refer to them separately. 3) Abstract, Background: \"be exposed to one or more STIs\" could be changed to \"two or more STIs\" 4) Abstract, Case: \"quantitative serological disease research laboratory test\" could be changed to \"quantitative Venereal disease research laboratory test\" 5) Abstract, Conclusions: Human papillomavirus is not correctly spelled and it does not cause genital ulcer diseases 6) Introduction: Anogenital warts are also called condylomata acuminata (not condyloma acuminatum, which is singular number) 7) Case report: \"Primary syphilis was treated with a single intramuscular injection...\" It is actually two injections, not a single one, as it is correctly described by the authors in the brackets.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "11076",
"date": "13 Apr 2024",
"name": "Kaveri Rusia",
"role": "Author Response",
"response": "Thank you for your responses. Necessary changes can be done according to your comments. I have used podophyllin as it is easily available in our setup."
}
]
},
{
"id": "266151",
"date": "07 May 2024",
"name": "Alessandra Latini",
"expertise": [
"Reviewer Expertise STIs"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper, Concomitant presence of two STIs in a male patient, by Rusia K et al describes the case of a young heterosexual student who presents with two sexually transmitted infections at the same time as ghenital warts and syphilis. The AA underline how condylomatosis is very common in sexually active young people while the epidemiology of syphilis describes higher prevalence curves in MSM and people with HIV infection. The case is well described and documented, the diagnostic and therapeutic process well described. The message that emerges is that syphilis should always be considered in the presence of another STI such as condylomatosis, even if genital warts have notoriously a high incidence in the general population. The authors also highlight the importance of HIV testing and contact tracing in at risk patients. (Ref-1). According to the ECDC, a large proportion of syphilis diagnoses in 2022 has been reported in subjects aged 45 years or older. However, while data on increasing STI rates among men who have sex with men have been increasingly reported, a scarce attention has been paid to populations with a lower sexual risk, such as heterosexual individuals. This paper considers the risk of syphilis in a heterosexual patient in line with the most recent epidemiological considerations.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-706
|
https://f1000research.com/articles/12-1156/v1
|
15 Sep 23
|
{
"type": "Research Article",
"title": "Prognostic role of tumor budding in oral squamous cell carcinoma: a retrospective study",
"authors": [
"Padmashri Kalmegh",
"Alka Hande",
"Madhuri Gawande",
"Swati Patil",
"Archana Sonone",
"Aayushi Pakhale",
"Alka Hande",
"Madhuri Gawande",
"Swati Patil",
"Archana Sonone",
"Aayushi Pakhale"
],
"abstract": "Background: Tumor budding (TB) is defined as a single cell or a cluster of up to five tumor cells at the invasion front of all oral squamous cell carcinoma (OSCC) cases. Tumor budding is considered a marker of many important events in oral carcinoma, including the epithelial-mesenchymal transition, invasion, metastasis, and for further prognosis. Methods: A total of 30 clinically and histopathologically diagnosed cases of OSCC were retrieved from the archival of the Department of Oral Pathology and Microbiology. After assessing the sections for the presence of TB, it is further categorized into high-intensity TB and low-intensity TB. Results: We found a strong association between lymph node metastasis, lymph node metastasis, and histopathological grading in the current study. There was no association between TB and a patient's survival rate. Conclusions: This study emphasizes the significance of tumor budding, its relevance to prognosis, and reproducibility, as well as the significance of its evaluation and incorporation into routine surgical pathology practice in the management of OSCC. As a result, we believe that tumor budding is a crucial factor in determining tumor behavior.",
"keywords": [
"Epithelial-mesenchymal transition",
"Histopathological marker",
"Histological evaluation",
"Invasive tumor front",
"Lymph node metastases",
"Oral squamous cell carcinoma",
"Prognosis",
"Tumor budding"
],
"content": "Introduction\n\nIn India, oral cancer contributes to two thirds of cancer cases. Oral squamous cell carcinoma (OSCC) has been categorized as the third most common malignancy and is considered a major risk factor because of increased consumption of tobacco and areca nut.1 OSCC has a low survival rate due to an early tendency to metastasize and recurrent recurrences. Therefore, early detection, correct diagnosis, and timely treatment are necessary to reduce morbidity and mortality. The invasive tumor front is the region where the most advanced layers of tumor reside, this gives the detailed prognosis of OSCC cases.2 OSCC cases are usually managed by surgery followed by postoperative radiation therapy. Although diagnostic techniques and treatment methods have improved, the mortality rates of patients with OSCC are still inadequately low with a poor survival rate of five years, challenging the current approaches of prognostic assessment. The aggressive clinical history of OSCC, which includes frequent locoregional relapses and lymph node metastasis (LNM) in more than 60% of cases, makes the prognosis uncertain.3,4 Tumor budding (TB) is the gold standard and reliable histomorphological parameter that has been studied in many cancers. TB is characterized by a dispersed invasive pattern in which epithelial tumor cells are visible at the invasive front as small clusters (up to five cells) spread throughout the stroma at different distances.5 In the 1950s, Imai et al.,6 originally described TB as “sprouting”, Gabbert et al.,7 termed this feature as “tumor dedifferentiation”. Later Morodomi et al.,8 and Hase et al.,9 coined the term “budding” as they observed the budding of undifferentiated cells and nests from larger tumor islands.1 TB is thought to represent the epithelial-mesenchymal transition (EMT), i.e., the important mechanism for the progression of epithelial cancers.10 As a result, we aimed to evaluate the importance of TB in the prognosis of OSCC in the current study.\n\nThis study aimed to perform an evaluation of TB, determine its association with various histopathological parameters, and thereby the prognosis in OSCC.\n\nThe objectives of this study were as follows: i) to assess TB in OSCC; ii) to evaluate TNM staging in OSCC; iii) to determine the association between TB with LNM in OSCC; iv) to determine the association between TB and the five year survival rate in OSCC; and v) to determine the association between TB with histopathological grade.\n\n\nMethods\n\nThe procedure that is employed the most frequently is the manual assessment of TB on hematoxylin and eosin (H&E) stained slides. For the classification of TB intensity, several authors have proposed a variety of techniques with a range of criteria. However, the technique by Wang et al.,5 from 2011, is one that is the most frequently acknowledged and used in OSCC. According to this approach, TB refers to isolated single cells or clusters of five tumor cells found at the invasive front. To locate the fields with the highest density of TB, a section is initially scanned at low power. Following this, the tumor buds are counted in a single field at a resolution of ×200 or ×20 objective. The samples are then divided into two groups: high-intensity TB (five or more buds) and low-intensity TB (five buds or fewer) or absence TB. Each section in the present study was reviewed by three observers, then by consensus to remove bias. The cases underwent follow-ups at intervals of two months. This study followed the STROBE guidelines.11\n\nDaniel formula for sample size estimation:\n\nWhere,\n\nZ2 - The level of significance at 5%\n\ni.e. 95% confidence interval =1.96\n\nP = Prevalence of OSCC in India = 80% = 0.80\n\nd = Desired error of margin = 10% = 0.10\n\nFormula Reference: Daniel et al.12\n\nThe present study was conducted from November 2022 at the Department of Oral Pathology and Microbiology, Sharad Pawar Dental College and Hospital, after receiving approval (dated, 05/10/2022) from the Institutional Ethical Committee [DMIMS (DU)/IEC/2022/292] of Datta Meghe Institute of Higher Education and Research, Sawangi (M), Wardha, Maharashtra, India. A total of 30 surgically operated cases of OSCC from the year 2010-2015 at this institute were retrieved from the archival of the department. There were 21 cases that had evaluated TB in OSCC, which included eight cases of well-differentiated squamous cell carcinoma (WDSCC), 12 cases of moderately differentiated squamous cell carcinoma (MDSCC), and one case of poorly differentiated squamous cell carcinoma (PDSCC) with their average age between 30-70 years. In order to assess the survival data, we had telephone conversations with patients or with their relatives. Informed written and verbal consent was taken from all participants involved in the study.\n\nThe histopathologically diagnosed and surgically operated cases of OSCC with various histopathological grades were retrieved from the departmental archives. The staging of the patients has been done according to the “American Joint Committee of Cancer” (AJCC) staging system.13 The cases who had undergone presurgical radiotherapy or chemotherapy, history of second primary or local and distant recurrence, and patients with any other systemic diseases and with coexisting malignancy were excluded from the study. The detailed information of the study population, including the clinical staging of the disease, comprehensive history of pertinent habits with their duration, and histopathological features such as grades of OSCC and lymph node metastasis had been noted.\n\nA chi-squared test was used to test the possible relationship between various clinicopathological variables. The statistical analysis was conducted using IBM SPSS Statistics (RRID: SCR_016479) v27.0 software, and p<0.05 is thought to be the threshold of significance. A chi-squared test, descriptive statistics, and inferential statistics were all used.\n\n\nResults\n\nEach clinical and histological feature and TB are cross-tabulated sequentially. Stromal TB was seen in each of the 21 cases. Nine out of the 21 cases (less than five tumor buds) had low-intensity TB, while 11 had high-intensity TB (more than five tumor buds) (Table 1).25 Out of 30 patients in the current study, 20 cases demonstrated an association between TB and lymph node metastases, while the other 10 cases did not (Table 2). We discovered that out of 20 cases that showed the presence of TB, 12 patients are dead and eight are alive, indicating that there is no connection between TB status and the likelihood of a patient surviving (Table 3). When compared to cases of WDSCC and PDSCC, cases of MDSCC demonstrated the presence of TB (Table 4). This finding suggests that TB can be used as a reliable histopathological parameter for early detection and diagnosis and to determine the prognosis of OSCC cases.\n\nThe H&E stained section of OSCC shows the presence of TB as indicated by the presence of cell nests containing single-cell infiltration. The invasive front of OSCC is shown by a histological investigation to have tumor buds that are spreading into the underlying connective tissue. High-intensity TB is the presence of >5 cell clusters at the invasive tumor front of the lesion (Figure 1, marked by black arrow), and low-intensity TB is the presence of <5 cell clusters at the invasive tumor front of the lesion (Figure 2, marked by black arrow).\n\nUnder (A) low power view (magnification, ×10) and (B) high power view (magnification, ×40). TB, tumor budding.\n\nUnder (A) low power view (magnification, ×10) and (B) high power view (magnification, ×40). TB, tumor budding.\n\n\nDiscussion\n\nOSCC contributes to 95% of oral cancers and predominantly metastasizes to the lymph nodes of the neck. Metastasis of cancer cells to lymph nodes i.e., positive lymph nodes (LN) is an important adverse prognostic factor for the survival of OSCC cases.14 In several studies of OSCC, TB has been recorded. Some of these studies have shown that TB is an important prognosticator of LNM, distant metastatic disease and local recurrence.15–18 Strong evidence linking TB and LNM has been established, and multivariate analysis shows that TB is associated with aggressive tumor activity and a bad prognosis in instances, suggesting that TB count can be used to gauge the risk of LNM.1,19 TB count does not require the use of any other expensive techniques or equipment because it is a simple procedure used on a daily basis with the help of H&E stained sections.15,20 TB is not a static histological feature, but it is a series of various processes occurring in an aggressive tumor with the potential to disseminate and metastasize. This biological phenomenon is a dynamic process carried out by a tumor with the potential to invade other tissues, spread and metastasize.16\n\nTB might be a sign of cells going through EMT, a process in which highly polarized epithelial cells become mobile mesenchymal cells. Therefore, EMT can be regarded as an indicating factor for invasion and subsequent metastasis.21 Metastasis can be evaluated from the increased distance of the tumor bud and reduced tumor bud size. Significantly more metastases were linked to decreased tumor bud size and increased tumor bud distance. The extent of EMT increased with the distance the tumor buds progressed. Thus, EMT has been related to poor prognostic outcomes in OSCC.22 Treatment plans and prognosis could be enhanced with precise histological grading and scoring of particular features. Sundar et al.,23 evaluated the prognostic value of TB in OSCC in 2019. They evaluated TB at the invasive tumor front in all OSCC cases. They discovered that advanced malignancies with tumor sizes larger than 4 cm exhibited high-intensity TB. They came to the conclusion that TB always manifested as an invasive front with cell infiltration in cords or groups. The fact that TB occurs before lymph node metastasis suggests that it is a reliable prognostic marker. They found a significant relationship between LNM and TB. Their research highlighted the significance of TB in the treatment of OSCC cases.23 The worst pattern of invasion (WPOI) and TB were two histological markers that were evaluated by Chatterjee et al., in 2019.17 The risk of LNM, recurrence, and death in early-stage OSCC were found to be best predicted by early detection of these characteristics. The treatment plan and outlook for OSCC are based on the tumor stage and LNM status. During the course of four and a half years, they examined the histological characteristics in 126 samples, including the histological grade, WPOI, TB, lymphovascular emboli, perineural invasion, depth of invasion, and host lymphocyte response. The findings of the study resulted in the recommendation that WPOI and TB be included in the guidelines for histopathological reporting as important risk factors for predicting LNM in all stages of OSCC and reliable prognostic markers.17 Almangush et al. (2014),15 investigated the effect of TB on prognosis in OSCC. They examined 16 studies to test this in a meta-analysis. For a better prognosis, they advised using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) criterion in histology reporting. They assessed the prognostic significance of TB in OSCC. Their research demonstrated a link between lymph node metastasis and TB. TB, which can be seen easily, is a valid prognostic indicator for OSCC and may help with individualized treatment, according to their findings.15 When compared to lymph nodes without metastasis, TB is significantly (P=0.003) associated with the presence of lymph node metastasis in our study (Tables 1 and 2), which is in accordance with previous studies by Sundar et al. (2019),23 Chatterjee et al. (2019),17 Almangush et al. (2014).15\n\nTB was examined by Joshi et al. (2020),16 as a potential predictive histopathological feature in oral squamous cell carcinoma. Overall, 30 OSCC cases from January 2018 to August 2019 were investigated. While analyzing invasive tumors, they considered both high-intensity tumor bud clusters of cancer cells and low-intensity tumor bud clusters of cancer cells. There found no evidence of a significant relationship between TB and the survival rate.16 Candanedo-Gonzalez et al. (2020),18 investigated incidences of OSCC in the tongue (TSCC), which had a susceptibility to early local spread and recurrence. They reported that TSCC at an early stage (T1/T2N0M0) is not necessarily associated with a favorable prognosis. It is essential to identify prognostic indicators that can be assessed using biopsies. They identified that the EMT, specifically in TSCC, is histologically represented by TB. As a result, they determined that TB in the TSCC was a biological marker that predicted a poor prognosis.18 The findings of our study (P = 0.59, not significant) (Table 3), demonstrated that there is no relationship between the presence or absence of TB and patient survival rates, which is in accordance with previous studies by Joshi et al. (2020)16 and Fernando Candanedo-Gonzalez et al. (2020).18\n\nNandita et al. (2016),24 investigated the contribution of TB to the diagnosis of OSCC. For this investigation, 30 histological samples of OSCC with a biopsy-proven diagnosis were chosen. They found tumor cells at the invasive front of the tumor. The number of tumor buds in which TB intensity was at its highest in the histological fields is counted. They used an independent t-test to compare prognostic variables with TB. As a result, they came to the conclusion that the relationship between TB and poor tumor differentiation, as well as its presence, could be crucial indicators to forecast the prognosis of patients with OSCC.22 Our research is consistent with that of Nandita et al. (2016).24 In the current study, we came to the conclusion that tumor buds are present in WDSCC and MDSCC at the invasive tumor front as compared to PDSCC (Table 4), suggesting the relevance of TB in early diagnosis of oral squamous cell carcinoma after assessing the existence of TB in various histological grading.\n\nThe study is limited by a small sample size, a relatively short follow-up period, and a small number of patients with available follow-up information.\n\nTB assessment serves as a potential histopathologic prognostic parameter in OSCC.\n\n\nConclusions\n\nTo conclude, tumour budding is an essential factor for determining the behaviour of tumours. TB refers to clusters of neoplastic cells at the invasive tumour front than the neoplastic cells in the primary tumour mass. TB is a frequent, repeatable, and easy-to-identify histological factor in OSCC. This study highlights the relevance of TB in prognosis as well as the significance of its evaluation and integration into the routine management of OSCC.",
"appendix": "Data availability\n\nFigshare: Short study data- Padmashri.csv. https://doi.org/10.6084/m9.figshare.22778228. 25\n\nZenodo: STROBE checklist for ‘Prognostic role of tumor budding in oral squamous cell carcinoma’. https://doi.org/10.5281/zenodo.7894541. 11\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe acknowledge the support of laboratory technicians from “Department of Oral & Maxillofacial Pathology and Microbiology”, “Sharad Pawar Dental College & Hospital”, “Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha”.\n\n\nReferences\n\nKale AD, Angadi PV: Tumor budding is a potential histopathological marker in the prognosis of oral squamous cell carcinoma: Current status and future prospects. J. Oral Maxillofac. Pathol. 2019 Sep; 23(3): 318. Publisher Full Text\n\nAngadi PV, Patil PV, Hallikeri K, et al.: Tumor budding is an independent prognostic factor for prediction of lymph node metastasis in oral squamous cell carcinoma. Int. J. Surg. Pathol. 2015 Apr; 23(2): 102–110. PubMed Abstract | Publisher Full Text\n\nWarnakulasuriya S: Global epidemiology of oral and oropharyngeal cancer. Oral Oncol. 2009 Apr 1; 45(4-5): 309–316. Publisher Full Text\n\nMassano J, Regateiro FS, Januário G, et al.: Oral squamous cell carcinoma: review of prognostic and predictive factors. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006 Jul 1; 102(1): 67–76. Publisher Full Text\n\nWang C, Huang H, Huang Z, et al.: Tumor budding correlates with poor prognosis and epithelial-mesenchymal transition in tongue squamous cell carcinoma. J. Oral Pathol. Med. 2011 Aug; 40(7): 545–551. PubMed Abstract | Publisher Full Text | Free Full Text\n\nImai T: The growth of human carcinoma: a morph anal. Fukuoka Igaku Zasshi. 1954; 45: 72–102.\n\nGabbert H, Wagner R, Moll R, et al.: Tumor dedifferentiation: an important step in tumor invasion. Clin. Exp. Metastasis. 1985 Oct; 3: 257–279. PubMed Abstract | Publisher Full Text\n\nMorodomi T, Isomoto H, Shirouzu K, et al.: An index for estimating the probability of lymph node metastasis in rectal cancers. Lymph node metastasis and the histopathology of actively invasive regions of cancer. Cancer. 1989 Feb 1; 63(3): 539–543. PubMed Abstract | Publisher Full Text\n\nHase K, Shatney C, Johnson D, et al.: Prognostic value of tumor “budding” in patients with colorectal cancer. Dis. Colon Rectum. 1993 Jul; 36: 627–635. Publisher Full Text\n\nDawson H, Lugli A: Molecular and pathogenetic aspects of tumor budding in colorectal cancer. Front. Med. 2015 Mar 10; 2: 11. Publisher Full Text\n\nKalmegh P: PROGNOSTIC ROLE OF TUMOR BUDDING IN ORAL SQUAMOUS CELL CARCINOMA (Version v1). [Dataset]. Zenodo. 2023. Publisher Full Text\n\nDaniel WW, Cross CL: Biostatistics: a foundation for analysis in the health sciences. Wiley; 2018 Nov 13.\n\nByrd DR, Brookland RK, Washington MK, et al.: AJCC cancer staging manual. Amin MB, Edge SB, Greene FL, editors. New York: springer; 2017 Jan.\n\nNorling R, Buron BM, Therkildsen MH, et al.: Staging of cervical lymph nodes in oral squamous cell carcinoma: adding ultrasound in clinically lymph node negative patients may improve diagnostic work-up. PLoS One. 2014 Mar 20; 9(3): e90360. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlmangush A, Salo T, Hagström J, et al.: Tumour budding in head and neck squamous cell carcinoma–a systematic review. Histopathology. 2014 Nov; 65(5): 587–594. PubMed Abstract | Publisher Full Text\n\nJoshi P, Pol J, Chougule M, et al.: Tumor budding–A promising prognostic histopathological parameter in oral squamous cell carcinoma–A comparative immunohistochemical study. J. Oral Maxillofac. Pathol. 2020 Sep; 24(3): 587. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChatterjee D, Bansal V, Malik V, et al.: Tumor budding and worse pattern of invasion can predict nodal metastasis in oral cancers and associated with poor survival in early-stage tumors. Ear Nose Throat J. 2019 Aug; 98(7): E112–E119. PubMed Abstract | Publisher Full Text\n\nCandanedo-Gonzalez F, Antonio OE, De JD: Tumor Budding in Oral Cavity Cancer. Breast Cancer. 2020; 5(1): 5–23.\n\nHo YY, Wu TY, Cheng HC, et al.: The significance of tumor budding in oral cancer survival and its relevance to the eighth edition of the American Joint Committee on Cancer staging system. Head Neck. 2019 Sep; 41(9): 2991–3001. PubMed Abstract | Publisher Full Text\n\nGrigore AD, Jolly MK, Jia D, et al.: Tumor budding: the name is EMT. Partial EMT. J. Clin. Med. 2016 Apr 29; 5(5): 51. Publisher Full Text\n\nChang JY, Wright JM, Svoboda KK: Signal transduction pathways involved in epithelial-mesenchymal transition in oral cancer compared with other cancers. Cells Tissues Organs. 2007; 185(1-3): 40–47. PubMed Abstract | Publisher Full Text\n\nKrisanaprakornkit S, Iamaroon A: Epithelial-Mesenchymal Transition in Oral Squamous Cell Carcinoma. ISRN Oncol. 2012 Mar 29; 2012: 1–10. Publisher Full Text\n\nSundar S: Prognostic value of tumor budding in oral squamous cell carcinoma. Eur. J. Mol. Clin. Med. 2019; 6(01): 2019.\n\nNandita KP, Boaz K, Srikant N, et al.: Tumour budding: A promising parameter in oral squamous cell carcinoma. Res. J. Pharm., Biol. Chem. Sci. 2016 Sep 1; 7(5): 2059–2063.\n\nKalmegh P: Short study data- Padmashri.csv. [Dataset]. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "248117",
"date": "07 Jun 2024",
"name": "Devendra Palve",
"expertise": [
"Reviewer Expertise Oral malignancies",
"Forensic Odontology",
"Odontogenic tumours"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article stresses on the tumour budding as a marker for prognosis in Oral Squamous cell carcinoma and checking its correlation with lymph node metastasis, TNM staging and five year survival rate. The authors have clearly presented their work that can be accessed online as well. The results have been mentioned clearly along with the statistical results. However, following parts of the article need corrections 1. In the Abstract- Result- \"We found a strong association between lymph node metastasis, lymph node metastasis, and histopathological grading in the current study.\" The message is unclear with repetition of words \"lymph node metastasis\".\n2. In Methods: \"high-intensity TB (five or more buds) and low-intensity TB (five buds or fewer)\" is not matching with grading shown under Histologic features \"High-intensity TB is the presence of >5 cell clusters and low-intensity TB is the presence of <5 cell clusters.\" The text is to be modified with correct parameters.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-1156
|
https://f1000research.com/articles/12-1563/v1
|
06 Dec 23
|
{
"type": "Case Report",
"title": "Case Report: Sebaceous carcinoma of the eyelid",
"authors": [
"Jayashree Bhawani",
"Samarth Shukla",
"Sourya Acharya",
"Sunita Vagha",
"Miheer Jagtap",
"Samarth Shukla",
"Sourya Acharya",
"Sunita Vagha",
"Miheer Jagtap"
],
"abstract": "Sebaceous carcinoma is an extremely rare malignant disease and it is more aggressive when it occurs in the eyelids and orbit. It can mimic several benign lesions, resulting in diagnostic delay. We present a case of sebaceous carcinoma in a 50-year-old male who presented with complaints of swelling of the upper eyelid, which was followed by appearance of an ulcerative growth over the eyelid. Magnetic resonance imaging (MRI) reports showed an ulcerated mass in the left periorbital and orbital region appearing heterogeneously hyperintense. Fine needle aspiration cytology (FNAC) showed malignant epithelial differentiation which was followed by exenteration of the eyeball. Histopathology showed the rare diagnosis of sebaceous carcinoma",
"keywords": [
"Sebaceous carcinoma",
"Muir- Torre syndrome",
"eyelid cancer"
],
"content": "Introduction\n\nSebaceous carcinoma originates from cutaneous sebaceous glands, gland of Zeis or the Meibomian glands.1 It is more commonly found in the Asian population.2 It has a syndromic association with Muir-Torre syndrome, with hereditary nonpolyposis colorectal cancer syndrome.3 It can occur secondary to radiation therapy for retinoblastoma.4 It clinically mimics the basal cell carcinoma or squamous cell carcinoma.5 Here, we report a case of sebaceous carcinoma of the upper eyelid on histopathology of orbital exenteration specimen.\n\nA 50-year-old male, farmer by occupation, presented with an 8-month history of an ulcerated growth over the left eye. The patient stated that the lesion started as a pea sized cystic swelling which gradually increased in size. He also gave a history of pain and maggot infestation in the same eye.\n\nRoutine investigations were performed, on ocular examination no light perception was present. Slit lamp examination of the left showed a mass of 6.3 × 3 × 1.5 cm with ulcerated appearance. Eyelashes were spared. The eyeball appeared as degenerated and distorted. On general examination no lymphadenopathy and organomegaly was noted.\n\nMRI reports showed an ulcerated mass in the left periorbital and orbital region appearing heterogeneously hyperintense on T2 and hypointense on T1 which was involving the left orbital group, adjacent intraorbital optic nerve and extraocular muscles.\n\nFine needle aspiration cytology (FNAC) was performed which showed polymorphs, lymphocytes and islands of tumor cells. These tumor cells appeared large in size, oval in shape and were arranged in groups. These cells had hyperchromatic nuclei. Cells also showed malignant epithelial differentiation.\n\nA surgical intervention named intraoperative frozen section was performed from the lesion and diagnosis suggestive of carcinoma either from sebaceous or squamous origin was made. After that, left eye exenteration was done.\n\nThe resected orbital exenteration specimen [Figure 1] was sent to histopathology. Specimen measured 6.2 × 6 × 3.5 cm. A tumor mass involving the upper eyelid extending from the medial margin measuring 5 × 2 × 1.5 cm was identified.\n\nMicroscopy showed pigmented lining epithelium. A scanner view of the section [Figure 2] also showed tumor cells arranged in lobules and sheets at places. High power view i.e. 40× showed sebaceous differentiation [Figure 3], individual tumor cells, which were polygonal in shape with scant, multivacuolated cytoplasm, it also showed round to oval, enlarged pleomorphic nuclei with 1–2 prominent nucleoli [Figure 4]. Deeper tissues showed fibro collagenous tissue, necrotic hemorrhagic tissue and infiltration by malignant cells.\n\n\nDiscussion\n\nSebaceous carcinoma is a great masquerader.6 Although sebaceous carcinoma has great tendency to arise in the ocular region, especially in the eyelids, it does occur in extraocular regions such as parotid. It accounts for 1 to 3% of malignant orbital tumors.7 Among the reported malignancies of eyelid tumors it is the third most common malignancy.8 It has a female predominance.9 The upper eyelid is affected more than the lower lid due to the abundance of meibomian glands.10 Periocular sebaceous carcinoma can clinically mimic a range of conditions and are misdiagnosed as basal cell carcinoma or squamous cell carcinoma.11\n\nThe most common presentation of sebaceous carcinoma in the eyelid is as round highly cellular nests of poorly differentiated tumor cells. Sometimes better differentiated cells with vacuolated cytoplasm are identified.12\n\nMany studies have shown that sebaceous carcinoma of the eyelid has a poor prognosis and if there is an orbital or vascular invasion present prognosis further worsens.13\n\nThe treatment of choice for sebaceous carcinoma is surgery, with complete excision verified by negative margins.14\n\n\nConclusions\n\nSebaceous carcinoma of the eyelid is a rare entity, but might be difficult to diagnose because of its ability to masquerade as the periocular lesions. However, accurate and prompt diagnosis is crucial for planning further management of the disease, therefore tissue diagnosis is the gold standard method and it can be aided by a panel of immunohistochemistry stains.\n\n\nCase report consent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patients.\n\n\nAuthor’s contributions\n\nJayashree Bhawani: drafting the case report and overview of patient management. Dr. Samarth Shukla: Reporting of the excised specimen sent for histopathological investigation and giving the suitable diagnosis. All the authors read and approved the final version of this manuscript.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nRao NA, Hidayat LC, McLean LC, et al.: Sebaceous carcinomas of the ocular adnexa: a clinicopathologic study of 104 cases, with five-year follow-up data. Hum. Pathol. 1982 Feb 1; 13(2): 113–122. PubMed Abstract | Publisher Full Text\n\nWu A, Rajak SN, Chiang CJ, et al.: Epidemiology of cutaneous sebaceous carcinoma. Australas. J. Dermatol. 2021 Feb; 62(1): 57–59. PubMed Abstract | Publisher Full Text\n\nJohn AM, Schwartz RA: Muir-Torre syndrome (MTS): an update and approach to diagnosis and management. J. Am. Acad. Dermatol. 2016 Mar 1; 74(3): 558–566. PubMed Abstract | Publisher Full Text\n\nKaliki S, Ayyar A, Dave TV, et al.: Sebaceous gland carcinoma of the eyelid: clinicopathological features and outcome in Asian Indians. Eye (Lond.). 2015 Jul; 29(7): 958–963. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKass LG, Hornblass A: Sebaceous carcinoma of the ocular adnexa. Surv. Ophthalmol. 1989 May 1; 33(6): 477–490. Publisher Full Text\n\nBuitrago W, Joseph AK: Sebaceous carcinoma: the great masquerader: emerging concepts in diagnosis and treatment. Dermatol. Ther. 2008 Nov; 21(6): 459–466. PubMed Abstract | Publisher Full Text\n\nShields JA, Demirci H, Marr BP, et al.: Sebaceous carcinoma of the ocular region: a review. Surv. Ophthalmol. 2005 Mar 1; 50(2): 103–122. PubMed Abstract | Publisher Full Text\n\nSlutsky JB, Jones EC: Periocular cutaneous malignancies: a review of the literature. Dermatol. Surg. 2012 Apr; 38(4): 552–569. Publisher Full Text\n\nYu SS, Zhao Y, Zhao H, et al.: A retrospective study of 2228 cases with eyelid tumors. Int. J. Ophthalmol. 2018; 11(11): 1835–1841. PubMed Abstract | Publisher Full Text\n\nShields JA, Demirci H, Marr BP, et al.: Sebaceous carcinoma of the eyelids: personal experience with 60 cases. Ophthalmology. 2004 Dec 1; 111(12): 2151–2157. Publisher Full Text\n\nSinard JH: Immunohistochemical distinction of ocular sebaceous carcinoma from basal cell and squamous cell carcinoma. Arch. Ophthalmol. 1999 Jun 1; 117(6): 776–783. PubMed Abstract | Publisher Full Text\n\nSadeghi S, Pitman MB, Weir MM, et al.: Cytologic features of metastatic sebaceous carcinoma: report of two cases with comparison to three cases of basal cell carcinoma. Diagn. Cytopathol. 1999 Nov; 21(5): 340–345. PubMed Abstract | Publisher Full Text\n\nHoffman GR, Jefferson ND, Reid CB, et al.: Orbital exenteration to manage infiltrative sinonasal, orbital adnexal, and cutaneous malignancies provide acceptable survival outcomes: an institutional review, literature review, and meta-analysis. J. Oral Maxillofac. Surg. 2016 Mar 1; 74(3): 631–643. Publisher Full Text\n\nGulleth Y, Goldberg N, Silverman RP, et al.: What is the best surgical margin for a Basal cell carcinoma: a meta-analysis of the literature. Plast. Reconstr. Surg. 2010 Oct 1; 126(4): 1222–1231. Publisher Full Text"
}
|
[
{
"id": "263242",
"date": "30 May 2024",
"name": "Jianmin Ma",
"expertise": [
"Reviewer Expertise Orbital Diseases"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall Assessment The case report on sebaceous carcinoma is comprehensive and detailed, providing valuable insights into the presentation, diagnostic process, therapeutic interventions, and outcomes of this rare condition. However, several areas require attention to improve clarity, accuracy, and readability. The following are my detailed comments and suggestions:\nAbstract Content and Clarity: The abstract is clear and summarizes the case effectively. Consider adding a sentence about the prognosis or significance of prompt diagnosis to underscore the clinical importance. Keywords: The keywords are appropriate but could include \"orbital exenteration\" and \"histopathology\" for better indexing.\nIntroduction Background Information: The introduction provides a good overview. Consider expanding on the clinical significance of sebaceous carcinoma and its diagnostic challenges. Patient Information Patient History: The patient history is well-detailed. Consider specifying the duration between the onset of symptoms and seeking medical advice to highlight any potential delays in diagnosis.\nClinical Findings Details and Clarity: The clinical findings section is clear. Consider specifying whether any other systemic examinations were performed, given the potential for metastasis in malignant conditions.\nDiagnostic Assessment Diagnostic Methods: The MRI and FNAC findings are described well. Ensure technical terms like \"heterogeneously hyperintense\" are explained or referenced for clarity. Figures: Ensure all figures are of high quality and properly referenced in the text. Consider providing a brief description of what each figure illustrates within the text. Therapeutic Interventions\nSurgical Details: The description of the surgical intervention is clear. Include any preoperative considerations or complications, if applicable.\nFollow-up and Outcomes Specimen Analysis: The analysis of the resected specimen is detailed. Ensure all histopathological findings are clearly described, and consider including a brief discussion on the typical histopathological features of sebaceous carcinoma.\nDiscussion Literature Review: The discussion provides a good review of the literature. Consider comparing this case to similar reported cases to highlight unique aspects or common patterns. Prognosis and Management: Expand on the prognosis and management strategies, including potential follow-up treatments or monitoring.\nConclusions Summary: The conclusions are concise. Emphasize the importance of early diagnosis and potential outcomes with timely intervention.\nReferences Formatting: Ensure all references are formatted according to the journal's guidelines. Completeness: Verify that all references cited in the text are included in the reference list and are correctly formatted. Specific Suggestions for Improvement Technical Terms: Define or reference all technical terms and acronyms (e.g., FNAC, MRI) upon their first use in the text. Grammar and Style: Review the manuscript for grammatical errors and ensure consistent scientific style. Figures and Tables: Ensure all figures and tables are clear, well-labeled, and properly referenced in the text. Flow and Structure: Ensure smooth transitions between sections for better readability.\nSuggested Citation To strengthen the discussion on sebaceous carcinoma of the eyelid, it would be beneficial to cite the following paper, which provides a comprehensive review of sebaceous gland hyperplasia and related conditions: Ma M. et. al., 2024 (Ref 1) This paper discusses the differential diagnosis and management strategies for sebaceous gland lesions, which can provide a comparative perspective to your case report on sebaceous carcinoma.\nConclusion This case report provides valuable insights into sebaceous carcinoma of the eyelid. With the above revisions, it will significantly enhance its clarity, impact, and contribution to the field. I recommend a revision to address the points mentioned above.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "11748",
"date": "11 Jun 2024",
"name": "Jayashree Bhawani",
"role": "Author Response",
"response": "Thank you for the suggestions Sir/Maam I am including your suggestions in the new version of the case report."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1563
|
https://f1000research.com/articles/10-628/v1
|
21 Jul 21
|
{
"type": "Research Article",
"title": "Screening for antifolate and artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea",
"authors": [
"Harriet Natabona Mukhongo",
"Johnson Kang'ethe Kinyua",
"Yishak Gebrekidan Weldemichael",
"Remmy Wekesa Kasili",
"Johnson Kang'ethe Kinyua",
"Yishak Gebrekidan Weldemichael"
],
"abstract": "Background: Antimalarial drug resistance is a major challenge hampering malaria control and elimination. Plasmodium falciparum, the leading causative parasite species, has developed resistance to basically all antimalarials. Continued surveillance of drug resistance using genetic markers provides important molecular data for treatment policies. This study sought to verify the genetic mechanism of resistance to sulfadoxine-pyrimethamine and assess the occurrence of point mutations associated with artemisinin resistance in P. falciparum clinical isolates from Eritrea. Methods: Nineteen dried blood spot samples were collected from patients visiting Adi Quala, Keren and Gash Barka Hospitals, Eritrea. The patients were followed up after receiving treatment with first line artesunate-amodiaquine. Nested polymerase chain reaction and Sanger sequencing techniques were employed to genotype point mutations in the P. falciparum bifunctional dihydrofolate reductase-thymidylate synthase (Pfdhfr, PF3D7_0417200), dihydropteorate synthase (Pfdhps, PF3D7_0810800) and kelch 13 (PfK13, PF3D7_1343700) genes. Results: Eight of nineteen (42%) of the dried blood spot samples were successful for PCR-amplification. Data analyses of the PCR-positive isolates revealed the following point mutations: Pfdhfr N51I in four isolates, C59R in one isolate, S108N in four isolates, a rare non-synonymous substitution V45A in four isolates and Pfdhps K540E in four isolates. No PfK13 point mutations were reported. Conclusions: Pfdhfr C59R and Pfdhps K540E point mutations are reliable markers for the sulfadoxine-pyrimethamine quintuple mutant haplotype combination. These findings highlight first reports in Eritrea, which verify the underlying genetic mechanism of antifolate resistance. Continuous monitoring of the PfK13 marker is recommended.",
"keywords": [
"drug resistance",
"Plasmodium falciparum",
"antifolate",
"artemisinin",
"genetic markers",
"Eritrea"
],
"content": "Introduction\n\nMalaria is a major vector-borne disease, endemic in 87 tropical and sub-tropical countries, causing over 400,000 deaths yearly (WHO World Malaria Report 2020). Eritrea, which is situated in the Horn of Africa, has experienced a significant decline in deaths and cases of malaria over the past 20 years (WHO World Malaria Report 2019). This reduction, according to the Ministry of Health (MOH) reports, is mainly due to extensive interventions employed towards the control of malaria since the establishment of the Eritrea National Malaria Control Program (NMCP) in 1995.1 Working hand-in-hand with Roll Back Malaria (RBM) collaborators and stakeholders,2 NMCP set up a combination of strategies including integrated vector management (IVM), early diagnosis and prompt treatment3 consequently leading to a remarkable decrease in incidence and mortality rates, following the gruesome 1998 malaria epidemic in the country.4 The disease is generally endemic in the Western lowlands of Gash Barka, Anseba, Debub and Semenawi Keih Bahri (Northern Red Sea) zobas (regions) whereas the Central highlands and Eastern lowlands of Maekel and Debubawi Keih Bahri (Southern Red Sea) zobas respectively have unstable, seasonal transmission. July–September is the common rainy season and hence malaria transmission peaks between October–November in a majority of the endemic areas while in the Coastal region the rainy season mostly occurs between December–January leading to a heightened transmission in March–April.5,6 About three-quarters of confirmed malaria cases in Eritrea are caused by Plasmodium falciparum and the remaining one-quarter is attributed to Plasmodium vivax, as well as small proportions of mixed infections (WHO African Region: Eritrea 2018). Currently, case management in Eritrea exclusively entails World Health Organisation (WHO) recommended first line treatment of uncomplicated malaria using artesunate-amodiaquine (AS-AQ), an artemisinin-based combination therapy (ACT) adopted in 2007, while quinine (Q) has been used for severe cases of infection since 2002 (WHO African Region: Eritrea 2018). Monitoring for drug resistance plays a major role in governing the efficacy of antimalarials, which subsequently influences their use in a population.\n\nThe emergence of drug resistance, especially among P. falciparum parasites, is a major hindrance to malaria control due to its increasing prevalence to essentially all antimalarials including sulfadoxine-pyrimethamine (SP) and lately artemisinins (ARTs).7 Genetic markers are invaluable tools in screening and detection of drug resistance, in addition to predicting the efficacy of antimalarials.8 Sulfadoxine-pyrimethamine P. falciparum resistance (SPR), which is well-studied, results from the occurrence and accumulation of mutations in the dihydrofolate reductase gene (Pfdhfr) and in the dihydropteorate synthase gene (Pfdhps) leading to a gradual reduction of sensitivity to pyrimethamine and sulfadoxine respectively.9 In vitro and in vivo studies have shown that SPR is mainly associated with point mutations at codons N51I, C59R, S108N and I164L of Pfdhfr and S436A, A437G, K540E, A581G and A613S of Pfdhps.10,11 Various combinations of these mutations have been used to classify SP resistant parasites according to different levels of resistance i.e. partially-, fully- or super resistant parasites and this has subsequently affected SP treatment policy. Partial resistance is demonstrated by a combination of triple mutant Pfdhfr, N51I, C59R, S108N and Pfdhps, A437G whereas full resistance is shown by a combination of triple mutant Pfdhfr, N51I, C59R, S108N and double mutant Pfdhfr, A437G, K540E. Finally, the sextuple mutant genotype involving a combination of triple mutant Pfdhfr, N51I, C59R, S108N and triple mutant Pdhfr, A437G, K540E and A581G defines super resistance.12\n\nThe development of artemisinin (ART) resistant P. falciparum parasites was first independently described in Western Cambodia, South East Asia.13 To date, resistance is commonly associated with five non-synonymous mutations including M476I, Y493H, R539T, I543T, and C580Y in the propeller domain of P. falciparum kelch 13 gene (Pfk13).14,15 ART resistance is primarily characterized by delayed parasite clearance rates in clinical studies as well as reduced in vitro drug susceptibility of the ring stage of parasite development.16,17 Considering the significant malaria control interventions accomplished in Eritrea, this pilot study aimed at availing supplementary molecular data by screening for SP and ART resistance-associated mutations from a cohort of patients, treated with first line AS-AQ, visiting selected hospitals located in malaria endemic regions of Eritrea. Generally, despite WHO’s change in treatment policy from the chloroquine (CQ) - sulfadoxine-pyrimethamine (SP) combination, adopted in 2002 to ACT, little is documented on the genetic mechanism underlying SPR using genetic markers. Additionally, a continuous detection for ART-resistance using genetic markers is important to keep track of changes at the genetic level.\n\n\nMethods\n\nThe ethical approval for this study was obtained from the Eritrea Institute of Technology, Research and Postgraduate Studies (RPS) Ethics Review Committee (Reference no. RPS/169/14) and the Ethics Review Board of the National Commission for Higher Education, Eritrea (NCHE) (Reference no. BHEAIL/3/656-568/14).\n\nSample collection was conducted from 1st July to 1st October 2014 at three hospitals located in malaria-endemic zobas of Eritrea: Adi Quala Hospital, Adi Quala (14°38′07′′N, 38°50′03′′E) in Zoba Debub, Keren Hospital, Keren (15°46′40′′N, 38°27′03′′E) in Zoba Anseba and Gash Barka Referral Hospital, Barentu (15°06′20′′N, 37°35′26′′E) in Zoba Gash Barka. Three time ranges were employed for the study at the three hospitals: from 1st July to 31st August 2014 for Adi Qualla Hospital, 16th July to 15th September 2014 for Keren Hospital and 15th August to 1st October 2014 for Gash Barka Referral Hospital.\n\nBlood samples were obtained from patients with febrile illness, who visited the three hospitals within the study period. The samples were spotted on Whatman 903TM paper (GE Healthcare Bioscience Corp.), stored in individual plastic bags with silica desiccant and transported for further molecular studies at the Institute for Biotechnology Research (IBR) in Jomo Kenyatta University of Agriculture and Technology (JKUAT), Kenya.\n\nGenomic DNA extraction was performed on the dried blood spot (DBS) samples using Schneeberger’s protocol with slight modifications, comprising 1.5M guanidine thiocyanate and 100mM Tris with 0.1% sodium dodecyl sulfate (SDS) at pH 8.18 Concentration of DNA ranged from 0.05 ng/uL to 6.03 ng/uL whereas the ratio obtained from analysis of DNA purity (260 nm/280 nm) ranged from 1.4 to 2.17. The DNA extracts were stored at -20°C and used for PCR amplification.\n\nOuter and nested PCR amplification was conducted using the AB 9800 Fast Thermocycler machine (Applied Biosystems, UK) on regions flanking identified point mutations of the following P. falciparum genes: bifunctional dihydrofolate reductase-thymidylate synthase – DHFR-TS (PF3D7_0417200), i.e. N51I, C59R, and S108N, hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase – PPPK-DHPS (PF3D7_0810800) i.e. K540E and kelch protein – kelch 13 (PF3D7_1343700) i.e. Y493H, R539T, I543T, and C580Y which confer drug resistance to SP and ART respectively. The respective gene sequences were retrieved from PlasmoDB release 46 (http://PlasmoDB.org) and primer design (Table 1) was performed using PrimerQuest and OligoAnalyzer tools from Integrated DNA technologies online platform (https://www.idtdna.com/). Selection of primers considered characteristics such as: Guanine-Cytosine (G+C) content of greater than 50, five degrees difference between melting temperatures and absence of hair-pin formation and self-annealing properties. A total PCR volume of 25 uL containing 12.5 uL of 2× DreamTaq PCR master mix (Thermo ScientificTM), 3.75 uL of the DNA template and 0.25 uL of the forward and reverse primers respectively were obtained for all the reactions. A volume of 3.75 uL of DNA template in the outer primary PCR reaction, as well as for the PCR amplicon in the nested secondary reaction was used. Step-down PCR cycling conditions for the outer and nested reactions were set as follows: an initial denaturation of 94°C for three minutes, a denaturation of 94°C for 15 seconds, an annealing temperature range of 55°C–60°C for 30 seconds, an elongation of 72°C for one minute and a final elongation of 72°C for 10 minutes.\n\nResolution of PCR amplicons was run in 1.5% agarose gel, 1× TAE buffer, at 70 V, 58 mA for one hour 30 minutes using a gel electrophoresis system (IBI-Shelton Scientific MP-1015 multipurpose) and an electrophoresis power voltage supplier (Pharmacia LKB ECPS 3000V/150mA). GelRed ® Nucleic Acid Gel stain (Biotium) was used for pre-cast gel staining, 1 kb DNA ladder (Thermo ScientificTM) for DNA quantification of resolved PCR amplicons. P. falciparum 3D7 purified DNA laboratory strain obtained from Kenya Medical Research Institute (KEMRI) was used as the main control for wild-type and mutant alleles of each gene. Purification of nested PCR amplicons depicting a single band was performed using the QIAquick PCR purification kit (Qiagen) whereas for amplicons showing double bands, the targets were processed using QIAquick gel extraction kit (Qiagen) as per the manufacturer’s protocol respectively. The PCR amplicons were shipped to Macrogen (Seoul, Korea) for Sanger sequencing.\n\nQIAGEN CLC Main Workbench v21.0.4 was used to perform sequence data editing, consensus sequence assembly and identification of nucleotide base conflicts against the 3D7 reference gene sequences of PF3D7_0417200, PF3D7_0810800 and PF3D7_1343700. Multiple sequence alignment (MSA), was carried out in MEGA v7.019 using the Muscle algorithm20 to identify nucleotide base changes, including translation to amino acid sequences using the standard genetic code for the identification of amino acid changes and their respective positions. Further visualisation of sequence alignments was performed in Jalview v2.11.1.421 to identify non-synonymous point mutations.\n\n\nResults\n\nAfter consent was given for participation and follow up, 19 dried blood spot (DBS) samples were successfully collected from a total of 131 patients who visited the three hospitals during the study period,22 10 samples from Adi Quala Hospital (AQH = 10), three samples from Keren Hospital (KH = 3) and six samples from Gash Barka Referral Hospital (GBH = 6). Eight DBS samples were from patients treated with ACT (artesunate [AS] 100 mg + amodiaquine [AQ] 200 mg) and did not respond to treatment. These underwent re-treatment with quinine (Q) and were cured. Five DBS samples were from patients who responded to ACT treatment. The remaining six were from patients presenting severe illness and were treated with quinine (Q) (Table 2).\n\nAS = artesunate, AQ = amodiaquine, Q = quinine.\n\nOn PCR amplification of targeted gene regions, sequence data from eight samples (AQH = 2, KH = 2, GBH = 4) was eventually analyzed for point mutations (Table 3). The nucleotide base changes comprised of four Pfdhfr substitutions, adenine (A) to cytosine (C) at position 152, thymine (T) to cytosine (C) at position 175, guanine (G) to adenine (A) at position 323, thymine (T) to cytosine (C) at position 134; one Pfdhps substitutions, adenine (A) to guanine (G) at position 1618 and none identified for PfK-13 (Table 4). Subsequent translation to amino acid sequences constituted changes as follows: asparagine (N) to isoleucine (I) at codon 51, cysteine (C) to arginine (R) at codon 59, serine (S) to asparagine (N) at codon 108 and valine (V) to alanine (A) at codon 45 for Pfdhfr; lysine (K) to glutamate (E) at codon 540 for Pfdhps and wild-type amino acids retained for Pfkelch-13 (Table 4). Multiple sequence alignment (MSA) and visualization of consensus sequence assemblies for Pfdhfr, Pfdhps and Pfkelch-13 against their 3D7 reference sequences distinguished four non-synonymous (nsy) point mutations for Pfdhfr (N51I, C59R, S108N, V45A), one non-synonymous (nsy) point mutation (K540E) for Pfdhps while Pfkelch-13 retained wild-type amino acids (Figure 1).\n\nJalview visualization of multiple sequence alignments depicting nsy-point mutations: Pfdhfr (N51I, S108N, V45A) occurred in all four isolates (KH013, GBH017, AQH010, AQH009), C59R was identified in one isolate (KH013); Pfdhps (K540E) occurred in all four isolates (KH013, GBH017, AQH010, AQH009), C59R was identified in one isolate (KH013) and Pfdhps (K540E) occurred in all four isolates (KH012, GBH014, GBH015, GBH017) PfK-13, established no point mutations in all six isolates, wild type amino acids retained at c.554(S), c.566(V), c.569(A), c.578(A), c.580(C), c.493(Y), c.539(R), c.543 (I).\n\nN = asparagine, I = isoleucine, C = cysteine, R = arginine, S = serine, V = valine, A = alanine.\n\nNote: The numeral ‘0’ indicates absence of isolates with the respective nucleotide/amino acid changes The dash (-) symbol implies no sequence data generated from the respective hospital sites.\n\n\nDiscussion\n\nIn this study, we present findings from a pilot survey assessing the occurrence of point mutations in PfK-13, Pfdhfr and Pfdhps genes from clinical isolates obtained from three zobas of Eritrea: Adi Quala (Adi Quala Hospital), Debub (Keren Hospital) and Anseba (Gash Barka Hospital). We targeted PCR-amplification of PfK-13 point mutations associated with artemisinin (ART) resistant phenotype in western Cambodia, South-East Asia Y493H, R539T, I543T, C580Y,14 non-synonymous point mutations, V566I, A578S, identified in isolates from five Sub-Saharan countries23 and N554S, A569S reported in a previous study from islands in Lake Victoria, Kenya.24 This study found none of the corresponding point mutations in PfK-13, which is similar to other studies from Eritrea25 and Kenya26,27 including other malaria endemic sub-Saharan countries.28 Data from the treatment outcome with the prescribed artemisinin (artesunate [AS]) indicated susceptibility responses corresponding with our findings and suggesting a likely absence of ART resistance. Only one isolate from these analyses was obtained from a patient who did not respond to first line treatment with AS-AQ – this could be attributed to possible causes of treatment failure such as non-compliance to the treatment regimen, incorrect drug usage, drug pharmacokinetics as well as host immunity.29,30\n\nPfdhfr point mutations, N51I, C59R and S108N observed in our study correspond with previous reports from Senegal,31 South Africa,32 Malawi, Mali, Kenya, Tanzania,33,34 including Venezuela in South America.35 Additionally, the single Pfdhfr C59R and Pfdhps K540E point mutations seen in our findings, have been shown to predict the occurrence of the Pfdhfr-Pfdhps quintuple mutant haplotype (Pfdhfr 51I/59R/108N + Pfdhps 437G/540E),36 which is associated with fully resistant SP parasites12 as well as SP treatment failure.37 The selection of these Pfdhfr-Pfdhps mutations from our findings, is attributable to the prior use of the CQ-SP combination as first-line treatment for clinical management of febrile disease especially at the primary health care level in Eritrea. Additionally, prior evidence shows that SP resistant parasites originated from South East Asia and consecutively spread into Sub-Saharan Africa,38,39 which eventually reached Eritrea too, as demonstrated in these findings. The valine (V) to alanine (A) change at codon 45 in Pfdhfr from this study, has not been previously reported, although, a converse occurrence of alanine (A) to valine (V) at codon 16 has been associated, both singly and doubly in combination to S108N mutation, with resistance to another antifolate, cycloguanil.40,41 Further investigation with a larger sample size is recommended to validate the selection of the V45A mutation in the population, as well as understand its implications to protein function in association with other established Pfdhfr mutations. Additionally, further detection of other SP resistance associated mutations not reported herein is recommended.\n\nAlthough this study design availed treatment outcome information to compare with corresponding generated molecular data, limitation of sample size as well as DNA quality and quantity constrained further detection of PfK13 mutations associated with artemisinin resistance. Nonetheless, the general findings reported here, are not affected by these limitations and essentially provides useful molecular inference for further investigations.\n\n\nConclusions\n\nHere, we provide molecular data verifying the genetic mechanism underlying SP resistance from selected participants of three regions of Eritrea. Pfdhfr C59R and Pfdhps K540E are reliable markers for the quintuple mutant haplotype conferring full resistance to SP. This study provides the molecular status of SP resistance in Eritrea. Continued monitoring of artemisinin resistance is recommended. Future studies should be carried out on a larger sample size since this study was a pilot survey involving a small sample size.\n\n\nData availability\n\nThis project contains the following underlying data:\n\nNCBI Gene: bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322415, https://www.ncbi.nlm.nih.gov/nuccore/MZ322415.\n\nNCBI Gene: bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322416, https://www.ncbi.nlm.nih.gov/nuccore/MZ322416.\n\nNCBI Gene: bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322417, https://www.ncbi.nlm.nih.gov/nuccore/MZ322417.\n\nNCBI Gene: bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322418, https://www.ncbi.nlm.nih.gov/nuccore/MZ322418.\n\nNCBI Gene: hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase (PPPK-DHPS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322419, https://www.ncbi.nlm.nih.gov/nuccore/MZ322419.\n\nNCBI Gene: hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase (PPPK-DHPS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322420, https://www.ncbi.nlm.nih.gov/nuccore/MZ322420.\n\nNCBI Gene: hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase (PPPK-DHPS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322421, https://www.ncbi.nlm.nih.gov/nuccore/MZ322421.\n\nNCBI Gene: hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase (PPPK-DHPS) [Plasmodium falciparum (malaria parasite)] Accession number MZ322422, https://www.ncbi.nlm.nih.gov/nuccore/MZ322422.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322423, https://www.ncbi.nlm.nih.gov/nuccore/MZ322423.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322424, https://www.ncbi.nlm.nih.gov/nuccore/MZ322424.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322425, https://www.ncbi.nlm.nih.gov/nuccore/MZ322425.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322426, https://www.ncbi.nlm.nih.gov/nuccore/MZ322426.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322427, https://www.ncbi.nlm.nih.gov/nuccore/MZ322427.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322428, https://www.ncbi.nlm.nih.gov/nuccore/MZ322428.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322429, https://www.ncbi.nlm.nih.gov/nuccore/MZ322429.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322430, https://www.ncbi.nlm.nih.gov/nuccore/MZ322430.\n\nNCBI Gene: kelch protein (K13) (Kelch13) [Plasmodium falciparum (malaria parasite)] Accession number MZ322431, https://www.ncbi.nlm.nih.gov/nuccore/MZ322431.\n\nDryad: Extended data for ‘Screening for Antifolate and Artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea’, https://doi.org/10.5061/dryad.sbcc2fr6q.22\n\nThis project contains the following extended data:\n\n• the total number of patients grouped according to age, who visited the three hospitals during the study period.\n\n• gel images of Pfdhfr, Pfdhps and PfK13 genetic markers.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nConsent\n\nAll participants were informed concerning the aim of the study, assent and written informed consent was given by patients, voluntary participation was allowed, and confidentiality of information collected ensured.",
"appendix": "Acknowledgements\n\nThe authors are grateful to all the participants of the study from the three hospitals and to Mr. Moses Ogugo (International Livestock Research Institute – Kenya) for the technical support.\n\n\nReferences\n\nMOH Ministry of Health: Malaria and other vector-borne diseases control strategy 2015-2019 in Eritrea. The national malaria control program . State of Eritrea: Ministry of Health; 2014; 2014.\n\nNabarro DN, Tayler EM: The “roll back malaria” campaign. Science. 1998; 280(5372): 2067–8. PubMed Abstract | Publisher Full Text Reference Source\n\nNMCP National Malaria Control Program Ministry of Health, State of Eritrea: Mandefera Declaration on Malaria control in Eritrea.2013.\n\nMufunda J, Nyarango P, Usman A, et al.: Roll back malaria - An African success story in Eritrea. S Afr Med J. 2007; 97(1): 46–50. PubMed Abstract Reference Source\n\nBerhane A, Mihreteab S, Ahmed H, et al.: Gains attained in malaria control coverage within settings earmarked for pre-elimination: malaria indicator and prevalence surveys 2012, Eritrea. Malar J. 2015; 14(467): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKifle MM, Teklemariam TT, Teweldeberhan AM, et al.: Malaria Risk Stratification and Modeling the Effect of Rainfall on Malaria Incidence in Eritrea. J Environ Public Health. 2019; 2019: 1–11. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nCui L, Mharakurwa S, Ndiaye D, et al.: Antimalarial drug resistance: Literature review and activities and findings of the ICEMR network. Am J Trop Med Hyg. 2015; 93: 57–68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVestergaard LS, Ringwald P: Responding to the challenge of antimalarial drug resistance by routine monitoring to update national malaria treatment policies. Am J Trop Med Hyg. 2007; 77(SUPPL. 6): 153–9. PubMed Abstract Reference SourceNBK1708/\n\nVinayak S, Alam MT, Mixson-Hayden T, et al.: Origin and evolution of sulfadoxine resistant Plasmodium falciparum. PLoS Pathog. 2010; 6(3): e1000830. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nConstanzo MS, Hartl DL: The evolutionary landscape of antifolate resistance in Plasmodium falciparum. J Genet. 2011; 90(2): 187–90. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nPlowe CV: The evolution of drug-resistant malaria. Trans R Soc Trop Med Hyg. 2009; 103(1 SUPPL): S11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNaidoo I, Roper C: Mapping “partially resistant”, “fully resistant”, and “super resistant” malaria. Vol. 29, Trends in Parasitology. Trends Parasitol. 2013: 505–15. PubMed Abstract | Publisher Full Text\n\nTakala-Harrison S, Jacob CG, Arze C, et al.: Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. J Infect Dis. 2015; 211(5): 670–9. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nAriey F, Witkowski B, Amaratunga C, et al.: A molecular marker of artemisinin- resistant Plasmodium falciparum malaria. Nature. 2013; 505(7481): 50–5. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nAshley EA, Dhorda M, Fairhurst RM, et al.: Spread of Artemisinin Resistance in Plasmodium falciparum Malaria. N Engl J Med. 2014; 371(5): 411–23. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nWitkowski B, Khim N, Chim P, et al.: Reduced Artemisinin Susceptibility of Plasmodium falciparum Ring Stages in Western Cambodia. Antimicrob Agents Chemother. 2013; 57(2): 914–23. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nDondorp AM, Nosten F, Yi P, et al.: Artemisinin Resistance in Plasmodium falciparum Malaria. N Engl J Med. 2009; 361(5): 455–67. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchneeberger C, Kury F, Larsen J, et al.: A simple method for extraction of DNA from guthrie cards. Genome Res. 1992; 2(2): 177–9. PubMed Abstract | Publisher Full Text Reference Source\n\nKumar S, Stecher G, Tamura K: MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016; 33(7): 1870–4. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nEdgar RC: MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004; 5. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nWaterhouse AM, Procter JB, Martin DMA, et al.: Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25(9): 1189–91. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMukhongo Natabona H, Kinyua Kang’ethe J, Gebrekidan Weldemichael Y, et al.: Extended data for: Screening for antifolate and artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea. Dryad. 2021. Publisher Full Text\n\nKamau E, Campino S, Amenga-Etego L, et al.: K13-propeller polymorphisms in Plasmodium falciparum parasites from sub-Saharan Africa. J Infect Dis. 2015; 211(8): 1352–5. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nIsozumi R, Uemura H, Kimata I, et al.: Novel mutations in K13 propeller gene of artemisinin-resistant Plasmodium falciparum. Emerg Infect Dis. 2015; 21(3): 490–2. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nMenegon M, Nurahmed AM, Talha AA, et al.: Molecular surveillance of antimalarial drug resistance related genes in Plasmodium falciparum isolates from Eritrea. Acta Trop. 2016; 157: 158–61. PubMed Abstract | Publisher Full Text Reference Source\n\nHemming-Schroeder E, Umukoro E, Lo E, et al.: Impacts of antimalarial drugs on plasmodium falciparum drug resistance markers, Western Kenya, 2003-2015. Am J Trop Med Hyg. 2018; 98(3): 692–9. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nWamae K, Okanda D, Ndwiga L, et al.: No Evidence of Plasmodium falciparum k13 Artemisinin Resistance-Conferring Mutations over a 24-Year Analysis in Coastal Kenya but a near Complete Reversion to Chloroquine-Sensitive Parasites. Antimicrob Agents Chemother. 2019; 63(12). PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaylor SM, Parobek CM, DeConti DK, et al.: Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis. 2015; 211(5): 680–8. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nKlein EY: Antimalarial drug resistance: A review of the biology and strategies to delay emergence and spread. Int J Antimicrob Agents . Elsevier B.V.; 2013; 41: p. 311–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPetersen I, Eastman R, Lanzer M: Drug-resistant malaria: Molecular mechanisms and implications for public health. FEBS Lett. 2011; 585(11): 1551–62. PubMed Abstract | Publisher Full Text\n\nNdiaye D, Daily JP, Sarr O, et al.: Mutations in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase genes in Senegal. Trop Med Int Heal. 2005; 10(11): 1176–9. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nRoper C, Pearce R, Bredenkamp B, et al.: Antifolate antimalarial resistance in southeast Africa: A population-based analysis. Lancet. 2003; 361(9364): 1174–81. PubMed Abstract | Publisher Full Text Reference Source\n\nPlowe CV, Cortese JF, Djimde A, et al.: Mutations in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase and epidemiologic patterns of pyrimethamine-sulfadoxine use and resistance. J Infect Dis. 1997; 176(6): 1590–6. PubMed Abstract | Publisher Full Text Reference Source\n\nWang P, Lee CS, Bayoumi R, et al.: Resistance to antifolates in Plasmodium falciparum monitored by sequence analysis of dihydropteroate synthetase and dihydrofolate reductase alleles in a large number of field samples of diverse origins. Mol Biochem Parasitol. 1997; 89(2): 161–77. PubMed Abstract | Publisher Full Text Reference Source\n\nUrdaneta L, Plowe C, Goldman I, et al.: Point mutations in dihydrofolate reductase and dihydropteroate synthase genes of Plasmodium falciparum isolates from Venezuela. Am J Trop Med Hyg. 1999; 61(3): 457–62. PubMed Abstract | Publisher Full Text Reference Source\n\nKublin JG, Dzinjalamala FK, Kamwendo DD, et al.: Molecular markers for failure of sulfadoxine-pyrimethamine and chlorproguanil-dapsone treatment of Plasmodium falciparum malaria. J Infect Dis. 2002; 185: 380–8. PubMed Abstract | Publisher Full Text Reference Source\n\nOkell LC, Griffin JT, Roper C: Mapping sulphadoxine-pyrimethamine-resistant Plasmodium falciparum malaria in infected humans and in parasite populations in Africa. Sci Rep. 2017; 7(1): 7389. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nMita T, Venkatesan M, Ohashi J, et al.: Limited geographical origin and global spread of sulfadoxine-resistant dhps alleles in plasmodium falciparum populations. J Infect Dis. 2011; 204(12): 1980–8. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nRoper C, Pearce R, Nair S, et al.: Intercontinental spread of pyrimethamine-resistant malaria. Science (80-). 2004; 305(5687): 1124. PubMed Abstract | Publisher Full Text Reference Source\n\nSirawaraporn W, Sathitkul T, Sirawaraporn R, et al.: Antifolate-resistant mutants of Plasmodium falciparum dihydrofolate reductase. Proc Natl Acad Sci U S A. 1997; 94(4): 1124–9. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nSridaran S, McClintock SK, Syphard LM, et al.: Anti-folate drug resistance in Africa: Meta-analysis of reported dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) mutant genotype frequencies in African Plasmodium falciparum parasite populations. Malaria Journal. BioMed Central. 2010; 9: 247. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source"
}
|
[
{
"id": "95573",
"date": "25 Oct 2021",
"name": "Olusola Ojurongbe",
"expertise": [
"Reviewer Expertise Medical Parasitology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMukhongo et al. presented a study highlighting the prevalence of P. falciparum dhfr, dhps, and K13 gene mutations in parasites collected in Eritrea. The subject of P. falciparum drug-resistant and gene mutations is very germane in malaria research, making this study a very important one. Unfortunately, this study is not well executed, and an extensive major review will be required.\nThe focus of this study is quite confusing. It is not clear why the authors are investigating dhfr and dhps mutations in this cohort. The country is not currently using sulfadoxine-pyrimethamine (SP) for treatment, and the cohort being investigated also did not use SP either. WHO currently recommends SP for prevention among pregnant women and children (in some cases). Neither of these groups is being studied. The author needs to justify the reason for SP mutation analysis in this study. What would have been more interesting would have been PFCRT gene mutations since amodiaquine is still being used as a partner drug for artesunate.\n\nThe authors stated in the abstract section that the \"study sought to verify the genetic mechanism of resistance to sulfadoxine-pyrimethamine.\" The genetic mechanism was not performed as stated by the authors in conclusion. All that the author did was report the mutations in dhps and dhfr genes. The identified mutations were not studied for their contributions to resistance in this cohort. While these mutations are well known for their contributions to resistance, many studies have reported these mutations without much compromise in SP cure rate, meaning that other additional factors are needed for resistance to occur. So for the authors to state that \"we provide molecular data verifying the genetic mechanism underlying SP resistance\" is not correct.\n\nThe authors stated that the patients were followed up. In Malaria studies, the standard WHO method of following up patients is to be observed on days 0,1,2,3, 7, 14, 21, and 28 or up to day 42. This will allow the definition of treatment failures (early, late, clinical, and parasitological) and adequate cure. The authors stated \"responded\" or \"Did not respond.\" How did they arrive at this outcome? Was this outcome based on fever or parasite detection? What type of failures are they considering? is it re-infection or recrudescence? All these are important in the analysis of and contribution of gene mutations to resistance. In my view, since the authors did not genotype the samples collected on the days that the patient \"Did not respond,\" this part should be expunged as it has little or no contribution to the data being presented.\n\nIt would be nice if the author could explain why only eight samples were successfully sequenced out of nineteen.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "8830",
"date": "01 May 2024",
"name": "Harriet Mukhongo",
"role": "Author Response",
"response": "Please find the authors' response to Reviewer 1 (Dr. Olusola Ojurongbe) linked here."
}
]
}
] | 1
|
https://f1000research.com/articles/10-628
|
https://f1000research.com/articles/13-625/v1
|
12 Jun 24
|
{
"type": "Study Protocol",
"title": "\"Effect of Immersive Virtual Reality in Adjunct to Conventional Physiotherapy on Static Balance, Dynamic Balance and Vertical Jump in Futsal Players with Lateral Ankle Sprain: A Protocol for Randomized Control Trial\"",
"authors": [
"Bharat Rathi",
"Swapnil Ramteke",
"Swapnil Ramteke"
],
"abstract": "Background As there is high expense of treatment and potential long-term consequences including chronic ankle instability (CAI), lateral ankle sprains (LAS) are common among athletes and represent a substantial healthcare burden. In terms of preventing more injuries and encouraging a full recovery, traditional treatments frequently fall short.\n\nMethods At the Department of Sports Physiotherapy, futsal athletes with grade I and grade II lateral ankle sprains will participate in a parallel-group, 1:1 allocation ratio trial. Individuals who fulfil the eligibility requirements will be randomized at random to either the experimental or control group. Conventional physiotherapy treatments will be administered to the control group, and IVR sessions utilizing certain games will be administered to the experimental group in addition to the same therapies. The Y Balance Tool is used to measure dynamic balance, the X Sens MVN system is used to measure vertical jump, and the Balance Error Scoring System (BESS) is used to assess static balance.\n\nResult This study aims to offer a new way to improving results for futsal players recovering from lateral ankle sprains by utilizing IVR technology in conjunction with traditional physiotherapy. The results could lead to the creation of more efficient sports-related injury rehabilitation programs, which would improve athlete performance and lessen the incidence of ankle sprains in athletic populations. CTRI Registration Number: CTRI/2024/04/065627 Name of registry: CTRI (Clinical Trials Registry) No. CTRI/2024/04/065627 Date: 12/04/2024 URL: https://ctri.nic.in/Clinicaltrials/rmaindet.php?trialid=102982&EncHid=78848.18761&modid=1&compid=19",
"keywords": [
"Ankle Sprain",
"Virtual Reality",
"Physiotherapy",
"Futsal",
"Athletes",
"Static Balance",
"Vertical jump",
"Dynamic Balance."
],
"content": "Introduction\n\nThe sports injury which is commonest in athletes is lateral ankle sprain (LAS). It causes a significant healthcare burden due to its high treatment costs as well as their long-term residual complications. Chronic ankle instability (CAI) is a syndrome that affects up to 40% of LAS patients. The characteristics of CAI are history of one severe LAS, repeated recurring sprains, incidents of the ankle giving way, or self-reported deficiencies in ankle function for more than a year after the initial sprain.1\n\nAnkle joint moves in the sagittal plane and is a hinge joint made of synovium. The distal epiphyses of the tibia and fibula form the hinge, which articulates in a highly congruent joint with the talus. It has mortise-like interlocks. Ankle sprains account for the majority of foot and ankle damage. The majority of people recover fully from them, but some experience chronic instability that makes it difficult for them to engage in strenuous activity.2\n\nAnkle sprains account for 70% or more of all reported ankle injuries in numerous sports, and ankle injuries itself make up 10% to 30% of all athletic injuries. Treatment for ankle sprains is frequently insufficient. Ankle sprains occur more frequently than 40% of the time, and repeated sprains might result in chronic ankle instability (CAI).3\n\nAn injury to the ankle joint’s lateral ligament complex is known as an ankle sprain. On the basis of severity of the injury, a grade is assigned. The ligament complex is partially ruptured with mild joint instability in grade II (one anterior talofibular ligament rupture, for example), slightly stretched in grade I without producing joint instability, and completely ruptured with joint instability in grade III. This classification has little practical ramifications because grade I injuries do not require particular treatment after diagnosis, and grade II and III injuries get the same therapy. The studies that were included in this analysis either did not specify which grades of injuries were included, or they included both grade II and III injuries.4\n\nAn athlete complains to have “rolled over” their outer ankle after spraining their lateral ankle ligament. The entire foot and ankle need to be examined to make sure there are no more injuries. Two clinical stability tests for ligamentous injury are the anterior drawer test for ATFL function and the inversion tilt test for both ATFL and CFL function. Radiographs can rule out treatable fractures when there are significant injuries or when there is no pain or sensitivity coming from the lateral ligaments. Stress radiography has no effect on the course of treatment.5\n\nTo improving athlete performance through movement recognition and technique correction, machine learning-based real-time prediction and feedback have the potential to evaluate injury promoting factors. This is especially important for athletes with impairments because it is possible to create customized monitoring systems that can foresee injuries unique to their condition. Additionally, it pushes the researchers to create more beneficial, accurate, and real-time data that is easy to use and provides coaches and athletes with actionable insights based on frameworks for context-specific evaluation and the capacity to recognize proper forms and common deviations of particular movements in accordance with established clinical consensus.6\n\nVirtual reality (VR) is defined as the computer-generated simulation of a three-dimensional. The cost of the new VR electrical technology, which is substantially less than that of the fixed virtual reality systems already in use, allows for high resolution, high frame rate, and sophisticated head tracking. It also includes a portable headset with an integrated screen. With such technology, it is considerably easier and more economical to adjust the sensory environment and regulate the variability of the experience’s intensity (dosing) inside “eyes open” task. The emphasis on sensory integration is consistent with studies conducted in 2008 by Kleim and Jones, who emphasized the significance of treating sensory deficiencies. Furthermore, it’s remarkable that the platform can provide these advantages without tipping over healthy young adults on a level surface. It demonstrates a careful effort to guaranteeing the technology’s usability for various user groups.7\n\nIvan Sutherland initially invented the notion of virtual reality in 1960.Thirteen virtual reality systems provide a window of interaction between users and a computer environment that mimics the real world. VR systems can be classified as immersive or non-immersive based on how much the user interacts with the virtual world and how many senses are engaged. Due to its three components interaction, immersion, and imagination—VR has been increasingly popular in rehabilitation over the past ten years. These factors have the potential to significantly improve motor learning. VR has certain benefits over traditional therapy. It gives patients a safe, virtual environment with functional tasks, immediate feedback, and appropriate incentives to boost adherence. Additionally, it offers customized programs for each patient and encourages them to take on challenging tasks in a secure environment, thereby increasing their capabilities. Because VR only needs minimal supervision, it can be used as a home-based program with unlimited repetitions, relieving physical therapists’ workload stress.8\n\nFutsal requires accurate movements, fast direction changes, and fast reactions. Proprioception of the knee is important, particularly following ankle injuries. Recovery from ankle sprains requires both static and dynamic balance. Maintaining stability, avoiding further injuries, and promoting joint healing are all part of static balance. Muscle strengthening and functional movement depend on dynamic balance. Virtual reality headsets like the Immersive Virtual Reality are imaginatively utilized in sports to facilitate quick transitions and teach skills through simulated games. Immersive Virtual Reality is used in conjunction with physiotherapy activities to gradually improve ankle performance following injury. The objectives of physical therapy for lateral ankle sprains include successful rehabilitation and a safe return to regular activity. Previous studies suggest that enhancing futsal players’ ankle performance with a conventional physiotherapy training that uses Immersive Virtual Reality. This calls for strength training, stability, plyometrics, and agility. With the help of this compelling technology, the use of cutting-edge technologies such as Immersive Virtual Reality into sports instruction being investigated. The objective of the research is to evaluate how well traditional physiotherapy and a technology-integrated method (Immersive Virtual Reality + Physiotherapy) improve athletes’ performance in the vertical jump, dynamic balance, and static balance following ankle injuries.\n\nTo evaluate the effect of immersive virtual reality (IVR) as an adjunct to conventional physiotherapy on static balance, dynamic balance, and vertical jump performance in futsal players recovering from lateral ankle sprain.\n\nPrimary objective:\n\n1. To evaluate the effect of Immersive Virtual Reality on static balance, dynamic balance and vertical jump in futsal players with lateral ankle sprain.\n\n2. To evaluate the effect of conventional training program on static balance, dynamic balance and vertical jump in futsal players with lateral ankle sprain.\n\n3. To compare the effect of immersive virtual reality in combination with conventional training program on static balance, dynamic balance and vertical jump in futsal players with lateral ankle sprain.\n\nSecondary objectives:\n\n1. Evaluation of subgroup analysis for finding the effect of intervention in males and females.\n\nThis protocol has been registered with CTRI: CTRI/2024/04/065627.\n\nInstitutional Ethical Committee approval number: DMIHER (DU)/IEC/2024/182.\n\nIEC approval date: 30/01/2024\n\nIt is a Two-arm parallel, single-center, Equal allocation superiority, Randomized controlled trial. This study will be conducted after obtaining informed consent from participants. Participants will be recruited from the Department of Sports Physiotherapy at Ravi Nair College of Physiotherapy in Sawangi, Meghe, Wardha, Maharashtra. Eligible participants will undergo screening based on predefined criteria, and individuals meeting the inclusion criteria will be enrolled. Allocation for both groups will be carried out via simple random selection to ensure fairness. This will be facilitated by a computer-generated random number system, utilizing the Sequentially Numbered Opaque Sealed Envelope Method for sample allocation. This study will be supervised by a departmental committee consisting of a PG Guide, the Head of the Department, the Principal of Ravi Nair Physiotherapy College (RNPC), and a member of the Research Guidance Cell. Patients will receive regular treatment sessions to adhere to recommended treatments, and if necessary, they will be reminded of therapy sessions via counselling or telephone contact. Athletes (Futsal Players) with the Lateral Ankle Sprain will be identified from Acharya Vinoba Bhave Rural Hospital as well as the from the Sports Department, Ravi Nair Physiotherapy College. Permission will be obtained from treating Doctors and then patient fulfilling the inclusion criteria will be randomly divided into two equal groups – Group A Group B. The Intervention given to Group A will be as per Physiotherapy Guidelines for Lateral ankle sprain (2021). The Intervention given to Group B will be as per Physiotherapy Guidelines for Lateral ankle sprain (2021) and it will be with the Immersive Virtual Reality.\n\nInclusion criteria\n\n1) Patient should be willing to participate in the study.\n\n2) Both male and female Futsal athletes.\n\n3) A diagnosis of Lateral Ankle Sprain in accordance with the diagnostic criteria for Ankle Sprain. (Grade I and Grade II)\n\nExclusion criteria\n\n1) Futsal players with grade III Ankle sprain.\n\n2) Athletes with pre-existing knee and hip injuries and Plantar fasciitis.\n\n3) Neurological conditions like Cerebellar Ataxia.\n\n4) Non-Futsal Athletes with Lateral Ankle Sprain.\n\n5) Previous history of Foot Drop.\n\nBoth groups will be receiving intervention for three sessions per week for a duration of four weeks. Pre- and post-intervention assessments will be taken, The CONSORT Flow chart, outlining participant flow from enrolment to analysis, is detailed in Figure 1.\n\nControl Group A: Conventional Physiotherapy\n\nFor Grade I ankle sprains, treatment involves cryotherapy, kinesiology taping, neuromuscular and balance training, strengthening exercises, and intrinsic muscle strengthening, all performed three times a week. Grade II treatment includes cryotherapy, therapeutic exercises, stretching, neuromuscular and balance training, strengthening exercises and intrinsic muscle strengthening exercises, also done three times a week. Motivational interviewing addresses psychological factors between sessions. These interventions aim to reduce pain, improve range of motion, restore strength, enhance balance, and boost self-efficacy for a safe return to activity. As shown in Table 1: Conventional Treatment Protocol.\n\nExperimental Group B: Immersive Virtual Reality in adjunct to Conventional Physiotherapy\n\nThe experimental group’s treatment protocol for Grade I and Grade II ankle sprains involves incorporating immersive virtual reality (VR) games alongside conventional physical therapy exercises. For Grade I sprains, Cryotherapy and Kinesiology Taping are combined with neuromuscular and balance training using the Clean Sheet game, and strengthening exercises are performed using the 2MD: VR Football game. For Grade II sprains, the same Cryotherapy and Kinesiology Taping protocols are followed, along with therapeutic exercises and stretching. Neuromuscular and balance training are integrated into the Clean Sheet game, while strengthening exercises are conducted using the 2MD: VR Football game. Motivational interviewing addresses psychological factors between sessions to enhance self-efficacy. As shown in Table 2: Immersive Virtual Reality in adjunct to Conventional Physiotherapy.\n\nThe Experimental Group will receive the following treatment protocol along with the help of following games in Immersive Virtual Reality.\n\n1) Clean Sheet\n\n2) 2MD: VR Football\n\nPrimary outcome\n\n1. Static Balance:\n\nBalance error scoring system (Static Balance) - A clinical assessment instrument called the Balance Error Scoring System (BESS) is used to measure balance and identify mild postural stability problems. It entails watching and rating particular mistakes made by an individual while they carry out different standing activities.\n\n2. Dynamic Balance:\n\nY Balance Tool - The Y balancing Test (YBT), which focuses on balancing ability, uses three directional motions (AT, PM, and PL) to assess lower limb muscle strength, flexibility, and proprioception. With one leg supporting the body and the other extended, the distance in centi-meters is measured from the midfoot to the tip of the extended leg. If the supporting foot lifts off the ground, if balance is dependent on the extended foot, or if the foot does not return to its starting position, the subject is considered to have failed. To account for any differences in limb length, measurements are taken from the anterior superior iliac spine (ASIS) to the medial malleolus.14\n\n3. Vertical Jump Test\n\nX Sens (Vertical Jump Test) - The X Sens MVN system typically consists of wearable motion capture suits featuring inertial sensors. The suit is equipped with inertial sensors, like gyroscopes and accelerometers, to record the movements of different body parts.\n\nMinimum sample size required.\n\nSample size by Cohen’s effect size by comparing two means.\n\nConsidering large effect size difference = 0.8 (Large effect size)\n\nZ1−α2 at 5% level of significance = 1.96\n\nZ1−β at 80% Power = 0.84\n\nRatio allocation (Group2/Group1) = 1\n\nConsidering 15% drop out total = 4\n\nA total of 30 samples are required per group.\n\nAdverse events if any, will be documented during each session.\n\n\nMethods\n\nData collection methods: Participants meeting the inclusion criteria will be enrolled in the study. Baseline data will be collected before the intervention begins. Post-intervention data will be collected after the completion of the four-week intervention period.\n\nThe full analysis data set will include all the study participants with no missing values for all the parameters in the data set. The study subjects will be the participants fulfilling inclusion and exclusion criteria\n\nOutcome variables: Primary outcomes\n\n1. Balance error scoring system (BESS)\n\n2. Y Balance test\n\n3. X Sens\n\nSecondary variables:\n\n1. Gender\n\nAll the data will be summarized with Baseline characteristics for demographic variables will be described by frequency and percentage for categorical data and with mean and standard deviation for continuous data.\n\nOutcome variables will be analysed over continuous variables will be summarised with the minimum, maximum, mean, standard deviation, standard error and CI at 95% for parametric data. Data over the continuous outcome variables will be firstly tested using normality test using Kolmogorov-Smirnov test at 5% level of significance (P≤0.05). If rejected data will be considered as normal otherwise non parametric test will be used for finding significance. T- test will be used to find the significance difference at 5% level (P≤0.05) for comparative groups.\n\n1) Immersive Virtual Reality in adjunct to Conventional Physiotherapy\n\n2) Conventional Physiotherapy\n\nNon normal data will be described by mean, median, lower and upper quartiles for using nonparametric test. And will be used for testing significance using Mann-Whitney test.\n\nCategorical variables will be summarised by frequency (N) and percentages value (%). Efficacy over the categorial variable will be analysed by chi square analysis for finding efficacy.\n\nDATA MONITORING: The data will be monitored by the Data Monitoring Committee of Ravi Nair Physiotherapy College.\n\nAny episode of the adverse events shall be reported to the Ethical Committee and the clinician in charge for assessing and managing the solicited and spontaneous adverse events and other unintended effects of trial interventions or trial conduct.\n\nConsent and assent:\n\nParticipants enrolled in the study will be fully informed about the study, and their written informed consent and assent will be obtained from each individual.\n\nConfidentiality: All information related to the study participants will be kept confidential. Patient-related data will only be utilized with explicit permission from the subjects.\n\nDeclaration of interests: There are no financial or competing interests to mention.\n\nAccess to data: The Principal Investigator (PI) will oversee the storage and maintenance of all data gathered throughout or after the study. The PI will retain access to the ultimate trial dataset, which will be shared in a de-identified format upon formal request, specifically for research and publication purposes only.\n\nAncillary and post-trial care: In the event of any occurrences resulting in harm from trial participation, care will be provided to the study subjects by the Principal Investigator (PI) following the policies outlined by Ravi Nair Physiotherapy College and DMIHER.\n\nDissemination policy: Data collected during or after the study will only be utilized for academic and research-related purposes culminating in a publication in a reputed journal.\n\nThe Recruitment of participants has not yet started.\n\n\nDiscussion\n\nLateral ankle sprain (LAS) is a common sports injury that frequently impacts physical performances of individuals involved in game like futsal where agility activities like accurate movements, fast direction changes, and fast reactions is required. While conventional physiotherapy approaches have been widely utilized in the Intervention of LAS, there is still a demand for innovative interventions to address this condition to optimize treatment outcomes, to reduced recurrence rates, and enhance patient satisfaction. Our study protocol introduces the integration of immersive virtual reality as an adjunct to conventional physiotherapy, aiming to address the multifaceted nature of LAS by targeting both physical symptoms and psychological factors in futsal athletes.\n\nWhen compared to traditional or no intervention, the meta-analysis of four clinical trials’ results demonstrated a strong and consistent impact of virtual reality (VR) on static balance. However, the research supporting the efficacy of VR apps for dynamic balancing is not entirely conclusive.15\n\nThe results demonstrate that impairments in proprioception, namely in the unconscious (reflexive) as opposed to the conscious (voluntary) component of proprioception, result in balance problems after Grade I and II lateral ankle sprains. This component probably has a major role in the recurrence of ankle sprains. Therefore, maintaining an effective rehabilitation program is crucial for managing proprioceptive deficits.16\n\nStudies have demonstrated the beneficial effects of incorporating virtual reality into rehabilitation programs on motor learning and functional recovery, especially when it comes to activities involving balance and coordination.17\n\nThis study offers some support for the use of Virtual reality assisted intervention in functional ankle instability rehabilitation but no insight into the clinical question of whether the Virtual reality (VR) approach may be used in place of standard physiotherapy procedures or vice versa. On the other hand, we would advise using the VR technique to supplement conventional physiotherapy techniques.10\n\nPhysiotherapists believe that Oculus Quest 2 can be a helpful virtual reality system for shoulder musculoskeletal therapy because it is user-friendly and entertaining for patients. To boost the likelihood that patients will use the system on their own, a few changes are necessary. Virtual reality (VR) can be used in orthopaedic rehabilitation, and the research supporting its effectiveness is generally positive.18\n\nThe purpose of our study is to determine whether using Immersive Virtual Reality (IVR) in adjunct with conventional physiotherapy can improve the performance of futsal players with lateral ankle sprains (LAS) in terms of static balance, dynamic balance, and vertical jump. This study will examine the possible effects of these interventions on sports rehabilitation and emphasize the value of using cutting-edge technology like IVR, by employing rigorous methodology, including randomization and outcome measures such as the Balance Error Scoring System (BESS) (static balance), Y Balance tool (dynamic balance) and X Sens (vertical jump performance). By using IVR for ankle rehabilitation process will probably lead to an early recovery and better prognosis in futsal athletes with LAS.\n\nEthical approval was received from the Datta Meghe Institute of Higher Education and Research (DU), Sawangi (Meghe), Wardha on January 30th 2024 Institutional Ethical Committee approval number: DMIHER (DU)/IEC/2024/182.\n\nParticipants enrolled in the study will be fully informed about the study, and their written informed consent and assent will be obtained from each individual.",
"appendix": "Data availability\n\nNo data were associated with this article.\n\nRepository Name: Figshare\n\nFile Name: SPIRIT Checklist for “Effect of Immersive Virtual Reality in Adjunct to Conventional Physiotherapy on Static Balance, Dynamic Balance and Vertical Jump in Futsal Players with Lateral Ankle Sprain: A Protocol for Randomized Control Trial”.\n\nDOI: 10.6084/m9.figshare.25826125.v1. 19\n\nURL: https://doi.org/10.6084/m9.figshare.25826125.v1.\n\nLicense: CC BY 4.0\n\n\nAcknowledgments\n\nThe authors express their gratitude to DMIHER, for there assistance in sample size calculation and data analysis.\n\n\nReferences\n\nDhillon MS, Patel S, Baburaj V: Ankle Sprain and Chronic Lateral Ankle Instability: Optimizing Conservative Treatment. Foot Ankle Clin. 2023 Jun; 28(2): 297–307. Publisher Full Text\n\nMarín Fermín T, Al-Dolaymi AA, D’Hooghe P: Acute Ankle Sprain in Elite Athletes: How to Get Them Back to the Game? Foot Ankle Clin. 2023 Jun 1; 28(2): 309–320. Publisher Full Text\n\nKobayashi T, Tanaka M, Shida M: Intrinsic Risk Factors of Lateral Ankle Sprain. Sports Health. 2016 Mar; 8(2): 190–193. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStruijs PA, Kerkhoffs GM: Ankle sprain. BMJ. Clin. Evid. 2010 May 13; 2010: 1115.\n\nLynch SA, Renström PAFH: Treatment of Acute Lateral Ankle Ligament Rupture in the Athlete. Sports Med. 1999 Jan 1; 27(1): 61–71. Publisher Full Text\n\nPreatoni E, Bergamini E, Fantozzi S, et al.: The Use of Wearable Sensors for Preventing, Assessing, and Informing Recovery from Sport-Related Musculoskeletal Injuries: A Systematic Scoping Review. Sensors. 2022 Jan; 22(9): 3225. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFeasibility and reliability of a virtual reality oculus platform to measure sensory integration for postural control in young adults: Physiotherapy Theory and Practice.[cited 2024 Jan 10]; 34(12): 935–950. PubMed Abstract | Publisher Full Text\n\nHoch MC, McKeon PO: Peroneal reaction time after ankle sprain: a systematic review and meta-analysis. Med. Sci. Sports Exerc. 2014 Mar; 46(3): 546–556. PubMed Abstract | Publisher Full Text\n\nMartin RL, Davenport TE, Fraser JJ, et al.: Ankle Stability and Movement Coordination Impairments: Lateral Ankle Ligament Sprains Revision 2021: Clinical Practice Guidelines Linked to the International Classification of Functioning, Disability and Health From the Academy of Orthopaedic Physical Therapy of the American Physical Therapy Association. J. Orthop. Sports Phys. Ther. 2021 Apr; 51(4): CPG1–CPG80. PubMed Abstract | Publisher Full Text\n\nKim K, Choi B, Lim W: The efficacy of virtual reality assisted versus traditional rehabilitation intervention on individuals with functional ankle instability: a pilot randomized controlled trial. Disabil. Rehabil. Assist. Technol. 2019 Apr 3; 14(3): 276–280. PubMed Abstract | Publisher Full Text\n\nWang Y, Gu Y, Chen J, et al.: Kinesio taping is superior to other taping methods in ankle functional performance improvement: a systematic review and meta-analysis. Clin. Rehabil. 2018 Nov 1; 32(11): 1472–1481. PubMed Abstract | Publisher Full Text\n\nCoughlan G, Caulfield B: A 4-Week Neuromuscular Training Program and Gait Patterns at the Ankle Joint. J. Athl. Train. 2007; 42(1): 51–59. PubMed Abstract\n\nTerada M, Pietrosimone BG, Gribble PA: Therapeutic Interventions for Increasing Ankle Dorsiflexion After Ankle Sprain: A Systematic Review. J. Athl. Train. 2013 Oct 1; 48(5): 696–709. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee SK, Ahn SH: Effects of balance evaluation comparison of dynamic balance and Y balance. J. Exerc. Rehabil. 2018 Dec 27; 14(6): 939–943. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElaraby AER, Shahien M, Jahan AM, et al.: The Efficacy of Virtual Reality Training in the Rehabilitation of Orthopedic Ankle Injuries: A Systematic Review and Meta-analysis. Adv. Rehabil. Sci. Pract. 2023; 12: 117957272311516. Publisher Full Text\n\nAkbari M, Karimi H, Farahini H, et al.: Balance problems after unilateral lateral ankle sprains. J. Rehabil. Res. Dev. 2006; 43(7): 819–824. PubMed Abstract | Publisher Full Text\n\nSaposnik G, Mamdani M, Bayley M, et al.: Effectiveness of Virtual Reality Exercises in STroke Rehabilitation (EVREST): rationale, design, and protocol of a pilot randomized clinical trial assessing the Wii gaming system. Int. J. Stroke. 2010 Feb; 5(1): 47–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLongo UG, Carnevale A, Andreoli F, et al.: Immersive virtual reality for shoulder rehabilitation: evaluation of a physical therapy program executed with oculus quest 2. BMC Musculoskelet. Disord. 2023 Nov 2; 24(1): 859. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRath B: SPIRIT Checklist for “Effect of Immersive Virtual Reality in Adjunct to Conventional Physiotherapy on Static Balance, Dynamic Balance and Vertical Jump in Futsal Players with Lateral Ankle Sprain: A Protocol for Randomized Control Trial”. figshare. 2024. Publisher Full Text"
}
|
[
{
"id": "299355",
"date": "05 Jul 2024",
"name": "Jente Wagemans",
"expertise": [
"Reviewer Expertise Sports medical & Rehabilitation sciences",
"physiotherapy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear author, Thank you for publishing your methods. With upcoming research regarding motor learning and brain involvement in ligament injuries, this type of interventions can make a real difference. I do have some concerns regarding the paper itself and the methods. I hope my feedback is constructive and useful: A Introduction: 1. May I suggest to use more references throughout the entire work: many statements are made without a reference. 2. Paragraph 1, sentence 2: Could you provide exact numbers regarding the socio-economic impact of lateral ankle sprains? 3. Paragraph 1: CAI is mentioned as a \"syndrome\" - may I suggest consulting the current state of the art regarding this semantics. 4. Paragraph 1: the characteristics of CAI: you mention history of a \"severe\" LAS - again, may I suggest consulting current literature. 5. Paragraph 2: \"ankle joint moves in the sagittal plane\" - the ankle movements are triplanar. 6. Paragraph 4: \"grade I injuries do not require particular treatment after diagnosis\" - please consult most recent literature. The majority of LAS are Grade I, and are considered innocuous; yet 40% develop CAI, and in some sports up to 47% have recurrent LAS.\nB. Methodology: The methods are very clear. I have one concern in terms of sample size. The calculation itself is correct. What is the basis for the considered effect size of 0.8? Please look at previously published RTC's or meta-analyses regarding exercise-based interventions for true found effects of interventions on balance tests or jump tests, and redo the sample size calculations. Arbitrarily considering a large effect can fuel power failure and statistical error.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
},
{
"id": "299357",
"date": "12 Jul 2024",
"name": "Aude Aguilaniu",
"expertise": [
"Reviewer Expertise physiotherapy",
"ankle sprain"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear author, Thank you for this interesting work entitled : « Effect of Immersive Virtual Reality in Adjunct to Conventional Physiotherapy on Static Balance, Dynamic Balance and Vertical Jump in Futsal Players with Lateral Ankle Sprain: A Protocol for Randomized Control Trial ».\nAuthors describe a protocol to evaluate the effect of Immersive Virtual Reality on static balance, dynamic balance and vertical jump in after a lateral ankle sprain in Futsal athletes. A control group will receive a conventional physiotherapy and an intervention group will receive immersive virtual reality in adjunct to conventional physiotherapy.\nHere is some comments and questions to help to improve the paper.\nIntroduction : Few citations are available in the introduction whereas a lot of information is given. I suggest associating more citation on what is said.\nMethodology - When the participant will be recruited? How many days/weeks after the injury? I suggest defining in the inclusion/exclusion criteria a timeline because rehabilitation in acute or subacute phase will be different. Then, I was also wondering when the baseline data will be recorded because in acute phase the athlete could probably not jump? - Do you plan to also include athletes who had a previous injury or only athletes who present an ankle sprain for a first time? Why do you include stretching for grade III and not for grade II ? - Concerning the dosage, I suggest increasing the global charge during the rehabilitation and explain how you will do it. How will you set the weight resistance and the time it will take at the first session and at the last session? Will it be the same weight for all or the weight will be set according to which parameters? Could you make an estimation of the time it will take for a session (is it longer or shorter with the VR ?, Is the global volume will be similar because it could impact the results) - In the table 2, it is specified that VR is used to strengthening part so it would be appropriate to add dorsiflexor, plantarflexor, evertor and invertor strength assessment in the outcome. I also suggest adding range of motion with the WBLT as an outcome (because a deficit in dorsiflexion is a risk factor to sustain an ankle sprain).\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-625
|
https://f1000research.com/articles/13-624/v1
|
12 Jun 24
|
{
"type": "Research Article",
"title": "The association between non-communicable diseases and COVID-19 severity and mortality among infected hospitalized healthcare workers in 29 countries: a cohort study",
"authors": [
"Yusuf Sheku Tejan",
"Jacklyne Ashubwe",
"Mher Beglaryan",
"Shermarke Hassan",
"Sartie Kenneh",
"Francis Moses",
"Abdulai Tejan Jalloh",
"Fassou Mathias Grovogui",
"Ibrahima Kaba",
"Sia Morenike Tengbe",
"Mustapha Kabba",
"Mamud Idriss Kamara",
"Santigie Sesay",
"Jonta Kamara",
"Jerry-Jonas Mbasha",
"Pryanka Relan",
"Innocent Nuwagira",
"Ibrahim Franklyn Kamara",
"Jacklyne Ashubwe",
"Mher Beglaryan",
"Shermarke Hassan",
"Sartie Kenneh",
"Francis Moses",
"Abdulai Tejan Jalloh",
"Fassou Mathias Grovogui",
"Ibrahima Kaba",
"Sia Morenike Tengbe",
"Mustapha Kabba",
"Mamud Idriss Kamara",
"Santigie Sesay",
"Jonta Kamara",
"Jerry-Jonas Mbasha",
"Pryanka Relan",
"Innocent Nuwagira",
"Ibrahim Franklyn Kamara"
],
"abstract": "Background Due to occupational exposure, healthcare workers (HCWs) have a higher risk of Coronavirus Disease 2019(COVID-19) infection than the general population. Non-communicable diseases (NCDs) may increase the risk of COVID-19-related morbidity and mortality among HCWs, potentially reducing the available health workforce. We examined the association between NCDs and COVID-19 disease severity and mortality among infected HCWs.\n\nMethods This cohort study used data from the International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) database. HCWs hospitalized between January 2020 and January 2023 due to clinically suspected or laboratory-confirmed COVID-19 were eligible for inclusion. Variables collected included demographic data, comorbidities, and hospitalization outcomes. Descriptive statistics were reported using mean/standard deviation (SD), median/interquartile range (IQR), or frequencies and proportions. For each NCD, the relative risk of death, adjusted for age and sex, was calculated using log-binomial regression as well as the population-attributable fraction.\n\nResults There were 17,502 HCWs, 95.7% of whom had a confirmed COVID-19 diagnosis. The majority were female (66.5%) and the mean age (SD) was 49.8 (14.3) years. Roughly, half (51.42%) of HCWs had no comorbidities, 29.28% had one comorbidity, 14.68% had 2 comorbidities and <5% had ≥3 comorbidities. The most common comorbidities were diabetes mellitus (49.40%) and cardiovascular disease (36.90%). Approximately one-fifth of the HCWs had severe COVID-19 (16.95%) and 10.68% of the HCWs with COVID-19 died. Being ≥45 years old, male gender, smoking, obesity, and certain NCDs increased the risk of COVID-19 severity and mortality. Obesity and diabetes mellitus were the leading risk factors in terms of the population-attributable risk for COVID-19 severity (6.89%) and mortality (36.00%) respectively.\n\nConclusions Many HCWs with COVID-19 had one or more NCDs. Obesity and diabetes mellitus increased COVID-19 severity and mortality risk. Reducing the prevalence of obesity and diabetes mellitus would yield the biggest reduction in COVID-19-related morbidity and mortality among HCWs.",
"keywords": [
"COVID-19",
"Healthcare workers",
"Noncommunicable diseases",
"Mortality",
"Disease severity",
"SORT IT"
],
"content": "Introduction\n\nThe world was grappling with the triple burden of communicable and non-communicable diseases (NCDs) and injuries, amplified by climate change effects, when it was struck by the Coronavirus Disease (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus- 2 (SARS-CoV-2) virus.1–5 In December 2019, the first case of COVID-19 was detected in Wuhan China. Within a short period the disease had spread to all regions of the world which compelled the World Health Organization (WHO) to declare it a public health emergency of international concern (PHEIC) in January 2020 and characterize it as a pandemic in March 2020 (WHO - COVID-19). This novel virus continued to evolve and spread with emerging strains accounting for increased risk of transmission and different degrees of disease severity within the community and in healthcare settings.6\n\nHealthcare workers (HCWs) bore the brunt of the pandemic through occupational exposure as they cared for COVID-19 patients.7 There is a growing body of evidence showing that HCWs were at higher risk of contracting the virus compared to the general population, as they cared for COVID-19 patients.8,9 The resultant negative physical and mental impacts of the disease on HCWs are well-documented.10,11\n\nHCWs serving in low-and-middle-income countries (LMICs), whose health systems are plagued by resource constraints, were more likely to be adversely affected due to gaps in infection prevention and control (IPC) mechanisms.11–13 A recent study conducted in Sierra Leone documented a high (29%) COVID-19 secondary infection rate among HCWs at three regional hospitals.14 Additionally, two other studies reported that HCWs experienced increased psychological stress including anxiety, isolation, fear, and being overwhelmed particularly in the first three months of the pandemic.15,16\n\nFurthermore, a recent systematic review documented geographical variations in COVID-19-related case fatality rates among HCWs.17 The highest mortality was seen in the Eastern Mediterranean (5.7%) followed by Southeast Asia (3.1%), Africa (1.2%), and Europe (0.6%).17 These differences in mortality rates might have been due to several factors including age, sex, comorbidities, and health system structures.18\n\nA country-based study in Egypt indicated that chronic diseases and home-based management were predictors of COVID-19 severity among HCWs.19 Evidence from a systematic review concurred with these findings that NCDs potentiated the severity of COVID-19 manifestations in the general population.20 These studies highlight the relationship between highly transmissible communicable diseases like COVID-19 and NCDs.\n\nGlobally, WHO reports that NCDs cause 41 million deaths annually.21 The most common NCDs are cardiovascular diseases including hypertension, diabetes mellitus, chronic obstructive pulmonary diseases, and cancers.21 LMICs, previously plagued primarily by infectious diseases, are now seeing an upward trend in NCDs and their attendant disabilities. A recent systematic review indicated that sub-Saharan African countries had seen an increase of 67% in disability-adjusted life years (DALYs) attributable to NCDs between 1990 and 2017.22\n\nThese trends have been associated with an increase in modifiable behavioural factors such as tobacco and harmful alcohol use, low consumption of fruits and vegetables, high intake of salts and sugar, low-fibre diets, obesity, and low physical activity. These behavioural factors are observed both in the general population and among HCWs.23 Several country-specific studies have documented evidence of risk factors for the development of NCDs among HCWs. A study conducted in Brazil estimated a high overall NCD prevalence (30%) among nurses.24 Another study conducted across several provinces in Zimbabwe documented that half (50%) of HCWs had at least one NCD with hypertension (36%) being the most common.25\n\nNCDs, when present as comorbidities, increase the risk of poor treatment outcomes and mortality. Evidence has shown that patients with pre-existing NCDs who were infected with COVID-19 had an increased risk of severe disease and mortality.8,26 A systematic review documented a two-fold increase in severity and a three-fold mortality risk in COVID-19 patients with underlying diabetes mellitus.26\n\nNCDs may increase the risk of COVID-19-related morbidity and mortality among HCWs, potentially reducing the available health workforce. Few studies have been conducted on the effects of NCDs on COVID-19 among HCWs, who have a higher exposure to the disease. Furthermore, no analysis has been conducted on the association between COVID-19 severity and mortality and risk posed by NCDs such as hypertension, diabetes mellitus, or other NCDs among HCWs from an multinational dataset.\n\nTo address this knowledge gap, we conducted a multi-country study among HCWs hospitalized for COVID-19 to (i) describe their demographic attributes and prevalence of NCDs and other risk factors, (ii) examine the association between NCDs and other risk factors and COVID-19 severity and mortality, and (iii) estimate the population-attributable fraction (PAF) of COVID-19 severity and death due to NCDs and other risk factors.\n\nThe findings and recommendations from this study may inform policies and strategies for reducing the vulnerability of HCWs in future public health emergencies and promote the resilience of health systems in the face of such shocks.\n\n\nMethods\n\nThis was a cohort study that used secondary data collected in 29 countries spread across different geographical regions. The study period ran from January 2020 to January 2023. Patients’ records were followed up from hospital admission to exit.\n\nGlobally, 60 countries distributed across Africa, Europe, North and South America, Australia, and the Arab and South-East Asian regions reported COVID-19 cases in healthcare facilities as part of the International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) study. Data collection, aggregation, curation, and harmonisation processes of the ISARIC study have been described previously.27\n\nTwenty-nine countries out of the 60 reporting COVID-19 data into the ISARIC database had reported information on HCWs hospitalized for COVID-19. The reporting countries were Egypt, Gambia, Ghana, Guinea, Libya, Malawi, South Africa, Estonia, Germany, Italy, Ireland, Luxembourg, Poland, Spain, United Kingdom, Argentina, Brazil, Canada, Peru, United States of America, Jordan, Kuwait, Palestine, United Arab Emirates, Australia, Hong Kong, Indonesia, Malaysia, and the Philippines.\n\nHCWs who were hospitalized with clinically suspected or laboratory-confirmed COVID-19 from the 29 countries that reported information on HCWs to the ISARIC database from January 2020 to January 2023 were eligible for inclusion.\n\nParticipating sites used the ISARIC-WHO case report form to enter data into a Research Electronic Data Capture (REDCap version 8.11.11, Vanderbilt University, Nashville, TN) database or the local databases before uploading to the Infectious Diseases Data Observatory (IDDO) database (Open Data Kit is a suitable open access alternative). Centrally collated data were wrangled and mapped to the structure and controlled terminologies of the Study Data Tabulation Model version 1.7, Clinical Data Interchange Standards Consortium, Austin, TX) using TrifactaVR software (OpenRefine is a suitable open access alternative). The independent variables were patient demographic information and the presence of NCD comorbidities; disease severity and patient outcomes were the dependent variables.\n\nSevere COVID-19 was defined as one or more of the following: admission to an intensive care unit (ICU), treatment with invasive mechanical ventilation (IMV), non-invasive ventilation (NIV), high-flow nasal cannulas (HFNC), extra-corporeal membrane oxygenation (ECMO), administration of inotropes and/or vasopressors. Severity was calculated for cases where all the components were not missing. The following comorbidities were assessed; diabetes mellitus (any type), asthma, cardiovascular disease, chronic pulmonary disease (not asthma), rheumatological disorder, chronic kidney disease, malignant neoplasm, chronic neurological disorder, chronic haematological disease, dementia, malnutrition, smoking status and obesity. The data on comorbidities (except obesity) were self-reported. Obesity was defined by the clinicians attending to the patients based on the Body Mass Index of ≥ 30.\n\nData was extracted from the IDDO database.27 R code was used to create a dataset for analysis (R version 4.3.2; R Core Team (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria). We used Stata v18.0 [StataCorp. 2023. Stata Statistical Software: Release 18. College Station, TX: StataCorp LLC] to prepare the data for analysis.\n\nTo estimate the relative risks (RR) of severity and death, we fitted log-binomial regression models (generalized linear models for the binomial family with the log link) for both severity and death outcomes using glm function of R. We omitted predictors with less than 15 outcome events in their exposed category. We adjusted comorbidities’ RR estimates for age and sex. To that end, we fitted a separate model for each comorbidity where predictors were the comorbidity, age, and sex. A P-value of 0.05 was used as the cut-off for statistical significance.\n\nTo estimate the proportion of deaths among HCWs that could be attributed to a specific NCD, we calculated the population attributable fraction (PAF). The PAF (and 95%CI) was calculated for comorbidities that were significant in the adjusted analysis and had RR estimates greater than 1. The R package ‘graphPAF’ R package version 2.0.0) was used to calculate age-and sex adjusted PAF estimates.28\n\nEthical approval was obtained via the global IDDO approval from different countries. The WHO Ethics Review Committee (RPC571 and RPC572, Apr 25, 2013) and the local or national Ethics Committees for participating sites approved the Execution of the ISARIC-WHO Clinical Characterization Protocol. Approvals included the South Central—Oxford C Research Ethics Committee for England (Ref. 13/SC/0149), the Scotland A Research Ethics Committee (Ref. 20/SS/0028) for Scotland, and the Human Research Ethics Committee (Medical) at the University of the Witwatersrand in South Africa as part of a national surveillance programme (M160667), which collectively represent most of the data. For patient data collected and used in research, patient consent was waived according to local norms determined by the responsible Ethics Committee. The IDDO governance processes covered the arrangements surrounding the pooling, storage, curation, and sharing of these data.\n\n\nResults\n\nA total of 841,640 records of patients admitted with COVID-19 were stored in the IDDO platform. Patients were hospitalized between January 2020 and January 2023. Of these, 17,502 (2.08%) were HCWs. Among these HCWs, a COVID-19 diagnosis was confirmed for 16,750 (95.70%). Of the 16,750 HCWs hospitalized with confirmed COVID-19, the majority (11,130, 66.45%) were females, and the mean age (SD) was 49.78 (14.33). Nearly all HCWs in this study were hospitalized in either South Africa or the United Kingdom (11,229, 67.04% and 4,782, 28.55% respectively) (Table 1, Figure 1).\n\n* Percentages of comorbidities are calculated among non-missing entries.\n\nAt the time of admission, half (8,613, 51.42%) of the HCWs had no comorbidities, more than a quarter (4,905, 29.28%) had one comorbidity, 2,459 (14.68%) had 2 comorbidities, and a small proportion had more than 3 comorbidities (773, 4.61%). The most common comorbidities were diabetes mellitus (3,308, 49.40%), cardiovascular disease (5,197, 36.9%), asthma (1,379, 9.80%), and chronic pulmonary disease (not asthma) (346, 2.50%). About a tenth of the HCWs were obese (1,478, 8.82%) (Table 1). Percentages of comorbidities were calculated among entries that had no missing data.\n\n2,839 (16.95%) of the HCWs suffered from severe COVID-19 during their period of hospitalization. Less than a quarter (2800, 16.72%) were admitted to the ICU, nearly one quarter (4,012, 23.95%) of the HCWs received oxygen via HFNC and less than one-tenth (1,293, 7.72%) received oxygen via IMV. The proportion of HCWs who died from COVID-19 was 10.68% (1,789) (Table 2).\n\nAfter adjustment for age and sex, the following factors were significantly associated with severe COVID-19. Age range 45-64 years (RR, 1.91; 95% CI, 1.76-2.07), age ≥ 65 years (RR, 2.02; 95% CI, 1.78-2.27), male gender (RR, 1.52; 95% CI, 1.42-1.62), obesity (aRR, 1.31; 95% CI, 1.21-1.41), smoking (aRR, 1.11; 95% CI, 1.01-1.22), asthma (aRR, 1.24; 95% CI, 1.14-1.35), cardiovascular disease (aRR, 1.14; 95% CI, 1.06-1.23), diabetes mellitus (aRR, 1.00; 95% CI, 0.93-1.08) and chronic pulmonary disease (not asthma) (aRR, 1.22; 95% CI, 1.04-1.41) (Table 3).\n\n† RR for age and sex are not adjusted.\n\n†† Population attributable fraction as percent.\n\n* p-value < 0.05.\n\n** p-value < 0.01.\n\n*** p-value < 0.001.\n\nAfter adjustment for age and sex, the following factors were significantly associated with mortality from COVID-19. Age range 45-64 years (RR, 3.42; 95% CI, 2.95-3.97), age ≥ 65 years (RR, 8.45; 95% CI, 7.28-9.85), male gender (RR, 1.73; 95% CI, 1.59-1.89), obesity (aRR, 1.34; 95% CI, 1.13-1.57), smoking (aRR, 1.09; 95% CI, 0.88-1.36), dementia (aRR, 1.33; 95% CI, 0.87-1.89), diabetes mellitus (aRR, 2.00; 95% CI, 1.73-2.33), chronic haematological disease (aRR, 1.48; 95% CI, 0.80-2.29), cardiovascular disease (aRR, 1.32; 95% CI, 1.20-1.44), chronic kidney disease (CKD) (aRR, 1.25; 95% CI, 0.98-1.54), malignant neoplasm (aRR, 1.34; 95% CI, 1.04-1.68), chronic neurological disorder (aRR, 1.07; 95% CI, 0.66-1.58), chronic pulmonary disease (not asthma) (aRR, 1.21; 95% CI, 0.97-1.46) and rheumatological disorders (aRR, 1.39; 95% CI, 1.01-1.84) (Table 4).\n\n† RR for age and sex are not adjusted.\n\n†† Population attributable fraction as percent.\n\n* p-value < 0.05.\n\n** p-value < 0.01.\n\n*** p-value < 0.001.\n\nObesity (PAF, 6.89%; 95% CI, 4.65-9.22) and cardiovascular disease (PAF,5.29%; 95% CI, 2.07-8.12) were found to have a relatively higher population-attributable risk for COVID-19 severity compared to the other factors (Table 3). Moreover, diabetes mellitus had the highest population-attributable risk for the mortality associated with COVID-19 (PAF, 36.00%; 95% CI, 28.8-44.5) (Table 4). The PAF for COVID-19 mortality associated with cardiovascular disease was also high, calculated at 12.70% (95% CI, 8.68-16.5).\n\nUnder the assumption of a causal relationship between the exposure and, severity and mortality outcomes, we estimated that approximately 6.89% of severe COVID-19 cases and 36.00% of COVID-19-related deaths could potentially be averted if obesity and diabetes mellitus respectively were eliminated as risk factors.\n\n\nDiscussion\n\nOur study is the most comprehensive multi-country study to evaluate the association between NCDs and COVID-19 severity and deaths. The findings add to the global body of evidence on the interaction between NCDs and COVID-19. About half of the HCWs had comorbidities at the time of admission, with the most common comorbidities being hypertension, diabetes mellitus, asthma, cardiac disease, and chronic pulmonary diseases (not asthma). A little over 50% of the HCWs suffered from severe COVID-19 during the period of hospitalization and roughly 11% died. Under the assumption of a causal relationship between the exposure and severity and mortality outcomes, we estimated that approximately 6.89% (95% CI, 4.65-9.22) of severe COVID-19 cases and 36.00% (95% CI, 28.8-44.5) of COVID-19-related deaths could potentially be averted if obesity and diabetes mellitus respectively were eliminated as risk factors.\n\nEvidence from our study showed that COVID-19 affected more female HCWs than males in terms of hospitalization. Other studies have documented similar findings to ours by demonstrating female predominance of HCWs admitted for COVID-19.17,29 A study conducted in Iran recorded a higher COVID-19 prevalence among female HCWs (53.5%) compared to males (46.5%), despite having a higher infection prevalence among males (56.4%) in the general population.29 The reasons for more COVID-19 infection among female HCWs might be due to women being overrepresented in patient-facing healthcare roles such as nursing. Furthermore, women tend to have better health-seeking behaviour than men.30 However, our finding has highlighted the need to explore more robust gender-focused IPC strategies to reduce this HCW vulnerability during infectious disease outbreaks.\n\nOur study identified that about half (49.58%) of HCWs had at least one comorbidity at the time of admission. In keeping with our findings, other studies have also demonstrated the presence of at least one comorbidity and associated risk factors in half of the HCWs.25,31 Furthermore, a 2021 systematic review examining the risk factors for SARS-CoV-2 infection among HCWs found an overall NCD prevalence of 18.4%; hypertension contributed the largest proportion (2.5%), followed by cardiovascular diseases (2.4%), chronic obstructive pulmonary disease (2.4%), and diabetes mellitus (1.4%).32 However, this review did not examine an association between the NCDs and COVID-19 severity and mortality. It is clear that the burden of NCDs is high among HCWs as documented by the present available evidence including our study. NCD prevention and treatment should be prioritized among HCWs.\n\nEvidence from our study indicated that there was an increased likelihood of the HCWs suffering from severe COVID-19 with older age (≥ 45 years), smoking, obesity, and being male. Additionally, we observed that asthma, cardiovascular diseases, and diabetes mellitus were positive predictors of COVID-19 severity. A 2021 study by Joo et al. documented an increased risk for severe COVID-19 in Malaysian HCWs with underlying comorbidities.33\n\nWhen HCWs are vulnerable to adverse health outcomes during an infectious disease outbreak it weakens the health systems’ response to and recovery from public health emergencies. This significant threat to the resilience of health systems highlights the imperative need for strategies to mitigate against the vulnerability of HCWs.34\n\nSpecific risk factors were identified in our study that increased the predisposition for mortality from COVID-19 among the HCWs with COVID-19. These included being older than 45 years, male gender, obesity, and smoking. A WHO study aimed at estimating the impact of COVID-19 on HCWs also highlighted higher mortality (60%) among male HCWs.35 Moreover, from a 2021 systematic review older age, male gender, and obesity heightened the risk of COVID-19 severity and mortality in the general population.36 The study on all the COVID-19 patient data in the ISARIC database documented that obesity led to a 24% increased risk for mortality.37 Looking at the increasing global burden of obesity, HCWs should embark on lifestyle modification activities that will avert the development of obesity.\n\nOur study also found that cardiovascular disease, dementia, diabetes mellitus, chronic haematological disease, chronic kidney disease, chronic pulmonary diseases (not asthma), malignant neoplasm, chronic neurological disorder, and rheumatological disorders significantly increased the risk of COVID-19 deaths. This finding concurred with other studies which showed a higher mortality risk for COVID-19 patients with concurrent cardiac disease and diabetes mellitus.26,38\n\nIn our analysis in terms of the PAF, obesity emerged as the leading risk factor for disease severity and diabetes mellitus as the leading risk factor for mortality associated with COVID-19. The PAF of 6.89% and 36.00% for severity and mortality respectively underscores the substantial impact that such modifiable factors could have on reducing COVID-19 severity and mortality rates. Similarly, a systematic review conducted in 2020 highlighted that the PAF for COVID-19 severity for obesity was 7.1% and that for diabetes mellitus within the general population was 6.5%.20 By focusing on interventions aimed at reducing the incidence of obesity and diabetes mellitus, public health authorities can potentially achieve a dual benefit of mitigating the immediate impact of COVID-19 and enhancing the overall resilience of the HCWs against future infectious disease outbreaks and other health threats.\n\nThe findings from this study have several important implications. Due to the risks posed by NCDs to HCWs, we recommend the establishment of effective occupational health and NCD prevention, screening, and treatment programmes for HCWs. Investing in lifestyle interventions for the prevention of NCDs and associated risk factors particularly obesity and diabetes mellitus amongst HCWs to reduce NCD burden will generate dividends in reducing their vulnerability during infectious disease outbreaks. Additionally, based on the increased gender-related risk of COVID-19 among HCWs, health stakeholders need to explore gender-focused IPC advocacy among HCWs.\n\nOur study had several strengths. First, we utilized a dataset collected from the largest cohort of hospitalized COVID-19 patients from 29 countries across 7 regions. This large sample size and the broad distribution of the HCW population give credence to the emerging evidence. This large and geographically broad sample also reduces biases that might be related to country-level data reporting which might underreport cases35,39 and thus weaken the validity of the evidence. Second, we adhered to Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines for reporting study findings. Third, we conducted a robust statistical analysis to generate the population-attributable fraction which will support the extrapolation of our study findings beyond our study population.\n\nDespite the strengths, our study had some limitations. The majority of the patient information in the ISARIC database was from South Africa and the United Kingdom, whereas the other countries reported limited data. Since reporting to the ISARIC database was voluntary, the reasons for limited data from the other countries remain unknown. However, this underlying reason needs further exploration to develop solutions that will improve data sharing by countries and increase the robustness and geographic generalisability of the database. Based on this limitation, our findings should be generalized with caution. Second, the high number of missing values for some of the comorbidities limited the statistical power concerning some of the comorbidities.\n\n\nConclusions\n\nOur study revealed that many of the HCWs at the frontline of managing COVID-19 had NCDs which increased their vulnerability in the face of infectious disease outbreaks. One fifth of the admitted HCWs suffered from severe COVID-19 and one-tenth of HCWs died due to COVID-19. Additionally, HCWs who were ≥45 years old, male, smokers, and obese had a higher risk of increased severity and/or dying from COVID-19 disease. We recommend the implementation of health education and promotion activities to reduce the NCD burden among HCWs to reduce their vulnerability during infectious disease outbreaks.",
"appendix": "Data availability\n\nThe data that underpin this analysis are available via a governed data access mechanism following a review of a data access committee. Data can be requested via the IDDO COVID-19 Data Sharing Platform (http://www.iddo.org/covid-19). The Data Access Application, Terms of Access and details of the Data Access Committee are available on the website. Briefly, the requirements for access are a request from a qualified researcher working with a legal entity who have a health and/or research remit; a scientifically valid reason for data access which adheres to appropriate ethical principles, and has plans to promote equity in the use of data. The full terms are at: https://www.iddo.org/ebola/data-access-guidelines. These data are a part of https://doi.org/10.48688/cpwp-ft84.\n\nThis article complied with the STROBE guidelines for reporting observational studies.\n\n\nAcknowledgments\n\nThis research was conducted through the Structured Operational Research and Training Initiative (SORT IT), a global partnership led by TDR, the Special Programme for Research and Training in Tropical Diseases hosted at the World Health Organization. The specific SORT IT program that led to this publication is a SORT IT partnership with the WHO Emergency Medical Teams (Geneva), WHO-AFRO (Brazzaville), WHO Country Offices and Ministries of Health of Guinea, Liberia, Sierra Leone, and the Democratic Republic of the Congo, the Infectious Diseases Data Repository (IDDO); The International Union Against Tuberculosis and Lung Diseases, Paris, France and South East Asia offices, Delhi, India; The Tuberculosis Research and Prevention Center Non-Governmental Organization, Yerevan, Armenia; I-Tech, Lilongwe, Malawi; Medwise solutions, Nairobi, Kenya; All India Institute of Medical Sciences, Hyderabad, India; and the National Training and Research Centre in Rural Health, Maferinyah, Guinea.\n\nThere should be no suggestion that the WHO endorses any specific organization, products or services. The views expressed in this article are those of the authors and do not necessarily reflect those of their affiliated institutions. The use of the WHO logo is not permitted.\n\n\nReferences\n\nOrtiz DAP, Abrigo MRM: The Triple Burden of Disease. Economic Issue of the Day. 2017; Vol. 17. Reference Source\n\nAmuyunzu-Nyamongo M: Noncommunicable diseases, injuries, and mental health: the triple burden in Africa. The Pan African medical journal. NLM (Medline). 2022; 43: 167. Publisher Full Text\n\nLadusingh L, Mohanty SK, Thangjam M: Triple burden of disease and out of pocket healthcare expenditure of women in India. PLoS One. 2018 May 1; 13(5): e0196835. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRossati A: Global warming and its health impact. International Journal of Occupational and Environmental Medicine. 2017; 8: 7–20. NIOC Health Organization.\n\nSemenza JC, Rocklöv J, Ebi KL: Climate Change and Cascading Risks from Infectious Disease. Infectious Diseases and Therapy. Adis. 2022; 11: 1371–1390. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeal J, O’Grady HM, Armstrong L, et al.: Patient and ward related risk factors in a multi-ward nosocomial outbreak of COVID-19: Outbreak investigation and matched case–control study. Antimicrob Resist. Infection Control. 2023 Dec 1; 12(1). Publisher Full Text\n\nShah ASV, Wood R, Gribben C, et al.: Risk of hospital admission with coronavirus disease 2019 in healthcare workers and their households: Nationwide linkage cohort study. The BMJ. 2020 Oct 28; 371.\n\nNguyen LH, Drew DA, Graham MS, et al.: Risk of COVID-19 among front-line health-care workers and the general community: a prospective cohort study. Lancet Public Health. 2020 Sep 1; 5(9): e475–e483. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbbas M, Robalo Nunes T, Martischang R, et al.: Nosocomial transmission and outbreaks of coronavirus disease 2019: the need to protect both patients and healthcare workers. Antimicrobial Resistance and Infection Control. 2021; 10. BioMed Central Ltd.\n\nShaukat N, Ali DM, Razzak J: Physical and mental health impacts of COVID-19 on healthcare workers: A scoping review. International Journal of Emergency Medicine. 2020; 13. BioMed Central Ltd.\n\nSaifullah MZ, Li M, Maqbool MQ: Impact of COVID-19 pandemic on health care workers (HCWs) in Sindh Province of Pakistan. Health Research Policy and Systems. 2023 Dec 1; 21(1). Publisher Full Text\n\nKamara IF, Tengbe SM, Fofanah BD, et al.: Infection Prevention and Control in Three Tertiary Healthcare Facilities in Freetown, Sierra Leone during the COVID-19 Pandemic: More Needs to Be Done!. International Journal of Environmental Research and Public Health. 2022 May 1; 19(9). Publisher Full Text\n\nAhmed J, Malik F, Bin Arif T, et al.: Availability of Personal Protective Equipment (PPE) Among US and Pakistani Doctors in COVID-19 Pandemic. Cureus. 2020 Jun 10; 12(6): e8550. PubMed Abstract | Publisher Full Text\n\nSquire JS, Dadzie D, Nyarko KM, et al.: Risk Factors for COVID-19 infection among Hospital Healthcare Workers, Sierra Leone.2020. Publisher Full Text\n\nTengbe SM, Kamara IF, Ali DB, et al.: Psychosocial impact of COVID-19 pandemic on front-line healthcare workers in Sierra Leone: an explorative qualitative study. BMJ Open. 2023 Aug 22; 13(8): e068551. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDzinamarira T, Murewanhema G, Mhango M, et al.: COVID-19 prevalence among healthcare workers. A systematic review and meta-analysis. International Journal of Environmental Research and Public Health. 2022; 19. MDPI.\n\nBandyopadhyay S, Baticulon RE, Kadhum M, et al.: Infection and mortality of healthcare workers worldwide from COVID-19: A systematic review. BMJ Global Health. 2020; 5: e003097. BMJ Publishing Group. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMisra-Hebert AD, Jehi L, Ji X, et al.: Impact of the COVID-19 Pandemic on Healthcare Workers’ Risk of Infection and Outcomes in a Large, Integrated Health System. The Journal of General Internal Medicine. 2020 Nov 1; 35(11): 3293–3301. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEl-Raey F, Alboraie M, Youssef N, et al.: Predictors for severity of sars-cov-2 infection among healthcare workers. Journal of Multidisciplinary Healthcare. 2021; 14: 2973–2981. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi X, Zhong X, Wang Y, et al.: Clinical determinants of the severity of COVID-19: A systematic review and meta-analysis. PLoS One. 2021; 16. Public Library of Science.\n\nNoncommunicable diseases WHO: [cited 2024 Mar 12]. Reference Source\n\nGouda HN, Charlson F, Sorsdahl K, et al.: Burden of non-communicable diseases in sub-Saharan Africa, 1990–2017: results from the Global Burden of Disease Study 2017. Lancet Global Health. 2019 Oct 1; 7(10): e1375–e1387. PubMed Abstract | Publisher Full Text\n\nKhargekar N, Singh A, Shruti T, et al.: A Cross Sectional Assessment of the Profile of Risk Factors of Non-Communicable Diseases Among Health Care Staff of a Tertiary Cancer Hospital. Journal of Lifestyle Medicine. 2022 May 31; 12(2): 98–103. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDomingues JG, da Silva BBC , Bierhals IO, et al.: Noncommunicable diseases among nursing professionals at a charitable hospital in Southern Brazil. Epidemiologia e Servicos de Saude. 2019; 28(2). Publisher Full Text\n\nCalderwood CJ, Marambire E, Nzvere FP, et al.: Prevalence of chronic conditions and multimorbidity among healthcare workers in Zimbabwe: Results from a screening intervention. PLOS Global Public Health. 2024 Jan 23; 4(1): e0002630. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNikoloski Z, Alqunaibet AM, Alfawaz RA, et al.: Covid-19 and non-communicable diseases: evidence from a systematic literature review. BMC Public Health. 2021 Dec 1; 21(1): 1068. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGarcia-Gallo E, Merson L, Kennon K, et al.: ISARIC-COVID-19 dataset: A Prospective, Standardized, Global Dataset of Patients Hospitalized with COVID-19. Science Data. 2022 Jul 30; 9(1).\n\nFerguson J, O’connell M: graphPAF: An R package to estimate and display population attributable fractions.\n\nSabetian G, Moghadami M, Hashemizadeh Fard Haghighi L, et al.: COVID-19 infection among healthcare workers: a cross-sectional study in southwest Iran. Virology Journal. 2021 Dec 1; 18(1): 58. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThompson AE, Anisimowicz Y, Miedema B, et al.: The influence of gender and other patient characteristics on health care-seeking behaviour: A QUALICOPC study. BMC Family Practice. 2016; 17(1): 38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFaruque M, Barua L, Banik PC, et al.: Prevalence of non-communicable disease risk factors among nurses and para-health professionals working at primary healthcare level of Bangladesh: A cross-sectional study. BMJ Open. 2021 Mar 19; 11(3): e043298. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGholami M, Fawad I, Shadan S, et al.: The COVID-19 Pandemic and Health and Care Workers: Findings From a Systematic Review and Meta-Analysis (2020–2021). International Journal of Public Health. 2023; 68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJoo LK, Sazali MF, Goroh M, et al.: Predictors of severe COVID-19 among healthcare workers in Sabah, Malaysia. BMC Health Services Research. 2022 Dec 1; 22(1): 1541. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOkoroafor SC, Asamani JA, Kabego L, et al.: Preparing the health workforce for future public health emergencies in Africa. BMJ Global Health. 2022; 7: e008327. BMJ Publishing Group. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe World Health Organization: The impact of COVID-19 on health and care workers: a closer look at deaths.2021.\n\nLi X, Zhong X, Wang Y, et al.: Clinical determinants of the severity of COVID-19: A systematic review and meta-analysis. PLoS One. 2021; 16. Public Library of Science.\n\nKartsonaki C, Baillie JK, Barrio NG, et al.: Characteristics and outcomes of an international cohort of 600 000 hospitalized patients with COVID-19. International Journal of Epidemiology. 2023 Apr 1; 52(2): 355–376. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPranata R, Henrina J, Raffaello WM, et al.: Diabetes and COVID-19: The past, the present, and the future. Metabolism: Clinical and Experimental. W.B. Saunders; 2021; 121. .\n\nGholami M, Fawad I, Shadan S, et al.: The COVID-19 Pandemic and Health and Care Workers: Findings From a Systematic Review and Meta-Analysis (2020–2021). International Journal of Public Health. 2023; 68. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "317489",
"date": "25 Sep 2024",
"name": "Max Carlos Ramírez-Soto",
"expertise": [
"Reviewer Expertise Infectious diseases"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study they evaluate risk factors for COVID-19 in health care workers. Their findings reveal that age, sex, diabetes and cardiovascular disease are risk factors for severity and death. These risk factors have been studied extensively, in the general population and in different risk groups. Although the study has interesting data, further analysis is needed to prove the association described above.\n\nMajor comments: Methods. To check for compliance with the STROBE guideline items. Statistical analysis. What assumptions were used to calculate the RR. Regarding the number of comorbidities, 2 or more should define multi-morbidity.\n\nResults They should include a flow chart with information on included and excluded cases with their respective reasons. Table 1 and 2. There are many unknowns, e.g., Current smoker, obesity, severity, Non-invasive ventilation, Inotropes, vasopressors, and High-flow oxygen nasal cannulas.\n\nTable 3. The authors should revise their analyses. This table includes data from 7858 patients, however in the comparisons of variables, none of the sums of yes and no variables match. Table 4. They do not include ratios because they include the population 16674.\nThe authors included the population between January 2020 and January 2023. Here, my main concern is that from 2021 onwards health workers were the first at-risk group to be vaccinated, but the authors did not include vaccination as an adjustment variable. Also, the study does not assess, nor does it compare variables before vaccination and after vaccination. It is likely that the highest number of cases occurred before vaccination (during 2020). For this year alone, a pre-vaccination analysis should be conducted to determine the association with risk factors, and another analysis in the vaccinated population (2021 to 2023), to assess whether the risk of age, sex, cardiovascular disease and diabetes persist in the vaccinated population compared to the unvaccinated.\n\nDiscussion and conclusions should be modified based on further analysis.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-624
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https://f1000research.com/articles/13-621/v1
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11 Jun 24
|
{
"type": "Research Article",
"title": "An Evaluation of Sagittal Balance and the Influence of Spinopelvic Components on Sagittal Balance through the Correction and Stabilization Using the Pedicle Screw Rod System on Patients with Adolescent Idiopathic Scoliosis",
"authors": [
"Ayiq Mahmud",
"Saifullah Asmiragani",
"Luthfi Gatam",
"Saifullah Asmiragani",
"Luthfi Gatam"
],
"abstract": "Background The pedicle screw rod system is believed to correction of 3-dimensional deformity and maintain the results of the correction, so the better sagittal balance correction can be expected.\n\nMethods We conducted a retrospective cohort study on 43 adolescent idiopathic scoliosis (AIS) patients who performed correction, stabilization and posterior fusion to determine the effect of spinal and spinopelvic components on sagittal balance correction. X-ray data were measured for thoracic kyphosis and lumbar lordosis as the spinal components and pelvic incidence (PI), pelvic tilt (PT), and sacral slope (SS) as the spinopelvic components. Further evaluations include sagittal spinal balance (C7PL), global sagittal balance, and sacrofemoral distance pre- and post-surgery. Statistical evaluation is performed to determine the correlation between the spinal and the spinopelvic components and the achievement of sagittal balance correction.\n\nResults TK/Sagittal Modifier obtained a significant correction with an average is 18.69° (±9.57), while LL (lumbar lordosis) has 44.58 ° (±11.94). Average of C7PL correction is 0.68 cm (±3.13), Global Sagittal Balance is -2.04 cm (±3.24), and SCFD is 2.69 cm (±2.48). The TK/LL degree doesn’t significantly influence on Global Sagittal Balance and C7PL. The TK degree significantly affects SCFD, whereas LL doesn’t significantly affect SCFD. Changes in each spinopelvic component are not significant in affecting Global Sagittal Balance.\n\nConclusions Correction and stabilization of AIS’s patients using the pedicle screw rod system resulted in significant Spinal Component TK/Sagittal Modifier and LL correction. Meanwhile, Spinopelvic Components didn’t achieve significant correction. Mean correction of C7PL is -2.66 (±4.4) and Global Sagittal is -3.11 cm (±4.94), SCFD only managed to correct 37.3%. Global Sagittal Balance is not significantly affected by all components of Spinopelvic components, while the C7PL is only affected by PT. Only PT and SS that significantly affected SCFD.",
"keywords": [
"Keywords: Adolescent Idiopathic Scoliosis",
"Spinal Component",
"Spinopelvic Component",
"Sagittal Spinal Balance",
"Sagittal Global Balance",
"SCFD"
],
"content": "Background\n\nThe correction of scoliosis deformities is a challenge for a spine surgeon related to the success of correction of coronal and sagittal deformities and, the cessation of progression, with no complications. The correction of scoliosis deformities followed by spinal fusion is a major action of almost the last century.1,2 Various types of instrumentation aim to achieve better 3-dimensional correction, including the correction maneuver, which was originally only pure distraction and compression, at this time, translation and derotation can also be done. Spinal sagittal balance, which is the accumulation of thoracic kyphosis and lumbar lordosis, is one of the parameters of success of the correction of the sagittal plane measured from the center of C7 and projected against posterosuperior corner S1.3,4\n\nChanges in sagittal balance that are not normal will first change the horizontal haze where the body will try to reach a normal point by not affecting the vision of the object in the front. Patients with an unbalanced sagittal balance, are unable to walk or stand perfectly without forcing the muscles to straighten up due to imperfect biomechanics.5 As a result of an imbalance in sagittal balance, the muscles will easily experience fatigue, and this causes pain.5\n\nMany instrumentations have been used, but not all instrumentation guarantees sagittal balance correction. Research on Harrington instrumentation found no satisfactory sagittal correction.6 Another generation is the CDI (Cottrel-Dubousset Instrumentation) which was first published by Richards et al., which only achieved a coronal balance correction of 49.6%12 and sagittal balance correction that was not significant.6\n\nThe pedicle screw rod system allows distraction, compression, translation and derotation. Therefore, it is believed to provide the correction of coronal, sagittal and axial plane deformities. In a study conducted by Vagmin Vora et al in adolescent idiopathic scoliosis (AIS) patients, which compared the use of a universal system with intraspinosus wire for pedicle screw use, it was found that pedicle screw was better in correcting the sagittal plane (thoracic kyphosis).7 However, that study did not explain achieving sagittal balance correction. Research conducted by Wimmer et al and Storer et al only compared the hook and pedicle screw system for coronal correction.8 Likewise, Kim et al only compared the coronal curve correction by the pedicle screw system vs hybrid instrumentation and hook system3,9 [Figure 1].\n\nThis figure/table has been reproduced with permission from Ref. 3.\n\nSagittal balance is the attainment of the balance of cervical lordosis, thoracic kyphosis and lumbar lordosis.10 Curves that are opposite of starting cervical lordosis, thoracic kyphosis, and lumbar lordosis allow for the absorption of load or efficient distribution of the spine and increase the efficiency of the spinal muscles. Of these curves, lumbar lordosis plays the most important role in maintaining efficient upright postures.2,11\n\nBroadly speaking, the sagittal balance of the body is determined by two components, namely the component of the spine (spine) and the pelvic component, which can be called spinopelvic components. Parameters in the spine as explained above include thoracic kyphosis and lumbar lordosis. Other parameters for determining the sagittal balance of the spine component include C7PL (C7 Plumb line), SCFD (Sacrofemoral distance), Sagittal global balance, thoracolumbar junction, T9 Sagittal offset, and L1 Tilt. As for determining the sagittal balance of the pelvic component, it can be measured from the pelvic tilt (PT), pelvic incidence (PI), and sacral slope (SS).\n\nSagittal balance measurements are obtained by measuring each sagittal balance parameter on the long standing film (standing full spine) by positioning the elbows at 90° and shoulder 45°.2 The measurement locations of thoracic kyphosis and lumbar lordosis from several different pieces of literature mention that, some measure from T1 - T12 or T2 - T12 as a thoracic component and L1 - L5 as a lumbar component.12 In the case of scoliosis, measurements of the sagittal plane components, according to King’s classification, are carried out on the thoracic spine of T4-T12. According to King’s classification, the selection of measurement of thoracic kyphosis and lumbar lordosis is carried out at this level because it is considered to have a neutral rotation.6 If the measurement obtained at the anterior angle of the spine is given a positive value, a negative value is obtained when measuring the posterior angle of the spine. The thoracic component measured at T4 - T12 is considered normal if the values obtained are in the range from +25° to +40°, while lumbar lordosis measured from L1 - L5 is considered normal if the values obtained are in the range from -35° to -55°.6 Other literature mentioned the term sagittal alignment with global sagittal alignment. Global sagittal alignment consists of global thoracic kyphosis measured from the upper endplate T2 and lower endplate T12, global lumbar lordosis is measured from the upper endplate L1 and upper endplate S1.13 TK/LL measurements are more often based on levels that have been determined according to the Lenke’s classification because they are more comprehensive, and these measurements are used by the authors. In accordance with Lenke’s classification, the measurement of thoracic kyphosis is at T5 - T12 with a normal mean value of 10-40 degrees,14 while lumbar lordosis is measured at the inferior end plate T12/L1 - S1 with normal values in the range of 40-60 degrees.14,15\n\nSagittal spinal balance or C7PL is another parameter besides thoracic kyphosis and lumbar lordosis that can be used to determine sagittal balance. Sagittal spinal balance (C7PL) is a measure of the horizontal distance between the C7 sagittal plumb line and the posterosuperior corner of S1. The distance that is considered within the normal limit is 3 cm or less from the posterior superior corner S1 (the plumb line is located in front of or behind the L5 – S1 disc).5 There is positive value if the C7 sagittal plumb line is > 2 cm in the anterior promontorium and there is negative value if the C7 sagittal plumb line is > 2 cm in the posterior promontorium.5,16,17 Global Sagittal Balance is the horizontal distance between the vertical line that passes through the HA (hip axis) and the vertical line that is parallel and passes through the promontorium and is known as the sacrofemoral distance (SCFD). The center of gravity, known as the hip axis, illustrates where the center of gravity falls along the body. The hip axis (HA) which is the center of gravity (CG) is the middle between the hip center or the middle of the line drawn from the two central head femurs. Global Sagittal Balance that can be considered within normal limits after correction is -2 to 3 cm.5 The closer the hip axis is, the less likely it is to translate body weight that causes compensation from the pelvis and spinal muscles.\n\nSpinopelvic components also affects sagittal balance, wherein some recent research, it is believed spinopelvic components are the key to achieving optimal balance.18 Spinopelvic alignment is translated as the interaction between the spine and pelvis that regulates such that weight falls on the hip axis18 [Figure 2]. Sagittal sacropelvic alignment can be assessed from PT (pelvic tilt), and SS (sacral slope), which is considered an embodiment of the mechanism of pelvic compensation against imbalance.\n\nThis figure/table has been reproduced with permission from Ref. 18.\n\nBecause spinopelvic alignment acts as a compensation reaction to the spine imbalance above it, a fixation construction will greatly affect the spinopelvic compensatory mechanism or even eliminate the compensatory mechanism. A pelvic tilt is an angle formed between a vertical line that passes through the hip axis and a line that connects the middle sacral end plate and the hip axis. Pelvic incidence is an angle formed from a line perpendicular to the sacral end plate and a line that passes through the hip axis (bicoxofemoral axis) and the midpoint of the sacral end plate. The sacral slope is the angle formed between the horizontal line and the sacral end plate. The normal values for each parameter considered normal are 41 ° ± 8.4 ° for sacral slope, 13 ° ± 6 ° for pelvic tilt, and 55 ° ± 10.6 ° for pelvic incidence.2 Other literature mentions values that are considered within the normal range, for pelvic tilt (PT) it is 10 ° to 25 °, for pelvic incidence (PI) it is 40 ° to 65 °, and for sacral slope (SS) it is 30 ° to 50 °.16\n\nThe incidences of scoliosis are known to be more common in women, with some conditions that cause a decrease in quality of life and pain, where some other conditions leads to balance disorders when standing and walking.19 This occurs because of the frontal and horizontal rotation which causes the interaction between the spine, trunk and pelvis. Delay in the correction of this deformity exacerbates pain and causes disc degeneration, joint degeneration, and flatbac.17 Patient with scoliosis have shorter stride lengths, varying muscle activation when walking, and less body stability. The correction of deformities in scoliosis remains a challenge, especially axial or rotational and sagittal. While coronal and axial or rotational will provide aesthetic effects related to the presence of a rib hump, sagittal deformity affects functionally that is more related to cervical balance, prevention of CHD (proximal junctional kyphotic), and thoracic volume effects,17 Patients with scoliosis with disturbed sagittal balance are relatively affected, experiencing defective natural backward balance. Normal sagittal balance allows one to walk upright with little effort. As a consequence of not having normal sagittal balance, the compensatory reaction will appear as being able to walk upright by reflecting one’s knee, which causes biomechanical changes in other structures.20 The restoration of sagittal balance, especially for thoracal kyphosis, is not only to prevent the occurrence of junctional degeneration (proximal or distal) but also to restore pulmonary function.17\n\nDecreased lordosis can occur due to an abnormality in the lumbar spine itself or due to a compensatory reaction due to an imbalance that results in a relative posterior translation of the vertebral disco structure21 [Figure 3]. Changes in abnormal lordosis do not mean that the patient is in a sagittal imbalance condition, but it can also occur as a compensatory reaction due to sagittal imbalance in another place, such as flat back or hyperkyphosis.21 For example if there is a change in the thoracic kyphosis outside the normal limits, which then changes the center of gravity, the body will then compensate by making the center of gravity return to the actual center of gravity, which is behind the femoral axis, by making changes in the lordosis to tolerable limits. If the compensatory reaction is not achieved, then the spinopelvic component will be included to achieve the maximum sagittal balance level [Figure 4].\n\nThis figure/table has been reproduced with permission from Ref. 21.\n\nAchievement of sagittal balance becomes highly important because of the effects that may occur due to imbalances in the sagittal plane of the spine. Flat back is one condition that is a form of compensation for the imbalance.22 The correction of the sagittal field should be followed by ensuring optimal sagittal balance. When the sagittal plane is within normal limits but is not followed by the achievement of the sagittal balance, this condition needs to be re-evaluated.\n\nThe spinopelvic factor has a close relationship with restoring the sagittal balance, meaning that if a normal sagittal plane is achieved but is not followed by sagittal balance, it is necessary to evaluate the pelvic component, which is one of the most important factors. Vice versa, when there is an imbalance in the spine, this will affect the pelvic component itself as a form of compensation for all the effects that may arise.\n\nLumbar lordotic (LL) is closely related to pelvic orientation expressed by the sacral slope, and it is strongly influenced by pelvic incidence. From this we can see a close relationship between the spinal parameters and the pelvic component. Lumbar lordotic changes, for example, will change pelvic incidence as a parameter determined by the sacral slope. As compensation for achieving pelvic incidence that remains within the normal range, the pelvic tilt will be enlarged by shifting the center sacral slope backward so that it is possible for slippage or spondylolisthesis. Another compensation is to reflect on the knee with all the consequences. Proper postoperative evaluation is highly necessary to determine the results of the correction of sagittal balance before various compensation including the appearance of slippage are made.23 The results of a retrospective study conducted by Giovanni Andrea La Maida on 76 AIS patients obtained the results of uncorrected sagittal balance, especially for Lenke’s type 1 curves and patients with hypokyphosis.23\n\nAll abnormalities that cause changes in sagittal balance need to consider components that affect changes in sagittal balance when operations are to performed so that normal sagittal balance is achieved. In the case of scoliosis, so far the only concern is how to achieve correction of coronal balance and sagittal balance. A corrective and instrumentation operation is said to be successful if short and long term evaluations are found with a sagittal balance within the normal range.24\n\nJackson and Hales stated that there is a close relationship between thoracic kyphosis, lumbar lordosis, pelvic position and sagittal plane malalignment which will be seen clinically if there is a loss of lordosis from the lumbar spine. Excessive kyphosis has the potential to increase intradiscal pressure and affect the workings of the spinal erector muscles. Clinical patients with an imbalance in the sagittal plane will experience pain, faster fatigue, body imbalance, and interference with horizontal vision.14 If this condition is left untreated, then the advanced condition will be compensated for by doing hip extension, genu flexion, and this will ultimately result in increasing susceptibility to fatigue.25\n\nThe influence of age, the presence of disc degeneration, or accompanying abnormalities that may be present in the hip and pelvis will further aggravate clinical complaints if found in patients with sagittal imbalance because the compensatory reactions that occur are not optimal.26 The return of sagittal balance to normal or near normal condition will reduce the work of the erector muscle of the spine and hamstring muscles to achieve balance.11,25\n\n\nMethods\n\nA retrospective cohort study was carried out by collecting secondary data on adolescent idiopathic scoliosis patients from the scoliosis registration, who had performed surgery and stabilization with a pedicle screw rod system from 1 July 2018 to 30 November 2018. The approval committee for the research is The Ethics Committee of Saiful Anwar General Hospital, Malang with approval number: 400/222/K.3/302/2023. The date of approval 12 September 2023. The data from the DICOM radiology file, long standing film and seen from C7 to the head of femur, then measured using the Horos software™ (https://horosproject.org/) for the research variables, namely spinal component (thoracic kyphotic and lumbar lordotic), spinopelvic component (PT, PI, and SS), and sagittal balance variables (sagittal spinal balance, sagittal global balance, and SCFD) pre-operative and post-operative.\n\n\nResults\n\nTable 1 shows that the coronal cobb angle obtained a significant correction of 37.93 ° (± 15.66 °) with the correction of the postoperative average curve at 19.94 ° (± 10.59). Meanwhile, the corrections for each coronal curve (PT, TL/L) obtained corrections exceeding 50% except for the MT (Main Thoracic) curve, which can only achieve around 45% correction, but, in general, the coronal balance correction reaches 50.15% and is significant. The TK/Sagittal Modifier component was successfully and significantly corrected at 8.93 ° (± 13.21) with a post-operative mean correction of 18.7 ° (± 9.57). The LL component achieved a significant correction of 7.51 ° (± 12.8) with a postoperative average achievement of 44.58 ° (± 11.94). PT (pelvic tilt) achieved a correction with an average of 10.23 ° (± 13.69 °), PI (pelvic incidence) achieved an average correction of 45.33 ° (± 15.35), and SS (sacral slope) achieved an average of 36.33 ° (± 8.67).\n\nSagittal spinal balance (C7PL) obtained a significant correction of -2.66 (± 4.4) with a postoperative average of 0.68 cm (± 3.13), Global Sagittal Balance achieved a significant correction of -3.11 cm (± 4.94) with a postoperative mean of -2.04 cm (± 3.24). SCFD obtained a correction of 0.18 (± 2.78) with a postoperative average of 2.69 cm (± 2.48) but this correction is not statistically significant with p > 0.05.\n\nTable 2 shows that the Global Sagittal Balance increases by 0.057 cm for each additional 1 ° of TK, and a decrease in the value of the Global Sagittal Balance of 0.04 cm for each additional 1 ° of LL. After testing the effect of a variable with the t-test, it shows that the addition of TK and LL degrees do not significantly influence or have weak effects on Global Sagittal Balance.\n\nWith regard to C7PL, every additional 1° of TK will reduce the C7PL value by 0.02 cm, and every additional 1° of LL will reduce the C7PL value by 0.03 cm. When the effect of variables is tested with the t-test, it shows that the addition of TK and LL degrees has no significant effect or has weak effects on C7PL. With respect to SCFD, for each additional 1 ° of TK, the SCFD value will decrease by 0.08 cm and for each additional 1 ° of LL, the SCFD value will increase by 0.02 cm. Based on the t-test, it showed that LL does not have a significant effect on all sagittal balance parameters and TK only had a significant effect on SCFD, while the effect of TK on Global Sagittal Balance and C7PL was not significant or had a weak effect.\n\nThe evaluation of the influence of spinopelvic components (PT, PI, and SS) on global sagittal balance using linear regression shows that every additional 1 ° of PT will increase the sagittal global balance by 0.02 cm, each additional 1 ° of PI will reduce the global sagittal balance by 0.02 cm, and each additional 1 ° of SS will reduce sagittal global balance by 0.02 cm. After testing the effect of the changes in each spinopelvic component (PT, PI, and SS) on the sagittal global balance, the value of each spinopelvic component (PT, PI, SS) has p> α =0.05, which means that the changes in each spinopelvic component are not significant in affecting global sagittal balance.\n\nThe evaluation of the influence of spinopelvic components (PT, PI, and SS) on C7PL using linear regression shows that each additional 1 ° of PT will increase C7PL by 0.189 cm, each additional 1 ° of PI will decrease C7PL by 0.109 cm, and each additional 1 ° of SS will increase C7PL by 0.105 cm. Then, the influence of each spinopelvic component (PT, PI, and SS) was tested on C7PL and the results show that only PT significantly affects C7PL changes with p = 0.029 < α = 0.05.\n\nThe evaluation of the influence of spinopelvic components on SCFD using linear regression shows that each additional 1 ° of PT will increase SCFD by 0.179 cm, each additional 1 ° of PI will reduce the SCFD value by 0.077 cm, and each additional 1 ° of SS will increase the SCFD value by 0.137 cm. Then, the t-test was performed to determine the effect of the changes in each spinopelvic component (PT, PI, and SS) on SCFD. From the t-test, it is found that PT significantly influences SCFD with a p-value of (0.005) < α = 0.05, SS significantly influences SCFD with a p-value of (0.034) < α = 0.05, while PI does not significantly influence SCFD with a p-value of (0.129) > α = 0.05. This means that the spinopelvic components that most influences SCFD changes are PT and SS [Table 3].\n\n\nDiscussion\n\nAchieving coronal balance correction is not much different from a meta-analysis study by Harrington instrumentation, which stated that the correction of coronal curves can be achieved with an average of 50%. Judging from the results of this study, instrumentation shows that the pedicle screw rod system is not significantly different from the results of coronal balance correction when compared with the use of Harrington instrumentation.28\n\nThe achievement of TK (thoracic kyphosis) correction in our study is almost the same as the results of previous studies that performed the addition of sublaminar bands with the achievement of TK (thoracic kyphosis) correction which was significant at 8 ° ± 7.17 The amount of SD (standard deviation) in our study was due to the large variation of data that we have or may also be caused by the insufficient number of samples. The percentage of the correction of TK/Sagittal modifier and LL (lumbar lordotic) reached 98.1% with a significant change in the paired t-test [Table 4]. Increasing or decreasing the TK/LL degree does not significantly influence or has weak influence on Global Sagittal Balance and C7PL. The increase or decrease in TK degree significantly affects SCFD, whereas LL does not significantly affect SCFD. As stated by Jackson and Hales in their paper,14 there is a close relationship between thoracic kyphosis, lumbar lordosis, pelvic position and sagittal plane malalignment which will be observed clinically. The loss of lordosis from the lumbar spine calls for more further evaluation and a clear explanation.\n\nOverall spinopelvic components (PI, PT, SS) obtain a 100% correction rate on each measurement variable, but the change was not significant. This can be caused by several possibilities, one of which is the number of samples that were not large enough or the wide range of normal spinopelvic values that were not proportional to the achievement of the correction.\n\nOnly Sagittal Spinal Balance (C7PL) and Global Sagittal Balance achieved significant correction while SCFD was not significantly corrected. Based on the percentage, SCFD was only managed to be corrected by 37.3%. Sagittal balance correction is affected by various factors and not merely instrumentation including the size and type of implant (rod) used. Techniques, strategies, and stages of correction as well as the experience of the operator also determine the success of the correction, including the objective conditions of the deformity.17 Changes in the contour of the rod at the time of the correction affect the results of the correction which automatically affects the post-operative clinical condition. In a study evaluating the correlation between pre-operative bending rods and the level of deformation of the rods during operation, finding show a close relationship in determining the sagittal balance correction results.17\n\n\nConclusion\n\nThe correction and stabilization of adolescent idiopathic scoliosis patients using a pedicle screw rod system show a significant correction of the spinal component TK/Sagittal Modifier and LL. Meanwhile, the spinopelvic components PT, and SS do not achieve a meaningful correction. Sagittal Spinal Balance (C7PL) and Global Sagittal Balance obtain a significant correction, while SCFD do not obtain a meaningful correction and only managed to be corrected by 37.3%. The correction of TK/LL does not significantly influence or has weak influences on Global Sagittal Balance and C7PL. The correction of TK only significantly affects SCFD, whereas LL does not significantly affect SCFD. The correction of all spinopelvic components (PT, PI, and SS) has no significant effect on Global Sagittal Balance. Only PT has a significant effect on Sagittal Spinal Balance (C7PL), while only PT and SS have a significant effect on SCFD.\n\nEthical approval for this research was obtained from approval committee: The Ethics Committee of Saiful Anwar General Hospital, Malang with approval number: 400/222/K.3/302/2023. The date of approval 12 September 2023.\n\nWritten informed consent for publication of their details and clinical images was obtained from the patient.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nPahys JM, Guille JT, D’Andrea LP, et al.: Neurologic injury in the surgical treatment of idiopathic scoliosis: guidelines for assessment and management. J. Am. Acad. Orthop. Surg. 2009; 17: 426–434. PubMed Abstract | Publisher Full Text\n\nVialle R, Levassor N, Rillardon L, et al.: Radiographic analysis of the sagittal alignment and balance of the spine in asymptomatic subjects. J Bone Jt Surg - Ser A. 2005; 87(2): 260–267. PubMed Abstract | Publisher Full Text\n\nKim YJ, Lenke LG, Cho SK, et al.: Comparative analysis of pedicle screw versus hook instrumentation in posterior spinal fusion of adolescent idiopathic scoliosis. Spine (Phila Pa 1976). 2004; 29(18): 2040–2048. PubMed Abstract | Publisher Full Text\n\nLykissas MG, Jain VV, Nathan ST, et al.: Mid- to long-term outcomes in adolescent idiopathic scoliosis after instrumented posterior spinal fusion: A meta-analysis. Spine (Phila Pa 1976). 2013; 38(2): E113–E119. Publisher Full Text\n\nChang KW, Leng X, Zhao W, et al.: Quality control of reconstructed sagittal balance for sagittal imbalance. Spine (Phila Pa 1976). 2011; 36(3): E186–E197. PubMed Abstract | Publisher Full Text\n\nHalm H, Castro WH, Jerosch J, et al.: Sagittal plane correction in “King-classified” idiopathic scoliosis patients treated with Cotrel-Dubousset instrumentation. Acta Orthop. Belg. 1995; 61(4): 294–301. PubMed Abstract\n\nVora V, Crawford A, Babekhir N, et al.: A pedicle screw construct gives an enhanced posterior correction of adolescent idiopathic scoliosis when compared with other constructs: Myth or reality. Spine (Phila Pa 1976). 2007; 32(17): 1869–1874. PubMed Abstract | Publisher Full Text\n\nSuk SI, Lee CK, Kim WJ, et al.: Segmental pedicle screw fixation in the treatment of thoracic idiopathic scoliosis. Spine (Phila Pa 1976). 1995; 20(12): 1399–1405. Publisher Full Text\n\nCuartas E, Rasouli A, O’Brien M, et al.: Use of all-pedicle-screw constructs in the treatment of adolescent idiopathic scoliosis. J. Am. Acad. Orthop. Surg. 2009; 17: 550–561. Publisher Full Text\n\nKim YJ, Bridwell KH, Lenke LG, et al.: An analysis of sagittal spinal alignment following long adult lumbar instrumentation and fusion to l5 or S1: Can we predict ideal lumbar lordosis?. Spine (Phila Pa 1976). 2006; 31(20): 2343–2352. PubMed Abstract | Publisher Full Text\n\nClaus AP, Hides JA, Moseley GL, et al.: Different ways to balance the spine: Subtle changes in sagittal spinal curves affect regional muscle activity. Spine (Phila Pa 1976). 2009; 34(6): E208–E214. PubMed Abstract | Publisher Full Text\n\nBenli IT, Akalin S, Kiş M, et al.: Frontal and sagittal balance analysis of late onset idiopathic scoliosis treated with third generation instrumentation. Kobe J. Med. Sci. 2001; 47(6): 231–253. PubMed Abstract\n\nUcar B: A new corrective technique for adolescent idiopathic scoliosis (Ucar′s convex rod rotation). J Craniovertebr Junction Spine. 2014; 5(3): 114–117. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nKim MK, Lee SH, Kim ES, et al.: The impact of sagittal balance on clinical results after posterior interbody fusion for patients with degenerative spondylolisthesis: a pilot study. BMC Musculoskelet. Disord. 2011; 12(England PT-Journal Article LG-English DC-20110421): 69. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLenke LG, Betz RR, Harms J, et al.: Adolescent idiopathic scoliosis. A new classification to determine extent of spinal arthrodesis. J Bone Jt Surg - Ser A. 2001; 83(8): 1169–1181. Publisher Full Text\n\nChi JH, Lee R, Mummaneni PV: idiopathic scoliosis. A new classification to determine extent of spinal arthrodesis. Neurosurg. Clin. N. Am. 2007; 18(2): 325–328. PubMed Abstract | Publisher Full Text\n\nBruce 2011: Idiopathic Scoliosis The Harms Study Group Treatment Guide. J. Chem. Inf. Model. 2013; 53: 1689–1699.\n\nBarrey C, Roussouly P, Le Huec JC, et al.: Compensatory mechanisms contributing to keep the sagittal balance of the spine. Eur. Spine J. 2013; 22(SUPPL.6): 834–841. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOhrt-nissen S, Bari T, Dahl B, et al.: Sagittal Alignment After Surgical Treatment of Adolescent Idiopathic Scoliosis d Application of the Roussouly Classification.2018; 6: 537–544.\n\nLeteneur S, Simoneau-Buessinger É, Barbier F, et al.: Effect of natural sagittal trunk lean on standing balance in untreated scoliotic girls. Clin. Biomech. 2017; 49(September): 107–112. PubMed Abstract | Publisher Full Text\n\nIlharreborde B, Pesenti S, Ferrero E, et al.: Influence of implant rod curvature on sagittal correction of scoliosis deformity. Eur. Spine J. 2018; 27(2): 350–357. PubMed Abstract | Publisher Full Text\n\nLee C-H, Chung CK, Jang J-S, et al.: Effectiveness of deformity-correction surgery for primary degenerative sagittal imbalance: a meta-analysis. J. Neurosurg. Spine. 2017; 27(5): 540–551. PubMed Abstract | Publisher Full Text\n\nSaha D, Gard S, Fatone S, et al.: The effect of trunk-flexed postures on balance and metabolic energy expenditure during standing. Spine (Phila Pa 1976). 2007; 32(15): 1605–1611. PubMed Abstract | Publisher Full Text\n\nLa Maida GA, Zottarelli L, Mineo GV, et al.: Sagittal balance in adolescent idiopathic scoliosis: Radiographic study of spino-pelvic compensation after surgery. Eur. Spine J. 2013; 22(SUPPL.6): 859–867. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO’Sullivan PB, Grahamslaw KM, Kendell M, et al.: The effect of different standing and sitting postures on trunk muscle activity in a pain-free population. Spine (Phila Pa 1976). 2002; 27(11): 1238–1244. PubMed Abstract | Publisher Full Text\n\nYagi M, Kaneko S, Yato Y, et al.: Walking sagittal balance correction by pedicle subtraction osteotomy in adults with fixed sagittal imbalance. Eur. Spine J. 2016; 25(8): 2488–2496. PubMed Abstract | Publisher Full Text\n\nLegaye J, Duval-Beaupère G: Sagittal plane alignment of the spine and gravity a radiological and clinical evaluation. Acta Orthop. Belg. 2005; 71(2): 213–220. PubMed Abstract\n\nPotter BK, Lenke LG, Kuklo TR: Prevention and management of iatrogenic flatback deformity. Journal of Bone and Joint Surgery - Series A. 2004; 86: 1793–1808. Publisher Full Text"
}
|
[
{
"id": "330131",
"date": "25 Oct 2024",
"name": "Yong Hai",
"expertise": [
"Reviewer Expertise Spine suregry",
"spinal deformity"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study evaluates the impact of the pedicle screw rod system on sagittal balance in adolescent idiopathic scoliosis (AIS) patients. It involved a retrospective cohort of 43 patients undergoing correction and stabilization. Key findings include significant improvements in thoracic kyphosis and lumbar lordosis, with average corrections of 18.69° and 44.58°, respectively. However, the study found that spinopelvic components had minimal influence on global sagittal balance. Specifically, while thoracic kyphosis positively affected sacrofemoral distance, other components did not yield significant corrections. Overall, the pedicle screw rod system effectively improves certain spinal parameters but has limited impact on spinopelvic alignment.\nHowever, several key areas could be improved to enhance the clinical utility and methodological rigor of the study. Please consider addressing the following points:\n1. Lack of innovation: There is a lot of literature on this topic. This article fails to provide significant innovations, and it is difficult to attract enough academic attention.\n2. Sample size problem: The study's small sample size negatively impacts the reliability of the correlation analysis and may lead to uncertainty in the results.\n3. Insufficient description of methodology: The introduction of the methodology part of the article is too brief and lacks detailed information, which may hinder other researchers from replicating and verifying the experiment.\n4. Clinical guidance significance: It is unclear whether this study has practical guidance significance for clinical practice. The author should clearly explain its potential impact on clinical application.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-621
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https://f1000research.com/articles/13-620/v1
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11 Jun 24
|
{
"type": "Research Article",
"title": "Association of LEP rs2167270 and LEPR rs1137100 genetic variants with obesity in the Jordanian population cohort",
"authors": [
"Manal Jarrar",
"Maen Hasan",
"Moawiya Haddad",
"Maher Obeidat",
"Ahmad Al-Qerem",
"M. Dulce Estêvão",
"Maria Palma Mateus",
"Manal Jarrar",
"Maen Hasan",
"Maher Obeidat",
"Ahmad Al-Qerem",
"M. Dulce Estêvão",
"Maria Palma Mateus"
],
"abstract": "Background Previous Genome Wide Association Studies (GWAS) of obesity susceptibility genes in different populations have confirmed the association of some variants with obesity, body mass index (BMI), and some related metabolic traits. To our knowledge, the current study is the first to investigate the genetic basis of obesity in the Jordanian population. The aim of our study is to investigate the occurrence and frequency of obesity-related genes in Jordanian individuals and any possible relationship between SNP genetic markers and phenotypic characteristics of studied individuals.\n\nMethods A total of 150 Jordanian unrelated adults, including 83 obese, 26 overweight, and 41 normal-weight subjects, were genotyped using the high resolution melt analysis (HRMA) and tested for the association of single nucleotide polymorphisms (SNPs), rs2167270 in LEP gene and rs1137100 in LEPR gene, with obesity risk, obesity/overweight risk, BMI, weight, height, total cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides, and blood level glucose.\n\nResults A significant association between obesity risk and the rs2167270 mutation in LEP gene was observed under a dominant model (odds ratio (OR) = 2.5147, 95% CI =1.0629 to 5.9494, p = 0.0358). A marginal (not significant) association between BMI and the rs2167270 mutation in LEP gene (p = 0.075), was also detected. Moreover, an association between rs2167270 mutation in LEP gene and glucose blood level was observed (p = 0.038). Total cholesterol and LDL-cholesterol also presented a weak association with the rs1137100 mutation in LEPR gene, with p = 0.071 and p = 0.078, respectively. Additionally, no significant association between LDL-cholesterol and the rs2167270 mutation in LEP gene was observed (p = 0.091). By contrast, there was no association between weight or height and the SNPs mutation evaluated in this study (p > 0.05).\n\nConclusions These results suggest that some SNPs in some obesity-related genes may contribute to obesity risk and its related anthropometric and metabolic traits in Jordanian population. To confirm these results, further studies on a larger Jordanian cohort should be carried out.",
"keywords": [
"Obesity",
"Overweight",
"LEP rs2167270",
"LEPR rs1137100",
"genetic variants",
"Jordan"
],
"content": "Introduction\n\nObesity is a multi-factorial disease resulting mainly from environmental and genetic factors, are defined as ‘abnormal or excessive fat accumulation that presents a risk to health’. A body mass index (BMI) over 25 is considered overweight, whereas over 30 is obese.1 According to the latest update of the Human Obesity Gene Map there are 253 quantitative trait loci related with obesity and obesity-related phenotypes that were identified from 61 genome-wide scans. Additionally, 127 candidate genes were associated with obesity phenotypes.2 Moreover, it has been reported that in genome wide association studies (GWAS) the authors analyze the interaction between genetic predisposition and the intake of sugar-sweetened beverages in relation to body-mass index, based on these 32 loci that were previously reported.3,4 Six new loci associated with BMI highlight a neuronal influence on body weight regulation,4 and association analyses of 249,796 individuals reveal 18 new loci associated with BMI.4,5 Association analyses of 249,796 individuals reveal 18 new loci associated with BMI.5 Leptin, a 16-kDa hormone of 167 amino acids, is encoded by LEP gene on chromosome 7,6 and is secreted mainly by the adipose tissue,7 is a member of the leptin-melanocortin pathway. Leptin plays a key role in energy homeostasis and in the control of satiety. Leptin exerts this action by binding to its receptor (LEPR) in the hypothalamus in a region responsible for energy homeostasis and appetite.8 Based on this mode of action, variations in the LEP or LEPR genes may have a role in the development of obesity or its markers.\n\nStudies evaluating the occurrence of single nucleotide polymorphisms (SNPs) in particular genes can provide insights into how changes in the genome may affect the risk of developing a disease such as obesity. SNPs are variations in a single nucleotide base in DNA that can occur between individuals, and some of these variations have been linked to an increased or decreased risk of developing certain diseases.9\n\nFor example, certain SNPs in genes that regulate appetite and energy expenditure have been found to be associated with an increased risk of obesity. These genes may play a role in how the body regulates food intake and energy balance, and variations in these genes may alter these processes, leading to an increased risk of developing obesity.10 By identifying specific SNPs associated with obesity risk, researchers can gain a better understanding of the genetic factors involved in the development of this disease. This knowledge can also be used to develop personalized approaches to preventing and treating obesity based on an individual’s genetic profile.5 However, it’s important to note that genetic factors alone cannot fully explain the development of obesity, and other factors such as lifestyle, environment, and epigenetic modifications also play a role.11\n\nTo our knowledge, this study is the first to investigate the putative genetic basis of obesity in the Jordanian population. This study aims to investigate if there is a relationship between mutation in the genome and the obesity risk in Jordanians through the analysis of two variants in leptin and leptin receptor genes namely, rs2167270 and rs1137100, respectively, and to investigate any possible relationship between these two variants and phenotypic characteristics of studied individuals.\n\n\nMethods\n\nThe study was approved by the Institutional Committee of the faculty of graduate studies at Al-Balqa Applied University on March 1, 2019 (Proposal Reference Number: session 6/2019). Human procedures were followed in accordance with the Helsinki Declaration of 1975 as revised in 2013. Written informed consent was obtained from all patients, indicating their agreement to take part in the study.\n\nA total of 150 Jordanians with no other diagnosed disease between the ages of 19-55 years participated in this study during the period of March and July 2019. The study was performed on volunteers from Al-Balqa Governorates and executed at Al-Balqa Applied University. Data on dietary habits, medical implication, physical activity, and family history for each participant were obtained by completing an interview questionnaire (face-to-face interactions).\n\nInclusion criteria include that the person belonged to the University, either students, academic teachers or members of the administration body. The exclusion criteria encompassed individuals with heart diseases, kidney issues, and metabolic syndrome. It also involved those who underwent bariatric surgeries or any stomach-related intervention for weight reduction, as well as individuals whose overweight or obesity result from hormonal disorders (i.e. hypothyroidism, Cushing’s disease, and hypogonadism) or the use of cortisone or other medications.\n\nHeight was measured with a portable Harpenden stadiometer® to the nearest millimeter (0.1 cm). Participants were barefoot, dressed in minimal clothing, standing with heels together, arms out to the side, legs straight, shoulders relaxed and the head in the Frankfurt plane. Body weight was measured using an Inbody™ 770 scale, to the nearest 0.1 kg with the subjects barefoot and wearing light clothes. BMI was calculated using the formula Weight/Height (kg/m2) and study participants were categorized normal (BMI 18.5–24.9) as overweight (BMI ≥ 25) and obese (BMI ≥ 30 according to the World Health Organization (WHO) standards for adults.12\n\nPeripheral venous blood samples after 10-12 hours fasting were collected in EDTA and plain tubes for SNPs genotyping and serological tests, respectively. Blood samples collected in plain tubes were centrifuged at 2,500 rpm for 15 minutes. The resulting serum was transferred to Eppendorf tubes and stored at -20°C until they were used for the serological analyses within a period not exceeding three months.\n\nSerum lipid levels, and fasting serum glucose (FSG) were analyzed with test kits (Biolabo) and expressed as mg/dl. Absorbance was measured using a Biovawe II spectrophotometer. FBG was determined by the glucose oxidase method and total cholesterol (TC) and triglyceride (TG) concentrations were determined using standard enzymatic methods. High density lipoprotein-cholesterol (HDL-C) was measured by precipitation method. Finally, low density lipoprotein-cholesterol (LDL-C) was calculated using Friedewald formula.\n\nGenomic DNA was extracted from white blood cells contained in 1.0 ml peripheral blood using Wizard® Genomic DNA Purification Kit (Promega) according to manufacturer’s instructions. DNA quality and concentration were assessed using a gel electrophoresis and a Biovawe II spectrophotometer. DNA solutions were prepared with a final concentration of 50 ng/ul and stored at -20°C until use.\n\nPrimers were designed to flank the selected SNP using Primer3 (RRID:SCR_003139) software applying the following criteria: product size: 40-100 bp, length: 19-23 bp, GC content: 45-60%, GC clamp: up to 3, annealing temperature: 55-60°C and an annealing temperature difference between each two pairs of primers of 1°C. The quality of the chosen primers, primer-dimer or cross dimer was assessed using DNAMAN software DNAMAN 10.0 – Integrated System for Sequence Analysis13 and Primer Premier 6.25 – PCR Primer Design Software.14 For the optimization of primers annealing temperature, PCR reactions for each pair of primers were performed at three different annealing temperatures above and below the calculated Tm (e.g., 50, 55 and 60°C, when the calculated Tm was 55°C). The optimal annealing temperature was the one that gave the lowest number of quantification cycles (Cq), with no nonspecific amplification or primer dimers formation. Then, the PCR product was evaluated using an 0.8% agarose gel electrophoresis and the PCR product with one single, bright band of the expected size on was chosen to be the optimized to PCR amplification. The selected primers used in this study are listed in Table 1. PCR amplification was carried out using a master mix from Kappa-bio Systems, prepared to fit the requirement of the High-Resolution Melt Analysis (HRMA) technology, in which a special dsDNA dye (EvaGreen) was included. The selected primers, related to each SNP, were used to amplify the region containing the respective SNP. DNA amplification was carried out using CFX96 real-time PCR applying the following cycling parameters: initial denaturation at 95.0°C for 4:00 min, denaturation at 95.0°C for 0:10 min, primers annealing step for 0:30 min (at different temperature according to the results of the primer annealing temperature optimization for each SNP as shown in Table 1). The extension step was carried out at 72.0°C for 0:30 min. A total of 37 cycles were used for both SNP amplification. The amplification step was followed by the melting step by raising the temperature from 65.0°C to 95.0°C (increment 0.5°C, 0:05) after a denaturation step at 95°C for 1:00 minute. The resulting melt curves were analyzed using Precision Melt Analysis™ software version 1.3.15 The SNPs for the selected genes were genotyped using the HRMA technique. Data were generated using CFX96 real-time PCR detection system and analyzed using Precision Melt Analysis™ software.\n\nStatistical analysis was performed using IBM SPSS Statistics (RRID:SCR_016479), version 23 (SPSS Inc., Chicago, IL, USA). The association of each SNP with the risk of obesity was assessed by calculating Person’s chi-square test and odds ratio (OR). The analysis was performed under the dominant, recessive, and co-dominant models. The associations of BMI and metabolic traits with genotypes were evaluated using the analysis of variance test (ANOVA) using t-test. P-values < 0.05 were considered statistically significant.\n\n\nResults\n\nThe biochemical and clinical characteristics of the participants in this study are summarized in Table 2. A total of 83 participants were identified as obese, 26 as overweight, and 41 as normal weight. There were significant differences in the BMI (p < 0.0005), weight (p < 0.0005), triglycerides (p = 0.005) between obese, overweight, and normal weight groups. Among the participants with obesity, 46 were within class I obesity, 20 within class II, and 17 within class III. BMI means were 32.3 ± 3.3, 36.6 ± 4.7, and 44.6 ± 7.4 for class I, class II and class III respectively.\n\nThe genotyping success rate for LEP rs2167270 for the 150 participants was 87% (131 participants were successfully genotyped), of which 41 (31.3%) were homozygous for the wild-type (GG) genotype, 59 (45.0%) were heterozygous (GA), and 31 (23.7%) were homozygous for the variant (AA) genotype (Figure 1). The genotypes of this SNP were in Hardy-Weinberg equilibrium (χ2 = 1.16, p > 0.05). The frequency of the rs2167270 (A) allele (minor allele frequency) for all participants was (46%). There was a significant difference (p ≤ 0.05) in the risk allele (A) frequency within normal, obese, and obese/overweight participants. The frequency for normal weight was 41%, for obese was 53%, and for the obese/overweight group was 48%.16\n\nData were generated using CFX96 real-time PCR detection system and analyzed using Precision melt analysis software. (A) Normalized melt curves. (B) Difference curves. GG genotype (wild type) is represented by the green curves cluster. AA genotype (mutant) is represented by the blue curves cluster. GAgenotype (heterozygote) is represented by the red curves cluster. (Each curve represents one single sample).\n\nThe mean values of BMI for GG, GA, and AA genotypes were 28.4, 31.6, and 31.2, respectively. ANOVA test was applied to evaluate the association between rs2167270 genotype and the anthropometric and metabolic characteristics. No association was observed between this SNP and the BMI, although a certain trend was detected (p = 0.075; Table 3). No other associations were observed with the BMI within the different participants groups considered but a certain trend toward significance within the female subgroup was determined (p = 0.09; Table 4). A significant association between the LEP rs2167270 with the fasting blood glucose levels (p = 0.038) was found. However, no associations were observed with the other metabolic traits evaluated in this study (Table 3). However, an association was found between the LEP rs2167270 and obesity under the dominant model (AA + GA vs. GG; OR = 2.52, 95% CI = 1.063-5.949, p = 0.036; Table 5). The Chi-square test was performed and a trend toward significance was found between the LEP rs2167270 and the risk of obesity under the additive model (χ2 (2, N = 109) = 4.895, p = 0.086; Table 5). Using the same model, no association was observed between this variant and the obesity/overweight risk, for all participants (χ2 (2, N = 131) = 4.09, p = 0.130; Table 6) nor for male or female subgroups (Table 7). The association between the LEP rs2167270 and the risk of obesity/overweight under the dominant and the recessive mutations (AA vs. GA + GG) was also tested (Table 6). No association was detected within all participants under these models, although the dominant model showed a certain trend toward significance (OR = 2.019, 95% CI = 0.901-4.524, p = 0.088; Table 6).\n\n* There is a significant difference between variables.\n\n* There is a significant difference between variables.\n\nThe genotyping success rate for LEPR rs1137100 was 94.7% (142 participants were successfully genotyped) of which 116 (81.7%) were homozygous for the wild-type (AA) genotype, 19 (13.4%) were heterozygous (GA), and 7 (4.9%) were homozygous for the variant (GG) genotype (Figure 2). The genotypes of this SNP were in Hardy-Weinberg equilibrium (χ2 = 17.25, p > 0.05). The minor frequency of the rs1137100 G allele for all (142) participants was 12%. There was a slight (not significant) difference in the risk allele (G) frequency within normal (12%), obese (13%), and obese/overweight participants (11%).\n\nData were generated using CFX96 real-time PCR detection system and analyzed using Precision melt analysis software. (A) Difference curves. (B) Normalized melt curves. AA genotype (wild type) is represented by the red curves cluster. GG genotype (mutant) is represented by the blue curves cluster. GA genotype (heterozygote) is represented by the green curves cluster. (Each curve represents one single sample).\n\nThe mean values of BMI for AA, GA, and GG genotypes were 31.0, 29.5, and 28.7, respectively. ANOVA test, which was applied to find the association between the LEPR rs1137100 genotype and the anthropometric and metabolic traits, showed no association of this SNP with BMI (p = 0.55; Table 8). However, marginal associations with total cholesterol (p = 0.071) and LDL cholesterol (p = 0.078) were observed (Table 8). Also, no associations were observed with BMI within participants groups (Table 9). The chi-square test was performed, and no relationship was found between the risk of obesity and the LEPR rs1137100 genotype using the additive model (X2 (2, N = 142) 0.26, p = 0.987). The association of LEPR rs1137100 with the risk of obesity using the dominant (AA vs. GA + GG), and recessive (AA + GA vs. GG) models were also tested (Table 9). No associations were detected within all participants groups using these models (Table 10), or within males or female separately (Table 11).\n\n\nDiscussion\n\nSince the discovery of leptin,6 many association studies have been carried out to identify the variations in the LEP gene that may be associated with obesity and its related anthropometric and metabolic characteristics.17,18 One of these variations was the rs2167270 (A19G), located in the first exon of the 5′ Untranslated Region.17 So far, few studies specifically concerning the association between the LEP rs2167270 genotype and obesity and its related anthropometric and metabolic characteristics are available.18–23 Table 2 shows a sample of these studies.\n\nThe genotype results for LEP rs2167270 obtained in this study are similar to the frequencies of the three LEP rs2167270 genotypes presented in several different populations studied in the International HapMap project.16\n\nSo far, most studies focused on the association of rs2167270 with serum leptin level, as this SNP might be involved in obesity by affecting leptin concentration.24 A systematic review and meta-analysis study25 addressing the associations of some adipokine genes variants with obesity susceptibility, revealed 10 studies that concerned with LEP variants. Four of these studies concerned the rs2167270 variant in particular.18–21 The overall results of these four studies, which included 553 obese and 365 controls, reported a non-significant association with obesity under dominant (OR = 1.14, 95% CI = 0.75–1.74 p = 0.53) and recessive models (OR = 0.89, 95% CI 0.67–1.20 p = 0.45). In the present study, the percentage of normal-weight participants who carried the GG genotype (42.9%) were larger than the percentage of obese/overweight participants (27.1%) who carried the same genotype, and the percentage of the normal-weight participants whose genotype is CC or CT (57.1%). It was also slightly smaller than the percentage of the obese/overweight participants (72.9%) whose carried these same genotypes. However, using the odds ratio under the dominant model, this difference did not reach the significant level of association with the risk of overweight/obesity, which is consistent with a Brazilian study22 and the four other studies included in the meta-analysis mentioned above, but it showed a certain trend toward significance (OR =2.019, 95% CI = 0.901-4.524, p = 0.0878), which was further verified to be restricted to the risk of obesity alone (OR =2.5147 95% CI =1.0629 to 5.9494, p = 0.0358). This result is consistent with an Indian study23 under dominant model (OR = 1.699, 95% CI =1.043–2.766, p = 0.03314). Association of LEP rs2167270 with obesity-related traits, i.e., BMI, has been the subject of many studies (Table 2) with contradictory results. While some studies confirmed the existence an association regarding to BMI,23,26 other studies revealed opposite results.18,20\n\nThe mean BMI of the participants not carrying any of the LEP rs2167270 risk alleles (GG) was 28.4, which is lower than the mean BMI of those carrying one risk allele (GA, 31.6), and carrying two risk alleles (AA, 31.2). This difference did not show a significant association but only a significant margin (p = 0.075), which may be due to the small sample size analyzed. However, these results are in line with those reported in other studies.18,20 Additionally, we observed that this small margin was maintained in the women’s group (p = 0.090) but was not observed when the men’s group was analyzed separately (p = 0.356), which suggests a Sex effect in this association between the LEP rs2167270 and the BMI. To validate these findings, studies involving a larger Jordanian cohort of each Sex should be conducted. To our knowledge, there are no studies reporting an association of LEP rs2167270 with serum lipid and glucose levels in adults, but a study including 136 Japanese children found no significant association of this SNP with serum lipids levels.27\n\nThe LEPR rs1137100 is a functional SNP in which the adenine (A) nucleotide is replaced by a guanine (G) nucleotide in exon two of the LEPR gene. As a result, lysine amino acid (K), encoded by the codon (AAG), is replaced by arginine (R), which is encoded by the codon (AGG). Rung et al., represents the distribution of the three LEPR rs1137100 genotypes in different populations studied in the International HapMap project.28 In general, it can be noted that the genotyping results for LEPR rs1137100 obtained in this study are similar to the genotyping frequencies in all populations, except for Japanese Tokyo (JPT), Han Chinese (CHB and HCB), and Chinese in Metropolitan Denver, Colorado (CHD). It can also be observed that the genotype frequencies are closer to Luhya, in Webuye, Kenya (LWK) and Maasai, in Kinyawa, Kenya (MKK) populations. An available review including previous studies that investigated the association of several known leptin and leptin receptor variants with obesity29 reported that the results of the included studies were inconclusive. This review shows that the LEPR rs1137100 SNP-obesity association was investigated in five studies and that in one them, the LEPR rs1137100 was associated with obesity in children but not in adults.30 Another study revealed that the LEPR rs1137100 is associated with obesity only in the presence of other two SNPs (LEPR rs8179183 (K656N) and SNP in the LEP gene 3’ flanking region).31 The other three studies related to LEPR rs1137100 included in the review showed no association with obesity or BMI.32–34 The results of the present investigation have shown that the percentage of normal-weight participants carrying the AA genotype is very close to the percentage of overweight and obese participants with the same genotype. In addition, the percentage of the normal-weight participants with the GA or GG genotype is also very close to that of the overweight and obese participants with the same genotype. Consequently, the current study revealed that there is no association between the LEPR rs1137100 and obesity under all the considered genetic models of inheritance. This result is in line with two studies that were conducted in 2011. A systematic review conducted by Bender et al.,34 evaluated the association of several common variants in LEPR including the rs1137100 with overweight while other systematic review and meta-analysis, including seven studies (five European and two Japanese), and enrolling 1,595 cases and 1,173 controls, also showed that there is no significant association of this SNP with obesity susceptibility.25\n\nThe mean BMI of participants not carrying any of the LEPR rs1137100 risk alleles (AA) was 31.0, while for those with one risk allele was (GA) the mean BMI was 29.5. For the participants carrying two risk alleles (GG) the determined BMI was 28.7, which is the lowest value. This result contrasts with what was expected, as the BMI decreased in those with both risk alleles. No changes were observed when analyzing the subgroups of participants (men and women, separately). This suggests that the G allele in the LEPR rs1137100 may have a protective effect against increased BMI, which is consistent with a Saudi study conducted in Jeddah city.35 However, they report a significant association with BMI in females but not in males, which contradicts the current study in which the BMI difference determined was not statistically significant. This lack of association with BMI is in line with the results of several other available studies.32,33,36\n\nWhile most studies have investigated the LEPR rs1137100-obesity association (Table 3), few studies that have analyzed the relationship of this SNP with serum lipid levels. A Japanese study carried out with 136 children reported a significant association between homozygous GG genotype and low levels of total cholesterol and low-density lipoprotein (LDL) cholesterol, but no association was found with triglycerides (TG) and high-density lipoprotein (HD) cholesterol.27 On the contrary, the current study showed a marginal significant association between the LEPR rs1137100 with total and LDL cholesterol, with the GG genotype being associated with higher total and LDL cholesterol levels. However, both studies agree that no association was observed with TG and HDL.\n\nThe findings of this study provide valuable insights into the potential role of the rs2167270 variant in the LEP gene as a contributing factor to obesity and metabolic parameters. The results indicate that under the dominant model, the rs2167270 variant is associated with an increased risk of obesity, as evidenced by higher BMI levels. This observation is consistent with previous research that has linked the LEP gene to obesity susceptibility.23 Moreover, the presence of the rs2167270 variant is associated with elevated blood glucose levels and LDL-cholesterol, highlighting its impact on glucose metabolism and lipid regulation. These findings align with other studies that have explored the influence of genetic variants on glucose metabolism and lipid profiles.23\n\nOf note, while the rs2167270 variant showed associations with BMI, blood glucose, and LDL-C, it did not exhibit significant correlations with total cholesterol, HDL-cholesterol, or triglyceride levels. This discrepancy might be attributed to the complex interplay of multiple genetic and environmental factors influencing lipid metabolism.23 Further investigations involving larger and more diverse populations are warranted to comprehensively elucidate the specific genetic determinants of these lipid parameters.\n\nOverall, this study highlights the potential significance of the rs2167270 variant in the LEP gene as a genetic marker for obesity risk and metabolic disturbances. Understanding the role of this genetic variant may aid in the development of targeted interventions and personalized approaches for the management and prevention of obesity-related complications.\n\n\nConclusions\n\nThe results of the current study suggest that the SNPs; rs2167270, in LEP gene, whereas rs1137100, in the LEPR gene, may not contribute to obesity risk and/or one or more of its related anthropometric and metabolic characteristics in the Jordanian population. This study suggests that the rs2167270 in the LEP gene may contribute to the risk of obesity, under the dominant model, and to higher blood glucose levels, BMI and LDL-C but it does not contribute to the higher total cholesterol, HDL-C or triglycerides. This study also revealed that the rs1137100 in LEPR gene may contribute to the higher total cholesterol and LDL-C blood levels, but that it is not associated with the risk of obesity (evaluated by the BMI value), HDL-C, triglycerides or blood glucose levels. No associations of both studied SNPs with weight or height were found in this study.\n\nThe limitations of the study include a small sample size, which limits the statistical power. To confirm the findings presented, studies involving larger Jordanian cohorts should be conducted.",
"appendix": "Data availability\n\nFigshare: Participants Data F1000Research.xlsx, https://doi.org/10.6084/M9.FIGSHARE.25284637.v1. 37\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nWorld Health Organization: Obesity and overweight.2021. Retrieved June 9, 2021. Reference Source\n\nRankinen T, Zuberi A, Chagnon YC, et al.: The human obesity gene map: the 2005 update. Obesity. 2006; 14(4): 529–644. PubMed Abstract | Publisher Full Text\n\nQi Q, Chu AY, Kang JH, et al.: Sugar-sweetened beverages and genetic risk of obesity. N. Engl. J. Med. 2012; 367(15): 1387–1396. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWiller CJ, Speliotes EK, Loos RJ, et al.: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat. Genet. 2009; 41(1): 25–34. 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}
|
[
{
"id": "290616",
"date": "27 Jun 2024",
"name": "Suzanne Al-Bustan",
"expertise": [
"Reviewer Expertise Human Genetics",
"Genetic Association of Metabolic disorders",
"Genetic structure of Arab populations"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper titled \"Association of LEP rs2167270 and LEPR rs1137100 genetic variants with obesity in the Jordanian population cohort\". The study describes a genetic association of two gene SNPS (LEP rs2167270 and LEPR rs1137100) with obesity in the Jordanian population and the main observed significance of LEP rs2167270 with obesity.\n\nAlthough the manuscript is well written and the experimental design is well described and executed, there are several issues that need to be addressed by the authors before considering its approval. One major issue is the sample size of the cohort (n=150) and the number of controls is less than the obese samples which can influence the overall outcome of the study. The authors have stated that this is a limitation of the study, however, the authors must support the results considering the low sample size. A minor issue to consider is to revise the manuscript for typo's and syntax errors. 1. Define the abbreviation for SNP in background as it appears before the methods and only use the abbreviation in the methods of the abstract. I suggest deleting \"genetic\" before markers as it is obvious. 2. First paragraph of the introduction: Line 7 refer to \"these loci\" but it is not clear what they are, consider rephrasing this statement. Lines 8 and 9, \"reveal\" should be in the past tense. 3. The correct nomenclature for the gene abbreviation is in italics. This should be corrected throughout the manuscript. 4. Paragraph 3, Line 1: The authors must cite the relevant reference. 5. The rationale behind selecting those specific SNPs is not clearly defined and how it formulated into the objectives. 6. In the methods under sampling and biochemical analysis, the authors need to provide the reference values for the sugar and lipid parameters. 7. The authors should perform power calculations to determine the power of the sample used in the study. The sample size is small and when classified into the three classes of obesity, I believe it maybe too small to draw sound conclusions. 8. As the number of the cohort samples is small, the authors should reconsider grouping the overweight samples (n=28) with the controls if their BMI is marginal. It is also not statistically sound to compare this group (n=28) with the obese and controls 9. The authors should provide some explanation on why numerous samples were unsuccessfully genotyped used the described method. 10. In the discussion, paragraph 4, line 6 and 8, the word \"Sex\" should be in a small letter. 11. The authors should elaborate on the role of the LEP SNP on the gene function in relation to obesity and support functional prediction. 12. The first line in the conclusion is inconsistent with the third line in reference to rs2167280. The authors should revise the statements.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "295233",
"date": "30 Aug 2024",
"name": "Siska Mayasari Lubis",
"expertise": [
"Reviewer Expertise Obesity",
"adrenal",
"thyroid",
"and diabetes"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nResearches should write down the research design used in this study clearly in the research method.\nFrom the results, the researcher wrote \"this study suggests that the rs2167270 in the LEP gene may contribute to the risk of obesity, under the dominant model, and to higher blood glucose levels, BMI and LDL-C but it does not contribute to the higher total cholesterol, HDL-C or triglycerides\" whereas, from the results we can see that there is only significant relationship with fasting plasma glucose but no associations were observed with the other metabolic traits evaluated in this study and also BMI (Table 3). It would be best for researchers to explain their reasons for making this conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-620
|
https://f1000research.com/articles/10-55/v1
|
29 Jan 21
|
{
"type": "Research Article",
"title": "Vaccination against hepatitis B virus in hemodialysis patients: trends in dialysis centers of Northern Pakistan",
"authors": [
"Muhammad Nadeem",
"Syed Asim Ali Shah",
"Naveed Arshad",
"Faiza Riaz",
"Rizwan Saeed Kiani",
"Muhammad Abdul Quddus",
"Syed Asim Ali Shah",
"Naveed Arshad",
"Faiza Riaz",
"Rizwan Saeed Kiani",
"Muhammad Abdul Quddus"
],
"abstract": "Background: Chronic kidney disease (CKD) patients, especially those on hemodialysis, are at increased risk of developing hepatitis B virus (HBV) infection. Guidelines suggest that all patients with CKD should be vaccinated against HBV, but these guidelines are usually not followed. We conducted this study to know the status of vaccination against HBV in CKD patients on regular hemodialysis. Methods: This observational descriptive study was conducted at the Department of Medicine, Sheikh Khalifa Bin Zayed Teaching Hospital, Poonch Medical College Rawalakot , and POF Teaching Hospital, Wah Medical College Wah Cantt, from March to July 2019. Patients reporting to the dialysis center of both hospitals on regular dialysis were included in the study. Patient information (HBV vaccination status, age, gender, education, socioeconomic status, duration of CKD and duration of dialysis) were collected on a specially designed questionnaire. The statistical analysis of data was done in SPSS for Windows, version 20. Results: A total 149 patients were included in the study, 63.1% were male and 36.9% were female. Out of these 24.2% were uneducated, 33.6% had 1-10 years school education, 38.2% had 10-14 years education, and 4% had more than 14 years education. About 35% patients were from low socioeconomic class, 54% from middle and 11% from higher class. Only 45.6% (n=68) of patients were vaccinated and 54.4% (n=81) were not vaccinated against HBV. Vaccination status was significantly associated with education (p=0.004) and socioeconomic status (p=0.008). Conclusion: The HBV status of patients on regular hemodialysis is not satisfactory at the two centers observed. It is associated with education and socioeconomic status of the patient.",
"keywords": [
"Dialysis",
"Education",
"Hepatitis B",
"Socioeconomic class",
"Vaccination"
],
"content": "Introduction\n\nChronic kidney disease (CKD) is a global health problem; estimated global prevalence is 11–13% with majority of the patients having stage 3 disease1. It is an immunosuppressive state, so CKD patients are at increased risk of developing many infections; some of these infections are vaccine preventable2. Hepatitis B virus (HBV) infection is among one of those infections. Like other high risk groups including IV drug abusers, homosexual men, having history of piercing and blood transfusions, it is more prevalent in CKD patients as compared to the general population3–5. High risk of HBV among hemodialysis patients is due to increased exposure to blood products, frequent cannulation and shared hemodialysis equipment6.\n\nHBV infection in CKD patients varies globally and correlates with the prevalence in the general population. Decreasing trends have been seen in developed countries; in the US it decreased from 7.8% in 1976 to 1% in 20023. The exact prevalence among CKD and dialysis patients in the developing world, including Pakistan, is not well known. There are scattered reports, mostly single-centre surveys; according to these surveys hepatitis B surface antigen (HBsAg) carrier rate ranges between 2% to 20%6. In Pakistan, the prevalence rate is about 4% in the general population7, indicating that it will be more than 4% in CKD patients.\n\nPrevention is the best option in the general population, as well as in high risk groups to reduce the prevalence of hepatitis B infection because treatment is lengthy, costly and not 100% effective. As HBV can be transmitted easily from the medical equipment used during dialysis, as it remains viable and stable in the environment for weeks at room temperature8, vaccination against HBV is most effective way to prevent it in CKD patients on hemodialysis. Complete vaccination was found to be protective in ≥90% in the general population, even 30 years after vaccination9. Although response is not good in chronic renal failure patients, up to 40% were found to be non-responders in some studies3,10. Still routine vaccinations of patients and healthcare workers has dramatically reduced the prevalence of HBV infection in hemodialysis patients11. It was found 70% lower among vaccinated patients as compared to non-vaccinated hemodialysis patients12.\n\nGuidelines from nephrology societies and Centers for Disease Control and Prevention suggest that all patients with CKD should be vaccinated against HBV2. Special formulation of recombinant vaccine is advised, either higher dosage or increased number of doses (4 doses) should be administered for good results2. Although guidelines strongly recommend vaccination of CKD patients against vaccine preventable diseases, it has been shown that they are not in fact routinely vaccinated against HBV. A study published in the UK showed that only 46% dialysis units were routinely immunizing patients according to the Renal Association’s recommendations13, while only 20% of patients were found to be vaccinated in a study conducted in Pakistan14.\n\nVaccination against HBV decreases the overall mortality in CKD patients, but, to the best of our knowledge, no recent data is available regarding the status of vaccination against HBV in CKD patients internationally. In developing countries, including Pakistan where hepatitis B is still a common problem, there is limited data available on this topic. The aim of this study was to observe the immunization status of CKD patients on regular hemodialysis against hepatitis B in Pakistan. The data can help in future for necessary measures to improve the vaccination against hepatitis B in CKD patients.\n\n\nMethods\n\nThis was an observational descriptive study conducted at the Department of Medicine, Sheikh Khalifa Bin Zayed Hospital, Rawalakot and POF Hospital, Wah Cantt, from March 2019 to July 2019. Sample size was calculated using the World Health Organization sample size calculator taking confidence level 95%, calculated sample size was 139 by using the formula n = (Z2 × P × (1 - P))/d2 for cross sectional studies15. Patients reporting to the dialysis centre of both hospitals with a diagnosis of CKD on regular dialysis of any age were included in the study by consecutive sampling. CKD was defined as individuals with markers of kidney damage or those with eGFR<60 mL/min per 1.73 m2 regardless of the cause16. Hepatitis B surface antigen positive, newly diagnosed CKD patients not on dialysis and patients not sure about their vaccination status were excluded from the study.\n\nData was collected using a structured questionnaire (Extended data17). The questionnaire included items intended to assess socio-demographic variables and hepatitis B vaccination status of the patients. The questionnaire was filled by the authors of the study after interviewing the participants. Every participant was interviewed before their dialysis session when they reported to the dialysis center for the scheduled dialysis.\n\nAge was entered in years, gender was entered as male or female, education level was considered as uneducated (those not able to read and write), up to secondary level education (1 to 10 years education), secondary level to graduation (10–14 years education) and post-graduation (more than 14 years education). Socioeconomic status was defined as lower class (monthly income ≤ 20000 Pakistani Rupees), middle class (monthly income 21000 to 99000 Pakistani Rupees) and upper class (monthly income ≥ 100000 Pakistani Rupees) based on gross monthly income and access to educational and healthcare facilities. Duration of CKD was considered in months.\n\nPatients were interviewed in detail about their vaccination status against hepatitis B. Only those were considered as vaccinated who completed the course of vaccination of 4 doses or 3 doses at an interval specified for hepatitis B vaccination. Those who did not receive vaccine at all and those who had an incomplete course were considered as unvaccinated.\n\nThe statistical analysis of data was done in SPSS for Windows, version 20. Means and standard deviations were calculated for quantitative variables like age and duration of CKD. Frequencies were calculated for gender, education, socioeconomic status and vaccination status of hepatitis B. Chi square test was applied to see the relation between different factors and status of vaccination. P ≤0.05 was considered as significant.\n\nEthical approval was obtained from Hospital Research Ethics Committee of POF Teaching Hospital, Wah Cantt (letter no. POFH/ERC/99053/05) and Hospital Research Ethics Committee of Sheikh Khalifa Bin Zayed Teaching Hospital (letter no. SKBZ/REC/019/08). Informed verbal consent to participate was obtained from the patients or their close relatives (when patients were unable to comprehend the researchers due to old age or uremic encephalopathy) where relevant. Verbal consent over written consent was taken because many patients were uneducated and unable to read a consent forms or were reluctant to sign a document. The ethics committee gave permission for this route of consent to be obtained. Consent for minors was taken from one of their parents.\n\n\nResults\n\nA total of 200 patients were asked to take part in the study, but only 149 responded. A total of 63.1% (n=94) were male and 36.9% (n=55) were female. Mean age was 50.5±16.7 years, with minimum age of 7 years and maximum 83 years. Mean duration of CKD was 38.9±47.2 months. Out of these 149 patients, 24.2% (n=36) were uneducated, 33.6% (n=50) had 1–10 years school education (up to secondary level), whereas 38.2% (n=57) had 10–14 years education (secondary level to graduation) and 4% (n=6) had more than 14 years education (post-graduation). About 35.6% (n=53) patients were from low socioeconomic class, 53.6% (n=80) from middle, and 10.8% (n=16) from higher class. Only 45.6% (n=68) patients were vaccinated and 54.4% (n=81) were not vaccinated against HBV (Table 1).\n\nA significant association was found between vaccination status and education of the patient; better educated patients were more likely to be vaccinated (Table 2). A significant association was also found between vaccination and socioeconomic status of the patients; patients from middle and upper classes were more likely to be vaccinated as compared to lower class. (Table 3). Vaccination status of the patients was not significantly associated with age (p= 0.540), gender (p= 0.517), and duration of CKD (p= 0.719).\n\n\nDiscussion\n\nIn our study, we found that 45.6% patients of CKD on regular dialysis were found to be vaccinated against HBV. We concluded that education and socioeconomic status are two important factors associated with status of vaccination, and was not associated with age, gender, and duration of CKD.\n\nResults showed that 63% patients were male, and the mean age of patients was 50 years. This suggests that more male patients are on hemodialysis and CKD is also more common in the older age group. This is the same as the United States Renal Data System 2011 Annual Data Report that showed that the initiation of dialysis was much higher in males as compared to females18. However, a meta-analysis reported that in some studies CKD was more common in females, while in other studies it was more common in males1. Many studies showed that CKD is more common in an older age group1, comparable with our findings. For example, in a study conducted in India19, the mean age was 51 years in CKD patients, while in a Chinese study it was found to 63.6 years20, almost the same as in our study. We did not find any association between status of vaccination and age or gender; this was also concluded by Amjad et al. in a study conducted in Pakistan14.\n\nNephrology societies and Centre for Disease Control and Prevention recommends that all CKD patients should be vaccinated against HBV2. These guidelines are not followed even in the developed world; 73.1% patients of CKD were found vaccinated in US21, and only 31% patients were vaccinated in a study conducted in Belgium22. Our results are also not encouraging, only 45.6% were found vaccinated, while in another study from Pakistan only 20% patients were vaccinated, consistent with our results14. A study conducted in Brazil showed better vaccination rates compared to our results, almost 60% patients were completely vaccinated, and another 15% were partially vaccinated22. The low vaccination rate in Pakistan indicates that dialysis centers and nephrologists are not following the guidelines of nephrology societies regarding vaccination against hepatitis B.\n\nOur study reported that vaccination status in dialysis patients was significantly associated with socioeconomic class and education of the patients. A vaccinated status was found to be higher in CKD patients with better socioeconomic status in another study conducted in Pakistan14. Another study conducted by Ertekin et al. showed that better socioeconomic status was associated with higher rates of vaccination in the general population23. These results are same as we found in our study. Low vaccination rates among lower socioeconomic groups may be due to non-affordability. As far as education is concerned, no association was found between vaccination against HBV of CKD patients and education in a study conducted by Amjad et al.14, which differs from our results. Studies from the general population and healthcare workers showed that education was significantly associated with vaccination status against HBV, comparable to our results24–26. Individuals who have more education may be better aware of the preventive role of vaccination, which may be the cause of better vaccination status in higher educated people.\n\nOur study is subject to some limitations. First, we only included those patients who were on regular dialysis. Second, only two dialysis centers were included in the study and few factors were studied related to vaccination status. We recommend future studies to include all patients of CKD from many centers.\n\n\nConclusion\n\nCurrently dialysis centers are not following guidelines regarding vaccination against HBV in hemodialysis patients. Vaccination status of patients on hemodialysis is not satisfactory in dialysis centers we sampled in Northern Pakistan. We found that vaccination status is significantly associated with education and socioeconomic status of the patients.\n\n\nData availability\n\nFigshare: Vaccination against hepatitis B virus in hemodialysis patients: trends in dialysis centers of Northern Pakistan, doi.org/10.6084/m9.figshare.13359713.v117.\n\nFigshare: Vaccination against hepatitis B virus in hemodialysis patients: trends in dialysis centers of Northern Pakistan, https://doi.org/10.6084/m9.figshare.13359713.v117.\n\nThis project contains the following extended data:\n\n- Copy of the questionnaire used in the study.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nHill NR, Fatoba ST, Oke JL, et al.: Global prevalence of chronic kidney disease - a systematic review and meta-analysis. PLoS One. 2016; 11(7): e0158765. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuidelines for vaccination in patients with chronic kidney disease. Indian J Nephrol. 2016; 26(Suppl 1): S15–S18. Free Full Text\n\nGrzegorzewska AE: Hepatitis B Vaccination in Chronic Kidney Disease: Review of Evidence in Non-Dialyzed Patients. Hepat Mon. 2012; 12(11): e7359. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFalla AM, Hofstraat SHI, Duffell E, et al.: Hepatitis B/C in the countries of the EU/EEA: a systematic review of the prevalence among at-risk groups. BMC Infect Dis. 2018; 18(1): 79. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZiaee M, Ebrahimzadeh A, Azarkar Z, et al.: Seroprevalence and risk factors for hepatitis B in an adult population: the first report from Birjand, South Khorasan, Iran. Hepat Mon. 2016; 16(9): e36452. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSomi MH, Hajipour B: Improving hepatitis B vaccine efficacy in end-stage renal diseases patients and role of adjuvants. ISRN Gastroenterol. 2012; 2012: 960413. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMehmood S, Raza H, Abid F, et al.: National prevalence rate of hepatitis B and C in Pakistan and its risk factors. J Public Health. 2019; 28: 751–764. Publisher Full Text\n\nThan TT, Jo E, Todt D, et al.: High Environmental Stability of Hepatitis B Virus and Inactivation Requirements for Chemical Biocides. J Infect Dis. 2019; 219(7): 1044–48. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBruce MG, Bruden D, Hurlburt D, et al.: Antibody Levels and Protection After Hepatitis B Vaccine: Results of a 30-Year Follow-up Study and Response to a Booster Dose. J Infect Dis. 2016; 214(1): 16–22. PubMed Abstract | Publisher Full Text\n\nMalaki M: Factors affecting on hepatitis B seroprotection in hemodialysis patients. Saudi J Kidney Dis Transpl. 2017; 28(3): 672–74. PubMed Abstract | Publisher Full Text\n\nWasley A, Kruszon-Moran D, Kuhnert W, et al.: The prevalence of hepatitis B virus infection in the United States in the era of vaccination. J Infect Dis. 2010; 202(2): 192–201. PubMed Abstract | Publisher Full Text\n\nGrzegorzewska AE: Prophylactic vaccinations in chronic kidney disease: Current status. Hum Vaccin Immunother. 2015; 11(11): 2599–2605. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRay S, Samuel T, Hawker J, et al.: Hepatitis B immunisation in renal units in the United Kingdom: questionnaire study. BMJ. 2002; 324(7342): 877–78. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmjad A, Kumar J, Chaudary N, et al.: Hepatitis B Vaccination Status in Chronic Kidney Disease: Experience at Pakistan Institute of Medical Sciences. Cureus. 2019; 11(7): e5282. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCharan J, Biswas T: How to calculate sample size for different study designs in medical research? Indian J Psychol Med. 2013; 35(2): 121–6. PubMed Abstract | Free Full Text\n\nWebster AC, Nagler EV, Morton RL, et al.: Chronic kidney disease. Lancet. 2017; 389(10075): 1238–1252. PubMed Abstract | Publisher Full Text\n\nNadeem M, Sha SAA, Arshad N, et al.: Vaccination against hepatitis B virus in hemodialysis patients: trends in dialysis centers of Northern Pakistan. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.13359713.v1\n\nUnited States Renal Data System: 2011 Annual Data Report. Accessed 21 September 2019. Reference Source\n\nRajapurkar MM, John GT, Kirpalani AL, et al.: What do we know about chronic kidney disease in India: first report of the Indian CKD registry. BMC Nephrol. 2012; 13: 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang L, Wang F, Wang L: Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012; 379(9818): 815–22. PubMed Abstract | Publisher Full Text\n\nAyoola R, Larion S, Poppers DM, et al.: Clinical factors associated with hepatitis B screening and vaccination in high-risk adults. World J Hepatol. 2019; 11(1): 86–98. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBoey L, Bosmans E, Ferreira LB, et al.: Vaccination coverage of recommended vaccines and determinants of vaccination in at-risk groups. Hum Vaccin Immunother. 2020; 16(9): 2136–43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuimarães MNC, Facincani T, de Sousa dos Santos S: Hepatitis B status in hemodialysis patients. Arq Gastroenterol. 2017; 54(4): 356–58. PubMed Abstract | Publisher Full Text\n\nErtekin V, Selimoglu MA: Effects of Several Socio-demographic factors on hepatitis B immunization rates. Eur J Gasteroenterol Hepatol. 2004; 16(7): 719. PubMed Abstract | Publisher Full Text\n\nOmotowo IB, Meka IA, Ijoma UN, et al.: Uptake of hepatitis B vaccination and its determinants among health care workers in a tertiary health facility in Enugu, South-East, Nigeria. BMC Infect Dis. 2018; 18(1): 288. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhan J, Shil A, Mohanty SK: Hepatitis B vaccination coverage across India: exploring the spatial heterogeneity and contextual determinants. BMC Public Health. 2019; 19(1): 1263. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "82554",
"date": "15 Apr 2021",
"name": "Chenhua Liu",
"expertise": [
"Reviewer Expertise Hepatitis B",
"hepatitis C",
"chronic kidney disease"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nNadeem et al. conducted an observational study about the vaccination status in Pakistan and to correlated the socioeconomic status with HBV vaccination.\nMajor concerns:\nThe authors interviewed the vaccination status in all patients. However, the patients had prone to have a high probability of recall bias, making sampling interviewing not reliable. Furthermore, patients who had HBsAg (-)/anti-HBs (+)/anti-HBc (-) or HBsAg (-)/anti-HBs (+)/anti-HBC (+) did not need vaccination. Furthermore, patients with isolated anti-HBc (+) may not need vaccination. The lack of HBV status in all patients is not scientific and should be comprehensively assessed.\n\nWhy did the author define CKD as eGFR < 60 on dialysis? Lots of patients with eGFR > 30 need not receive hemodialysis. The authors poorly defined the patient in this study.\n\nSince this was an observational study without any pre-specified hypothesis, a sample size calculation was not needed. The author erroneously cited and used the sample size calculation in the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "6588",
"date": "29 Apr 2021",
"name": "Muhammad Nadeem",
"role": "Author Response",
"response": "I would like to thank the reviewer for reviewing the article and giving his precious time and valuable comments. Reviewer had few concerns regarding the study, as a corresponding author I want to respond on this report. 1. Main concern of the reviewer was about data collection. According to reviewer interviewing the patient regarding vaccination is not a reliable method, it is a genuine concern but due to unavailability of formal certification of hepatitis B vaccination in our setup we were left only with this method. Although we counter checked the information provided by the patient from record of dialysis centers which we did not mention in methodology. I would like to add this in data collection procedure. 2. According to reviewer “patients who had HBsAg (-)/anti-HBs (+)/anti-HBc (-) or HBsAg (-)/anti-HBs (+)/anti-HBC (+) did not need vaccination. Furthermore, patients with isolated anti-HBc (+) may not need vaccination.” This statement does not match the recommendations of CDC, WHO and Nephrology societies, as they recommend the vaccination of all CKD patients [1,2,3,4]. Routine pre vaccination serology is also not recommended by WHO especially when it is not cost effective [5]. The only logical cost effective serological test is HBsAg as there is no benefit of vaccination in HBsAg positive patients not the HBsAg negative as mentioned by reviewer, we did this and excluded the HBsAg positive patients mentioned in data collection procedure. If reviewer can provide the reference regarding the recommendation of all these serological tests before vaccination in CKD and exclusion of patients with serological results mentioned in his statement it will help us and other researchers in future. 3. Another observation was regarding definition of CKD. Definition provided is internationally accepted definition established by The Kidney Disease Outcomes Quality Initiative (KDOQI) of the National Kidney Foundation (NKF) and Kidney Disease Improving Global Outcomes (KDIGO) [4]. This definition cannot be changed; if reviewer can provide some other definition with reference we can include that definition. As for as selection of patients for this study is concerned it is clearly mentioned that only those patients of CKD were included who were on regular hemodialysis, so the observation of reviewer “Lots of patients with eGFR > 30 need not receive hemodialysis. The authors poorly defined the patient in this study” is not justified. 4. As for as details of sample size calculation are concerned, these were not included in initial manuscript. These details were provided on the demand of journal. References: 1. Recommendation of the Immunization Practices Advisory Committee (ACIP). Inactivated hepatitis B virus vaccine. MMWR Morb Mortal Wkly Rep. 1982;31(24):317–22. , 27-8. 2. Recommendations of the Advisory Committee on Immunization Practices (ACIP): Use of vaccines and immune globulins for persons with altered immunocompetence. MMWR Recomm Rep. 1993;42:1–18. 3. Guidelines for vaccination in patients with chronic kidney disease. Indian J Nephrol. 2016; 26(Suppl 1): S15–S18. 4. Kidney Disease: Improving Global Outcomes (KDIGO) CKD Work Group. KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease. Kidney Int Suppl 2013; 3: 1-150; http://dx.doi.org/10.1038/kisup.2012.73 5. World Health Organization. Hepatitis B vaccines: WHO position paper, July 2017 – Recommendations [published online July 22, 2017]. Vaccine. doi: 10.1016/j.vaccine.2017.07.046)"
}
]
}
] | 1
|
https://f1000research.com/articles/10-55
|
https://f1000research.com/articles/13-619/v1
|
11 Jun 24
|
{
"type": "Research Article",
"title": "Overcoming barriers to career progression for mid-career female physician-scientists: Insights and solutions",
"authors": [
"Derya Yakar",
"Marieke Haan",
"Yfke P Ongena",
"Mithra Hesselink",
"Stephanie CE Schuit",
"Thomas C Kwee",
"Marian JE Mourits",
"Marieke Haan",
"Yfke P Ongena",
"Mithra Hesselink",
"Stephanie CE Schuit",
"Thomas C Kwee",
"Marian JE Mourits"
],
"abstract": "Background Gender equity in academia is a significant challenge. To investigate career advancement perspectives of mid-career female physician-scientists, identify their needs and barriers, and develop a mentor-sponsorship strategy to improve their representation in higher academic ranks.\n\nMethods In this qualitative study, conducted at a Western European academic medical center, we interviewed 19 mid-career female physician-scientists across all specialties, including radiology. Data were analyzed using thematic analysis.\n\nResults Four themes were identified: 1. Horizontal and vertical ambitions, (i.e., knowledge expansion and hierarchical advancement) 2. Evaluation of talent, 3. Career path needs, and 4. Receiving support. These themes revealed barriers to women's advancement, including limited talent recognition, inadequate leadership support, self-limiting beliefs, structural issues, and lack of networking opportunities. To address these challenges, a mentor-sponsorship program should prioritize sponsor training, start immediately at the beginning of the mid-career phase (attainment of assistant professorship), emphasize horizontal and vertical development, take work-life balance into account, establish mentor networks, and allow individuals to choose mentors and sponsors based on their needs and aspirations.\n\nConclusions This study has identified key needs and barriers that impede the advancement of female physician-scientists in academia. To address these challenges, a tailored mentor-sponsorship program is recommended. Key program elements include training leadership to recognize talent and offer proactive support, starting at the onset of the mid-career phase, emphasizing horizontal and vertical development, and establishing a strong mentor-sponsor network with thoughtful matching. These actions can help to overcome obstacles and facilitate the progress of women in academia.",
"keywords": [
"Gender inequality",
"talent development",
"sponsorship",
"academic advancement"
],
"content": "Introduction\n\nGender equity in academia, especially at senior levels like full professorships and leadership roles, remains a significant challenge. The European Union's She figures indicate a marginal increase in women's representation at these levels, from 24% in 2015 to 26% in 2018.1 This “leaky pipeline” phenomenon is particularly evident during the mid-career phase, where women's advancement disproportionately declines.1 Narrowing our focus to medicine, women constitute half or more of medical students in Europe and the USA.2,3 Moreover, the proportion of female physician-scientists, for example in the Netherlands (ranging from 60% to 70%), significantly surpasses the number of male physician-scientists.4\n\nTo understand and address this pipeline leak, we investigate the barriers that women perceive to develop a formal program tailored specifically to the needs of mid-career physician-scientist women. Earlier literature shows that gender exerts a dual impact on women's medical careers, operating both internally by shaping women's ambitions and externally through societal pressures that perpetuate gender stereotypes.5 To harmonize work-life responsibilities and needs, women navigate through choices leading to discernible career gaps in specialty selection, promotional opportunities, and leadership positions.5–7 In previous years, mentorship programs have emerged from the international literature as effective tools for facilitating individual progress and increasing skills.8 However, mentorship alone is not sufficient for climbing the academic ladder.9 Previous studies in the business community have revealed that the lack of sponsorship emerges as an important factor preventing women from advancing into leadership positions, rather than their lack of quality or suitability.10 Sponsorship, which involves encouraging, supporting, and protecting individuals,10,11 can play a significant role in academic settings by narrowing the gender gap.12,13\n\nGiven the limited experience with this concept in academic settings, there is a need to adapt sponsorship approaches specifically for academia.14 Conducting in-depth interviews with female physician-scientists serves as an initial step towards identifying their specific needs. The purpose of this study was to identify perspectives related to career advancement in academia of mid-career female physician-scientists, understand the needs, explore perceived barriers, and ultimately develop a mentor-sponsorship strategy to enhance their representation in higher academic ranks and leadership positions.\n\n\nMethods\n\nTo achieve a comprehensive view of mid-career women's perspectives on their careers, we conducted qualitative semi-structured interviews using a thematic analysis approach, combining deductive and inductive reasoning.15,16 This approach allowed us to explore pre-identified topics from the literature and to construct themes ourselves which were relevant to womens’ career and talent development. In this section we give complete details of our methods. The presented qualitative study meets the SRQR17 and COREQ18 guidelines for reporting on qualitative research.\n\nThis research was conducted at a Dutch medical center (University Medical Center Groninen (UMCG)) and approved by the local medical ethics review board of the UMCG (IRB number: 11009, approval date and number 17/10/2022, and approval number METc 2022/498). Based on the hospital's administrative records, a sampling frame was constructed comprising all female mid-career medical specialists who fulfilled the inclusion criteria of being a physician, holding a PhD degree, and supervising at least one PhD student. A purposive sampling method was employed, aiming for a balanced representation of assistant professors, associate professors, post-docs, various medical specialties, and residency program leaders. Initially, the response rate in the first round of data collection was not sufficient. As a result, in the second round, one of the inclusion criteria, the requirement of supervising at least one PhD student, was removed. The overall response rate was 73% (19 participants out of 26 approached physicians). Each potential participant received an invitation letter containing information about the study. Subsequently, they were contacted by phone and invited to participate. Upon agreement, interviews were scheduled. The interviews were conducted by four experienced and trained interviewers from the hospital's Human Resources department, consisting of one male and three females. Prior to the interviews, all participants provided verbal consent. In total, 19 interviews were conducted. For qualitative health research, a minimum sample size of 9-17 interviews is recommended to achieve data saturation.19,20 The interviews had an average duration of 54 minutes, with a range of 38-72 minutes.\n\nThe interview guide, developed by the research team, covered four topics derived from the literature5–7: 1. The significance of work in life, 2. Expectations and needs regarding career development, 3. Current support and encouragement for career development, including formal policies, and 4. Opportunities for career development. Each topic included open-ended questions and follow-up probes to encourage detailed responses. Interviews were held between November 2022 and March 2023.\n\nAll 19 audio recordings were automatically transcribed using Amberscript (www.amberscript.com), and subsequently, the transcripts underwent manual correction by three coders (Second author, fourth author, and one research-master student trained in qualitative coding), marking the initiation of the data familiarization process. During this process, all identifying information was removed from the transcripts to ensure privacy. To address our research question, a thematic analysis was employed.11–12 The coding process was facilitated by the use of ATLAS.ti version 23 for Windows.20 To commence the coding process, all three coders inductively coded an identical interview keeping the deductive themes in mind. The double-coded interview was subsequently compared and discussed among the three coders. The coders also together reflected on their own subjectivity and positionality to be aware of possible bias while coding the data. This discussion led to the final set of codes. A codebook was developed based on these codes for structuring the analysis process. The coding process continued as each coder individually applied the codes from the codebook and incorporated new inductive codes as needed while coding a set of interviews. On two occasions, the coded interviews were merged in ATLAS.ti to discuss the ungoing coding process and to assess data saturation. Data saturation was achieved after coding 16 interviews. To ensure the robustness of our findings, interviews 17-19 were also conducted and coded. No new information emerged from these additional interviews, increasing the likelihood of data saturation. Finally, the codes were utilized to construct themes that reflected the needs and barriers to talent development in the career paths of the interviewed women.\n\n\nResults\n\nInterviews were conducted with a diverse group of women: 3 associate professors, 6 assistant professors, 4 postdocs, and 6 residency program leaders. The mean number of years working at the hospital was 14 with a range of 5-23. The specialities of the participants were: pathology (2), nuclear medicine, oncology (2), gastroenterology, clinical genetics, interventional cardiology, pediatrics (3), pulmonology, radiology (3), rheumatology, psychiatry, anaesthesiology, and gynaecology.\n\nFour main themes were constructed in the data: 1. Horizontal and vertical ambitions, 2. Evaluation of talent, 3. Career path needs, and 4. Receiving support.\n\nWithin this theme, participants displayed two types of ambitions: horizontal (knowledge expansion) and vertical (career progression).21 Focusing on horizontal ambition, participants indicated they work at an academic hospital because they want to increase and innovate their knowledge and skills. Learning is a process that is ongoing and never finished. Participant 9 phrased it as follows: “I think that you are constantly learning, right? That was also the reason why I wanted to work in an academic setting. It's a constant learning process, you have to teach others what you know”. Talent development is often intrinsically motivated. Participants explicitly mentioned they enjoy self-development and the choice for knowledge expansion does not have to be related to higher academic positions. Not only self-development but also contributing to a higher cause and improving clinical skills to become better medical specialists is important for the interviewed women.\n\nVertical ambitions refer to aspiring specific positions such as assistant-, associate- and full professor and other leadership roles. Many participants already took management and leadership courses, some specifically aimed at being a female leader. This indicates that these women want to advance their skills on this front and see themselves in these leadership positions. For example, one participant strived to be the chairwoman of her professional association and another participant had the ambition to become residency program leader. The female physicians are aware of their position at the department and some anticipate on possible chances that will appear in the future, like participant 8: “I do have plans for the next five years. There will definitely be some changes happening in our team, so I would like to be involved or jump in, so to speak”. The women that are already in associate professor positions have the ambition to become full professor, mostly because it is part of the academic process and reaching the professor position feels as if the process is completed.\n\nThough for those in other positions than associate professor (i.e., post-doc, assistant-professor) vertical ambitions were expressed with some hesitations. The participants mentioned that it is very time-consuming to climb the hierarchical academic ladder and that promotion depends on many different aspects which makes it hard to become an associate or full professor. Participant 6 expressed her feelings about the academic positions as follows: “Yes, so I did want to become a good specialist. But, apart from that, well, I didn't really have ambitions to reach the highest levels of academia. I did want to do some research, perhaps conduct my own studies, but not necessarily become a professor. I didn't see myself in that role because I thought, well, everything is already so busy, and that would make it even busier.”\n\nThis theme addresses women's perceptions of the hospital's promotion regulations, crucial in evaluating talent for career advancement. The hospital outlines specific criteria in a policy document for academic positions, such as supervising PhD students, research conceptualization, scientific impact, acquiring grants, publications, international recognition, outreach, and educational contributions. Moreover, Dutch knowledge institutes and funding bodies seek to modernize the recognition of researchers.22 They emphasize evaluating quality beyond publication numbers and impact factors, aiming to recognize teaching, societal impact, leadership, patient care, open science practices, and team collaboration.\n\nParticipants prioritizing horizontal growth or feeling their research did not align with academic standards often did not review the hospital's policy document. They believed that lacking a robust research background made pursuing academic positions unrealistic, as talent is predominantly assessed based on research achievements. They also sensed that the absence of early career research could significantly impact their academic trajectory, participant 4 described this as follows: “In my opinion, if you miss out on that initial grant, then you can forget about the rest. That's how it feels, I think. If you haven't immediately jumped on that train, then you'll be playing catch-up for the rest of your career”.\n\nWomen who did read the policy document and who were working towards a higher academic position had mixed feelings about the hospital’s policy. On the one hand, they find the policy clear and transparent and like that the rules are the same for everyone. On the other hand, participants thought the policy encourages box-checking. They disliked policies’ uniformity and believed more tailored rules should be applied because in some fields it is more challenging to secure funding or achieve certain milestones. Participants did not see the new Dutch policy, valuing skills beyond research, reflected in the hospital's policy or embraced by their department chairs (DCs). They seek assurance that diverging from the promotion policy will not hinder academic progression, emphasizing the need for recognizing and rewarding teaching and clinical contributions more consistently.\n\nIn this theme, we explore the vital career needs constructed from women's perspectives. They express a desire to influence hospital policies and shape the work environment, believing it would aid their career growth. Specifically, they advocate for a more balanced workload distribution and increased staffing to facilitate dedicated time for professional development in which balancing personal demands and professional wishes should be possible as well. Despite encouragement for self-development, participants find themselves investing personal time in talent growth. Additionally, they seek peer discussions—collaborations with colleagues at similar career stages, albeit not necessarily from the same department. These conversations encompass a range of topics from career decisions to specific tasks, exemplified by participant 7 discussing grant writing: “I really miss having a meeting or a structure or maybe a mentor, but also a discussion with, let's say, peers or colleagues because I've heard of groups that have that, for example within the [department], where they gather together to write a proposal, for instance”.\n\nNot all women were certain about their career aspirations and specific needs. They were unsure about the appropriate steps to take or the most advantageous direction for their talent development. This suggests that the participants require additional or different support in order to advance their careers. Participant 1 mentioned the challenges she faced during the annual performance review when discussing her needs with her DC: “It's always a question during the annual performance review of what you will do next year and what you want then. But it's always… Well, I think it's a mutual interaction because I'm not particularly outspoken about it and I don't really know myself what I want”.\n\nOne of the potential needs that was explicitly discussed with the women during the interviews pertained to the availability of career support in their work life. This theme explores whether the women receive support and, if so, their feelings about it.\n\nGenerally, women held positive views about their annual performance reviews with their DC or clinical director. These sessions facilitated discussions on department satisfaction and skill enhancement through recommended courses or training. However, many felt responsible for navigating their career advancement independently. While their DC directed them to the hospital's policy document, participants desired a more proactive approach, seeking personalized conversations about the promotion process aligned with their unique strengths. Moreover, participants noted a lack of ample recognition beyond research and insufficient discussions on leveraging these talents for career growth. For instance, participant 5 stated: “Yeah, what I really miss and what I need is indeed that at some point it is also expressed like, hey, we see in you this or that talent or that particular potential. And how can we help you get there? And that's not there. That's really unfortunate because you, you simply can't do it alone, it's as simple as that”.\n\nThe participants voiced a need for a dedicated confidant to discuss their careers, offer reflective feedback, and aid in expanding their professional network—a role where feeling safe to address job-related matters was paramount. They highlighted challenges when their mentors changed positions or relationships shifted with their DC, impacting confidentiality. Participants noted the limitations of their DC as a sponsor due to potential conflicts of interest and expressed a desire to choose their own sponsor from a list of potential candidates. They stressed the importance of a compatible match between the employee and this confidant, emphasizing shared career paths and personalities. This sparring partner should empower the employee, respecting their aspirations, be they focused on horizontal, vertical advancement, or both.\n\n\nDiscussion\n\nIn this qualitative study conducted at a Western European academic medical center, we interviewed 19 mid-career female physician-scientists, including radiologists. Through thematic analysis, we constructed four key themes that capture their perspectives on work needs and future career paths.\n\nFirstly, it explores ambition, highlighting the importance of both horizontal and vertical aspirations without assuming immediate leadership roles. By recognizing qualifications and not solely focusing on immediate vertical ambition, more women can engage and thrive.23,24\n\nSecondly, talent evaluation was a theme. Participants emphasized horizontal skill development and those feeling misaligned with academic profiles lacked information on specific requirements. Women familiar with the policy were generally satisfied with the clear criteria. However, some saw the policy as a checklist and criticized its failure to recognize talents beyond research achievements. Aligning criteria beyond research achievements cannot only promote a more comprehensive and holistic approach but also nurture more versatile leaders in academic medical centers.\n\nThe third theme addresses career path needs, focusing on influencing hospital policies, balancing personal demands and professional needs, and seeking peer discussions across departments. Uncertainty about aspirations calls for varied support structures. In a mentor-sponsorship program, these issues could be effectively addressed by providing opportunities for advising in institutional policymaking, discussing flexible career paths and facilitating networking opportunities.\n\nThe fourth theme examines the support received by the participants. While they valued annual reviews, they sought more proactive guidance from DC’s for career advancement. They desired confidentiality in a chosen mentor-sponsor relationship, aligning with their personality and career paths.\n\nFrom our study, significant barriers impeding the progression of women in an academic medical center have surfaced. These encompass limited recognition of talents, insufficient support from DCs, self-imposed limitations, and institutional hurdles such as limited possibilities to combine work with personal demands and rigid promotion policies. To counter these obstacles, prioritizing sponsor training becomes pivotal when crafting mentor-sponsorship programs. This aligns with Williams et al.'s proposition,12 advocating for the integration of sponsorship activities into academic metrics, signalling a commitment to institutional change at higher levels. A well-structured formal program, ideally initiated during mid-career stages, should not only emphasize both horizontal and vertical development but also foster mentor networks and encourage participation in institutional policymaking. These strategies aim to create an environment conducive to women's advancement without assuming immediate leadership roles.\n\nTo our knowledge, this is the first qualitative study that specifically targets mid-career female physician-scientists across an academic medical center. Previous qualitative research has predominantly focused on the experiences of women who were already in leadership positions and has been limited to specific subspecialties,7,25–27 making direct comparisons with previous research inappropriate. In another quantitative study on sponsorship by Williams et al.,12 findings recognized sponsorship as a potential solution to address the underrepresentation of women and minorities. The majority of respondents were familiar with sponsorship, had received it, and expressed satisfaction. However, there was a need for systematic changes to enhance transparency, equity, and impact, as respondents perceived a bias against sponsoring women. Levine et al.14 affirmed in a qualitative study sponsorship's importance in academic progression, particularly its gender-specific nuances, warranting further exploration in academic medicine. These findings support the objective of our study, which is to design a tailored formal program to support women in their careers.\n\nAcknowledging limitations, this study was conducted at a single Western European academic medical center, which may limit the generalizability of the findings to other medical centers worldwide. However, given that issues of gender inequity are prevalent globally, the insights gained from this study could be valuable to institutions in other countries. Furthermore, the diversity and inclusion debate extends beyond gender, and other underrepresented groups may require specialized programs to support their advancement in academia. Future studies can explore the specific needs of these groups and design strategies accordingly.\n\nIn conclusion, this study has identified key needs and barriers that impede the advancement of female physician-scientists in academia. To address these challenges, a tailored mentor-sponsorship program is recommended. Key program elements include training leadership to recognize talent and offer proactive support, starting at the onset of the mid-career phase, emphasizing horizontal and vertical development taking into account a work-life balance, and establishing a strong mentor-sponsor network with thoughtful matching. These actions can help to overcome obstacles and facilitate the progress of women in academia.\n\nThis research was conducted at a Dutch medical center and approved by the local institutional review board (IRB number: 11009). Verbal informed consent was obtained from all participants. Based on the documents reviewed, the medical ethics review committee of the UMCG determined that this study did not constitute clinical research with human subjects as defined under the Medical Research Involving Human Subjects Act (WMO). Given the low-risk and non-invasive nature of the research, verbal informed consent was deemed appropriate. All participants were comprehensively briefed on the study's objectives, procedures, and potential implications, and their verbal consent was obtained prior to their participation, ensuring they were fully aware and agreeable to the terms of the study.",
"appendix": "Data availability\n\nAccess to the data supporting the findings of this study is restricted due to the sensitive nature of the information and the small number of participants, which heightens the need to maintain confidentiality and adhere to ethical standards. The IRB has stated that the General Data Protection Regulation (GDPR) may apply to this scientific research. Therefore, to ensure compliance with ethical guidelines and the GDPR there is a strict limitation on data sharing.\n\nThose wishing to request access to the data may submit a formal application to the Principal Investigators of the study. Approval of such requests will be contingent upon the demonstration of a legitimate scientific purpose and a commitment to maintaining the confidentiality and security of the data as stipulated by the overseeing IRB. Direct supervision by the research's Principal Investigators will be required throughout the data access period.\n\nApplications for data access should be directed to the Principal Investigators via [d.yakar@umcg.nl]. Each application will be evaluated on a case-by-case basis, considering the sensitivity of the data and the proposed use. Access, if granted, will be subject to conditions that align with both ethical standards and legal requirements under the GDPR.\n\n\nAcknowledgements\n\nThe authors would like to thank the interviewers, Dineke ten Dolle, Martijn van Dijk, Janneke Carriere, and Reineke Kins, for their significant contributions and commitment to this study. The authors would also like to express their gratitude to Michiel Kahmann, Director of HR, for his support throughout the research process.\n\n\nReferences\n\nEuropean Commission: Research and Innovation SHE FIGURES 2021: Gender in Research and Innovation Statistics and Indicators.2021. Accessed 23 June 2023. Reference Source\n\nAssociation of American Medical Colleges (AAMC): AAMC press release (2022) Diversity Increases at Medical Schools in 2022. Accessed 23 June 2023. Reference Source\n\nEurostat: Health statistics.2022. Accessed 23 June 2023. Reference Source\n\nWolters FJ: Academische carrièreperspectieven van gepromoveerde dokters: Een landelijk cohortonderzoek in de periode 1992-2018. Ned Tijdschr Geneeskd. 2020; 164: D5300.\n\nWinkel AF, Telzak B, Shaw J, et al.: The role of gender in careers in medicine: A systematic review and thematic synthesis of qualitative literature. J Gen Intern Med. 2021; 36(8): 2392–2399. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLewiss RE, Silver JK, Bernstein CA, et al.: Is academic medicine making mid-career women physicians invisible? J Womens Health (Larchmt). 2020; 29(2): 187–192. PubMed Abstract | Publisher Full Text\n\nPiltch-Loeb R, Rosenkrantz AB, Merdjanoff AA: Identifying barriers and facilitators of success for female radiology researchers: An analysis of in-depth interviews with nationally recognized leaders of the field. J Am Coll Radiol. 2020 Oct; 17(10): 1344–1351. PubMed Abstract | Publisher Full Text\n\nSambunjak D, Straus SE, Marusić A: Mentoring in academic medicine: a systematic review. JAMA. 2006; 296(9): 1103–1115. Publisher Full Text\n\nShakil S, Redberg RF: Gender disparities in sponsorship-how they perpetuate the glass ceiling. JAMA Intern Med. 2017; 177: 582. PubMed Abstract | Publisher Full Text\n\nHewlett SA, Perraino K, Sherbin L, et al.: The sponsor effect: Breaking through the last glass ceiling. Cambridge, Massachusetts: Harvard Business Publishing; 2011.\n\nYakar D, Schuit SCE, Kahmann MTG, et al.: The issue of diversity in Dutch Academic medical centers: A role for professionals in leadership position. Ned Tijdschr Geneeskd. 2022; 166: D6659.\n\nWilliams MF, Yank V, O’Sullivan P, et al.: Faculty knowledge, actions, and perceptions of sponsorship: An institutional survey study. Med Educ Online. 2023; 28(1): 2218665. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeitte LA, McGinty GB, Canon CL, et al.: Shifting from mentorship to sponsorship—A game changer! J Am Coll Radiol. 2019; 16(4 Pt A): 498–500. PubMed Abstract | Publisher Full Text\n\nLevine RB, Ayyala MS, Skarupski KA, et al.: “It’s a Little Different for Men”—Sponsorship and Gender in Academic Medicine: a Qualitative Study. J Gen Intern Med. 2021; 36: 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBraun V, Clarke V: Is thematic analysis used well in health psychology? A critical review of published research, with recommendations for quality practice and reporting. Health Psychol Rev. 2023; 17: 695–718. Publisher Full Text\n\nKing N, Brooks J: Thematic analysis in organisational research.Cassell C, Cunliffe AL, Grandy G, editors. The Sage handbook of qualitative business and management research methods: Methods and challenges. Sage; 2018; pp. 219– 236. Publisher Full Text\n\nO'Brien BC, Harris IB, Beckman TJ, et al.: Standards for reporting qualitative research: a synthesis of recommendations. Acad Med. 2014; 89(9): 1245–1251. Publisher Full Text\n\nTong A, Sainsbury P, Craig J: Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups. Int J Qual Health Care. 2007; 19(6): 349–357. PubMed Abstract | Publisher Full Text\n\nHennink M, Kaiser BN: Sample sizes for saturation in qualitative research: A systematic review of empirical tests. Soc Sci Med. 2022; 292: 114523. PubMed Abstract | Publisher Full Text\n\nVasileiou K, Barnett J, Thorpe S, et al.: Characterising and justifying sample size sufficiency in interview-based studies: Systematic analysis of qualitative health research over a 15-year period. BMC Med Res Methodol. 2018; 18(1): 148. PubMed Abstract | Publisher Full Text | Free Full Text\n\nATLAS.ti Scientific Software Development GmbH [ATLAS.ti 23 Windows]: 2023. Reference Source\n\nArthur MB, Inkson K, Pringle JK: The New Careers: Individual Action and Economic Change. London: Sage Publications; 1999. Publisher Full Text\n\nAssociation of Universities in the Netherlands, Netherlands Organisation for Scientific Research, Netherlands Federation of University Medical Centres and ZonMw (Netherlands Organisation for Health Research and Development): Room for everyone's talent. Towards a new balance in the recognition and rewards for academics. Accessed 22 June 2023. Reference Source\n\nTheobald J, Gaglani S, Haynes MR: The association between confidence and accuracy among users of a mobile web platform for medical education. Ann Intern Med. 2015; 162(5): 395–396. PubMed Abstract | Publisher Full Text\n\nGuptill M, Reibling ET, Clem C: Deciding to lead: A qualitative study of women leaders in emergency medicine. Int J Emerg Med. 2018; 11(1): 47. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGottenborg EW, Yu A, McBeth LJ, et al.: The experience of women in hospital medicine leadership: A qualitative study. J Gen Intern Med. 2021; 36(9): 2678–2682. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAyyala MS, Skarupski K, Bodurtha JN, et al.: Mentorship Is Not Enough: Exploring Sponsorship and Its Role in Career Advancement in Academic Medicine. Acad Med. 2019; 94(1): 94–100. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "300676",
"date": "20 Sep 2024",
"name": "Linda Elizabeth Ruiz",
"expertise": [
"Reviewer Expertise gender in management"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis research addresses the important subject of women in mid-career development. The study is focused on the academy within physician-scientists. The authors explore barriers and enablers in career development. Using a qualitative perspective, they identify essential themes within this important topic of study. Similar studies have addressed the topic within the corporate umbrella. Still, not so many within the medical sciences and with a focus on scientists, and that's why this research brings an innovative perspective.\nIntroduction The introduction is well-developed; you included relevant information that attracts the reader's attention. However, it will benefit from adding some more information within other fields. Since this subject has been explored in different social sciences and management areas, you can add relevant information that supports your study. For example, women are taking high-ranking positions. Still, many of them remain in middle management levels because of the glass ceiling effect, problems with balancing work-life responsibilities, or maybe because they simply have other interests. Your main goal is to identify perspectives related to career advancement in academia of mid-career female physician-scientists, understand the needs, explore perceived barriers, and ultimately develop a mentor-sponsorship strategy to enhance their representation in higher academic ranks and leadership positions. Make sure you address all these elements in your results section. You may benefit from refining the goal.\nMethods The method is well defined, I suggest you add: 1-\n\nExamples of questions during your interviews. 2-\n\nDescribe the process of coding (e.g., open coding), grouping, and defining major themes.\nResults The results are well structured. The document clearly defines the four main elements identified during this study, highlighting horizontal and vertical ambitions, talent evaluation, career path needs, and receiving support. All the categories were supported with representative quotes.\nDiscussion It would help if you supported your second, third, and fourth themes with other studies. If you do not find literature within the medical field, please look into the management field. While the themes are well-developed, linking your findings more explicitly to the existing literature or theoretical frameworks would strengthen your analysis. It would be best if you also highlighted how your findings relate to the goal of the paper.\nOverall, I found the article very interesting. The major strength is that your thematic method is straightforward and well-organized, and the findings contribute to the field. However, you need to include more literature or theory to support your analysis and findings.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-619
|
https://f1000research.com/articles/13-618/v1
|
11 Jun 24
|
{
"type": "Research Article",
"title": "Evaluating the Malay version of NIOSH WellBQ: A study on reliability and construct validity for enhanced workplace well-being assessment",
"authors": [
"Aswandi Omar",
"Ng Yee Guan",
"Sindhu Nair Mohan",
"Siti Aisah Mokhtar",
"Lim Poh Ying",
"Aswandi Omar",
"Sindhu Nair Mohan",
"Siti Aisah Mokhtar",
"Lim Poh Ying"
],
"abstract": "This study aimed to validate the Worker Well-Being Questionnaire, originally developed by the US National Institute for Occupational Safety and Health, in the Malay language. The translation process involved an initial independent translation by a professional translator, followed by a comparison of translations to synthesize a unified version, which was subsequently back-translated. The back-translations were then reviewed by an expert committee to create a finalized questionnaire version. The results of this validation study indicate a high level of satisfaction, demonstrating an excellent fit with confirmatory factor analysis (CFI and TLI values ranging from 0.96 to 0.99) and a low root mean square error of approximation (RMSEA values ranging from 0.03 to 0.07). Moreover, the questionnaire exhibits sound internal consistency, with Cronbach’s alpha values exceeding 0.7, and the factor structures align with theoretical expectations. In conclusion, the Malay version of the questionnaire faithfully reproduces the original instrument, enabling a robust and efficient assessment of workers’ well.",
"keywords": [
"workers well-being",
"validation",
"realibility",
"occupational health and safety",
"Malay version"
],
"content": "Introduction\n\nAlthough workplace safety aspects have traditionally focused on biological, chemical, and radiological risks, psychosocial risk factors have recently garnered attention from researchers due to the impact of poor psychosocial working conditions on workers’ well-being and productivity.1 Developing and underdeveloped nations have shown a lack of awareness regarding addressing psychosocial working conditions and workers’ well-being.2 Conducting relevant studies becomes crucial in tackling psychosocial working conditions and workplace well-being issues.3–5 These studies can provide a more informed understanding of the challenges faced by these countries in terms of understanding, measuring, and managing well-being in general and in the workplace specifically.5 Additionally, research is needed to address the emerging risks and perils in workplace settings in developing and underdeveloped countries.3 By exploring the associations between psychosocial work factors and well-being, these studies can contribute to a better understanding of the impact of psychosocial factors on workers’ health and productivity.4\n\nThe NIOSH WellBQ, developed by the National Institute for Occupational Safety and Health (NIOSH), is a tool designed to assess the well-being of workers, with a primary focus on psychosocial working conditions.6 Constructed based on insights derived from occupational safety and health principles, this instrument provides a comprehensive understanding of employee well-being.7 The questionnaire, consisting of 126 questions distributed across five domains—work evaluation and experience, workplace policies and culture, workplace physical environment and safety climate, health status, and home, community, and society—also includes optional inquiries about work arrangements and demographics.6 The WellBQ is specifically tailored to measure a holistic understanding of worker well-being, encompassing both work and life dimensions.8 It seeks employees’ perspectives on various aspects, including the quality of their work life, circumstances beyond the workplace, support from supervisors, as well as their physical and mental health status.9\n\nA study by Ref. 6 established its psychometric properties, showing it as a reliable instrument. Organizations can use the NIOSH WellBQ to understand and improve workplace conditions. Researchers can explore the link between psychosocial conditions and outcomes like job satisfaction and stress, while individuals can assess their well-being for self-improvement.\n\nThe NIOSH WellBQ assesses psychosocial working conditions and their impact on employee well-being. Organizations use it for targeted interventions, researchers investigate relationships with job satisfaction, stress, and health, and individuals self-assess well-being.6 In summary, the NIOSH WellBQ aids well-being assessment and improvement in psychosocial work conditions.\n\nIn the course of history, the paramount importance of preserving the health and safety of workers has been manifested through the evolution of a robust framework for assessing and mitigating occupational hazards. This approach has consistently aimed at establishing secure work environments and safeguarding employees from adverse health effects resulting from occupational exposure.10 However, despite sustained efforts, the International Labour Office recently reported an alarming global annual toll of over two million fatalities due to accidents and occupational diseases. This statistic highlights the inadequacies and limitations of existing safety measures and calls for more effective, comprehensive strategies in occupational risk assessment, management, and prevention.11\n\nThe psychosocial work environment encompasses various risks, including psychosocial risk, hazards, factors, or stressors, as highlighted in previous research.12 These risks are pivotal considerations in fostering a healthy workplace environment, with a focus on optimizing worker health and well-being, as endorsed by organizations such as the International Labour Organization (ILO), World Health Organization (WHO), European Union Occupational Safety and Health (EU-OSHA) agency, Health and Safety Executive (HSE), and related entities.13\n\nTo ensure the applicability of the NIOSH WellBQ in Malaysia, it is imperative to conduct comprehensive research on occupational stress. This research aims to establish the validity and reliability of a Malay version of the NIOSH WellBQ. The study focuses on evaluating the consistency and construct validity of the Malay adaptation among civil servants in Kuala Lumpur, Putrajaya, and Selangor, Malaysia. Such research is crucial for the advancement of occupational stress assessment in the region and can significantly contribute to the well-being of the workforce.\n\nThis cross-sectional study used a Google Form to validate the NIOSH WellBQ among civil servants. The inclusion criteria encompass permanent staff, while the exclusion criteria pertain to temporary and contract-basis staff. The survey was widely distributed to various ministries and departments located in Kuala Lumpur, Putrajaya, and Selangor. Before participating in the study, all respondents provided written informed consent. In October 2022, a self-administered Malay version of the NIOSH WellBQ was distributed to 100 employees from various ministries and departments. The decision to include 100 respondents was driven by the aim to achieve a sufficiently diverse and representative sample, allowing for a robust analysis of psychosocial working conditions and employee well-being across different organizational settings and roles. This sample size is considered adequate for statistical significance, ensuring that the findings from the survey can be generalized to a broader population of employees within the targeted ministries and departments. Additionally, the practical consideration of participant burden and time constraints led to the selection of a manageable sample size, enabling a more feasible administration of the questionnaire, and ensuring a reasonable completion time of approximately 30 minutes per participant.\n\nThe NIOSH WellBQ, comprising a total of 68 items, was translated into the Malay language. It encompasses 16 scales, five indices, and 31 individual items that span across five domains: (1) work evaluation and experience; (2) workplace policies and culture; (3) workplace physical environment and safety climate; (4) health status; and (5) experiences and activities outside of work related to home, community, and society.\n\nThe NIOSH WellBQ was translated using a back-to-back method from English to Malay and then back to English by a certified translator from Universiti Pendidikan Sultan Idris (UPSI). This rigorous translation process ensured the accuracy and quality of the Malay version of the NIOSH WellBQ. This translation version has undergone content validity assessment by four experts prior to the distribution of this questionnaire.\n\nThe study’s protocol received approval from the Ethics Committee for Research Involving Human Subjects at Universiti Putra Malaysia on 2nd February 2023 (Reference No: JKEUPM-2022-986). The questionnaire distribution in October 2022 occurred prior to obtaining ethical approval on 2nd February 2023, due to unforeseen administrative delays, which arose because at that time, the University was in a transitional phase between the COVID-19 control order and transitioning to a hybrid work phase. Delays were encountered in obtaining official letters, compounded by difficulties in accessing Government premises during the distribution of questionnaires at that time. However, ethical considerations were strictly adhered to throughout the data collection process to safeguard participant welfare and maintain research integrity.\n\nData collection was facilitated through the utilisation of a specific questionnaire. Prior to commencing the study, authorisation was sought and obtained from the pertinent Human Resources Departments within the involved ministries. The respondents received the questionnaire via their official WhatsApp group. Accompanying the questionnaire distribution, written informed consent was meticulously provided to and obtained from each respondent. Prior to their participation, each participant in the study was required to provide written informed consent. This process involved presenting participants with a paper-based consent form that outlined the purpose, procedures, and potential risks and benefits of the study. Participants were given ample time to review the information provided in the consent form and had the opportunity to ask any questions they may have had. Subsequently, those who agreed to participate in the study signed the consent form, signifying their voluntary agreement to take part in the research.\n\nData entry and analysis were performed using SPSS version 25, a widely-used statistical software package for social sciences. Descriptive statistics were calculated to summarise the data, including means and standard deviations for continuous variables and frequencies with percentages for categorical variables. The internal consistency of the measurement scales was evaluated using Cronbach’s alpha coefficients, a commonly used measure of reliability.\n\nAn exploratory factor analysis with principal components and varimax rotation was conducted to assess the construct validity of the measurement instrument. This technique helps to identify the underlying factors or dimensions captured by the items in the instrument and to assess how well they align with the theoretical framework.\n\nHowever, it should be noted that SPSS cannot directly compute more advanced model fit indices such as TLI, RMSEA, and CFI, commonly used in Structural Equation Modeling (SEM). Therefore, the software AMOS was utilised to obtain pertinent findings regarding the goodness-of-fit of the structural models. AMOS is specifically designed for SEM analysis and provides robust tools to evaluate the model fit and test complex relationships among latent variables.\n\n\nResults\n\nThis study encompasses civil servants from diverse grades and service groups in Kuala Lumpur, Selangor, and Putrajaya. Initially, 100 questionnaires were distributed, out of which 95 participants responded. Among the final 95 respondents, 44 were classified as male, and 51 were female. It is important to note that these classifications refer to biological sex, not gender identity. Additionally, the majority of respondents were 37 years old and held a Bachelor’s Degree (30.5%).\n\nThe Malay version of the work evaluation and experience domain exhibited remarkable conformity with the data, as indicated by the following statistical indicators: RMSEA, TLI, and CFI values of 0.075, 0.99, and 0.97, respectively (Table 1). Most subdomains within this specific domain demonstrate consistently good internal consistency, as evidenced by Cronbach’s coefficients exceeding 0.70. However, it is essential to highlight that the assessment of work conditions indicates poor internal consistency, with a Cronbach’s alpha coefficient of 0.159. This discovery is similar to the study conducted while validating the NIOSH Work Well-being Questionnaire in Italian.14\n\nBased on the findings, the Supportive Work Culture scale demonstrates good reliability, with a Cronbach’s alpha coefficient of 0.895. Meanwhile, the Health Culture at Work scale shows an acceptable level of internal consistency, with a Cronbach’s alpha coefficient of 0.631. The subdomain assessing benefits exhibits a Cronbach’s alpha coefficient of 0.727, indicating good internal consistency. Additionally, the Organization of Work and Life subdomain achieves a Cronbach’s alpha coefficient of 0.780, signifying a satisfactory level of internal consistency. Unfortunately, the RMSEA, CFI, and TLI values cannot be computed for this domain, as it contains only single items or fewer than three observed variables per latent construct. These fit indices necessitate an adequate number of indicators to evaluate the model’s goodness of fit effectively. Moreover, it is worth noting that the original developers of this questionnaire did not report the RMSEA, CFI, and TLI values.6\n\nThe findings revealed that all scales demonstrated good internal consistency. The Cronbach’s alpha coefficients were 0.931, 0.823, and 0.688 for workplace safety climate, physical work environment satisfaction, and interpersonal conflict and incivility, respectively. Additionally, the validation of the third domain yielded excellent results, indicating a high level of fit for the model, with an RMSEA of 0.086, while the TLI and CFI values were 0.989 and 0.981, respectively.\n\nStatistical findings on domain 4 indicate a very good model fit with RMSEA = 0.079, TLI = 0.922, and CFI = 0.977. However, it is essential to note that during our validation analyses, certain subdomains (“general health” and “injury”) and constructs (“physical activity,” “tobacco use,” “alcohol consumption,” “work-related injury,” and “injury consequences”) were taken into consideration. Expressly, the “injury” subdomain and its constructs were excluded from the validation analyses due to the extremely low variability in responses provided by the respondents. Respondents found it challenging to accurately assess the effects of work-related injuries in the last 12 months. Similarly, the construct “alcohol consumption” was removed because all responses were coded as 0, indicating no variability. Likewise, the “tobacco use” construct was excluded due to some modalities’ low frequency of affirmative responses.\n\nRegarding the construct “physical activity,” statistical analysis revealed a weak correlation between the two items of the scale. This result can likely be attributed to the diverse and varying nature of work activities performed by the population enrolled in this study. The participants in this study engaged in various and distinct tasks, which may have influenced their responses to the two items on this scale. As for the subdomain “general health,” its inclusion in the validation analyses led to decreased CFI and TLI values; hence, it was excluded from the analyses. Only the subdomains “overall stress (health, finance, relationships, work)” and “cognitive functioning limitations” under mental health exhibited acceptable internal consistency with Cronbach’s alpha values of 0.821 and 0.782, respectively.\n\nOverall, the findings indicate a robust model fit for domain 4. However, excluding certain subdomains and constructs was necessary to ensure the validity and reliability of the validation analyses. These exclusions were made based on the limited variability, low frequency of responses, and weak correlation observed for certain items in the assessment, as well as considerations of the unique characteristics of the study population and their work activities.\n\nWhile Fontana et al.’s study14 did not include factor analysis for this domain, we chose to incorporate it into our research. This domain consists of two single items, one 2-item index, and one 7-item index. Chari et al.,6 the developers of NIOSH WellBQ, reported a low Cronbach’s alpha value of 0.62 for this domain in their original study. However, in our current investigation, both subdomains, namely “Financial security” and “Activities outside of work,” exhibited higher Cronbach’s alpha values of 0.811 and 0.810, respectively, indicating stronger internal consistency. It is important to acknowledge the potential limitations of using a combination of single and multiple items in this domain, as it may impact the interpretation of results and the underlying constructs being measured. Further research and validation studies may be warranted to enhance the measurement of this domain within the context of well-being assessments.\n\nIn this study, similar to the research conducted by Chari et al.6 and Fontana et al.,14 an analysis of correlations among selected scales and items was performed to verify concurrent, convergent, and discriminant validity (results presented in Table 2). The primary distinctions when comparing this study with the research conducted by Chari et al.1 were observed for the following items and scales: “time paucity/work overload,” “meaningful work,” “availability of health programs at work,” “availability of job benefits,” “physical activity,” “tobacco use,” “risky drinking,” “healthy diet,” “support outside of work,” and “activities outside of work.”\n\nRegarding this matter, it is reasonable to expect that the differences in domains 4 (health status) and 5 (home, community, and society) are predominantly correlated to social and cultural differences between the population enrolled in the study. Furthermore, based on the findings, the differences observed in domains 1(work evaluation and experience) and 2 (workplace policies and culture) mainly result from the uniqueness and variations in the work environments of the respondents in the public service, who come from various types of services and positions.\n\n\nDiscussion\n\nPsychosocial working conditions play a crucial role in promoting workers’ well-being and ensuring the implementation of health and safety standards in the workplace.2 Research has shown that high job demands, low job control, and poor social support in the workplace are associated with increased stress levels and negative health outcomes among workers.2 These factors can lead to decreased job satisfaction, increased absenteeism, and reduced productivity.2 Addressing psychosocial working conditions involves implementing policies and practices that promote a healthy work-life balance, provide opportunities for skill development and career advancement, and encourage positive social interactions among employees.2 By creating a supportive work environment, organizations can enhance workers’ well-being and contribute to their overall job satisfaction and engagement.2\n\nPolicymakers and occupational health practitioners play a crucial role in ensuring that psychosocial working conditions are considered and addressed.2 They can develop and enforce regulations and guidelines that promote a healthy work environment, conduct inspections and audits to assess compliance with these standards, and provide resources and support to organizations in implementing effective psychosocial risk management strategies.2\n\nBased on the findings of this study, it is evident that the NIOSH WellBQ demonstrates strong qualities as a measurement tool for assessing worker well-being and psychosocial working conditions. The study’s results support the assertions made by the creators of NIOSH WellBQ, stating that the instrument’s content is theoretically driven and grounded in existing concepts of well-being. The instrument encompasses a wide range of well-being measures across various dimensions. This comprehensive approach results from its development through an extensive review of the literature on occupational stress, health, and well-being and input from subject-matter experts.\n\nThe research outcomes support the notion that the NIOSH WellBQ is a robust and reliable instrument for assessing the well-being of workers and their psychosocial working conditions. The instrument’s theoretical foundation and its inclusion of diverse well-being dimensions further strengthen its utility as a valuable tool for researchers and practitioners.\n\nNevertheless, there are several limitations that the developers of NIOSH WellBQ can improve upon in the future. One notable limitation is the presence of single items for certain constructs. Single-item measures may not fully capture the complexity of these constructs, and therefore, it is crucial to exercise caution when interpreting findings based solely on these single items. Alternative measures can be considered to address this limitation, such as supplementing single-item measures with multiple-item scales that have established psychometric properties. These multiple-item scales provide more reliable and valid assessments of the constructs.15\n\nIt would be prudent for the developer of NIOSH WellBQ to take these limitations into consideration and explore opportunities to enhance the measurement of constructs within the instrument in the future revision. By incorporating multiple-item scales and conducting further validation studies, the NIOSH WellBQ can potentially strengthen its psychometric properties and provide a more comprehensive and accurate assessment of worker well-being and psychosocial working conditions.16\n\nIn conclusion, this study provides compelling evidence supporting the reliability and validity of the Malay version of the NIOSH WellBQ as a comprehensive instrument for evaluating worker well-being. The results demonstrate its effectiveness in capturing the multifaceted dimensions of well-being within the studied population. Nonetheless, it is important to acknowledge that the current findings should be considered preliminary. Further comprehensive validation is warranted to ensure the instrument’s robustness and applicability, involving larger sample sizes and more sophisticated methodologies.\n\nTo strengthen the psychometric properties of the Malay version of NIOSH WellBQ, future research should consider conducting test-retest reliability assessments. Test-retest reliability assesses the stability of responses over time by administering the instrument to the same group of participants on two separate occasions and examining the consistency of their responses. This will help determine whether the instrument produces consistent results over time and establish its reliability. Confirmatory factor analysis (CFA) should also be conducted to examine the model fit of the Malay version of NIOSH WellBQ. CFA is a statistical technique that tests the fit between the observed data and the hypothesized factor structure of the instrument. By conducting CFA, researchers can assess whether the items in the instrument are measuring the intended constructs and establish its construct validity.\n\nFurthermore, exploring the convergent validity of the Malay version of NIOSH WellBQ would enhance its credibility. Convergent validity refers to the degree to which the instrument correlates with other measures that assess similar constructs. By comparing the results of the Malay version of NIOSH WellBQ with other established well-being measures, researchers can examine the extent to which the instrument converges with existing measures and validate its effectiveness in assessing worker well-being. By undertaking these crucial steps, researchers can enhance confidence in the Malay version of NIOSH WellBQ and extend its generalizability to broader populations. Test-retest reliability assessments will provide evidence of the instrument’s stability over time, while CFA will establish its construct validity. Exploring convergent validity will further validate the instrument by comparing its results with other established measures of well-being. As the study advances and these psychometric properties are strengthened, the Malay version of NIOSH WellBQ has the potential to become a valuable tool for assessing worker well-being in diverse settings. Its reliability, validity, and generalizability will contribute to its credibility and usefulness in promoting workers’ well-being and informing occupational health interventions.\n\n\nConclusion\n\nGenerally, the study demonstrated that the version of the WellBQ validated in this research exhibits more than satisfactory psychometric qualities. This suggests that it is a reliable tool to measure and assess the well-being of workers in Malaysian working populations and workplaces. Referring to the findings of this study, with a few exceptions that were extensively discussed earlier, our statistical analyses revealed a good model fit and internal consistency for the WellBQ. These results further support the suitability of the WellBQ for use in evaluating the well-being of workers in various Malaysian contexts.\n\nIt is crucial to note that the findings of this study are highly comparable and practically correspond with those obtained by Chari et al.6 and Fontana et al.14 These similarities reinforce the results previously reported by the developers of the WellBQ. Consequently, the outcomes presented in this research significantly contribute to the existing knowledge concerning workers’ well-being.6,14 The findings generated in this study can be valuable in enhancing our understanding of the topic related to workers’ well-being and may have implications for improving workplace well-being assessments and interventions.",
"appendix": "Data availability\n\nFigshare: NIOSH WELLBQ QUESTIONNAIRE ENGLISH AGE GROUP…https://doi.org/10.6084/m9.figshare.25426279.v1. 17\n\nThis project contains the following underlying data:\n\n- NIOSH WELLBQ QUESTIONNAIRE.csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nJavaid, et al.: Does psychosocial work environment factors predict stress and mean arterial pressure in the malaysian industry workers? Biomed. Res. Int. 2018; 2018: 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKowalski, Loretto: Well-being and hrm in the changing workplace. The International Journal of Human Resource Management. Int. J. Hum. Resour. Manag. 2017; 28(16): 2229–2255. Publisher Full Text\n\nIsha, et al.: Malay validation of copenhagen psychosocial work environment questionnaire in context of second generation statistical techniques. Biomed. Res. Int. 2020; 2020: 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSlany, et al.: Psychosocial work factors and long sickness absence in europe. International Journal of Occupational and Environmental Health. Int. J. Occup. Environ. Health. 2014; 20(1): 16–25. PubMed Abstract | Publisher Full Text\n\nKowalski, Loretto: Well-being and hrm in the changing workplace. Int. J. Hum. Resour. Manag. 2013; 28(16): 2229–2255. Publisher Full Text\n\nChari R, Sauter SL, Sayers ELP, et al.: Development of the national institute for occupational safety and health worker well-being questionnaire. J. Occup. Environ. Med. 2022; 64(8): 707–717. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDobson M, et al.: The healthy work survey. J. Occup. Environ. Med. 2023; 65(5): e330–e345. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeters S, et al.: Thriving from work questionnaire: dimensionality, reliability, and validity of the long and short form questionnaires. Am. J. Ind. Med. 2023; 66(4): 281–296. PubMed Abstract | Publisher Full Text\n\nTerry P: The stare decisis doctrine and total worker health®: prior precedent and continuous improvement in health promotion. Am. J. Health Promot. 2022; 37(3): 296–299. PubMed Abstract | Publisher Full Text\n\nChari, et al.: Expanding the paradigm of occupational safety and health a new framework for worker well-being. J. Occup. Environ. Med. 2018; 60(7): 589–593. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: WHO/ILO joint estimates of the work-related burden of disease and injury, 2000–2016: global monitoring report.2021.\n\nWagner, et al.: Healthcare professionals’ perspectives on working conditions, leadership, and safety climate: a cross-sectional study. BMC Health Serv. Res. 2019; 19(1): 1–14. Publisher Full Text\n\nJavaid, et al.: Does psychosocial work environment factors predict stress and mean arterial pressure in the malaysian industry workers?. Biomed. Res. Int. 2018; 2018: 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFontana, et al.: Validation of the NIOSH Worker Well-being Questionnaire in Italian Language. J. Occup. Environ. Med. 2023; 65(6): e402–e412. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpector: Industrial and organizational psychology: Research and practice. John Wiley & Sons; 2021.\n\nWanous, Hudy: Single-item reliability: A replication and extension. Organ. Res. Methods. 2001; 4(4): 361–375. Publisher Full Text\n\nOmar A: NIOSH WELLBQ QUESTIONNAIRE ENGLISH AGE GROUP. [Dataset]. figshare. 2024. Publisher Full Text"
}
|
[
{
"id": "295243",
"date": "28 Jun 2024",
"name": "Remy Magnier-Watanabe",
"expertise": [
"Reviewer Expertise Subjective well-being",
"knowledge management",
"international business"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript aims to validate the Worker Well-Being Questionnaire, a scale originally developed by the US National Institute for Occupational Safety and Health (NIOSH), in the Malay language. The results show that the Malay version is a reliable tool for assessing worker well-being in the Malaysian context.\nThe introduction provides a solid background on the importance of assessing psychosocial working conditions and the necessity of having a validated tool in the Malay language. However, the literature review could be expanded to include more recent studies that have validated similar instruments in different languages and contexts to strengthen the justification for this study. For instance, recent studies such as those by Berthelsen et al. (2020) [Ref 1] or the validation of the Copenhagen Psychosocial Questionnaire in Sweden and Şahan et al. (2019) on [Ref 2] the Turkish version could provide valuable insights and methodologies relevant to the current manuscript.\nIn the methodology, the expertise and qualifications of the translators and the expert committee members should be detailed to add credibility to the process. The results are well-organized and presented, with clear tables summarizing the key findings. The low internal consistency for certain subdomains (work conditions) is acknowledged, but the manuscript should give potential reasons for this and suggest ways to address these issues in future research. The practical implications for occupational health practitioners and policymakers are briefly mentioned. Expanding this section to provide more concrete recommendations based on the authors' study would enhance the manuscript’s impact. For example, the recent guidelines by the International Labor Organization (ILO) and World Health Organization (WHO) on addressing mental health at work offer practical strategies that could be adapted for implementing the findings of this study(https://www.who.int/publications/i/item/9789240057944) Overall, the manuscript makes a valuable contribution to the literature on workplace well-being assessment tools.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-618
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https://f1000research.com/articles/13-180/v1
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11 Mar 24
|
{
"type": "Research Article",
"title": "Effect of Maraviroc and/or Favipiravir plus systemic steroids versus systemic steroids only on the viral load of adults with severe COVID-19: clinical trial",
"authors": [
"Elba Medina",
"Ana Laura Sanchez-Sandoval",
"Eira Valeria Barrón-Palma",
"Ana María Espinosa-García",
"Alma Maria de la Luz Villalobos-Osnaya",
"Mireya León-Hernández",
"María Luisa Hernández-Medel",
"Joselin Hernández-Ruiz",
"Mara Medeiros",
"Alberto Cedro-Tanda",
"Adolfo Pérez-García",
"Lucía Monserrat Pérez-Navarro",
"Elba Medina",
"Ana Laura Sanchez-Sandoval",
"Eira Valeria Barrón-Palma",
"Ana María Espinosa-García",
"Alma Maria de la Luz Villalobos-Osnaya",
"Mireya León-Hernández",
"María Luisa Hernández-Medel",
"Joselin Hernández-Ruiz",
"Mara Medeiros",
"Alberto Cedro-Tanda",
"Adolfo Pérez-García"
],
"abstract": "Background Coronavirus disease 2019 (COVID-19) has created the need to evaluate drugs such as favipiravir (FPV), an antiviral inhibitor of RNA-dependent RNA-polymerase (RdRp), and Maraviroc (MVC), an antiretroviral that antagonizes the chemokine receptor CCR5, which could affect the modulation of inflammation and viral replication in the treatment of COVID-19. We sought to evaluate the effect of MVC and/or FPV plus systemic steroid (SS) vs. SS alone on the viral load and progression to critical disease.\n\nMethods Sixteen patients with severe COVID-19 were evaluated in three treatment arms: 1) SS only (n=6), 2) SS plus one test drug MVC or FPV (n=5), and 3) SS plus both test drugs (MVC and FPV, n=5). The viral load was determined for N, E, and RdRp viral genes.\n\nResults A significant decrease in viral load was observed in the three treatment groups, with a larger effect size in the group that combined SS with both test drugs. The E, N, and RdRp genes with Cohen’s d were 120%, 123%, and 50%, respectively.\n\nConclusions The largest effect on viral load reduction, as measured by effect size, was observed in the combination treatment group; however, no statistical significance was found, and it did not prevent progression to critical illness.",
"keywords": [
"Steroids",
"Treatment",
"antiviral drugs",
"COVID-19",
"Favipiravir",
"Maraviroc",
"severe disease"
],
"content": "Introduction\n\nIn hospitalized patients with coronavirus disease 2019 (COVID-19), five percent of patients with severe disease can progress to critical condition; therefore, the WHO designed a 10-point progression and severity score.1 Most patients who progress to severe disease have at least one risk factor, such as old age, type 2 diabetes mellitus (T2DM), obesity, hypertension (HTN),2 and high viral load with a cycle threshold (Ct) <25.3 High viral load at admission and within the first 12 days, as well as old age and comorbidities, are independently associated with the risk of intubation and mortality.3,4 The severity of COVID-19 prompted both new therapeutic strategies; dexamethasone helped to reduce mortality5 and at the same time, in silico studies revealed an area of opportunity for Favipiravir (FPV), a prodrug developed in 2002 for the influenza virus as a ribonucleotide analog that inhibits the viral replication by inhibiting the viral enzyme RNA-dependent RNA-polymerase (RdRp).6–8 Moreover, its known adverse effects include thoracic pain, diarrhea, hyperuricemia, and liver damage.9–13 Another repositioned drug is Maraviroc (MVC), developed for human immunodeficiency virus (HIV), which antagonizes the chemokine receptor CCR5,14 additionally modulates inflammation,15–17 and could have a dual block of CCR5 and the NSP5 (3CLpro or Mpro) viral protease of the SARS-CoV-2 virus, which is responsible for the regulation of replication.18,19 It could also inhibit S-protein-mediated cell fusion and syncytia-forming capacity.17 The most frequent adverse effects were skin rash, infections, bronchitis, cough, and fever.20 Subsequently, the development of vaccines has reduced mortality,21 and the antivirals approved thus far are not fully effective, and their availability is limited.22,23 Notwithstanding, new infections continue to occur in vulnerable people, so there is still a need for effective drugs. Therefore, this study aimed to assess the effect of MVC and/or FPV plus systemic steroids (SS) vs. SS only on the viral load and progression to critical disease in COVID-19 patients.\n\n\nMethods\n\nThis was a randomized, unicentric, parallel, single-blinded study (only the patient was blinded to the allocation). The participants were severe, non-critical COVID-19 patients admitted between July 2021 and June 2022 who met the following inclusion criteria: Age 18-80 years, within the first 12 days of onset of symptoms, oxygen saturation ≤90%, positive test for SARS-CoV-2, and at least one risk factor for progression to critical: T2DM, Body mass index (BMI) ≥30, HTN, and age ≥65 years. The women agreed to use contraceptives for up to 90 days. Exclusion criteria were breastfeeding or pregnant women, encephalopathy, renal function ≤ 30 ml/min/1.73 m2 estimated by CKD-EPI, acute coronary disease, any state of immunosuppression, and treatment with psychotropics. All the participants signed an informed consent form. We screened 237 patients, of which 19 met the inclusion criteria, 16 completed the assigned treatment, and were analyzed, as shown in Figure 1—CONSORT flow diagram.\n\nDue to the low recruitment rate, the treatment group with only MVC plus SS or FPV plus SS was grouped into a single treatment group named only one antiviral. Three patient was not included in the analysis because one patient of the FPV group developed severe sinus bradycardic (35 bpm) on the second day of treatment, so it was suspended for the patient's safety; this patient was on concomitant treatment with an antitussive (dropropizine), which has been associated with bradycardia due to its alpha-blocker effect, and therefore was also suspended; three days after suspension, the patient recovered heart rate without additional further treatment or procedure, another patient also development severe sinus bradycardia (<40 bpm) on the third day parallel to the intubation process, demanding the use of vasopressors, and dobutamine, recovered heart rate the same day; the remaining patient escaped from the hospital, then only analyzed 16 patients.\n\nSS, Systemic Steroid only; MVC+SS, Maraviroc, and Systemic Steroid; FPV+SS, Favipiravir, and Systemic Steroid; FPV+MVC+SS; Favipiravir plus Maraviroc and Systemic Steroid; bpm, beats per minute.\n\nPatients were recruited from the emergency room, infectology, or pneumology services. They were randomly assigned to one of four parallel groups in a 1:1:1:1 ratio; patients were allocated according to a chart of aleatory numbers stratified by sex; using your hospital record number, randomization was by a computer-generated random number list prepared by an investigator with no clinical involvement in the trial. After the researcher obtained the patient’s consent, the research nurse telephoned a contact independent of the recruitment process for allocation consignment. The nurses and investigators were trained in good clinical practice. Treatments were defined as follows: only (SS), MVC+SS, FPV+SS, and MVC+FPV+SS. Due to the low recruitment rate and adverse events of FPV, the clinical trial was closed, and the treatment groups with only MVC plus SS or FPV plus SS were gathered as a single group called treatment with only one antiviral for statistical analysis, as shown in Figure 1.\n\nOutcomes\n\nPrimary outcomes: Decrease the viral load, and progression to critical disease.\n\nSample size calculation was performed using the statistical package GPower 3.1.9®, applying an F-family test for between-factors repeated measures ANOVA considering three treatment groups, three viral load measurements, and an effect size of 0.5, (odds ratio: 6) by Magleby et al.,4 and 0.8 power, obtaining a total of 24 patients: six per group, plus an additional 20% for losses, thus summing eight per group.\n\nDosing: MVC (300 mg Selzentry, GSK) was administered orally at 300 mg twice a day for ten days.24 FPV (200 mg Avigan, Fujifilm Pharma) was administered orally, 1600 mg twice daily on the first day, and 600 mg twice daily on days 2-7.25 SS: All patients received intravenous steroids: dexamethasone (6 mg daily) or its steroid equivalent,5 enoxaparin, or fractioned heparin. Patients who missed two dose administrations for any reason were excluded from the protocol. The patients’ participation could also end before term due to a complication or life-threatening adverse event, and clinical assessment was performed daily for seven days, and on day 28.\n\n\nResults\n\nRNA was extracted from nasopharyngeal exudates using QIAamp® and the QIAGEN kit. Viral genes E, N, and RdRp were identified by qRT-PCR using the GeneFinder™ COVID-19 Plus RealAmp kit (OSANG Healthcare, South Korea), according to the manufacturer’s protocol. The results were analyzed using QuantStudioTM Design & Analysis version 1.5.1 (Thermo Fisher Scientific, USA). The Ct was determined in duplicate to identify the concordance between measurements, and the reported values are the means of measurements. The viral load was calculated from calibration curves and reported as the number of copies per microliter of RNA extracted per sample. Briefly, primer pairs were designed to amplify each of the three viral genes detected with the kit (E, N, and RdRp) using one of the positive samples with a Ct value of <25 for all three genes. The PCR amplification products were purified and quantified, and 1:10 dilutions with known copy numbers were generated for subsequent analysis by qRT-PCR. The Ct values obtained were plotted against log (number of copies/μl) to calculate a linear fitting equation (R2>0.97) for each viral gene. Finally, the Ct values for each gene in the samples were used to calculate the number of copies/μl of RNA, using the fitting equations of the calibration curve for each gene sequence. Libraries were prepared using the Illumina COVIDSeq test protocol, following the manufacturer’s instructions. First-strand synthesis was performed using the RNA samples. The synthesized cDNA was amplified using ARTIC primers v4 for multiplex PCR, generating 98 amplicons across the SARS-CoV-2 genome. The PCR-amplified product was tagged and adapted using IDT for Illumina Nextera UD Indices Set A, B, C, and D (384 indices) (Illumina, San Diego, CA, USA). Sequencing was performed on the NextSeq 2000 platform (Illumina, San Diego, CA, USA).\n\nAll adverse events, related or unrelated to the study drugs, were analyzed by the Pharmacovigilance Service of the Hospital and duly notified to the competing authorities.\n\nGiven that the patients were discharged before ten days, we analyzed the data up to day seven; chi-square and Kruskal-Wallis tests were used to compare clinical and laboratory characteristics in the three treatment groups. The effect of the three treatments on viral load was measured using effect size (Cohen’s d). T-tests for related samples were performed to compare the clinical and laboratory characteristics within the groups. SPSS version 26 (IBM, Chicago, IL, USA) was used for all the statistical analyses. The significance level was set at p < 0.05 for all statistical tests.\n\n\nEthics\n\nThis clinical trial was approved by the Committee of Bioethics, Research, and Biosafety of Hospital General de Mexico “Dr. Eduardo Liceaga” (registration number DI/20/407/04/38) and by the Federal Commission for Protection Against Sanitary Risk (COFEPRIS). The procedures followed were in accordance with the ethical standards of the responsible institutional committee on human experimentation, World Medical Association, and Helsinki Declaration.\n\n\nResults\n\nWe included 16 patients with severe COVID-19 (9 women, seven men) with a mean age of 53±14 years. The clinical characteristics, viral loads, and adverse events of each treatment group are summarized in Table 1.\n\na Kruskal-Wallis (compared to three treatments on day 0, and day 7).\n\nb Chi-square test.\n\nc T test for related samples.\n\nd This patient had four risk factors for critical disease, received treatment with MVC, required invasive mechanical ventilation, and died at 10 days.\n\ne The patient was not vaccinated, he does not accept invasive mechanical ventilation and died at 9 days.\n\nf Started day seven and recovered normal heart rate on day 12.\n\n* p < 0.05 with statistical significance.\n\nFour of 16 patients reached a decrease of ≥ 2 points in the WHO score on day seven; 50 percent of which were in the single antiviral group; however, no statistically significant difference was found.\n\nThe largest viral load reduction was observed in the MVC and FPV+MVC groups (days three, and seven compared with day 0) (Figure 2). The delta variant was identified in 10 of 16 patients, and the remaining six patients were infected with the Omicron variant.\n\nPercentage of change on day 3 vs day 0 in nasopharyngeal exudate in the three treatment groups. The most considerable percentage of reduction in the number of copies per microliter of RNA was observed in the MVC and FPV+MVC groups. Percentage of change on day 7 vs day 0 in nasopharyngeal exudate in the three treatment groups. The decrease in viral load measured in the percentage of the gene copies per microliter of RNA of nasopharyngeal exudate on day seven was larger in the MVC and FPV+MVC groups.\n\nThree patients had bradycardia, two had FPV, and one had FPV+MVC. According to the Pharmacovigilance Service, these are related to FPV. All patients recovered; however, two patients were excluded from the study because of severe bradycardia and were not included in the analysis. Figure 1—CONSORT flow diagram.\n\n\nCombined antiviral group\n\nThis group included five patients (three women and two men). Of the five patients, one received two doses of vaccination, and in the remaining four patients, none received at least one dose. The mean patient age was 58±8 years.\n\nThe viral load was analyzed in five patients. This group had a larger effect size in reducing the viral load at day seven compared with the other treatment groups; genes E, N, and RdRp with Cohen’s d of 120%, 123%, and 50%, respectively (Table 2). One of the five patients maintained a persistently high viral load, and this patient survived. The Omicron variant was found in four out of five patients; the remaining patient had the delta variant.\n\na Sample nasopharyngeal exudate.\n\n\nSingle antiviral group\n\nFive patients were included (three women and two men), with a mean age of 52±14 years. Four of the five patients received two doses of the vaccine, and one received only one dose.\n\nWe did not identify a statistically significant difference in the viral load. The delta variant was found in four of five patients, and the other had the Omicron variant. One out of five patients maintained a persistently high viral load (≤ 25 Ct) and died.\n\n\nNon-antiviral treatment\n\nSix patients were included in this group (3 women and 3 men). The patients’ age was 48±18 years. Three of the six patients were vaccinated, two of the three had two doses, the other had one dose, and the other three patients were not vaccinated vs. final.\n\nWe analyzed the viral load in six patients and found no statistical significance. The delta variant was found in five of six patients, and the remaining patient had the Omicron variant.\n\n\nDiscussion\n\nIn this study respect to the effect of three treatments on the viral load, and to avoid progress to critical disease in patients with severe COVID-19 found a reduction, and a quicker decrease in viral load in the combined treatment group (FPV+MVC) notwithstanding this did not prevent the progression to critical disease which could be attributed to the small size of the sample, notwithstanding several factors may affect the results; regarding Favipiravir, three significant factors that may affect the results: heterogeneity in doses, and duration of treatment (loading dose from 1600 to 4800 mg, maintenance dose of 1200 to 2000 mg, 2, 3, 4 doses for the next 4-13 days), older age, baseline disease severity.9,10,26–28 In one study, FPV slightly improved clinical and radiological manifestations or decreased viral load10 but in another study, it failed to improve viral elimination.27 Siripongboonsitti et al 2023 found in patients with mild to moderate COVID-19, the use of favipiravir prevented severe COVID-19 when personalized, early treatment was performed, and dose adjustment was made based on ethnicity and body weight.28\n\nCurrently, some antiviral drugs are approved by the FDA for emergency use,22,23 whose main objective is to avoid hospital admission and death in unvaccinated, with mild to moderate disease, and without a requirement of oxygen, within the first seven days of the onset of symptoms. In contrast, our study focused primarily on patients with severe clinical symptoms, in which the objective was to prevent their evolution to be critical.\n\nAnalysis of the epidemic waves of COVID-19 suggests that the SARS-CoV-2 virus evolved into less lethal variants, and the start of vaccination modified the severity of the infection; the oxygen requirement decreased from 80% to 17%, as well as a decrease in admission to the ICU, average days of hospital stay, and mortality.29 Therefore, conditions changed dramatically for the benefit of our population since 42% of the subjects in this study were recruited between the third and fourth COVID-19 waves when Delta and Omicron were the predominant variants. The Omicron variant has been described to have a 44% reduction in hospital admissions and a 69% lower risk of death than confirmed cases of the delta variant.30 Delta and Omicron variants have shorter incubation periods, whereas higher infectious viral loads were detected in patients infected with Delta than in patients infected with Omicron.31,32\n\nThe clearance time of viral load is slower in non-vaccinated individuals.33 After one dose of vaccine, the number of Ct increased by 4.5 Ct, and with a booster, it increased by 2.4 Ct34; therefore, the start of vaccination could be a factor that influenced our results; nevertheless, the combined treatment reached the effect faster in Ct, and a larger effect size in reducing viral load at seven days; some antivirals found a significant reduction in viral load,22,23 remdesivir no provoke reduction, only positive clinical outcome.35\n\nThe most prevalent risk factors in the population were T2DM or HTN (63%), followed by obesity and age >65 years, which differs from other studies in which 79% had a BMI ≥ 30, followed by age >60 years, and T2DM.23\n\nRegarding adverse events, we did not find hyperuricemia frequently reported in treatment with FPV36; three of our patients developed bradycardia; and there are two case reports that associate the development of bradycardia with FPV as a possible rare adverse event.37,38\n\nThe limitations were that pharmacokinetics could not be performed, and the study could not be double-blinded. Finally, the sample size was small, which limited statistical analysis. The public health emergency mainly generated this, adding to the lack of finances, shortage of human resources, and obstacles of the regulatory system.\n\nRegarding MVC in COVID-19, there are few registered clinical trials on ClinicalTrials.gov, including this, and none have evaluated its combination with favipiravir. The development of drugs, whether approved or not, requires time and funding to determine the therapeutic target, the drug’s toxicity, and how to use it properly.39,40 It has been challenging to draw any consistently valid conclusions about the efficacy of drugs in the treatment of COVID-19 disease41,42; so far the cure has not been achieved with the use of a single particular drug.39,43\n\nRegister in Clinical Trials (NCT04475991). https://clinicaltrials.gov/study/NCT04475991?cond=NCT04475991&rank=1\n\nFor pre-registered analysis in clinical trials, we planned the analysis of data to be between the four treatment groups. However, because of the low recruitment rate and small sample size, it was necessary for statistical analysis to join the group of favipiravir plus systemic steroids with the group of Maraviroc plus systemic steroids in one antiviral treatment group.\n\n\nData and software availability\n\nFigshare: Medina, Elba; Sanchez, Laura; Barron, Valeria; Espinosa, Ana Maria; Villalobos, Alma; Leon, Mireya; et al. (2024). Repository COMVIVIR.xlsx. figshare. Dataset. https://doi.org/10.6084/m9.figshare.25017992.v3\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReviewers\n\n1. Doi Y. https://pubmed.ncbi.nlm.nih.gov/?term=Doi+Y&cauthor_id=36307058 Department of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. E-mail: yoheidoi@fujita-hu.ac.jp\n\n2. Siripongboonsitti, T. Division of Infectious Diseases, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand. Taweegrit.sir@cra.ac.th\n\n3. Manuel Iván Girón-Pérez Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Nayarit, Mexico. ivan_giron@hotmail.com\n\n4. Carlos Eduardo Covantes-Rosales Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Nayarit, Mexico carlos.covantes@uan.edu.mx.\n\n5. Michael J Satlin. Department of Medicine, Division of Infectious Diseases. Weill Cornell Medicine, New York, New York USA. mjs9012@med.cornell.edu",
"appendix": "Acknowledgments\n\nCONAHCYT, CVU 785859. GlaxoSmithKline donated Maraviroc, and CCINSHAE (Comisión Coordinadora de Institutos Nacionales de Salud y Hospitales de Alta especialidad) donated Favipiravir. Hospital General de México “Dr. Eduardo Liceaga”.\n\n\nBibliography\n\nCharacterisation WHO, infection MoC-: A minimal common outcome measure set for COVID-19 clinical research. Lancet Infect. Dis. 2020; 20(8): e192–e197.\n\nKompaniyets L, Pennington AF, Goodman AB, et al.: Underlying Medical Conditions and Severe Illness Among 540,667 Adults Hospitalized With COVID-19, March 2020-March 2021. Prev. Chronic Dis. 2021; 18: E66. Publisher Full Text\n\nLiu Y, Yan LM, Wan L, et al.: Viral dynamics in mild and severe cases of COVID-19. Lancet Infect. Dis. 2020; 20(6): 656–657. 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(1533-4406 (Electronic)).\n\nLevine-Tiefenbrun MA-O, Yelin IA-O, Katz R, et al.: Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine. (1546-170X (Electronic)).\n\nGottlieb RL, Vaca CE, Paredes R, et al.: Early Remdesivir to Prevent Progression to Severe Covid-19 in Outpatients. N. Engl. J. Med. 2022; 386(4): 305–315. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPilkington V, Pepperrell T, Hill A: A review of the safety of favipiravir - a potential treatment in the COVID-19 pandemic? J. Virus Erad. 2020; 6(2): 45–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHabib MB, Elshafei M, Rahhal A, et al.: Severe sinus bradycardia associated with favipiravir in a COVID-19 patient. Clin. Case Reports. 2021; 9(8): e04566. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSzigeti J: Sinusbradycardia mint lehetséges favipiravir-mellékhatás. Orv. Hetil. 2022; 163(7): 267–270. PubMed Abstract | Publisher Full Text\n\nMartinez MA: Efficacy of repurposed antiviral drugs: Lessons from COVID-19. Drug Discov. Today. 2022; 27(7): 1954–1960. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartinez M: Clinical Trials of Repurposed Antivirals for SARS-CoV-2. Antimicrob. Agents Chemother. 2020; 64(9): e01101–e01120. Publisher Full Text\n\nBartoli A, Gabrielli F, Alicandro T, et al.: COVID-19 treatment options: a difficult journey between failed attempts and experimental drugs. Intern. Emerg. Med. 2021; 16(2): 281–308. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEsmail LC, Kapp P, Assi R, et al.: Sharing of Individual Patient-Level Data by Trialists of Randomized Clinical Trials of Pharmacological Treatments for COVID-19. JAMA. 2023; 329: 1695–1697. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEdwards A: What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen? J. Chem. Inf. Model. 2020; 60(12): 5727–5729. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "266453",
"date": "08 May 2024",
"name": "Amgad M Rabie",
"expertise": [
"Reviewer Expertise Medicinal Chemistry & Drug Discovery"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe TOP MAJOR CONCERN: The current work lacks many extremely important references in the Introduction section and discussion parts about new compounds/drugs (especially similar antiviral drugs, e.g., ensitrelvir, simnotrelvir, cordycepin, riboprine, molnupiravir, remdesivir, teriflunomide, strychnine bush ingredients, pineapple ingredients, ginger ingredients, oxadiazoles, gallates, and other similar nucleoside/nucleotide analogs) that are effective against the different variants of SARS-CoV-2, especially the Omicron variant, as well as discussing the last reports for COVID-19 disease treatment in general; all of them must be adequately cited and added to this work to strengthen its validity and to be publicly accepted. The references are: (RABIE A, 2023[Ref 1]), (Rabie AM, 2022[Ref 2]), (Rabie AM, et al., 2022[Ref 3]), (Eltayb WA, et al., 2023[Ref 4]), (Rabie A, 2021[Ref 5]), (Rabie AM, 2021[Ref 6]), (Rabie AM, et al., 2023[Ref 7]), (Rabie AM, 2022[Ref 8]), (Rabie AM, et al., 2023[Ref 9]), (Rabie AM, et al., 2023[Ref 10]), (Rabie A, 2022[Ref 11]), (Rabie AM, 2024[Ref 12]), (Rabie AM, 2021[Ref 13]), (Rabie A, 2022[Ref 22]). - https://doi.org/10.22034/ijnc.2022.3.10\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11697",
"date": "11 Jun 2024",
"name": "Elba Medina",
"role": "Author Response",
"response": "Amgad M Rabie Mansoura University, Mansoura, Dakahlia Governorate, Egypt We thank the reviewer for the positive feedback and helpful comments. The necessary changes have been incorporated into the manuscript. We have included many important references in the introduction section and discussion parts about new compounds/drugs, that are effective against the different variants of SARS-CoV2, as well as the last reports for COVID-19 disease treatment in general."
}
]
}
] | 1
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https://f1000research.com/articles/13-180
|
https://f1000research.com/articles/11-851/v1
|
28 Jul 22
|
{
"type": "Research Article",
"title": "Effects of different concentrations of reversine to enhance conversion of dedifferentiated fat cells into mature cardiomyocytes",
"authors": [
"Budi Baktijasa Dharmadjati",
"Djanggan Sargowo",
"Aulanni’am .",
"Budi Susetyo Pikir",
"Yudi Her Oktaviono",
"Oryza Sativa",
"Kandita Arjani",
"Ricardo Adrian Nugraha",
"Djanggan Sargowo",
"Aulanni’am .",
"Budi Susetyo Pikir",
"Yudi Her Oktaviono",
"Oryza Sativa",
"Kandita Arjani",
"Ricardo Adrian Nugraha"
],
"abstract": "Background: There is an essential need for cardiomyocyte regeneration among patients with heart failure. Transplantation of dedifferentiated fat (DFAT) cells may lead to an improvement of cardiomyocyte regeneration among heart failure patients. We believe that DFAT cells are promising candidate cell sources for cardiac regeneration. However, the pathway underlying how DFAT cells of the adipose lineage differentiate into mature cardiomyocytes isn’t fully understood. Methods: We conducted an experimental laboratory study on isolated DFAT cells from adipose tissue of healthy adults. Then, we treated cells with different concentrations of reversine (10, 20 and 40 nM), and performed RNA extraction and cDNA synthesis. Next, we used a ceiling culture method based on the buoyancy properties of mature lipid-filled adipocytes. Stemness expression (Octamer-binding transcription factor 4 [Oct4], brachyury, Fetal liver kinase 1 [Flk-1]) was quantified by reverse transcription-quantitative (RT-q)PCR, while cardiomyocyte expression (Transcription factor GATA-4 [GATA4] and cardiac troponin T [cTnT]) was quantified by immunocytochemistry. Results: ANOVA with Tukey’s post-hoc found that 10 nM reversine increased greater Flk-1 expression compared to the control group (MD: 5.037 + 0.998; p < 0.001), but there were no significant changes among Oct4 (MD: 0.013 + 1.244; p = 0.99) and brachyury expression (MD: 0.157 + 0.084; p = 0.252). Kruskal-Wallis revealed that the expression of GATA4 (1.65 [0.41-1.98] to 0.015 [0.007-0.034]; p = 0.017) reduced significantly from day 7 until day 21 and cTnT (5.07 [6.62-8.91] to 8.22 [6.81-9.40]; p = 0.001) increased significantly from day 7 until day 21. Conclusions: Reversine could increase the expression of Flk-1, but it was unable to stimulate the expression of Oct4 and brachyury related to stem cell-ness. An optimal concentration of 10 nM reversine may have the greatest effect on enhancing the differentiation of DFAT cells into mature cardiomyocytes, as indicated by higher cTnT expression between cells.",
"keywords": [
"Cardiomyocyte",
"cTnT",
"DFAT cells",
"GATA4",
"Reversine"
],
"content": "Abbreviations\n\nACE: Angiotensin Converting Enzyme\n\nASCs: Adipose derived Stem Cells\n\nBMSCs: Bone Marrow Mesenchymal Stem Cells\n\nCMC: Cardiac Mesodermal Cell\n\nCPC: Cardiac Progenitors Cell\n\ncTnT: Cardiac troponin T\n\nDFAT: Dedifferentiated Fat Cell\n\nEND-2: Endoderm-like cell line\n\nESCs: Embryonic Stem Cells\n\nEPCs: Endothelial Progenitor Cells\n\nFBS: Fetal Bovine Serum\n\nFlk-1: Fetal Liver Kinase 1\n\nHAT: Histone Acetylation Transferase\n\nHeSCs: Human Embryonic Stem Cells\n\nhMSC: human Mesenchymal Stem Cell\n\nHSCs: Hematopoietic Stem Cells\n\nHSC: Hepatic Stellate Cell\n\niPSC: Induced Pluripotent Stem Cells\n\nMEK: Mitogen activated extra cellular signal regulated kinase\n\nMPC: Mesodermal Progenitor Cell\n\nMPS1: Mono-polar Spindle 1\n\nMSC: Mesenchymal Stem Cell\n\nμMM: Non-Muscle Myosin II\n\nOct4: Octamer-binding transcription factor 4\n\nPBS: Phosphate Buffer Saline\n\nPSC: Pluripotent Stem Cell\n\nSVF: Stromal Vascular Fraction\n\nTMSC: Tonsil Mediated Stem Cell\n\nUVSCs: Umbilical Vein Stem Cells\n\n\nIntroduction\n\nHeart failure is a complex health problem due to its high morbidity and mortality, so a definite and efficient approach to heart failure is a long-term hope and goal in the development of heart disease therapy. The population of those with heart failure increases as the number of older individuals grows and life expectancy generally increases due to the advances in pharmacology, interventions, and cardiac surgery. Classic interventions focus on controlling factors that might worsen cardiac function. These interventions do not solve the real problem, because widespread and progressive cardiomyocyte dysfunction has still taken place. Thus, novel approaches that modify the remodelling process, focus on the regeneration of cardiomyocytes, and improve the performance of cardiomyocytes are required.1\n\nRegenerative medicine combines an interdisciplinary research and clinical application that aims to repair, replace, and/or regenerate cells, tissues and/or organs to restore disturbed function.1,2 These approaches include, but are not limited, to the use of small and/or soluble molecule, gene therapy, stem cell-based therapy, organ tissue engineering, and reprogramming of cells.3,4 As a precursor for stem cell harvesting in cell-based therapy, adipose tissue has unique advantages in terms of abundant availability, ease of isolation, high degree of homogeneity, and decent ability to differentiate into multipotent cells.5,6 With the current development of isolation and culture techniques, ceiling culture and insert culture will produce adipose-derived stem cells (ASCs) but with a higher percentage of the expressed quantity of the mesenchymal stem cell marker known as dedifferentiated fat (DFAT) cells.7,8\n\nSimilar to ASCs, DFAT cells have been proven to be able to differentiate into various cells in the mesenchymal lineage.9,10 DFAT cells have plasticity to differentiate into several cell types derived from the three germ layers, including skeletal myoblasts,11 vascular endothelial cells,12 neurons,13 and urethral smooth muscle cells.14\n\nReversine is a purine-derived small molecule that has been shown to be able to induce the dedifferentiation of unipotent myoblast cells to progenitor cells, which are more multipotent.15,16 Reversine as an inductor of stem cell dedifferentiation has the ability to increase the potential level of a cell, so that the cell can be directed to differentiate into another cell in the same lineage or even from a different lineage with exposure to the appropriate stimulus and medium.17,18\n\nTo date there has been no research that proves the effect of reversine on the process of further dedifferentiation of adipocyte cells, which causes a reduction in the commitment lineage so that it can be relatively more easily directed towards target cells, so this study aims to analyse the effect of reversine exposure and differences in passages of DFAT cells related to their differentiation into cardiomyocytes, characterized by the expression of the marker Transcription factor GATA-4 (GATA4) and cardiac troponin T (cTnT).\n\nWe did a pilot study to understand the mechanism of dedifferentiation and differentiation of DFAT cells. We explored the role of reversine in enhancing the dedifferentiation of DFAT cells and the optimal concentration of reversine to maximise the potency of DFAT cell dedifferentiation into cardiac progenitor stem cells. We used different concentrations of reversine (10, 20 and 40 nM) in the DFAT cell cultures.\n\n\nMethods\n\nOur study obtained a letter of approval from Health Research Ethics Council of Faculty of Medicine, Universitas Airlangga (reference number: 062/EC/KEPK/FKUA/2021) issued on March 22nd 2021, under the name of Budi Baktijasa Dharmadjati as the principal investigator. All procedures were approved by the relevant ethics committees, and written informed consent was obtained from all study participants.\n\nThe study design is an observational, analytical laboratory study using different concentrations of reversine in DFAT cell cultures from human adipose tissue. This type of analytical laboratory study is a post-test only controlled group design. The independent variables consist of various concentrations of reversine (10, 20, 40 nM). The dependent variables consist of the expression of stemness biomarkers (Octamer-binding transcription factor 4 [Oct4], brachyury, Fetal liver kinase 1 [Flk-1]), early cardiomyocytes (GATA4) and mature cardiomyocytes (cTnT).\n\nOur research was conducted at Institute of Stem Cell Laboratory Airlangga University, Suraaya, East Java and Dr. Soetomo General Academic Hospital, Surabaya, East Java. The duration between study enrolment until data completion lasted for 12 months.\n\nThe number of replicates that will produce this interval half-length according to Berthouex and Brown (2002)19 is:\n\nThis formula assumes random sampling. It also assumes that n is large enough that the normal distribution can be used to define the confidence interval. Then, the number of replications for each group is four, so the total sample needed is 16 replications.\n\n\n\n1. DFAT cells from adipose tissue were collected from the lower abdominal area of patients during laparoscopic surgery with small incisions (3-5 cm) under local anaesthesia by a digestive surgeon. Cells were collected from adult patients who were in a stable condition and were not taking anti-platelets or anti-coagulants. Patients were prepared for clinical application of stem cell therapy at the Network Bank Dr. Soetomo General Hospital, Surabaya. DFAT cells were multiplied in vitro at the 3rd and 6th passage.\n\n2. Reversine (2-(4-morpholinoanilino)-6-cyclohexylaminopurine) is an Aurora kinase inhibitor that is able to dedifferentiate DFAT cells into mesodermal stem cells. The control group (P0) had four culture cells and were not treated with reversine. The treatment groups (REV10, REV20, REV40) included 12 culture cells treated with different concentrations of reversine (10, 20 and 40 nM).\n\n3. Washing buffer containing phosphate-buffered saline (Sigma-Aldrich, Milan, Italy), 0.1% sodium azide (Sigma-Aldrich, Milan, Italy), and 0.5% bovine serum albumin (BSA) Sigma-Aldrich, Milan, Italy) was used for all washing steps (3 ml washing buffer and centrifugation, 400 × g for 8 minutes at 4°C). Briefly, 5×105 cells/sample were incubated with 100 ml of 20 mM ethylene-diaminetetraacetic acid (EDTA, Sigma-Aldrich) at 37°C for 10 minutes and washed.\n\n4. Proliferation media with α-Minimum Essential Medium (MEM) (Sigma-Aldrich, Milan, Italy), which contains non-essential amino acids, sodium pyruvate, lipoic acid, vitamin B12, biotin, and ascorbic acid.\n\n5. Differentiation media with CDM3-C medium (with CHIR99021) (Sigma-Aldrich, Milan, Italy).\n\n6. Transport media with 3% gentamicin (Thermo Fisher Scientific, Inc., Waltham, MA, USA)\n\n7. Collagenase type I (Worthington Biochemical Corporation, Lakewood, NJ, USA)\n\n8. Triple express, trypan blue and PSC Cardiomyocyte Differentiation Kit (Gibco, Thermo Fisher Scientific, Inc., Waltham, MA, USA)\n\n9. Mouse IgG Monoclonal Antibody against Cardiac troponin T Recombinant (1:300 dilution; LSBio (LifeSpan) Cat# LS-C89784-200, RRID:AB_1936961) and F(ab')2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 488 (Thermo Fisher Scientific Cat# A48282, RRID:AB_2896345)\n\n10. Anti-Rabbit GATA4 Polyclonal Antibody (1:100 dilution; Thermo Fisher Scientific, Inc., Waltham, MA, USA: Catalog # BS-1778R) and F(ab')2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 488 (Thermo Fisher Scientific Cat# A48282, RRID:AB_2896345)\n\n11. 2 mL aspiration pipettes individually wrapped (Greiner, cat. no. 710183)\n\n12. 5, 10, 25 mL pipettes sterile, individually wrapped (Corning Falcon, cat. nos. 357543, 357551, 357535)\n\n13. 250-, 500-, and 1,000-mL PES 0.2 μm filters (Thermo Scientific Nalgene, cat. no. 568-0020, 569-0020, 567-0020)\n\n14. 100 μm cell strainer (Corning Falcon, cat. no. 352360)\n\n15. 0.6 mL sterile microtubes (E&K Scientific, cat. no. 280060-S)\n\n16. 2 mL sterile microtubes (E&K Scientific, cat. no. 280200-S)\n\n17. 100 mL glass beaker (Fisher Scientific)\n\nCollection and isolation of DFAT cells from adipose tissue\n\nAdipose tissue obtained from loose subcutaneous tissue through abdominoplasty procedure with a size of ~3x3 cm with an estimated weight of 10 g and stored in a 50 mL conical tube. Adipose tissue was minced into small pieces and dissociated with 0.1% (w/v) collagenase, then sent to the laboratory using a container containing an ice pack at a temperature of 4°C without the addition of other cryopreservation agents. When the tissue was received in the laboratory, the adipocyte tissue was put into a 50 mL plastic tube to be washed with D-PBS (-) twice at room temperature. The tissue was then placed into a 10 cm glass petri dish, then chopped until smooth.\n\nInsert culture strategy was performed to collect mature lipid-filled adipocytes based on the property of buoyancy. Approximately 1 g adipose tissue was chopped and mixed into 0.1% collagenase solution (collagenase type I) at 37°C for 1 hour with stirring/shaking slowly. After centrifugation at 135 × g for 3 minutes, the supernatant layer containing DFAT cells floated on the culture medium or plastic tube to allow other non-adipocytes to separate and sink to the bottom and can be discarded after centrifugation, then filtered using a nylon filter (core size 100 m). Adipose was then washed repeatedly (3 times) in MEM supplemented with 20% foetal bovine serum (FBS) before further use. A total of 30-50 L was then transferred to 6-well plates with 70 m filters and incubated for 5 days in MEM. DFAT cells from adipocytes will sink through the filter and stick to the bottom of the dish. The filter and residual adipocytes were discarded after day 5.\n\nCells were treated with different concentrations of reversine (10, 20 and 40 nM). Reversine (StemCell Technologies) at a dose of 10, 20 and 40 was administered to DFAT cell sub-groups passage 3 and 6 on the first day of DFAT cells entering the passage. Then, DFAT cells were incubated for 15 minutes at room temperature.\n\nRNA extraction and cDNA synthesis\n\nFor extraction of RNA, single cell pellets from each well in the first group were transferred to a conical tube for further centrifugation at 13000 rpm for 3 minutes (Wisespin CF10, WISD). The pellets formed were separated and 200 μL liquid was left in the tube. Pellets were rinsed with PBS, and then 5.6 microns carrier RNA and 560 micros AVL buffer (QiAmp® Viral RNA Kit) were added. Vortexing (Wisemix VM-10, WISD) was performed for 15 seconds followed by spin down (Vision VS-100 BN) before incubation at room temperature for 15 minutes. After the incubation process was completed, 600 μL of 96% ethanol was added to the sample tube. Vortexing was again performed for 15 seconds followed by spin down. The solution in the tube was then transferred to a spin column and centrifuged at 8000 rpm for 1 minute. After the supernatant layer was removed, the contents of the tube were transferred to a 2 mL collection tube. Wash buffer AW1 was added to the collection tube before centrifugation at 8000 rpm for 1 minute. After rinsing with wash buffer 2, the supernatant layer was removed and centrifuged at 12000 rpm for 1 minute in order to dry the filter, with a target concentration in the filter of 1-2 ng/μL. Then the solution was transferred to a 1.5 mL tube and 60 μL AVE buffer was added. After incubation at room temperature for 3 minutes, centrifugation was carried out at 8000 rpm for 1 minute. The solution was then stored in a collecting tube in a cooler at -20°C.\n\nFor cDNA synthesis, the RNA samples and reagents were thawed at room temperature and the PCR tubes were prepared and labelled. Vortexing was carried out to ensure that the solution mixture was homogeneous, and a spin down process was carried out to ensure that all liquids remained at the bottom. A total of 2 L reagent was added to the PCR tube, then 3 L RNA sample was added to the same PCR tube. After vortexing and spin down, the next tube was inserted into the PCR machine at 70°C for 5 minutes. cDNAs were generated from 1 mg total RNA and amplified using the ReverTra Ace qPCR-RT Kit (Toyobo, Osaka, Japan) according to the manufacturer’s instructions.\n\nReverse transcription-quantitative (RT-q)PCR\n\nQuantification of stemness expression (Oct4, brachyury, Flk-1) was performed via RT-qPCR. Primer sequences of Oct4, brachyury and Flk-1 can be seen in Table 1. Primer reagent (0.5 μL) with nuclease-free water (1.5 μL) were vortexed and span down at 70°C for 5 minutes. Another reagent consisted of 4 μL Go Script buffer, 4 μL MgCl2, 1 μL PCR Nucleotides, 1 μL Reverse transcriptase, 0.5 μL RNA sin and 4.5 μL nuclease-free water. A concentration of 7.5 pmoles/μL primer reagent was resuspended with the primer pairs in 50 μL autoclaved deionized water and 0.1X TE buffer (1 mM Tris HCl, pH 8.0 at 25°C; 0.1 mM EDTA, pH 8.0 at 25°C). After the PCR reaction process was completed, the cDNA samples were stored in a refrigerator at -20°C. Expression was quantified using the 2-ΔΔCt method and the fold-difference of expression levels of genes were calculated and compared in cycle threshold (Ct) values.20 The melting curve was generated immediately after amplification by holding the reaction mixture at 95°C for 60 seconds, and then lowering the temperature to 45°C at a transition rate of 0.1°C/second and maintained for 120 seconds. Then, the samples were heated slowly at a transition rate of 0.05 to 80°C with continuous collection of fluorescence at 640 nm.\n\nImmunocytochemistry\n\nQuantification of cardiomyocyte expression (GATA4 and cTnT) was performed by immunocytochemistry. Assessment of the expression of the differentiation marker of GATA and cTnT in DFAT culture at this stage using the FITC-labelled immunocytochemical method, was carried out on days 7, 14 and 21 after the cells were exposed to differentiation medium. DFAT cells were incubated with a target unmasking fluid (Accurate Chemical & Scientific Corp., Westbury, NY, USA) for 15 minutes using a microwave oven for antigen retrieval.\n\nThe slides were reconstituted in PBS, pH 7.4 and blocked with 10% normal goat serum (v/v). For double staining, the slides were incubated with Anti-Rabbit GATA4 Polyclonal Antibody (1:100 dilution; Thermo Fisher Scientific, Inc., Waltham, MA, USA: Catalog # BS-1778R) and Mouse IgG Monoclonal Antibody against Cardiac troponin T Recombinant (1:300 dilution; LSBio (LifeSpan) Cat# LS-C89784-200, RRID:AB_1936961) at 4°C overnight and then washed three times with PBS. Some of the sections were incubated with 1% BSA as negative controls. Next, the sections were incubated with F(ab')2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 488 (Thermo Fisher Scientific Cat# A48282, RRID:AB_2896345) respectively, for 1 h at 25°C (room temperature).\n\nThis was followed by incubation with DAPI (Vector Laboratories). The incubated monolayer cells were fixed with 4% formalin buffer for 15 minutes, then the object glass was washed with PBS and dried. Followed by blocking with 10% PBS for 15 minutes. Immunocytochemistry in the DFAT preparation was intended to observe the expression of cTnT where the cells were then incubated with fluorophore-labelled secondary antibody with F(ab')2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 488 (Thermo Fisher Scientific Cat# A48282, RRID:AB_2896345). The staining process was carried out in a dark room because it was sensitive to light, then incubated at 37°C for 1 hour and then observed using an excitation filter of 450–560 nm under a fluorescence microscope (Nikon) at a magnification of 200×.\n\nWe analysed the association between various concentrations of reversine (10, 20 and 40 nM) with the expression of stemness biomarkers (Oct4, brachyury, Flk-1), and early cardiomyocyte (GATA4) and mature cardiomyocyte (cTnT) markers. Firstly, we did a normality test using Shapiro-Wilk test. For normally distributed data, we performed a comparison test using Analysis of Variance (ANOVA) with Tukey’s post-hoc analysis. For data that was not normally distributed, we performed Kruskal Wallis followed by a Mann-Whitney U test. Path analysis was carried out using multiple linear regression to determine the pathway mechanism of the influence of the concentration of reversine on the dedifferentiation of DFAT cells and differentiation into mature cardiomyocytes. Statistical tests were performed using IBM SPSS Statistics (RRID:SCR_016479) version 25.0 software.\n\n\nResults\n\nThe surface markers used in the DFAT cell characterization process were CD90 and CD105, which are specific markers for mesenchymal stem cells, and CD45 and CD34, which are specific markers for hematopoietic cells. Examination by immunocytochemistry showed that the DFAT cell population showed positive expression (>95% luminescence of cells per field of view) of CD105 and CD90 and negative expression (<2% luminescence per field of view) of CD45 and CD34 (Figure 1).21–23\n\nREV, reversine.\n\nDFAT cells were analysed using the RT-qPCR method on days 3, 5, and 7. The mean data from the experiment is in Table 2. As seen in Table 2, the REV10, REV20, and REV40 groups had a lower mean value of Oct4 expression compared with group K. Similarly, for the mean expression of brachyury, all reversine groups had lower values than the control group. The opposite occurred for Flk-1 expression, where REV10 had a higher mean value than the control, while the other two doses had a lower mean than the control. Analysis using the ANOVA test showed that there were significant differences in the mean values of markers (Oct4, brachyury, and Flk-1) at each reversine dose (REV10, REV20, and REV40) as can be seen in Table 2.\n\nThe mean value for Oct4 expression showed a decreasing trend with the addition of reversine. There was a statistically significant difference between the concentration of reversine and the expression of Oct4 (p = 0.004), with the greatest Oct4 expression in the control group and the lowest Oct4 expression in the REV40 group, as can be seen in Figure 2.\n\nOct4, Octamer-binding transcription factor 4; REV, reversine.\n\nThe mean value for brachyury expression showed a decreasing trend with the addition of reversine. There was a statistically significant difference between the concentration of reversine and the expression of brachyury (p < 0.001), with the greatest brachyury expression in the control group and the lowest brachyury expression in the REV40 group, as can be seen in Figure 3.\n\nREV, reversine.\n\nFor Flk-1 expression, REV10 increased the mean value of Flk-1 expression from the 3rd day of observation until the 7th day of observation, whereas REV20 and REV40 did not show any statistically significant differences (Figure 4).\n\nFlk-1, Fetal liver kinase 1; REV, reversine.\n\nIf the REV20 and REV40 variables are omitted, it can be concluded that REV10 significantly increased the mean value of Flk-1 on the 5th and 7th day of observation (p < 0.001). These data were obtained through analysis using independent t-test and paired t-test, with a bar chart in Figure 5.\n\nFlk-1, Fetal liver kinase 1.\n\nThe quantity of GATA-4 and cTnT expression analysed on day 21 showed an abnormal data distribution, so we used the Kruskal-Wallis test for further data processing. The median value of GATA-4 decreased from day 7 until day 21, while the median value of cTnT increased from day 7 until day 21. Kruskal-Wallis test revealed that the expression levels of GATA-4 and cTnT were different between control group, REV10, REV20 and REV40 groups (p < 0.001) as can be seen in Table 3. Figure 6 revealed a trend of decreasing value of GATA4 in all groups between 21 days of observation (p = 0.017). Figure 7 revealed a trend of increasing value of cTnT in all group between 21 days of observation (p = 0.001).\n\nGATA4, Transcription factor GATA-4; REV, reversine.\n\ncTnT, Cardiac troponin T; REV, reversine.\n\nWhen path analysis was performed on all variables, it was found that at phase 3, the dose of reversine had a significant effect on the quantity of cTnT (p = 0.015) and GATA4 (p = 0.011) expression. Meanwhile, in passage six, the reversine dose only had a significant effect on GATA4 expression (p = 0.004). Meanwhile, the reversine dose had a significant effect on the quantity of Flk-1 expression (p < 0.001), which indicates how strong the effect of the dose is (a positive sign means it has a positive effect as can be seen in Figure 8.\n\nOct4, Octamer-binding transcription factor 4; Flk-1, Fetal liver kinase 1; GATA4, Transcription factor GATA-4; cTnT, Cardiac troponin T.\n\n\nDiscussion\n\nThe ability of DFAT cells to differentiate into multiple derived cells from the three germ layers raises questions about the stem cell-ness properties of DFAT cells. Previous studies have shown that DFAT cells have similar properties to mesenchymal stem cells.24–29 DFAT cells show the expression of several cell potential markers such as Oct4, Sox2, Nanog, Rex-130 SOX9, ACAN31 and Flk-1.32 In this study, DFAT cells were exposed to different doses of reversine with the assumption that the reversine would affect the potential level of DFAT cells. There were three markers analysed in this study, namely Oct4, which represents stemness transcription factor (SRTF) at the pluripotent level, brachyury, which represents mesodermal cell transcription factor at the multipotent level, and Flk-1, which is a marker of mesodermal endothelial cells. Meanwhile, the doses of reversine used were 10, 20 and 40 nM. The concentration selection was made based on a preliminary study that had been carried out previously using reversine at the concentration of 10, 20 and 40 nM. Analysis of these three markers showed that reversine, especially at the concentration of 10 nM, was able to increase Flk-1 expression consistently during the three days of observation. Reversine at the concentration of 10 nM was also superior to other doses in increasing the expression of Oct4 and brachyury markers even though it had a lower mean value than the control group in all observation groups.\n\nFlk-1 is one of the potential markers of mesodermal endothelial cells that are essential in the development of endothelial and other hematopoietic derivatives. The detection of this marker confirms the assumption that DFAT cells undergo dedifferentiation from mature mesenchymal cells into more “younger” cells. Expression of Flk-1 in DFAT cells indicates the potential of these cells to differentiate into cardiomyocytes. This is in line with previous studies using an embryonic stem cell differentiation model in mice, showing that progenitor cells expressing Flk-1 can differentiate into contractile cardiomyocytes, whereas cells that do not express Flk-1 are unable to differentiate into contractile cardiomyocytes.\n\nBrachyury is a transcription factor that indicates the ability of mesodermal differentiation. Brachyury expression in DFAT cells notably decreases when compared to AMSC cells.33 In this study, the administration of reversine did not increase the expression of brachyury. Perhaps this indicates the ability of reversine to induce further de-differentiation in DFAT cells not to the mesodermal level. Brachyury is also a specific and sensitive marker for the diagnosis of chordoma and has been shown to play a role in the carcinogenesis and development of several epithelial carcinomas.34 A further question that needs to be investigated is whether the low expression of brachyury is associated with a lower risk of DFAT cell carcinogenesis.35\n\nOct4 is one of the markers of cell pluripotency that plays a role in the differentiation of the three germ layers. Oct4 expression in this study is lower than in several previous studies.34 This could be due to several reasons, the first being the lack of observation days and the second being that the dose in this study was not able to induce an increase in Oct4 expression.\n\nOne of the main objectives in this study was to find out the optimal dose for differentiation of DFAT cells into cardiomyocytes. The results of this study indicate that reversine had a significant effect on the expression of cardiomyocyte cell markers. Among the three doses used, reversine at a dose of 10 nM was consistently able to increase the expression of GATA4 and cTnT markers in two different passage groups. Meanwhile, the other two doses, namely the concentration of 20 nM and 40 nM, showed inferior results when compared with the concentration of 10 nM. This supports the assumption that the dose of reversine is concentration dependent on the differentiation ability of DFAT cells.\n\nIf you look at the median values of GATA4 and cTnT in each subgroup, you will see a tendency to decrease the median value of GATA4 and increase the median value of cTnT on each day of observation. This is consistent with the theory that states that GATA4 as a marker of cardiac progenitor cells will decrease when DFAT cells differentiate into cardiomyocytes, which are characterized by the detection of cTnT, so it is assumed that GATA4 and cTnT have a negative association, i.e., the lower GATA4 expression the higher the levels of cTnT. However, a different reality was found in this study, particularly in the cTnT group. In the GATA4 group, all concentrations of reversine consistently showed a lower median value as the days of observation increased, with reversine at a concentration of 10 nM having the largest effect on decreasing GATA4 values in culture cells.36–38\n\nIn the cTnT group, inconsistency was seen in each passage group, reversine at a concentration of 10 nM increased the median value on days 7 and 14, but decreased values on day 21 in passage three, while in passage six the median value consistently increased. The same thing happened in the 40 nM reversine group. Meanwhile, at a concentration of 20 nM, the median value at passages three and six seemed to decrease with increasing days of observation.\n\nThe inconsistencies mentioned above can be caused by several technical factors that were not controlled by the researchers, including cell density, which causes false negative results, the emergence of artifacts during staining, which causes false positive results and less than perfect absorption of antibody/Alexa Fluor due to insufficient membrane recovery time achieved. Although passages three and six are still classified as early passages, there are several things that can cause differences in the quality of each of these passages. Senescence is one of the causes of decreased differentiation ability of DFAT cells. It can be concluded that the differentiation ability decreases as cells age.\n\n\nConclusions\n\nReversine could increase the expression of Flk-1, yet it was unable to stimulate the expression of Oct4 and brachyury related to stem cell-ness. An optimal concentration of 10 nM reversine may have the greatest effect on enhancing the differentiation of DFAT cells into mature cardiomyocytes, as can be seen by higher cTnT expression between cells.\n\n\nData availability\n\nFigshare: Raw Data - Effects of Different Concentration of Reversine to Enhance Conversion of Dedifferentiated Fat Cells into Cardiomyocyte. https://doi.org/10.6084/m9.figshare.20000426.21\n\nThe project contains the following underlying data:\n\n• ICC-BB.sav (immunocytochemistry data)\n\n• RTqPCR.sav\n\nFigshare: Raw Ct values and standard curves for all samples and replicates.\n\nhttps://doi.org/10.6084/m9.figshare.20109680.22\n\nFigshare: Raw, unedited, uncropped immunocytochemistry images.\n\nhttps://doi.org/10.6084/m9.figshare.20109629.23\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe thank the dedicated team of laboratory/experiments/microscope/archives from the Institute of Stem Cell Laboratory Airlangga University for their technical contribution. Special thanks to Prof. Maria Inge Lusida and Prof. Fedik Abdul Rantam for their reviews and excellent insights on an earlier version of our manuscript, although any errors are our own responsibilities and should not tarnish the reputations of these esteemed persons.\n\n\nReferences\n\nSampogna G, Guraya SY, Forgione A: Regenerative medicine: Historical roots and potential strategies in modern medicine. J. Microsc. Ultrastruct. 2015; 3: 101–107. PubMed Abstract | Publisher Full Text\n\nDuarte MS, Bueno R, Silva W, et al.: Triennial growth and development symposium: Dedifferentiated fat cells: Potential and perspectives for their use in clinical and animal science purpose. J. Anim. Sci. 2017; 95(5): 2255–2260. 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PubMed Abstract | Publisher Full Text\n\nQu G, von Schroeder HP : Preliminary Evidence for the Dedifferentiation of RAW 264.7 Cells into Mesenchymal Progenitor-Like Cells by a Purine Analog. Tissue Eng. A. 2012; 18: 1890–1901. PubMed Abstract | Publisher Full Text\n\nSantaguida S, Tighe A, D’Alise AM, et al.: Dissecting the role of MPS1 in chromosome biorientation and the spindle checkpoint through the small molecule inhibitor reversine. J. Cell Biol. 2010; 190: 73–87. PubMed Abstract | Publisher Full Text\n\nSaraiya M, Nasser R, Zeng Y, et al.: Reversine enhances generation of progenitor-like cells by dedifferentiation of annulus fibrosus cells. Tissue Eng. Part A. 2010; 16: 1443–1455. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBerthouex PM, Brown LC: Statistics for Environmental Engineers. 2nd ed.Boca Raton, FL:Lewis Publishers;2002.\n\nLivak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta C(T)) Method. Methods. 2001 Dec; 25(4): 402–408. PubMed Abstract | Publisher Full Text\n\nNugraha RA, Baktijasa B, Sargowo D: Raw Data - Effects of Different Concentration of Reversine to Enhance Conversion of Dedifferentiated Fat Cells into Cardiomyocyte. figshare. [Dataset].2022. Publisher Full Text\n\nNugraha RA, Baktijasa B, Sargowo D, et al.: Raw Ct values and standard curves for all samples and replicates. figshare. Dataset.2022. Publisher Full Text\n\nNugraha RA, Baktijasa B, Sargowo D, et al.: Raw, unedited, uncropped immunocytochemistry images. figshare. Figure.2022. Publisher Full Text\n\nShah SR, David JM, Tippens ND, et al.: Brachyury-YAP Regulatory Axis Drives Stemness and Growth in Cancer. Cell Rep. 2017; 21(2): 495–507. PubMed Abstract | Publisher Full Text\n\nShall G, Menosky M, Decker S, et al.: Effects of Passage Number and Differentiation Protocol on the Generation of Dopaminergic Neurons from Rat Bone Marrow-Derived Mesenchymal Stem Cells. Int. J. Mol. Sci. 2018; 19(3): 1–31. PubMed Abstract | Publisher Full Text\n\nSoltani L, Rahmani HR, Daliri Joupari M, et al.: Effects of Different Concentrations of Reversine on Plasticity of Mesenchymal Stem Cells. Ind. J. Clin. Biochem. December 2018; 35: 188–196. PubMed Abstract | Publisher Full Text\n\nvon Schubert C , Cubizolles F, Bracher JM, et al.: Plk1 and Mps1 Cooperatively Regulate the Spindle Assembly Checkpoint in Human Cells. Cell Rep. 2015; 12(1): 66–78. PubMed Abstract | Publisher Full Text\n\nWei S, Duarte MS, Zan L, et al.: Cellular and Molecular Implications of Mature Adipocyte Dedifferentiation. J. Genomics. 2013; 1: 5–12. PubMed Abstract | Publisher Full Text\n\nZiaeian B, Fonarow GC: Epidemiology and aetiology of heart failure. Nat. Rev. Cardiol. 2016; 13(6): 368–378. PubMed Abstract | Publisher Full Text\n\nZuk PA, Zhu M, Ashjian P, et al.: Human Adipose Tissue Is a Source of Multipotent Stem Cells. Mol. Biol. Cell. 2002; 13(12): 4279–4295. PubMed Abstract | Publisher Full Text\n\nSaler M, Caliogna L, Botta L, et al.: hASC and DFAT, multipotent stem cells for regenerative medicine: A comparison of their potential differentiation in vitro. Int. J. Mol. Sci. 2017; 18. PubMed Abstract | Publisher Full Text\n\nJumabay M, Zhang R, Yao Y, et al.: Spontaneously beating cardiomyocytes derived from white mature adipocytes. Cardiovasc. Res. 2010; 85(1): 17–27. PubMed Abstract | Publisher Full Text\n\nJumabay M, Abdmaulen R, Urs S, et al.: Endothelial differentiation in multipotent cells derived from mouse and human white mature adipocytes. J. Mol. Cell. Cardiol. 2012; 53: 790–800. PubMed Abstract | Publisher Full Text\n\nFigiel-dabrowska A, Radoszkiewicz K, Rybkowska P, et al.: Neurogenic and neuroprotective potential of stem/stromal cells derived from adipose tissue. Cells. 2021; 10(6): 1–27. PubMed Abstract | Publisher Full Text\n\nChen M, Wu Y, Zhang H, et al.: The Roles of Embryonic Transcription Factor BRACHYURY in Tumorigenesis and Progression. Front. Oncol. 2020; 10(June): 1–9. PubMed Abstract | Publisher Full Text\n\nBadimon L, Oñate B, Vilahur G: Adipose-derived mesenchymal stem cells and their reparative potential in ischemic heart disease. Rev. Esp. Cardiol. 2015; 68: 599–611. Publisher Full Text\n\nChen L, Qin F, Ge M, et al.: Application of Adipose-Derived Stem Cells in Heart Disease. J. Cardiovasc. Transl. Res. 2014; 7(7): 651–663. PubMed Abstract | Publisher Full Text\n\nJumabay M: Dedifferentiated fat cells: A cell source for regenerative medicine. World J. Stem Cells. 2015; 7: 1202–1214. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "243563",
"date": "22 Feb 2024",
"name": "Francesco Galli",
"expertise": [
"Reviewer Expertise Regenerative Medicine",
"gene/cell therapy",
"Muscular Dystrophy",
"Molecular and cell biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors address an important issue in the heart disease therapy the need of novel approach for the regeneration of damage cardiomyocytes to reduce that factor that might worsen cardiac function.\nThe approach of the author looks promising and easy to apply to cells. it addresses both the problem to have an easy and abundant cells' source (using adipose stem cells) and to have an easy protocol of de-differentiation using only one molecule (reversine) instead a cocktail of small molecules. While the study is of interest, there are few experimental concerns with this manuscript in its present form.\n1-In figure 1 Author states that only 2% of cells are CD45 and CD35 +. While the figure confirms this data for CD35, for CD45 you can see in the figure around 30-40% of positive cells. How can this result be address? Also expression of DAPI is a key information if the percentage of positive cells needs to be established.\n\n2-In figure 2 the author showed by RT-qPCR the expression of Oct4 after treatment with different concentration of REV and at different time. While for the highest concentration of REV40 is possible to observe a trend in the gene expression for the other 2 concentration REV10 and REV20 is observed a random expression during the time course. has the author an explanation for this result? If yes it could be important to be added in the manuscript.\n3-Result in figure 3 is very clear. It well known that downregulation of brachury genes results in down regulation of different mesenchymal marker (e.g. SMA,Vimentin, Desmin) did the author analysis. the expression of this gene? Showing the regulation also of these downstream genes could strength this data and the paper.\n4-How can the author correlate the increase of expression of FLK-1 after a treatment with REV10 with the result obtained for Oct4 gene in figure 1 where the expression was affected only after treatment with REV40?\n5-The level of expressions of GATA4 and cTnT protein are essential to demonstrate the fully differentiation of stem-cell in cardiomyocyte. To strengthen his result the author has to show the immunofluorescence, to observe also if the cells have also the typical cardiac phenotype (expression of sarcomere, and the shape of the cells).\nAuthor wrote a paragraph about limitations, could be useful for the reader if these limitations are indicated in the results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11269",
"date": "04 Apr 2024",
"name": "Ricardo Adrian Nugraha",
"role": "Author Response",
"response": "1-In figure 1 Author states that only 2% of cells are CD45 and CD35 +. While the figure confirms this data for CD35, for CD45 you can see in the figure around 30-40% of positive cells. How can this result be address? Also expression of DAPI is a key information if the percentage of positive cells needs to be established. Answer: According to our laboratory analysts, which is supported by Auto Image Analysis Toolbox Software, immunocytochemistry showed that the DFAT cell population showed positive expression (>95% luminescence of cells per field of view) of CD105 and CD90 and negative expression (<2% luminescence per field of view) of CD45 and CD34. 2-In figure 2 the author showed by RT-qPCR the expression of Oct4 after treatment with different concentration of REV and at different time. While for the highest concentration of REV40 is possible to observe a trend in the gene expression for the other 2 concentration REV10 and REV20 is observed a random expression during the time course. has the author an explanation for this result? If yes it could be important to be added in the manuscript. Answer: Although the expression of Oct4 is reduced with the concentration of Reversine and time extended, the cells had got sufficient differentiation potential. In the concentration REV10 and REV20, Oct4 expression was reduced at the 7th day after reversine removal, supporting a possible reversine-induced change in lineage commitment. Moreover, Oct4 signalling is shown to be essential in reversine's activity. 3-Result in figure 3 is very clear. It well known that downregulation of brachury genes results in down regulation of different mesenchymal marker (e.g. SMA,Vimentin, Desmin) did the author analysis. the expression of this gene? Showing the regulation also of these downstream genes could strength this data and the paper. Answer: Yes, in summary, these data clearly suggested that reversine possess a dual activity as it promotes the dedifferentiate into stem-cell-like progenitors, but reduce brachyury expression and results in down regulation of different mesenchymal marker. 4-How can the author correlate the increase of expression of FLK-1 after a treatment with REV10 with the result obtained for Oct4 gene in figure 1 where the expression was affected only after treatment with REV40? Answer: Increase of expression of Flk-1 in DFAT cells indicates the potential of these cells to differentiate into cardiomyocytes. Results suggested that increasing concentration and time extended leads to the increasing level of Flk-1. However, level of Oct4 doesn’t incease, suggesting that mesochymal genes were difficulty up-regualated in this experiments. 5-The level of expressions of GATA4 and cTnT protein are essential to demonstrate the fully differentiation of stem-cell in cardiomyocyte. To strengthen his result the author has to show the immunofluorescence, to observe also if the cells have also the typical cardiac phenotype (expression of sarcomere, and the shape of the cells). Answer: Thank you for your suggestion, authors have added Figure 9 (Immunofluorescence of GATA4 in the cell culture) and Figure 10 (Immunofluorescence of cTnT in the cell culture) to support the results."
}
]
}
] | 1
|
https://f1000research.com/articles/11-851
|
https://f1000research.com/articles/12-1222/v2
|
09 Oct 23
|
{
"type": "Data Note",
"title": "Identification of high-performing antibodies for tyrosine-protein kinase SYK for use in Western Blot, immunoprecipitation and immunofluorescence",
"authors": [
"Walaa Alshafie",
"Maryam Fotouhi",
"Riham Ayoubi",
"Kathleen Southern",
"Carl Laflamme",
"NeuroSGC/YCharOS collaborative group",
"Walaa Alshafie",
"Maryam Fotouhi",
"Riham Ayoubi",
"Kathleen Southern"
],
"abstract": "Tyrosine-protein kinase SYK, encoded by the SYK gene, is a non-receptor type protein kinase which mediates immune signal transduction through immunoreceptors. Tyrosine-protein kinase SYK expression has been associated with the development of various inflammatory diseases, cancer and neurodegenerative conditions. The reproducibility of tyrosine-protein kinase SYK research would help elucidate the mechanism in which it causes neuroinflammation as well as its potential as a novel target to treat Alzheimer’s disease. This would be facilitated with the availability of high-quality tyrosine-protein kinase SYK. In this study, we characterized thirteen tyrosine-protein kinase SYK commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.",
"keywords": [
"Uniprot ID P43405",
"SYK",
"tyrosine-protein kinase SYK",
"spleen tyrosine kinase",
"antibody characterization",
"antibody validation",
"Western Blot",
"immunoprecipitation"
],
"content": "Introduction\n\nTyrosine-protein kinase SYK, also known as spleen tyrosine kinase (SYK), is a non-receptor type of protein-tyrosine kinase (PTK) predominantly recognized for its role in amplifying immune responses.1 Unique to other families of PTKs, SYK has tandem N-terminal Src homology 2 (SH2) domains as well as a tyrosine kinase domain at its C-terminal region. Binding of the SH2 domains to di-phosphorylated immunoreceptor tyrosine-based activating motif (ITAM) activates SYK, triggering downstream inflammatory signalling cascades.1–3\n\nFunctioning as a vital mediator of cellular inflammatory responses, SYK is primarily known to contribute to allergies,4 autoimmune diseases5,6 and B-cell malignancies.7 Emerging research has suggested SYK may be implicated in the development in neuroinflammatory symptoms that are characteristic of Alzheimer’s disease (AD).8,9 As such, studies have demonstrated that inhibition or down-regulation of SYK increases amyloid-beta (Aβ) clearance and decreases Tau hyperphosphorylation, highlighting it’s potential as a therapeutic target to treat AD.9–11 Further investigation is required to elucidate the mechanism in which SYK influences Tau pathology and Aβ deposition.8\n\nMechanistic studies would be greatly facilitated with the availability of high-quality antibodies. Here, we compared the performance of a range of commercially available antibodies for tyrosine-protein kinase SYK and validated several antibodies for Western Blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of tyrosine-protein kinase SYK properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type and knockout cells.12–22 To identify a cell line that expresses adequate levels of tyrosine-protein kinase SYK protein expression to provide sufficient signal to noise, we examined public proteomics databases, namely PaxDB23 and DepMap.24 THP-1 was identified as a suitable cell line and thus THP-1 was modified with CRISPR/Cas9 to knockout the corresponding SYK gene (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and SYK KO cell extracts and probed them side-by-side with all antibodies in parallel13–22 (Figure 1).\n\nLysates of THP-1 (WT and SYK KO) were prepared, and 30 μg of protein were processed for Western Blot with the indicated tyrosine-protein kinase SYK antibodies. The Ponceau stained transfers of each blot are presented to show equal loading of WT and KO lysates and protein transfer efficiency from the acrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. An exception was given for antibody GTX633910*, which was titrated to 1/250 as the signal was too weak when following the supplier’s recommendations. Antibody dilutions used: MA1-19332* at 1/1000, 13198** at 1/1000, 80460* at 1/1000, 12358** at 1/1000, GTX633910* at 1/250, MAB7166* at 1/250, NBP1-03250* at 1/500, 66721-1-lg* at 1/2000, AFFN-SYK-5A10* at 1/200, ab3993* at 1/500, ab40781** at 1/1000, ab244701** at 1/1000, ab244968** at 1/1000. Predicted band size: 72 kDa. *Monoclonal antibody, **Recombinant antibody.\n\nFor immunoprecipitation experiments, we used the antibodies to immunopurify tyrosine-protein kinase SYK from THP-1 cell extracts. The performance of each antibody was first evaluated by detecting whether they could immunocapture tyrosine-protein kinase SYK. Antibodies that successfully captured the protein were further evaluated by immunoprecipitation13–22 (Figure 2).\n\nTHP-1 lysates were prepared, and immunoprecipitation was performed using 2.0 μg of the indicated tyrosine-protein kinase SYK antibodies pre-coupled to Dynabeads protein G or protein A. A) Ability of the antibodies to immunocapture tyrosine-protein kinase SYK was first assessed by comparing the level of protein available in the starting material to the level remaining in the unbound fractions. B) The immunoprecipitates for antibodies which would immunocapture tyrosine-protein kinase SYK in (A) are shown. For Western Blot, 80460* and ab244968** were used at 1/3000. The Ponceau stained transfers of each blot are shown. SM = 10% starting material; UB = 10% unbound fraction; IP = immunoprecipitated. *Monoclonal antibody, **Recombinant antibody.\n\nFor immunofluorescence, as described previously, antibodies were screened using a mosaic strategy.25 In brief, we plated WT and KO cells together in the same well and imaged both cell types in the same field of view to reduce staining, imaging and image analysis bias (Figure 3).\n\nTHP-1 WT and SYK KO cells were labelled with a green or a far-red fluorescent dye, respectively. WT and KO cells were mixed and plated to a 1:1 ratio on coverslips. Cells were stained with the indicated tyrosine-protein kinase SYK antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (WT), red (antibody staining) and far-red (KO) channels was performed. Representative images of the merged blue and red (grayscale) channels are shown. WT and KO cells are outlined with yellow and magenta dashed line, respectively. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Exceptions were given for antibodies GTX633910* and 66721-1-lg*, which were titrated to 1/2000 and 1/1000, respectively, as the signals were too weak when following the supplier’s recommendations. When the concentration was not indicated by the supplier, which was the case for antibodies ab3993*, ab244701**, and ab244968**, we tested antibodies at 1/1000. At this concentration, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: MA1-19332* at 1/1000, 13198** at 1/400, 80460* at 1/400, 12358** at 1/400, GTX633910* at 1/2000, MAB7166* at 1/500, NBP1-03250* at 1/500, 66721-1-lg* at 1/1000, AFFN-SYK-5A10* at 1/60, ab3993* at 1/1000, ab40781** at 1/700, ab244701** at 1/1000, ab244968** at 1/1000. Bars = 10 μm. *Monoclonal antibody, **Recombinant antibody.\n\nIn conclusion, we have screened tyrosine-protein kinase SYK commercial antibodies by Western Blot, immunoprecipitation and immunofluorescence and identified several high-quality antibodies under our standardized experimental conditions. Under our standardized experimental conditions, several high-quality antibodies were identified, however, the authors do not engage in result analysis or offer explicit antibody recommendations. A limitation of this study is the use of universal protocols - any conclusions remain relevant within the confines of the experimental setup and cell line used in this study. Our primary aim is to deliver top-tier data to the scientific community, grounded in Open Science principles. This empowers experts to interpret the characterization data independently, enabling them to make informed choices regarding the most suitable antibodies for their specific experimental needs. The underlying data supporting this study is found on Zenodo, an open access repository.26,27\n\n\nMethods\n\nAll tyrosine-protein kinase SYK antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly.28 Peroxidase-conjugated goat anti-rabbit and anti-mouse antibodies are from Thermo Fisher Scientific (cat. number 65-6120 and 62-6520). Alexa-555-conjugated goat anti-rabbit and anti-mouse secondary antibodies are from Thermo Fisher Scientific (cat. number A21429 and A21424). The AFFN-SYK-5A10* antibody was deposited to the Developmental Studies Hybridoma Bank (DSHB) by EU Program Affinomics (DSHB Hybridoma Product AFFN-SYK-5A10).\n\n* Monoclonal antibody.\n\n** Recombinant antibody.\n\n1 Refers to RRID that were recently created (July 2023) and will be added to the Antibody Registry in the coming weeks.\n\nCell lines used are listed in Table 1. THP-1 SYK KO clone was generated with low passage cells using an open-access protocol available on Zenodo.org: https://zenodo.org/record/3875777#.ZA-Rxi-96Rv. Two guide RNAs were used to knockout SYK in THP-1 using the CRISPR-Cas9 technology (sequence guide 1: TTTCGGCAACATCACCCGGG, sequence guide 2: GCTCCCGCTCGATGGTGTAG).\n\nBoth THP-1 WT and SYK KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.29 Cells were cultured in DMEM high-glucose (GE Healthcare cat. number SH30081.01) containing 10% fetal bovine serum (Wisent, cat. number 080450), 2 mM L-glutamate (Wisent cat. number 609065, 100 IU penicillin and 100 μg/mL streptomycin (Wisent cat. number 450201).\n\nWestern Blots were performed as described in our standard operating procedure.30 THP-1 WT and SYK KO were collected in RIPA buffer (25 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) (Thermo Fisher Scientific, cat. number 89901) supplemented with protease inhibitor. Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 × g for 15 min at 4°C and equal protein aliquots of the supernatants were analyzed by SDS-PAGE and Western Blot. BLUelf prestained protein ladder (GeneDireX, cat. number PM008-0500) was used.\n\nWestern Blots were performed with large 5–16% gradient polyacrylamide gels and transferred on nitrocellulose membranes. Proteins on the Blots were visualized with Ponceau S staining (Thermo Fisher Scientific, cat. number BP103-10) which is scanned to show together with individual Western Blots. Blots were blocked with 5% milk for 1 hr, and antibodies were incubated overnight at 4°C with 5% bovine serum albumin (BSA) (Wisent, cat. number 800-095) in TBS with 0.1% Tween 20 (TBST) (Cell Signalling Technology, cat. number 9997). Following three washes with TBST, the peroxidase conjugated secondary antibody was incubated at a dilution of ~0.2 μg/mL in TBST with 5% milk for 1 hr at room temperature followed by three washes with TBST. Membranes were incubated with Pierce ECL (Thermo Fisher Scientific, cat. number 32106) prior to detection with the HyBlot CL autoradiography films (Denville, cat. number 1159T41).\n\nImmunoprecipitation was performed as described in our standard operating procedure.31 Antibody-bead conjugates were prepared by adding 2 μg or 10 μL of antibody at an unknown concentration to 500 μL of Pierce IP Lysis Buffer (Thermo Fisher Scientific, cat. number 87788) in a 1.5 mL microcentrifuge tube, together with 30 μL of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse antibodies) (Thermo Fisher Scientific, cat. number 10002D and 10004D). Tubes were rocked for ~ 2 hrs at 4°C followed by several washes to remove unbound antibodies.\n\nTHP-1 WT were collected in Pierce IP buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol) supplemented with protease inhibitor. Lysates were rocked 30 min at 4°C and spun at 110,000 × g for 15 min at 4°C. One mL aliquots at 1.0 mg/mL of lysate were incubated with an antibody-bead conjugate for ~2 hrs at 4°C. The unbound fractions were collected, and beads were subsequently washed three times with 1.0 mL of IP lysis buffer and processed for SDS-PAGE and Western Blot on 5–16% gradient polyacrylamide gels.\n\nImmunofluorescence was performed as described in our standard operating procedure.13–22,25 THP-1 WT and SYK KO were labelled with a green and a far-red fluorescence dye, respectively (Thermo Fisher Scientific, cat. number C2925 and C34565). The nuclei were labelled with DAPI (Thermo Fisher Scientific, cat. number D3571) fluorescent stain. WT and KO cells were plated on glass coverslips as a mosaic and incubated for 24 hrs in a cell culture incubator at 37oC, 5% CO2. Cells were fixed in 4% paraformaldehyde (PFA) (Beantown chemical, cat. number 140770-10 ml) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL). Cells were permeabilized in PBS with 0,1% Triton X-100 (Thermo Fisher Scientific, cat. number BP151-500) for 10 min at room temperature and blocked with PBS with 5% BSA, 5% goat serum (Gibco, cat. number 16210-064) and 0.01% Triton X-100 for 30 min at room temperature. Cells were incubated with IF buffer (PBS, 5% BSA, 0,01% Triton X-100) containing the primary tyrosine-protein kinase SYK antibodies overnight at 4°C. Cells were then washed 3 × 10 min with IF buffer and incubated with corresponding Alexa Fluor 555-conjugated secondary antibodies in IF buffer at a dilution of 1.0 μg/mL for 1 hr at room temperature with DAPI. Cells were washed 3 × 10 min with IF buffer and once with PBS. Coverslips were mounted on a microscopic slide using fluorescence mounting media (DAKO).\n\nImaging was performed using a Zeiss LSM 700 laser scanning confocal microscope equipped with a Plan-Apo 20x air objective (NA = 0.8). All cell images represent a single focal plane. Figures were assembled with Adobe Photoshop (version 24.1.2) to adjust contrast then assembled with Adobe Illustrator (version 27.3.1).",
"appendix": "Data availability\n\nZenodo: Antibody Characterization Report for tyrosine-protein kinase SYK, https://doi.org/10.5281/zenodo.6566940. 26\n\nZenodo: Dataset for the tyrosine-protein kinase SYK antibody screening study, https://doi.org/10.5281/zenodo.8164709. 27\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAcknowledgments\n\nWe would like to thank the NeuroSGC/YCharOS collaborative group for their important contribution to the creation of an open scientific ecosystem of antibody manufacturers and knockout cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources and collaboration. Members of the group can be found below.\n\nNeuroSGC/YCharOS collaborative group: Aled M. Edwards, Peter S. McPherson and Chetan Raina.\n\nThank you to the Structural Genomics Consortium, a registered charity (no. 1097737), for your support on this project. The Structural Genomics Consortium receives funding from Bayer AG, Boehringer Ingelheim, Bristol-Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute (grant no. OGI-196), the EU and EFPIA through the Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant no. 875510), Janssen, Merck KGaA (also known as EMD in Canada and the United States), Pfizer and Takeda.\n\nAn earlier version of this of this article can be found on Zenodo (doi: 10.5281/zenodo.6566940).\n\n\nReferences\n\nSada K, Takano T, Yanagi S, et al.: Structure and function of Syk protein-tyrosine kinase. J. Biochem. 2001; 130(2): 177–186. Publisher Full Text\n\nLiu D, Mamorska-Dyga A: Syk inhibitors in clinical development for hematological malignancies. J. Hematol. Oncol. 2017; 10(1): 145. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMócsai A, Ruland J, Tybulewicz VL: The SYK tyrosine kinase: a crucial player in diverse biological functions. Nat. Rev. Immunol. 2010; 10(6): 387–402. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMeltzer EO, Berkowitz RB, Grossbard EB: An intranasal Syk-kinase inhibitor (R112) improves the symptoms of seasonal allergic rhinitis in a park environment. J. Allergy Clin. Immunol. 2005; 115(4): 791–796. PubMed Abstract | Publisher Full Text\n\nWeinblatt ME, Kavanaugh A, Burgos-Vargas R, et al.: Treatment of rheumatoid arthritis with a Syk kinase inhibitor: a twelve-week, randomized, placebo-controlled trial. Arthritis Rheum. 2008; 58(11): 3309–3318. PubMed Abstract | Publisher Full Text\n\nPodolanczuk A, Lazarus AH, Crow AR, et al.: Of mice and men: an open-label pilot study for treatment of immune thrombocytopenic purpura by an inhibitor of Syk. Blood. 2009; 113(14): 3154–3160. PubMed Abstract | Publisher Full Text\n\nFriedberg JW, Sharman J, Sweetenham J, et al.: Inhibition of Syk with fostamatinib disodium has significant clinical activity in non-Hodgkin lymphoma and chronic lymphocytic leukemia. Blood. 2010; 115(13): 2578–2585. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchweig JE, Yao H, Coppola K, et al.: Spleen tyrosine kinase (SYK) blocks autophagic Tau degradation in vitro and in vivo. J. Biol. Chem. 2019; 294(36): 13378–13395. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchweig JE, Yao H, Beaulieu-Abdelahad D, et al.: Alzheimer's disease pathological lesions activate the spleen tyrosine kinase. Acta Neuropathol. Commun. 2017; 5(1): 69. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCombs CK, Johnson DE, Cannady SB, et al.: Identification of microglial signal transduction pathways mediating a neurotoxic response to amyloidogenic fragments of beta-amyloid and prion proteins. J. Neurosci. 1999; 19(3): 928–939. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParis D, Ait-Ghezala G, Bachmeier C, et al.: The spleen tyrosine kinase (Syk) regulates Alzheimer amyloid-β production and Tau hyperphosphorylation. J. Biol. Chem. 2014; 289(49): 33927–33944. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaflamme C, McKeever PM, Kumar R, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8: 8. Publisher Full Text\n\nAlshafie W, Fotouhi M, Shlaifer I, et al.: Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence. F1000Res. 2022; 11: 977. Publisher Full Text\n\nAlshalfie W, Fotouhi M, Ayoubi R, et al.: The identification of high-performing antibodies for RNA-binding protein FUS for use in Western Blot, immunoprecipitation, and immunofluorescence. F1000Res. 2023; 12: 376. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorrall D, Ayoubi R, Fotouhi M, et al.: The identification of high-performing antibodies for TDP-43 for use in Western Blot, immunoprecipitation and immunofluorescence. F1000Res. 2023; 12: 277. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcDowell I, Ayoubi R, Fotouhi M, et al.: The identification of high-preforming antibodies for Ubiquilin-2 for use in Western Blot, immunoprecipitation, and immunofluorescence. F1000Res. 2023; 12: 355. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAyoubi R, Fotouhi M, Southern K, et al.: The identification of high-performing antibodies for Vacuolar protein sorting-associated protein 35 (hVPS35) for use in Western Blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 452. Publisher Full Text\n\nAyoubi R, Alshafie W, Southern K, et al.: The identification of high-performing antibodies for Coiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10) for use in Western Blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 403. Publisher Full Text\n\nAyoubi R, Alshafie W, You Z, et al.: The identification of high-performing antibodies for Superoxide dismutase [Cu-Zn] 1 (SOD1) for use in Western blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 391. Publisher Full Text\n\nAyoubi R, McDowell I, Fotouhi M, et al.: The identification of high-performing antibodies for Profilin-1 for use in Western blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 348. Publisher Full Text\n\nAyoubi R, Alshafie W, Shlaifer I, et al.: The identification of high-performing antibodies for Sequestosome-1 for use in Western blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 324. Publisher Full Text\n\nAlshafie W, Ayoubi R, Fotouhi M, et al.: The identification of high-performing antibodies for Moesin for use in Western Blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 172.\n\nWang M, Herrmann CJ, Simonovic M, et al.: Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics. 2015; 15(18): 3163–3168. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDepMap, Broad: DepMap 19Q3 Public ed2019.\n\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence.2021.\n\nAlshafie W, Fotouhi M, Ayoubi R, et al.: Antibody Characterization Report for tyrosine-protein kinase SYK. Zenodo. 2022. Publisher Full Text\n\nSouthern K: Dataset for the tyrosine-protein kinase SYK antibody screening study. [Data set]. Zenodo. 2023. Publisher Full Text\n\nBandrowski A, Pairish M, Eckmann P, et al.: The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res. 2023; 51(D1): D358–D367. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBairoch A: The Cellosaurus, a Cell-Line Knowledge Resource. J. Biomol. Tech. 2018; 29(2): 25–38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAyoubi R, McPherson PS, Laflamme C: Antibody Screening by Immunoblot.2021.\n\nAyoubi R, Fotouhi M, McPherson P, et al.: Antibody screening by Immunoprecitation.2021."
}
|
[
{
"id": "228375",
"date": "03 Jan 2024",
"name": "Kiyonao Sada",
"expertise": [
"Reviewer Expertise Signal transduction"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe importance of the protein-tyrosine kinase Syk has been highlighted in new research areas for studying the pathogenesis and developing treatments of neurological diseases. In this study, the authors compare the usefulness of anti-Syk antibody-based approaches using wild-type and Syk-deficient THP-1 cells, established by genome editing.\nIt is very important to know which antibodies commercially available are useful for a particular protein, not just Syk. This paper does not indicate which antibodies are recommended, but allows experts reading this paper to make their own interpretations. The experimental conditions are based on the recommended dilution factors, and in practice, further investigation by the researcher is required. However, it is not practical for many researchers to purchase and compare all antibodies, so the Syk results provide very important information.\nWestern blot results were relatively uniform, but differences in the usefulness of each antibody were observed in immunoprecipitation and immunofluorescence. In particular, the reader is provided with the information that some antibodies could detect Syk effectively despite the lack of company recommendations for immunofluorescence.\nRegarding Table 2, in discussing the experimental results, it is also necessary to present information about the antigens of these antibodies. This is because it is assumed that when immunoprecipitation is performed, the antibodies mask the antigenic sites, making it difficult to detect proteins that associate with the same sites.\nOverall, I can conclude that this is a very useful paper for researchers who are pioneering new studies on Syk.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": []
},
{
"id": "235832",
"date": "16 Feb 2024",
"name": "Araujo Nelson A",
"expertise": [
"Reviewer Expertise Structure and function of protein kinases A"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFull Report.\nThe data note entitled \"Identification of high-performing antibodies for tyrosine-protein kinase SYK for use in Western Blot, immunoprecipitation, and immunofluorescence\" compares thirteen commercial antibodies against tyrosine-protein kinase SYK using three different immunodetection techniques to provide relevant data regarding the sensitivity and specificity of these antibodies for SYK protein tyrosine kinase. My main criticism is that the results and discussion section is little developed; for example, are not briefly described the most relevant results of any of the three experiments and are not discussed the results that were different, for example, why the GTX633910 antibody detects a polypeptide band above 75 kDa while the 72 kDa band corresponding to the Tyrosine-protein kinase SYK is very poorly detected; why is not detected with the AFFN-SYK-5A10 antibody the Tyrosine-protein kinase SYK; why in immunoprecipitation the 80460 and ab244968 antibodies were used to immunodetect the unbound fraction and not other antibodies. The authors should provide answers in the text to these questions. In immunofluorescence results, place the white light micrograph of the cells next to the fluorescence image to observe the cell outline is recommended and can then be followed by the colored segmented lines in the fluorescence image. Write in the protocol how the total protein concentration in the supernatant was determined and how many the volume in microliters used to obtain 30 mg of protein from WT cells as from SYK KO cells in each lane to do better reproducible the experiment. Also the conclusion is observed underdeveloped. I recommend the authors to conclude by offering their own recommendations on bioanalytical applications of the antibodies analyzed and compare with the vendor-recommended applications read in Table 2.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "11724",
"date": "20 Jun 2024",
"name": "Kathleen Southern",
"role": "Author Response",
"response": "Thank you Araujo Nelson A. for your comprehensive reviewer report for our article. Please see below our responses to your specific comments and concerns. The data note entitled \"Identification of high-performing antibodies for tyrosine-protein kinase SYK for use in Western Blot, immunoprecipitation, and immunofluorescence\" compares thirteen commercial antibodies against tyrosine-protein kinase SYK using three different immunodetection techniques to provide relevant data regarding the sensitivity and specificity of these antibodies for SYK protein tyrosine kinase. My main criticism is that the results and discussion section is little developed; for example, are not briefly described the most relevant results of any of the three experiments and are not discussed the results that were different, for example, why the GTX633910 antibody detects a polypeptide band above 75 kDa while the 72 kDa band corresponding to the Tyrosine-protein kinase SYK is very poorly detected; why is not detected with the AFFN-SYK-5A10 antibody the Tyrosine-protein kinase SYK; why in immunoprecipitation the 80460 and ab244968 antibodies were used to immunodetect the unbound fraction and not other antibodies. The authors should provide answers in the text to these questions. While the authors understand your concern regarding the lack of result analysis, we must re-iterate, that the authors do not engage in result analysis nor offer explicit antibody recommendations. The format of this article is a Data Note, with the goal being to provide brief descriptions of research data for potential reuse or to benefit for the scientific community without providing any analyses or conclusions, as explained in their article guidelines (https://f1000research.com/for-authors/article-guidelines/data-notes). The GTX633910 antibody detecting bands above the 75 kDa molecular marker in both the wild-type (WT) and the knockout (KO) could indicate that this antibody is non-selective, binding to epitopes other than the intended target. The Western blot assessment of antibodies in the unbound fraction as well as the immunoprecipitation are carried out with antibodies previously KO-validated by Western blot (Figure 1), which is why antibodies 8060 and ab244968 were selected. We understand that this last point was not made clear in the text. In the newly submitted version of this article we have included a statement in the results and discussion section to clarify this part of the protocol. In immunofluorescence results, place the white light micrograph of the cells next to the fluorescence image to observe the cell outline is recommended and can then be followed by the colored segmented lines in the fluorescence image. With our immunofluorescence protocol described in the methods section of this article, the goal is not to define the cellular location of the target protein but rather to determine where or not ratio of signal between the WT and KO cells is significantly different. This is why we outline of the cell is not as significant compared to the signal produced by the cells themselves. Write in the protocol how the total protein concentration in the supernatant was determined and how many the volume in microliters used to obtain 30 mg of protein from WT cells as from SYK KO cells in each lane to do better reproducible the experiment. The protocol describing how the total protein concentration was determined as well as the method to obtain 30 mg of protein has been included in the Methods section describing Antibody screening by Western blot. Also the conclusion is observed underdeveloped. I recommend the authors to conclude by offering their own recommendations on bioanalytical applications of the antibodies analyzed and compare with the vendor-recommended applications read in Table 2. The authors to not offer their own recommendations nor compare the antibody performance in each application to the vendors recommended application. The reason being that the antibodies are tested under one specific set of conditions, therefore summarizing the performance of the antibodies would only be valid under these precise experimental set-up and cell lines used. The goal of the YCharOS initiative is to present antibody characterization data to the scientific community, using a standardized protocol that allows researchers to select high-performing antibodies. This enables researchers who specialize in the target of interest, in this case Tyrosine -protein kinase SYK, to conduct further studies. This intention is clearly defined in the concluding paragraph of the results and discussion section. We hope that with our clarifications, responses to your concerns, and the statements included in the latest version of the article, you no longer have reservations about the status of this article. The presented antibody characterization data will be highly beneficial for researchers aiming to enhance their studies on tyrosine-protein kinase SYK."
}
]
}
] | 2
|
https://f1000research.com/articles/12-1222
|
https://f1000research.com/articles/13-614/v1
|
11 Jun 24
|
{
"type": "Case Report",
"title": "Case Report: A Case Report on an 18-Year-Old Female with Cerebral Vasculitis in Systemic Lupus Erythematosus (SLE).",
"authors": [
"Sakshi Dudhe",
"Gaurav V Mishra",
"Pratap Singh Parihar",
"Devyansh Nimodia",
"Dhananjay Shinde",
"Anjali Kumari",
"Gaurav V Mishra",
"Pratap Singh Parihar",
"Devyansh Nimodia",
"Dhananjay Shinde",
"Anjali Kumari"
],
"abstract": "Cerebral vasculitis is a rare but severe complication of Systemic Lupus Erythematosus (SLE), presenting significant challenges in management due to its potential for devastating neurological consequences and poor prognosis. We present a case of an 18-year-old female with known SLE who presented with seizures, declining cognitive function, and unresponsiveness. Neurological examination, laboratory investigations, and radiological imaging supported the diagnosis of cerebral vasculitis secondary to SLE. Despite aggressive immunosuppressive therapy, the patient’s neurological status continued to deteriorate, leading to respiratory failure and multiorgan dysfunction. Ultimately, the patient succumbed to multiorgan failure attributed to severe CNS vasculitis and its complications. This case underscores the importance of early recognition and aggressive management of cerebral vasculitis in SLE while highlighting the need for further research into more effective therapeutic strategies to improve patient outcomes.",
"keywords": [
"treatment challenges",
"multiorgan failure",
"immunological dysfunction",
"neurological complications",
"systemic lupus erythematosus (SLE)",
"cerebral vasculitis"
],
"content": "Introduction\n\nSystemic Lupus Erythematosus (SLE) is a chronic autoimmune disease characterized by immune dysregulation, leading to inflammation and tissue damage in multiple organs and systems. Though mostly SLE primarily affects women of childbearing age, its clinical presentation can vary widely, ranging from mild symptoms to life-threatening complications.1 Neurological manifestations occur in approximately 50% of SLE patients during the course of their illness, with varying degrees of severity and clinical presentations.2 Cerebral vasculitis, although rare, is one of the most severe neurological complications of SLE, leading to significant morbidity and mortality.3 SLE impacts numerous organ systems, such as the muscles and peripheral and central neurological systems. While involvement of the central nervous system (CNS) is widespread in SLE patients, resulting in a variety of neuropsychiatric symptoms, cerebral vasculitis is uncommon; postmortem investigations have shown that its frequency is less vasculitis in SLE is characterized by inflammation of the blood vessels supplying the brain, resulting in impaired blood flow, ischemia, and tissue damage. This condition can manifest clinically as seizures, focal neurological deficits, cognitive impairment, and altered consciousness.4 Diagnosing cerebral vasculitis in SLE often requires clinical assessment, laboratory investigations, and neuroimaging studies. Laboratory findings may include positive antinuclear antibodies (ANA), elevated inflammatory markers, and evidence of multiorgan involvement.5 Neuroimaging studies such as magnetic resonance imaging (MRI) are crucial in detecting cerebral vasculitis-related abnormalities, including white matter lesions, infarcts, and haemorrhages.6 Treatment of cerebral vasculitis in SLE typically involves aggressive immunosuppressive therapy aimed at suppressing the underlying autoimmune process and reducing inflammation. Corticosteroids, cyclophosphamide, and other immunomodulatory agents are commonly used to achieve disease control and prevent further neurological deterioration.7 Despite advances in the management of SLE and its complications, cerebral vasculitis remains a challenging condition associated with high rates of morbidity and mortality. Early recognition, prompt intervention, and close monitoring are essential to optimize outcomes in affected patients.8 In this context, we present a case report of an 18-year-old female with SLE who developed cerebral vasculitis, highlighting the clinical features, diagnostic challenges, and management strategies associated with this rare but severe complication of the disease.\n\n\nCase presentation\n\nAn 18-year-old female patient, previously diagnosed with Systemic Lupus Erythematosus (SLE) one year back, presented to the emergency department with episodes of seizures characterized by clenching of the jaw and abnormal movements of the upper and lower limbs, accompanied by severe headache, declining cognitive function, and decreased responsiveness for 6 hours. For one year she was a known SLE case and in between this time period, she had symptoms like painful joints, fatigue, malar rashes, photosensitivity, oral ulcers and hair loss. There was no notable family history of autoimmune diseases or neurological disorders.\n\nDuring the general physical examination in Emergency Department, her blood pressure was measured at 140/80 mm Hg, with a pulse rate of 84 bpm and oxygen saturation of 98%. The neurological assessment revealed generalized tonic-clonic seizures, limited spontaneous movements, and non-reactive pupils. Deep tendon reflexes were found to be sluggish to absent. Systemic examination of Cardiovascular system, Respiratory system and Gastrointestinal system yielded normal findings. An erythematous malar rash, sparing the nasolabial folds, consistent with SLE, was observed.\n\nThe patient underwent comprehensive laboratory and radiological investigations, revealing significant findings, including positive Anti Smith antibody (Anti Sm) which is the most specific antibody in SLE and Antinuclear antibody (ANA) which is most sensitive antibody in SLE, with low complement levels (C3, 51 mg/dL; C4, 6 mg/dL). She was under suspicion of presenting with iron deficiency anemia (Hb 4.6 gm%), leading to the prescription of iron protein succinylate oral solution for a duration of 4.5 weeks; however, there was no improvement was noted. A blood smear analysis revealed an elevated quantity of spherocytes, suggesting the presence of an autoimmune hemolytic mechanism that necessitated the administration of corticosteroid therapy.\n\nLeukocytosis and thrombocytopenia were noted, likely caused by ongoing infection or immunosuppressive therapy drugs. Elevated serum creatinine levels (4.1 mg/dL), which was indicative of poor kidney function was also a finding. Arterial blood gas analysis indicated metabolic acidosis (serum bicarbonate 10 mEq/L, pH 7), blood lactate levels were 4.5 mmol/requiring bicarbonate correction. Cerebrospinal fluid (CSF) analysis demonstrated elevated protein levels and pleocytosis, indicative of CNS inflammation.\n\nRadiological examinations comprised abdominal and pelvic ultrasonography and MRI Brain imaging. Ultrasonography revealed increased ecotexture of kidneys with loss of cortico-medullary junction, suggestive of chronic kidney disease. MRI Brain, conducted on a 3 Tesla MRI machine, revealed T2WI/FLAIR hyperintensities in the cerebral cortex and subcortical white matter in the left frontal, bilateral parietal, and high parietal regions. Additionally, multiple diffusely scattered petechial hemorrhages were noted in the bilateral cerebral lobes, predominantly involving the splenium of the corpus callosum and bilateral internal capsule as shown in Figure 1.\n\nThe patient received treatment including antiepileptics (in. Levipil 1 gm IV BD) for seizure control, corticosteroids (in. Methylprednisolone 1 gm IV OD) for inflammation control, and cyclophosphamide (in. Cyclophosphamide) according to the Eurolupus protocol to address the ongoing autoimmune process. Given persistently falling blood pressure, intravenous Norad was administered. Despite aggressive medical intervention for SLE, the patient’s neurological status continued to deteriorate. She developed respiratory failure with pulmonary edema, necessitating ventilation support. Despite maximal supportive care, she remained comatose and unresponsive, ultimately succumbing to multiorgan failure secondary to severe CNS vasculitis and its complications, including seizures, with SLE considered as the attributing cause of death.\n\n\nDiscussion\n\nCerebral vasculitis is a rare but severe complication of Systemic Lupus Erythematosus (SLE), characterized by inflammation of the brain’s blood vessels. It presents a significant challenge in management due to its potential for devastating neurological consequences and poor prognosis.9 In this case, the patient presented with a myriad of neurological symptoms, including seizures, declining cognitive function, and unresponsiveness, indicative of CNS involvement in SLE. The presence of a malar rash, positive Antismith antibody (Anti Sm), Antinuclear antibody (ANA), and other laboratory findings consistent with SLE further supported the diagnosis. Additionally, radiological imaging revealed findings of cerebral vasculitis, including T2WI/FLAIR hyperintensities and petechial hemorrhages in the brain parenchyma.10 However, secondary infections needs to be ruled out using contrast enhanced MRI. In addition to conventional MRI, vessel wall MRI (VW-MRI) may be helpful in differentiating between vascular narrowing caused by intracranial atherosclerotic disease (ICAD) plaque, reversible cerebral vasoconstriction syndrome, dissection, and moyamoya disease, as well as vasculitis, which is characterized by contrast enhancement of the affected arterial wall. Treatment strategies for cerebral vasculitis in SLE typically involve aggressive immunosuppressive therapy to suppress the underlying autoimmune process and reduce inflammation. In this case, the patient received a combination of corticosteroids and cyclophosphamide, to control disease activity and prevent further neurological deterioration.11 However, despite these interventions, the patient’s neurological status continued to deteriorate, highlighting the challenges in managing this complication of SLE. The development of subsequent respiratory failure and multiorgan dysfunction further compounded the complexity of the case with classic SLE findings. Despite maximal supportive care of this known SLE patient, including ventilation support and hemodynamic management, the patient succumbed to multiorgan failure, CNS vasculitis and its complications.12\n\n\nConclusions\n\nIn conclusion, the presented case underscores the formidable challenge of cerebral vasculitis in the context of Systemic Lupus Erythematosus (SLE). Despite aggressive medical intervention, including immunosuppressive therapy and supportive care, the patient’s neurological status continued to deteriorate, ultimately leading to multiorgan failure and a fatal outcome. This case highlights the limitations of current treatment approaches and the urgent need for further research into more effective therapeutic strategies for managing cerebral vasculitis in SLE. Additionally, it emphasizes the importance of early recognition and prompt initiation of treatment to improve outcomes in such cases. Ultimately, the complexity and severity of cerebral vasculitis in SLE underscore the necessity for a multidisciplinary approach involving rheumatologists, neurologists, and critical care specialists to optimize patient care and mitigate the devastating consequences of this condition.\n\n\nDisclosure\n\nHuman subjects: Consent was obtained or waived by all participants in this study.\n\n\nConsent to publish\n\nWritten informed consent for publication of their clinical details and images was obtained from the patient, who volunteered to participate in this study and gave permission for this study. She was explained the possible risks and benefits of this study and provided adequate information concerning the study in her language.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nD’Cruz DP, Khamashta MA, Hughes GRV: Systemic lupus erythematosus. Lancet. 2007; 369: 587–596. Publisher Full Text\n\nBertsias GK, Ioannidis JP, Aringer M, et al.: EULAR recommendations for the management of systemic lupus erythematosus with neuropsychiatric manifestations: report of a task force of the EULAR standing committee for clinical affairs. Ann. Rheum. Dis. 2010; 69(12): 2074–2082. PubMed Abstract | Publisher Full Text\n\nHanly JG, Urowitz MB, Sanchez-Guerrero J, et al.: Neuropsychiatric events at the time of diagnosis of systemic lupus erythematosus: an international inception cohort study. Arthritis Rheum. 2007; 56(1): 265–273. PubMed Abstract | Publisher Full Text\n\nZhang X, Dong Y, Tang F, et al.: Central nervous system involvement in systemic lupus erythematosus. Zhonghua Nei Ke Za Zhi. 1999; 38(10): 681–684. PubMed Abstract\n\nGovoni M, Bortoluzzi A, Padovan M, et al.: The diagnosis and clinical management of the neuropsychiatric manifestations of lupus. J. Autoimmun. 2016; 74: 41–72. Publisher Full Text\n\nThirunavukkarasu B, Gupta K, Nada R, et al.: Neuropathological spectrum in systemic lupus erythematosus: A single institute autopsy experience. J. Neuroimmunol. 2021; 353: 577518. PubMed Abstract | Publisher Full Text\n\nEmerson JS, Gruenewald SM, Gomes L, et al.: The conundrum of neuropsychiatric systemic lupus erythematosus: Current and novel approaches to diagnosis. Front. Neurol. 2023; 14: 1111769. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPalines RV, Esfahani F, Baer AN: Reversible posterior leukoencephalopathy syndrome in systemic lupus erythematosus. J. Clin. Rheumatol. Pract. Rep. Rheum. Musculoskelet. Dis. 2000; 6(4): 204–209. Publisher Full Text\n\nJennette JC, Falk RJ, Bacon PA, et al.: 2012 revised International Chapel Hill Consensus Conference Nomenclature of Vasculitides. Arthritis Rheum. 2013; 65(1): 1–11. PubMed Abstract | Publisher Full Text\n\nBertsias GK, Tektonidou M, Amoura Z, et al.: Joint European League Against Rheumatism and European Renal Association-European Dialysis and Transplant Association (EULAR/ERA-EDTA) recommendations for the management of adult and paediatric lupus nephritis. Ann. Rheum. Dis. 2012; 71(11): 1771–1782. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFanouriakis A, Kostopoulou M, Alunno A, et al.: 2019 update of the EULAR recommendations for the management of systemic lupus erythematosus. Ann. Rheum. Dis. 2019; 78(6): 736–745. PubMed Abstract | Publisher Full Text\n\nLassere MN, Johnson KR, Boers M, et al.: Definitions and validation criteria for biomarkers and surrogate endpoints: development and testing of a quantitative hierarchical levels of evidence schema. J. Rheumatol. 2007; 34(3): 607–615. PubMed Abstract"
}
|
[
{
"id": "298294",
"date": "28 Aug 2024",
"name": "Angel Justiz-Vaillant",
"expertise": [
"Reviewer Expertise Clinical Immunology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is scientifically sound and very interesting. It will be served to other practitioners in the field of rheumatology and/or immunology to manage a case like this one. The workout of SLE was done correctly and clinically there is not doubt that we are in front of an interesting case of lupus. I invite the readers to access it by themselves.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "12316",
"date": "29 Aug 2024",
"name": "Sakshi Dudhe",
"role": "Author Response",
"response": "Thank you!"
}
]
},
{
"id": "313640",
"date": "03 Sep 2024",
"name": "Ke Xu",
"expertise": [
"Reviewer Expertise Clinical Rheumatology Immunology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is scientifically and clinically sound. Cerebrovascular inflammation is a severe neurological complication of systemic lupus erythematosus (SLE), making this patient particularly significant for clinicians, especially those specializing in rheumatology and immunology. The case involves a young female with SLE presenting with acute onset symptoms, requiring aggressive treatment that eventually led to neurological deterioration. A comprehensive physical examination of the patient remains necessary, emphasizing the importance of clinician vigilance. Furthermore, considering the patient's one-year history of SLE, it is crucial to explore her medication regimen during this period and evaluate its efficacy. Additionally, details regarding the duration and implementation of this treatment plan are still required. A full supplementary explanation is recommended. In addition, the references cited are old, and new advances in diagnosis and treatment remain to be fully elucidated.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-614
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https://f1000research.com/articles/13-116/v1
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19 Feb 24
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{
"type": "Research Article",
"title": "Wings of Change: aPKC/FoxP-dependent plasticity in steering motor neurons underlies operant self-learning in Drosophila",
"authors": [
"Andreas Ehweiner",
"Carsten Duch",
"Björn Brembs",
"Andreas Ehweiner",
"Carsten Duch"
],
"abstract": "Background Motor learning is central to human existence, such as learning to speak or walk, sports moves, or rehabilitation after injury. Evidence suggests that all forms of motor learning share an evolutionarily conserved molecular plasticity pathway. Here, we present novel insights into the neural processes underlying operant self-learning, a form of motor learning in the fruit fly Drosophila.\n\nMethods We operantly trained wild type and transgenic Drosophila fruit flies, tethered at the torque meter, in a motor learning task that required them to initiate and maintain turning maneuvers around their vertical body axis (yaw torque). We combined this behavioral experiment with transgenic peptide expression, CRISPR/Cas9-mediated, spatio-temporally controlled gene knock-out and confocal microscopy.\n\nResults We find that expression of atypical protein kinase C (aPKC) in direct wing steering motoneurons co-expressing the transcription factor FoxP is necessary for this type of motor learning and that aPKC likely acts via non-canonical pathways. We also found that it takes more than a week for CRISPR/Cas9-mediated knockout of FoxP in adult animals to impair motor learning, suggesting that adult FoxP expression is required for operant self-learning.\n\nConclusions Our experiments suggest that, for operant self-learning, a type of motor learning in Drosophila, co-expression of atypical protein kinase C (aPKC) and the transcription factor FoxP is necessary in direct wing steering motoneurons. Some of these neurons control the wing beat amplitude when generating optomotor responses, and we have discovered modulation of optomotor behavior after operant self-learning. We also discovered that aPKC likely acts via non-canonical pathways and that FoxP expression is also required in adult flies.",
"keywords": [
"insect",
"flight",
"learning",
"memory",
"operant",
"molecular",
"gene",
"CRISPR"
],
"content": "Introduction\n\nMotor learning is an essential component of human behavior and is ubiquitous throughout the animal kingdom. The process of learning a motor skill can be influenced by a number of factors, such as the amount of training, type of feedback, or the presence/absence of environmental cues. Regaining lost motor functions after brain or spinal cord injury is considered a crucial component of rehabilitation. Human language is acquired by a form of motor learning, and motor learning also appears to be a key invention that allowed the newly evolved animals in the Cambrian to become ambulatory.1–3 Vocal learning, such as learning to speak, is a form of motor learning4 that involves the Forkhead Box transcription factor family P (FoxP) in vertebrates.5–15 Other, nonvocal forms of motor learning also involve FoxP genes in vertebrates16–19 and invertebrates.20 Vocal learning also shares the involvement of protein kinase C (PKC) with other forms of motor learning,21–25 raising the possibility of a conserved motor learning pathway extending beyond these two components.\n\nWhile motor learning shares various features with other forms of learning, such as operant learning producing habits or skill-learning, it is debated how many common biological mechanisms these different concepts share.26–29 Understanding motor learning in a numerically smaller nervous system in a genetically tractable organism where one can not only study the motor learning process itself, but also its interactions with other forms of learning,30 may help inform these debates.\n\nHere we provide further evidence about the specific manner in which FoxP and PKC are involved in a form of motor learning in the fruit fly Drosophila, operant self-learning at the torque meter. In this experiment, motor learning dissociates from other forms of learning such that genes involved in motor learning are not involved in other forms of learning and vice versa.31–33 At the torque meter, a fly is tethered between head and thorax such that it can move all other appendages. When beating its wings, the fly generates forces, some of which can be measured by the torque meter. Specifically, the torque meter measures torque around the vertical body axis, yaw torque.34 Even in the absence of any guiding cues, flies can learn to associate one torque domain (e.g., roughly corresponding to left or right, respectively, turning maneuvers) with a punishing heat beam.35 This experiment not only conceptually mimics other motor learning paradigms in that feedback is made immediately contingent on specific motor actions, but also via its dependence on FoxP and PKC genes.20,21 This form of motor learning has been termed operant self-learning to distinguish it from other forms of operant learning and to denote that the subject is learning about its own behavior, as opposed to some stimulus associated with the behavior.32\n\nFor operant self-learning in Drosophila, it is not known in which neurons the FoxP gene is required and which PKC gene is involved. It is also unknown which pathway is engaged by PKC and whether FoxP expression is also required acutely in adult flies for this form of motor learning. In this work, we addressed all three research questions.\n\n\nMethods\n\nIf not stated otherwise, flies were raised on standard cornmeal/molasses medium36 at 25°C and 60% humidity under a 12-hour light/dark cycle. For experiments requiring the expression of temperature-sensitive Gal80, animals were raised at 18°C. To set up crosses for behavioral experiments, 20 females were placed together with five to eight males and were allowed to lay eggs for 24 h. They were flipped daily into fresh vials, to ensure appropriate larval density. In 30 years of research on learning and memory in tasks like ours, no difference was ever observed between male and female flies in terms of learning ability. Whenever genetically appropriate, we used female flies for practical reasons. The flies were prepared the day before the experiment, allowing them time to recover (Table 1). Female flies (24 to 48 h old) were briefly immobilized under cold anesthesia. A thin triangular copper hook (0.05 mm diameter) was glued (3m Espe Sinfony, 3M Deutschland GmbH) between head and thorax, fixing both body parts to each other.37 Each animal was kept individually in a small moist chamber with a few grains of sugar. For tub-Gal80ts expression, animals were raised at 18°C and incubated at 30°C for two days. Experiments were always conducted at room temperature. For experiments using the gene-switch system, newly hatched flies were placed on Drosophila instant medium (351.204, Schlüter Biologie, Eutin-Neudorf, Germany) containing the steroid hormone RU486 (200 μg/ml, CAS No.: 84371-65-3, Sigma-Aldrich, St. Louis, MO) for two days.\n\nThe UAS-g-KIBRA line was generated in the laboratory of Michael Krahn, Universität Münster (Table 1). They cloned the following guide RNAs from KIBRA Intron-2: GTACTTACGACTGCTTCGAC and KIBRA Intron-4: GGGCACCGTGCAGATCAGCA in pCDF6 and inserted them in attP40.\n\nTwo different torque meters and setups had to be used for technical reasons, not by choice. Both torque meters were described previously: The ‘Tang’ meter38 and the ‘Götz’ meter34(RRID:SCR_017276), named after the authors. With flies attached to the torque meter via a clamp, all devices measure the rotational force (torque) around the animal’s vertical body axis. While the Götz meter is older than the Tang meter, it is technically more advanced because of its rotational compensation, and was included in a more modern version of the setup that was used in the later experiments, after the first data were collected using the Tang setup. Even later, the wild type experiments shown in Figure 4 were conducted with a third torque meter, still in the prototype phase, which combines the laser-based measurement of the Tang meter with induction-based compensation of the Götz meter. Documentation of this setup is in preparation, but the operating principles remain the same as for the two referenced devices. In all setups, the animal is surrounded by a cylindrical panorama (arena; diameter 58 mm Tang, 90 mm other setups), homogeneously illuminated from behind by either a projector (new setups: DLPLCR4500EVM, Texas Instruments) or a halogen lamp (Tang: OSRAM 100W/12V), such that stationary flight in a controlled environment was achieved. An infrared laser (Stocker Yale Lasiris SNF series; 825 nm, 150 mW) was used as punishment in all setups. The laser was pointed from above onto the animal’s head, pulsed (approximately 200 ms pulse width ~4 Hz) and the intensity adjusted empirically for maximal heat avoidance and learning. The experiment is fully computer controlled, using custom software (Tang: LabView, National Instruments, RRID:SCR_014325. New setups: DOI: 10.5281/zenodo.7102195).\n\nBefore each self-learning experiment, the yaw torque range was adjusted using optomotor stimuli for each fly tethered to the torque meter. The optomotor response (OMR) is an innate, orienting behavior evoked by whole-field visual motion and is common to vertebrates and invertebrates. The OMR has algorithmic properties such that the direction of the whole-field coherent motion dictates the direction of the behavioral output (e.g., leftward visual stimuli lead to turning left, and rightward visual stimuli lead to turning right). For instance, when tethered Drosophila are surrounded by vertical black and white grating patterns rotating along the fly’s azimuth (i.e, around the fly’s vertical body axis), the fly will turn (i.e., produce yaw torque) in the direction of perceived motion. Typical OMRs for tethered flies responding to horizontally rotating vertical stripes are depicted in Figure 4A1.\n\nFor the ‘Tang’ setup, arena rotation for the optomotor stimulus was operated by hand. The direction of the rotation was reversed after the fly reached its asymptotic optomotor torque. During optomotor presentations before the self-learning experiment, the torque was adjusted to be zero-symmetric. This was to facilitate unbiased torque preferences before training. Torque traces during OM presentations were not stored in experiments using the ‘Tang’ setup. Optomotor stimuli (15 vertical black stripes on a white background taking about 3.5s for a full rotation, i.e., a pattern wavelength of 24° at a pattern frequency of about 4.3 Hz) were presented for a duration of 30 s in each turning direction for flies in the new setups and recorded in the raw data files together with all other data from each experiment. Because of this difference, as experiments recorded with the Tang device did not record optomotor periods, periods in ‘Tang’ experiments are numbered from 1 to 9 (Table 2), while optomotor periods for the new setups were included, such that the periods in the new setups were numbered 1-17 (Table 3). Because we used four optomotor periods each before and after training in the new setup, periods 5 to 13 were the periods in which self-learning was studied in this setup.\n\nAll periods lasted 120s.\n\nOM - optomotor. Torque learning periods (5-13) lasted 120s, while OM periods lasted 30s.\n\nThe main self-learning experiment then consisted of nine periods of two minutes duration in both setups. The laser was permanently off during the first two periods, so that the fly could freely choose its direction of turning maneuvers without any feedback. In the following two training periods either the left or the right torque domain was associated with the punishing laser, without any hysteresis. The punished torque domain was alternated between experiments. The first two training periods were followed by one test period without punishment. Afterwards, the fly was trained again with the same side punished as before for another two 2-min. periods. Finally, no heat was applied in the final two test periods, allowing the fly to express its spontaneous yaw torque preference. The figures always show the preference in the first test period after the last training period, i.e., period 8 (performance index, PI8) in the Tang setup and period 12 (PI12) in the new setups (Tables 2, 3). When the axis labels in the figures differ with regard to PI8 or PI12, these differences only indicate which setup was used. In all cases, the same first test period after the last training period was used to test for learning, irrespective of setup.\n\nData selection\n\nTo ensure proper punishment by the laser, each fly was exposed to the laser after the experiment, to ensure it was adjusted correctly. If the fly survived the laser for 15 s or longer, the data were excluded from analysis. Data that did not show any or shifted OMRs, indicating either an unhealthy fly or an error with the measuring device, were also excluded. Data were also excluded if the fly had not experienced the laser at least once during training. Finally, flies with poor flight performance (constant stopping of flight) were also excluded from analysis. While these data were excluded from analysis, all complete traces are nevertheless included in the published data sets, such that the inclusion criteria can be independently tested.\n\nData availability and analysis\n\nThe preference of a fly for right or left torque domain was quantified as the performance index PI = (ta − tb)/(ta + tb). During training periods, tb indicates the time the fly is exposed to the heat and ta the time without heat. During tests, ta and tb refer to the times when the fly chose the formerly (or subsequently) unpunished or punished situation, respectively. Thus, a PI of 1 indicates the fly spent the entire period in the situation not associated with heat, whereas a PI of −1 indicates that the fly spent the entire period in the situation associated with heat. Accordingly, a PI of zero indicates that the fly distributed the time evenly between heated and non-heated situations and a PI of 0.5 indicates that 90 of the 120 s in that period were spent in the unpunished situation.\n\nAnalogously, optomotor (Table 3, OM) behavior was quantified by computing an OM asymmetry index from the torque traces. Straight lines or double sigmoidal models were fitted to individual torque traces from OM periods, depending on the detected slope of the OMR. Each fit was generated separately for each turning direction. From the fitted lines/models, optomotor magnitude was derived as either the intercept (lines) or the asymptote (double sigmoidal model) for each turning direction. The magnitude of left-turning torque was subtracted from the magnitude of right-turning torque and divided by the sum of the two values. This optomotor asymmetry index becomes -1 for OMRs where clockwise (‘right-turning’) stimuli elicit no or left-turning torque (while counter-clockwise stimuli elicit left-turning torque). It becomes 1 for OMRs where counter-clockwise (‘left-turning’) stimuli elicit no or right-turning torque (while clockwise stimuli elicit right-turning torque). The OM asymmetry index becomes zero if the absolute magnitudes of OMRs in both directions are equal. In brief, a positive optomotor asymmetry index indicates shifts away from symmetrical torque towards right-turning torque and a negative index indicates shifts towards left-turning torque.\n\nAll behavioral data were analyzed using R (R Project for Statistical Computing) (RRID:SCR_001905). The collection of R-scripts evaluating the time series data can be found at DOI 10.5281/zenodo.10041052.39 The data model pertaining to the XML raw data files and the YAML data set files can be found at 10.5281/zenodo.7101734.39 In brief, the XML data files contain both the meta-data for each single fly experiment as well as the time-series data covering the entire experiment. The single YAML file per dataset contains the experimental design, such as which data files belong to which experimental group, the type of statistics to be performed, significance levels used, experimenter comments and data inclusion/exclusion. The main R-Script reads the YAML dataset files and performs the appropriate computations for quality control, analysis and statistics.\n\nQuality control is performed on each single-fly XML file and included in the published datasets. Each single-fly experiment XML file is thus accompanied by a single-fly HTML quality control report sheet containing plots of the raw time series data, as well as a number of evaluations necessary to assess the proper execution of the experiment and the quality of the resulting data.\n\nData analysis and statistics for each dataset are reported in an HTML dataset evaluation sheet. Thus, a complete dataset consists of one XML raw data file and one HTML quality control sheet for each fly, plus a single YAML dataset file and one HTML dataset evaluation sheet.\n\nThe datasets were published using a custom Python script (DOI: 10.5281/zenodo.7101741)39 that synchronizes the collected data on the local computer with the University of Regensburg publication server. The persistent identifiers for each dataset are listed in the figure legends.\n\nStatistics\n\nMotivated by ongoing efforts to improve statistical inference in science (e.g.,,40–54 we chose to statistically evaluate PIs in two complementary ways, using both frequentist and Bayesian statistics.55–61 Following previous studies,30,31,62–65 individual PIs of the first test after the last training period were tested against zero to evaluate the ability of the manipulated flies to show a preference towards the unpunished torque domain. The rationale behind estimating a group of flies as either showing learning or not is to trade-off statistical power with a more nuanced measure of learning performance: comparing between experimental groups may yield more nuance, but also requires impractically large sample sizes for adequate (>80%) statistical power. To further reduce the chance of statistical error, we used both Wilcoxon tests in a frequentist scenario and computed the equivalent Bayes Factors for a Bayesian version. We set the alpha value for the Wilcoxon test to 0.5% as suggested by,46 such that p-values below 0.005 and Bayes factors above 5 for the same group of flies would be considered compelling evidence that the flies were able to learn. Conversely, Bayes Factors below one together with p-values higher than 0.05 were considered evidence that the flies were not able to show self-learning. Finally, groups where the two statistics were in conflict or intermediate, were considered inconclusive. Thus, both the Bayesian and the frequentist criteria had to be met in order to claim that a genetic manipulation interfered with operant self-learning. These criteria were chosen to quantitatively distinguish between effective and ineffective manipulations without neglecting the uncertainty associated with all experimentation. At the same time, our evaluations were chosen to specifically identify large contributions to the learning processes that can be identified with sufficient statistical power (i.e., large effect sizes). All statistical results are published with the raw data and the code used to compute them is openly available.\n\nDissection\n\nThe axon terminals on flight steering muscles were tested immunocytochemically for the expression of FoxP and aPKC in flies expressing LexAop RFP under the control of FoxP-Lex and UAS td-GFP under the control of aPKC-trojan GAL4 (LexAop RFP, UAS td-GFP/aPKC-Trojan-GAL4; FoxP-LexA/+). In addition, synapses at neuromuscular junctions were labeled with the active zone marker bruchpilot (brp,66). Animals were dissected in normal saline along the dorsal midline and bent open with minute pins inserted through the dorsalmost edge of the dorsal longitudinal flight muscles (DLMs). The heart, gut, fat tissue, and other connective tissue were removed to expose the ventral nerve cord (VNC) and the musculature. Next, on both sides the DLMs and dorsoventral flight muscles (DVMs) were carefully removed layer-by-layer to expose the direct flight steering muscles, which are located close to the lateral cuticle of the thorax. Preparations were rinsed 5-10 times in saline to remove debris from the dissection procedure, and specimens were fixed for 1 h in 4 % paraformaldehyde in 0.1 M PBS buffer at room temperature (22°C). After fixation specimen paraformaldehyde was exchanged with 0.1 M PBS buffer.\n\nImmunohistochemistry of motor terminals\n\nFollowing fixation, specimens were washed 6 × 20 min in 0.1 M PBS buffer at room temperature. Next, preparations were washed 3 × 1 h in 0.1 M PBS-Tx (0.3%) buffer at room temperature and incubated with primary antibodies (mouse α-brp, 1:500 (Hybridoma bank, NC82)); chicken α-GFP (1:1000, Life Technologies A10262), and rabbit α-mCherry, (1:500, PAS-34974)) in 0.1 M PBS-Tx (0.3 %) buffer at 4° C for 24 to 36 h. Following primary antibody incubation, preparations were washed 6 × 1 h in 0.1 M PBS buffer at room temperature. Next animals were incubated in secondary antibodies: donkey α-mouse Alexa 647 (JacksonImmunoResearch 715-605-150), donkey α-chicken Alexa 488 (Dianova 703-545-155), and donkey α-rabbit Alexa 568 (Invitrogen A10042) in 0.1 M PBS-Tx (0.15%) buffer at 4°C for 24 to 36 h. Following secondary antibody incubation, preparations were washed 3 × 1 h in 0.1 M PBS buffer at room temperature, dehydrated in an ascending ethanol series (50, 70, 90, and 2 × 100 % EtOH, 15 min each), and cleared for 5 min in methyl salicylate. Finally, preparations were mounted in methyl salicylate in between two coverslips that were glued onto both sides of a round hole (10 mm diameter) drilled into custom-made metal slides of 188 μm thickness.67 Briefly, one cover slip was fixated with superglue underneath the hole, the space was filled with methyl salicylate, the preparation transferred into the mounting media, and another coverslip was carefully placed on top of the hole, so that no air remained in the methyl salicylate filled hole. The top coverslip was fixed to the metal slide using transparent nail polish (DM Markt, Mainz, Germany). After 20 min to let the nail polish dry the preparation was transferred to the microscope. In total 11 animals were subjected to immunocytochemistry on direct flight muscles. In nine of these 11 preparations, we were able to identify only subsets of the direct wing steering muscles under investigation. These subsets yielded identical results with respect to aPKC and FoxP expression as the two preparations with complete sets of direct muscles as shown in Figure 3.\n\nConfocal laser scanning microscopy\n\nPreparations were scanned using a Leica (Leica Microsystems, Germany) SP8 confocal laser scanning microscope (CLSM) under either a 20x oil (NA = 0.75) or a 40x oil (NA = 1.3) lens at an image format of 1024 × 1024 pixels. Z-step size was 2 μm for the 20x lens (resulting in voxel dimensions of 0.57 × 0.57 × 2 μm) and 1 μm for the 40x lens (resulting in voxel dimensions of 0.28 × 0.28 × 1 μm). Alexa 488 was excited with an argon laser at 488 nm and detected with a photomultiplier between 495 and 530 nm wavelength. Alexa 488 was excited with a solid state laser at 561 nm and detected with a photomultiplier between 570 and 610 nm wavelength. Alexa 647 was excited with a red helium neon laser at 633 nm and detected with a photomultiplier between 640 and 670 nm wavelength. All image stacks were stored as.lei files and further analyzed using Las X software (Leica Microsystems, Germany). Selected fields of view were used for maximum intensity projection views, which were exported as 24 bit three color tiff images and further processed with Corel Draw 11.\n\nData availability\n\nConfocal image stacks can be found at: 10.5281/zenodo.10606166.68\n\n\nResults\n\nColomb and Brembs (2016) discovered that blocking all protein kinase C (PKC) isoforms in neurons using the inhibitory peptide PKCi abolished operant self-learning. We replicated their results by pan-neuronal expression of PKCi. In one group, PKCi was expressed both during development and in the adult flies. In the other group, PKCi expression was restricted to adulthood only, by using the temperature-sensitive Gal4 inhibitor tub-Gal80ts (see Methods for details). Temporally unrestricted pan-neural expression did not impair self-learning, whereas expression restricted to neurons in adult flies abolished self-learning (Figure 1A). This result may seem surprising, but compensation for experimental manipulations of PKC activity through development has been reported numerous times in the literature69–73 and our data reproduced our previously published, identical experiments with PKCi,21 demonstrating the PKCi construct is still performing as expected. Expressing PKCi only in cells expressing isoform B of the FoxP gene also abolished self-learning, even without temporal control, suggesting that PKC activity is required in FoxP-positive neurons.\n\nPerformance indices for the first period after training (PI8/PI12) are plotted. Each colored dot represents a single fly experiment. Red dots denote experiments where the fly was punished on its left turning torque domain, blue dots denote flies that were punished on their right turning domain. Box plots denote medians, quartiles and non-outlier range. Statistical analyses test for differences of PIs against zero. A. Inhibiting all protein kinase C isoforms with the inhibitory peptide PKCi. Constitutive, pan-neuronal expression PKCi (left, yellow), leads to high PIs and a large Bayes Factor, indicating this manipulation left self-learning intact. Expressing PKCi either in FoxP-isoform B positive neurons without temporal control (middle, green), or in all neurons but restricted to adulthood using tub-Gal80ts (right, blue, see Methods for details) yields low PIs, high p-values and low Bayes factors, indicating self-learning was impaired. Data: 10.5283/epub.52958.74 B. Pan-neuronal knock-out of two different PKC genes with CRISPR/Cas9 in adulthood (using the GeneSwitch system and feeding RU486 to adult flies, see Methods for details) suggests aPKC is necessary for operant self-learning. Knocking out atypical PKC (yellow, left) yields moderate PIs, p-values and Bayes factors, indicating some effect on operant self-learning, while the high PIs, low p-values and high Bayes factor of the group where PKC53E was knocked out (right, green) indicate their self-learning was intact. Data: 10.5283/epub.52957.75 C. Knocking out aPKC in motor neurons or FoxP-neurons impairs operant self-learning. Expressing the CRISPR/Cas9 components either in FoxP isoform B-positive neurons (green, middle) or in motor neurons (blue, right) leads to low PIs, high p-values and low Bayes Factors, indicating their self-learning is strongly impaired. Control flies with only the CRISPR/Cas9 genetic elements but no driver, showed high PIs, a low p-value and a high Bayes Factor, indicating their self-learning was intact. Data: 10.5283/epub.52944.76 D. Bayesian statistics for the three datasets.\n\nColomb and Brembs (2016) also discovered that restricting PKCi expression to motoneurons (MNs) was sufficient to impair self-learning. The FoxP-iB driver line replicated these results as well, as FoxP isoform B is prominently expressed in motor neurons.77 To help determine which PKC may be involved in this mechanism, we screened RNA-Seq databases for PKC genes expressed in MNs. Restricting candidates to those where gRNA lines were available for CRISPR/Cas9-mediated gene knockout yielded only two genes: the atypical PKC (aPKC) and the diacylglycerol-activated PKC53E. Knocking out each gene pan-neuronally in adult flies and testing the manipulated animals for operant self-learning showed excellent learning performance in PKC53E-manipulated flies (Figure 1B), clearly ruling out PKC53E as the gene involved in operant self-learning. The performance of the aPKC-manipulated flies was inconclusive: their preference scores were somewhat lower, not reaching our criteria for significant learning, but at the same time too high to be confident in the result (Figure 1B).\n\nAs PKC activity is required in MNs,21 we limited the aPKC knockout to these neurons which abolished self-learning (Figure 1C). To test the hypothesis articulated above that aPKC activity is required in FoxP neurons, we also knocked out aPKC in FoxP neurons, which also abolished self-learning. (Figure 1C). Using two different driver lines also controls for driver-specific effects and potential expression outside of motor neurons. Both driver lines support operant self-learning in principle (article in preparation, data at DOI: 10.5283/epub.52962), with C380-Gal4 also already in the peer-reviewed literature.21 To our knowledge, C380 and FoxP-iB expression overlaps only in MNs.\n\nThus, the behavioral data presented above support the hypothesis that the plasticity mediating operant self-learning takes place in neurons that co-express both FoxP and aPKC. Whole-mount confocal microscopy of fly central nervous systems with aPKC-Gal4 and Foxp-LexA expression suggested that neurons expressing both aPKC and FoxP exist only in the ventral nerve cord (VNC, Figure 2A, B). We identified co-expressing neurons in all neuromers of the VNC, with the ventral location of the mesothoracic aPKC/FoxP neurons suggesting potential wing MNs (Figure 2C).78 To ascertain the identity of this ventral cluster of co-expressing neurons, we marked MNs with the driver line D42-Gal4 and used FoxP-LexA to stain all FoxP neurons. With these labels, we identified a ventral sub-population of putative wing MNs expressing FoxP, which matched the location of the aPKC/FoxP neurons identified before (Figure 2D). The overlap (or lack thereof) may not be clearly visible in these 2D renderings presented in this text, which is why we made the 3D image stacks available for closer scrutiny (DOI: 10.5281/zenodo.10047941).79 Both the C380 driver used in Figure 1 and the D42 driver used here, label not only MNs but also other neurons, in particular cholinergic neurons. However, the lines overlap in MNs in the VNC. FoxP is also expressed in these MNs and knocking out aPKC in these neurons also impaired operant self-learning. While each line of evidence is suggestive, at best, together, these lines of evidence converge on the hypothesis that wing steering MNs expressing both aPKC and FoxP may be important for operant self-learning. These suggestive results, together with the recently published draft VNC connectome,80 motivated us to analyze the direct wing steering muscles for innervation by MNs with both aPKC and FoxP expression, instead of further quantifying the VNC dataset.\n\nConfocal stacks of whole mount preparations of central nervous systems; A-C: green - aPKC-Gal4>CD8::GFP, red - FoxP-LexA>CD8::RFP; D: green - D42-Gal4>CD8::GFP, red - FoxP-LexA>CD8::RFP. Confocal image stacks available at: 10.5281/zenodo.10047941. A. Adult brain (top) with ventral nerve cord (VNC, bottom) attached. No co-expressing cells can be observed in the brain, whereas such neurons (yellow) are readily observable in all neuromers of the VNC (arrowheads). B. VNC with aPKC/Foxp co-expression (yellow) both in cell bodies and fiber tracts in nerves (arrowheads). C. C1: Dorsal view of motor neuron reconstruction (modified from Ref. 78) C2: Confocal image stack of dorsal view of the mesothoracic neuromer with putative wing MNs expressing both aPKC (green) and FoxP (red) marked. D. D1: Lateral view of motor neuron reconstruction (modified from Ref. 78). D2: Confocal image stack of mesothoracic neuromer with all MNs (green) and FoxP neurons (red) marked. This lateral view supports the hypothesis that the ventral cluster of aPKC/FoxP neurons comprises wing MNs.\n\nEach direct steering muscle is innervated by one single identified MN.81 Thus, identifying the muscles reveals the identity of the corresponding MNs. To test for the expression of aPKC and FoxP in MNs that innervate direct wing muscles, we expressed UAS-GFP under the control of aPKC-Gal4 (Figure 3, second column) and RFP under the control of FoxP-lexA (Figure 3, third column). The signal of each fluorescent reporter was further enhanced by immunocytochemistry, and the active zone marker bruchpilot (brp66; was used to label the neuromuscular synapses in flight MN axon terminals (Figure 3, fourth column). In total, Drosophila is equipped with 12 flight steering muscles each of which likely contributes to a distinct function in flight control.82 The activation patterns of four of these muscles have been analyzed in response to optomotor stimulation during flight (first and second basalar muscles b1 and b2, as well as first pterale I muscle (i1) and third pterale II muscle (iii1).82–84 A schematic of these four direct flight muscles plus five adjacent ones that were analyzed in this study illustrates their spatial arrangement, shapes, and depicts which ones are innervated by steering MNs that express both aPKC (green) and FoxP (magenta), only one of both, or neither of them (grey; Figure 3A1).\n\nRepresentative projection view of MN terminals on the direct flight steering muscles in animals with GFP label in aPKC expressing cells (aPKC-Gal4>CD8::GFP, green), RFP expression in FoxP expressing cells (FoxP-LexA>CD8::RFP, magenta), and immunolabeling for the presynaptic active zone marker bruchpilot (brp, cyan) reveal which direct flight steering MNs express either aPKC, FoxP, or both, or none of them but only brp in presynaptic active zones. (A1) depicts the orientation, shape, and abbreviated names of direct flight steering muscles and summarizes which ones are innervated by aPKC expressing MNs (green), by FoxP-expressing MNs (magenta), or by MNs without FoxP and aPKC expression (grey). (A2) Projection view of direct flight muscles and their innervation with GFP expression under the control of aPKC-GAL4 (green) at 20x magnification. (A3) Same preparation, image stack, and field of view but with RFP expression under the control of FoxP-lexA (magenta). (A4) Same preparation, image stack, and field of view with brp immunolabel (cyan) in presynaptic active zones of flight steering MNs. (B1-B4). Same preparation but with selective enlargement of the three basalare muscles (b1-b3), with all three labels in (B1), GFP label in aPKC-expressing cells (green, B2), RFP label in FoxP expressing cells (magenta, B3), and Brp label in presynaptic active zones (cyan, B4). Muscles b1 and b3 are innervated by steering MNs with aPKC and FoxP expression, but b2 is devoid of FoxP-expressing innervation. (C1-C4) Same preparation but with selective enlargement of second basalare (b2) and the adjacent pterale 1 (i1) and pterale II (iii3) muscles with all three labels (C1), GFP label in aPKC-expressing cells (green, C2), RFP label in FoxP-expressing cells (magenta, C3), and brp label in presynaptic active zones (cyan, C4). Only i1 is faintly labeled for terminals with aPKC FoxP expression. (D1-D4) Same preparation but with selective enlargement of the pterale II muscles iii3 and iii4, the adjacent pleurosternal muscle (ps1), and the posterior notal wing process muscles (hg) with all three labels (D1), GFP label in aPKC-expressing cells (green, D2), RFP label in FoxP-expressing cells (magenta, D3), and Brp label in presynaptic active zones (cyan, C4). The pterale II muscles iii3 and iii4 are innervated by terminals with aPKC and FoxP expression. Image stacks available at: 10.5281/zenodo.10606166.\n\nRepresentative maximum intensities projection views at 20x magnification allow us to visualize all nine flight steering muscles investigated in one field of view (Figures 3A2-A4). Except the pleurosternal muscle 1 (ps1) and the posterior notal wing process muscles (hg), all other steering muscles are innervated by aPKC-positive MNs (Figures 3A1, A2, green). In contrast, six of the nine steering muscles are innervated by FoxP-positive MNs, including the basalars b1 and b3, the pterale i1, iii3, and iii4, as well as the pleurosternal muscle ps1 (Figures 3A1, A3, magenta). A subset of five flight steering muscles is innervated by MNs that express both genes required for operant self-learning. These are b1, b3, i1, iii3, and iii4 (Figure 3A).\n\nSelective enlargements at 40x magnification were used to better visualize the axon terminals on those steering muscles of particular interest, with Figure 3 panels B1-B4 focussing on the three muscles that insert at the basalar sclerite and are thus named basalar 1-3 (b1-b3). Prominent labels of both aPKC (green) and FoxP (magenta) are present in the MNs to steering muscles b1 and b3, but the motor axon innervating b2 is devoid of FoxP signals (Figure 3, B1-B4).\n\nMuscle b1 has been reported to fire once every wingbeat83 during straight flight, during the transition from up- to downstroke. Optomotor stimulation causes phase shifts of b1 firing in the wing beat cycle, which in turn cause changes in wing beat amplitude both in the fruit fly Drosophila83 as well as in the blowfly, Calliphora.85 The activity of b3 during flight has not been recorded electrophysiologically, but the muscle exhibits very similar morphological properties compared to b1. Both b1 and b3 are orientated similarly relative to the body axis and the wing hinge, and both are innervated by MNs with particularly large diameter axons (Figures 3B1-B3) and particularly large active zones (Figure 3B4), suggesting similar functional roles. Steering muscle b2 is also innervated by large diameter axons (Figure 3C1) with large presynaptic active zones (Figure 3C4). Although some aPKC reporter label is detected in the MN to b2 (Figures 3C1, C2, C4), labeling intensity is considerably fainter than that in b1 and b3 MNs (Figures 3B1-B3). Fainter reporter labeling indicates weaker aPKC-Gal4 expression. The b2 MN is devoid of the FoxP reporter label (Figure 3C3). Although b2 has been reported to respond to optomotor stimulation, its phasic bursting responses correlate with rapid changes in wing beat amplitude as observed during body saccades.83\n\nFigure 3 panels C1-C4 move the field of view posteriorly and show the pterale 1 muscle i1 and the pterale 2 muscle iii1. Muscle i1 is innervated by a MN with faint aPKC (Figure 3C2) and faint FoxP (Figure 3C3) label. i1 has been reported to respond to optomotor stimulation, but its specific role in optomotor control remains largely unknown.83 Steering muscle iii1 shows some faint aPKC signal (Figure 3C2) but is devoid of any FoxP label (Figure 3C3) and does not participate in optomotor flight control.83\n\nThe roles in flight control of the remaining four steering muscles (ps1, iii3, iii4, and hg; Figures 3D1-D4) in Drosophila are not fully understood. However, iii3 and iii4 are innervated by MNs with aPKC (Figure 3D2) and FoxP (Figure 3D3) expression. Axon terminals on ps1 are FoxP positive (Figure 3D3) but lack any aPKC label (Figure 3D2). Active zones on steering muscle hg are visible through the brp label (Figure 3D4) but the motor axon on hg is devoid of both aPKC (Figure 3D2) and FoxP (Figure 3D3).\n\nBecause it is not known at which torque meter reading the fly actually generates zero angular momentum, before each torque learning experiment, it is crucial to set the average of the asymptotic left and right optomotor response (OMR) magnitudes to zero (Figure 4A1, see Methods for details). This is to avoid an initial bias in the torque preference before training and with the assumption that the mid-point between the maximal OMRs roughly corresponds to flying straight (i.e, zero angular momentum). During the ensuing conditioning procedure, flies show spontaneous torque fluctuations that can reach or even exceed those elicited by optomotor stimulation in magnitude. Within each torque domain (i.e., ‘left’ or ‘right’, respectively), the temporal patterns (i.e., slow or fast) of torque fluctuations and their relative direction (i.e., more or less torque) are irrelevant for the heat stimulus as long as the zero point is not crossed: heat remains either on or off until the fly switches torque domains. Until this research, there was no reason to assume any relation between elicited OMRs and spontaneous torque fluctuations, neither conceptually nor anatomically. Now, however, the described role of the steering MNs co-expressing aPKC and FoxP (Figure 3) in large torque fluctuations elicited by optomotor stimuli prompted the hypothesis that there may be a neuroanatomical connection between spontaneous torque fluctuations and elicited OMRs after all: the motor neurons that innervate the steering muscles may be involved in both elicited and spontaneous torque fluctuations. If these neurons were indeed common to elicited OMRs and spontaneous torque fluctuations, we should observe a change in the OMRs after operant yaw torque learning.\n\nA. Measurements before training. A1 Averaged optomotor traces of flies punished either on the ‘left’ (yellow) or on the ‘right’ (green) torque domain. Both groups show similar response magnitudes in either direction of the optomotor stimulus. Errors are standard deviations. A2 Optomotor asymmetry indices for flies punished either on the ‘left’ (yellow) or on the ‘right’ (green) torque domain. The values for both groups spread around zero. Positive values indicate a shift towards positive (right-turning) torque. Both frequentist and Bayesian analyses are displayed to the right of the plots and indicate no difference between the groups. A3 Regression analysis between torque preference and optomotor asymmetry. Optomotor values were adjusted such that positive values indicate a shift towards the unpunished torque domain. No significant correlation was observed. Left-pointing arrowheads (yellow) denote flies punished on left-turning torque and right-pointing arrowheads (green) denote flies punished on right-turning torque. A4 Comparison of optomotor asymmetry (left, yellow) and torque preference (right, green) indices. Here again, optomotor values were adjusted such that positive values indicate a shift towards the unpunished torque domain. Both measures vary around the zero point and Wilcoxon tests against zero are not significant (p-values above each plot). Left- and right-pointing arrowheads denote punishment directions as before. B. Measurements after training. B1 Averaged optomotor traces of flies punished either on the ‘left’ (yellow) or on the ‘right’ (green) torque domain. A reduction in the OMR magnitude can be observed on the punished, but not on the unpunished side. Errors are standard deviations. B2 Optomotor asymmetry indices for flies punished either on the ‘left’ (yellow) or on the ‘right’ (green) torque domain. Positive values indicate a shift towards positive (right-turning) torque. The values for each group have now shifted towards the unpunished side compared to the values before training. Both frequentist and Bayesian analyses are displayed to the right of the plots and indicate a significant difference between groups. B3 Regression analysis between torque preference and optomotor asymmetry. Optomotor values were adjusted such that positive values indicate a shift towards the unpunished torque domain. A significantly positive correlation was observed, such that higher torque preferences entailed larger optomotor asymmetry. Left-pointing arrowheads (yellow) denote flies punished on left-turning torque and right-pointing arrowheads (green) denote flies punished on right-turning torque. B4 Comparison of optomotor asymmetry (left, yellow) and torque preference (right, green) indices. Here again, optomotor values were adjusted such that positive values indicate a shift towards the unpunished torque domain. Both measures are shifted towards more positive values and Wilcoxon tests against zero are now significant for both variables (p-values above each plot). Left- and right-pointing arrowheads denote punishment directions as before. Data available at: 10.5283/epub.54804.86\n\nTo test this hypothesis, we analyzed the OMRs after training of a cohort of wild type Berlin flies (Figure 4B; control flies from a separate research project). We found that the asymptotic magnitude of the OMR on the punished side was reduced after operant training, while the OMR on the unpunished side remained unaltered compared to before training (Figure 4B1). Quantifying this observation revealed a significant difference in optomotor asymmetry after training (Figure 4B2) but not before training (Figure 4A2) between the two experimental groups.\n\nAn important question regarding the functional significance of this change in optomotor asymmetry is whether the amount of torque preference after training reflects the amount of optomotor asymmetry. There was no significant correlation between torque preference and optomotor asymmetry before training (Figure 4A3; as expected as the OMR was adjusted to be as symmetrical as practically possible). Once the flies have completed the training phase, torque preference becomes a significant predictor of optomotor asymmetry (Figure 4B3). These results corroborate our hypothesis that the wing MNs identified above, specifically those that have been shown to be involved in generating OMRs,82,83 constitute a site of the plasticity mediating operant self-learning in Drosophila. We also tested whether it would be sufficient to test for optomotor asymmetry after training as a proxy measure for torque preference. Before training, as expected, both measures showed similar values ranging around the zero point (Figure 4A4). After training, both measures did deviate from zero towards the unpunished direction, however, the effect was noticeably larger for torque preference than for optomotor asymmetry (Figure 4B4). Together with the correlation explaining about a third of the variance (Figure 4B3), these data may indicate that the MNs are an important, but not the only site of plasticity in this form of learning.\n\nOptomotor analysis (Figure 4) suggests there may be additional sites of plasticity besides wing steering MNs. FoxP-positive neurons in the brain are straightforward potential candidates for such additional sites. Therefore, we performed spatial CRISPR/Cas9-based genome editing without restricting the manipulation to the adult stage. At the time of these experiments, no driver lines with FoxP-overlapping expression in the Saddle and Vest regions were available. Therefore, we tested driver lines expressing in the protocerebral bridge (PCB, Figure 5A), the PCB and adjacent central complex neuropils (see Materials and Methods for details, Figure 5B) and the dorsal cluster neurons (Figure 5C). Overlap of Gal4 expression patterns with FoxP expression was verified using the FoxP-LexA line77,87 and FoxP-knockout efficiency was quantified previously.77 No self-learning impairment was observed following FoxP knockout in these brain areas, suggesting that FoxP expression is not necessary in these areas for operant self-learning.\n\nPerformance indices for the first period after training (PI8/12) are plotted. Each colored dot represents a single fly experiment. Red dots denote experiments where the fly was punished on its left turning torque domain, blue dots denote flies that were punished on their right turning domain. Box plots denote medians, quartiles and non-outlier range. Statistical analyses test for differences of PIs against zero (above plots and D). A. Flies with FoxP knocked out in the protocerebral bridge (left, yellow) as well as the gRNA (middle, green) and Cas9 (right, blue) control flies showed high PIs, large Bayes factors (D) and small p-values, indicating their self-learning was intact. Data: 10.5283/epub.52956.88 B. Flies with FoxP knocked out in the protocerebral bridge and additional components of the central complex (left. yellow) as well as the gRNA (middle, green) and Cas9 (right, blue) control flies showed high PIs, large Bayes factors (D) and small p-values, indicating their self-learning was intact. Data: 10.5283/epub.52951.89 C. Flies with FoxP knocked out in the dorsal cluster neurons (left, yellow) as well as the gRNA (middle, green) and Cas9 (right, blue) control flies showed high PIs, large Bayes factors (D) and small p-values, indicating their self-learning was intact. Data: 10.5283/epub.52946.89,90 D. Bayesian statistics for the three datasets.\n\nWe discovered that aPKC is required in MNs for operant self-learning (see above). As FoxP is also expressed in MNs, we knocked FoxP out in MNs using two different driver lines, C380 and D42. However, CRISPR/Cas9-mediated FoxP knockout in MNs disrupted flight-performance of manipulated flies to an extent that precluded any torque learning experiments. Our results above (Figure 3) will now allow us to select more specific driver lines, expressing only in the identified wing steering MNs,91 which may yield FoxP knock-out flies (or any other manipulation) with sufficient flight performance.\n\nFoxP was shown to be important for normal development.77,92 Strong motor impairments have been reported after a developmental FoxP knockout, for instance rendering the animals unable to fly (see above). Since the ability to fly is a basic requirement for torque learning, we used a CRISPR/Cas9-based approach to pan-neuronally knock out FoxP in adult flies. No effect was observed on self-learning two days after the start of the knock-out induction (Figure 6A), but waiting for 14 days after the pan-neural knock-out yielded a significant self-learning impairment (Figure 6B). As a test seven days after induction was also without effect (DOI: 10.5283/epub.52965), self-learning remains functional for at least 7-14 days after cessation of FoxP gene transcription in all neurons.\n\nPlotted are performance indices for the first period after training (PI12). Each colored dot represents a single fly experiment. Red dots denote experiments where the fly was punished on its left turning torque domain, blue dots denote flies that were punished on their right turning domain. Box plots denote medians, quartiles and non-outlier range. Statistical analyses test for differences of PIs against zero. A. Self-learning two days after FoxP knockout induction with RU486. Experimental animals (left, yellow) as well as gRNA (middle, green) and Cas9 (left, blue) control animals showed all high PIs as well as large Bayes Factors above 1000 and p-values below 0.005, indicating that all groups showed unimpaired self-learning. Data: 10.5283/epub.52963.93 B. Self-learning 14 days after FoxP knockout induction with RU486 and 12 days after cessation of RU486 administration. Experimental animals (left, yellow) showed low PIs as well as a Bayes Factor of less than one together with a large p-value, whereas both the genetic control animals without RU486 treatment (middle, green) and the pooled RU486-treated gRNA and Cas9 controls (right, blue) showed high PIs, large Bayes Factors and p-values smaller than 0.005, indicating an impairment in self-learning only in the experimental group. Data: 10.5283/epub.52964.94\n\nHaving established that aPKC is required in FoxP-positive MNs, we sought to identify further components of the aPKC-dependent plasticity underlying operant self-learning in Drosophila. It is not uncommon for plasticity mechanisms in the adult animal to recruit genes with a function during neuronal development.95–97 With PKCs being notorious for being able to compensate for genetic manipulations,69–73 one reliable countermeasure has proven to shorten the time period between manipulation and testing sufficiently to ensure compensation has no time to take place.21,31 Following this tried-and-tested approach, our manipulations of prominent PKC interaction partners were thus restricted to adult neurons. One such prominent interaction partner of aPKC during Drosophila nervous system development is bazooka (baz), a crucial component of the highly conserved PAR complex.98,99 However, knocking out baz in all adult neurons did not disrupt operant self-learning (Figure 7A), suggesting that the Par complex signaling pathway is not involved in operant self-learning. A second prominent aPKC interaction partner is the kidney and brain protein (KIBRA), which acts in the conserved Hippo pathway100,101 and also proposed to be involved in learning/memory.102–106 Knocking out KIBRA in all adult neurons also did not disrupt operant self-learning (Figure 7B).\n\nPlotted are performance indices for the first period after training (PI12). Each colored dot represents a single fly experiment. Red dots denote experiments where the fly was punished on its left turning torque domain, blue dots denote flies that were punished on their right turning domain. Box plots denote medians, quartiles and non-outlier range. Statistical analyses test for differences of PIs against zero. A. Knocking out bazooka using CRISPR/Cas9-mediated genome editing in adult animals had no effect on operant self-learning. Both flies that were fed the steroid hormone RU486 (left, yellow) and the genetically identical flies without the hormone (right, green), showed high PIs, low p-values and high Bayes Factors, indicating a preference for the unpunished torque domain. Data: 10.5283/epub.52947.107 B. Knocking out KIBRA using CRISPR/Cas9-mediated genome editing in adult animals had no effect on operant self-learning. Both flies that were fed the steroid hormone RU486 (left, yellow) and the genetically identical flies without the hormone (right, green), showed high PIs, low p-values and high Bayes Factors, indicating a preference for the unpunished torque domain. Data: 10.5283/epub.53685.108\n\n\nDiscussion\n\nOperant self-learning in Drosophila is a form of motor learning that appears to be conserved among bilaterians. The transcription factor FoxP is involved in various forms of motor learning in chordates,5–9,11,13,16–18 as is PKC.22–24,109–112 PKC is also involved in motor learning in the feeding behavior of the lophotrochozoan Aplysia113 and both are involved in motor learning in the ecdysozoan Drosophila (this work and.20,21,31 This wealth of evidence supports what has been called ‘deep homology’ for motor learning in bilaterians.12\n\nIn this work, we present new insights into the neurobiological mechanisms underlying this form of motor learning.\n\nWhile previous evidence suggested that some PKC activity was required in some MNs for operant self-learning,21 it was not clear which PKC gene was involved and in which MNs. Improving upon the previous attempts to identify the responsible PKC gene, here we used CRISPR/Cas9 to first rule out that PKC53e is involved and then show that the atypical PKC (aPKC) is necessary for operant self-learning (Figure 1). Restricting transgenic manipulations to FoxP isoform-B positive neurons and using anatomical experiments to confirm behavioral results suggesting that FoxP is not necessary in the brain for operant self-learning (Figures 2, 5), we now hypothesize that aPKC activity is required in aPKC/FoxP-positive direct wing steering MNs in the ventral nerve cord (VNC). Our analysis of these direct wing muscles, responsible for, e.g. wing beat amplitude (a major contributing factor to yaw torque),114 revealed aPKC/FoxP co-expressing MNs innervating a specific subset of these muscles (Figure 3), corroborating our hypothesis.\n\nSpecifically, the basalar muscle b1 which is known to regulate wing beat amplitude during optomotor stimulation through phase shifts of its action potential within the wing beat cycle83 is innervated by a MN with very strong aPKC and FoxP expression in all 11 animals analyzed. Similarly, b3 is also innervated by a MN with very strong aPKC and FoxP expression and the b3 muscle is reported to increase activity when the ipsilateral wing decreases its amplitude.115 The b1 and the b3 muscles thus both share similar sizes and morphologies, are innervated by MNs with particularly thick processes and presynaptic active zones, insert at opposite sides of the basalar sclerite and act in a push-pull fashion in controlling wing beat amplitude,115 a major contributor to yaw torque. Although the MN innervating the third basalar muscle, b2, also expresses aPKC along the axon, we did not detect aPKC signal in axon terminals or active zones, and it does not show FoxP label, thus ruling out a function of b2 in aPKC/FoxP mediated operant self-learning. In contrast to b1 and b3, b2 firing is not linked to the wingbeat cycle; instead, it fires in bursts during turning maneuvers.82 Corroborating the conclusion that it is not involved in mediating operant self-learning, b2 is silent during straight flight, but it is likely involved in regulating body saccades (Heide, Götz, 1996), which are by themselves not relevant for controlling the heat in our experiments. For the basalar muscles the emerging picture is that b1 and b3 are the top candidates for self-learning because they likely regulate wingbeat amplitude and thus also yaw torque on a wingbeat cycle by cycle basis. Strikingly, the MNs innervating these two muscles show high levels of aPKC and FoxP expression. Although much less is known about the pterale muscles, and neither iii3 nor iii4 (both with aPKC and FoxP co-expression) have been recorded electrophysiologically during flight, a similar picture begins to emerge. The MN to the left muscle i1 is known to be active during right turns83 and co-expresses aPKC and FoxP, whereas iii1 reportedly83 does not participate in OMRs and is innervated by a MN with weak aPKC and no FoxP label. In summary, flight steering muscles that are known to regulate flight steering in response to optomotor stimulation receive aPKC and FoxP positive motor innervation.\n\nGiven that MNs innervating muscles important for controlling wingbeat amplitudes during OMRs coexpress aPKC and FoxP, the genes necessary for our operant experiments where the animals learn to generate specific wingbeat amplitudes, a straightforward hypothesis emerges: if operant self-learning altered the properties of MNs that also happen to be involved in OMRs, we should be able to observe training-induced modifications in the flies’ optomotor behavior after training. Analyzing the OMRs of a separate cohort of wild-type flies corroborated this hypothesis (Figure 4). The optomotor magnitude was reduced in the punished turning direction, but unaltered in the unpunished direction. This result is both expected and unexpected: it is expected because these MNs express both genes necessary for operant self-learning. The result is unexpected because OMRs were not trained and the magnitude of the effect is not large enough to prevent the flies from flying straight.30 So unexpected was this result, in fact, that our study, triggered by the expression results (Figures 2, 3), is the first to analyze OMRs after conditioning since the initial description of these operant experiments more than 30 years ago,35 even though that capability existed from the very beginning. This surprising result from wild type flies raises the question of whether the changes observed in the OMR could have their cause outside of the steering MNs? With emerging evidence that OMRs are mediated via (both identified and yet to be identified) descending neurons from the brain with direct synaptic connections onto the steering MNs in the VNC,116,117 additional neuroanatomical overlap between the circuitry controlling elicited OMRs and the circuitry giving rise to spontaneous yaw torque fluctuations becomes very unlikely. In particular, in the light of this evidence, any such overlap would need to be localized to the brain, where we did not find any neurons expressing both aPKC and FoxP. The remote possibility remains that OMR plasticity after operant learning may be caused by non-aPKC/Foxp-dependent plasticity mechanisms in the brain. Future research will address this possibility. Taken together, our results and the available evidence on OMRs strongly suggest that the changes we have detected in wild-type OMRs after operant self-learning are caused by steering MN plasticity, in turn brought about by the operant training.\n\nThen again, only about a third of the variance in the torque preference after training can be explained by this optomotor asymmetry. This result explains the observations that there are flies with a strong conditioned torque preference but with an optomotor asymmetry in the opposite direction, as well as flies with a weak conditioned torque preference and large optomotor asymmetry (Figure 4B3). Clearly, plasticity in steering MNs appears to be important, but it does not reflect the entirety of the learning processes.\n\nPlasticity in steering movements such as OMRs have been observed before, such as in classic “inversion goggles” experiments where the coupling between the fly’s movements and the environment was reversed118 or in a more recent experiment revealing adaptation processes.119 It has long been recognized that insects with asymmetrical wing damage need to adjust the neural commands for generating torque to compensate for the changed physical torque (e.g., Refs. 116, 117, 120–124). Plasticity in wing steering motor neurons provides a potential mechanism for such adjustments.\n\nTaken together, these results converge on the hypothesis that plasticity in MNs that innervate the direct muscles involved in generating yaw torque, but not other steering MNs, mediates an important aspect of operant self-learning in Drosophila. The importance of MN plasticity is emphasized by FoxP-dependent plasticity apparently not being required in the brain (Figure 5). This MN plasticity could either be implemented by (a) postsynaptic plasticity of the input synapses to these MNs, postsynaptic because the MNs but not the interneurons express the proteins required for self-learning, or (b) on the level of the intrinsic excitability of flight steering motoneurons, or (c) on the level of the output synapses to the respective steering muscles. However, the mechanism and subcellular localization of self-learning in MNs remains to be determined.\n\nA second interesting, yet unstudied population of aPKC/FoxP co-expressing neurons resides in the abdominal neuromer of the VNC. As flies use their abdomen analogously to a rudder during turns in flight,125,126 involvement of these neurons seems plausible in addition to wing MNs.\n\nWhile few studies in insects have shown MN plasticity, the Aplysia sensorimotor synapse is a classical model for research on plasticity mechanisms. There is a rich literature on MN plasticity in this preparation, some of which reports PKC-dependent mechanisms.104,127–137 Also in mammals (including humans) MN plasticity in the spinal cord is a readily observable phenomenon in nonclinical and clinical settings.138–147 The discovery of aPKC-dependent plasticity in Drosophila MNs expands this body of literature to a genetically tractable organism and inasmuch as clinical practice relies on MN plasticity, may even help instruct the development of clinical applications.\n\nUntil our work, PKC activity had only been shown to be important for memory consolidation/maintenance in world-learning experiments in flies, but not for learning/acquisition.148,149 Also in Drosophila at the torque meter, PKCs are dispensable for world-learning.31 The literature on PKCs in learning and memory in other animals is complex and multifaceted. In some preparations, PKC isoforms are required during memory maintenance, in some also during acquisition and in others different isoforms distinguish between acquisition and consolidation.69,70,102,104,128,133,135,150–158 As the manipulations in our experiments lasted throughout training together with the tests immediately following training and we did not test for long-term memory, we can only ascertain that aPKC is required in a very narrow time window of minutes around training. Future research will address whether aPKC must be present during training, test, or both.\n\nNotably, there is one other preparation where PKC activity is involved and which is also conceptually most closely resembling the one we used here, operant reward learning in Aplysia feeding behavior. However, in this preparation, the calcium-dependent Apl-I PKC not the atypical Apl-III PKC appears to be mediating the plasticity.113 Given the degeneracy between the different PKC genes and the fact that they can not only compensate for long-term PKCi-mediated inhibition (this work and,21 but also for each other,69 more research is needed to elucidate how these different mechanisms of plasticity evolved and are related to each other.\n\nNeither bazooka (baz) nor the kidney and brain gene (KIBRA), two prominent interaction partners of aPKC,98–104,106,159,160 showed an effect on operant self-learning when they were knocked out in the adult nervous system (Figure 7), potentially raising doubts about the effectiveness of the CRISPR/Cas9 method in these cases. In particular, one may question the approach of temporally limiting the manipulation to adult neurons. Although this had been effective with previous PKC manipulations using an inhibitory peptide, PKCi,21,31 it only yielded an intermediate effect with a CRISPR-mediated knockout targeting aPKC (Figure 1B). In contrast, temporally uncontrolled knockout of aPKC in MNs of the VNC (Figure 1C) proved surprisingly effective, given expectations from prior experience.\n\nNonetheless, we are confident that both manipulations successfully knocked out each of these genes. First, we found that the baz knockout, rather than impairing self-learning, increases learning performance (manuscript in preparation), suggesting the PAR complex may be sequestering aPKC and thereby limiting its availability for self-learning. Thus, these data suggest that baz is indeed not directly involved in mediating the aPKC activity contributing to plasticity in steering MNs; instead, it may be binding aPKC in the PAR complex, preventing it from playing its role in MN plasticity. Second, our KIBRA knock-out had a severe effect on flight performance when elicited during development, suggesting that also this manipulation was, in principle, effective. That being said, without clear evidence that the baz and KIBRA proteins are completely absent, these results remain suggestive rather than conclusive. In addition to protein-level analysis of CRISPR efficacy (as we have performed in CRISPR-mediated FoxP knock-out77), future experiments will use FoxP-iB and c380 drivers to drive baz and KIBRA knockouts.\n\nInterestingly, at least during development, baz and KIBRA have been reported to have opposite effects on the function of aPKC, with the PAR complex (baz) and the Hippo pathway (KIBRA) mutually inhibiting each other.161 While baz is thought to mediate aPKC activity, KIBRA is thought to exert negative regulatory effects on aPKC. Thus, knocking out each one of them should have revealed a decrement in self-learning in at least one of them, if the processes during development were recapitulated during self-learning. On the other hand, experiments in which KIBRA has been shown to be involved in learning/memory have suggested a positive rather than a negative regulatory role,104,153 albeit with an emphasis on long-term memory rather than learning.162 Whichever way aPKC may be interacting with components of these canonical pathways, the literature predicts that at least one of our manipulations should have revealed a decrement in operant self-learning. The fact that this prediction was falsified may suggest that aPKC exerts its function in a non-canonical manner in operant self-learning plasticity. We are currently pursuing research into the possibility that bazooka may be a negative regulator of aPKC activity during operant self-learning.\n\nAs FoxP mutants are impaired in operant self-learning,20 two hypotheses about the role of this prominent transcription factor arise. First, FoxP may be directly involved in the learning process via some unknown, cytosolic function. A transcription factor function appears unlikely, because of the short duration of our experiments. Second, FoxP may exert its effects as a developmental regulator, being crucial for the development of the circuits mediating operant self-learning. As the developmental role of FoxP genes is well documented7,14,77,92,163,164 and there are few domains in the gene that would lend themselves to a hypothetical cytosolic function, the latter hypothesis appeared more plausible. The result that adult knockout of FoxP had no immediate effect on operant self-learning (Figure 6A) seemed to corroborate this hypothesis. In contrast, supporting a continued role of FoxP genes in motor learning also after development are data from songbirds where FoxP2 gene expression is not only regulated by singing,15,165–167 but where normal FoxP2 expression is necessary in adults to maintain learned song.8,168 To also test the second hypothesis, we aged the flies after the FoxP knockout and tested them 7 and 14-days later. Flies still showed operant self-learning after seven days without FoxP transcription (DOI: 10.5283/epub.52965), but were impaired after 14 days (Figure 6B). These results suggest a role for adult FoxP expression in maintaining operant self-learning capabilities after development, analogous to the role of FoxP2 in songbird vocal learning.8,168 This result may be explained by the temporal dynamics of the genes regulated by FoxP169 or by the half-life of FoxP itself. Further research is needed to distinguish between these two options.",
"appendix": "Data availability\n\nUnderlying data for ‘Wings of Change: aPKC/FoxP-dependent plasticity in steering motor neurons underlies operant self-learning in Drosophila’,\n\nUniversity of Regensburg: 1A: https://www.doi.org/10.5283/epub.52958 74\n\nUniversity of Regensburg: 1B: https://www.doi.org/10.5283/epub.52957 75\n\nUniversity of Regensburg: 1C: https://www.doi.org/10.5283/epub.52944 76\n\nZenodo: 2: https://www.doi.org/10.5281/zenodo.10047941 79\n\nZenodo: 3: https://www.doi.org/10.5281/zenodo.10606166 68\n\nUniversity of Regensburg: 4: https://www.doi.org/10.5283/epub.54804 86\n\nUniversity of Regensburg: 5A: https://www.doi.org/10.5283/epub.52956 88\n\nUniversity of Regensburg: 5B: https://www.doi.org/10.5283/epub.52951 89\n\nUniversity of Regensburg: 5C: https://www.doi.org/10.5283/epub.52946 90\n\nUniversity of Regensburg: 6A: https://www.doi.org/10.5283/epub.52963 93\n\nUniversity of Regensburg: 6B: https://www.doi.org/10.5283/epub.52964 94\n\nUniversity of Regensburg: 7A: https://www.doi.org/10.5283/epub.52947 107\n\nUniversity of Regensburg: 7B: https://www.doi.org/10.5283/epub.53685 108\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe thank Thomas Kopp in the electronics workshop of the University of Regensburg, without whose tireless support this work could not have been accomplished. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nWolpaw JR: Harnessing neuroplasticity for clinical applications. Brain. 2012 Apr; 135(Pt 4): e215. author reply e216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEftekhar A, Norton JJS, McDonough CM, et al.: Retraining Reflexes: Clinical Translation of Spinal Reflex Operant Conditioning. Neurotherapeutics. 2018 Jul; 15(3): 669–683. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKane NS, Robichon A, Dickinson JA, et al.: Learning without performance in PKC-deficient Drosophila. Neuron. 1997 Feb; 18(2): 307–314. PubMed Abstract | Publisher Full Text\n\nDrier EA, Tello MK, Cowan M, et al.: Memory enhancement and formation by atypical PKM activity in Drosophila melanogaster. Nat. Neurosci. 2002 Apr; 5(4): 316–324. PubMed Abstract | Publisher Full Text\n\nMichel M, Green CL, Lyons LC: PKA and PKC are required for long-term but not short-term in vivo operant memory in Aplysia. Learn. 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Proc. Natl. Acad. Sci. USA. 1991 Mar 1; 88(5): 2016–2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEtcheberrigaray R, Matzel LD, Lederhendler II, et al.: Classical conditioning and protein kinase C activation regulate the same single potassium channel in Hermissenda crassicornis photoreceptors. Proc. Natl. Acad. Sci. USA. 1992 Aug 1; 89(15): 7184–7188. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMuzzio IA, Talk AC, Matzel LD: Incremental redistribution of protein kinase C underlies the acquisition curve during in vitro associative conditioning in Hermissenda. Behav. Neurosci. 1997; 111(4): 739–753. PubMed Abstract | Publisher Full Text\n\nBlackwell KT: Subcellular, cellular, and circuit mechanisms underlying classical conditioning in Hermissenda crassicornis. Anat. Rec. B New Anat. 2006 Jan; 289(1): 25–37. PubMed Abstract | Publisher Full Text\n\nGao PP, Goodman JH, Sacktor TC, et al.: Persistent Increases of PKMζ in Sensorimotor Cortex Maintain Procedural Long-Term Memory Storage. iScience. 2018 Jul 27; 5: 90–98. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSoriano EV, Ivanova ME, Fletcher G, et al.: aPKC Inhibition by Par3 CR3 Flanking Regions Controls Substrate Access and Underpins Apical-Junctional Polarization. Dev. Cell. 2016 Aug 22; 38(4): 384–398. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWieschaus E, Noell E: Specificity of embryonic lethal mutations in Drosophila analyzed in germ line clones. Rouxs Arch. Dev. Biol. 1986 Jan; 195(1): 63–73. PubMed Abstract | Publisher Full Text\n\nZhang L, Wei X: The Roles of Par3, Par6, and aPKC Polarity Proteins in Normal Neurodevelopment and in Neurodegenerative and Neuropsychiatric Disorders. J. Neurosci. 2022 Jun 15; 42(24): 4774–4793. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZha C, Sossin WS: The molecular diversity of plasticity mechanisms underlying memory: An evolutionary perspective. J. Neurochem. 2022 Dec; 163(6): 444–460. PubMed Abstract | Publisher Full Text\n\nRocca DL, Wilkinson KA, Henley JM: SUMOylation of FOXP1 regulates transcriptional repression via CtBP1 to drive dendritic morphogenesis. Sci. Rep. 2017 Apr 13; 7(1): 877. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBowers JM, Perez-Pouchoulen M, Roby CR, et al.: Androgen modulation of Foxp1 and Foxp2 in the developing rat brain: impact on sex specific vocalization. Endocrinology. 2014 Dec; 155(12): 4881–4894. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTeramitsu I, White SA: FoxP2 regulation during undirected singing in adult songbirds. J. Neurosci. 2006 Jul 12; 26(28): 7390–7394. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThompson CK, Schwabe F, Schoof A, et al.: Young and intense: FoxP2 immunoreactivity in Area X varies with age, song stereotypy, and singing in male zebra finches. Front. Neural. Circuits. 2013 Feb 28; 7: 24. Publisher Full Text\n\nChen Q, Heston JB, Burkett ZD, et al.: Expression analysis of the speech-related genes FoxP1 and FoxP2 and their relation to singing behavior in two songbird species. J. Exp. Biol. 2013 Oct 1; 216(Pt 19): 3682–3692. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXiao L, Merullo DP, Koch TMI, et al.: Expression of FoxP2 in the basal ganglia regulates vocal motor sequences in the adult songbird. Nat. Commun. 2021 May 11; 12(1): 2617. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKuo HY, Chen SY, Huang RC, et al.: Speech- and language-linked FOXP2 mutation targets protein motors in striatal neurons. Brain. 2023 May 4; 146: 3542–3557. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "258497",
"date": "04 Apr 2024",
"name": "Efthimios M C Skoulakis",
"expertise": [
"Reviewer Expertise Associative and non associative learning and memory and associated disorders modeled in Drosophila"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Ehweiner et al advances previous findings of the Brembs lab. They provide evidence that the atypical PKC with FoxP positive wing steering neurons is necessary for operant self-learning as the authors define it. The manuscript is rather long, and the discussion should be shortened as to not reiterate results. Although I have no argument that the phenotypes, they see are consistent with a performance reduction in the trained operant response, I am uncertain about the following: 1. Can the authors differentiate expression of the learned steering response from the site of actual integration of signals required to change the base line response? In other words, are the motor neurons identified required for expression/performance of the maneuvers necessary to demonstrate the learned behavior?\n\nBut is this the actual locus where the learning occurs? If so, what are the afferent neurons encoding the punishment that should impinge on these motoneurons? Is it possible that the site of learning is elsewhere within the nervous system a possibility also consistent with the Elav-driven knock out data? This should at least be discussed in the appropriate section. Perhaps not at this point but differential (side specific) photo activation of the identified neurons might provide necessary evidence on their sufficiency to drive optomotor bias. 2. I do not understand the result in Fig 6. How can the effect be 12 days after removal of the RU486 inducer?!!! If I remember correctly from the original paper detailing the GS system, the effect of RU486 wears out within 24 hrs post removal of the drug. However, does induction poison the FoxP neurons and it takes that long for them to degenerate? Are the neurons there post treatment? Have the authors tried RU486 induction for more than 2 days??\nMinor points: 1. Please list on table 1 where each driver is expressed. 2. On page 8 in the opening paragraph of the results section. Please summarize (for the naive reader) previous findings that led you to look specifically at the FoxP neurons.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11571",
"date": "02 Jul 2024",
"name": "Björn Brembs",
"role": "Author Response F1000Research Advisory Board Member",
"response": "Thank you very much for these very useful suggestions and comments! We have now uploaded three new versions of the manuscript for you to choose from: 1. The version required by the publisher. This file is likely not very useful for reviewers, as it contains many formatting changes. 2. The new manuscript without marked changes (apkc_foxp_6.docx) 3. The new manuscript with marked changes from the previous version (apkc_foxp_difference_v5v6.pdf) Please find below our point-by-point replies to your comments, with your comments marked in bold: The manuscript by Ehweiner et al advances previous findings of the Brembs lab. They provide evidence that the atypical PKC with FoxP positive wing steering neurons is necessary for operant self-learning as the authors define it. The manuscript is rather long, and the discussion should be shortened as to not reiterate results. We have now taken out the summarized results. Although I have no argument that the phenotypes, they see are consistent with a performance reduction in the trained operant response, I am uncertain about the following: 1. Can the authors differentiate expression of the learned steering response from the site of actual integration of signals required to change the base line response? In other words, are the motor neurons identified required for expression/performance of the maneuvers necessary to demonstrate the learned behavior? But is this the actual locus where the learning occurs? If so, what are the afferent neurons encoding the punishment that should impinge on these motoneurons? Is it possible that the site of learning is elsewhere within the nervous system a possibility also consistent with the Elav-driven knock out data? This should at least be discussed in the appropriate section. This is one of the crucial research questions! We have already tried to address this in our discussion, but obviously did not find the right words to explain what our data show and where additional data is still needed. We have therefore deleted this part of the discussion and re-written it from scratch. We are confident that it now better addresses this issue. Only after this review was received, the detailed function of the steering muscles was elucidated: 10.1038/s41586-024-07293-4 (published April 17, 2024). We have incorporated some of the new information in our manuscript. We now first establish that the neurons that are doubly labeled indeed are those involved in generating slow, ‘baseline’ yaw torque fluctuations of the type seen in both OMRs and rewarded/punished in our learning experiments. Then we discuss the evidence for the literature that suggests that the only place where OMR and learning overlap is the steering MNs, such one can only see learning effects on OMRs if the learning took place in the steering MNs. Perhaps not at this point but differential (side specific) photo activation of the identified neurons might provide necessary evidence on their sufficiency to drive optomotor bias. There is recently published work that confirms the work detailing the role of the neurons we already cite: https://www.nature.com/articles/s41586-024-07293-4 So we are very confident about the role of these neurons in torque modulations. The two last authors are currently preparing a grant proposal to find out what physiological changes occur in these neurons due to learning and there, yes, absolutely, side-specific work will be proposed. Without such experiments it is impossible to find out how the memory operates. 2. I do not understand the result in Fig 6. How can the effect be 12 days after removal of the RU486 inducer?!!! If I remember correctly from the original paper detailing the GS system, the effect of RU486 wears out within 24 hrs post removal of the drug. However, does induction poison the FoxP neurons and it takes that long for them to degenerate? Are the neurons there post treatment? Have the authors tried RU486 induction for more than 2 days?? We have now added text to explain that we have no reason to assume that the technique isn’t working as expected. We take these results to mean that the 2-day RU486 exposure knocks out the FoxP gene as expected (and the protein data we have published show that the CRISPR construct is working properly!). Unfortunately, the one antibody that reliably detects FoxP protein and that we used in our previous publication is no longer available, so what we don’t know is whether the FoxP protein stays around for so long and this is why the flies can learn fine without a FoxP gene The genes regulated by FoxP keep performing their function without FoxP for so long or A combination of the two. We are confident to have clarified these three options in the current version of the manuscript. Minor points: 1. Please list on table 1 where each driver is expressed. Done (and deleted one row with a line we had not used in this publication). Thank you for this suggestion! 2. On page 8 in the opening paragraph of the results section. Please summarize (for the naive reader) previous findings that led you to look specifically at the FoxP neurons. We now explain that our FoxP drivers show overlap with the MN drivers that unveiled the role of PKC in MNs."
}
]
},
{
"id": "258492",
"date": "17 Apr 2024",
"name": "Kathrin Vogt",
"expertise": [
"Reviewer Expertise Neurogenetics",
"Neuroethology",
"Drosophila",
"Neuromodulation",
"Learning & Memory"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nEhweiner et al. describe a potential neural circuit mechanism underlying operant motor learning in Drosophila melanogaster. They trained flies to avoid certain flight directions in a flight simulator by punishing steering maneuvers either to the right or left. In line with previous studies, PKC is required for this kind of self-learning, and the current study suggests that specifically the aPKC gene is required in FoxP-positive motor neurons. The overlapping expression of these two genes is described in wing motor neurons in the VNC. To test for further effects of operant conditioning on flight behavior, the authors test if the optomotor response is affected after training and find a preference shift, suggesting that motor learning does even affect this generally very hardwired and stereotypic behavioral response. Further experimental data investigates the role of FoxP in the brain and the temporal requirements of adult-restricted FoxP knock-out induction.\nThe data presented in this manuscript suggests a plastic mechanism, dependent on FoxP and aPKC, within wing motor neurons of the fly required for operant motor learning. The authors provided all raw data and performed rigorous statistical analysis. However, some of the data shows weak phenotypes and thus, excluding a role for some of the genes tested based on a single negative result seems not to be appropriate (PKC53, Baz, Kibra). The authors discuss some of these possibilities, however more experiments are required. Several manipulations in more refined sets of neurons during development might also avoid compensation mechanisms kicking in or the problem of prolonged viability of proteins. The effect of motor learning on OMR is very interesting and it will be exciting to see if FoxP is required for the OMR shift, or if it only affects operant learning and the two behaviors are modulated separately.\nFigure 1: aPKC is required in FoxP positive and C380-GAL4 neurons – but the effect upon whole brain KO is small and they still show significant learning. PKC53 KO shows also significant learning is not further tested. To confirm that specifically aPKC is required, the authors should also perform a more restricted manipulation with PKC53 KO -either in FoxP or C380 labeled neurons. Did the authors look at expression patterns of PKC53 in the VNC?\nFigure 2: FoxP expression in the VNC overlaps with aPKC. FoxP is also expressed in many motor neurons. However, as there are many FoxP cells without aPKC expression, the figure cannot clearly indicate that aPKC and FoxP are expressed in the same specific wing motor neurons.\nFigure 3: Co-expression of aPKC and FoxP in specific neuromuscular synapses onto wing muscle cells. It will be interesting to see if the found genes will be specifically required in different wing motor neurons – potentially also dependent on the motor task.\nFigure 4: Flies that have been trained with the operant motor learning paradigm, also have been tested for OMR before and after training. After training, their preference towards the punished side is shifted according to the trained behavior. Maybe the authors could even increase the OMR effect with a more difficult OMR task. Potentially, strong OMR stimuli also induce strong OMR responses, however, if OMR stimuli are less salient or lower in contrast, the flies could maybe more easily suppress specific flight directions. This might enhance the training effect.\nFigure 5: The authors show that FoxP KO in the brain does not influence motor learning. aPKC also seems to have a strong expression in the brain and might be additionally required for plasticity there, however, this has not been tested.\nFigure 6: Here, the authors show that a FoxP-KO restricted to adult flies only shows a phenotype after 14 days. Overall, older flies seem to get worse in operant conditioning. Can the authors exclude that this effect is due to the older age of flies – which might make them more vulnerable to manipulations or weak expression?\nFigure 7: KO of Baz and Kibra in all neurons = no effect on operant learning. In addition to compensation mechanisms, it might be that a cell-specific KO also here might reveal a phenotype – similar to aPKC KO in all neurons, which still showed significant learning. In Figure 6, the authors showed that FoxP adult restricted KO did not reveal any phenotype, could the same problem arise here – maybe the authors can test these effects also in older flies.\nMinor comments: Figure 2:\nC2 = The overlap between aPKC and FoxP is very hard to see – a zoom-in with both channels separate would be helpful. Same for Panels D. As there are different drivers for GFP across panels, please indicate this in the labels in the figure. In Panel D, D42-GAL4 was used to label wing MNs. What is the difference between c380-GAL4 used for behavior and D42-GAL4? Also, D42-GAL4 is not listed in the methods.\nFigure 4:\nColors in the legend are assigned as yellow and green for panel A4/B4, please change this to blue and red.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11572",
"date": "02 Jul 2024",
"name": "Björn Brembs",
"role": "Author Response F1000Research Advisory Board Member",
"response": "Thank you very much for these very useful suggestions and comments! We have now uploaded three new versions of the manuscript for you to choose from: 1. The version required by the publisher. This file is likely not very useful for reviewers, as it contains many formatting changes. 2. The new manuscript without marked changes (apkc_foxp_6.docx) 3. The new manuscript with marked changes from the previous version (apkc_foxp_difference_v5v6.pdf) Please find below our point-by-point replies to your comments, with your comments marked in bold: Figure 1: aPKC is required in FoxP positive and C380-GAL4 neurons – but the effect upon whole brain KO is small and they still show significant learning. PKC53 KO shows also significant learning is not further tested. To confirm that specifically aPKC is required, the authors should also perform a more restricted manipulation with PKC53 KO -either in FoxP or C380 labeled neurons. Did the authors look at expression patterns of PKC53 in the VNC? According to our criteria, only the PKC53E flies showed significant learning (see M&M). These results also confirmed results we had obtained with PKC53E mutant flies, so we now have two experiments ruling out PKC53E. It seems excessive to test PKC53E yet a third time. The aPKC results were inconclusive, as the flies did not meet both of our criteria for learning. This is the reason we performed further tests with these flies. If they had shown significant learning, we would not have tested them with different drivers either. We now emphasize in the text that the additional experiments merely replicated the first result to minimize the probability of the aPKC result being a false-positive. Figure 2: FoxP expression in the VNC overlaps with aPKC. FoxP is also expressed in many motor neurons. However, as there are many FoxP cells without aPKC expression, the figure cannot clearly indicate that aPKC and FoxP are expressed in the same specific wing motor neurons. That is correct and we also do not claim this in this figure, yet. We only use this to justify and motivate the thorough analysis in Fig. 3. We have made this more explicit in the text. Figure 3: Co-expression of aPKC and FoxP in specific neuromuscular synapses onto wing muscle cells. It will be interesting to see if the found genes will be specifically required in different wing motor neurons – potentially also dependent on the motor task. Once we have access to more specific GAL4 lines (they should arrive soon), we could test whether, for instance, aPKC knock-out in the MNs for muscle b1 and b3 alone is sufficient to impair self-learning. However, as it stands right now, there does not seem to be a line for just b1/b3 alone, so there are some technical challenges ahead with this approach. See also our brief mention of the abdominal MNs and the function of the abdomen as a rudder. We now mention these future experiments in the discussion. Figure 4: Flies that have been trained with the operant motor learning paradigm, also have been tested for OMR before and after training. After training, their preference towards the punished side is shifted according to the trained behavior. Maybe the authors could even increase the OMR effect with a more difficult OMR task. Potentially, strong OMR stimuli also induce strong OMR responses, however, if OMR stimuli are less salient or lower in contrast, the flies could maybe more easily suppress specific flight directions. This might enhance the training effect. Excellent suggestion! Yes, indeed we use maximally effective OMR stimuli and it is possible that we hit a ceiling effect such that the numerical difference between trained and untrained becomes small. Yes, we will definitely test this! We now mention this experiment in the discussion. Figure 5: The authors show that FoxP KO in the brain does not influence motor learning. aPKC also seems to have a strong expression in the brain and might be additionally required for plasticity there, however, this has not been tested. The reason why we only tested FoxP in the brain and not aPKC is historical: these tests were performed before we had identified aPKC. Since we now know that there is no co-expression of aPKC and FoxP in the brain, these data only serve to corroborate the conclusion that this type of plasticity appears not to be required in the brain. We now make this aspect more explicit in the text. Figure 6: Here, the authors show that a FoxP-KO restricted to adult flies only shows a phenotype after 14 days. Overall, older flies seem to get worse in operant conditioning. Can the authors exclude that this effect is due to the older age of flies – which might make them more vulnerable to manipulations or weak expression? This could be possible. Difficult to say how plausible this is. One would need to knock out a gene that we know is not involved in self-learning in such old flies and see what happens. Given that it is quite a large effort to get such old flies to make it through the experiment, it’s not quite obvious if the potential answer is worth the effort. At this point, as we do not have anyone in the laboratory who could take on this project, we would probably rather take this result out than try to experimentally rule this explanation out. Figure 7: KO of Baz and Kibra in all neurons = no effect on operant learning. In addition to compensation mechanisms, it might be that a cell-specific KO also here might reveal a phenotype – similar to aPKC KO in all neurons, which still showed significant learning. In Figure 6, the authors showed that FoxP adult restricted KO did not reveal any phenotype, could the same problem arise here – maybe the authors can test these effects also in older flies. For bazooka we now make it more explicit that the manipulated flies actually learn better than controls (manuscript in preparation) and link to Andreas Ehweiner’s dissertation that contains the result. For KIBRA we now emphasize that as long as the KIBRA gRNA strain is not officially published (it was a gift), these results are preliminary. Minor comments: Figure 2: C2 = The overlap between aPKC and FoxP is very hard to see – a zoom-in with both channels separate would be helpful. Same for Panels D. I have raised this repeatedly with graduate student Andreas Ehweiner and he reiterated that this was the best he could do. He emphasized that viewing the confocal stacks, the overlap would be clearly visible, but in 2D it was always difficult form him to get a similarly convincing view/perspective. As Fig. 3 shows more detail and the image stacks are available, we feel that we have provided sufficient evidence for the aPKC/FoxP overlap, when combining Fig. 2 and Fig. 3. As there are different drivers for GFP across panels, please indicate this in the labels in the figure. Done In Panel D, D42-GAL4 was used to label wing MNs. What is the difference between c380-GAL4 used for behavior and D42-GAL4? Also, D42-GAL4 is not listed in the methods. D42 line is now listed among the used fly lines, thank you! Both c380 and d42 are both motorneuron lines and in this work, we have been using them interchangeably, without any particular reason for one or the other. We try to say as much in the Results text for Fig. 2 and have no re-worded the sentence to make it even more explicit. Figure 4: Colors in the legend are assigned as yellow and green for panel A4/B4, please change this to blue and red. Done"
}
]
},
{
"id": "258493",
"date": "10 May 2024",
"name": "Wayne Sossin",
"expertise": [
"Reviewer Expertise Molecular mechanisms of memory formation and maintenance."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper makes important contributions to the field of molecular mechanisms underlying memory formation. I had previously reviewed this paper for a separate journal and this revised version has addressed all the issues I previously had raised and I have no more issues to raise.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-116
|
https://f1000research.com/articles/13-613/v1
|
10 Jun 24
|
{
"type": "Correspondence",
"title": "Empowering Maneuvers: Boldly Mobilizing Military Medical Research and Training within the Kingdom of Saudi Arabia to Safeguard a Nation and its People.",
"authors": [
"Yasser Mandourah",
"Richard Mottershead",
"Nafi Alonaizi",
"Hasan Alriaini",
"Essam Burhan",
"Nabeel Al-Yateem",
"Yasser Mandourah",
"Nafi Alonaizi",
"Hasan Alriaini",
"Essam Burhan",
"Nabeel Al-Yateem"
],
"abstract": "In 2023 Alkhathami and colleagues from the Prince Sultan Military College of Health Sciences highlighted the Kingdom of Saudi Arabia’s transformative upgrades across various sectors, notably including enhancements to the healthcare system, and called for action to extend these upgrades to the military healthcare field. Prompted by this call to action, the leadership of the military healthcare system swiftly commenced initiatives, acting in less than three months from this pivotal appeal. In January 2023 the first author ordered a decree via the General Directorate of Armed Forces Medical Services of Saudi Arabia, in collaboration with US central Command and international partners, to host the 3rd International Conference of Military Medicine. The event graciously welcoming more than 1000 military representatives from 20 participating nations. The Military Medical Conference, fostering a global military community dialogue on the necessity to explore collective capacities to endure and overcome humanitarian challenges, thereby sustaining health, promoting well-being, and nurturing life through strategies that align with the insights of Alkhathami et al. (2023). The response and the need underlined by the original article are discussed by the Major General, staff of the Saudi Military Medical Services and academics from the University of Sharjah.",
"keywords": [
"Medical Research",
"Health Training",
"National Strategies",
"Digital Health",
"Humanitarian Response"
],
"content": "Introduction\n\nAlkhathami et al. (2023) underscored the imperative to progress and advance military medical research and training within the Saudi Armed Forces to meet the nation’s research and development needs. Considering the significant financial investments in the Kingdom of Saudi Arabia’s (KSA) Armed Forces (Trending Economics, 2021), aligning research and training policy and practice is crucial to devising an effective and empowering strategy. This response aims to not only resonate with the original article but also to attest to the evidence of the plan’s progression, supporting and accelerating the military medical services’ contributions towards achieving the Kingdom’s Vision 2030 targets (Saudi Vision, 2021).\n\nThis significant advancement towards these goals showcases the collaboration between Saudi Arabian researchers and international experts, laying a foundation for success through mutual support and comradery—a theme highlighted by the lead author at this year’s military medical conference. However, this response also calls for a continued confidence in leadership and celebrates the knowledge and capabilities of Arab states, drawing upon international partnerships to advance military medical research and training. This ethos underscores the region’s collaborative spirit and dedication to enhancing the medical services’ bespoke needs, ensuring the safety and sovereignty of Saudi Arabia and its neighboring states (Mottershead & Alonaizi, 2022a). The Ministry of Defense Health Military Medical Services (MODMMS) and the Saudi Ministry of Defense have demonstrated innovation and foresight in enhancing military healthcare services through research and training initiatives, a commitment this response applauds as evidence of the Vision’s blueprint for economic and social success by 2030. This progress is realized within national initiatives to progress the digital health strategy through the progression of digitalization. This method is a comprehensive solution that provides the scalable and interoperable tactical medical architecture required to collect, collate, analyze, and distribute critical medical data across the All-Domain Military Operations. This endeavor spearheaded by the first author and his team is a direct reference to the needs discussed by Alkhathami et al. (2023) in the goal for Saudi Arabia is actively pursue localizing its military industries as part of its Vision 2030 plan, intending to localise 50% of military industries by 2030.\n\nThis national project’s digital health strategy will provide documentation through interoperability of medical communications for combat casualty care systems. The authors acknowledge and heed the concerns of Alkhathami et al. (2023), in their belief that traditional clinical medical research, alone is insufficient to meet the specific needs of the military. A comprehensive and solution focused strategy has been mobilized to accelerate the research and training needs of the nation as evidenced with the recent joint Forces conference. This event showcased the digital health strategy and how innovation will now automate and synchronize the collection of medical data to support medical regulating. Digitalization will further integrate and allow bidirectional exchange within existing military satellite networks, inadvertently, enabling the transmission and receiving of medical data via the Ministry of Defense (MoD) communication Network and other secure networks. Crucially important is that it shall provide Situational Awareness (SA) and understanding using a Common Operational Picture (COP) for command systems. The authors highlight how within this research and training initiative, intelligence from the area of operations shall integrate medical devices to provide casualty heat maps, Command and Control and medical evacuation (MERT).\n\nAlkhathami et al. (2023) counsel that there is a lack of comprehensive research and evidence specifically tailored to the military context in Saudi Arabia. The authors advocate forward planning and a collaborative and cohesive response to these opportunities to further advance the achievements of the nation. Mottershead and Alonaizi (2022b) evidence attempts to progress healthcare treatments and therapeutic alliances to empower new health and well-being strategies within the region. The recent conference focusing on a Multinational Medical Response themed on Emergency Disaster Management, Humanitarian Assistance & Relief Operations, Major General Yasser Mandourah, General Director of Armed Forces Medical Services (first author) has sought to combat against a regression in military medicine readiness that occurs between periods of active service. This pattern, referred to as Walkers Dip (2018) results in a diminished ability to respond. MODMMS has therefore shown great insight by creating a strategy to safeguard the lives of young service personnel by maintaining the effectiveness of not only the Saudi but also all participating nations military medical services. This ability resonates with the nation’s executive leadership, acknowledging the valued insight from colleagues such as Alkhathami et al. (2023) and celebrates the nation’s proud ability to listen and respond to the ever-present need for the continuation of knowledge embraced within the solidarity of comradeship.\n\nIn conclusion, this article celebrates the progress made in investing in military medical research and training as vital components of the readiness and effectiveness of Saudi military medical services. This agenda promises to enhance care for military personnel, and foster improved training, research, and development. The inherent need to innovate, woven into the fabric of the region’s people, has always necessitated resourcefulness. This empowering capability has been a cornerstone of prosperity and identity for the Kingdom of Saudi Arabia and its people. Finally, the authors advocate for the mobilization towards an agenda that populates research designed to meet the contextualized needs of the military research landscape, creating a rallying call to meet and exceed the ambitions set forth by the Kingdom of Saudi Arabia’s Vision 2030.\n\n\nAuthor contributions\n\nYM and RM conceived the article. YM and RM prepared the first draft of the manuscript. All authors were involved in the revision of the draft manuscript and have agreed the content.",
"appendix": "References\n\nAlkhathami MG, Al Naam YA, Al Zahrani EM: Advancing military medical research and training in the Saudi Armed Forces: a call to action. BMJ Mil Health. 2023 Nov 3; e002528. Epub ahead of print. PubMed Abstract | Publisher Full Text\n\nMottershead R, Alonaizi N: A narrative inquiry into the resettlement of armed forces personnel in the Arabian Gulf: a model for successful transition and positive mental well-being [version 2; peer review: 2 approved]. F1000Res. 2022a; 10: 1290. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMottershead R, Alonaizi N: Empowering social prescribing and peer support: A proposed therapeutic alliance against addictions and substance misuse within the middle east. J. Drug Alcohol Res. 2022b; 11. Publisher Full Text\n\nSaudi Vision 2030: Kingdom of Saudi Arabia. KSA: Saudi Vision; 2021. Reference Source\n\nTrending Economics: Saudi Arabia Military Expenditure. 2021. Accessed Feb 2024.\n\nWalker AJ: The ‘Walker dip’. J. R. Nav. Med. Serv. 2018; 104: 173–176. Publisher Full Text"
}
|
[
{
"id": "291516",
"date": "23 Jul 2024",
"name": "Ali Alhaiti",
"expertise": [
"Reviewer Expertise Community Health Nursing"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: The authors should not give any citations in the abstract section.\nAre arguments sufficiently supported by evidence from the indexed literature or by new data and results?\nThe arguments are partly sufficient because there is a paucity of literature supporting this study. Furthermore, the authors have not stated sufficient data that supports this article. I therefore urge the authors to clearly address this issue to make this article scientifically sound.\nThis article is relevant because it addresses the challenges and limitations of the previous article indexed by Alkhathami et al. (2023). Moreover, it led to an international collaboration that laid a foundation via mutual support and camaraderie. The article also yields a positive result by making the Saudi Government invest heavily in military medical research and training. However, the author stated that “it was highlighted how this research and training initiative, intelligence from the area of operations shall integrate medical devices to provide casualty heat maps, Command and Control and medical evacuation”. What did the author highlight?\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Partly\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "12069",
"date": "26 Jul 2024",
"name": "Dr. Richard Mottershead",
"role": "Author Response",
"response": "On behalf of the honourable Dr. Yasser Mandourah and the team, I would like to sincerely thank Dr. Ali Alhaiti as a respected academic within the Kingdom of Saudi Arabia for his review of our article. If I may respond on behalf of the team. A decision was taken to include the reference Alkhathami et al. (2023) within the abstract. This was with the agreement of the editors, as it was believed that this guided the reader to the originating research article and hence, positioned the focus of our article to acknowledgment their relevant and worthwhile views with an evidence trail that progress has and will continue to be maintained within the Kingdom. The article highlights the international conference and strategy to address the research and training needs of Saudi Arabia and disseminates to the reader the focus of the mentioned event. This is what is being highlighted and disseminated with examples such as the integration of medical devices to provide casualty heat maps, Command and Control and medical evacuation strategies. Again, thank you for your valued contribution, time and energy on this review. Dr. Richard Mottershead."
}
]
},
{
"id": "291517",
"date": "24 Jul 2024",
"name": "Neil Kitchiner",
"expertise": [
"Reviewer Expertise Military mental health"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nEmpowering Maneuvers: Boldly Mobilizing Military Medical Research and Training within the Kingdom of Saudi Arabia to Safeguard a Nation and its People.\nThe above paper builds on a previous indexing by (Alkhathami et al. 2023) regarding the Kingdom of Saudi Arabia's plans to transform the military healthcare system amongst other sectors. It calls for action to extend these upgrades to the military healthcare field. They hosted an international partners conference who attended the 3rd International Conference of Military Medicine with delegates from over 20 countries attending.\nThe indexing highlights Saudi Arabia's national project to enhance it's digital health strategy allowing for medical documentation to flow from the combat arena via combat casualty care systems enhancing the command and control and medical evacuation. The indexing also promotes research designed to meet the above's needs as described in the Kingdom of Saudi Arabia's Vision 2023.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "12070",
"date": "26 Jul 2024",
"name": "Dr. Richard Mottershead",
"role": "Author Response",
"response": "On behalf of the honourable Dr. Yasser Mandourah and the team, I would like to sincerely thank Dr. Neil Kitchener of Cardiff University for his review of our article. We are fortunate to have a reviewer of such note, blessed as a respected academic, clinician and with a military background. Thank you for your valuable insight into our response to highlight a rapidly emerging evidence base for the enhancement of the research and development strategy led by the Major General. Your valued opinion is of great merit, especially due to your own contributions to leading the creation of national services to enhance care and safeguard communities within the United Kingdom. On behalf of the team, thank you for your time, energy and consideration of our article. Dr. Richard Mottershead"
}
]
}
] | 1
|
https://f1000research.com/articles/13-613
|
https://f1000research.com/articles/12-1352/v1
|
17 Oct 23
|
{
"type": "Research Article",
"title": "Effect of fluticasone-impregnated throat packs on postoperative sore throat (POST) and hoarseness of voice: A randomized clinical trial",
"authors": [
"Arjun Talapatra",
"Shaji Mathew",
"Sushma Thimmaiah Kanakalakshmi",
"Rama Rani",
"Arjun Talapatra",
"Shaji Mathew",
"Rama Rani"
],
"abstract": "Background: Post-operative sore throat (POST) is one of the most common complaints post-endotracheal intubation and can be decreased through various interventions. This study aimed to determine the effect of fluticasone-impregnated versus saline throat packs on the occurrence and severity of POST and voice hoarseness. Methods: This prospective, randomized, double-blinded trial was conducted on patients undergoing nasosinus surgeries at Kasturba Medical College and Hospital. Patients were randomized to groups based on a computer-generated table of random numbers post-intubation after placing a definite length of oropharyngeal packs into group F (fluticasone) who received four puffs of fluticasone furoate-soaked throat packs and group C (control) wherein normal saline-soaked throat packs were used. Determining the incidence of POST and voice hoarseness was the primary outcome; severity of POST and voice hoarseness, patient satisfaction scores at 24 hours post-surgery and adverse events were secondary outcomes. Results: Overall, 86 patients were randomized and 43 patients were included in each group. Incidence of POST (%) and voice hoarseness (%) were 55.8, 55.6, 55.8, 53.4 and 30.2, 28, 28, 28 in group C. Incidence of POST (%) and voice hoarseness (%) were 37.2, 37.2, 37.2, 34.8 and 14, 14, 14,14 in group F at 1, 2, 6 and 24 hours, respectively, however, the p values were not found to be significant at any time interval. There was no significant difference in terms of severity of POST and voice hoarseness, patient satisfaction scores between the groups and there were no reported adverse events. Conclusions: In patients undergoing nasosinus surgery under general anesthesia with endotracheal intubation, fluticasone furoate-impregnated throat packs failed to show any significant reduction in the incidence and severity of POST as well as hoarseness of voice, and even though it was not statistically significant, the fluticasone impregnated group had higher patient satisfaction scores. Registration: CTRI (CTRI/2020/09/027946; 22/09/2020).",
"keywords": [
"Endotracheal intubation",
"Fluticasone furoate",
"Hoarseness of voice",
"Nasosinus surgeries",
"Postoperative sore throat"
],
"content": "Introduction\n\nTracheal intubation is mostly performed under general anesthesia to secure the airway and is usually associated with variable degrees of trauma. Postoperative sore throat (POST), which ranges from 12.1% to 70%, is one of the commonest consequences of intubation, while hoarseness of voice varies from 4–43%.1–3 The eighth worst possible post-anesthesia effect is POST, which imparts a strongly negative influence on the overall experience of surgery and stay in the hospital postoperatively.4 POST is caused by a number of different factors, including vocal cord damage, congestive blood loss, and damage to the epithelium and mucosal cells caused by airway secretion.5 In recent years, it has been reported that the shape of tracheal tubes, the size of the cuffs, the endotracheal intubation technique, the cuff pressure, and the use of inhalation anesthesia as contributing factors to POST.6–11\n\nMany surgical subspecialties use throat packs for various reasons. During surgery, they gather blood, secretions, and bone and cartilage fragments. It is asserted that doing so will lessen their inhalation and swallowing after surgery, which will lessen the likelihood of postoperative complications.12 Even though there are several advantages of inserting throat packs there are certain drawbacks and POST is major among them.13\n\nTo reduce the frequency of POST, many interventions can be used, including the use of compact tracheal tubes,14 using video laryngoscopy during intubation,15 limiting endotracheal cuff pressure,16 using steroids during surgery,17–19 topically applying non-steroidal anti-inflammatory drugs (NSAIDs),20 or using different gargles (magnesium and ketamine) during surgery.21\n\nThe topical administration of nonsteroidal anti-inflammatory drugs, lidocaine, steroids, N-methyl-d-aspartate receptor antagonists, and Glycyrrhiza have all been used to prevent POST through various mechanisms of action, according to systematic reviews.22 However, a thorough search of the literature showed no evidence of studies involving the use of throat packs soaked with steroid sprays.23 Our study drug, fluticasone furoate is typically available as a nasal spray and studies have not shown any adverse effects associated with the application of this spray. Therefore, the specific objectives of our study was to determine the effect of fluticasone-impregnated throat packs versus saline throat packs on the incidence and severity of POST and hoarseness of voice as well as to assess patient satisfaction at 24 hours in the postoperative period and any adverse events.\n\n\nMethods\n\nThis clinical trial received approval from the Institutional Ethics Committee (Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee (IEC no: 714/2019, dated 18/09/2019) and was registered with the Clinical Trials Registry - India (CTRI; Registration no: CTRI/2020/09/027946; 22/09/2020). Patients provided written informed consent.\n\nBetween September 2020 and July 2021, patients scheduled for nasosinus surgeries under general anesthesia with endotracheal intubation at Kasturba Medical College and Hospital participated in this prospective, 1:1 randomized, double-blinded clinical trial. After receiving approval from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee and registering with the CTRI, 86 patients were enrolled using the inclusion and exclusion criteria after providing written informed consent without any deviation from the original trial protocol and the trial was conducted according to the principles expressed in the Declaration of Helsinki. This study adheres to the CONSORT guidelines, and the proforma, model consent form and protocol can be found as Extended data.39\n\nParticipants classified as I or II according to the American Society of Anaesthesiologists (ASA) physical status classification, patients aged 18–60 years of both sexes were included in the study. Whereas those with a pre-existing sore throat and/or hoarseness of voice, anticipated difficult airway, already on steroids, requiring more than two attempts at endotracheal intubation and trauma during intubation were excluded.\n\nSimple randomization with a 1:1 allocation ratio was carried out using an online randomization service. After patients had finished all baseline assessments and observer one had been blinded, sequentially numbered, opaque, and sealed envelopes were opened to reveal the allocation sequence.\n\nPatient preparation: On the morning of operation, all patients were given tab ranitidine 150 mg and tab metoclopramide 10 mg. Nil per oral orders of 6 hours for solids and 2 hours for clear fluids was advised. The patient was identified on the day of surgery, fasting status was confirmed and they were shifted to the operating room. The monitors included a 5-electrode ECG, a non-invasive blood pressure monitor, and a pulse oximeter before induction of anaesthesia. Baseline blood pressure, heart rate and peripheral oxygen saturation were noted. The intravenous line was secured with a suitable gauge intravenous catheter under aseptic precautions, and the Ringer’s lactate infusion was started.\n\nAll the patients were pre-oxygenated for 3 minutes with 100% oxygen before being induced with intravenous 2 μg/kg fentanyl, induction with 2-3 mg/kg propofol, and neuromuscular blockade (NMB) with 0.1 mg/kg vecuronium. When the train-of-four count was zero, the patient was intubated under direct laryngoscopy (7 mm tube for females and 8 mm tube for males), which was inflated with air to a pressure of 25 mmHg. The demographic characteristics in terms of age, sex, BMI, smoking history and the mean duration of surgery were analyzed.\n\nObserver one performed a preoperative evaluation and obtained informed consent. He was blinded to the group the patient was allotted. Additionally, he evaluated the patient after surgery and recorded the occurrence and severity of POST, voice hoarseness, and patient satisfaction score based on a predetermined score. Observer two performed the intubation and intervention according to the group allotted. Based on the group allocated, the patient received the throat pack soaked with either four puffs (400 mcg) of fluticasone furoate spray for group F and normal saline for group C. With the aid of Magill’s forceps and direct laryngoscopy, packs with standard dimensions of 120 cm × 7.5 cm were inserted. The use of steroids was avoided intraoperatively. Anesthesia was maintained with isoflurane, 40% oxygen and 60% air. Cuff pressure was kept below 25 cm H2O throughout the operation. In the end, the anesthetic agents were tapered and stopped, and 0.05 mg/kg of neostigmine was used to counter residual NMB. None of the patients received glycopyrrolate preoperatively or during the procedure. The throat pack was removed under direct laryngoscopy once the surgery was completed after gentle oral suctioning. Once the extubation criteria were satisfied, the patient was extubated and moved to the postoperative recovery room.\n\n\n\n• Age, sex, BMI, smoking history and the mean duration of surgery were documented.\n\n• Post-operative sore throat at 1 hour, 2 hours, 6 hours and 24 hours using a 4-point scale.\n\n• Hoarseness of voice at 1 hour, 6 hours and 24 hours using a 4-point scale.\n\n• Patient satisfaction score at 24 hours in the postoperative period.\n\nObserver 1 interviewed patients at 1, 2, 6, and 24 hours to assess the incidence and severity of postoperative sore throat and hoarseness of voice, patient satisfaction level as well as any adverse events.\n\nThe post-operative sore throat severity18 was graded as follows: i) Grade 0, no sore throat at any time since the operation; ii) Grade 1, no pain, only discomfort or itchy sensation in the throat; iii) Grade 2, pain on swallowing or attempt at swallowing; and iv) Grade 3, pain at rest.\n\nThe severity of the hoarseness of voice19 was graded as follows: i) Grade 0, no evidence of hoarseness of voice at any time since the operation; ii) Grade 1, no evidence of hoarseness at the time of the interview; iii) Grade 2, hoarseness at the time of interview noted by the patient only; and iv) Grade 3, hoarseness that is easily noted by the assessor at the time of the interview.\n\nPatient satisfaction score was graded as follows: i) Score 0, poor; ii) Score 1, fair; iii) Score 2, good; and iv) Score 3, excellent.\n\nThe primary outcome analyzed was the incidence of POST and post-operative voice hoarseness at 1, 2, 6 and 24 hours in both group C and group F. The secondary outcomes analyzed were severity of POST and voice hoarseness at 1, 2, 6 and 24 hours in both the groups including patient satisfaction scores at 24 hours post-surgery and any adverse events.\n\nObserver one was the principal investigator who did the preoperative evaluation, after checking suitability for inclusion criteria in the study and obtaining written informed consent. He was blinded to the group the patient was allotted. He explained to the patient about the study and assessed the patient postoperatively on their grade of postoperative sore throat, hoarseness of voice and patient satisfaction score according to a pre-existing scoring scale.\n\nObserver two was the Consultant anaesthesiologist, who performed the laryngoscopy and intubation and performed the intervention according to the group allotted.\n\nA pilot study with 10 patients in each group revealed that the control group had a 60% incidence of POST and the experimental group had a 40% incidence, which was used to determine the sample size. We required 96 patients in each group with a 20% difference between the two groups, assuming 85% power and a 5% level of significance. However, given the ongoing COVID-19 pandemic, due to a drastic reduction in the number of elective nasosinus surgeries in our institute, we were able to conduct our trial only in 86 patients (43 per group), despite extending our study period for three more months. For continuous variables, the data were presented as mean, and for categorical variables, as a percentage of frequency. To analyze significant differences between dichotomous variables, the chi-squared test was used. The term “p-value <0.05” denoted a statistically significant result. IBM SPSS Statistics (RRID:SCR_016479) 20.0 for Windows (SPSS Inc., Chicago, IL, US), a statistical software program, was used to conduct the statistical analysis.\n\n\nResults\n\nA total of 106 ASA I–II patients were screened in our study of which only 86 patients were included in our study. Of the 20 excluded, 11 patients required repeated attempts for intubation while nine required airway adjuncts (Figure 1).\n\nGroup C, Control group; Group F, Fluticasone group.\n\nThere were 43 patients in each group and their demographic characteristics were comparable with no significant difference in terms of age, sex, and smoking history. The majority of patients in either group had ASA physical status II. The mean duration of surgery among both groups was also similar (Table 1).\n\nBetween September 2020 and July 2021, patients scheduled for nasosinus surgeries under general anesthesia with endotracheal intubation at Kasturba Medical College and Hospital participated in this prospective, 1:1 randomized, double-blinded clinical trial.\n\nIncidences of postoperative sore throat were 55.8, 55.6, 55.8 and 53.4% in group C at 1, 2, 6 and 24 hours and 37.2, 37.2, 37.2 and 34.8% in group F at 1, 2, 6 and 24 hours, respectively (Table 2, Figure 2). Incidences of postoperative hoarseness of voice were found to be 30.2, 28.0, 28.0 and 28.0% in group C at 1, 2, 6 and 24 hours and 14.0, 14.0, 14.0 and 14.0% in the group F at 1, 2, 6 and 24 hours, respectively (Table 2, Figure 3). Although there was a lower incidence of POST and hoarseness of voice in the fluticasone group at 1, 2, 6 and 24 hours, the p values were not found to be significant at any time interval.\n\nPOST, postoperative sore throat.\n\nAccording to the criteria outlined in the methodology, the degree of POST and hoarseness of voice were graded.\n\nGrade 0 sore throats were present in 20 patients in group F (46.5%) and 28 patients in group C (65.1%). Grade 1 sore throats were present in 14 patients in group C (32.5%), 10 patients in group F (23.2%), and seven patients in group C (16.2%) and five patients in group F (11.6%). At 24 hours after surgery, only two patients in group C (4.6%) and none of the patients in group F had grade 3 sore throats. Nevertheless, there was no statistically significant difference between the groups (Table 3).\n\nA total of 23 patients in group C (53.4%) and 18 patients in group F (41.8%) both experienced grade 0 hoarseness of the voice. Grade 1 was present in 10 patients in group C (23.2%) and nine patients in group F (20.9%). Grade 2 hoarseness of voice affected 14 patients in group C (32.5%) and 10 patients in group F (23.2%). At 24 hours after surgery, there was one patient in group C (2.3%) and one patient in group F (2.3%) who both had grade 3 hoarseness of voice. The difference between the groups was present, but it was not statistically significant (Table 3).\n\nMost of the patients in both groups had excellent patient satisfaction scores, however, patients in group F had higher satisfaction scores 24 hours postoperatively but were not statistically significant (Table 4).\n\nNeither group experienced any adverse effects.\n\n\nDiscussion\n\nEndotracheal intubation is the most definitive way of securing the airway. Many anesthesiologists consider POST, a frequent anesthetic complication, to be a minor complication. However, for some patients, it might be their initial complaint as soon as they regain consciousness, hence reduction of POST enhances postoperative patient comfort, satisfaction and overall hospital stay.24\n\nThroat packs are used in oronasal procedures mainly to prevent intraoperative aspiration of blood into the respiratory and digestive tract. It is common knowledge that using pharyngeal packs makes recovery from surgery more painful and uncomfortable. POST brought on by oropharyngeal packs is unclear. It is postulated that the hard, abrasive cotton fibers of the pack can cause dryness of the surrounding tissues as well as the instrumentation per se can cause local inflammation eventually leading to POST and hoarseness of voice.25 Even though various pharmacological modalities of attenuating POST have been studied in the past14–21 there is no extensive literature documenting the use of steroid-impregnated throat packs. Since steroids have an anti-inflammatory effect, we analyzed their effect in mitigating POST and hoarseness of voice.\n\nIn prior studies, patient factors predicting POST included young age, being female and having a smoking history.26,27 Lautenbacher et al.,28 and Petrini et al.,29 revealed that older patients when compared to the younger age group had a lesser response to pain stimulus as ageing reduces pain sensitivity and intensity, thus suggesting young age as a predictor of POST. However, in our study, we found no difference among the groups as the majority of the patients in both groups were young. According to Feine et al.,30 women are more sensitive to the intensity of the pain and men typically have higher pain tolerance thresholds28 suggesting that female patients tend to have a higher incidence of POST. Similar to the study by Jaensson et al.,31 who found no appreciable difference in POST incidence between men and women, there is no effect of sex on POST and hoarseness of voice in this study. Smoking is a significant predictor because it is known to cause airway inflammation on its own,32,33 which contributes to POST, however, due to the small sample size in this study, we were unable to detect any influence on POST, which is similar to the study by Lee et al.34\n\nIn the study by Higgins et al.,2 he found that the incidence of POST was higher in those with ASA physical status III when compared to those with ASA I/II (p≤0.05), however in our study all the patients had ASA status of I/II, thus no difference could be recorded. Longer surgery times have been shown in earlier studies35,36 to affect the occurrence of POST, with factors including surgical manipulation of the airway and surrounding tissue, repeated suctioning, high anesthetic gas flow rates, and lack of airway humidity as contributors. However, in our study, there was no such difference because all of the patients were posted for nasosinus surgery and the surgical times in the two groups were comparable.\n\nThe overall incidence of POST and hoarseness of voice in our study was similar to the study done in 2017 on Korean patients by Lee et al.,34 wherein 207 patients were analyzed, among whom 119 patients (57.5%) developed POST and 80 patients (38.6%) developed hoarseness of voice. However, many prior studies have shown that the incidence of POST may be up to 70% and that of hoarseness is reported to range from 4–43%.1–4 Even though the incidence of POST and hoarseness of voice was lower in the fluticasone group than in the control group in this study, there was never a postoperative difference that was statistically significant. This study is comparable to one by Park SY et al.,37 which compared the incidence of POST in patients with tracheal tubes impregnated with triamcinolone acetonide (n=72) and chlorhexidine (n=72) during intubation. His research demonstrated that when compared to the chlorhexidine group (71.8%; 51/72) the incidence of POST was significantly lower in the steroid-impregnated group (19.4%; 14/72) (p<0.001).\n\nThe overall severity of POST as well as hoarseness of voice was lower fluticasone group but was not statistically significant. These results are similar to the study by Park SY et al.,37 wherein the severity of POST was analyzed at 1, 6 and 24 hours and found that among 72 patients in the steroid-soaked throat pack group majority (68/72) had grade 0 severity at 1 hour and 24 hours and very few (10/72) had grade 1 severity of POST, which is similar to our study, however, their study revealed significant difference (p<0.001), which is unlike our study and probably can be explained by the small sample size in each group.\n\nThe majority of patients in this study reported positive experiences with fluticasone-impregnated throat packs when compared to the placebo group, but the findings were not statistically significant. The analysis of POST in 140 patients who needed intubation by Macintosh laryngoscope versus GlideScope in the study by Aqil M et al.,38 also included patient satisfaction scores at 24 hours following surgery, which was similar to our study.\n\nThis was a single center study with a relatively small sample size. Our study included only nasosinus surgeries and with respect to the endotracheal tube, the number of attempts, time taken for insertion and cuff pressure were not analyzed in this study.\n\nRandomized controlled trials (RCTs) provide the highest level of evidence. In this study we utilised the anti-inflammatory property of fluticasone furoate on reducing POST, which is one of the most disturbing after effects post-endotracheal intubation. Even though our study showed lesser incidence and severity of POST as well as hoarseness of voice it was not statistically significant, which might be due to small sample size in each group. Thus, after proving with an adequate sample size, our intervention could be applicable and would be beneficial in reducing the incidence of POST in patients undergoing endotracheal intubation.\n\n\nConclusions\n\nThe frequency and severity of POST and hoarseness of voice in patients undergoing nasosinus surgery under general anesthesia with endotracheal intubation were not significantly reduced by fluticasone furoate-impregnated throat packs. It gave a higher satisfaction score after 24 hours even though it was statistically insignificant.",
"appendix": "Data availability\n\nDue to the fact that open posting of data on a repository was not included in the study information sheet at the time the study was done, data access will be granted once users have consented to the data sharing agreement and provided written plans and justification for what is proposed with the data. Data access may be obtained by submitting a request to the corresponding author.\n\nFigshare: Protocol, https://doi.org/10.6084/m9.figshare.23850630.v4. 39\n\nThis project contains the following extended data:\n\n- CONSORT Checklist.doc\n\n- Proforma.docx\n\n- Informed consent.docx\n\n- Protocol.doc\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nTanaka Y, Nakayama T, Nishimori M, et al.: Lidocaine for preventing postoperative sore throat. Cochrane Database Syst. Rev. 2015; 7. Publisher Full Text\n\nHiggins PP, Chung F, Mezei G: Postoperative sore throat after ambulatory surgery. Br. J. Anaesth. 2002 Apr 1; 88(4): 582–584. Publisher Full Text\n\nSharma S, Bhardwaj V, Sharma S, et al.: Dexamethasone to decrease post-anesthesia sore throat (POST) and hoarseness-which is the most effective route: intravenous, topical, or nebulization? A prospective randomized trial. Ain-Shams J. Anesthes. 2021 Dec; 13(1): 1–7. Publisher Full Text\n\nEl-Boghdadly K, Bailey CR, Wiles MD: Postoperative sore throat: a systematic review. Anaesthesia. 2016 Jun; 71(6): 706–717. Publisher Full Text\n\nWinkel E, Knudsen J: Effect on the incidence of postoperative sore throat of 1 percent cinchocaine jelly for endotracheal intubation. Anesth. Analg. 1971 Jan 1; 50(1): 92–94. PubMed Abstract | Publisher Full Text\n\nSaeki H, Morimoto Y, Yamashita A, et al.: Postoperative sore throat and intracuff pressure: comparison among endotracheal intubation, laryngeal mask airway and cuffed oropharyngeal airway. Masui. 1999 Dec 1; 48(12): 1328–1331. PubMed Abstract\n\nLee J, Park HP, Jeong MH, et al.: Combined intraoperative paracetamol and preoperative dexamethasone reduces postoperative sore throat: a prospective randomized study. J. Anesth. 2017 Dec; 31: 869–877. PubMed Abstract | Publisher Full Text\n\nHu B, Bao R, Wang X, et al.: The size of endotracheal tube and sore throat after surgery: a systematic review and meta-analysis. PLoS One. 2013 Oct 4; 8(10): e74467. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChang JE, Kim H, Han SH, et al.: Effect of endotracheal tube cuff shape on postoperative sore throat after endotracheal intubation. Anesth. Analg. 2017 Oct 1; 125(4): 1240–1245. PubMed Abstract | Publisher Full Text\n\nSato K, Tanaka M, Nishikawa T: Changes in intracuff pressure of endotracheal tubes permeable or resistant to nitrous oxide and incidence of postoperative sore throat. Masui. 2004 Jul 1; 53(7): 767–771. PubMed Abstract\n\nJoe HB, Kim DH, Chae YJ, et al.: The effect of cuff pressure on postoperative sore throat after Cobra perilaryngeal airway. J. Anesth. 2012 Apr; 26: 225–229. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFennessy BG, Mannion S, Kinsella JB, et al.: The benefits of hypopharyngeal packing in nasal surgery: a pilot study. Ir. J. Med. Sci. 2011 Mar; 180: 181–183. Publisher Full Text\n\nKarbasforushan A, Hemmatpoor B, Makhsosi BR, et al.: The effect of pharyngeal packing during nasal surgery on the incidence of post-operative nausea, vomiting, and sore throat. Iran J. Otorhinolaryngol. 2014 Oct; 26(77): 219–223. PubMed Abstract\n\nZhang W, Zhao G, Li L, et al.: Prophylactic administration of corticosteroids for preventing postoperative complications related to tracheal intubation: a systematic review and meta-analysis of 18 randomized controlled trials. Clin. Drug Investig. 2016 Apr; 36: 255–265. Publisher Full Text\n\nNajafi A, Imani F, Makarem J, et al.: Postoperative sore throat after laryngoscopy with macintosh or glide scope video laryngoscope blade in normal airway patients. Anesthesiol. Pain Med. 2014 Feb; 3(1). Publisher Full Text\n\nAnsari L, Bohluli B, Mahaseni H, et al.: The effect of endotracheal tube cuff pressure control on postextubation throat pain in orthognathic surgeries: a randomized double-blind controlled clinical trial. Br. J. Oral Maxillofac. Surg. 2014 Feb 1; 52(2): 140–143. PubMed Abstract | Publisher Full Text\n\nSun L, Guo R, Sun L: Dexamethasone for preventing postoperative sore throat: a meta-analysis of randomized controlled trials. Ir. J. Med. Sci. 2014 Dec; 183: 593–600. PubMed Abstract | Publisher Full Text\n\nCanbay O, Celebi N, Sahin A, et al.: Ketamine gargle for attenuating postoperative sore throat. Br. J. Anaesth. 2008 Apr 1; 100(4): 490–493. PubMed Abstract | Publisher Full Text\n\nKadar MA: Assessment of the efficacy of dexamethasone, lignocaine or placebo in the prevention of post intubation sore throat. Int. J. Biomed. Res. 2015; 6(07): 493–503. Publisher Full Text\n\nChang JE, Min SW, Kim CS, et al.: The effect of benzydamine hydrochloride prophylaxis on postoperative sore throat and hoarseness after tracheal intubation using a double-lumen endobronchial tube: a randomized controlled trial. Can. J. Anaesth. 2015 Oct; 62: 1097–1103. PubMed Abstract | Publisher Full Text\n\nTeymourian H, Mohajerani SA, Farahbod A: Magnesium and ketamine gargle and postoperative sore throat. Anesth. Pain Med. 2015 Jun; 5(3): e22367. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang G, Qi Y, Wu L, et al.: Comparative efficacy of 6 topical pharmacological agents for preventive interventions of postoperative sore throat after tracheal intubation: A systematic review and network meta-analysis. Anesth. Analg. 2021 Jul; 133(1): 58–67. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThompson MJ, Hayward G, Heneghan CJ, et al.: Corticosteroids for sore throat. Cochrane Database Syst. Rev. 2010; 1. Publisher Full Text\n\nSmarius BJ, Guillaume CH, Jonker G, et al.: The use of throat packs in pediatric cleft lip/palate surgery: a retrospective study. Clin. Oral Investig. 2018 Dec; 22: 3053–3059. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBajwa SJ: Prevention of aspiration of blood with a unique pharyngeal packing method. Anesth. Essays Res. 2012 Jul; 6(2): 251–252. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMencke T, Echternach M, Kleinschmidt S, et al.: Laryngeal morbidity and quality of tracheal intubation: a randomized controlled trial. The Journal of the American Society of Anesthesiologists. 2003 May 1; 98(5): 1049–1056. Publisher Full Text\n\nBiro P, Seifert B, Pasch T: Complaints of sore throat after tracheal intubation: a prospective evaluation. Eur. J. Anaesthesiol. 2005 Apr; 22(4): 307–311. Publisher Full Text\n\nLautenbacher S, Peters JH, Heesen M, et al.: Age changes in pain perception: a systematic-review and meta-analysis of age effects on pain and tolerance thresholds. Neurosci. Biobehav. Rev. 2017 Apr 1; 75: 104–113. PubMed Abstract | Publisher Full Text\n\nPetrini L, Matthiesen ST, Arendt-Nielsen L: The effect of age and gender on pressure pain thresholds and suprathreshold stimuli. Perception. 2015 May; 44(5): 587–596. PubMed Abstract | Publisher Full Text\n\nFeine JS, Bushnell MC, Miron D, et al.: Sex differences in the perception of noxious heat stimuli. Pain. 1991 Mar 1; 44(3): 255–262. Publisher Full Text\n\nJaensson M, Gupta A, Nilsson U: Gender differences in sore throat and hoarseness following endotracheal tube or laryngeal mask airway: a prospective study. BMC Anesthesiol. 2014 Dec; 14(1): 1–8. Publisher Full Text\n\nJayes L, Haslam PL, Gratziou CG, et al.: SmokeHaz: systematic reviews and meta-analyses of the effects of smoking on respiratory health. Chest. 2016 Jul 1; 150(1): 164–179. PubMed Abstract | Publisher Full Text\n\nThomson NC: Asthma and smoking-induced airway disease without spirometric COPD. Eur. Respir. J. 2017 May 1; 49(5): 1602061. PubMed Abstract | Publisher Full Text\n\nLee JY, Sim WS, Kim ES, et al.: Incidence and risk factors of postoperative sore throat after endotracheal intubation in Korean patients. J. Int. Med. Res. 2017 Apr; 45(2): 744–752. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPatil BO, Sonavdekar SR, Mathur R: A Relative Study on Laryngeal Mask Airway Lubrication with 0.005% Beclomethasone Cream v/a 2% Lidocaine.\n\nSultan SS, Fahmy NM, Hassan MI, et al.: Soaking oro-pharyngeal pack with triamcinolone acetonide lowers discomfort in functional endoscopic sinus surgeries. Rev. Chil. Anest. 2020; 49: 889–895. Publisher Full Text\n\nPark SY, Lee SJ: Application of triamcinolone acetonide paste to the endotracheal tube reduces postoperative sore throat: a randomized controlled trial. Can. J. Anesth. 2011 May 1; 58(5): 436–442. PubMed Abstract | Publisher Full Text\n\nAqil M, Khan MU, Mansoor S, et al.: Incidence and severity of postoperative sore throat: a randomized comparison of Glidescope with Macintosh laryngoscope. BMC Anesthesiol. 2017 Dec; 17(1): 1–8. Publisher Full Text\n\nKanakalakshmi ST: Protocol. [Dataset]. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "241363",
"date": "07 Feb 2024",
"name": "Ajinkya Pawar",
"expertise": [
"Reviewer Expertise Clinical Trial"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe introduction of the manuscript titled \"Effect of fluticasone-impregnated throat packs on postoperative sore throat (POST) and hoarseness of voice: A randomized clinical trial\" provides a comprehensive overview of the background, rationale, and objectives of the study. Overall, the introduction is well-structured and informative. However, here are some comments on potential flaws or areas for improvement: The introduction mentions the incidence of POST ranging from 12.1% to 70% and hoarseness from 4–43%. However, it would be helpful to provide the sources of these statistics to lend credibility to the claims. This is important for readers to evaluate the reliability and generalizability of the reported incidence rates. The statement that POST is the eighth worst possible post-anesthesia effect is intriguing, but the source or reference for this specific ranking is not provided. While the introduction mentions that throat packs have advantages, it briefly touches on the drawbacks, with POST being a major concern. Expanding on the drawbacks and potential complications associated with throat packs could provide a more balanced view and help readers understand the context for investigating alternative interventions. The introduction discusses various interventions to reduce the frequency of POST, such as compact tracheal tubes, video laryngoscopy, cuff pressure control, steroids, NSAIDs, and different gargles. It might be beneficial to briefly mention the effectiveness or limitations of these interventions. The introduction mentions a thorough search of the literature showing no evidence of studies involving the use of throat packs soaked with steroid sprays. While this highlights the novelty of the study, it would be helpful to elaborate on why this gap exists and why it is essential to address it. The introduction mentions that fluticasone furoate is typically available as a nasal spray with no reported adverse effects. While this information is relevant, it might be helpful to briefly explain why fluticasone furoate is being considered for impregnating throat packs, especially in comparison to other available steroids or anti-inflammatory agents. The specific objectives of the study are outlined at the end of the introduction, but the wording could be refined for clarity. Consider rephrasing to clearly state each objective and its significance in the context of the study.\nDiscussion The section provides a thorough analysis of the study results and offers valuable insights. However, there are a few areas that could be addressed for clarity and completeness: While the discussion emphasizes the significance of reducing POST for postoperative patient comfort, satisfaction, and overall hospital stay, it would be beneficial to delve deeper into the specific impact of POST on patients' experiences. Providing anecdotes or examples could help readers better understand the practical implications of mitigating POST. The discussion briefly mentions the use of steroids for their anti-inflammatory effect in preventing POST. It would be helpful to expand on the rationale behind choosing fluticasone furoate specifically, considering its anti-inflammatory properties and its potential advantages over other steroids. This could strengthen the justification for the study intervention. The discussion compares the results of the current study with findings from previous research, particularly the study by Park SY et al (Ref1). However, it would be beneficial to discuss any differences in study design, patient populations, or interventions that may contribute to variations in results. The limitations section provides essential information about the constraints of the study, such as the single-center design and relatively small sample size. However, there is a mention of not analyzing certain aspects related to endotracheal tubes, such as the number of attempts, time for insertion, and cuff pressure. The discussion touches upon the small sample size as a potential reason for the lack of statistical significance in certain outcomes. It would be beneficial to discuss the implications of the study's limitations on the generalizability of the findings. Additionally, addressing the types of patients or surgeries to which the results may be more applicable could enhance the discussion. Considering the study's findings and limitations, it would be helpful to suggest potential avenues for future research. This could include recommendations for larger multi-center trials, exploring different patient populations, or investigating variations in the intervention protocol. Ensure consistency in reporting findings. For instance, the discussion mentions a lower incidence and severity of POST in the fluticasone group, but then notes that the results were not statistically significant. Clarify whether these observed differences are clinically meaningful even if not statistically significant. Acknowledge the strengths of the study, such as the randomized controlled trial design and the use of a specific intervention that has not been extensively studied before. Recognizing these strengths reinforces the scientific rigor of the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11539",
"date": "21 Jun 2024",
"name": "Sushma Thimmaiah Kanakalakshmi",
"role": "Author Response",
"response": "The introduction of the manuscript titled \"Effect of fluticasone-impregnated throat packs on postoperative sore throat (POST) and hoarseness of voice: A randomized clinical trial\" provides a comprehensive overview of the background, rationale, and objectives of the study. Overall, the introduction is well-structured and informative. However, here are some comments on potential flaws or areas for improvement: Comment The introduction mentions the incidence of POST ranging from 12.1% to 70% and hoarseness from 4–43%. However, it would be helpful to provide the sources of these statistics to lend credibility to the claims. This is important for readers to evaluate the reliability and generalizability of the reported incidence rates. Response Many thanks for your suggestion. We have changed the prevalence of POST and hoarseness of voice and have mentioned them in the revised manuscript. Comment The statement that POST is the eighth worst possible post-anesthesia effect is intriguing, but the source or reference for this specific ranking is not provided. Response Many thanks for your suggestion. We have changed the statement and have mentioned in the revised manuscript. Comment While the introduction mentions that throat packs have advantages, it briefly touches on the drawbacks, with POST being a major concern. Expanding on the drawbacks and potential complications associated with throat packs could provide a more balanced view and help readers understand the context for investigating alternative interventions. Response Many thanks for your suggestion. We have added supporting study and have mentioned them in the revised manuscript. Comment The introduction discusses various interventions to reduce the frequency of POST, such as compact tracheal tubes, video laryngoscopy, cuff pressure control, steroids, NSAIDs, and different gargles. It might be beneficial to briefly mention the effectiveness or limitations of these interventions. Response Many thanks for your suggestion. We have added supporting studies and have mentioned in the revised manuscript. Comment The introduction mentions a thorough search of the literature showing no evidence of studies involving the use of throat packs soaked with steroid sprays. While this highlights the novelty of the study, it would be helpful to elaborate on why this gap exists and why it is essential to address it. Response Many thanks for your suggestion. We have added the supporting study and have mentioned in the revised manuscript. Comment The introduction mentions that fluticasone furoate is typically available as a nasal spray with no reported adverse effects. While this information is relevant, it might be helpful to briefly explain why fluticasone furoate is being considered for impregnating throat packs, especially compared to other available steroids or anti-inflammatory agents. Response Many thanks for your suggestion. We have added the supporting study and have mentioned it in the revised manuscript. Comment The specific objectives of the study are outlined at the end of the introduction, but the wording could be refined for clarity. Consider rephrasing to clearly state each objective and its significance in the context of the study. Response Many thanks for your suggestion. We have made the necessary changes and have mentioned them in the revised manuscript. Discussion The section provides a thorough analysis of the study results and offers valuable insights. However, there are a few areas that could be addressed for clarity and completeness: Comment While the discussion emphasizes the significance of reducing POST for postoperative patient comfort, satisfaction, and overall hospital stay, it would be beneficial to delve deeper into the specific impact of POST on patients' experiences. Providing anecdotes or examples could help readers better understand the practical implications of mitigating POST. Response Many thanks for your suggestion. We have added the studies and have mentioned them in the revised manuscript. Comment The discussion briefly mentions the use of steroids for their anti-inflammatory effect in preventing POST. It would be helpful to expand on the rationale behind choosing fluticasone furoate specifically, considering its anti-inflammatory properties and its potential advantages over other steroids. This could strengthen the justification for the study intervention. Response Many thanks for your suggestion. We have made the necessary changes and have mentioned them in the revised manuscript. Comment The discussion compares the results of the current study with findings from previous research, particularly the study by Park SY et al (Ref1). However, it would be beneficial to discuss any differences in study design, patient populations, or interventions that may contribute to variations in results. Response Many thanks for your suggestion. We have made the necessary changes and have mentioned them in the revised manuscript. Comment The limitations section provides essential information about the constraints of the study, such as the single-center design and relatively small sample size. However, there is a mention of not analyzing certain aspects related to endotracheal tubes, such as the number of attempts, time for insertion, and cuff pressure. The discussion touches upon the small sample size as a potential reason for the lack of statistical significance in certain outcomes. It would be beneficial to discuss the implications of the study's limitations on the generalizability of the findings. Additionally, addressing the types of patients or surgeries to which the results may be more applicable could enhance the discussion. Response Many thanks for your suggestion. We have made the necessary changes and have mentioned them in the revised manuscript. Comment Considering the study's findings and limitations, it would be helpful to suggest potential avenues for future research. This could include recommendations for larger multi-centre trials, exploring different patient populations, or investigating variations in the intervention protocol. Response Many thanks for your suggestion. We have made the necessary changes and have mentioned them in the revised manuscript Comment Ensure consistency in reporting findings. For instance, the discussion mentions a lower incidence and severity of POST in the fluticasone group, but then notes that the results were not statistically significant. Clarify whether these observed differences are clinically meaningful even if not statistically significant. Response Many thanks for your suggestion. Although the observed differences were clinically meaningful they were not statistically significant as mentioned in our study. Comment Acknowledge the strengths of the study, such as the randomized controlled trial design and the use of a specific intervention that has not been extensively studied before. Recognizing these strengths reinforces the scientific rigor of the research. Response Many thanks for your suggestion. We have made the necessary changes and have mentioned them in the revised manuscript"
}
]
},
{
"id": "217314",
"date": "09 Feb 2024",
"name": "Mathew George",
"expertise": [
"Reviewer Expertise Neuro anaesthesia",
"Paediatric Anaesthesia",
"Intraoperative evoked potential monitoring"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is well designed and executed. The background research is also commendable. If possible it would be better to continue patient enrolment to achieve the calculated sample size of 96 patients per group as it would possibly improve the power of the study and likely bring out a significant difference between the groups as there is a trend towards fluticasone decreasing the incidence of the primary outcome.\nThe paragraph on secondary outcome needs some correction as the number of patients with grade 2 soreness is not mentioned appropriately, or has been missed.\nAltogether the paper is well designed and reasonably well written but is underpowered to reveal the true benefits if any for the treatment being studied.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11315",
"date": "13 Apr 2024",
"name": "Sushma Thimmaiah Kanakalakshmi",
"role": "Author Response",
"response": "Mathew George Comment The study is well designed and executed. The background research is also commendable. If possible it would be better to continue patient enrolment to achieve the calculated sample size of 96 patients per group as it would possibly improve the power of the study and likely bring out a significant difference between the groups as there is a trend towards fluticasone decreasing the incidence of the primary outcome. Response Many thanks for your comments. We are continuing the patient enrollment as suggested so as to improve the power of our study and trying to find any significant differences between the groups. Comment The paragraph on secondary outcome needs some correction as the number of patients with grade 2 soreness is not mentioned appropriately, or has been missed. Response Many thanks for your comments. We have made the necessary changes and highlighted the same. Comment Altogether the paper is well designed and reasonably well written but is underpowered to reveal the true benefits if any for the treatment being studied. Response Many thanks for your comments. We agree with your suggestion and thus are continuing recruiting patients so as to improve the overall number and power of the study."
}
]
},
{
"id": "237023",
"date": "09 Feb 2024",
"name": "Riniki Sarma",
"expertise": [
"Reviewer Expertise AIrway",
"resuscitation",
"Pain management"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis randomized controlled trial takes into account an innovative drug to find the outcome of sore throat and hoarseness of voice postoperatively in patients undergoing endotracheal intubation. Fluticasone is a known treatment method used in rhinosinusitis due to its anti-inflammatory properties. Though not statistically significant, in view of the incidence of POST being lesser with fluticasone group, the findings from this study are encouraging.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11314",
"date": "13 Apr 2024",
"name": "Sushma Thimmaiah Kanakalakshmi",
"role": "Author Response",
"response": "Riniki Sarma This randomized controlled trial takes into account an innovative drug to find the outcome of sore throat and hoarseness of voice postoperatively in patients undergoing endotracheal intubation. Fluticasone is a known treatment method used in rhinosinusitis due to its anti-inflammatory properties. Though not statistically significant, in view of the incidence of POST being lesser with fluticasone group, the findings from this study are encouraging. Response Many thanks for your comments madam. Thank you for your motivating comments."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1352
|
https://f1000research.com/articles/12-1467/v1
|
13 Nov 23
|
{
"type": "Systematic Review",
"title": "Association between nitric oxide and cancer and stroke risk: A meta-analysis",
"authors": [
"Abdul Rohim Tualeka",
"Juliana Jalaludin",
"Janvier Gasana",
"Nor Ashikin Sopian",
"How Ran Chao",
"Mohd Yusmaidie",
"Velu Perumal",
"Suardi Zurimi",
"Pudji Rahmawati",
"Ahsan Ahsan",
"Salsabila Novianti",
"Juliana Jalaludin",
"Janvier Gasana",
"Nor Ashikin Sopian",
"How Ran Chao",
"Mohd Yusmaidie",
"Velu Perumal",
"Suardi Zurimi",
"Pudji Rahmawati",
"Ahsan Ahsan",
"Salsabila Novianti"
],
"abstract": "Background: Numerous case-control studies have been carried out to test the mechanism by which nitric oxide, specifically the polymorphism 894G>T in the eNOS gene, or endothelial nitric oxide synthase, raises the possibility of stroke and cancer. Methods: The aim of this meta-analysis was to describe the correlation between cancer and stroke risk with nitric oxide, by implementing a comprehensive search in various digital databases, including Science Direct, PubMed, and Google Scholar, in the period 2012-2023 to observe the published results of all related studies. Results: The meta-analysis included a total of fifteen case-control studies. These studies involved 3,019 cases and 3,333 controls in total. This study found that the GG versus GT+TT genotype of eNOS 894G>T polymorphism was significantly positively correlated with cancer risk. Additionally, the significance of this association was further attributed to the specific type of polymorphism involved, as well as the risk of stroke in the T versus G model, followed by TT versus GG+GT. Conclusions: The results of the eNOS 894G>T polymorphisms have been correlated with cancer, and in particular, the GT+TT versus GG model yielded an odds ratio (OR of 1.96, a 95% CI of 1.22 to 3.15, and a p-value of 0.0005. Moreover, the mentioned polymorphisms were found to be associated with stroke risk in the T versus G model, which had an OR of 1.20; 95% CI of 1.01 to 1.43 with a p-value of 0.04; and TT versus GG+GT with an OR of 0.09; 95% CI of 0.03 to 0.30 with a p-value of 0.0001.",
"keywords": [
"Nitric oxide",
"eNOS 894G>T",
"polymorphism",
"cancer",
"stroke",
"meta-analysis",
"safe work"
],
"content": "Introduction\n\nNitric oxide, or NO, is a chemical compound found in organisms such as mammals. For example, in humans, NO acts as a signaling molecule in various physiological and pathological processes in the body and simultaneously, becomes a diatomic free radical, produced by the enzymatic activity of NOS itself on the L-Arginine compound, yielding the production of L-citrulline along with NO (Korde Choudhari et al., 2013). The NOS family consists of three members, namely eNOS, nNOS, and finally iNOS (Sachdev, 1999). NO influences the coagulation process, neuronal activity, and cerebral blood flow (Korde Choudhari et al., 2013). NO has the potential to induce cellular inflammation, which can delay the onset of stroke. Additionally, NO can act as a carcinogen, increasing cancer risk.\n\nNO plays a substantial role in cancer’s progression and development. NO promotes cancer progression and metastasis via polyamine synthesis or inhibition of NO-mediated tumor cytotoxicity (Gào and Schöttker, 2017; Gào et al., 2019). The roles and functions of NO have been extensively investigated in numerous types of cancer. The response to hypoxia involves NO, which plays a crucial role in inducing angiogenesis and promoting cancer cell defense, and is attributed to the mutagenic behavior exhibited by NO. When cells are exposed to NO for a considerable duration, it is commonly a result of iNOS being produced during chronic inflammation, which gives it a role in carcinogenesis (Utispan and Koontongkaew, 2020). iNOS is considered to have an impact on the mechanism of carcinogenesis.\n\niNOS plays a multifaceted role in tumor building through its involvement in genetic changes, angiogenesis, proliferation, metastasis, and immunosuppression (Erlandsson et al., 2018). Several studies have proven NO’s influence on both illnesses. NO has been demonstrated to contribute to lung cancer’s progression (Chen et al., 2008). NO can potentially promote the progression of pulmonary carcinoma through a process called protein nitration. NO can also cause head-neck cancer in smokers and people with alcohol use disorders (Patel et al., 2009). The subtype NO, which is iNOS/NOS2, is considered to be correlated with a raised risk of development of prostate cancer (Aaltoma, Lipponen and Kosma, 2001). NO can also result in the onset of breast cancer (Loibl et al., 2002).\n\nNO has a critical part in regulating cerebral circulation and modulating neuronal activity. Microvascular endothelial cells in the brain, also known as the endothelium, are capable of producing and releasing various vasoactive substances, among which NO. The continuous production of NO by the endothelium in basal situations and its reactions to vasoactive stimuli provide knowledge of the complex regulation of cerebral circulation and the maintenance of vascular health in the brain. This dysfunction in NO production and release could be a factor in the progression of stroke. Stroke refers to a clinical condition characterized by unexpected loss of cerebral responsibility as a result of vascular pathology in the brain (Demaerschalk et al., 2016). NO is essential to stroke as an important signaling molecule. The harmful effects of NO derived from iNOS and nNOS primarily stem from the generation of nitrates and free radicals (Zhao et al., 2000). nNOS and iNOS are involved in causing nerve injury during both the beginning and final stages of brain ischemia. Conversely, when eNOS is activated, it has a neuroprotective effect (Chen et al., 2017).\n\nThe NOS isoform responsible for producing NO in the vascular endothelium is known as endothelial NOS (eNOS), which in its isoform is expressed through cells and actively contributes to normal vascular tone in physiological conditions. eNOS has also been extensively investigated in the context of carcinogenesis, particularly its involvement in mediating tumor maintenance (Lim et al., 2008). Furthermore, limited levels of NO produced by eNOS can have a neuroprotective effect on stroke through increased vasodilation and cerebral circulation (Yang et al., 2019). Recently, several single nucleotide polymorphisms have been found in eNOS, among which 894G>T in exon 7.\n\nSeveral case-control studies aimed to check whether the NO correlation with cancer and stroke risk exists, especially its polymorphism eNOS, as well as how these factors may impact the development of cancer and stroke risk. Hence, we conducted a meta-analysis to provide a clearer understanding of the association between NO levels and both cancer risks.\n\n\nMethods\n\nThe research method used was a meta-analysis. Our meta-analysis adhered to the criteria recommended in the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, or PRISMA. To discover relevant primary articles, we performed a comprehensive search of digital databases, including PubMed, Science Direct, and Google Scholar, to identify all relevant studies on the correlation of NO especially eNOS 894>GT, and risk to cancer and stroke. The search period was limited from December 2022 to January 2023. We applied the following keywords: NO or NOS or eNOS or “eNOS 894G>T” AND “polymorphism” AND “cancer risk” AND “stroke risk”. To ensure a comprehensive review of the literature, we conducted a thorough examination of the reference lists included in the recognized literature.\n\nDetermination of inclusion and exclusion criteria followed PICOS (Problem, Intervention, Comparison, Outcome, and Study design). The included studies were carefully examined to ensure their relevance and quality for our study. No national restrictions were imposed, meaning studies from all countries were considered eligible for inclusion. The research that met the eligibility criteria was carefully selected for our analysis: 1) Articles published in the English language that investigated the correlation between NO, especially eNOS 894G>T, and the risk of cancer and stroke; 2) Designed as a case-control study; 3) Articles that provided detailed data on genotype and allele frequencies of eNOS gene polymorphisms, which has sufficient data for the calculation of the odds ratio (OR) and the confidence interval of 95%. Therefore, studies were excluded according to as the following criteria: 1) Qualitative research; 2) No available genotype frequency; 3) Studies without control; 4) Meta-analysis studies; and 5) Animal studies.\n\nThe data in all studies were extracted when sufficient criteria were met. We then used Microsoft Excel to record the year of publication, the last name of the authors, control, and case sample sizes, and the country of the study. The results were then compared after being extracted, and an assessment was carried out along with the resolution of matters that were not appropriate through consensus. We extracted data from the nine articles meeting eligibility criteria for cancer risk and the seven articles for stroke risk association with NO.\n\nA statistical review was implemented using RevMan, Cochrane with version 5.4 to investigate the association between NO and the risk of stroke and cancer. Crude ORs and a CI of 95% were utilized. Pooled ORs were computed for various genetic models of the eNOS G894T gene polymorphism, including GT+TT versus GG, GT versus GG, TT versus GG, T versus G, and G versus T. The eNOS gene encodes for endothelial nitric oxide synthase and has a polymorphism at position 894G>T that can result in GG, GT, or TT variants (Buldreghini et al., 2010). G represents the homozygous wild-type genotype, where the individual has two copies of the G allele. GT represents the heterozygous genotype, where the individual has one copy of the G allele and one copy of the T allele. TT represents the homozygous variant genotype, where the individual has two copies of the T allele (Hinz et al., 2013). The calculation of pooled ORs allowed to perform a Z test with a significance level of p≤0.05.\n\nThe presence of heterogeneity among the studies included was assessed with a Q test score. If there was no significant hterogeneity, i.e., p>0.10, the effect model was applied consistently. Otherwise, when (p<0.10), the random-effects model was utilized. The diversity of the included research was assessed using the I2 test, which quantifies the degree of heterogeneity. If the I2 value was less than 25%, it indicated no heterogeneity. If the I2 value ranged from 25% to 50%, it showed moderate heterogeneity. If the I2 was greater than 50%, it indicated extreme heterogeneity. The 50% p-value indicating the existence of heterogeneity between the studies and a random effects model (Mantel-Haenszel technique) was implemented; conversely, if no significant heterogeneity was found, the fixed effect model is applied. Publication bias assessment was not conducted in this study based on the limited number of articles included in meta-analysis (less than 10).\n\n\nResults\n\nThe flow diagram in Figure 1 summarises the study workflow. A total of 145 articles were identified in the databases. After removing duplicates, a total of 105 studies remained. These studies were further screened by reviewing the titles and abstracts, leading to the exclusion of 56 articles that did not meet the predetermined exclusion and inclusion conditions. After carefully examining the full text of the remaining 43 records, an additional 21 articles were excluded based on both exclusion and inclusion conditions. Ten other studies (da Costa Escobar Piccoli et al., 2012; Jang et al., 2013; Rah et al., 2013; Akhter et al., 2014; Kang et al., 2014; Özçelik et al., 2014; Ben Chaaben et al., 2015; Hung et al., 2019; Lee, 2019; Tsay et al., 2019) were also excluded because of unavailable genotype frequency. Six studies (Hao, Montiel and Huang, 2010; Yao et al., 2013; Guo, 2014; Zhao et al., 2014; Abedinzadeh et al., 2020; Akbar et al., 2022) were not included in the analysis because they were meta-analysis studies.\n\nFinally, 15 qualified articles met the eligibility criteria. Nine case-control studies examined the association between NO and cancer risk, and six case-control studies analyzed the association between NO and stroke risk. Table 1 shows the features of the 15 studies incorporated in our analysis.\n\nA total of 15 studies investigating an association between NO, cancer, and stroke risk, especially, the endothelial nitric oxide G894T polymorphism, were included. In our analysis, we identified a total of 2,013 cases and 2,187 control subjects for assessing cancer risk, as well as 1006 cases and 1146 control subjects for evaluating stroke risk. Table 2 presents the aggregated outcome polymorphism through meta-analysis and its association with cancer risk. The results showed a substantial correlation of cancer risk and the eNOS polymorphism G894T, with comparisons of T versus G yielding an OR of 1.00 (95% CI 0.44 to 2.27, where p=1.00), G versus T, where the OR was 1.00 (95% CI 0.44 to 2.27) with p=1.00, and TT versus GG+GT, where the OR was 0.51 (95% CI is 0.22 to 1.17 and p=0.11), comparison of GT versus GG+TT with an OR of 1.21; 95% CI is 0.77 to 1.91, and p=0.41).\n\na The p value of the Z test was found to be less than 0.05.\n\nTable 3 presents the consolidated findings of the meta-analysis, demonstrating the significant association between the eNOS G894T gene and the risk of stroke where the comparison is T versus G, namely the OR of 1.20 (95% CI=1.01 to 1.43) with a p of 0.04 and the TT versus GG+ GT comparison with an OR of 0.08 (95% CI, namely 0.03 to 0.30), where p is 0.0001. However, a significant correlation was not found in G versus T, where the OR is 0.88 (95% CI, namely 0.74 to 1.05) with p=0.15, and in TT versus GG+GT, where the OR was 0.68 (95% CI was 0.24 to 1.93 and p=0.47) compared with GT versus GG+TT, where the OR was 1.03 (95% CI was 0.40 to 2.64, and p=0.95).\n\na The p value of the Z test was found to be less than 0.05, indicating statistical significance.\n\nHeterogeneity was observed among the studies in every allele and gene, as depicted in Figures 2 and 3 (T versus G, G versus T, GT+TT versus GG, TT versus GG + GT, and GT versus GG + TT). Tables 2 and 3 provide information on the selected model (random or fixed effect) utilized in order to review universal genetic model correlations.\n\n\nDiscussion\n\nNO acts as a crucial part of numerous pathological and psychological processes. NO is extensively implicated in various events related to cancer, including angiogenesis, metastasis, invasion, and apoptosis, which various studies have investigated; results have provided evidence that increased concentrations of NO within cancer cells can effectively suppress tumor angiogenesis and metastasis (Zhao et al., 2014). Conversely, low levels of NO in tumor cells may facilitate tumor growth by reducing NO-induced apoptosis (Heller, 2008). These observations suggest that the effects of NO on cancer development may be strongly dependent on the local NO concentration. NO is the result of three types of NOS isoforms, namely nNOS, eNOS, and iNOS. These enzymes facilitate the conversion of l-arginine to l-citrulline through oxidation (Vanini, Kashfi and Nath, 2015). eNOS is one of the three isoforms of NOS responsible for synthesizing NO in humans. Moreover, this particular isoform is closely linked to angiogenesis, which is associated with NO synthesis in both normal and cancerous cells (Song et al., 2013). A polymorphism was found in the gene encoding eNOS that could alter the production of NO. The G894T variation, also known as the guanine polymorphism to thymine with position 894 and exon 7 (rs1799983), is of particular interest (Akbar et al., 2022).\n\nFrom several studies that were selected for our meta-analysis, the polymorphism was correlated with increased cancer risk in both African, European, and Asian countries. Adibmanesh et al. (2020) stated that the eNOS polymorphism 894G>T showed a significant correlation with colorectal cancer existing in the T allele genotype. Aouf et al. (2019) stated that NOS3 G894T substantially increases the risk of nasopharyngeal carcinoma (NPC) in a population from Tunisia. Furthermore, research conducted by Branković et al. (2013) suggested that NOS3 894G>T genetic polymorphisms were not associated with the risk of prostate tumor in a community in Serbia but may be relevant as prognostic factors for the progression of prostate cancer and patients’ outcome. In the study by Carkic et al. (2020), the results proved that eNOS had a significant impact on oral squamous cell cancer (OSCC) in the Serbian population. Koçer et al. (2020) stated that there was no significant association between the eNOS G894T gene and the risk of lung cancer, where p was greater than 0.05. Research by Su et al. (2018) found no relationship between OSCC and eNOS holotypes in Taiwan. Research by Verim et al. (2013) proved the existence of NOS3 is crucial in increasing the susceptibility to bladder cancer within the Turkish population. Based on the research by Yadav et al. (2019), it is suggested that eNOS 894G > T polymorphisms play a role in influencing the risk of epidermoid cell cancer of the head and neck in the population of North India. Additionally, a study conducted by Yanar et al. (2016) suggests a potential association between the G894T variation of NOS3 and the possibility of laryngeal cancer (LC), possibly due to the involvement of impaired redox homeostasis.\n\nThe role of nitric oxide in cancer can be seen in Figure 4. Based on Figure 4, overproduction of NO can facilitate tumor angiogenesis and metastasis. The NOS isoforms that produce NO in the vascular endothelium are defined as endothelial NOS (eNOS), which is found in the endothelium and carries out a crucial role in regulating vascular tone under normal conditions, which is involved in carcinogenesis and contributes to tumor protection (Lim et al., 2008). One possible explanation for the role of this enzyme in cancer progression is that reduced eNOS enzyme activity may lead to a functional decrease in NO levels within the tumor microenvironment, thereby promoting tumor growth. Recently, single nucleotide polymorphisms (SNPs) have been discovered in the eNOS gene. One of these SNPs, located at exon 7 (894G>T). Regarding to the functional role of NO in regulating angiogenesis in cancer, it is possible that this SNP might be positively correlated with the cancer progress by affecting NO synthesis.\n\nStroke ranks as the second-leading major contributor to mortality and disability in adults, after coronary heart disease (WHO, 2020). Stroke is a multifactorial disease; Epidemiological studies and animal experiments have provided indications of a genetic impact on the development of ischemic stroke (IS) (Hassan and Markus, 2000). Family history also serves as a crucial factor in assessing the potential for stroke. Endothelial NO, synthesized by eNOS, acts as a significant part of regulating blood flow and exhibits anti-proliferation and anti-inflammatory substances. eNOS polymorphism has a significant impact on endothelial dysfunction. The G894T variant of eNOS has been implicated in the development of diverse conditions, consisting of cardiovascular diseases and erectile dysfunction. A compromised NO-dependent vasomotor response is believed to be involved in the pathophysiology of stroke (Kaur, Uppal and Kaur, 2015). Because of its significant role in vascular physiology, genetic mutations may contribute to stroke pathogenesis by altering the expression and enzymatic activity of eNOS.\n\nExternal influences that affect eNOS cause cancer and stroke through chronic stress. eNOS activity is regulated by adrenaline (Seya et al., 2006; Kou and Michel, 2007; Figueroa et al., 2009; Barbieri et al., 2012). Prolonged stress can act as a contributing factor in the onset and advancement of cancer. Stress is also considered a relevant factor in cancer development (Antoni et al., 1978; Chida et al., 2008; Desaive and Ronson, 2008). eNOS plays an essential role in ensuring vascular homeostasis, which includes regulating vascular integrity, blood flow, cell adhesion, angiogenesis, vascular permeability, immune response, and metabolism. Additionally, chronic stress can elevate the production of specific growth factors that enhance blood supply (Heid, 2014). This can accelerate the progression of cancerous tumors. Furthermore, stress can lead to increased cardiac burden, elevated blood pressure, and raised levels of sugar and fat in the bloodstream (Heart and Stroke, 2023). These factors can elevate the risk of cerebral blood clot formation, resulting in increased susceptibility to stroke.\n\nFrom for the studies examined for the present meta-analysis, the presence of the eNOS polymorphism 894G>T has been correlated with a raised susceptibility to stroke in individuals of African, Asian, and European ancestry. Research conducted by Anliaçik et al. (2019) indicates there is no significant relationship between eNOS G894T and ischemia stroke among the Anatolia population. Diakite et al. (2014) stated that a significant relationship has been observed between the eNOS polymorphism 894G>T and ischemia stroke found in dominant, recessive, and additive models in the Moroccan population. Furthermore, research conducted by El Gohary, El Azab, and Kamal El-Din (2017) stated that no significant association was found between the eNOS polymorphism G894T and immediate stroke in Egyptian patients.\n\nResearch conducted by Kaur, Uppal, and Kaur (2015) stated that the G894T variant has been found to be associated with ischemic stroke and may contribute to ischemic stroke susceptibility in the Northern Indian population Kumar et al. (2016) suggest that the G894T eNOS can be a determinant of ischemic stroke, mainly for the large vessel disease (LVD) subtype, in the Northern Indian population. Additionally, a study by Shyu et al. (2017) reported that genotypic polymorphisms of the eNOS G894T polymorphism were given or used as an optimization of the risk of atherosclerotic stroke in Taiwan.\n\nThe role of nitric oxide in stroke can be seen in Figure 5. Based on Figure 5, low levels of NO derived from eNOS may exert neuroprotection in stroke by promoting vasodilatation and increasing cerebral blood flow (Yang et al., 2019). However, at the same time, there is an enhancement in superoxide production due to eNOS uncoupling. This leads to a significant increase in peroxynitrite formation, which damages lipids, proteins, and DNA and can trigger activation of poly adenosine diphosphate rribose (ADP-ribose) polymerase (PARP), which all contribute to neurotoxicity in stroke.\n\nWe conducted a meta-analysis considering the association or correlation of nitric oxide, especially NOS 894G>T polymorphism with stroke, and cancer risk. A total of 15 studies included 3,333 controls and 3,019 cases were selected for this meta-analysis. Overall, eNOS polymorphism 894G>T was found to be significantly correlated with increased cancer risk in the GG versus GT+TT genetic model. However, there were no substantial associations in the genetic model as examined in G versus T, T versus G, GT versus GG+TT, and TT versus GG+GT. The polymorphism has a relationship with a substantially higher risk of stroke in the genetic models of both TT versus GG+GT and T versus G.\n\n\nConclusions\n\nIn conclusion, the recent meta-analysis found that nitric oxide-related polymorphisms with the eNOS 894G>T gene are associated with a substantial risk of cancer in the total population based on the GG vs. GT+TT genetic model and significantly correlated with the manifestation of stroke in the genetic models T vs. G, and TT vs. GG + GT. G vs. T, and GG + GT vs. TT. Considering the conclusion, these results should be reassessed in the coming days through studies with a larger sample population.",
"appendix": "Data availability\n\nAll underlying data are available as part of the article and no additional source data are required.\n\nZenodo: PRISMA Checklist for “Association between nitric oxide and cancer and stroke risk: A meta-analysis”, https://doi.org/10.5281/zenodo.8031323 (Tualeka et al., 2023).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nAaltoma SH, Lipponen PK, Kosma VM: Inducible nitric oxide synthase (iNOS) expression and its prognostic value in prostate cancer. Anticancer Res. 2001; 21(4B): 3101–3106. PubMed Abstract\n\nAbedinzadeh M, Dastgheib SA, Maleki H, et al.: Association of endothelial nitric oxide synthase gene polymorphisms with susceptibility to prostate cancer: A comprehensive systematic review and meta-analysis. Urol. J. 2020; 17(4): 329–337. 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Stroke. 2016; 47: 581–641. PubMed Abstract | Publisher Full Text\n\nDesaive P, Ronson A: Stress spectrum disorders in oncology. Curr. Opin. Oncol. 2008; 20(4): 378–385. Publisher Full Text\n\nDiakite B, Hamzi K, Slassi I, et al.: G894T endothelial nitric oxide synthase polymorphism and ischemic stroke in Morocco. Meta Gene. 2014; 2(1): 349–357. PubMed Abstract | Publisher Full Text | Free Full Text\n\nErlandsson A, Carlsson J, Andersson SO, et al.: High inducible nitric oxide synthase in prostate tumor epithelium is associated with lethal prostate cancer. Scand. J. Urol. 2018; 52(2): 129–133. PubMed Abstract | Publisher Full Text\n\nFigueroa XF, Poblete I, Fernández R, et al.: NO production and eNOS phosphorylation induced by epinephrine through the activation of β-adrenoceptors. Am. J. Physiol. Heart Circ. Physiol. 2009; 297(1): H134–H143. PubMed Abstract | Publisher Full Text\n\nGào X, Schöttker B: Reduction-oxidation pathways involved in cancer development: A systematic review of literature reviews. Oncotarget. 2017; 8(31): 51888–51906. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGào X, Xuan Y, Benner A, et al.: Nitric Oxide Metabolites and Lung Cancer Incidence: A Matched Case-Control Study Nested in the ESTHER Cohort. Oxidative Med. Cell. Longev. 2019; 2019: 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEl Gohary EA, El Azab AA, Kamal El-Din MMM: Study of Relationship between G894T Variant of Endothelial Nitric Oxide Synthase Gene and Acute Ischemic Stroke. Egyptian J. Hosp. Med. 2017; 69(1): 1607–1613. Publisher Full Text\n\nGuo X: Endothelial nitric oxide (eNOS) gene G894T and VNTR polymorphisms are closely associated with the risk of ischemic stroke development for Asians: Meta-analysis of epidemiological studies. Mol. Biol. Rep. 2014; 41(4): 2571–2583. PubMed Abstract | Publisher Full Text\n\nHao Y, Montiel R, Huang Y: Endothelial nitric oxide synthase (eNOS) 894 G>T polymorphism is associated with breast cancer risk: A meta-analysis. Breast Cancer Res. Treat. 2010; 124(3): 809–813. PubMed Abstract | Publisher Full Text\n\nHassan A, Markus HS: Genetics of ischaemic stroke. J. Neurol. Neurosurg. Psychiatry. 2000; 84(12): 1302–1308. Publisher Full Text\n\nHeart&Stroke: Stress basics.2023.\n\nHeid M: How stress affects cancer risk.2014.\n\nHeller A: Apoptosis-inducing high •NO concentrations are not sustained either in nascent or in developed cancers. ChemMedChem. 2008; 3(10): 1493–1499. Publisher Full Text\n\nHinz J, Schöndorf D, Bireta C, et al.: The eNOS 894G/T gene polymorphism and its influence on early and long-term mortality after on-pump cardiac surgery. J. Cardiothorac. Surg. 2013; 8(1): 199. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHung WC, Wu TF, Ng SC, et al.: Involvement of endothelial nitric oxide synthase gene variants in the aggressiveness of uterine cervical cancer. J. Cancer. 2019; 10(12): 2594–2600. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJang MJ, Jeon YJ, Kim JW, et al.: Association of eNOS polymorphisms (-786T>C, 4a4b, 894G>T) with colorectal cancer susceptibility in the Korean population. Gene. 2013; 512(2): 275–281. PubMed Abstract | Publisher Full Text\n\nKang MK, Kim OJ, Jeon YJ, et al.: Interplay between polymorphisms in the endothelial nitric oxide synthase (eNOS) gene and metabolic syndrome in determining the risk of ischemic stroke in Koreans. J. Neurol. Sci. 2014; 344(1–2): 55–59. PubMed Abstract | Publisher Full Text\n\nKaur K, Uppal A, Kaur A: An exonic G894T variant of endothelial nitric oxide synthase gene as a risk factor for ischemic stroke in North Indians. Acta Neurobiol. Exp. 2015; 75(4): 339–350. PubMed Abstract\n\nKoçer C, Benlier N, Balci SO, et al.: The role of endothelial nitric oxide synthase gene polymorphisms in patients with lung cancer. Clin. Respir. J. 2020; 14(10): 948–955. PubMed Abstract | Publisher Full Text\n\nKorde Choudhari S, Chaudhary M, Bagde S, et al.: Nitric oxide and cancer: A review. World J. Surg. Oncol. 2013; 11: 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKou R, Michel T: Epinephrine regulation of the endothelial nitric-oxide synthase: Roles of RAC1 and β3-adrenergic receptors in endothelial no signaling. J. Biol. Chem. 2007; 282(45): 32719–32729. PubMed Abstract | Publisher Full Text\n\nKumar A, Misra S, Kumar P, et al.: Association between Endothelial nitric oxide synthase G894T gene polymorphism and risk of ischemic stroke in North Indian population: A case-control study. Neurol. Res. 2016; 38(7): 575–579. PubMed Abstract | Publisher Full Text\n\nLee P-C: A Case-Control Study and Meta-Analysis of the Association of eNOS rs1799983 SNP with Stroke Risk. Med. Health. 2019; 14(1): 118–134. Publisher Full Text\n\nLim KH, Ancrile BB, Kashatus DF, et al.: Tumour maintenance is mediated by eNOS. Nature. 2008; 452(7187): 646–649. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLoibl S, Von Minckwitz G, Weber S, et al.: Expression of endothelial and inducible nitric oxide synthase in benign and malignant lesions of the breast and measurement of nitric oxide using electron paramagnetic resonance spectroscopy. Cancer. 2002; 95(6): 1191–1198. PubMed Abstract | Publisher Full Text\n\nÖzçelik AT, Can Demirdöʇen B, Demirkaya Ş, et al.: Importance of NOS3 genetic polymorphisms in the risk of development of ischemic stroke in the Turkish population. Genet. Test. Mol. Biomarkers. 2014; 18(12): 797–803. PubMed Abstract | Publisher Full Text\n\nPatel JB, Shah FD, Shukla SN, et al.: Role of nitric oxide and antioxidant enzymes in the pathogenesis of oral cancer. J. Cancer Res. Ther. 2009; 5(4): 247–253. PubMed Abstract | Publisher Full Text\n\nRah H, Jeon YJ, Lee WS, et al.: Association of nitric oxide synthase gene polymorphisms (-786T>C, 4a4b, 894G>T) with primary ovarian insufficiency in Korean women. Maturitas. 2013; 74(2): 160–165. PubMed Abstract | Publisher Full Text\n\nSachdev K: Clinical Pathology and Clinical Bacteriology. J. Clin. Pathol. Bacteriol. 1999; 22(1). Publisher Full Text\n\nSeya Y, Fukuda T, Isobe K, et al.: Effect of norepinephrine on RhoA, MAP kinase, proliferation and VEGF expression in human umbilical vein endothelial cells. Eur. J. Pharmacol. 2006; 553(1–3): 54–60. PubMed Abstract | Publisher Full Text\n\nShyu HY, Chen MH, Hsieh YH, et al.: Association of eNOS and Cav-1 gene polymorphisms with susceptibility risk of large artery atherosclerotic stroke. PLoS One. 2017; 12(3): e0174110–e0174112. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSong Y, Zhao XP, Song K, et al.: Ephrin-A1 Is Up-Regulated by Hypoxia in Cancer Cells and Promotes Angiogenesis of HUVECs through a Coordinated Cross-Talk with eNOS. PLoS One. 2013; 8(9): e74464–e74468. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSu CW, Chien MH, Lin CW, et al.: Associations of genetic variations of the endothelial nitric oxide synthase gene and environmental carcinogens with oral cancer susceptibility and development. Nitric Oxide. 2018; 79(May): 1–7. PubMed Abstract | Publisher Full Text\n\nTsay MD, Hsieh MJ, Wang SS, et al.: Impact of endothelial nitric oxide synthase polymorphisms on urothelial cell carcinoma development. Urol. Oncol. 2019; 37(4): 293.e1–293.e9. PubMed Abstract | Publisher Full Text\n\nTualeka AR, Jalaludin J, Gasana J, et al.: PRISMA Checklist for Article Association between nitric oxide and cancer and stroke risk: A meta-analysis. Zenodo. 2023. Publisher Full Text\n\nUtispan K, Koontongkaew S: High nitric oxide adaptation in isogenic primary and metastatic head and neck cancer cells. Anticancer Res. 2020; 40(5): 2657–2665. Publisher Full Text\n\nVanini F, Kashfi K, Nath N: The dual role of iNOS in cancer. Redox Biol. 2015; 6(August): 334–343. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerim L, Toptaş B, Özkan NE, et al.: Possible relation between the NOS3 gene GLU298ASP polymorphism and bladder cancer in Turkey. Asian Pac. J. Cancer Prev. 2013; 14(2): 665–668. PubMed Abstract | Publisher Full Text\n\nWHO: The top 10 causes of death. World Health Organization; 2020.\n\nYadav SK, Gupta S, Yadav A, et al.: Endothelial nitric oxide synthase gene polymorphisms modulate the risk of squamous cell carcinoma of head and neck in north Indian population. Meta Gene. 2019; 21(October 2018): 100575. Publisher Full Text\n\nYanar K, Çakatay U, Aydin S, et al.: Relation between Endothelial Nitric Oxide Synthase Genotypes and Oxidative Stress Markers in Larynx Cancer. Oxidative Med. Cell. Longev. 2016; 2016: 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang C, Hawkins KE, Doré S, et al.: Neuroinflammatory mechanisms of blood-brain barrier damage in ischemic stroke.2019.\n\nYao YS, Chang WW, Jin YL, et al.: An updated meta-analysis of endothelial nitric oxide synthase gene: Three well-characterized polymorphisms with ischemic stroke. Gene. 2013; 528(2): 84–92. PubMed Abstract | Publisher Full Text\n\nZhao C, Yan W, Zu X, et al.: Association between endothelial nitric oxide synthase 894G>T polymorphism and prostate cancer risk: a meta-analysis of literature studies. Tumor Biol. 2014; 35(12): 11727–11733. PubMed Abstract | Publisher Full Text\n\nZhao X, Haensel C, Araki E, et al.: Gene-dosing effect and persistence of reduction in ischemic brain injury in mice lacking inducible nitric oxide synthase. Brain Res. 2000; 872(1–2): 215–218. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "233428",
"date": "12 Feb 2024",
"name": "Eric Tzyy Jiann Chong",
"expertise": [
"Reviewer Expertise Gene polymorphisms",
"meta-analysis",
"risk association",
"molecular epidemiology",
"medical biotechnology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Tualeka et al. aims to associate the eNOS rs1799983 SNP with the risk of cancer and stroke using a meta-analysis approach. The authors concluded that this SNP is associated with the risk of cancer and stroke in some genetic model comparisons. Overall, the manuscript is poorly written, with many unclear statements and grammatical errors, although it has been reviewed and edited by many authors. There are many concerns that should be addressed by the authors.\nTitle - The current title is not specific enough to reflect the contents of the manuscript. Please include the specific gene and polymorphism in the title.\nAbstract -Why is the objective of the study is written in the Methods instead of the Background? - The Results section is not clear. Among the 3019 cases and 3333 controls, how many are derived from cancer and stroke cases, respectively?\n\n- What is meant by “significantly positively correlated with cancer risk”? Does it mean an increase or decrease in risk? -The conclusion is more like describing the results of this study than a conclusion. Please rephrase.\nIntroduction - The authors mentioned that several SNPs have been identified in the eNOS gene but failed to justify why they focused on the rs179983 SNP. - What is meant by “….especially its polymorphism eNOS, as well as…..”? -What is meant by “…and both cancer risks” in the last sentence of this section?\n\nMethods - What is meant by “The search period was limited from December 2022 to January 2023”? Were only studies published within this period included in the meta-analysis? - The authors did not include some essential keywords in the literature search, such as “rs1799983”, “carcinoma”, and “cerebrovascular disease”, which are frequently used in scientific publications. - Please remove the G vs. T allelic model in the statistical analysis, as it did not yield any meaningful results. The T. vs. G allelic model is sufficient to determine if the recessive T allele is a risk factor for cancer or stroke susceptibility. - The authors mentioned that a publication bias test cannot be performed due to fewer than 10 studies. This is incorrect, as more than or equal to 3 studies are sufficient for a publication bias test. - The quality scoring of the studies is not included in the meta-analysis. - A sensitivity analysis is not included in the meta-analysis.\nResults - It is very confusing to look at the Figure 1 alone. For example, the reports assessed for eligibility are 43, after excluding 21 reports, it should remain at 22. Why are studies included in the meta-analysis only 15? -The caption for Figures 2 and 3 is not clear. What does A-E mean? - Many studies published between the years 2012-2023 are not included in the meta-analysis. A few examples are listed below. This shows that the literature search is not comprehensive, probably due to the keywords used. i) Fadi et al. 2018. World Journal of Neuroscience, 8(1): 98-107. ii) Phneh et al. 2019. Medicine & Health, 14(1): 118-134. iii) Jelel et al. 2020. Biological Research for Nursing, 23(3): 408-17.\nDiscussion - The second, sixth, and seventh paragraphs are restating the findings of previous studies; they are not comparing to the data of this meta-analysis. - The last paragraph should be removed and replaced with a paragraph that states the limitations of this study.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
},
{
"id": "233438",
"date": "16 Feb 2024",
"name": "Katrina Miranda",
"expertise": [
"Reviewer Expertise NO and cancer"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Tualeka and colleagues provides a meta-analysis on the correlation of a polymorphism in the eNOS gene on cancer and stroke. The analysis itself is fine. However, presentation of the complex relationship of NO and cancer or stroke is cursory. References include randomly chosen reviews rather than the original literature. It would be beneficial to include an expert on NO in preparation of a revision. For example, the levels of NO produced by the isoforms is not well presented. The polymorphism is also not described sufficiently. Lately, in Figure 5, if eNOs is uncoupled, where does the NO come from to produce peroxynitrite? In sum, more details are needed in this manuscript.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-1467
|
https://f1000research.com/articles/12-1389/v1
|
20 Oct 23
|
{
"type": "Research Article",
"title": "A stability indicating method development and validation of a rapid and sensitive RP-HPLC method for Nintedanib and its application in quantification of nanostructured lipid carriers",
"authors": [
"Varalakshmi Velagacherla",
"Yogendra Nayak",
"K Vijaya Bhaskar",
"Usha Yogendra Nayak",
"Varalakshmi Velagacherla",
"Yogendra Nayak",
"K Vijaya Bhaskar"
],
"abstract": "Background: Nintedanib (NTB) is a multiple tyrosine kinase inhibitor, been investigated for many disease conditions like idiopathic pulmonary fibrosis (IPF), systemic sclerosis interstitial lung disease (SSc-ILD) and non-small cell lung cancer (NSCLC). NTB is available as oral capsule formulation, but its ability to detect degradants formed through oxidative, photolytic and hydrolytic processes makes it difficult to quantify. In the current work, a novel reversed-phase high-performance liquid chromatography (RP-HPLC) method was developed and validated. Methods: The developed method is simple, precise, reproducible, stable and accurate. The inherent stability of NTB was evaluated using the proposed analytical method approach and force degradation studies were carried out. NTB was separated chromatographically on the Shimadzu C18 column as stationary phase (250 ×4.6 mm, 5 µm) using an isocratic elution method with 0.1% v/v triethyl amine (TEA) in HPLC grade water and acetonitrile (ACN) in the ratio 35:65% v/v. The mobile phase was pumped at a constant flow rate of 1.0 ml/min, and the eluent was detected at 390 nm wavelength. Results: NTB was eluted at 6.77±0.00 min of retention time (tR) with a correlation coefficient of 0.999, the developed method was linear in the concentration range of 0.5 µg/ml to 4.5 µg/ml. The recovery rate was found to be in the range of 99.391±0.468% for 1.5 µg/ml concentration. Six replicate standards were determined to have an % RSD of 0.04. Conclusion: The formulation excipients didn't interfere with the determination of NTB, demonstrating the specificity of the developed method. The proposed approach of the analytical method developed can be used to quantify the amount of NTB present in bulk drugs and pharmaceutical formulations.",
"keywords": [
"Nintedanib",
"RP-HPLC",
"Validation",
"Stress degradation",
"Nanostructured lipid carriers",
"Entrapment efficiency"
],
"content": "Introduction\n\nNintedanib (NTB) is an oral multiple tyrosine kinase inhibitor that competitively inhibits vascular endothelial growth factor, fibroblasts growth factor receptor, and platelet-derived growth factor receptor due to the nature of its ATP-binding pocket property. 1 NTB is used to treat a variety of illnesses, including Idiopathic pulmonary fibrosis (IPF), Systemic sclerosis-associated lung disease, non-small cell lung cancer (NSCLC), several Interstitial Lung Diseases, and COVID-19 linked with IPF. NTB works by preventing the cascaded autophosphorylation of tyrosine kinase receptors.1 NTB has an anti-angiogenic action, making it a potential drug for cancer treatment. It is selectively used in conjunction with docetaxel to treat NSCLC.2 NTB is given at a dose of 120–150 mg and the dosage are once or twice a day. NTB is classified as a class II drug under the biopharmaceutical classification system (BCS). Due to first-pass metabolism by enzymes including CYP3A4 and P-gp inhibition, NTB has an extremely low oral bioavailability of 4.7%. NTB reaches its peak plasma concentration in 2-4 hours with 97.8% protein binding. NTB has a half-life of approximately 9.5 hours when it is given orally.3 With a dose of 150 mg twice daily NTB, uncommon colitis is also seen in certain patients.4\n\nNTB is having very low aqueous solubility of 0.0309 mg/ml with pKa of 7.23 The chemical structure of NTB is represented in Figure 1. A patent is available on NTB quantification by using high sensitivity analytical method through high-performance liquid chromatography (HPLC) mass spectrometry where they have used formic acid, methanol and ammonium salt as mobile phase and silica gel as stationary phase.5 Pasquini et al have reported a quality by design (QbD) based LC-MS method for estimating NTB and its impurities in soft gelatin capsules.6 Several investigators have reported various methods like RP-UPLC,7 LC-MS,8 RP-HPLC in formulation, and determination of NTB and its stress degradation,9 and which help in estimating the NTB. Some of the methods also reported degradation pathways and the degradation nature of NTB in various solvents with time. As per the existing literature search, none of the methods have reported the usage of the lower organic phase, salt-free analysis, less retention time and less flow rate. These are the parameters that we have focused upon to produce a cost-effective and less time-consuming method.9,10 The method is precise, rapid, simple and accurate to estimate NTB as per ICH Q2 (R1) guidelines.8 The developed method is used to quantify NTB in Nanostructured lipid carriers (NLCs) loaded with NTB. NLCs are the modified form of solid lipid nanoparticles. NLCs are the combination of liquid and solid lipids in a particular ratio and are known as hybrid nanocarriers. NLCs possess advantages like less particle size, high drug loading, improved solubility, permeation, increased stability and bioavailability. They also have the property of bypassing first-pass metabolism as the absorption takes through the lymphatic system but not from the stomach.11 Some of the lipids like oleic acid and linolic acid which are used in the formulation of NLCs have properties of inhibiting P-gp protein.12 Thus, this current study deals with the development of the analytical method and its validation along with degradation studies and the application of the developed analytical method for estimating the NTB in NLCs based nano-formulations.\n\n\nMethods\n\nNTB ≥98% (HPLC) was procured from Sigma-Aldrich, Triethylamine (TEA), orthophosphoric acid (OPA), acetonitrile (ACN) and sodium hydroxide (NaOH) were procured from Merck Ltd. (Mumbai, India). Hydrochloric acid (HCl) is from Loba Chemie (Mumbai, India) and hydrogen peroxide (H2O2) 30% v/v was procured from Himedia Labs (Mumbai, India). Methanol was got from Finar Ltd. (Ahmedabad, India). HPLC grade water (milli Q water) was procured from the Millipore Direct-Q3 system in the lab (Millipore Pvt. Ltd., Bangalore, India).\n\nStandards and chemicals were weighed by using a sensitive balance (Sartorius AG, Germany). Mobile phases were filtered by using membrane filters 0.22 μm. Mobile phase pH was checked by pH meter (Eutech Instruments pH 510) and sonicated by ultrasonic bath sonicator (GT Sonic, Servewell Instruments). The analytical method was developed in HPLC, Shimadzu LC-2010 CHT (Shimadzu Corporation, Kyoto, Japan) make with quaternary pumps, autosampler, degasser, column oven and dual-wavelength prominence photodiode array (PDA) and ultraviolet (UV) detectors.\n\nFor the development of an analytical method, different columns like Luna, Phenomenex, Chromasol and Shimadzu C18 were used. Effect of various mobile phases like pH 4.5 acetate buffer, pH 6.8 phosphate buffer, 0.1% Trifluoroacetic acid (TFA) and 0.1% TEA were used along with organic solvent ACN. The effect of mobile phase flow rate and temperature of the column was also considered for the method development. The method was optimized by checking all parameters like tailing factor, replicates of standard solution, percentage relative standard deviation (%RSD), theoretical plate count, amount of organic solvent ratio to the aqueous mobile phase, run time and asymmetry of peaks.\n\nThe isocratic method was used for the analytical method development. Shimadzu C18 column was stationary phase and the mobile phase was phosphate buffer (0.1% TEA and the pH was adjusted to 3 with OPA) and ACN with a wavelength of 390 nm at the operating temperature of 25°C. The flow rate of the mobile phase was 1ml/min and injection volume was 20 μl. Each sample run time was 10 min. The optimized chromatographic conditions for the analytical method are given in Table 1.\n\nAccurately weighed 5 mg of NTB was added to a 10 ml volumetric flask and dissolved in 80% of methanol in Milli Q water. Further dilutions were made to get 1 μg/ml concentration and from this stock solution, the remaining concentrations were prepared.\n\n10 mg NTB containing nanostructured lipid carriers were centrifuged and the supernatant was decanted where the pellet was dissolved in 1 ml of methanol and necessary dilutions were made with diluent (methanol).\n\nSelection of wavelength\n\nWavelength was determined by preparing a primary stock solution of NTB (2 mg/ml) in diluent and further dilutions were made to acquire a working standard NTB solution of 2 μg/ml. A UV–Visible spectrophotometer (UV-1601PC, Shimadzu, Japan) was used to scan the NTB standard solution in between the wavelength range of 190-800 nm which helps in the determination of absorption maxima (λmax) where water was used as blank.\n\nAll the parameters of the developed analytical method were validated according to ICH Q2(R1) regulatory guidelines.\n\nSix samples of 1.5 μg/ml concentration were injected and analyzed by the developed method. After analysis, theoretical plates, tailing factor, retention time and % RSD were calculated from peaks.13\n\nBlank and sample solutions were injected separately, and the peaks were seen to determine the specificity.14\n\nTo estimate the range and linearity of the analytical method, various concentrations of NTB solutions (0.5 to 4.5 μg/ml) were prepared. Each concentration was analyzed three times (n=3) under the same chromatographic conditions. The calibration curve linearity was evaluated by linear regression analysis.15\n\nPrecision of the analytical method was determined by performing analysis of six samples on two different days intraday and inter-day with three concentrations (0.5, 2 and 4 μg/ml) and the range of concentrations were taken from the linearity curve which was categorized into lower quality control (LQC), middle quality control (MQC) and higher quality control (HQC). All samples were analyzed at optimized chromatographic conditions and % RSD was calculated after calculating the average area of the three concentrations.16\n\nAccuracy study is an assay method where percentage recovery is calculated. The study was performed by the addition of three different known concentrations at three levels 50%, 100% and 150%. Three injections of each concentration (1.5, 2 and 2.5 μg/ml) were injected and analyzed under the optimized chromatographic conditions. % RSD was calculated for all samples.17\n\nThe Limit of Detection (LOD) and Limit of Quantification (LOQ) were determined from the linearity curve by measuring the ratio of signal to noise. LOD is the concentration that comes as a result of measuring the 3:1 signal-to-noise ratio. LOQ is the concentration that comes as a result of measuring the 10:1 signal-to-noise ratio.18\n\nThe effect of intended changes that were made in chromatographic conditions like the composition of mobile phase, wavelength, column temperature and flow rate in the analytical method were studied. The changes considered for analysis are given below.19\n\ni. Organic phase ratio 33% and 37%\n\nii. Column temperature 22°C and 28°C\n\niii. Wavelengths 388 and 392 nm\n\nBenchtop stability was determined for analytical samples of the same concentration (3.5 μg/ml). The samples were kept at room temperature and injected three times at different time points (4, 8, 12 and 24 h). The peak area, retention time and %RSD were determined.20\n\nForce degradation studies were performed to determine the stability of NTB in the developed analytical method by exposing it to various stress as discussed below.21\n\nAcid degradation\n\n0.1 N HCl was added into 4 μg/ml of standard NTB solution, and the solution was subjected to heating by using the reflux condensing method for 60 min at 85°C temperature. One standard control sample was prepared in the same conditions by eliminating the heating step. Three replicates of each sample were injected by neutralizing with base.\n\nBase degradation\n\n0.1 N NaOH was added into 4 μg/ml of standard NTB solution, and the solution was subjected to heating by using the reflux condensing method for 60 min at 85°C temperature. One standard control sample was prepared in the same conditions by eliminating the heating step. Three replicates of each sample were injected by neutralizing them with acid.\n\nOxidative degradation\n\n3% Hydrogen peroxide was added to 4 μg/ml NTB standard solution. Three replicates of each sample were injected.\n\nThermal degradation\n\n2 μg/ml NTB standard solution was exposed to 105°C temperature for 24 h. Three replicates of each sample were injected. % assay and % RSD were calculated.\n\nPhotolytic degradation\n\n1.5 μg/ml NTB standard solution was exposed to UV light for 24 h and the energy given was 200-watt hours/square meter. Three replicates of each sample were injected. The % assay and % RSD were calculated.\n\nThe developed analytical method was applied for assessing the encapsulation efficiency of optimized NLCs formulation. NLCs were prepared by melt emulsification sonication method. Formulation was centrifuged for 30 min at 22,000 rpm by maintaining the temperature at 4°C. After centrifugation, the pellet was collected and ruptured with methanol and necessary dilutions were made by using diluent. Placebo was prepared in a similar manner excluding drug and analyzed.\n\n\nResults and discussion\n\nA stability indicating HPLC method for the determination of NTB in the formulation was developed and validated in the current investigation. The approach was focused primarily on lowering the amount of organic solvents used, making the mobile phase simple and feasible without the inclusion of buffer salts and shortening the run time. To determine whether the created approach of the analytical method was reliable for the analysis of NTB, it was validated as per ICH Q2(R1) recommended guidelines. The optimized method comprised of mobile phase ratio 35:65 (organic: aqueous) where the organic phase was ACN and the aqueous phase was 0.1% TEA and pH was adjusted to 3 with OPA and run time for 10 min. Chromatogram of the NTB peak with optimized chromatographic conditions is represented in Figure 2.\n\nAcetate buffer with pH 4.5 and phosphate buffer with pH 6.8 have not shown proper elution of the NTB. An increase in ACN in the mobile phase to 40 and 45% have shown less theoretical plate count which was not suggestable for a precise method. 0.1% TFA with more ACN ratio in the mobile phase has shown broader peaks and fronting was seen which is not acceptable. 0.1% TFA with less ACN ratio in the mobile phase has shown broader peaks with fronting and it was seen that the peak was eluted earlier with less retention time which is not acceptable. At lower ACN ratios, the NTB peak was found to be satisfactory. A sharp NTB peak was observed with 0.1% TEA with pH 3 adjusted with OPA, this might be due to the high polarity of NTB, and fronting was reduced due to the addition of 0.1% TEA. These findings led to the finalization of the procedure using 0.1% TEA and ACN as the mobile phase in a ratio of TEA:ACN (65:35%v/v). Chromatograms showing the effect of different mobile phases (A) 0.1% TEA:ACN (65:35%v/v), B) 0.1% TEA:ACN (55:45%v/v), C) 0.1% TEA:ACN (60:40%v/v), D) 0.1% TFA:ACN (60:40%v/v) and E) 0.1% TFA:ACN (55:45%v/v) are represented in Figure 16.\n\nTo elute NTB, various columns like Luna, Phenomenex, Chromasol and Shimadzu C18 were tested. The increased affinity of NTB was seen in the chromasol C18 column as peaks obtained were larger and broad even at the high organic ratio in the mobile phase. NTB peaks obtained by Luna C18 column have shown less theoretical plate count. In Shimadzu C18 column NTB peaks have shown clear and sharp peaks without any noise and with high theoretical plate count. The sharp peaks in the Shimadzu C18 column may be due to the ability of high hydrophobic affinity towards Shimadzu column (as NTB is a hydrophobic drug) and core-shell technology (www.Shimadzu.com).22\n\nWhen the flow rate was increased from 1 ml/min to 1.2 ml/min, the NTB peak shape not changed significantly. Hence, the flow rate was kept constant at 1 ml/min as it will be economical when compared to 1.2 ml/min.\n\nThe temperature of the column oven had no discernible effect on the shape of the peak when it was increased from 25°C to 40°C. Therefore, the temperature of the column oven was regulated at around 25°C (room temperature), as greater temperatures could shorten the column’s lifespan.\n\nThere was no interference from the peaks of the placebo, diluent and standard NTB solution at the retention time of NTB, indicating that the suggested analytical method was precise and specific in the quantification of NTB in the formulation (Figure 3 and 15). The correlation coefficient showed that the developed analytical method was linear from the range of 0.5 μg/ml to 4.5 μg/ml. System suitability, precision and accuracy studies revealed that the technique produces precise findings for analyzing NTB. The % RSD of the formulation which was discovered to be less than 2% when compared with the optimized analytical method, provided further evidence of the analytical method’s robustness. Variations in flow rate, wavelength, column oven temperature, and mobile phase composition (% buffer) were made to test the method’s robustness, and their impact on the peak area, plate count, tailing factor, and retention duration was measured. All measured % RSD values were within the limit.\n\nParameters like theoretical plates, tailing factor, retention time and % RSD were calculated from peaks are tabulated in Table 2. All parameters were within the limits which shows that the developed analytical method was accurate and suitable for analyzing other samples.\n\nThere was no interference seen in the peaks of blank when compared to the sample solution and the chromatograms of blank and NTB showing without interference were represented in Figure 3.\n\nThe relation between the concentration of NTB samples and peak area to the developed method was directly proportional and proved the linearity. The linear equation obtained for analytical samples was given in Table 3 and the regression equation was y = 98912x+50683 whereas goodness of fit R2 is 0.999. The calibration curve for analytical samples is given in Figure 4.\n\nPrecision results have shown a close relationship between inter-day and intraday samples in all three LQC, MQC and HQC ranges. % RSD acceptance range for precision was less than 2% and all samples have fallen under this category and the results are given in Table 3.\n\nThe lowest concentration of the analyte in analytical samples which can be detected but not compulsorily quantitated is known as LOD. The lowest concentration of the analyte which can be quantified precisely is known as LOQ. The results of LOD and LOQ are given in Table 3.\n\nIt was shown that there was not much change in the results by changing the composition of mobile phase, wavelength, column temperature and flow rate. There was no distinct change in peak area and % RSD values of samples were in the acceptable range. %RSD and peak area values for analytical are given in Table 3.\n\nThere was no change in the retention time of the peaks till 24 h, the chromatograms at different time intervals can be seen in Figure 5 and % RSD values were in an acceptable range which shows that NTB is stable, and the peak area, % RSD values are given in Table 3.\n\nForce degradation studies were carried out to determine if any degradants were formed due to exposure to stress conditions.\n\nAcid degradation\n\n0.1N HCl treated NTB standard solutions which were kept at room temperature have not shown any degradant peaks. 0.1 N HCl treated NTB solutions which were subjected to 85°C temperature for 30 min have not shown any degradant peaks. There was a change in retention time (6.45±00) where the acid-treated sample was eluted slightly earlier than the NTB elution peak at optimized chromatographic conditions. % Assay of the acid degradation samples was found to be 86.62±2.48 and peaks are represented in Figure 6.\n\nSince there are five nitrogen atoms and three carbonyl groups there would have been protonation on the lone pair of electrons on the nitrogen and oxygen. Hence the resulted protonated structure has more or less similar but not the same Rt value compared to NTB standard peak. The degradant formed due to acid is given in Figure 7 and this acid degradation was supported by the literature.23\n\nBase degradation\n\n0.1 N NaOH NTB standard solution treated NTB standard solutions which were kept at room temperature have not shown any degradant peaks, 0.1N NaOH treated NTB solutions that were subjected to 85°C temperature for 30 min have shown four degradant peaks and peaks are represented in Figure 8.\n\nNTB is susceptible to undergo degradation in the presence of basic media. The carbonyl groups are attacked by hydroxyl ions via nucleophilic addition mechanism yielding the major degradants. Also, the alkene bond is susceptible to being cleaved. Degradants formed due to base are given in Figure 9. Degradation of NTB due to base/alkali was also reported in the literature.8\n\nOxidative degradation\n\n3% hydrogen peroxide standard solution at ambient temperature for 24 h has shown four degradant peaks, % assay of the peroxide degradation samples was not calculated as the peak area values are very less than the linearity curve range. The degradant peaks are represented in Figure 10. The oxidative stressing of NTB is clearly showing the formation of four degradation products. The two nitrogen’s of piperazine undergoing N-oxidation and peroxidation of alkene is another major degradation product. Degradation of NTB due to oxidation is given in Figure 11 and oxidative degradation of NTB is also reported in the literature.9\n\nThermal degradation\n\nThere were no degradant peaks observed in thermal degradation indicating thermal stability of NTB and the % assay of the thermal degradation samples was found to be 98.22±0.267. % RSD values and peak area were given in Table 3. And peaks are represented in Figure 12.\n\nPhotolytic degradation\n\nThere was one very small degradant peak observed in photolytic degradation and the % assay of the photolytic degradation samples was found to be 95.7.3±0.137. % RSD values and peak area were given in Table 3. The degradant peak is represented in Figure 13. Most of the drug was stable to photolytic stress conditions but a small percentage of the drug has undergone degradation at the alkene bond.\n\nBy injecting the stressed sample and unstressed sample into the HPLC instrument, the degradation peaks were identified. To ascertain the specificity of the NTB peak and peak purity of the corresponding substance, NTB was subjected to many stress conditions like thermal, light, acid, alkali, and oxidative stresses. To produce a measurable level of degradation, the stressing agent concentration and exposure time were optimized. The investigation was conducted to evaluate other degradant peaks as well as the purity of the NTB peak. It was discovered that NTB was more prone to alkali degradation, which was also reported in other literature.24 The electrophilic attack of oxygen radicals which will promote the development of degradant products causes the oxidative degradation of NTB. UV rays may induce NTB to isomerize and result in the formation of degradant (Figure 14). NTB was stable at room temperature which was confirmed by chromatograms which were taken at different time intervals till 24 h. The Stability-indicating RP-HPLC Method for NTB verified that the developed analytical method was specific for the determination or quantification of NTB and the retention time of NTB is free of interference from degradant peaks.\n\nCharacterization of nanostructured lipid carriers\n\nThe particle size of NLCs was found to be 290.5 ± 3.41 nm and the polydispersity index (PDI) was found to be 0.394 ± 0.028. From the PDI result it was confirmed that the formulation was monodisperse, whereas zeta potential was found to be -19.8±2.185 mV.\n\nSpecificity of validated method\n\nIt was seen that the drug, the formulation’s excipients, and the blank peaks (methanol) did not interfere with one another. Chromatograms of formulation, placebo and blank are represented in Figure 15.\n\nEncapsulation efficiency\n\nEncapsulation efficiency was found to be 88.241±0.155% and the % RSD value was in the acceptable range with the value of 0.176. There was no change in retention time and theoretical plate count in all the samples.\n\nThe amount of NTB in the NLCs formulation was measured using the RP-HPLC technique established in the current investigation. It was discovered that the developed analytical method was precise because there was no interference from a blank peak, placebo peak and NTB standard peak. It was difficult to recover the drug from the formulation excipients,25 but the current developed analytical method demonstrated a recovery that was well within the allowable range.\n\nThe outcomes of the present analytical method point to the possibility of effectively analyzing the amount of NTB in the NLCs formulation.\n\n\nConclusion\n\nThe developed HPLC method for determining NTB was found to be sensitive, precise, and repeatable. The technique was verified against the various concentration ranges of NTB (0.5-4.5 μg/ml. It was discovered to provide good accuracy and precision for the quantification of the NTB. The procedure was very reliable because the outcomes were unaffected by minor adjustments to the instrument’s settings or the composition of the mobile phase. The developed analytical method was discovered to have lower LOD and LOQ than the methods that were previously published. Also, it was discovered that the approach suggested in this study was very specific for the identification of NTB even when other formulation excipients were present. Our study will be helpful for the quantitative evaluation of NTB by this stability-indicating HPLC method because there are currently no publications on this topic with complete degradation studies which are advantageous for the quantification of NTB in bulk drugs and pharmaceutical preparations.",
"appendix": "Data availability\n\nFigshare: Validation of RP-HPLC for Nintedanib, https://doi.org/10.6084/m9.figshare.23565852.v1. 26\n\nThis project contains the following underlying data:\n\n- HPLC_analytical validation_2023.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nAuthors would like to thank Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India for providing Dr. TMA Pai fellowship to Ms. Varalakshmi Velagacherla and research facilities to carry out this work.\n\n\nReferences\n\nWongkarnjana A, Yanagihara T, Kolb MR: Treatment of idiopathic pulmonary fibrosis with Nintedanib: an update. Expert Rev. Respir. Med. 2019; 13(12): 1139–1146. PubMed Abstract | Publisher Full Text\n\nPopat S, Mellemgaard A, Reck M, et al.: Nintedanib plus docetaxel as second-line therapy in patients with non-small-cell lung cancer of adenocarcinoma histology: a network meta-analysis vs new therapeutic options. Future Oncology (London, England). Jun. 2017; 13(13): 1159–1171. PubMed Abstract | Publisher Full Text\n\nProesmans VLJ, Drent M, Elfferich MDP, et al.: Self-reported Gastrointestinal Side Effects of Antifibrotic Drugs in Dutch Idiopathic Pulmonary Fibrosis patients. Lung. 2019; 197(5): 551–558. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAli M, Barash M, Mohammed A, et al.: SEVERE PANCOLITIS: A RARE ADVERSE EFFECT OF NINTEDANIB. Chest. Oct. 2018; 154(4): 446A. Publisher Full Text\n\nZhu X: The high-sensitivity analysis method of genotoxicity impurity in ethyl sulfonic acid Nintedanib. CN106841495A. Jun. 13, 2017 Jan. 21, 2023. Reference Source\n\nPasquini B, Orlandini S, Furlanetto S, et al.: Quality by Design as a risk-based strategy in pharmaceutical analysis: Development of a liquid chromatography-tandem mass spectrometry method for the determination of nintedanib and its impurities. J. Chromatogr. A. Jan. 2020; 1611: 460615. Publisher Full Text\n\nJayagopal B, Murugesh S: QbD-mediated RP-UPLC method development invoking an FMEA-based risk assessment to estimate nintedanib degradation products and their pathways. Arab. J. Chem. Sep. 2020; 13(9): 7087–7103. Publisher Full Text\n\nDutta D, Das S, Seijas JA, et al.: VALIDATED STABILITY- INDICATING HPTLC METHOD FOR NINTEDANIB & CHARACTERIZATION OF DEGRADANTS BY LC-MSn. Proceedings of The 23rd International Electronic Conference on Synthetic Organic Chemistry, Sciforum. Nov. 2019. Publisher Full Text\n\nPurnachand D, Veerareddy A, Ramadevi B, et al.: Development and validation of a simple and sensitive stability indicating RP-HPLC assay method for determination of Nintedanib and stress degradation studies. J. Chem. Pharm. Res. 2015; 7(8): 774–782. Reference Source\n\nSantosh AW, Sumithra M: QbD Based Development and Validation of RP-HPLC Method for Nintedanib Esylate: Application to Bioanalytical and Stability Study in Plasma. Anal. Chem. Lett. May 2021; 11(3): 392–408. Publisher Full Text\n\nHaider M, Abdin SM, Kamal L, et al.: Nanostructured Lipid Carriers for Delivery of Chemotherapeutics: A Review. Pharmaceutics. Mar. 2020; 12(3): E288. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoushaymi B, Nasreddine N, Kedees M, et al.: Oleic acid increases uptake and decreases the P-gp-mediated efflux of the veterinary anthelmintic Ivermectin. Drug Res (Stuttg). Feb. 2019; 69(3): 173–180. PubMed Abstract | Publisher Full Text\n\nRaut R, Shaji J: HPLC method validation for quantification of tetrahydrocurcumin in bulk drug and formulation. Future J. Pharm. Sci. Feb. 2021; 7(1): 42. Publisher Full Text\n\nAlquadeib BT: Development and validation of a new HPLC analytical method for the determination of diclofenac in tablets. Saudi Pharm J. Jan. 2019; 27(1): 66–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNaseef H, Moqadi R, Qurt M: Development and Validation of an HPLC Method for Determination of Antidiabetic Drug Alogliptin Benzoate in Bulk and Tablets. J. Anal. Methods Chem. Sep. 2018; 2018: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSankar PR, Viswanath A, Eswarudu MM, et al.: Development and Validation of RP-HPLC Method for the Determination of Sorafenib in Pharmaceutical Dosage Form. IJPSRR. Jul. 2021; 69(1). Publisher Full Text\n\nBakhshi F, Molavi O, Rashidi MR, et al.: Developing a high-performance liquid chromatography fast and accurate method for quantification of silibinin. BMC. Res. Notes. Nov. 2019; 12(1): 743. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPakalapati S, Rumalla CS, Gudapati AR, et al.: A novel RP-HPLC method development and validation for determination and estimation of eluxadoline drug with its impurities. SN Appl. Sci. May 2020; 2(6): 1036. Publisher Full Text\n\nEpshtein N, Sevastianova V, Koroleva A: INVESTIGATION OF ROBUSTNESS AT VALIDATION OF HPLC AND UPLC METHODS: A MODERN APPROACH INCLUDING RISK ANALYSIS. Drug Development & Registration. Feb. 2018; 1: 96–109.\n\nNavamanisubramanian R, Panchagiri S, Nerella R, et al.: STABILITY INDICATING RP-HPLC METHOD FOR ESTIMATION OF REPAGLINIDE IN RABBIT PLASMA. Int. J. Appl. Pharm. Apr. 2019; 206–210. Publisher Full Text\n\nBatrawi N, Naseef H, Al-Rimawi F: Development and Validation of a Stability-Indicating HPLC Method for the Simultaneous Determination of Florfenicol and Flunixin Meglumine Combination in an Injectable Solution. J. Anal. Methods Chem. Jul. 2017; 2017: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShim-pack Velox C18: (accessed Mar. 01, 2023). Reference Source\n\nDhiman V, Balhara A, Singh S, et al.: Characterization of stress degradation products of nintedanib by UPLC, UHPLC-Q-TOF/MS/MS and NMR: Evidence of a degradation product with a structure alert for mutagenicity. J. Pharm. Biomed. Anal. May 2021; 199: 114037. PubMed Abstract | Publisher Full Text\n\nJayagopal B, Murugesh S: QbD-mediated RP-UPLC method development invoking an FMEA-based risk assessment to estimate nintedanib degradation products and their pathways. Arab. J. Chem. 2020; 13(9): 7087–7103. Publisher Full Text\n\nGadag S, Narayan R, Mehta CH, et al.: Development and Validation of a Rapid and Sensitive Stability-indicating RP-HPLC Method for Resveratrol Quantification in Pharmaceutical Formulation. Indian J. Pharm. Educ. Res. 2021; 55(3s): S825–S836. Publisher Full Text\n\nVelagacherla V, Nayak Y, Bhaskar KV, et al.: Validation of RP-HPLC for Nintedanib. Dataset. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "217521",
"date": "27 Nov 2023",
"name": "Rubi Mahato",
"expertise": [
"Reviewer Expertise Synthesis of platform molecules",
"naturopathy",
"homeopathic treatments",
"curriculum research (Pharmaceutical Sciences )"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReviewer’s Comments:\nTitle: A stability indicating method development and validation of a rapid and sensitive RP-HPLC method for Nintedanib and its application in quantification of nanostructured lipid carriers\nOverall, this research article is very well presented and provided with detailed research methodology and outcomes. Authors have provided elaborated procedures for each experiment done, and have provided the data and appropriate figures for all of them. I also like how the authors have listed the different types of columns they have tried before finalizing to use one. Also, the quantifiable range of Nintedanib (μg/ml) concentrations are provided.\nThe stability studies of Nintedanib in presence of various factors such as acid, base, oxidation, elevated temperature, and light are provided as well. Moreover, authors have evaluated their newly developed RP-HPLC in evaluation of encapsulation efficiency of nanostructured lipid carrier, which serves as a validation of their newly developed method.\nTaken together, the findings are new, and a reliable and accurate method was developed to quantify the drug Nintedanib.\nDecision: accept as it is.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "272267",
"date": "23 May 2024",
"name": "Mohana Vamsi Nuli",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n# Page-7: Chromatograms of A and B are altered. # Page-7: There is no placebo chromatogram # Page-8: LOD and LOQ concentrations are in ppm? But standard concentration is 1ppm? # Page-9: Solution stability peak area is double than Robustness and other peak areas? Supposed to be the same peak area? # Page-16: Chromatogram B and C with increase in ACN when compared with, there is no change in NTB retention time. Also, Blank peak retention time increased with increase in ACN which supposed to decrease the Retention time.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11716",
"date": "20 Jun 2024",
"name": "Usha Yogendra Nayak",
"role": "Author Response",
"response": "Reviewer Comment 1: # Page-7: Chromatograms of A and B are altered. Answer to comment 1: In this chromatogram, peak A is blank methanol, and peak B is Nintedanib. Peak B chromatogram results from the Nintedanib in the sample, which causes variations in retention duration, intensity, and composition. The blank peak in the chromatogram is caused by methanol. By distinguishing it from impurities and background noise, this distinction guarantees precise identification and quantification of the analyte. Reviewer Comment 2: # Page-7: There is no placebo chromatogram. Answer to the comment 2: As in figure 1 is only of method development the placebo peak is not given only pure Nintedanib drug chromatogram is given, the placebo peak is given in figure 15 where the drug from nano structured lipid carriers was determined. Reviewer Comment 3: # Page-8: LOD and LOQ concentrations are in ppm? But standard concentration is 1ppm? Answer to comment 3: In the linearity curve, Nintedanib was found to have LOD of 2.45 μg/ml and LOQ of 7.45 μg/ml. Reviewer Comment 4: # Page-9: Solution stability peak area is double than Robustness and other peak areas? Supposed to be the same peak area? Answer to comment 4: Stability solutions chromatograms and robust chromatograms were done at different concentration ranges. Hence the areas are different. Reviewer Comment 5: # Page-16: Chromatogram B and C with increase in ACN when compared with, there is no change in NTB retention time. Also, Blank peak retention time increased with increase in ACN which supposed to decrease the Retention time. Answer to comment 5: The consistent retention duration of NTB implies that variations in ACN content do not substantially impact it, possibly because of its unique chemical characteristics. On the other hand, the conventional trend of decreased retention with rising ACN concentration is overridden by an increase in the blank peak's retention time with greater ACN, which suggests distinct interactions between the impurities and the stationary phase or a change in solubility dynamics."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1389
|
https://f1000research.com/articles/12-1093/v1
|
01 Sep 23
|
{
"type": "Research Article",
"title": "Impact of coenzyme Q10 as an adjuvant therapy to letrozole on spermiogram results and sex hormone levels in Iraqi men with infertility; randomized open label comparative study",
"authors": [
"Essa Bahauldeen Fadhil",
"Mohammed Mahmood Mohammed ",
"Ula M. Alkawaz",
"Mohammed Mahmood Mohammed ",
"Ula M. Alkawaz"
],
"abstract": "Background: Worldwide, infertility affects about 15% of reproductive-age couples. In many cases, infertility can't be treated, however new treatment options with promising value have been involved in recent clinical trials. The aim of this clinical trial was to evaluate the impacts of adding coenzyme Q10 (CoQ10) to letrozole on the results of spermiogram and sex hormone tests in men diagnosed with idiopathic oligoasthenoteratozoospermia (iOAT) syndrome, which is a type of male defective spermatogenesis of unknown etiology. Methods: This randomized, open-label, parallel two-arm interventional study included 67 adult male patients aged 18-60 years with a confirmed diagnosis of iOAT syndrome recruited from The High Institute for Infertility Diagnosis & Assisted Reproduction Technologies/Nahrain University. Patients were randomly separated into two groups, Group A included 29 patients treated with letrozole 2.5 mg tablet orally twice a week, Group B included 38 patients treated with a combination of letrozole 2.5 mg tablet orally twice a week plus CoQ10 400 mg per day. Both groups completed treatment for three months. Semen samples, serum follicle-stimulating hormone (FSH), estradiol (E2), and testosterone (T) were analyzed at day one, and at the end of month one, two and three. Results: Both groups showed that sperm concentration, normal morphology, total sperm count and motility, serum testosterone and FSH levels, and T/E2 ratio were significantly increased, while estradiol levels significantly decreased after three months of treatment. Seminal fluid volume changed significantly in group A only. In comparing between the two groups, all measured parameters, apart from sperm motility and FSH level, demonstrated a significant difference after three months of treatment, while sperm volume reached significant value after only two months of therapy. Conclusions: CoQ10 as adjuvant treatment to letrozole effectively improved most of the tested sperm parameters in Iraqi men with iOAT. Registration: ClinicalTrials.gov (NCT05847257, May 6, 2023).",
"keywords": [
"Male",
"infertility",
"spermatogenesis",
"idiopathic"
],
"content": "Introduction\n\nThe World Health Organization (WHO) defines infertility as “the incapability of a couple to conceive in spite of having regular sexual activity for at least one year without using any contraceptive methods”.1 Around the world, approximately 15% of reproductive-age couples are struggling with infertility,2 about half of these issues are related to male factors.3 There are many causes contributing to male infertility, including infection,4 alteration in organ function,5 environmental factors, genetic factors,6 and sex hormone disturbance.7\n\nIdiopathic oligoasthenoteratozoospermia (iOAT) is associated with faulty spermatogenesis and is characterized by unusually low sperm count, motility, and a large number of dysmorphic spermatozoa in the ejaculate, The etiology of which is unclear and is frequently considered undetectable by standard laboratory techniques. About 30% of OAT patients are identified as idiopathic, and idiopathic testicular abnormalities cause the most severe cases of OAT.8 Although established disorders such as varicocele, cryptorchidism, and hypogonadism are identifiable causes of OAT and infertility, approximately 25% of these individuals do not have a known explanation behind their irregular semen analysis.9,10\n\nA complex interaction of hormones that act centrally and intratesticular is necessary for spermatogenesis. In response to the activity of gonadotropin-releasing hormone (GnRH) from the hypothalamus, the anterior pituitary secretes luteinizing hormone (LH) and follicle-stimulating hormone (FSH). In the testis, FSH operates on Sertoli cells to stimulate the maturation of spermatogonia. LH has an influence on Leydig cells promoting testosterone synthesis. Local testosterone concentrations must be significantly greater than serum levels for effective spermatogenesis. Then, by its effects on Sertoli cells, this intratesticular testosterone indirectly promotes the development of germ cells.7\n\nMany hormones are participating in the regulation of spermatogenesis. LH stimulates Leydig cells to release testosterone to promote the production of sperm and virilization and exerts negative feedback to suppress the release of LH and FSH from the pituitary gland. FSH promotes Sertoli cells to support spermatogenesis to release inhibin B that has negative feedback effects to inhibit FSH secretion. FSH is required to establish spermatogenesis and it’s very important to understand that testes will produce lower numbers and poorer quality of sperm with only FSH stimulation, while LH is necessary to obtain both quantity and quality of sperm production, as a result neither FSH alone nor LH alone is sufficient to produce high quality sperm.11\n\nAromatase is a cytochrome p-450 enzyme present in the adipose tissue, testes, liver, and female reproductive organs that has roles in converting testosterone (T) to estradiol (E2) and androstenedione to estrone. Aromatase inhibitors block the conversion of T to E2; therefore, the level of testosterone is increased while the estrogen level is suppressed. As the endogenous testosterone levels rise, and in combination with the reduction in the estrogen suppressing role on the hypothalamic–pituitary–gonadal (HPG) axis, spermatogenesis is further stimulated.12 In men, the modification of plasma E2 levels to the normal physiological range results in a positive impact on FSH, LH and testosterone levels mediated by an effect on the pituitary gland derived by this reduction.13 Therefore in men with low testosterone levels, aromatase inhibitors enhance testosterone secretion.14\n\nLetrozole belongs to third-generation aromatase inhibitors that inhibit estrogen biosynthesis reversibly and act as an anti-cancer agent for advanced breast cancer.15 The medication dosage form is tablet 2.5 mg and when taken orally it is absorbed readily (bioavailability 99.9%); food has no effects on its absorption. Letrozole is rapidly distributed, its excreted mainly through the urine (about 90%) and its half-life is about two days.16\n\nOxidative stress (OS) and reactive oxygen species (ROS) are believed to damage the spermatozoa and account for 30 to 80% of infertility cases in men.17 ROS in semen originates from different endogenous and exogenous sources, the endogenous sources include round cells, epithelial cells and leukocytes, while lifestyle factors including drinking alcohol, smoking and ecological factors (such as radiation and toxins) are considered sources of exogenous ROS.18 Increased ROS production causes oxidative stress and reduces the antioxidant capacity of spermatozoa.19 Spermatozoa have plasma membranes that are made up of lipids and polyunsaturated fatty acids, increased levels of ROS make the membrane vulnerable to lipid peroxidation and damage.20 The lower motility and reduced fluidity of membranes in sperm occur due to lipid peroxidation and are associated with reduced ability of sperm to fertilize.21 Coenzyme Q10 (CoQ10) is a fat soluble vitamin-like molecule naturally found in cell membranes in the human body and it is naturally found in our diet and can be synthesized endogenously.22 CoQ10 has antioxidant effects and is involved in the production of mitochondrial energy, which is important for maintaining the power source of spermatozoa and provide protection to their membranes from damage through lipid peroxidation. Therefore, it’s considered among the most extensively utilized antioxidants as an option to treat idiopathic infertility in men.23 The aim of the current clinical trial was to evaluate the impacts of adding CoQ10 to letrozole on spermiogram results and sex hormone levels in men diagnosed with iOAT syndrome.\n\n\nMethods\n\nWritten informed consent was obtained from each participant for participation and publication of clinical information. The study was approved by both the institutional regulation board of the Department of Clinical Pharmacy/College of Pharmacy/Mustansiriyah University (ID number: 3983, date: 14th December 2021), and the High Institute for Infertility Diagnosis & Assisted Reproductive Technologies/Nahrain University (Date: 3rd November 2021; Ethical code: A21024).24 The recruitment period started on the 1st of January 2022 after both faculties approved the study. The study followed the Declaration of Helsinki (2008) for research on human subjects and its later amendments. This trial was registered with ClinicalTrials.gov (NCT05847257) on May 6, 2023. Due to the recent introduction of required clinical trials registration in Iraq, we registered the study retrospectively to assure its transparency. This study adhered to the CONSORT guidelines,38 no harms or unintended effects have been reported for this study.\n\nThis study was a randomized, open-label, parallel two-arm interventional study. The study initially included 74 patients, on follow-up seven cases were lost and the final analysis involved 67 cases. These patients were further divided into two groups randomly, group A (29) patients received letrozole 2.5 mg (Letrozole® 2.5 mg, Accord Healthcare Limited, UK) twice weekly for three months, and group B (38) patients received letrozole 2.5 mg twice a week plus CoQ10 400 mg (CoQ-10®, Natrol, USA) once per day (200 mg twice daily) for three months as illustrated in Figure 1.\n\nPatients with iOAT syndrome were selected during their visit to The High Institute for Infertility Diagnosis & Assisted Reproduction Technologies/Nahrain University. Before taking part, each subject provided their written, informed consent. The duration of this study was from the 1st of December 2021 until 1st of October 2022.\n\nInclusion criteria\n\n1. Adult male patients.\n\n2. Aged 18–60 years.\n\n3. Confirmed diagnosis of iOAT syndrome.\n\nExclusion criteria\n\n1. Patients who have been found to have additional infertility causes, such as varicocele or obstruction of the ejaculatory duct.\n\n2. Those who have had surgery for male factor infertility.\n\n3. Patients with infections such as sexually transmitted infections (STIs).\n\n4. Patients with renal or liver disease.\n\n5. Incomplete patient data.\n\nThe seminal fluid analysis (SFA) and hormone profile (FSH [VIDAS®FSH, bioMerieux SA, France Cat no.:30 407-01], estradiol [VIDAS®E2II, bioMerieux SA, France Cat no.: 30 431], and testosterone [VIDAS® Testosterone II, bioMerieux SA, France Cat no.:414320]) were assessed at the beginning of the study (baseline value) and at the end of months one, two and three for three consecutive months after taking the medication to measure the possible changes in the studied parameters. The measurement of FSH, LH, and testosterone was performed using enzyme linked florescent assays (ELFAs) (mini VIDAS, bioMerieux SA, France).\n\nThe randomization process was done utilizing the online software Research Randomizer. First, the patients were sequentially numbered during the interview and then randomly assigned to one of two groups using the online software.\n\nPrimary outcomes\n\nSeminal fluid analysis\n\nAssessment of sperm volume/ ml, sperm concentration/ ml, total sperm count/ml, progressive sperm motility (%), non-progressive sperm motility (%), immotile sperm (%), normal sperm morphology (%). Time Frame: changes in value from baseline to the end of the first, second or third month for three consecutive months of treatment.\n\nSecondary outcomes\n\nHormone profile\n\nAssessment of concentration of serum FSH, concentration of serum estradiol, and concentration of serum testosterone. Time Frame: change in value from baseline to the end of the first, second and third month for three consecutive months of treatment.\n\nA previous study by Peivandi et al.,25 showed that letrozole 2.5 mg increases sperm concentrations over three months and demonstrated an in improvement by 33% for sperm parameters (concentration after three months of therapy) so we assumed that the use of CoQ10 will increase this value to 55%. Using MedCalc (RRID:SCR_015044) software version 14.8.1, we arrived at 64 patients for both groups to confirm the null hypothesis (with type I error 5% and type II error of 10%), we increased the sample to 74 to account for maximum possible loss in patients being around 15% without affecting the accuracy of the results.\n\nAll analyses were carried using IBM SPSS Statistics (RRID:SCR_016479) version 28.1 (Chicago, USA), repeated measures ANOVA was used to assess the differences in each group across four time periods with post hoc Tukey’s test to assess the pair wise comparisons. An independent t-test was used to assess the difference between each treatment group. A chi-squared test was used to assess the difference in categorical variables. The level of significance was 0.05 (alpha level), and all p-values were two tailed. For sample size calculations MedCalc (RRID:SCR_015044) software version 14.8.1 was used.\n\n\nResults\n\nThe demographic data and baseline characteristics of all participants are summarized in Table 1.38 In this table, there were non-significant variations among all parameters between the two groups.\n\nTable 2 shows the results of letrozole effects alone and with CoQ10 on sperm production after one, two and three months. The effects on both groups showed a significant growth in the mean value of sperm concentration and total sperm count in respect to the baseline (p<0.01). However, significant (p<0.05) and non-significant (p>0.05) changes in seminal fluid volume in group A and B were reported, respectively. At the end of the current study, the results revealed significant (P˂0.05) differences between the two groups for all parameters (sperm concentration and total sperm counts) except seminal fluid volume, which was significant only after two months (P>0.05).\n\nA t-test used to test statistical differences between 2 groups (Horizontally).\n\nB One way repeated measures ANOVA used for comparison between (Time-wise values) within each group. Different small case letters indicate significant difference. NS: No significant changes (p≥0.05).\n\n* significant changes (p<0.05).\n\n** highly significant changes (p<0.01). CoQ10, coenzyme Q10.\n\nTable 3 illustrates the effects of letrozole alone and with CoQ10 on sperm motility and morphology after one, two and three months. Statistically, significant improvement was reported in both groups regarding sperm motility and morphology after three months of treatment. However, comparison between the groups, showed no significant differences (P>0.05) in all parameters except the only sperm morphology was significantly improved in group B compared to that of group A (p<0.05).\n\nA t-test used to test statistical differences between 2 groups (Horizontally).\n\nB One way repeated measures ANOVA used for comparison between (Time-wise values) within each group. Different small case letters indicate significant difference. NS: No significant changes (p≥0.05).\n\n* significant changes (p<0.05).\n\n** highly significant changes (p<0.01). CoQ10, coenzyme Q10.\n\nResults of comparing the effect of letrozole alone and in combination with CoQ10 on sex hormones after one, two and three months are demonstrated in Table 4. In both groups, a highly significant (p<0.01) increase in testosterone and FSH levels was noticed. Conversely, estradiol levels were significantly decreased (p<0.01). Between the two groups, significant (p<0.05) and highly significant (p<0.001) changes in testosterone and estradiol levels were noticed, respectively, with no significant (p>0.05) changes for FSH levels. Regarding the ratio of T/E2, the growth was about 190% and 312% for group A and B from the base line, respectively, the statistical significancy was achieved between the two groups (p<0.05).\n\nA t-test used to test statistical differences between 2 groups (Horizontally).\n\nB One way repeated measures ANOVA used for comparison between (Time-wise values) within each group. Different small case letters indicate significant difference. NS: No significant changes (p≥0.05).\n\n* significant changes (p<0.05).\n\n** highly significant changes (p<0.01). CoQ10, coenzyme Q10.\n\n\nDiscussion\n\nThe male reproductive capacity is affected by many demographic factors, with age seemingly the most sensitive factor since aging is negatively correlated with spermatogenesis.26 In the current study, most participants were in their thirties; consequently, a correlation may be present relating to the quantity and quality of sperm. The second important factor is smoking, a study by Jin-Bo Dai et al., (2015) confirmed that tobacco smoking is considered a risk factor for developing infertility, smoking cigarettes, water pipes or vapes may contain many harmful chemicals that disrupt the antioxidant status of testes and consequently lead to the interruption of spermatogenesis.27 However, in spite of the adverse consequences of smoking on male fertility, many men are still fertile but they are at risk for becoming infertile.28 More than half of the patients in the current study were smokers and this may have a great influence on the quality of sperms.\n\nIn this study, most of the patients were overweight and obese, this may have an association with low quality of spermatozoa. Belloc et al., (2014) showed a correlation between high BMI and low semen quality, whereas sperm morphology is not affected.29 In previous clinical trials, letrozole was used alone at a dose of 2.5 mg per day to treat infertility in men,30,31 while another previous study used a weekly dose of 2.5 mg letrozole to improve testosterone.32 However, the dose of letrozole used in the current study was 2.5 mg twice a week for all patients, this came from the experience of consultants in an attempt to decrease the expected side effects, including loss of libido, which was reported in earlier studies.31,33\n\nA study by Kooshesh et al., (2020) concluded that the use of letrozole in the treatment of men with iOAT and T: E2 ratio ≤ 10, can successfully increase sperm quality and chromatin integrity, and consequently increase spontaneous pregnancy.12 To a large extent, these finding are in agreement with the current results.\n\nIn men, estrogen is mainly produced by the conversion of testosterone to E2 via aromatase enzymes,34 an excess of estrogens can block the HPG axis, therefore, infertility occurs due to reduced release of FSH and LH. Administration of letrozole can lead to increased testosterone and decreased estradiol production. So by improving the T/E2 ratio, this can have positive effects on spermatogenesis and obtaining high quality and quantity of sperm.7\n\nThe addition of CoQ10 to letrozole showed notable improvement in the ratio of T/E2 (312%) compared to that of using letrozole alone (190%) after three months of treatment. Peivandi et al., (2019) showed a correlation between the improvement in spermatogenesis to the increase in the ratio of T/E2.25 Appasamy et al., (2007) suggested that the increased ROS levels may have potential to disrupt hormonal balance and reduce the levels of male sex hormones, therefore resulting in infertility.35 However, administration of CoQ10, which has notable antioxidant properties to scavenge ROS and reverse oxidative stress, results in the improvement of spermiogram parameters.36\n\nSafarinejad (2009) illustrated the effects of CoQ10 on sperm parameters, using 300 mg CoQ10 a day for six months to show enhancement in sperm count, motility and morphology, while decreasing the levels of FSH.37 In the present study, a combination of CoQ10 and letrozole were used for three months, the results indicated improvement in sperm motility, morphology and concentration. Furthermore, assessment of sex hormone levels showed an increase in FSH and testosterone and a decrease in E2 levels.\n\nThe combined administration of letrozole and CoQ10 led to significant improvements of all spermiogram parameters, this combination appears to have a synergistic effect to obtain higher quality spermatogenesis.\n\nA limitation of this study includes the small sample size for both groups due to missing many patients during follow-up periods and exclusion criteria mentioned above. In addition, there was a lack of control group due to the difficulty in convincing men who have not been diagnosed with infertility to undertake SFA and hormone analysis. Thirdly, no sensitivity analyses were conducted for the confounding variables. Finally, ROS in seminal fluid was not measured due to the lack of availability of tools to measure ROS in semen.\n\n\nConclusions\n\nThe combined use of letrozole and CoQ10 was found to improve sperm parameters and patients showed a boosted improvement in all spermiogram parameters compared to that of patients administered letrozole alone. Based on the results of this study, letrozole plus CoQ10 is recommended to treat patients with iOAT syndrome who have high estradiol and low testosterone levels.",
"appendix": "Data availability\n\nZenodo: Impact of coenzyme Q10 as an adjuvant therapy to letrozole on spermiogram results and sex hormone levels in Iraqi men with infertility; randomized open label comparative study. https://doi.org/10.5281/zenodo.8191739. 38\n\nThis project contains the following underlying and extended data:\n\n- Raw spreadsheet data\n\n- Completed CONSORT checklist\n\n- Ethical approval of both committees\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe researchers would like to thank Mustansiriyah University (www.uomustansiriyah.edu.iq) Baghdad/Iraq and the fertility center of Nahrain University, and Dr Hayder A. Fawzi for its support and encouragement to complete the present work.\n\n\nReferences\n\nXiao-yan C, Jie L, Dang J, et al.: A highly sensitive electrochemiluminescence immunoassay for detecting human embryonic human chorionic gonadotropin in spent embryo culture media during IVF-ET cycle. J. Assist. Reprod. Genet. 2013; 30: 377–382. Publisher Full Text\n\nAgarwal A, Mulgund A, Hamada A, et al.: A unique view on male infertility around the globe. Reprod. Biol. Endocrinol. 2015; 13: 37. Publisher Full Text\n\nAston KI, Krausz C, Laface I, et al.: Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. Hum. Reprod. 2010; 25: 1383–1397. PubMed Abstract | Publisher Full Text\n\nPenna Videaú S, Cermeño Vivas J, Salazar N: IgA antibodies to Chlamydia trachomatis and seminal parameters in asymptomatic infertile males. Arch. Androl. 2001; 46: 189–195.\n\nElzanaty S, Richthoff J, Malm J, et al.: The impact of epididymal and accessory sex gland function on sperm motility. Hum. Reprod. 2002; 17: 2904–2911. Publisher Full Text\n\nCavallini G: Male idiopathic oligoasthenoteratozoospermia. Asian J. Androl. 2006; 8: 143–157. Publisher Full Text\n\nSengupta P, Dutta S, Karkada IR, et al.: Endocrinopathies and Male Infertility. Life (Basel). 2021; 12: 12. Publisher Full Text\n\nSingh R, Kaleem AM, Narayana SS, et al.: A case of oligoasthenoteratozoospermia with AZFc deletion and persistent oxidative stress. Indian J. Hum. Genet. 2012; 18: 359–362. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSiddiq FM, Sigman M: A new look at the medical management of infertility. Urol. Clin. North Am. 2002; 29: 949–963. PubMed Abstract | Publisher Full Text\n\nSharlip ID, Jarow JP, Belker AM, et al.: Best practice policies for male infertility. Fertil. Steril. 2002; 77: 873–882. Publisher Full Text\n\nSilber SJ: Fundamentals of male infertility. Springer; 2018.\n\nKooshesh L, Bahmanpour S, Zeighami S, et al.: Effect of Letrozole on sperm parameters, chromatin status and ROS level in idiopathic Oligo/Astheno/Teratozoospermia. Reprod. Biol. Endocrinol. 2020; 18: 47. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRaven G, de Jong FH , Kaufman JM, et al.: In men, peripheral estradiol levels directly reflect the action of estrogens at the hypothalamo-pituitary level to inhibit gonadotropin secretion. J. Clin. Endocrinol. Metab. 2006; 91: 3324–3328. PubMed Abstract | Publisher Full Text\n\nSchlegel PN: Aromatase inhibitors for male infertility. Fertil. Steril. 2012; 98: 1359–1362. Publisher Full Text\n\nHe DX, Ma X: Clinical utility of letrozole in the treatment of breast cancer: a Chinese perspective. Onco. Targets. Ther. 2016; 9: 1077–1084. PubMed Abstract | Publisher Full Text\n\nDellapasqua S, Colleoni M: Letrozole. Expert Opin. Drug Metab. Toxicol. 2010; 6: 251–259. Publisher Full Text\n\nAlahmar AT, Calogero AE, Singh R, et al.: Coenzyme Q10, oxidative stress, and male infertility: A review. Clin. Exp. Reprod. Med. 2021; 48: 97–104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGharagozloo P, Aitken RJ: The role of sperm oxidative stress in male infertility and the significance of oral antioxidant therapy. Hum. Reprod. 2011; 26: 1628–1640. PubMed Abstract | Publisher Full Text\n\nAlahmar AT: Role of Oxidative Stress in Male Infertility: An Updated Review. J. Hum. Reprod. Sci. 2019; 12: 4–18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRao M, Zhao XL, Yang J, et al.: Effect of transient scrotal hyperthermia on sperm parameters, seminal plasma biochemical markers, and oxidative stress in men. Asian J. Androl. 2015; 17: 668–675.\n\nEftekhari A, Ahmadian E, Azami A, et al.: Protective effects of coenzyme Q10 nanoparticles on dichlorvos-induced hepatotoxicity and mitochondrial/lysosomal injury. Environ. Toxicol. 2018; 33: 167–177. PubMed Abstract | Publisher Full Text\n\nSood B, Keenaghan M: Coenzyme Q10. StatPearls. StatPearls Publishing; 2022.\n\nSalvio G, Cutini M, Ciarloni A, et al.: Coenzyme Q10 and Male Infertility: A Systematic Review. Antioxidants (Basel). 2021; 10: 10. Publisher Full Text\n\nFadhil EB: Ethical approval. Zenodo. 2023.\n\nPeivandi S, Jafarpour H, Abbaspour M, et al.: Effect of letrozole on spermogram parameters and hormonal profile in infertile men: A clinical trial study. Endocr. Regul. 2019; 53: 231–236. Publisher Full Text\n\nGunes S, Hekim GN, Arslan MA, et al.: Effects of aging on the male reproductive system. J. Assist. Reprod. Genet. 2016; 33: 441–454. Publisher Full Text\n\nDai JB, Wang ZX, Qiao ZD: The hazardous effects of tobacco smoking on male fertility. Asian J. Androl. 2015; 17: 954–960.\n\nSharma R, Harlev A, Agarwal A, et al.: Cigarette Smoking and Semen Quality: A New Meta-analysis Examining the Effect of the 2010 World Health Organization Laboratory Methods for the Examination of Human Semen. Eur. Urol. 2016; 70: 635–645. PubMed Abstract | Publisher Full Text\n\nBelloc S, Cohen-Bacrie M, Amar E, et al.: High body mass index has a deleterious effect on semen parameters except morphology: results from a large cohort study. Fertil. Steril. 2014; 102: 1268–1273. Publisher Full Text\n\nCavallini G, Beretta G, Biagiotti G: Preliminary study of letrozole use for improving spermatogenesis in non-obstructive azoospermia patients with normal serum FSH. Asian J. Androl. 2011; 13: 895–897. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShuling L, Sie Kuei ML, Saffari SE, et al.: Do men with normal testosterone-oestradiol ratios benefit from letrozole for the treatment of male infertility? Reprod. Biomed. Online. 2019; 38: 39–45. PubMed Abstract | Publisher Full Text\n\nLoves S, Ruinemans-Koerts J, de Boer H : Letrozole once a week normalizes serum testosterone in obesity-related male hypogonadism. Eur. J. Endocrinol. 2008; 158: 741–747. PubMed Abstract | Publisher Full Text\n\nDel Giudice F, Busetto GM, De Berardinis E, et al.: A systematic review and meta-analysis of clinical trials implementing aromatase inhibitors to treat male infertility. Asian J. Androl. 2020; 22: 360–367. PubMed Abstract | Publisher Full Text\n\nBoon WC, Chow JD, Simpson ER: The multiple roles of estrogens and the enzyme aromatase. Prog. Brain Res. 2010; 181: 209–232. Publisher Full Text\n\nAppasamy M, Muttukrishna S, Pizzey AR, et al.: Relationship between male reproductive hormones, sperm DNA damage and markers of oxidative stress in infertility. Reprod. Biomed. Online. 2007; 14: 159–165. PubMed Abstract | Publisher Full Text\n\nAlahmar AT: The impact of two doses of coenzyme Q10 on semen parameters and antioxidant status in men with idiopathic oligoasthenoteratozoospermia. Clin. Exp. Reprod. Med. 2019; 46: 112–118. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSafarinejad MR: Efficacy of coenzyme Q10 on semen parameters, sperm function and reproductive hormones in infertile men. J. Urol. 2009; 182: 237–248. Publisher Full Text\n\nFawzi HA: Impact of coenzyme Q10 as an adjuvant therapy to letrozole on spermiogram results and sex hormone levels in Iraqi men with infertility; randomized open label comparative study.2023. Publisher Full Text"
}
|
[
{
"id": "204199",
"date": "13 Sep 2023",
"name": "Isarin Thanaboonyawat",
"expertise": [
"Reviewer Expertise Infertility",
"in vitro fertilization",
"fertility preservation",
"IVM",
"embryo culture",
"ovarian tissue cryopreservation",
"implantation",
"probiotics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a randomized, open-label comparative study of sperm quality assessment following combined treatment with coenzyme Q10 and letrozole versus letrozole alone. OAT is widely studied, however, the causes and treatment guidelines are not established. This study suggested a possible combination treatment, however, some key points need to be modified.\nBackground: The first two sentences are not relevant to the heading. It would be better to describe what is known, such as the effect of CoQ10 on sperm quality or male sex hormones; and what aspects need further exploration. Are there any similar studies published? It is better to summarize the results here.\nIntroduction: The content is well-written and easy to understand. Although the mechanisms of sperm protection by CoQ10 and letrozole are elucidated, a thorough review of published articles on the effects of CoQ10 and letrozole treatment on OAT is more important. The rationale for using both drugs in this study should be rigorously discussed. Did the author expect the synergistic function? The present introduction is better summarized to avoid a lengthy introduction.\nCited references are usually those that provide evidence or information for the first time, rather than articles that reuse that information.\nReference 1 needs to be the statement of WHO. Please check it carefully.\nReferences 2 and 3 are not the original articles that reported the prevalence of 15% or the prevalence of malefactors. Please cite the original article and authors who reported this information.\nReference 6 is a minireview, not the original article that provided the information as cited. Please cite the original article and authors who reported this information.\nReference 7 is a review of the significant aspects of irisin actions and its involvement in energy homeostasis and male reproduction. Please cite a more relevant article.\n“Idiopathic oligoasthenoteratozoospermia (iOAT) is associated with faulty spermatogenesis and is characterized by unusually low sperm count, motility, and a large number of dysmorphic spermatozoa in the ejaculate” Please define iOAT clearly with proper reference.\nReference 17: “Oxidative stress (OS) and reactive oxygen species (ROS) are believed to damage the spermatozoa and account for 30 to 80% of infertility cases in men,” The original article needs to be cited.\nMethods: “This registered with ClinicalTrials.gov (NCT05847257) on May 6, 2023.” The RCT was retrospectively registered.\nThe authors are required to provide the details of methods to make the process reproducible.\nHow to randomize the participants? Sealed envelope? How many sets? The proportion of the control and intervention groups is better stated. I suppose it was 1:1?\nHow to determine the sample size? Did you estimate the sample size based on the semen concentration? What is the initial semen concentration and the expected concentration after treatment? If the authors used the semen concentration of Peivandi’s study, did you include the same kind of participants Peivandi included male patients with abnormal parameters of semen fluid based on WHO criteria, which were serum T/E2 ratio < 10 (testosterone mg/dl and estradiol pg/ml).\nFor sample estimation: If the authors assessed multiple parameters, concentration, motility, and morphology, the largest sample size estimated from each parameter will be used. That means if the sample size needed based on concentrations is less than the sample size calculated based on motility, the sample size used for motility should be used. Could you please provide the process of sample calculation?\nIt is better to provide the definition of OAT? How many semen samples per patient were used? How much is the lag time between each sample collection?\nVIDAS® automated quantitative tests are used for plasma and serum. Semen has different components. Using the same instrument may produce different results compared to plasma. Could you please show the evidence to support to use of this instrument?\nHow to measure the semen fluid volume, concentration, motility, etc. Please describe the procedures.\nThe technique of semen preparation for hormonal measurement is crucial. Could you please state the procedures, such as any dilution or centrifugation? Were cryopreservation needed? How?\nFor hormone measurements, please describe how the instrument was used, the settings used, and positive/negative control samples. How to interpret the results of the read. How about the CV of the measurement? What is the measurement range and sensitivity? This information will provide the validity of the study.\nResults:\nCONSORT FLOW CHART Thirty-four and 40 patients were randomized in groups A and B, respectively. There were 5 and 2 patients lost in each group. Why were only 29 patients/group analyzed? Where were the other 9 patients in Group B?\nThe authors presented the protocol analysis. If possible, ITT analysis will be more useful.\nDiscussion:\nWell written.\nAre there any explanations for the mechanisms of CoQ10 in improving sperm concentration?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "10393",
"date": "06 Nov 2023",
"name": "Hayder Fawzi",
"role": "Author Response",
"response": "Answer to reviewer 1 Background: Q/ The first two sentences are not relevant to the heading. It would be better to describe what is known, such as the effect of CoQ10 on sperm quality or male sex hormones; and what aspects need further exploration. Are there any similar studies published? It is better to summarize the results here. A/ This article focuses first and most on infertility, so we started our article in defining the main issue based on well-known definition of WHO, and after we defined infertility, we introduced the intervention as you mentioned. Next the new background. “Infertility is common problem affecting many couples, still many interventions directed to treat infertility with varying outcomes. The aim of this clinical trial was to evaluate the impacts of adding coenzyme Q10 (CoQ10) to letrozole on the results of spermiogram and sex hormone tests in men diagnosed with idiopathic oligoasthenoteratozoospermia (iOAT) syndrome, which is a type of male defective spermatogenesis of unknown etiology.” Introduction: Q/ The content is well-written and easy to understand. Although the mechanisms of sperm protection by CoQ10 and letrozole are elucidated, a thorough review of published articles on the effects of CoQ10 and letrozole treatment on OAT is more important. The rationale for using both drugs in this study should be rigorously discussed. Did the author expect the synergistic function? The present introduction is better summarized to avoid a lengthy introduction. A/ During our initial proposal of the research, we kept in mind possible additive effect at least and at best synergic effect. Cited references are usually those that provide evidence or information for the first time, rather than articles that reuse that information. Q/ Reference 1 needs to be the statement of WHO. Please check it carefully. A/ We changed Ref 1 to more appropriately, as listed below: World Health Organisation. Infertility [Internet]. www.who.int. 2022. Available from: https://www.who.int/health-topics/infertility#tab=tab_1 [Accessed: February 2022] Q/ References 2 and 3 are not the original articles that reported the prevalence of 15% or the prevalence of malefactors. Please cite the original article and authors who reported this information. A/ Ref 2, changed to the following: “Sharlip ID, Jarow JP, Belker AM, Lipshultz LI, et al. Best practice policies for male infertility. Fertility and sterility. 2002;77(5):873-82.DOI:10.1016/S0015-0282(02)03105-9” Ref 3, changed to the following: Q/ Reference 6 is a minireview, not the original article that provided the information as cited. Please cite the original article and authors who reported this information. A/ Ref 6, changed to the following: Ma Y, He X, Qi K, Wang T, et al. Effects of environmental contaminants on fertility and reproductive health. Journal of Environmental Sciences. 2019;77:210-7.DOI:https://doi.org/10.1016/j.jes.2018.07.015 Q/ Reference 7 is a review of the significant aspects of irisin actions and its involvement in energy homeostasis and male reproduction. Please cite a more relevant article. A/ Ref 7, changed to the following: “Kim HH, Schlegel PN. Endocrine manipulation in male infertility. The Urologic clinics of North America. 2008;35(2):303-18, x.DOI:10.1016/j.ucl.2008.01.003” Q/ “Idiopathic oligoasthenoteratozoospermia (iOAT) is associated with faulty spermatogenesis and is characterized by unusually low sperm count, motility, and a large number of dysmorphic spermatozoa in the ejaculate” Please define iOAT clearly with proper reference. A/ New definition: “Idiopathic male infertility is referred to the impairment of sperm parameters without clear male-associated cause, Although physical examination, endocrine, genetic, and biochemical laboratory results for these men are normal, semen analysis can show abnormal findings, they do not have a history of disorders that influence fertility” [1] Minhas S, Bettocchi C, Boeri L, Capogrosso P, et al. European Association of Urology Guidelines on Male Sexual and Reproductive Health: 2021 Update on Male Infertility. European urology. 2021;80(5):603-20.DOI:10.1016/j.eururo.2021.08.014 Q/ Reference 17: “Oxidative stress (OS) and reactive oxygen species (ROS) are believed to damage the spermatozoa and account for 30 to 80% of infertility cases in men,” The original article needs to be cited. A/ Ref 17, changed to the following [2]: Showell MG, Mackenzie-Proctor R, Brown J, Yazdani A, et al. Antioxidants for male subfertility. Cochrane Database Syst Rev. 2014(12):Cd007411.DOI:10.1002/14651858.CD007411.pub3 Methods Q/ “This registered with ClinicalTrials.gov (NCT05847257) on May 6, 2023.” The RCT was retrospectively registered. We gave our explanation inside the article, please refer to the designated section inside “ethical statement”, “ Due to the recent introduction of required clinical trials registration in Iraq, we registered the study retrospectively to assure its transparency.” Q/ The authors are required to provide the details of methods to make the process reproducible. We included all possible methodologies and we adhered to the CONSORT checklist, again if something specific is/are unclear please ask specifically and we will provide an answer. Q/ How to randomize the participants? Sealed envelope? How many sets? The proportion of the control and intervention groups is better stated. I suppose it was 1:1? We implemented a block randomization design in which we divided the participants into 14 blocks (sets) each with a block size of 6 patients stratified by treatment groups, see Link table. The proportion of the control and intervention groups was 1:1 (balanced design). Q/ How to determine the sample size? Did you estimate the sample size based on the semen concentration? What is the initial semen concentration and the expected concentration after treatment? If the authors used the semen concentration of Peivandi’s study, did you include the same kind of participants Peivandi included male patients with abnormal parameters of semen fluid based on WHO criteria, which were serum T/E2 ratio < 10 (testosterone mg/dl and estradiol pg/ml). We estimated the sample by A previous study by Peivandi et al., showed that letrozole 2.5 mg increases sperm concentrations over three months and demonstrated an in improvement by 33% for sperm parameters (concentration after three months of therapy) so we assumed that the use of CoQ10 will increase this value to 55%. Using MedCalc (RRID:SCR_015044) software version 14.8.1, we arrived at 64 patients for both groups to confirm the null hypothesis (with type I error 5% and type II error of 5%), we increased the sample to 74 to account for maximum possible loss in patients being around 15% without affecting the accuracy of the results. Keep in mind that sample size is a method to estimate the sample size, within certain levels of certainty and best to relay on the trial outcomes. Q/ For sample estimation: If the authors assessed multiple parameters, concentration, motility, and morphology, the largest sample size estimated from each parameter will be used. That means if the sample size needed based on concentrations is less than the sample size calculated based on motility, the sample size used for motility should be used. Could you please provide the process of sample calculation? Yes, the largest sample size for sperm concentrations was used. And attached is the output of the MedCal program. See linked figure. Q/ It is better to provide the definition of OAT? How many semen samples per patient were used? How much is the lag time between each sample collection? We included a definition of OAT in the introduction The semen sample was collected four times per patient (once at baseline, after 1 month, after 2 months, and after 3 months) each time we took a single semen sample at each visit. All this information is stated in the article already! Q/ VIDAS® automated quantitative tests are used for plasma and serum. Semen has different components. Using the same instrument may produce different results compared to plasma. Could you please show the evidence to support to use of this instrument? VIDAS is used for assessing serum markers which we mentioned in the “variable measurement” section, it can not measure the semen parameters we measured which include: “sperm volume/ ml, sperm concentration/ ml, total sperm count/ml, progressive sperm motility (%), non-progressive sperm motility (%), immotile sperm (%), normal sperm morphology (%).” We measured using the WHO methods for assessing semen parameters, we added the details inside the new version of the article under the new section “semen fluid analysis”. The samples were collected via masturbation after abstinence of 3 to 4 days directly into a dry, clean disposable wide-mouth plastic container in a private room close to the laboratory in the institute. Immediately after that the samples were carried to laboratory of semen examination then put in an incubator at 37ºC for 30 minutes. After complete liquefaction, the semen analysis was done by macroscopic and microscopic examination according to standard criteria of WHO (2021) Ref: World Health Organization. WHO laboratory manual for the examination and processing of human semen Sixth Edition. 2021. Q/ How to measure the semen fluid volume, concentration, motility, etc. Please describe the procedures. We add a new section that explains seman measurement. Q/ The technique of semen preparation for hormonal measurement is crucial. Could you please state the procedures, such as any dilution or centrifugation? Were cryopreservation needed? How? Regarding these points, we only used VIDIS to assess the hormonal levels, we used the manual methods for assessing the semen parameters and we separated these details inside the article. Q/ For hormone measurements, please describe how the instrument was used, the settings used, and positive/negative control samples. How to interpret the results of the read. How about the CV of the measurement? What is the measurement range and sensitivity? This information will provide the validity of the study. FSH [VIDAS®FSH, bioMerieux SA, France Cat no.:30 407-01, (Measurement range: 0.1–110 mIU/mL, Detection limit: ≤0.1, Intra-assay CV: ≤5%, Inter-assay CV: ≤6%)” estradiol [VIDAS®E2II, bioMerieux SA, France Cat no.: 30 431, “Measurement range: 9 – 3000 pg/mL, Detection limit: 9 pg/mL, Intra-assay CV: ≤7.5%, and Inter-assay CV: ≤9.5%)”] testosterone [VIDAS® Testosterone II, bioMerieux SA, France Cat no.:414320], “Measurement range: 0.1 – 13 ng/mL, Detection limit: 0.1 ng/mL, Intra-assay CV: ≤10%, and Inter-assay CV: ≤4.5%)”] VIDAS is an automated device that gives you the interpretation directly, please refer to the manufacturer's website (https://www.biomerieux-nordic.com/product/vidasr-fertility-panel ). Results: Q/ CONSORT FLOW CHART Thirty-four and 40 patients were randomized in groups A and B, respectively. There were 5 and 2 patients lost in each group. Why were only 29 patients/group analyzed? Where were the other 9 patients in Group B? The authors presented the protocol analysis. If possible, ITT analysis will be more useful. Thank you for your note we had an error in filling the flow chart and we updated it in the article, see linked figure. Discussion: Well written. Q/ Are there any explanations for the mechanisms of CoQ10 in improving sperm concentration? Co Q10 has a powerful antioxidant scavenging free radical and involved in production of mitochondrial energy which is important for maintaining spermatozoa's energy, also protects its membrane from damage by peroxidation of lipid. Ref: Salvio G, Cutini M, Ciarloni A, Giovannini L, Perrone M, Balercia G. Coenzyme Q10 and Male Infertility: A Systematic Review. Antioxidants (Basel, Switzerland) 2021;10( References 1. Minhas S, Bettocchi C, Boeri L, Capogrosso P, et al. European Association of Urology Guidelines on Male Sexual and Reproductive Health: 2021 Update on Male Infertility. European urology. 2021;80(5):603-20.DOI:10.1016/j.eururo.2021.08.014 2. Showell MG, Mackenzie-Proctor R, Brown J, Yazdani A, et al. Antioxidants for male subfertility. Cochrane Database Syst Rev. 2014(12):Cd007411.DOI:10.1002/14651858.CD007411.pub3"
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https://f1000research.com/articles/12-1093
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https://f1000research.com/articles/13-609/v1
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10 Jun 24
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{
"type": "Research Article",
"title": "Validation of the self-report classification tool to determine language dominance in Kannada-English bilinguals",
"authors": [
"Chanchal Chaudhary",
"Gopee Krishnan",
"Chanchal Chaudhary"
],
"abstract": "Background In recent times, the efforts to profile the language characteristics of bilinguals have been extended from mere documentation of proficiency in each language to the determination of language dominance that captures both proficiency and usage (i.e., frequency & contexts) of each language. In multilingual countries, individuals are immersed in various languages in different contexts. With the broader intention to improve the linguistic profiling of bilinguals in countries with similar characteristics, we aimed to adapt and validate the Self-report classification tool in Indian Kannada-English bilinguals.\n\nMethods A group of 88 adult Kannada-English bilingual participants self-rated their language proficiency. We measured their language dominance with the adapted tool. Finally, to objectively measure their language abilities, we used the short version of the Bilingual Aphasia Test.\n\nResults Discriminant analysis of the ratings showed that the self-report classification tool accurately classified our participants into three groups based on language dominance. Both the self-rating and the objective measure of language proficiency supported the (dominance) classifications by the adapted tool.\n\nConclusion Findings show that the adapted self-report classification tool is valid for determining language dominance in Kannada-English bilinguals. Further, the current study shows that this tool is adaptable to novel bilingual language dyads.",
"keywords": [
"Bilingualism",
"Dominance",
"Proficiency",
"Self-report",
"dominance classification"
],
"content": "Introduction\n\nBilinguals are one of the fastest-growing populations worldwide (Puebla et al., 2022; Shin, 2022), and their number is on the constant rise (Guo & Yao, 2022). With approximately half of the world’s population being bilingual (Grosjean, 1992, 2010; Romaine, 2012), bilingualism is becoming a norm (Marian et al., 2007). Being a bilingual has different definitions in the literature. Initially, early studies classified a bilingual as one with equal proficiency in two languages (Lambert et al., 1959). However, the current understanding defines a bilingual as an individual who possesses different levels of proficiency and exposure to two languages (Kremin & Byers-Heinlein, 2021). Bilinguals, being a significant proportion of the population, are employed in research across various disciplines (Gertken et al., 2014). Hence, in studies where the role of language may impact the outcome of research, it becomes essential to understand and thoroughly document the language characteristics of bilinguals (Vicente et al., 2019).\n\nLanguage proficiency and language dominance are essential (Vicente et al., 2019), yet separable (Birdsong, 2014) constructs that should be assessed while recruiting bilinguals for research. Language proficiency denotes the “extent to which a bilingual’s skills in one or two languages meet the age-based native speaker” (Bedore et al., 2012) where a native language can be defined as the language that is acquired from a naturalistic exposure in early childhood (Rothman & Treffers-Daller, 2014). Proficiency also incorporates knowledge of the languages in terms of vocabulary, syntax, and semantics which can be assessed through several linguistic tasks such as vocabulary, oral comprehension, and reading fluency (Gullifer et al., 2020; Marian et al., 2007). As “language is not produced in a vacuum” (Baker, 2011), the structure of languages, their patterns, and contexts of usage all deem relevant measures of communication (Baker, 2011; Lim et al., 2008; Treffers-Daller, 2019) and hence the duration of exposure to languages and the context in which these languages are spoken influence the bilinguals’ proficiency in these languages.\n\nIn the past, subjective tools were the primary means to document language proficiency (Flege et al., 2002; Jia et al., 2006; Li et al., 2006; Marian et al., 2007). Some of these tools (e.g. Flege et al., 2002; Li et al., 2006; Vaid & Menon, 2000) collected language background history, where bilinguals reported information on the age of acquisition of languages, frequency of exposure to language, and usage of languages in different contexts. Other methods include the use of (a) standardized questionnaires (e.g., Language Experience and Proficiency Questionnaire (LEAP-Q), Marian et al., 2007), (b) vocabulary tests, or (c) naming or verbal fluency tasks (Haman et al., 2015; Milton & Alexiou, 2009). Though numerous studies use proficiency as the only construct, studies also show that language dominance factors can alter these proficiency measures. For example, rating lower proficiency for a language when it is used less frequently (Bruin, 2019).\n\nLanguage dominance is a measurable construct that can be coherently determined by dimensions and domains of language (Birdsong, 2014; Treffers-Daller, 2019; Wang 2013). Dimensions of language are determined by competence in a language along with its production and processing, whereas domains of language refer to the context and use of language (Birdsong, 2014; Treffers-Daller, 2019). Studies that have measured language dominance in bilinguals report distinct aspects of bilingualism that are used to determine dominance. While two studies (Flege et al., 2002; Tsui et al., 2019) used self-rating of proficiency along with linguistic tests, others (Bilingual Language Profile: Bedore et al., 2012; Bilingual Dominance Scale: Dunn & Tree, 2009) determined dominance based on self-ratings of proficiency along with ratings on experience, attitude, and language use. Solís-Barroso and Stefanich (2019) compared some of the most used language dominance methods (Bedore et al., 2012; Dunn & Tree, 2009; Flege et al., 2002; Gertken et al., 2014) on Spanish-English bilinguals to determine whether these methods would yield same dominance classification in the participants. The results of the correlation analysis revealed some overlaps between the classification of participants using the Bilingual Language Profile (Bedore et al., 2012) and the Bilingual Dominance Scale (Dunn & Tree, 2009). Flege et al.’s (2002) method of determining dominance with the repetition tasks did not surface to be a good predictor of dominance. Though similarities existed, many bilinguals (20 out of 29) were incorrectly classified. It can be concluded that the currently existing methods for measuring language dominance are not unified and may not provide comparable results when used on the same population (Solís-Barroso & Stefanich, 2019; Birdsong, 2014; Flege et al., 2002). It is also possible that even if the same tool is used across studies, the information used in each tool would yield a different dominance classification in participants (Kremin & Byers-Heinlein, 2021). Hence, it becomes essential that the measurement of dominance in bilinguals uses some systematic guidelines that can be replicated across studies and populations (Lim et al., 2008).\n\nThough English is not the primary language in many countries, it is used (i.e., spoken & written) essentially in formal and educational settings (Harris et al., 2006; Lim et al., 2008). Many individuals are, thus, exposed to a second (often, e.g., English) language from the commencement of their schooling. Similarly, in many multilingual South Asian countries like India and Singapore, individuals relocate to different states for employment purposes (Gullifer, 2020). In such scenarios, they either learn a new language or communicate in a common language. For instance, India is a linguistically diverse country (Upadhyay & Hasnain, 2017), and most states have unique languages. Migration from one state to another for education and employment is frequently observed (Treffers-Daller, 2019) which changes the language experience of such migrants (Bialystok, 2009; Lim et al., 2008). Many individuals experience multilingualism in such countries (Siemund et al., 2021) and necessitates documentation of these linguistic experiences systematically. The measurement method should include proficiency ratings that can be used in any language, as it is difficult to find standardized measures in multiple languages used in such countries (Arun et al., 2013; Lim et al., 2008).\n\nLanguage dominance is an important construct for many researchers, academicians, and clinicians (Schmid & Yılmaz, 2018; Vicente et al., 2019). Considering the language status of Asian population, Lim et al. (2008) proposed a systematic way to determine and document the language dominance. Lim et al. (2008) systematically included dimensions and domains in their language dominance tool that categorizes a person as dominant in a language when he/she fulfils the proficiency criteria along with language frequency and domain. That is, a language is identified as dominant only when it is used frequently (spoken, heard, read, or written) and in a majority of environments (e.g., work, social, and home). For example, individuals were identified as dominant in a language when their proficiency rating in that language varied ‘significantly’ from another. In addition to this, the same language should be spoken and heard daily as well as be read or written at least weekly. Finally, for a language to be dominant, it needs to be used in a minimum of two of the following environments: work, social, and home. In bilinguals,’usage-based approaches’ along with proficiency ratings are recommended to determine language dominance (Birdsong, 2014; Treffers-Daller, 2019). As the language characteristics of the bilinguals used in the Lim et al. (2008) study are quite similar to those in India and many other Asian countries, this tool could serve as a sensitive measure of language dominance in Asian bilinguals. Further, it may be used to document language dominance in individuals speaking different language combinations in many multilingual and multicultural contexts. The non-reliance on any vocabulary, naming, or fluency tests to determine language dominance would greatly facilitate its usage in many languages that do not possess such tests. Thus, the study aimed to validate the self-report classification tool (Lim et al., 2008) in Kannada-English bilinguals.\n\n\nMethods\n\nWe conducted this study in a district of a southern state in India. This is a multilingual district where three languages are spoken primarily by the local population (Kannada, Tulu, & Konkani). Kannada, being the official language of the state of Karnataka, is the common choice among native speakers of all three languages. As stated in the introduction, English is primarily introduced through formal academic means as the second language. The usage of English for communicative purposes in young and middle-aged adults is fostered by the presence of several educational institutions where national and international students pursue their education in this district.\n\nEthical approval (IEC 900/2018) was obtained from the Institutional Ethics Committee (Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee) of the parent institute on December 11, 2018. All the participants signed a written consent form before participating in this study. We recruited 100 native Kannada speakers through word-of-mouth, these included university-going students, research scholars, and working professionals residing in the district. The participants were above 18 years of age and had exposure to English before seven years of age. All individuals that were recruited for the study had Kannada and English as their first or second language. None of them had a history or complaint of any communication/neurological disorder. Median age of all the participants was 22 (18,32) with 61 females [22(18,30)] and 27 males [22 (18,34)].\n\nIn this study, we used the self-report classification tool developed by Lim et al. (2008). With permission from the corresponding author (Dr. Lim, September 11, 2018), this tool (see Lim et al., 2008, pg. 405-410) was minimally modified to suit the linguistic premises of the current study. These changes comprised replacing “Mandarin” with “Kannada” throughout the questionnaire and changing school examination grades. It categorizes the language dominance of a bilingual using three sections: “language proficiency, frequency of language use, and domain of language use” in a self-reporting manner.\n\nTo measure the language performance objectively, pertinent sections from the short version (Krishnan & Mathew, 2017) of the Bilingual Aphasia Test (BAT: Paradis & Libben, 1987) were used in English and Kannada. The BAT was originally developed to assess language deficits in bilinguals with aphasia (Paradis & Libben, 1987). However, it is a cumbersome test battery that requires several hours to administer all subtests. In this context, several languages have short versions of BAT, following the recommendations of Paradis & Libben (1987), including Kannada (Krishnan & Mathew, 2017), one of the languages considered in this study. The short version includes five main categories from the original version, viz. auditory comprehension, reading, repetition, naming, and metalinguistic ability. We used this tool as it is validated in Kannada-English bilinguals (Krishnan & Mathew, 2017).\n\nThe participants were provided with the printed form of the self-report classification tool. They were given two weeks to return the filled forms. We sent reminders every three days up till they returned filled forms or till the end of the response period. No participants were excluded during this phase, as we received the forms from all the participants. Among the 100 respondents, data from 12 participants were excluded due to incomplete information (e.g. not filling the age of exposure (n=7), incorrectly filling the domain of language use (n=5)).\n\nThe rating of language dominance rating procedure:\n\nLanguage Proficiency: The participants self-rated their language proficiency in four sections, viz. understanding (U), speaking (S), reading(R), and writing (W), on a 7-point rating scale in both languages. In addition to the proficiency rating, the participants filled in information on their age of first exposure to both languages and the rankings (1 or 2) on the four sections mentioned above.\n\nFrequency of language use: In this section, the participants indicated how frequently (i.e., every day, every week, every month, every year, or less than once/year) they heard, spoke, read, or wrote each of the two languages.\n\nThe Domain of language use: Here, the participants indicated their usage of the two languages across three domains: viz., home, work, and social.\n\nFollowing this, to obtain the objective measure of language proficiency, we administered the short version (Krishnan & Mathew, 2017) of the BAT (Paradis & Libben, 1987) to the valid (n=88) respondents in Kannada and English. Participants were informed regarding the test time, and an appointment was scheduled within the same week of obtaining the filled form. We scheduled the time slots for test administration based on participants’ convenience. The test took approximately 50-60 minutes to administer.\n\n\nResults\n\nThe participants (n=88) were divided into three groups based on their dominance rating such as: a) English-dominant (ED: n=25), b) Kannada-dominant (KD: n=16), and c) balanced bilinguals (BB: n=47). The median age of the participants in each group, their age of exposure, duration of exposure, and years of formal education in Kannada and English languages, are given in Table 1. The median age of participants across the groups was comparable. All the participants in this study were exposed to Kannada before one year of age. The participants in the ED group were exposed to English at an earlier age than the KD and BB groups. The duration of exposure to both languages across the groups was comparable. However, the number of years of formal education varied between the groups. The participants in the KD and BB groups had similar years of formal education. Most of the individuals in the ED group reported a greater number of years of formal education in English compared to the other groups. This might be due to their early enrolment in the English medium of instruction.\n\nSubjectively, the participants self-rated their language proficiency on a seven-point rating scale (Lim et al., 2008). As an objective measure of the language proficiency, we administered the short version of bilingual aphasia test (Paradis & Libben, 1987) to the participants. The findings of both these measures are described below.\n\nThe participants self-rated their proficiency in understanding, speaking, reading, and writing in both the languages on a seven-point rating scale. Following Lim et al. (2008), we categorized a language as dominant if it fulfilled two of the three following criteria: “a) the difference in total scores between the languages >0, b) the difference in the scores between the languages for understanding, speaking, or reading is > +1 or < -1, and c) the difference in the scores between the languages for understanding, speaking, or writing is > +1 or <-1.” In addition to these criteria, the dominant language had to be used frequently (Spoken or heard daily, along with either reading or writing weekly). Similarly, the dominant language should be used in at least two of the three environments (i.e., home, school/work, or social).\n\nThe visual inspection of the data showed that the ED group reported higher proficiency in English [24(23,27)] compared to Kannada [18(16,20)], and the KD group reported higher proficiency in Kannada [26(24.50, 27.50)] compared to English [19.50(17, 22)]. To determine if these scores were significantly different from each other, Kruskal-Wallis test was administered as the data followed a non-normal distribution. This test is a non-parametric test that compares medians of two or more groups. The balanced group participants reported similar proficiency ratings in both Kannada and English languages (p<0.001). On English proficiency scores, significant differences were observed between ED and KD groups (p<0.001) and KD and BB groups (p<0.001), however, no (significant) differences were found between ED and BB groups (p=0.11). On Kannada proficiency, KD and BB showed similar ratings (p=0.089), whereas significant differences were observed between ED and KD (p<0.001) and ED and BB groups (p<0.001).\n\nThe scoring of BAT was done per the instructions provided by the test adapters. All correct responses were scored +1, and wrong/no responses were scored zero. Raw scores were calculated for BAT in English and Kannada by adding the respective subtest scores.\n\nThe Kruskal-Wallis test was administered to determine whether there was any significant difference in the average BAT scores in English among the three dominance groups (ED, KD, & BB) as data violated the normality assumption. Findings revealed a significant difference in the average BAT scores in English between different dominance groups (p<0.001). Similarly, the BAT scores in Kannada were compared among the three dominance groups (ED, KD, & BB) and were found to be significant (p<0.001) (see Table 2). Bonferroni adjustments were used to determine the difference between BAT scores in English and Kannada across three groups. Except for the Kannada BAT scores between KD and BB groups (p=0.075), all other groups showed significant differences in English and Kannada BAT scores.\n\nAs the frequency and domain data were categorical, mode values were used for the analysis. For the frequency of language usage, similar modal values showed that all participants spoke and heard Kannada and English languages daily (mode=1). However, stark differences were seen in English and Kannada writing. Participants across all three groups rarely used Kannada for writing (KD and BB modal value=3; ED: modal value=5) compared to English (modal value=1). This is consistent with the participants having English as the medium of formal language instruction. However, the participants in the KD group read Kannada (modal value=1) more frequently than the ED and BB groups (mode value=2). In the domain of language use, all participants across the three groups used Kannada at home. The ED group used English at work and socially, whereas the other groups (KD & BB) used Kannada at work and in social settings. Invariably at work, most of the participants spoke in English.\n\nAkin to the original study (Lim et al., 2008) and other studies that classify bilinguals based on the language profile (Li et al., 2006; Schmid & Yılmaz, 2018), we used discriminant analysis to determine the accuracy of the classification tool to determine the language dominance of Kannada-English bilinguals recruited for this study. In data where dependent variable is categorical in nature (e.g., groups), discriminant analysis can be used to understand how the independent (or predictor) variables contribute to these categories. Further, such an analysis can determine whether significant differences exist in these categories based on the independent variables (Al-Karkhi & Alqaraghuli, 2019; Timm, 2002). Thus, the discriminant analysis may be used to predict the accuracy of classification. The discriminant analysis was performed by keeping language dominance (based on the classification tool) as the grouping variable and the independent variables were raw scores of language proficiency, frequency of language use, and domain of language use in both languages. The results showed an overall 88.6% classification rate, which was significant (p<0.001). The results are provided in Table 3.\n\nThe discriminant analysis classified the three groups of participants as follows: the English-dominant group - 96% (24/25), the Kannada-dominant group - 69% (11/16), and the balanced bilingual group - 91.5% (43/47). To determine if the objective language test scores supported these classifications, scores of the Bilingual Aphasia Test in English and Kannada languages were compared across the groups. The measures used for the test were auditory comprehension, reading, repetition, naming, and metalinguistic ability in both languages. The participants in the BB group obtained identical scores in their performance in English [303(296-308)] and Kannada [303(291-306)]. Participants in the English-dominant group obtained higher scores in English [310(308-312)] compared to Kannada [278(276-285)], whereas those in the Kannada-dominant group obtained higher scores in Kannada [308(305-312)] compared to English [286(276-293)].\n\n\nDiscussion\n\nAcross the world, the linguistic background of the bilingual population is constantly changing due to the increase of such population (Vicente et al., 2019) and migrations (Moyer & Rojo, 2007). In many countries, bilingualism is becoming a norm rather than an exception (Ramírez-Esparza et al., 2020). The effect of this increase is more apparent in multilingual Asian countries where English is becoming the language of instruction from an early stage of academic training and subsequent as well as for employment (Bhattacharya & Chandrasekhar, 2020). To quantify the language abilities of bilinguals, objective measures/tools are needed. Language dominance has gained the attention of several researchers across the globe as this construct takes into account the frequency and domains of language use in bilinguals. In today’s world, bilinguals are immersed in different linguistic environments throughout their day, which requires the usage of different languages in different contexts (Romaine, 2012). Hence, dominance becomes a more relevant measure to document the language profile of bilinguals.\n\nThe current study was an attempt to validate the self-report classification tool (Lim et al., 2008) to determine language dominance for use in an Indian population. With permission from the original authors, we (minimally) modified the tool to suit the linguistic premises of the current study. Subsequently, we administered this tool to 88 Kannada-English bilingual adults to examine its suitability to determine the language dominance in these bilinguals. We chose this tool for our participants as the language characteristics in India resemble to that of the participants recruited to the original study (Mandarin-English bilinguals residing in Singapore). Further, we used a similar analysis by Lim et al. (2008) to examine if the results could be replicated. Findings from the discriminant analysis showed that the tool was able to classify the Kannada-English bilinguals used in our study as English-dominant, Kannada-dominant, and balanced bilinguals with an overall correct classification score of 88.6% that was found to be significant (p<0.001). The self-ratings of proficiency, frequency of language use, and domain of use emerged as effective measures of dominance classification.\n\nThe Bilingual Aphasia Test (Paradis & Libben, 1987) scores supported the accuracy of the language dominance-based classification of our participants. In the Asian context, there is a generalized dearth of culturally and linguistically standardized tests to determine language abilities (Grosjean, 2010; Lim et al., 2008). We chose the Bilingual Aphasia Test as this test has been validated for use in the Indian population (Bhat & Chengappa, 2003; Krishnan & Mathew, 2017). In addition to these advantages, BAT in both languages has similar items and scoring that making it easier to administer and compare the scores between languages. The participants in the English-dominant and Kannada-dominant groups performed better in English and Kannada languages, respectively. The participants in the balanced bilingual group obtained similar scores in their Kannada and English language performance. Most of the comparisons between the Kannada and English Bilingual Aphasia Test scores showed significant differences across the three dominance groups, except for the Kannada scores of Kannada-dominant and balanced bilingual groups. This could have been due to certain similarities in the participants in terms of the usage of languages. Compared to the English-dominant group who used Kannada only at home, participants in the Kannada-dominant and balanced bilingual groups used Kannada at home and in their social circles. This finding is like the participants’ performance in Lim et al. (2008), where the receptive vocabulary scores (on the “Multilingual British Picture Vocabulary Scale”, Dunn et al., 1982) between Mandarin-dominant group and the balanced bilingual group were not distinguishable. Together, these findings highlight the similarities between the language profiles of bilinguals in different Asian countries.\n\nOther factors like age of acquisition (Paap et al., 2014), formal years of instruction, and length of exposure to both languages did not support the language dominance findings. This shows that these factors may not play a vital role in differentiating the bilingual population in terms of their language dominance when the bilinguals are exposed to both languages early in their years (Bruin, 2019).\n\nFindings from this study show that the self-report classification tool can serve as a potential tool to accurately classify the Kannada-English bilinguals into their language dominance groups. It is essential to have such a classification tool in multilingual Asian countries like India, where bilinguals are used for research routinely. Further, the current findings entail that this tool could be confidently used to determine the language dominance in bilingual participants from bi-multilingual contexts like the one in the current study.\n\nKannada is spoken across the Karnataka state of India. However, the participants were recruited from a single district where the prominent bilingual dyad was Kannada-English. Though Kannada is the native language considered in this study, the dialectical variations of this language could not be addressed due to the sampling frame.\n\nEthical approval (IEC 900/2018) was obtained from the Institutional Ethics Committee (Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee) of the parent institute on December 11, 2018.\n\nAll the participants signed a written consent form before participating in this study.",
"appendix": "Data availability statement\n\nOpen Science Framework: Self-report classification tool data, https://doi.org/10.17605/OSF.IO/8Z79D (Krishnan & Chaudhary, 2024a).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nOpen Science Framework: Extended Data_Self report classification tool questionnaire, https://doi.org/10.17605/OSF.IO/KZWHT (Krishnan & Chaudhary, 2024b).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nWe thank the authors of the original article, for permitting us to use the tool for this study and for providing clarifications whenever needed on the dominance determination criteria.\n\n\nReferences\n\nAl-Karkhi AF, Alqaraghuli WA: Applied statistics for environmental science with R. Elsevier; 2019.\n\nArun P, Chavan BS, Bhargava R, et al.: Prevalence of specific developmental disorder of scholastic skill in school students in Chandigarh, India. Indian J. Med. Res. 2013; 138(1): 89–98. PubMed Abstract\n\nBaker C: Foundations of bilingual education and bilingualism. Multilingual matters; 2011.\n\nBedore LM, Peña ED, Summers CL, et al.: The measure matters: Language dominance profiles across measures in Spanish–English bilingual children. Biling. Lang. Congn. 2012; 15(3): 616–629. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBhat S, Chengappa S: Code Switching in Normal and Aphasic Kannada-English Bilinguals.2003.\n\nBhattacharya L, Chandrasekhar S: India’s search for link language and progress towards bilingualism (No. 2020-015). Mumbai, India: Indira Gandhi Institute of Development Research; 2020.\n\nBialystok E: Bilingualism: The good, the bad, and the indifferent. Biling. Lang. Congn. 2009; 12(1): 3–11. 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Publisher Full Text\n\nGrosjean F: Bilingualism, biculturalism, and deafness. Int. J. Biling. Educ. Biling. 2010; 13(2): 133–145. Publisher Full Text\n\nGullifer JW, Kousaie S, Gilbert AC, et al.: Bilingual language experience as a multidimensional spectrum: Associations with objective and subjective language proficiency. Appl. Psycholinguist. 2020; 42(2): 245–278. Publisher Full Text\n\nGuo W, Yao S: Cognitive Benefits of Being Bilingual for Young Children: A Literature Review. 2021 International Conference on Social Development and Media Communication (SDMC 2021). Atlantis Press; 2022, January; pp. 654–660.\n\nHaman E, Łuniewska M, Pomiechowska B: Designing cross-linguistic lexical tasks (CLTs) for bilingual preschool children. Assessing multilingual children: Disentangling bilingualism from language impairment. 2015; pp. 196–240. Publisher Full Text\n\nHarris CL, Gleason JB, Aycicegi A: When is a first language more emotional? Psychophysiological evidence from bilingual speakers. 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Publisher Full Text\n\nLi P, Sepanski S, Zhao X: Language history questionnaire: A web-based interface for bilingual research. Behav. Res. Methods. 2006; 38(2): 202–210. PubMed Abstract | Publisher Full Text\n\nLim VP, Liow SJR, Lincoln M, et al.: Determining language dominance in English–Mandarin bilinguals: Development of a self-report classification tool for clinical use. Appl. Psycholinguist. 2008; 29(3): 389–412. Publisher Full Text\n\nMarian V, Blumenfeld HK, Kaushanskaya M: The Language Experience and Proficiency Questionnaire (LEAP-Q): Assessing language profiles in bilinguals and multilinguals.2007; 50(4): 940–967.\n\nMilton J, Alexiou T: Vocabulary size and the common European framework of reference for languages. Vocabulary studies in first and second language acquisition: The interface between theory and application. 2009; pp. 194–211. Publisher Full Text\n\nMoyer MG, Rojo LM: Language, migration, and citizenship: New challenges in the regulation of bilingualism. Bilingualism: A social approach. 2007; pp. 137–160. Publisher Full Text\n\nPaap KR, Johnson HA, Sawi O: Are bilingual advantages dependent upon specific tasks or specific bilingual experiences? J. Cogn. Psychol. 2014; 26(6): 615–639. Publisher Full Text\n\nParadis J, Libben G: The assessment of bilingual aphasia: the Bilingual Aphasia Test.1987.\n\nPuebla C, Fievet T, Tsopanidi M, et al.: Mobile-assisted language learning in older adults: Chances and challenges. ReCALL. 2022; 34(2): 169–184. Publisher Full Text\n\nRamírez-Esparza N, García-Sierra A, Jiang S: The current standing of bilingualism in today’s globalized world: A socio-ecological perspective. Curr. Opin. Psychol. 2020; 32: 124–128. PubMed Abstract | Publisher Full Text\n\nRomaine S: The bilingual and multilingual community. The handbook of bilingualism and multilingualism. 2012; pp. 443–465. Publisher Full Text\n\nRothman J, Treffers-Daller J: A prolegomenon to the construct of the native speaker: Heritage speaker bilinguals are natives too!. Appl. Linguist. 2014; 35(1): 93–98. Publisher Full Text\n\nSchmid MS, Yılmaz G: Predictors of language dominance: An integrated analysis of first language attrition and second language acquisition in late bilinguals. Front. Psychol. 2018; 9: 1306. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShin JH: Adolescent Korean returnees’ perceptions of the change of language learning contexts as bilingual learners. Applied Linguistics Review. 2022.\n\nSiemund P, Al-Issa A, Leimgruber JR: Multilingualism and the role of English in the United Arab Emirates. World Englishes. 2021; 40(2): 191–204. Publisher Full Text\n\nSolís-Barroso C, Stefanich S: Measuring language dominance in early Spanish/English bilinguals. Languages. 2019; 4(3): 62. Publisher Full Text\n\nTimm NH: Discriminant and classification analysis. Applied Multivariate Analysis. New York, USA: Springer-Verlag; 2002; pp. 419–444.\n\nTreffers-Daller J: What defines language dominance in bilinguals? Annu. Rev. Linguist. 2019; 5: 375–393. Publisher Full Text\n\nTsui RKY, Tong X, Chan CSK: Impact of language dominance on phonetic transfer in Cantonese–English bilingual language switching. Appl. Psycholinguist. 2019; 40(1): 29–58. Publisher Full Text\n\nUpadhyay RK, Hasnain SI: Linguistic diversity and biodiversity. Lingua. 2017; 195: 110–123. Publisher Full Text\n\nVaid J, Menon R: Correlates of bilinguals’ preferred language for mental computations. Spanish Appl. Linguist. 2000; 4(2): 325–342.\n\nVicente M, Calandruccio L, Miller MK, et al.: Language proficiency and dominance considerations when working with Spanish–English bilingual adults. Am. J. Audiol. 2019; 28(3): 724–729. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang X: Language dominance in translation priming: Evidence from balanced and unbalanced Chinese–English bilinguals. Q. J. Exp. Psychol. 2013; 66(4): 727–743. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "294859",
"date": "09 Jul 2024",
"name": "Dr Vandana V P",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe current study adapts and validates an existing self-report -based classification tool developed for language dominance.\n\nThe authors used discriminant function analysis to determine the validity of the adapted tool, and they claim that it can accurately categorize dominant and balanced bilinguals, which is supported by an objective measure (Bilingual Aphasia test). It is crucial to determine language dominance while selecting the language of intervention in a bilingual context, such as India. Conducting objective measures to determine language dominance is time-consuming. Hence, self-reported questionnaires that include measures of proficiency, frequency, and language use context are quick, easy and more reliable. Here are some comments and clarifications which will improvise the article. Major:\n\nThe clinical application/ utility of the classification tool is majorly missing in this article. We would recommend you to highlight on the this. For the initial recruitment of participants, what was the standard criteria/definition of bilinguals used by the researcher? Were these participants true bilinguals or did they know any more languages? If we consider the age and education of these participants, they all would have studied three languages in school. Further, the average scores on proficiency, frequency and domain (context of use) of the three language groups can be provided in a table format for the readers for better understanding (can be added within Table 1). Post hoc comparisons for proficiency, frequency and domain can also be added in the analysis. Even though the rating and scoring for language proficiency is mentioned in the results section we would recommend you to include the rating and overall scoring in detail under the materials section.\nThe subheading “The rating of language dominance rating procedure” in the procedure section and the linguistic proficiency (under results section), first paragraph of Self-reported language proficiency (under results section) can be combined together and moved under the subheading of materials. This will bring clarity in how you have decided the language dominance and classified the participants before reading the results.\nPlease mention who administered Bilingual Aphasia Test and were they proficient in both the languages? English and Kannada versions of the test were conducted on the same day? Also, who divided the participants into subgroups based on the self-ratings? The one who analysed and classified them into ED, KD and BB and the one who administered Bilingual Aphasia Test were same? Authors can add an example to explain how the decision of language dominance based on the score obtained in the self -report classification tool. Authors have reported the overall 88.6% classification rate, which was significant (p<0.001). The classification rate for each subgroup would also provide some insights.\nAs mentioned in the article Table 3 is not providing the results of Discriminant Function analysis. This needs rectification.\nThe authors have done BAT separately to support the classification accuracy in the study. Was there any correlation done between total score obtained on proficiency, frequency and context of use with BAT total score? Have the authors carried out any correlation between the age of exposure, years of language instructions, years of language exposure in the current study to say that these factors “may not play a vital role in differentiating the bilingual population in terms of their language dominance when the bilinguals are exposed to both languages early in their years” even in Indian context?\n\nMinor:\nThe authors have provided the factors that are used to determine language dominance. It would be better to state a clear definition of language dominance and the distinction between language dominance and proficiency also in the introduction section. It is written in the article that “Studies that have measured language dominance in bilinguals report distinct aspects of bilingualism that are used to determine dominance.” Please mention which studies they are referring to and what are the distinct aspect that they refer to. “As the language characteristics of the bilinguals used in the Lim et al. (2008) study is quite similar to those in India and many other Asian countries, this tool could serve as a sensitive measure of language dominance in Asian bilinguals.” It is better to elaborate the similarities with respect to sociolinguistic environment in India and other Asian country you are referring to. In your observation, was the highly proficient language and the dominant language were same for the participants included in the study? Does L1 and L2 differed among all the subgroups? The self-report classification tool was only in English? Was it comprehensive to all participants (even Kannada dominant group)?\nIn the results “The balanced group participants reported similar proficiency ratings in both Kannada and English languages (p<0.001)”. when the groups perform similar there should not be any significance difference in scores. In that sense, p value you have mentioned seems incorrect. Please rectify.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "294862",
"date": "16 Jul 2024",
"name": "Manaswita Dutta",
"expertise": [
"Reviewer Expertise Adult Neurogenic Communication Disorders",
"Bilingualism in healthy aging and neurological impairment."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this interesting work. The study aims to validate a self-report language dominance classification tool developed by Lim et al. (2008) for Kannada-English bilinguals in India. While the study is well-executed, the manuscript would benefit from further revisions. Specifically, it is recommended that the introduction be expanded to provide a more comprehensive overview of the existing literature. Additionally, more details are needed in the methodology and results section to enhance clarity and ensure replicability. Furthermore, in the discussion section, it would be helpful to explore how this classification tool could advance the field and its potential applications in clinical and research settings. It is also important to address the study's limitations in more detail. Please see below for my detailed comments/suggestions:\n\nAbstract: 1. Please cite \"the self-report classification tool\" since it is the original measure you are referring to here. Or else it is not clear which tool you are referring to.\nIntroduction: 1. \"Bilinguals, being a significant proportion of the population, are employed in research across various disciplines (Gertken et al., 2014).\" -- such as? Which \"various disciplines\" are being to referred to here? 2. \"While two studies (Flege et al., 2002; Tsui et al., 2019) used self-rating of proficiency along with linguistic tests, others (Bilingual Language Profile: Bedore et al., 2012; Bilingual Dominance Scale: Dunn & Tree, 2009) determined dominance based on self-ratings of proficiency along with ratings on experience, attitude, and language use. Solís-Barroso and Stefanich (2019) compared some of the most used language dominance methods (Bedore et al., 2012; Dunn & Tree, 2009; Flege et al., 2002; Gertken et al., 2014) on Spanish-English bilinguals to determine whether these methods would yield same dominance classification in the participants.\" -- this is a an awkward framing of the sentence. Please consider rephrasing. Also, when summarizing studies consider providing more information for the reader. For instance, what populations did Flege et al., 2002; Tsui et al., 2019) investigate? Do you mean all studies cited here were done on Spanish-English bilinguals? 3. \"The results of the correlation analysis revealed some overlaps between the classification of participants using the Bilingual Language Profile (Bedore et al., 2012) and the Bilingual Dominance Scale (Dunn & Tree, 2009).\" -- correlations among what variables. Please specify. 4. \"Flege et al.’s (2002) method of determining dominance with the repetition tasks did not surface to be a good predictor of dominance.\" -- Please clarify for the reader what this \"repetition tasks\" entailed? Were these word repetition tasks or phrase level tasks? How would this help determine dominance? 5. \"Though similarities existed, many bilinguals (20 out of 29) were incorrectly classified.\" -- You will need to add more information to clarify these findings for the reader. For instance, in this context, what does \"though similarities existed\" mean? When you say \"bilinguals\" what languages did they speak? 6. \"It is also possible that even if the same tool is used across studies, the information used in each tool would yield a different dominance classification in participants (Kremin & Byers-Heinlein, 2021).\" - Why is that? Please state the causes for these discrepancies clearly in the text. 7. Since you are talking about English in the preceding sentence, would it be better to say, \"Many individuals are, thus, exposed to English (often as a second language) from the commencement of their schooling.\"? 8. \"For example, individuals were identified as dominant in a language when their proficiency rating in that language varied ‘significantly’ from another. -- Please rephrase - isn't this obvious? How does this sentence add to the discussion? 9. \"In addition to this, the same language should be spoken and heard daily as well as be read or written at least weekly. Finally, for a language to be dominant, it needs to be used in a minimum of two of the following environments: work, social, and home.\" -- This is similar to what you have said in the earlier sentence starting with \"That is, a language is identified as dominant...\" I recommend merging this and the previous sentence with the information you have provided before. 10. \"As the language characteristics of the bilinguals used in the Lim et al. (2008) study are quite similar to those in India and many other Asian countries, this tool could serve as a sensitive measure of language dominance in Asian bilinguals.\" -- Not all Asian languages are similar to Indian languages structurally. So please specify the languages studied in the Lim et al. (2018) paper and elaborate on how you think there is similarity among Indian and these Asian languages. This is particularly helpful for readers who are not familiar with these Asian languages. 11. \"the study aimed to validate the self-report classification tool (Lim et al., 2008) in Kannada-English bilinguals.\" -- Considering that your study leverages the tool developed by Lim et al. (2008), it would be important to provide more information on this tool for readers for purposes of clarity and replication. The information provided in its current form is bare minimum. 12. The rationale for the study needs to be stronger. It is not entirely clear in the manuscript how your study extends and adds to the existing literature. For instance, a discussion of tools that are commonly used in the Indian context is missing. What tools have been used in studies to evaluate Kannada-English speakers in prior studies (healthy aging and neurological impairments)? Furthermore, self-report tools have been used previously in Indian languages (e.g., Bilingual Dominance Scale by Dunn & Tree, 2009 (Ref 1) in Bose et al., 2022 (ref 2); Dutta et al., 2024(Ref 3) ; Patra A, et.al., 2020 (Ref 4) aphasia paper). Such studies are not represented in the authors' review of literature. Citing the existing studies, it would be helpful if you can highlight the shortcomings of these tools and how your validated tool would fill these empirical gaps.\nMethods: 1. Consider adding some citations in the first paragraph where you introduce the language of Kannada to support your claims. Ethnography and Indian Census stats may be helpful here. Also, a brief description of the language structure (and how distinct it is from English) would be helpful. Again, this is helpful for readers unfamiliar with the languages. 2. Consider adding this adapted tool as an Appendix material just like Lim and colleagues did. It would be helpful to see how exactly the original tool was adapted for Kannada-English speakers? 3. Language was assessed using the BAT. Was any hearing/vision or cognitive screenings done to ensure participants were able to perform the study tasks appropriately? If so, please report this data.\nResults: Well-summarized and appropriate statistical analyses conducted. 1. Table 1: Remind the readers the sample size in each subgroup. 2. Clarify to the reader how linguistic proficiency is different from self-reported language proficiency? Both are self-reported. Linguistic looks at overall proficiency vs. language proficiency looks at each language domain? 3. Multiple comparisons were carried out. Were the p-values corrected for in all analyses? 4. Please provide the total BAT scores for each subgroup in Table 2. 5. \"The participants in the BB group obtained identical scores in their performance in English [303(296-308)] and Kannada [303(291-306)]. Participants in the English dominant group obtained higher scores in English [310(308-312)] compared to Kannada [278(276-285)], whereas those in the Kannada-dominant group obtained higher scores in Kannada [308(305-312)] compared to English [286(276-293)].\" -- Are these median values and ranges? Please label the numeric data within the text.\nDiscussion: 1. Further discussion of the potential clinical and research implications of this validated tool is warranted. How does this validation extend the literature whereas other tools have been used in Indian languages? How does your study address the research gap? 2. Other limitations and potential directions that need to be addressed: 2.a. This tool its present form only be used with Kannada-English bilinguals; therefore there is a need for future research in other Indian languages. 2.b. Was power analysis done? If so, please report. 2.c. One of your subgroups (BB) had almost double the number of participants compared to the rest two subgroups. This could have potentially influenced the results and needs to be acknowledged in the limitations.\nMinor comments: 1. \"Many individuals experience multilingualism in such countries (Siemund et al., 2021) and necessitates documentation of these linguistic experiences systematically.\" -- it should be \"this necessitates\". 2. \"Considering the language status of Asian population, Lim et al. (2008) proposed a systematic way to determine and document the language dominance.\" -- add \"the\" before Asian population. 3. \"We administered the short version of bilingual aphasia test (Paradis & Libben, 1987) to the participants. -- Standardized test names should be in upper case (i.e., Bilingual Aphasia Test).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "294865",
"date": "18 Jul 2024",
"name": "Brendan Stuart Weekes",
"expertise": [
"Reviewer Expertise Bilingualism"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThere are two problems with this study that merit further discussion. First, the BAT is known to be quite limited in reliability and validity. I think it is necessary to explain how this tool was translated into Kannada. Specifically, data on the reliability and validity of the translation for use with non-brain injured participants is essential (1). Second, there is general agreement among psycholinguists that naming objects is the gold standard for measuring proficiency in bilingual speakers. It is certainly a more reliable method and also ecologically valid. I recommend further work to examine the validity of the self rating instrument using an objective method of language proficiency. Another relevant point is the lack of methodological rationale and theoretical context provided for the research. I recommend Ramanujan and Weekes (Ref 1) 2)on proficiency measures in Hindi speakers as one possible solution.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-609
|
https://f1000research.com/articles/13-608/v1
|
10 Jun 24
|
{
"type": "Research Article",
"title": "Corneal tissue engineering: From research to industry, quality of life impact, and Latin American ophthalmologists' perspectives",
"authors": [
"David E Rodríguez Fuentes",
"Katiana Flores Nucamendi",
"Jorge E. Valdez-García",
"Cuevas Díaz Duran Raquel",
"Vidal-Paredes Isaac Alejandro",
"Oneill Cirian",
"Judith Zavala",
"David E Rodríguez Fuentes",
"Katiana Flores Nucamendi",
"Jorge E. Valdez-García",
"Cuevas Díaz Duran Raquel",
"Vidal-Paredes Isaac Alejandro",
"Oneill Cirian"
],
"abstract": "Background Tissue engineering research aims to address the global shortage of donated corneal tissue, yet challenges persist in clinical translation. This study assesses the pathway from basic research to clinical adoption in corneal tissue engineering.\n\nMethods Bibliometric and patent analyses were conducted using the Web of Science-Core Collection and Lens databases to identify top authors, countries, journals, publication trends, inventors, patent statuses, and affiliated companies. A quality-adjusted life year (QALY) analysis compared engineered corneal endothelium to full keratoplasty. A pilot study surveyed thirty ophthalmologist surgeons from eight Latin American countries.\n\nResults A strong upward publication trend (R2 = 0.89, p = 1.53x10^-9) in corneal endothelium engineering was observed over the past decade, led by the USA, China, and Japan. Among 614 research papers, 26 patents and 10 companies were identified. Engineered corneal endothelium showed a QALY gain of 0.74 versus 0.07 of corneal transplants. Most survey respondents (97%) expressed interest in adopting engineered corneal endothelium for transplantation if affordability, biocompatibility, and functionality were assured.\n\nConclusions While tissue engineering offers promise in alleviating corneal scarcity, a significant gap remains between scientific advancements and clinical adoption, presenting “death valleys.” Addressing this requires more efficient navigation of the interplay between scientific progress, technology adoption, and clinical practice.",
"keywords": [
"corneal tissue engineering",
"bibliometric analysis",
"patent analysis",
"clinical adoption",
"technology transfer"
],
"content": "1. Introduction\n\nAlthough corneal transplants are the most common type of transplant worldwide, a shortage of tissue donors hinders the need for necessary surgeries, leaving most patients without access to surgery that could restore their vision. Currently, only one cornea is available globally for every 70 individuals who are needed, and the majority of low- and middle-income countries lack access to eye banks.1 The International Agency for the Prevention of Blindness reports 12.7 million people on the waiting list for corneal tissue donors, making this a global need.2 Along with full cornea transplantation (penetrating keratoplasty), other surgical techniques involving only the transplantation of the corneal endothelium, such as Descemet membrane endothelial keratoplasty (DMEK) and Descemet stripping endothelial keratoplasty (DSEK), have been developed. However, all these surgical procedures have common limitations, such as rejection of the graft, graft detachment, and loss of cell viability in the middle term, which results in the need for an additional graft in most cases.3,4\n\nIn response to this issue, the field of tissue engineering applied to the corneal endothelium has emerged as a significant and potentially effective therapeutic intervention path. Several methods have emerged for isolating and harvesting corneal endothelial cells, as have approaches for producing scaffolds for the transplantation of these cells, such as decellularized stroma and other biomaterials.5 This is demonstrated by the growing trend in publications in the field in the last 20 years.6 Although these developments hope to alleviate the current scarcity of corneal tissue for transplants, the pathway for adopting emergent technologies in clinical practice faces two “death valleys”: the transition between academic research and technology transfer and then clinical practice adoption.7,8 Several factors influence this, including a shortage of multidisciplinary approaches, lack of funding, and practices in the technology transfer process, leading to a gap between scientific advances and practical implementation.\n\nThe goal of scientific progress is to benefit society. Quality-adjusted life years (QALYs), which enable us to estimate the potential impact of a novel treatment in contrast with the gold standard treatment in terms of quality of life beyond cost-effectiveness, serve as helpful tool to support the clinical adoption of emerging technologies.9 Prior research evaluated two surgical methods for transplanting corneal endothelium in terms of QALYs10 and the results of cost reduction between the use of donor corneal tissue obtained from eye banks and the transplantation of engineered corneal endothelium.11\n\nWe aimed to trace the trajectory from fundamental research to practical clinical application in the realm of corneal transplantation. We delve into the intricate interplay between scientific progress, technology adoption, and clinical practice to shed light on the barriers hindering the translation of innovative technologies into practical applications. This exploration is not merely a pursuit of academic curiosity but also a call for action, emphasizing the urgent need for sustained collaboration, financial support, and further in-depth studies. The aim of this study was to bridge the persistent gap between theoretical promise and practical implementation, ultimately revolutionizing the landscape of corneal transplantation for the improvement of global eye health.\n\n\n2. Methods\n\n2.1.1 Search strategy\n\nWe searched the Web of Science-Core Collection (WOS-SCC)12 database using topic as a field of search with the following keywords: tissue engineering, regenerative, reconstruction, corneal endothelium, and descement in the following query: TS=(“tissue* engineer*” OR regener* OR reconstruct*) AND TS=((cornea* AND endothel*) OR descement*). This search yielded a total of 1030 articles. The documents were then filtered by document type, including only original articles published in any language between 2003 and 2023. The data were searched and extracted on the same day (June 29, 2023).\n\nThe full records, including the cited references of all 614 selected articles in plain text format from the WOS-SCC, were exported. The raw file was uploaded to VOS-Viewer Software13 https://www.vosviewer.com/ to screen the author’s names and to create a thesaurus file. The ‘found and replace’ function was used in open-line software to update all the information in the database and to make the metadata consistent between the VOS-Viewer and Biblioshiny formats.\n\nThe bibliometric analysis was conducted using VOS-Viewer software 313 and the bibliometrix and biblioshiny R packages14 https://www.bibliometrix.org/home/index.php/layout/biblioshiny. VOS-Viewer Software was used to filter the top 25 most relevant authors and journals by creating a list according to their selection thresholds of the minimum number of documents and citations. Biblioshiny was used to perform a descriptive analysis of the bibliometric indicators, evaluate the citations of the top 25 authors and journals, and determine the impact factor and collaboration networks between the top authors and countries.\n\nWe searched the Patent Public Search (USPTO)15 database. We used the following query: “corneal endothelium” AND (“tissue engineering” OR “regenerative” OR “reconstruction”) AND (biomaterials OR cell therapy OR scaffold OR membrane) NOT (“organoids” OR “epithelium”). This search yielded a total of 126 patents. A search of the European Patent Office database16 using the following query: “corneal endothelium in the title AND tissue engineering OR scaffold OR biomaterial in the title or abstract” retrieved 6 results. Given the difference in the number of results retrieved from these two databases, we conducted a third search using the Lens database17 with the following query: (title:((cornea AND endothelium) AND (cell therapy OR scaffold OR biomaterial OR tissue engineering OR membrane OR reconstruction NOT epithelium)) OR abstract:((cornea AND endothelium) AND (cell therapy OR scaffold OR biomaterial OR tissue engineering OR membrane OR reconstruction NOT epithelium)) OR claim:((cornea AND endothelium) AND (cell therapy OR scaffold OR tissue engineering OR membrane OR reconstruction NOT epithelium))). This search retrieved 181 results. The data search was conducted on August 28, 2023. The “analysis” function of the Lens database was used to generate graphs about the number of patents over time, type of documents, legal status, top inventors, jurisdiction, and most cited documents from 1980 to present.\n\nWe used the results on Biblioshiny based on the publication affiliation from the bibliometric analysis search. We chose the affiliations that were companies, and then we selected those that had an active website. From those companies, we chose those that had products related to engineered corneal tissue. Data relating to the company’s country, type of product, year of foundation, clinical use and phase of production were analyzed.\n\nFor the QALY analysis, we created a Markov model18 that considered both the quality and quantity of life in the Mexican population using parameters such as life expectancy, cost of corneal transplant, and mean age of transplant. We considered three categories of vision health: blindness, sight, and mortality. Each category has several transition possibilities. Patients can transition from “sight” to “blind” and vice versa and then to death, referring to the end as the absorbing state, given that once an individual enters the state, they remain there.19 Only the transition from blindness to sight incurs expenses, including the cost of obtaining cells from one corneal donor and generating the necessary cells for up to ten engineered corneal endothelium constructs.20 We used a hypothetical cohort of 1000 blind patients aged 35 years and ran the program for 40 years to calculate life expectancy. A discount rate of 3.5% over a 10-year period was used in the computations. We projected that the intervention would reduce the waiting list from three to one year since more transplants would be accessible. We calculated the cost per QALY gained for each intervention and compared it to Mexico’s GDP per capita (8,346.7 USD) to determine whether the interventions were cost-effective, assuming the same cost per patient. The reference cost for a corneal transplant was $6000 USD,21 and the calculated cost of an engineered corneal endothelium tissue was $2400 USD (taken from a preliminary cost analysis from data not shown considering donor cornea acquisition, laboratory consumables, reagents, biocompatible scaffold production cost, QA testing, and a GMP-compliant laboratory, among others). The transplant survival rate/duration was 87% after one year, 72% after three years, 54% after six years, and 42% after ten years.22\n\nWe created an online 10-question formulary using Survey Monkey, an online software platform with free license options, to assess Latin American ophthalmology surgeons’ attitudes toward the use of engineered tissue for corneal endothelium restoration. The formulary was distributed during October 2022 by email throughout the community of Latin American ophthalmology surgeons, and information about the respondent’s location, willingness to use a synthetic biocompatible membrane to transplant corneal endothelial cells, preferred characteristics (thickness, insertion port size, presentation, rigidity, and transparency level), and price range of the bioengineered tissue was recorded to assess the potential of transplanting engineered corneal endothelium instead of donated corneal endothelium. The replies were analyzed using descriptive statistics.\n\n\n3. Results\n\nA total of 416 of the 1030 screened articles were excluded (those published before 2003, review articles, meeting abstracts, proceedings papers, book chapters, editorial material, letters, early access, corrections, or retracted publications), and 614 were included in the bibliometric analysis. A flow diagram describing the flow information used for article screening and selection is shown in Figure 1.\n\nThe articles were published by 2,572 authors from 49 different countries in six different languages—English, French, German, Korean, Portuguese, and Russian—in 206 different journals and used a total of 17,194 references. In total, these articles had 12,042 citations, excluding self-citations. To analyze the trend in the number of publications and correlate it to the year, we performed a polynomial regression. Using a log transformation of the year as an independent variable, we observed a continuous annual growth rate that stabilized in 2021. We fitted a squared polynomial equation to predict the number of articles as a function of year, and we obtained a statistically significant R-squared value of 0.89 and a p value of 1.53×10-9, demonstrating a trend toward an increase in the number of articles related to corneal endothelium regeneration, as shown in Figure 2a.\n\na) Annual growth rate of the number of publications on corneal endothelium regeneration. b) Top 25 authors. c) Top 25 Journals. d) Author collaboration.\n\nThe analysis included a total of 2,572 authors contributing to the 614 selected original articles, resulting in an average of 0.23 documents per author. Eight authors had single-authored documents. The average number of coauthors per document was 6.34, and the average number of international coauthorships was 25.57%. Figure 2b shows the top 25 authors according to their publication rate, and Figure 2c shows the relationships between the top authors in the field who had more than 8 publications and 159 citations. The most productive authors on this specific topic are Metha JS (28 articles), Peh GSL (24 articles), Kinoshita S (23 articles), Koizumi N (23 articles), and Okumura N (23 articles). There is a strong coauthor relationship between Peh GS and Metha JS, as well as between Kinoshita S, Koizumi N, and Okumura, all of whom currently form the most productive research groups in the field.\n\nThe study included 206 journals with 614 published papers, yielding a total of 0.33 documents per journal. The top 25 journals with at least 5 articles and 35 citations are shown in Figure 2d. According to JCR 2022, these 25 journals have an average impact factor of 4.238 and are in quartile 2; 11 (52%) are in the category of ophthalmology, 5 (20%) are in the category of cell & tissue engineering, 3 (12%) are in the category of multidisciplinary sciences, 2 (8%) are in the category of material science, and 2 (8%) are in other categories. These journal articles have been referenced more than 558 times and have a local H-index greater than 13. Exp. Eye Res. (47) is the most relevant journal.\n\nA search of the Lens database returned 181 results. We applied the categorization filter to the following: A61f2/14 (eye parts, e.g. lenses, corneal implants; artificial eyes making thereof from organic plastic material), A61f2/142 (artificial or natural cornea replacement implant for repair of defective corneal tissue), A61p27/02 (Drugs for disorders of the senses, ophthalmic agents) A61l27/24 (materials for {grafts or} prostheses or for coating {grafts or} prostheses, collagen) A61l27/3604 (materials for {grafts or} prostheses or for coating {grafts or} prostheses, {characterized by the human or animal origin of the biological material, e.g. hair, fascia, fish scales, silk, shellac, pericardium, pleura, renal tissue, amniotic membrane, parenchymal tissue, fetal tissue, muscle tissue, fat tissue, enamel}), A61l27/38 (materials for {grafts or} prostheses or for coating {grafts or} prostheses, {containing added animal cells}), A61l27/3834 (materials for {grafts or} prostheses or for coating {grafts or} prostheses {Cells able to produce different cell types, e.g. hematopoietic stem cells, mesenchymal stem cells, marrow stromal cells, embryonic stem cells}, and C12n5/071 (Vertebrate cells or tissues, e.g. human cells or tissues). There were 26 patents who continued to be examined. The top inventors were Cong R., Fan T., Kinoshita S., Ueno M., Zhao J., Koizumi, Gutermuth A., Yang X., Duang H., and Hori J (Figure 3a). Among those, Kinoshita, Ueno, Koizumi, and Duan were also among the most cited authors in the bibliometric analysis. Four patents were granted, one was an additional patent, and twenty-one were patent applications between 1992 and 2024 (Figure 3b). The legal status of 10 of the patents was active, with only three being discontinued (Figure 3c). The jurisdiction with the largest number of patents is the United States, followed by the World Intellectual Property Organization (WIPO) and European patents (Figure 3d). The most cited patent, with 62 citations, was “Methods employed in replacement of the corneal endothelium”, of White T., granted in 1992; it was followed by “Human Corneal Endothelial Cell-Derived Precursor Cells, Cellular Aggregates, Methods for Manufacturing the Same, and Methods for Transplanting Precursor Cells and Cellular Aggregates”, of Amano, published in 2009, with 19 citations, currently discontinued; and “In Vitro Cornea Equivalent Model”, of Parenteau, published in 1994, with 6 citations.\n\na) Number of documents per inventor. b) Document type versus publication date. c) Number of documents by legal status. d) Number of documents per jurisdiction (data and images retrieved from Lens.org).\n\nThe affiliations of the articles included in the bibliometric analysis yielded 53 companies. Twenty of those had an active webpage. Of those, 10 had products related to the original research paper from which the affiliation was taken (Table 1). These companies were founded from 2001 to 2022. These countries are in four different regions: five in the USA, two in Japan, two in China and one in Spain. Five of these companies have products on the market (Linkocare, CorneaGen, Takara Bio, BioTissue, and Cell Science & Technology Institute); two are developing phase II clinical trials (Trefoil Therapeutics and Emmecell); and one is in a phase I clinical trial (Body Organ Biomedical Corp); two of them are in the preclinical phase (Vissum Group and Cellusion). Three of these companies have products whose main use is corneal transplantation (Linkocare, CorneaGen, and Cellusion). One of the companies (Corneagen) appears as the affiliation of three documents with five of the top authors from the bibliometric analysis (Kinoshita, Hamuro, Ueno, Okumura, and Koizumi); two of them are also among the top patent inventors (Kinoshita and Koizumi).\n\nThe Markov model based QALY study showed that engineered corneal endothelium intervention is associated with greater QALY gains than full keratoplasty is. The analysis revealed that endothelial corneal transplant had a QALY increase of 0.07 compared to that of engineered corneal endothelium intervention (0.74 QALY gain on a scale of 0 to 1). Table 2 shows the comparison between the QALYs gained and the cost of the transplantation of engineered tissue and full keratoplasty.\n\nA total of 30 ophthalmology surgeons with subspecialties in the cornea answered the questionnaire. The participants were from 8 Latin American countries: Colombia, Ecuador, Venezuela, Mexico, Spain, Costa Rica, Paraguay, and the Dominican Republic (Figure 4a). In a question with open answers, the key features for selecting an engineered corneal endothelium as the first choice for transplantation were biocompatibility, cost, manipulability, and transparency. More respondents mentioned efficacy, ease of insertion, orientation, resistance during manipulation, accessibility, thickness, adherence, and viability time (Figure 4b).\n\na) Nationality distribution of the survey respondents. b) Features favoring engineered corneal endothelium for transplantation over full keratoplasty.\n\nThe majority of participants (97%) expressed the belief that synthetic membrane-based engineered tissue would be beneficial for corneal endothelium transplantation. The participants’ preferences for key characteristics of an engineered corneal endothelium are outlined in Table 3.\n\n\nDiscussion\n\nThe cornea is one of the most common transplanted tissues worldwide, primarily because corneal opacity is among the leading causes of blindness and vision impairment.44 As the global population continues to grow and life expectancy increases, the persistent scarcity of corneal tissue donors remains a primary obstacle to accessing corneal transplantation. Presently, there is a significant deficit in the availability of corneal grafts, with just one cornea accessible for every 70 individuals in need.1 Penetrating keratoplasty has traditionally served as the conventional and widely practiced surgical method for managing diverse corneal conditions, irrespective of the specific layer affected, including endothelial issues. However, recent advancements in technology and innovations in the field have given rise to endothelial keratoplasty techniques over the past two decades.4 These techniques entail the transplantation of specific corneal components and present an alternative and progressive approach to treating such conditions. Despite these surgical advances, the issue of donor tissue scarcity remains unresolved. This study aimed to trace the trajectory from fundamental research to practical clinical application.\n\nEfforts to address the tissue donor shortage are now underway through comprehensive basic, translational, and clinical research initiatives. Tissue engineering has made significant strides, marked by notable developments in the isolation and culture of corneal endothelial cells, coupled with the production of biocompatible scaffolds, which have improved the prospects of tissue-engineered grafts.45 As demonstrated in the bibliometric analysis, there has been continuous growth in publications related to corneal endothelial engineering over the past two decades,6 which aligns with the data that indicate a decline in publications on penetrating keratoplasty.46 However, challenges persist in translating this scientific progress to clinical application due to diverse factors, such as limited research time and financial constraints. The median time to receive the first independent grant was 8 years only among ophthalmology clinician scientists. Nevertheless, the time taken to achieve independence as a researcher correlates with greater institutional support and earlier success in obtaining extramural grants.47 Furthermore, addressing the challenge of collaboration and integration between basic and clinical research is crucial for successful translational medicine.7 This is proven in our bibliometric analysis, where most of the documents were located in ophthalmology journals, with fewer contributions in fields such as cell and tissue engineering, multidisciplinary studies, and material sciences. This gap may signify a potential shortage of multidisciplinary approaches within the field, which is crucial for addressing the ongoing challenge of corneal tissue scarcity.\n\nThe first “Death Valley” in the path to clinical application occurs during the transitory period between technology transfer and academic research.7,8 This aligns with the findings of our patent study, which reduced the number of patents from 614 publications to 26 using a search strategy akin to the one utilized in the bibliometric analysis. Only four of the 25 most cited authors in the bibliometric analysis were among the top 10 inventors in the patents. This could be related to several factors, referred to as obstacles to the growth of technology transfer, such as the lack of engagement and cooperation between scientists and technologists.48 Several surgical techniques have been developed in the field of ophthalmology to improve visual health. Collaboration with experts in the fields of material sciences, nanotechnology, biotechnology, robotics, etc., was necessary for these advancements. This necessitates strengthening the training of research personnel doing eye surgery in transdisciplinary teams, providing access to financial resources for funding, and exchanging practices that enhance the work of Institutional Review Boards to improve the technology transfer pathway.49\n\nBetween the stage of technology transfer and clinical application, there is a second “Death Valley ”.7,8 Robust research and actual use of breakthrough technologies in the rapidly evolving medical technology landscape are significantly out of alignment, especially in the field of ophthalmology. Despite the abundance of research articles demonstrating advancements in disciplines such as artificial intelligence (AI), tissue engineering, and surgical improvements, the translation of these discoveries into practical applications has been remarkably poor. Industry 5.0 is anticipated to meet the demands of the ophthalmology sector by combining artificial intelligence and telemedicine.49,50 This difference is emphasized by the fact that, out of more than 600 research articles, only 26 patents and 10 companies are actively utilizing technology focused on engineering the corneal endothelium. This disparity demands a thorough examination of the barriers hindering the straightforward translation of test findings into therapeutic settings. This phase, which involves a lack of financing throughout the pre-seed and seed stages of the implementation of innovative ideas, is a well-discussed aspect that affects the translation of scientific breakthroughs.48 Five of the 10 companies analyzed are in the midst of ongoing research, while the other five already have products on the market. Particularly noteworthy is the presence of Corneagen, which was the affiliation for three documents authored by three of the most cited researchers in our bibliometric analysis. These companies are actively engaged in various aspects of the field, such as cell therapy, engineered tissue, devices designed for tissue transplantation, specialized media, and biomaterials used as bandages.\n\nConsidering the challenges that limit the practical application of novel technologies in ophthalmology, a thorough analysis of their potential impact on patient outcomes is crucial. As we investigate the field of engineered corneal endothelium, an evaluation assessing the benefits of this alternative strategy in comparison to traditional corneal transplantation is necessary. A prior study underscored the economic and accessibility advantages of the engineered corneal endothelium, positioning it as a more viable and cost-effective choice for patients.11 The application of QALY analysis, a metric gauging health outcome based on both length and quality of life,51 has been previously employed to assess the cost-effectiveness of ultrathin DSAEK (10). In the present study, the QALY analysis was tailored to the specific parameters of the Mexican population, given that it is the country with the most corneal transplants in Latin America according to the 2019 report of the Eye Bank Association of America,52 which established a foundational perspective. This approach not only accentuates the regional advantages of engineered corneal endothelium in terms of cost but also extends its benefits to life expectancy, graft survival rates, and the reduction of transplant waiting lists. These assumptions are likely applicable to other Latin American nations contending analogous challenges related to corneal blindness and donor scarcity.53–55\n\nEffective collaboration among a variety of stakeholders, including patients, doctors, public health specialists, machine learning engineers, data scientists, statisticians, and field scientists, is required for the successful integration of cutting-edge technology into clinical practice.56 Notably, a clear framework for decision-making is often missing from the implementation of such technologies. In earlier research, the importance of “flexibility of usage” became a top priority criterion in “physician-specific” factors in the framework used to make decisions about the adoption of new surgical technologies.57 To bridge this conceptual understanding with tangible insights, we conducted a survey into the perspectives of Latin American ophthalmology surgeons. Despite limitations in terms of respondent numbers and survey questions, the data obtained offer initial insights into factors deemed crucial by these surgeons when contemplating the adoption of engineered corneal endothelium. Safety, effectiveness, cost, and procedural viability emerged as paramount criteria, aligning with the prioritization criteria for surgical technology adoption.57,58 This finding confirms the promise of this technology by bridging the gap between theoretical advantages and real-world attitudes among practitioners. Further in-depth studies with a wider group of respondents will confirm these preliminary data.\n\n\nConclusion\n\nIn summary, this study highlights the existing gap between the significant scientific advancements in corneal endothelium engineering and its practical application in clinical contexts. This study emphasizes the need to reconsider traditional research pathways and academic models, emphasizing a shift toward prioritizing healthcare impact and patient outcomes. Recognizing corneal transplantation as a crucial public health concern, the adoption of novel technologies should extend beyond research labs and actively target real-world implementation. While bibliometric analysis indicates a noticeable shift toward corneal endothelial engineering and emphasizes the importance of multidisciplinary collaboration, certain limitations exist. The database constraints hindered a comprehensive understanding of the types of studies analyzed, limiting our insight into the evolving evidence for engineered corneal tissue in clinical applications. Additionally, our company analysis was based solely on bibliometric affiliations, potentially overlooking other technologies. The examination of patents revealed challenges in translating innovations, emphasizing obstacles to practical applications. Industry trends underscore the misalignment between research production and real-world technology use, particularly in ophthalmology. The QALY analysis demonstrated the benefits of adopting engineered corneal endothelium in clinical practice. A Latin American survey among ophthalmologists offered valuable perspectives on the factors influencing technology adoption. Overall, these findings emphasize the complex interplay among scientific progress, technology adoption, and clinical practice, calling for sustained collaboration, financial support, and further in-depth studies to bridge the gap between theoretical promise and practical implementation in corneal transplantation.",
"appendix": "Data availability\n\nFigshare: Corneal Endothelium Bibliometric and Patent Analysis. https://doi.org/10.6084/m9.figshare.25697556.v1 59\n\nThe project contains the following underlying data:\n\n• Supplementary File 1.xlsx. (Web of Science Raw File Bibliometric Analysis)\n\n• Supplementary File 2.xlsx. (Bibliometric Analysis Top 25 Journals)\n\n• Supplementary File 3.xlsx. (List of 26 patents from Lens.org)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nGain P, Jullienne R, He Z, et al.: Global Survey of Corneal Transplantation and Eye Banking. JAMA Ophthalmol. 2016 Feb 1 [cited 2024 Jan 4]; 134(2): 167–173. PubMed Abstract | Publisher Full Text\n\nCorneal Surgery, Transplant Tissue, and Eye Banking - The International Agency for the Prevention of Blindness.[cited 2024 Jan 14]. Reference Source\n\nKhattak A, Fouad A: Five-year endothelial cell count post penetrating keratoplasty using internationally transported corneal donor tissue.2019 [cited 2024 Feb 4]. Publisher Full Text\n\nMoshirfar M, Thomson AC, Ronquillo Y: Corneal Endothelial Transplantation. StatPearls; 2023 Jul 24 [cited 2024 Feb 4]. Reference Source\n\nSmeringaiova I, Paaske Utheim T, Jirsova K: Ex vivo expansion and characterization of human corneal endothelium for transplantation: a review. Stem Cell Res. Ther. 2021 Dec 1 [cited 2024 Feb 4]; 12(1): 521–554. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNiu HQ, Yang Y, Wang BB, et al.: A global bibliometric and visualized analysis in the status and trends of corneal tissue engineering research from 1991 to 2021. J. Tissue Eng. 2022 Jan 1 [cited 2024 Jan 8]; 13: 204173142211381. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nBartakova A, Kuzmenko O, Alvarez-Delfin K, et al.: A Cell Culture Approach to Optimized Human Corneal Endothelial Cell Function. Invest. Ophthalmol. Vis. Sci. 2018 Mar 1 [cited 2024 Jan 3]; 59(3): 1617–1629. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRafat M, Jabbarvand M, Sharma N, et al.: Bioengineered corneal tissue for minimally invasive vision restoration in advanced keratoconus in two clinical cohorts. Nat. Biotechnol. 2022 Aug 11 [cited 2024 Jan 3]; 41(1): 70–81. PubMed Abstract | Publisher Full Text Reference Source\n\nToda M, Ueno M, Hiraga A, et al.: Production of Homogeneous Cultured Human Corneal Endothelial Cells Indispensable for Innovative Cell Therapy. Invest. Ophthalmol. Vis. Sci. 2017 Apr 1 [cited 2024 Jan 3]; 58(4): 2011–2020. PubMed Abstract | Publisher Full Text\n\nHamuro J, Toda M, Asada K, et al.: Cell Homogeneity Indispensable for Regenerative Medicine by Cultured Human Corneal Endothelial Cells. Invest. Ophthalmol. Vis. Sci. 2016 Sep 1 [cited 2024 Jan 3]; 57(11): 4749–4761. PubMed Abstract | Publisher Full Text\n\nHamuro J, Ueno M, Toda M, et al.: Cultured Human Corneal Endothelial Cell Aneuploidy Dependence on the Presence of Heterogeneous Subpopulations With Distinct Differentiation Phenotypes. Invest. Ophthalmol. Vis. Sci. 2016 Aug 1 [cited 2024 Jan 3]; 57(10): 4385–4392. PubMed Abstract | Publisher Full Text\n\nHamuro J, Ueno M, Asada K, et al.: Metabolic Plasticity in Cell State Homeostasis and Differentiation of Cultured Human Corneal Endothelial Cells. Invest. Ophthalmol. Vis. Sci. 2016 Aug 1 [cited 2024 Jan 3]; 57(10): 4452–4463. PubMed Abstract | Publisher Full Text\n\nSchlötzer-Schrehardt U, Zenkel M, Strunz M, et al.: Potential Functional Restoration of Corneal Endothelial Cells in Fuchs Endothelial Corneal Dystrophy by ROCK Inhibitor (Ripasudil). Am. J. Ophthalmol. 2021 Apr 1 [cited 2024 Jan 3]; 224: 185–199. PubMed Abstract | Publisher Full Text\n\nHanson C, Arnarsson A, Hardarson T, et al.: Transplanting embryonic stem cells onto damaged human corneal endothelium. World J. Stem Cells. 2017 Aug 8 [cited 2024 Jan 3]; 9(8): 127–132. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu YT, Chen HC, Chen SY, et al.: Nuclear p120 catenin unlocks mitotic block of contact-inhibited human corneal endothelial monolayers without disrupting adherent junctions. J. Cell Sci. 2012 Aug 1 [cited 2024 Jan 3]; 125(Pt 15): 3636–3648. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu YT, Li F, Han B, et al.: Activation of RhoA-ROCK-BMP signaling reprograms adult human corneal endothelial cells. J. Cell Biol. 2014 [cited 2024 Jan 3]; 206(6): 799–811. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu YT, Han B, Li F, et al.: Knockdown of both p120 catenin and Kaiso promotes expansion of human corneal endothelial monolayers via RhoA-ROCK-noncanonical BMP-NFκB pathway. Invest. Ophthalmol. Vis. Sci. 2014 [cited 2024 Jan 3]; 55(3): 1509–1518. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu Y, Sun H, Hu M, et al.: Human Corneal Endothelial Cells Expanded in vitro Are a Powerful Resource for Tissue Engineering. Int. J. Med. Sci. 2017 Feb 7 [cited 2024 Jan 3]; 14(2): 128–135. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu Y, Sun H, Guo P, et al.: Characterization and Prospective of Human Corneal Endothelial Progenitors. Int. J. Med. Sci. 2017 [cited 2024 Jan 3]; 14(8): 705–710. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu Q, Zhu Y, Tighe S, et al.: Engineering of Human Corneal Endothelial Cells In Vitro. Int. J. Med. Sci. 2019 [cited 2024 Jan 3]; 16(4): 507–512. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu Q, Sun H, Yang D, et al.: Cellular Substrates for Cell-Based Tissue Engineering of Human Corneal Endothelial Cells. Int. J. Med. Sci. 2019 [cited 2024 Jan 3]; 16(8): 1072–1077. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeant J, Eveleth DD, Subramaniam A, et al.: Regenerative responses of rabbit corneal endothelial cells to stimulation by fibroblast growth factor 1 (FGF1) derivatives, TTHX1001 and TTHX1114. Growth Factors. 2021 [cited 2024 Jan 3]; 39(1–6): 14–27. PubMed Abstract | Publisher Full Text\n\nAlió del Barrio JL, De la Mata A, De Miguel MP, et al.: Corneal Regeneration Using Adipose-Derived Mesenchymal Stem Cells. Cells. 2022 Aug 1 [cited 2024 Jan 3]; 11(16). PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang EY, Kong X, Wolle M, et al.: Global Trends in Blindness and Vision Impairment Resulting from Corneal Opacity 1984–2020: A Meta-analysis. Ophthalmology. 2023 Aug 1; 130(8): 863–871. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoshirfar M, Thomson AC, Ronquillo Y: Corneal Endothelial Transplantation. StatPearls; 2023 Jul 24 [cited 2024 Jan 4]. Reference Source\n\nCatalà P, Thuret G, Skottman H, et al.: Approaches for corneal endothelium regenerative medicine. Prog. Retin. Eye Res. 2022 Mar 1; 87: 100987. PubMed Abstract | Publisher Full Text\n\nPekel E, Pekel G: Publication trends in corneal transplantation: a bibliometric analysis. BMC Ophthalmol. 2016 Nov 8 [cited 2024 Jan 4]; 16(1): 194–196. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRusakevich AM, Protopsaltis NJ, Rao RC, et al.: Research Funding, Income, and Career Satisfaction among Clinician-Scientists in Ophthalmology in the United States. Am. J. Ophthalmol. 2021 Jul 1 [cited 2024 Jan 4]; 227: 254–264. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShmeleva N, Gamidullaeva L, Tolstykh T, et al.: Challenges and Opportunities for Technology Transfer Networks in the Context of Open Innovation: Russian Experience. J. Open Innov.: Technol. Mark. Complex. 2021 Sep 3 [cited 2024 Jan 7]; 7(3): 197. Publisher Full Text Reference Source\n\nOspina PD, Díaz MCC, Lara S, et al.: New Technologies in Eye Surgery — A Challenge for Clinical, Therapeutic, and Eye Surgeons. Advances in Eye Surgery. IntechOpen; 2016 [cited 2024 Jan 7]. Reference Source\n\nChourasia S, Pandey SM, Murtaza Q, et al.: Redefining Industry 5.0 in Ophthalmology and Digital Metrology: A Global Perspective.[cited 2024 Jan 8]; 38: 527–545. Publisher Full Text\n\nWhitehead SJ, Ali S: Health outcomes in economic evaluation: the QALY and utilities.[cited 2024 Jan 8]. Reference Source\n\nBank E: 2019 EYE BANKING STATISTICAL REPORT 2019 Analysis of Surgical Use and Indications for Corneal Transplant.2019 [cited 2024 Jan 9]. Reference Source\n\nMuñoz B, West SK: Blindness and visual impairment in the Americas and the Caribbean. Br. J. Ophthalmol. 2002 May 1 [cited 2024 Jan 8]; 86(5): 498–504. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nSilva JC, Mújica OJ, Vega E, et al.: A comparative assessment of avoidable blindness and visual impairment in seven Latin American countries: prevalence, coverage, and inequality. Rev. Panam. Salud Publica. 2015 [cited 2024 Jan 8]; 37(1): 13–20. PubMed Abstract Reference Source\n\nFurtado JM, Lansingh VC, Carter MJ, et al.: Causes of Blindness and Visual Impairment in Latin America. Surv. Ophthalmol. 2012 Mar 1 [cited 2024 Jan 8]; 57(2): 149–177. Publisher Full Text Reference Source\n\nRedd TK, Al-Khaled T, Chan RVP, et al.: Technology and Innovation in Global Ophthalmology: The Past, the Potential, and a Path Forward.2023 [cited 2024 Jan 14]. Reference Source\n\nShoman H, Almeida ND, Tanzer M: Ranking Decision-Making Criteria for Early Adoption of Innovative Surgical Technologies. JAMA Netw. Open. 2023 Nov 1 [cited 2024 Jan 11]; 6(11): e2343703–e2343703. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nZavala J, Rodríguez Fuentes DE: Corneal Endothelium Bibliometric and Patent Analysis. [Dataset]. figshare. 2024. Publisher Full Text"
}
|
[
{
"id": "291729",
"date": "09 Jul 2024",
"name": "Denise Loya Garcia",
"expertise": [
"Reviewer Expertise Cornea",
"Refractive Surgery and External Diseases"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a comprehensive and intricate manuscript detailing the progression from basic research to clinical adoption in the field of corneal tissue engineering.\n\nThey provide clear and precise data on the current state of technology transfer pathways and their clinical applications. The manuscript emphasizes the importance of multidisciplinary collaboration in corneal tissue engineering, identifying several key strategies necessary to overcome challenges such as the \"valley of death\" and facilitate clinical applications.\n\nThe authors conclude that strengthening industry-academia partnerships is essential for enhancing the transition from research to clinical practice. This collaborative effort is crucial in effectively addressing the scarcity of corneal tissue.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "291732",
"date": "19 Jul 2024",
"name": "Chris Sampson",
"expertise": [
"Reviewer Expertise Health economics"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article has worthwhile ambitions but constitutes a strange hotchpotch of uncoordinated research activities. My most significant concern relates to the lack of clarity in the reporting. Ultimately, the paper does not succeed in its objective to 'trace the trajectory from fundamental research to practical clinical application'. My specific points are as follows.\nNote that I am reviewing this manuscript as a health economist. For certain parts of the manuscript (e.g. the section on patent analysis), I cannot provide expertise.\nMajor / required 1) The whole paper, as captured succinctly in the methods section of the abstract, constitutes a seemingly random collection of methods. Justification must be provided for the choice of methods. The study would be better reframed as a kind of scoping analysis without any specific hypothesis or prespecified focus. 2) Significant parts of the paper appear not to have been written by a human. In particular, the final paragraph of the introduction and the Conclusion section both read as if they are entirely computer (AI) generated, and are wholly lacking in meaning or substance. The entire manuscript should be reviewed for accuracy and conciseness. 3) Section 2.4 (QALY analysis) does not provide an adequate description of methods. This section makes reference to a model, but the structure of the model is not described (there is an implication that the model is based on three states, but this is not explicit). Aspects of the model such as the waiting list are not explained. Parameters (e.g. those relating to certain costs) are seemingly assumed with no justification. Almost every detail that one would expect to see is missing. I will not list them all here, but will simply refer the authors to the CHEERS checklist [1], which they should use to ensure completeness of reporting. 4) Similarly, the results of the QALY analysis are extremely unclear. The authors make claims about QALY gains, but it is not clear what this is in comparison to (I suspect it is in comparison to baseline, though this is not really a 'gain' unless the comparator is death at baseline). Note also that 'QALY gain' is not measured 'on a scale of 0 to 1'. 5) There is a tendency in the manuscript to report results in the methods section. For example, the first section 2.2 (there are two section 2.2s) describes the results of literature searches. All results should be presented in the Results section. 6) The conclusions stated in the abstract are not derived from the results as described in the abstract. This should be rewritten. 7) Claims about the number of actors in this space, e.g. \"only 26 patents and 10 companies\", require convincingly systematic methods, and there is little reason provided in this manuscript to believe that the review was systematic and comprehensive. The authors need to more clearly describe the limitations of their study in this regard.\nMinor / optional 8) The title should be edited to provide some signal of what the research actually entailed, rather than a vague topic. 9) The passage - on page 3 - that introduces QALYs does not make sense. It does not accurately characterise the role or purpose or construction of QALYs. QALYs do not go 'beyond' judgments of cost-effectiveness (they are an input to them). They also tend not to be used directly in 'clinical adoption' decisions. 10) There are errors and inconsistencies in the use of headings. For example, there are two section 2.2s. 11) A graphic pipeline representation of Table 1 would be a valuable addition to the paper. 12) There are errors in the citations that should be corrected. See, for example, citation 52. 13) Reference 11 requires completion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-608
|
https://f1000research.com/articles/12-631/v1
|
08 Jun 23
|
{
"type": "Research Article",
"title": "The effect of green mussel (Perna viridis) shells’ hydroxyapatite application on alkaline phosphatase levels in rabbit femur bone defect",
"authors": [
"Kevin Christian Tjandra",
"Robin Novriansyah",
"Edward Kurnia Setiawan Limijadi",
"Lydia Kuntjoro",
"Meita Hendrianingtyas",
"Kevin Christian Tjandra",
"Robin Novriansyah",
"Edward Kurnia Setiawan Limijadi",
"Lydia Kuntjoro"
],
"abstract": "Background: A non-union fracture is one of the most common complications arising from an untreated fracture. Bone grafts are able to fasten bone healing which can prevent and cure non-union fractures. Therefore, alternative hydroxyapatite bone grafts from waste resources are needed to increase the availability of bone grafts in the healthcare system. A bone substitute, hydroxyapatite (HA), has the ability to prevent non-union fractures. Green mussel shell contains 95.69 percent HA, allowing for an annual production of 133.97–287.07 tons per ha of HA, and is a potent alternative material in the manufacture of HA. Methods: This research was conducted for four months using a true experimental research method with a post-test-only control group design. This study used 36 New Zealand rabbits (Oryctolagus cuniculus) which were divided into 9 groups: positive control, negative control, and intervention at weeks 2, 4 and 6 after the intervention. All groups were subjected to three general procedures: pre-surgery, surgery, and post-surgery. Results: The findings demonstrated that green mussel shell HA has efficacy in accelerating bone healing, better than HA bovine, as compared to the 6-week negative control group and demonstrated a significant difference (p < 0.05). Conclusions: Green mussel hydroxyapatite is proven to be able to fasten and maximize the bone healing process as fast as bovine HA, and even has higher efficacy than bovine HA.",
"keywords": [
"Hydroxyapatite",
"green mussel shell",
"bone substitute",
"bone healing",
"alkaline phosphatase"
],
"content": "Introduction\n\nThe incidence of traffic accidents has increased in Indonesia, which often cause disability in the form of fractures.1,2 Based on data recorded by the Directorate of Traffic of the Regional Police of Central Java in 2018, the prevalence of fractures due to traffic injury is 5.5% in Indonesia.3 Data recorded by the World Health Organization (WHO) shows that there was an increase in the number of fractures from 2008 to 2009, from 13 million cases to 18 million cases along with a prevalence rate of 2.7% to 5.5%.4 If these conditions are not handled, the decline in quality of life and activity limitations cannot be avoided.\n\nFracture is a condition where there is a discontinuity of bone.5 Meanwhile, bones have the ability to heal.1 Fracture healing necessitates a combination of mechanical stability from appropriate fixation, adequate bone vascularization, osteoprogenitors and growth factors from bone cells, and interaction between shattered bone fragments. Non-union fractures can occur if a combination of these conditions is not met.6,7 As a result, bone grafts with osteogenesis, osteoinduction, and osteoconduction characteristics are required to assist in the healing of acute fractures and non-union fractures.\n\nA substance called hydroxyapatite (HA) is frequently utilized in the development of bone substitutes. This is because HA makes up 50% of the mineral components of bone. Bone consists of 69% mineral components, 22% organic matrix, and 9% water. HA is a key component needed in the process of bone regeneration and healing.8 Virgin clam shells and green mussel shells are just two examples of wastes that could serve as a source of HA for bone substitutes.9,10 The virgin clam shell (Anadara granosa) has been suggested as a viable material for the synthesis of HA.10 On the other hand, no recent studies related to green mussel shells have been conducted. Therefore, the potential of green mussel shells as a material for HA synthesis will be examined in this research.11\n\nAccording to Sangwaranatee (2016), green mussel shells contain two polymorphs of calcium carbonate (CaCO3), namely calcite and aragonite. Most organic compounds can be found among the crystallites (intercrystalline), but some organic molecules (intercrystalline) are also intercalated in the crystal lattice. More specifically, green mussel shells consist of 95-99% CaCO3 (calcite, aragonite, or vaterite) with lesser amounts of MgCO3, Al (Fe2O3), SiO2, Ca3P2O8, CaSO4, proteins, and mucopolysaccharides. This CaCO3 content will then be processed into the hydroxyapatite.12\n\nIndonesia is able to produce 140 – 210 tons per hectare of green mussel shell waste every year.13 Green mussel shells consist of 95.69% HA, so 133.97 – 287.07 tons per hectare of HA can be produced annually.14 Therefore, green mussel shells have the potential to be an alternative material in the production of HA.\n\nAlkaline phosphatase (ALP), an enzyme that contributes to the process of bone mineralization, is produced by osteoblasts with increased activity in the third stage. As one of the elements of a complete blood count, ALP can therefore serve as a biomarker that is frequently evaluated and easily accessed to detect bone healing.15\n\nIn this research, serum ALP levels will be measured in the weeks 2, 4, and 6 to see how the distribution of green mussel shell HA affects the ALP levels. This retrieval was timed in accordance with findings from Rathwa et al. (2021), who noted that peak serum ALP levels in fracture patients occurred in the sixth week.16 This research aims to observe the effectiveness of green mussel shell HA as a bone substitute material and to provide knowledge for further research.\n\n\nMethods\n\nEthical clearance was issued by the Medical and Health Research Ethics Commission Faculty of Medicine, University of Diponegoro (Komite Etik Penelitian Kesehatan Fakultas Kedokteran Universitas Diponegoro), with serial number 03/EC/H/FK-UNDIP/I/2022 approved on January 11th 2021. All methods and protocol, including the research question, key design features, and analysis plan, were performed in accordance with the relevant guidelines and regulations and the study is reported in accordance with ARRIVE guidelines. All efforts were made to ameliorate any suffering of animals. All the efforts aim for acclimatization to account for their diverse origins; each rabbit was kept separately in polycarbonate cages (0.90 0.60 0.60 m) for a week on a 12-hour light/dark cycle at a constant temperature of 25°C and humidity of 50%. Animals were routinely observed for food consumption and fecal characteristics while being fed a conventional pellet diet and drinking tap water at will.\n\nThis research was carried out at the Animal Test Laboratory in the Lembah Kalipancur Tourism Village, Semarang, and the Healthy Animal Clinic Laboratory in Malang. This research was carried out for four months from September to December 2021. This study used a true experimental study with a post-test-only control group design.\n\nThe experimental animals used in this study were New Zealand guinea rabbits (Oryctolagus cuniculus) obtained from rabbit breeders in Ambarawa, Semarang Regency. The inclusion criteria in this study were skeletally matured, male New Zealand rabbits (Oryctolagus cuniculus), aged 6-12 months, with a weight of 2.5 – 3 kg. The exclusion criteria in this study were there being anatomical abnormalities, signs of infection, and rabbits that died during treatment. The required sample size was calculated using a resource equation. The equation showed that each group (9 groups) should consist of 3 rabbits with 1 additional rabbit to account for drop out (10%). Thus, 36 rabbits were used in this study.\n\nSampling was conducted by simple random sampling to avoid bias due to variations in age and weight. Rabbits that met the inclusion and exclusion criteria were assigned randomly after being determined to be homogeneous using a simple randomization method. Then the 4 stages of blinding were conducted which included blinding during allocation, during the experiment, during the outcome assessment, and during the data analysis. After a week of adaptation, samples were obtained randomly from the group of rabbits (Oryctolagus cuniculus). Then the 36 rabbits were divided into 9 groups (4 rabbits for each group) as shown in Figure 1.\n\nDescription:\n\nn: Sample\n\nK1: Negative control\n\nK1.1: Negative control observed sixth week after intervention\n\nK1.2: Negative control observed fourth week after intervention\n\nK1.3: Negative control observed second week after intervention\n\nK2: Positive control\n\nK2.1: Positive control observed sixth week after intervention\n\nK2.2: Positive control observed fourth week after intervention\n\nK2.3: Positive control observed second week after intervention\n\nP: Intervention group\n\nP1: Intervention group observed sixth week after intervention\n\nP2: Intervention group observed fourth week after intervention\n\nP3: Intervention group observed second week after intervention\n\nX0: No Intervention\n\nX1: Bovine HA implantation in rabbit femur\n\nX2: Green mussel shell HA implantation in rabbit femur\n\nSeven rabbits from seven different groups (P1, K1.1, P2, K2.2, P3, K2.3, K1.3) were found dead during daily monitoring several days after the surgery with no specific cause of death. None of the humane endpoint criteria (Table 1) were noted prior to their death nor found on examination after death. Rabbits from P1 and K1.1 were found dead two days after the surgery, rabbits from P2 and K2.2 were found dead three days after the surgery, and rabbits from P3, K2.3, and K1.3 were found dead five days after the surgery. The final data does not include their information. However, the data is still credible since each group achieved the minimum sample of three rabbits for each of these groups.\n\nThe rabbits were selected according to the inclusion criteria after each rabbit was weighed. A total of 36 rabbits that met the inclusion criteria were then adapted, given food and drink as necessary for a week. During the adaptation period, rabbits were given vitamins A, D, E (0.1 mL/kg BW IM), vitamin B complex (0.1 mL/kg BW IM), and ivermectin (0.4 mg/kg BW IM) for disease prevention. After a week-long adaptation period, the rabbits were separated each into one cage according to their group. The rabbits were monitored for their humane endpoint conditions before and after the intervention for 2 hours per day (16:00 – 18:00). Those rabbits that reached their humane endpoint will be terminated by the administration of ≥100 mg/kg of pentobarbital (lethal dose) intravascularly (IV). The humane endpoint criteria can be seen in this table below, from Montgomery (1990).\n\nThe research data obtained were primary data from the observation of blood serum alkaline phosphatase levels as a bone healing biomarker on rabbit femur bones from the treatment group compared to the negative and positive control groups. The collection of blood serum alkaline phosphatase levels as biomarkers of bone healing was carried out in week 2, week 4, and week 6 after surgery.\n\nThe green mussel shell HA used in this study is obtained from the production led by Rifky Ismail et al. at the Center of Biomechanics, Biomaterials, Biomechatronics, and Biosignal Processing (CBIOM3S).17 Then the obtained HA was powdered into a mortar and then the particle size was reduced using a stamper. In order to prevent infection, UV sterilization for ±3 hours was conducted. Before the implantation process, HA should be measured to prevent bias. The required amount of HA is calculated by the following calculation:\n\nFrom the calculation, the mass of HA required for implantation of a tubular defect with a diameter of 5 mm and a depth of 5 mm is 300 mg.\n\nThere are two location options for making bone lesions in order to apply bone grafts, the metaphysis and the diaphysis. Both locations have advantages and disadvantages. There is a cushioning effect that prevents the risk of fracture due to the presence of layers of pars spongiosa and pars compacta which is an advantage of the metaphyseal section, but this section also has the disadvantage of being close to several large arteries and so there is risk of bleeding. In addition, the metaphysis has a lower volume and density than the diaphysis, making it easier to fracture.18,19 The diaphysis location was chosen as the surgery site because it is far from the great artery and it is not easily fractured.\n\nThe surgical procedure began by shaving the hair at the incision area followed by injection of enrofloxacin 5 mg/kg IV in the rabbit’s ear through the v. auricularis lateralis as prophylactic antibiotics, and ketamine 10-40 mg/kg and acepromazine 3-5 mg/kg intramuscularly in m. longissimus dorsi caudal as the anesthetic. After that, an incision was made in the lateral area of the distal diaphysis of the femur with blade no. 22 by incising the fascia and periosteum of the rabbit femur according to the treatment group.\n\nThe procedure was conducted according to each of the experimental groups. K1.1, K1.2, K1.3: make a defect in the lateral body of the femoris using a drill with a diameter of 5 mm and a depth of 5 mm. K2.1, K2.2, K2.3: make a defect in lateral corpus femoris using a drill with a diameter of 5 mm and a depth of 5 mm and fill the defect with bovine HA. P1, P2, P3: make a defect in the lateral part of the corpus femoris using a drill with a diameter of 5 mm and a depth of 5 mm and fill the defect with green mussel shell HA.\n\nThe fascia was sutured using absorbable catgut sutures, and the skin was sutured using non-absorbable silk. After that, the rabbits were examined until the time of data collection to know whether the rabbit showed any sign of infection, anatomical abnormalities, or died, so we could determine whether they met the exclusion criteria or not. The rabbits that showed exclusion criteria would be dropped out of the study.\n\nThe rabbits were taken care of properly by giving them food and drink as necessary until the time of blood serum data collection. The blood serum samples were taken two, four, and six weeks after surgery, depending on the intervention group of the rabbit. The intervention group is fully described in Figure 1. During this time, they were also given analgesic carbogen 2 mg/kg orally and antibiotic enrofloxacin 35mg/kg orally once per three days to keep their quality of life up.\n\nThe blood sampling was conducted by inserting needle parallel to the lateral marginal auricular vein. Once the needle reached the vein, blood will flow into the catheter. The vacutainer tube was pushed so that blood can enter the 1-2 ml tube. After collecting the required sample, the needle was immediately removed from the rabbit’s lateral marginal vein. The injected area was pressed with an alcohol swab at the end of this process.20\n\nAfter the blood samples were collected, the rabbits were killed by the administration of ≥100 mg/kg of pentobarbital (lethal dose) intravascularly (IV). Then, they were monitored until a lack of heartbeat was noted for >60 seconds prior to carcass disposal.\n\nExamination of ALP is selected due to its availability in most health centers. Detection of the ALP level from blood serum was carried out using the Mindray BC2800Vet series and blood chemistry analyzer with the brand Ubio-iChem-535 at the Animal Clinic Laboratory of Healthy Animals in Malang. In a previous study, this procedure was carried out based on measuring serum ALP levels in rabbit blood through the marginal vein. Then, the alkaline phosphatase is tested using 4-nitrophenol phosphate as a substrate and 2-amino-2-methyl-1-propanol (AMP) or diethanolamine (DEA) as a buffer, with DEA yielding higher ALP results. ALP isoenzymes can be differentiated using electrophoresis, HPLC, and other techniques.21\n\nThe data obtained from the biochemical assessment were described by the ratio of serum alkaline phosphatase (ALP) levels.\n\nThe Shapiro-Wilk test analyzed the normality of the data distribution. This test was chosen because the sample size in this study was <50. The data of this study were normally distributed with a p-value ≥0.05. The analysis was carried out using a one-way ANOVA test to see differences between groups because the data were normally distributed. A post hoc LSD test followed the results of the ANOVA test to find out more conclusively the relationship between variables that caused the data to be significant at the p-value <0.05. The comparison between the negative control group and the intervention group only shows a significant difference in the week 6.\n\nIn addition, data analysis was also carried out to compare the data for the week 2 and week 4; week 2 and week 6; and week 4 and week 6 using one-way ANOVA. The data of this study were considered insignificant at the p-value < 0.05.\n\n\nResults\n\nIn this study, a total of 36 New Zealand rabbits (Oryctolagus cuniculus) were chosen and split into 9 groups. Each group consisted of four rabbits and were treated according to their group. The alkaline phosphatase blood serum level data was collected from the remaining 29 rabbits after 7 died before samples could be taken. The timing of data collection for rabbits was carried out according to the group, namely in the week 2, week 4, and week 6 after the intervention.\n\nTable 2 shows the serum alkaline phosphatase (ALP) levels in rabbits in each treatment group. Differences in ALP levels were found vertically at weeks 2, 4, and 6. Horizontally, differences in ALP levels can be seen between the positive control, treatment, and negative control groups.\n\nTable 3 shows that the results of the one-way ANOVA test, which reported a p-value = 0.483 and a Levene value = 0.244. Because the p-value was > 0.05, this analysis test showed no significant difference in serum ALP levels at week 2, week 4, and week 6 in the bovine group (K2.3, K2.2, and K2.1).\n\nTable 4 shows the results of the one-way ANOVA test which reported a p-value = 0.052 and a Levene value = 0.034. Because the p-value was > 0.05, this analysis test showed no significant difference in serum ALP levels at week 2, week 4, and week 6 of the green mussel shell group (P3, P2, and P1).\n\nTable 5 shows the results of the one-way ANOVA test reported a p-value = 0.510 and the Levene value = 0.772. Because the p-value was > 0.05, it can be concluded that the serum ALP levels in the negative control group (K1.3, K1.2, and K1.1) were not significantly different.\n\nTable 6 shows that from the one-way ANOVA test results, the p-value = 0.416 and the Levene value = 0.192. Because the p-value was > 0.05, it can be concluded that the serum ALP levels in the week 2 were not significantly different.\n\nTable 7 shows that the results of the one-way ANOVA test reported a p-value = 0.959 and the Levene value = 0.454. Because the p-value was > 0.05, it can be concluded that the serum ALP levels in the week 4 were not significantly different.\n\nTable 8 shows that from the one-way ANOVA test results, the p-value = 0.030 and the Levene value = 0.087. Because the p-value was < 0.05 and a Levene value > 0.05, it can be concluded that the serum levels of ALP in the positive control, treatment, and negative control groups at week 6 had significant differences and were homogeneous. The test was continued with the LSD post hoc test to find out the differences between the treatment groups.\n\nTable 9 above shows that the results of the post hoc LSD test reported the positive control group (bovine) (K2.1) against the treatment group (green mussel shells) (P1) and the negative control group (K1.1) were not significantly different, while the treatment group (green mussel shells) (P1) against the negative control group (K1.1) had significant results.\n\n\nDiscussion\n\nThe osteoconductive matrix is one of the elements that influences the bone healing process. It serves as a scaffold or mineralizing agent for bone and helps in the adherence of osteoconductive and osteogenic cells to the fracture site. Hydroxyapatite is one form of an osteoconductive matrix (HA). Hydroxyapatite is a substance made up of calcium (Ca2+), hydroxy (OH-), and phosphate (PO43-) ions that form a crystal structure with the chemical formula Ca5(PO4)3(OH). The body will naturally generate hydroxyapatite from Ca2+ ions in the blood and inorganic phosphate compounds (Pi or PO43-). Compound Pi is generated by dephosphorylating organic phosphate compounds (PPi), which are phosphates that happen at the ALP dephosphorylation process. As a result, the presence of a hydroxyapatite scaffold reduces ALP activity since the body no longer needs to synthesize hydroxyapatite from PPi.16,22\n\nBecause of that, ALP levels in a bone healing union will be normal or slightly elevated since the hydroxyapatite in green mussel shells functions well as a scaffold. In contrast to non-union fractures, the bone healing process takes longer, and more phosphate is required to compensate for the failure of bone healing, causing ALP levels to grow higher than in union fractures. This condition serves as the study’s measurement basis.16,22 However, ALP does not only play a role in the bone healing process, but also plays a role in other organ systems, such as hepatobiliary, genitourinary, and gastrointestinal.22,23 As a result, it is important to ensure that these body functions are in good condition so that false negatives or false positives do not occur.\n\nThis study aims to determine the effect of green mussel shell hydroxyapatite on blood alkaline phosphatase (ALP) levels in bone grafting procedures in New Zealand rabbits. The total sample was 36 New Zealand rabbits which were then divided into 9 groups. Following this, observations were made in the groups of negative control, positive control groups, and intervention groups in the weeks 2, 4, and 6. Using a surgical procedure and drilling with a width and depth of 5 mm, all groups produced lesions on the femoral diaphysis. The treatment group received green mussel shell hydroxyapatite (HA), while the negative control group did not get any HA as a follow-up intervention. The positive control group received bovine hydroxyapatite (HA). Drill lesions were made to develop the femoral diaphysis to replicate a fracture and to provide a suitable area to apply HA to the cavity formed by the drilling process. In this experiment, an effective dose of bone healing was up to 300 mg of the bone graft.10\n\nThis experiment had a number of methodological limitations, including fractures in the rabbits and post-interventional infections that were not equally exposed to all of the rabbits. This may impact the trial outcomes by increasing the time it takes for bones to recover, which could prevent all treatment groups from showing significant results between the weeks 2, 4, and 6. Even though all groups received an appropriate dose of 300 mg at the area of the lesion, the prolonged bone healing time meant that the test between the positive control group and the negative control group did not produce significant results in the week 6.\n\nAccording to data analysis, the only test that produced significant results with a p-value less than 0.05 on the post-hoc LSD test was the comparison between the week 6 negative control group (K1.1) and the week 6 treatment group (P1). This demonstrates the effectiveness of green mussel shell HA in accelerating and maximizing the healing of bone fractures. however, it could not detect a significant difference between the week 2 and 4. This shows that the week 6, when ALP activity is at its peak, is the optimal week to observe how HA treatment affects the bone-healing process in femoral fractures as compared to weeks 2 and 4.16\n\nAdditionally, even though there were no statistically significant differences between the week 6 positive control group (K2.1) and the week 6 negative control group (K1.1) in the test, K2.1’s ALP level was lower than K1’s. This demonstrates that bovine HA can speed up bone repair, but its effectiveness is lower than that of HA from green mussel shells.\n\nA comparison test of the serum ALP levels at the weeks 2, 4, and 6 in each treatment group’s results did not reveal any significant differences. This indicates that while ALP activity varied at weeks 2, 4, and 6, the differences were not statistically significant. This means that the effect of giving HA works evenly in the weeks 2, 4, and 6.\n\n\nConclusion\n\nGreen mussel hydroxyapatite (HA) is proven able to fasten and maximize the bone healing process as fast as bovine HA and even has higher efficacy than bovine HA.",
"appendix": "Data availability\n\nMendeley Data: Green Mussel Shell Hydroxyapatite ALP Data Set, https://data.mendeley.com/datasets/gvhpb34kkr/1. 24\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nARRIVE checklist for ‘The effect of green mussel (Perna viridis) shells’ hydroxyapatite application on alkaline phosphatase levels in rabbit femur bone defect’, https://doi.org/10.17632/vyw756k44g.1.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAndrzejowski P, Giannoudis PV: The ‘diamond concept’ for long bone non-union management. J. Orthop. Traumatol. 2019; 20(1): 1–3.\n\nQamar N, Aswari A: Healing or Hurting: development of highway public transportation technology. J. Dinamika Huk. 2018; 18(3): 319–328.\n\nKementerian Kesehatan RI, Hasil Riset Kesehatan Dasar (Riskesdas): 2018. Badan Penelitian dan Pengembangan Kesehatan Kementerian RI.2018.\n\nAmin S, Achenbach SJ, Atkinson EJ, et al.: Trends in fracture incidence: a population-based study over 20 years. J. Bone Miner. Res. 2014; 29(3): 581–589. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNoorisa R, Apriliwati D, Aziz A, et al.: The characteristic of patients with femoral fracture in Department Of Orthopaedic And Traumatology RSUD Dr. Soetomo Surabaya 2013–2016. J. Orthop. Traumatol. Surabaya. 2017; 6(1): 1–1.\n\nBabcock S, Kellam JF: Hip fracture nonunions: diagnosis, treatment, and special considerations in elderly patients. Adv. Orthop. 2018; 2018: 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFrölke JP, Patka P: Definition and classification of fracture non-unions. Injury. 2007; 38: S19–S22. PubMed Abstract | Publisher Full Text\n\nKattimani VS, Kondaka S, Lingamaneni KP: Hydroxyapatite–-Past, present, and future in bone regeneration. Bone Tissue Regen. Insights. 2016; 7: BTRI.S36138–BTRI.S36119. Publisher Full Text\n\nBhatt RA, Rozental TD: Bone graft substitutes. Hand Clin. 2012; 28(4): 457–468. Publisher Full Text\n\nVecchio KS, Zhang X, Massie JB, et al.: Conversion of bulk seashells to biocompatible hydroxyapatite for bone implants. Acta Biomater. 2007; 3(6): 910–918. PubMed Abstract | Publisher Full Text\n\nDhanaraj K, Suresh G: Conversion of waste sea shell (Anadara granosa) into valuable nanohydroxyapatite (nHAp) for biomedical applications. Vacuum. 2018; 152: 222–230. Publisher Full Text\n\nSangwaranatee NW, Teanchai K, Kongsriprapan S, et al.: Characterization and analyzation of chitosan powder from Perna Viridis shell. Materials Today: Proceedings. 2018; 5(6): 13922–13925.\n\nFitriah E, Maryuningsih Y, Roviati E: Pemanfaatan daging dan cangkang kerang hijau (Perna viridis) sebagai bahan olahan pangan tinggi kalsium. Proceeding of The URECOL. 2018; pp. 412–423.\n\nLiemawan AE, Tavio T, Raka IG: Pemanfaatan limbah kerang hijau (Perna Viridis L.) sebagai bahan campuran kadar optimum agregat halus pada beton mix design dengan metode substitusi. Jurnal Teknik ITS. 2015; 4(1): F128–F133.\n\nNazht HH, Omara RA, Al Dahhan MR, et al.: Estimation of alkaline phosphatase enzymes level in the femoral transverse fractures healing in rabbits.2019. Publisher Full Text\n\nRathwa HS, Verma T, Chavali VH: Assessment of union in fractures: Role of Serum Alkaline Phosphatase and Ultrasonography. J. Clin. Orthop. Trauma. 2021; 14: 94–100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIsmail R, Laroybafih MB, Fitriyana DF, et al.: The effect of hydrothermal holding time on the characterization of hydroxyapatite synthesized from green mussel shells. Journal of Advanced Research in Fluid Mechanics and Thermal Sciences. 2021; 80(1): 84–93. Publisher Full Text\n\nAjayi IE, Shawulu JC, Zachariya TS, et al.: Osteomorphometry of the bones of the thigh, crus and foot in the New Zealand white rabbit (Oryctolagus cuniculus). Ital. J. Anat. Embryol. 2012; 117(3): 125–134. PubMed Abstract\n\nBagi CM, Berryman E, Moalli MR: Comparative bone anatomy of commonly used laboratory animals: implications for drug discovery. Comp. Med. 2011; 61(1): 76–85. PubMed Abstract\n\nNazht HH: Estimation the alkaline phosphatase (ALP) level in partial hepatectomy rabbits. Al-Qadisiyah Journal of Veterinary Medicine Sciences. 2015; 14(1): 10–14.\n\nWashington IM, Van Hoosier G: Clinical Biochemistry and Hematology. The Laboratory Rabbit, Guinea Pig, Hamster, and Other Rodents. 2012; pp. 57–116. Publisher Full Text\n\nOrimo H: The mechanism of mineralization and the role of alkaline phosphatase in health and disease. J. Nippon Med. Sch. 2010; 77(1): 4–12. PubMed Abstract | Publisher Full Text\n\nStigbrand T, Wahren B: Alkaline Phosphatases. Serological Cancer. Markers. 1992; 11: 135. Publisher Full Text\n\nTjandra KC, Novriansyah R, Limijadi EKS, et al.: The effect of green mussel (Perna viridis) shells’ hydroxyapatite application on alkaline phosphatase levels in rabbit femur bone defect. Mendeley Data. 2023; V1. Publisher Full Text\n\nTjandra KC, Novriansyah R, Limijadi EKS, et al.: The effect of green mussel (Perna viridis) shells’ hydroxyapatite application on alkaline phosphatase levels in rabbit femur bone defect. Mendeley Data. 2023; V1. Publisher Full Text"
}
|
[
{
"id": "195140",
"date": "24 Aug 2023",
"name": "George J Dias",
"expertise": [
"Reviewer Expertise Biomaterials",
"in-vitro and in-vovo investigations.Implants for surgical applications."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Abstract needs to be improved.\nPage 5: Seven rabbits from seven different groups (P1, K1.1, P2, K2.2, P3, K2.3, K1.3) were found dead during daily monitoring several days after the surgery with no specific cause of death. This is a relatively high number of deaths, 7 out of 36 - ~20%. Very surprising that cause of death such as infection, haemorrhage was not determined?\n..., UV sterilization for 3 hours was conducted. I consider this sterilization method to be inadequate for a material to be surgically implanted. Because UV light will only disinfect the surface and will not have an effect of the interior of the implant particles. Authors need to provide evidence about how this sterilization method was selected using general surgical principals.\nPage 6: ... using a drill. Give more details of the bone drilling process. What was the speed of the motor? The type and size of the bur? Was the bur irrigated during drilling?\nfill the defect with green mussel shell HA. What was the form of HA? Was it a powder? If so what is the size of the particles?\nThe blood sampling was conducted by inserting needle parallel to the lateral marginal auricular vein. Once the needle reached the vein, blood will flow into the catheter. The vacutainer tube was pushed so that blood can enter the 1-2 ml tube. After collecting the required sample, the needle was immediately removed from the rabbit’s lateral marginal vein. The injected area was pressed with an alcohol swab at the end of this process. It is not necessary to provide minute details on venopuncture. It would have been preferable if this much of details were provided for the surgical technique of HA implantation.\nExamination of ALP is selected due to its availability in most health centers. Question is blood samples tested in Animal Health Centres are that of common companion animals such as dogs and cats. Therefore, can testing ALP in rabbit blood in a health centre be accurate?\nPage 9: As a result, the presence of a hydroxyapatite scaffold reduces ALP activity since the body no longer needs to synthesize hydroxyapatite from PPi. It can also be argued that the low ALP level indicate that the rate of bone remodelling is slow, leading to the rate of new bone formation to be also being low.\nThis experiment had a number of methodological limitations, including fractures in the rabbits and post-interventional infections that were not equally exposed to all of the rabbits. This may impact the trial outcomes by increasing the time it takes for bones to recover, which could prevent all treatment groups from showing significant results between the weeks 2, 4, and 6. Even though all groups received an appropriate dose of 300 mg at the area of the lesion, the prolonged bone healing time meant that the test between the positive control group and the negative control group did not produce significant results in the week 6. If most of the animals in this study experienced delayed healing of surgical sites due to infections, then the outcome of the complete investigation is brought into question?\n..... negative control group (K1.1) In the negative control, although there was no implant material in the surgical site, the bone defect would not have been empty, it would have been filled with blood clot that eventually got organised, leading to bone healing with new bone formation. Therefore, the significant difference between negative group and the treatment group may indicate that the green mussel shell hydroxyapatite may not be effective as the natural blood clot?\nA comparison test of the serum ALP levels at the weeks 2, 4, and 6 in each treatment group’s results did not reveal any significant differences. This indicates that while ALP activity varied at weeks 2, 4, and 6, the differences were not statistically significant. This means that the effect of giving HA works evenly in the weeks 2, 4, and 6. It is very curious why the authors did not take bone tissue biopsies from the surgical sites at these time points and investigate the histology, and compare these findings with that of the ALP values?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "200163",
"date": "06 Sep 2023",
"name": "Happy Kurnia Permatasari",
"expertise": [
"Reviewer Expertise In silico",
"in-vitro and in-vivo studies",
"natural biomaterials",
"nutraceuticals",
"functional food",
"biochemistry and biomolecular",
"natural product"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWe have fully and carefully evaluated this manuscript, \"The effect of green mussel (Perna viridis) shells' hydroxyapatite application on alkaline phosphatase levels in rabbit femur bone defect\" by Tjandra et al.\nHere are our comments:\n1. First of all, we agree with the other reviewer who requires the authors to re-edit the abstract section. The aims of this research are not yet visible in the abstract. This \"better than HA bovine\" refers to control? Or which intervention? Because it is not mentioned in the abstract methods, but appears in the results.\n2. Introduction:\nProvide the latest data and a wider area, it is stated that the authors adapted data from \"Regional Police of Central Java in 2018\". This is a small part of Indonesia and does not reflect the urgency in the world; and some data got \"2008 to 2009\", please fix it to be more updated.\n\nThe aim of the study must also be addressed from the perspective of describing the contribution to the field under analysis and the elements of scientific novelty presented, as the last, separate paragraph of this section, to make it more easily visible. Develop it better. What differentiates your paper from others on the same topic? Give a reason for interest in this paper.\n\n3. Methods:\nRegister this research protocol at https://preclinicaltrials.eu and mention the registration number in the methods section; it can be registered at any time and for free, this is to increase the readability value of this article.\n\nWriting the Latin name Oryctolagus cuniculus at the beginning can be long, but from now on it must be O. cuniculus; and just write the Latin name without \"Rabbits\"; to be more efficient.\n\nAnalysis: Data analysis is processed using what software? With what CI? It should be clear and detailed.\n\nHow is the sample size calculated? What formula do the authors use?\n\nWhat is the HA dosage given based on?\n\n4. Results:\nIt would be more valid to display tissue histology figure observation data from Animal Experimental to prove the authors' claim to the conclusion that \"Green mussel hydroxyapatite (HA) is proven able to fasten and maximize the bone healing process as fast as bovine HA and even has higher efficacy than bovine HA.\"\n5. Discussion:\nA possible mechanism for the bone healing process must be discussed in a comprehensive manner, due to the long research, this raises the question of whether Green mussel hydroxyapatite (HA) really contributes to the healing process or if it is due to the healing process over time.\n6. Very brief conclusion, elaborate it with the findings that have been observed in the research.\nWe conclude that this article needs to be extensively revised.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "200155",
"date": "06 Sep 2023",
"name": "Maria Apriliani Gani",
"expertise": [
"Reviewer Expertise Biomaterials",
"biomedical pharmacy",
"pharmacology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript “The effect of green mussel (Perna viridis) shells’ hydroxyapatite application on alkaline phosphatase levels in rabbit femur bone defect” was aimed to observe the effectiveness of green mussel shell HA as a bone substitute material.\nBefore being indexed, the article must go through a major revision, including data addition and extensive English editing.\nAbstract:\nIt is recommended to summarize the background section in the abstract and detail the aim of the study.\n\nIn the method section of the abstract, kindly briefly mention the kind of evaluation that was used in the study (histology, etc.).\n\nThe results section in the abstract should be written in the past tense.\n\nIntroduction:\nKindly check and revise the grammar in this section. Please be aware of when to use past tense etc.\n\n“If these conditions are not handled, the decline in quality of life and activity limitations cannot be avoided.” Kindly add the data based on another study regarding quality of life and fracture incidence rate before this sentence.\n\n“As a result, bone grafts with osteogenesis, osteoinduction, and osteoconduction characteristics are required to assist in the healing of acute fractures and non-union fractures.” Please add the reference for this.\n\n“A substance called hydroxyapatite (HA)”. I recommend the authors to change the word “substance” to “material.”\n\n“Virgin clam shells and green mussel shells are just two examples of wastes that could serve as a source of HA for bone substitutes.” Kindly delete the word “just.”\n\nThe author should explain why virgin clam shells and green mussel shells are recommended to be used as HA sources. What are the differences between them with other natural sources of HA?\n\nThe author should detail the hypothesis of the use of green mussel shells in the bone healing process, in terms of the chemical and physical characteristics of this material.\n\n“Alkaline phosphatase (ALP), an enzyme that contributes to the process of bone mineralization, is produced by osteoblasts with increased activity in the third stage.” Delete the “third stage” or keep it with prior explaining about bone healing stages.\n\n“As one of the elements of a complete blood count, ALP can therefore serve as a biomarker that is frequently evaluated and easily accessed to detect bone healing.” The authors should detail the correlation of bone healing processes with ALP serum levels not only in humans but also in animal models. Does it really have a positive correlation of not statistically differ based on other papers?\n\nMethods:\nI recommend the authors summarize the methods section.\n\n“The inclusion criteria in this study were skeletally matured, male New Zealand rabbits (Oryctolagus cuniculus), aged 6-12 months, with a weight of 2.5 – 3 kg. The exclusion criteria in this study were there being anatomical abnormalities, signs of infection, and rabbits that died during treatment.” The inclusion and exclusion criteria mean that any criteria chosen before the study begins. Rabbits who died during the treatments are not included in the criteria. Any animals that died during the treatment must be noted, observed, and reported in the manuscript.\n\nThere was a high number of deaths of the animal and it is a must that the authors should clearly explain the cause of death in the manuscript.\n\nDoes the defect model present the “non-union fractures”? The authors should mention the criteria of non-union fracture and match it with the defect model that was created in the study.\n\nThe authors treated the rabbit with HAs in powder form. How do the authors ensure that the material can serve as a scaffold in the defective tissue? Since HAs may combine with the blood in the defect site it makes the “scaffold” and the treatment fail.\n\nPlease explain why the authors use bovine HA as the positive control, as well as the company of the bovine HA that was used in this study.\n\nTable 1 is not needed to be included in the manuscript, it is enough to mention and cite the source.\n\nThe authors should detail the product code and company that provided the ALP kit.\n\nResults:\nTable 2-9 came from the same data set, which was the ALP levels. These tables can be present in one graph only.\n\nThe authors must add another data set in the manuscript, including:\n\nCharacteristics of green mussel shells HA and bovine HA. Cytotoxic test for the HAs. Other in vivo evaluation results such as radiology and histology to support the current findings.\n\nDiscussion:\nThe authors should detail the concept of ALP levels in each timeline in the bone healing process. When usually the ALP reaches its peaks etc. and why.\n\n“As a result, the presence of a hydroxyapatite scaffold reduces ALP activity since the body no longer needs to synthesize hydroxyapatite from PPi.” This process occurs in the bone tissue. The authors should include the correlation of the tissue and serum ALP levels.\n\nSince the HA came from shells, is there any potential allergic reactivity of the developed material in the human body?\n\nReferences:\nPlease update the references with the up-to-date articles.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-631
|
https://f1000research.com/articles/11-990/v1
|
02 Sep 22
|
{
"type": "Systematic Review",
"title": "Women’s access to health care for non-communicable diseases in South Africa: A scoping review.",
"authors": [
"Jacob Gizamba",
"Jess Davies",
"Chad Africa",
"Candice Choo-Kang",
"Julia Goedecke",
"Hlengiwe Madlala",
"Estelle Lambert",
"Dale Rae",
"Landon Myer",
"Amy Luke",
"Lara R. Dugas",
"Jacob Gizamba",
"Jess Davies",
"Chad Africa",
"Candice Choo-Kang",
"Julia Goedecke",
"Hlengiwe Madlala",
"Estelle Lambert",
"Dale Rae",
"Landon Myer",
"Amy Luke"
],
"abstract": "Background: Non-communicable diseases (NCDs) such as obesity, hypertension (HPT), and type II diabetes (T2D) are of increasing concern in South Africa (SA), with women being more at risk. Authors conducted a scoping review to identify and map the evidence available about the barriers of access to obesity, HPT, and T2D care among women in SA. Methods: Arksey and O'Malley's framework for scoping review was used. The search of the literature was completed in the Scopus, Web of Science, and PubMed databases between April and May 2022. Only studies conducted among women in SA were eligible for inclusion. Identified barriers were mapped onto Levesque’s framework of access to health care to determine which points along the chain of accessing NCD health care among women are mostly impacted. Results: Seven articles were included in the review: qualitative (n=2), quantitative (n=2), mixed methods (n=2), and grey literature (n=1). The included studies reported barriers of access to HPT and T2D care only, and no study reported barriers to obesity care. Supply-side barriers included lack of knowledge about available services, physician heavy workloads, medicine stock-outs, limited availability of testing equipment, unaffordable transport costs, travelling longer distances, inefficiently longer waiting times, and delayed referral. Demand-side barriers included women having low self-awareness of NCD status, concerns about confidentiality, perceived discrimination, and poverty. Conclusions: Access to HPT and T2D services is impacted from perception of need to benefitting from care. Articles included identified barriers affecting the availability and accommodation dimension of access to care, suggesting that HPT and T2D care is often unavailable or that women are unable to reach health facilities or service providers. There is need for more and better-quality research about access to NCD health care in SA, especially among women having a disproportionately high burden of obesity, T2D, and HPT.",
"keywords": [
"Womens health",
"non-communicable disease epidemiology",
"obesity",
"hypertension",
"type 2 diabetes",
"access to care"
],
"content": "Introduction\n\nThe ultimate focus of any health care system is effective and efficient provision of evidence-based health care services fulfilling the needs of the clients and satisfying their expectation for receiving better quality services. Preferably, services should be approachable, acceptable, affordable, available, and appropriate to all users in situations of perceived need.1 This is relevant particularly among women who are more likely to have specific health care needs across their life course and given that approximately two out of three women die from non-communicable diseases (NCDs) globally, possibly more in sub-Saharan Africa (SSA).2–4 Driving this increased risk among women, is persistent exposure to the leading modifiable risk factors for NCDs, coupled with other health conditions such as reproductive, maternal, child, and adolescent health.3,5–7 Further, in the process of seeking health care services, women are subject to gender bias inherent within health systems, resulting in women receiving fewer examinations, screening, and diagnostic tests for NCDs compared to men with similar symptoms.3\n\nThe burden of NCDs among women in SSA has doubled in the recent years.7 Specifically, there has been dramatic increase in the prevalence of NCDs such as type II diabetes (T2D) and hypertension (HPT),8,9 with concomitant increase in NCD-related morbidity and mortality. According to the International Diabetes Federation, the projected rate of increase in T2D cases is highest in SSA compared to other regions. Further, in this region, South Africa (SA) has the highest proportion of people with T2D10 and T2D is the second leading cause of death in the country and the leading cause of death among women.11 The high burden of NCDs among women in SA is exacerbated by the fact that the prevalence of obesity among adults residing in SSA is now higher than the global obesity prevalence for adults,8 with SA having the highest prevalence of obesity, particularly in women.12 Additionally, postpartum weight gain and gestational diabetes are prevalent in SA, resulting in an increased burden of NCDs among women, and demanding availability of specialized services during their life course.13–15 The NCD burden is further compounded by evidence of substantial disparities in women’s health indicators, based on place of residence (rural/urban), socioeconomic status and other indicators of inequities in access to health care.16,17\n\nThe key to averting NCDs and their associated outcomes among women is ensuring availability of regular and holistic NCD-related health care throughout their life course and particularly during critical periods such as pregnancy.3,18,19 For this to be effectively achieved, it’s imperative to first recognize and address any factors that impede access to NCD health care and utilisation among women. The concept of access is better explained as an interaction between characteristics of persons, social and physical environments and the characteristics of health systems and providers.1 All initiatives to promote health equity in access to NCD-related health care need to consider factors from both the supply-side of the health system and the demand-side of the population as highlighted in the Levesque’s dimensions of access to health care framework.1,20 Approaching access to health care with such perspective addresses the fact that access to health services depends not only on availability of the services but also on socioeconomic and sociocultural factors.3 These factors have a direct influence on barriers to access, hence necessitating exploration of access to health care from different perspectives and on different levels, which may require varying solutions to address.\n\nThe aim of this scoping review was to systematically map the evidence available regarding barriers to women’s access to health care for NCDs, focusing on obesity, HPT and T2D, over their life course in SA. The following research questions guided the review process: (a) What are the impediments of access to NCD-related health care services from demand-side (patient/client) perspective? (b) What are the impediments of access to NCD-related health care services from supply-side (provider/health system) perspective? (c) Which points along the chain to accessing NCD-related health care according to the Levesque framework of access to health care is mostly adversely impacted? The identified barriers were mapped onto the Levesque et al.,1 framework of access to health care. The framework suggests a multidimensional view of health care access with five supply-side dimensions of accessibility: approachability, acceptability, availability/accommodation, affordability, and appropriateness and five demand-side corresponding individuals’ and population’s abilities: to perceive, to seek, to reach, to pay and to engage in health care (Figure 1).1 Integrating this framework into this review will assist in highlighting the weak points along the chain of access to health care for NCDs in South African women, which may help to inform strategies, policies, and practices that ultimately lead to a lower NCD burden.\n\n\nMethods\n\nThe methodology of the scoping review was informed by the Arksey and O’Malley framework for scoping reviews.21 Given the complexity of research on access to health care for NCDs, a scoping review was deemed appropriate for collating and synthesizing the available literature on the topic. Studies were included if they (i) involved women; (ii) were conducted in SA; (iii) assessed barriers or facilitators to obtaining NCD-related health care (obesity, HPT, and T2D); (iv) were peer-reviewed or grey literature; and (v) the study explored perceptions from a provider or patient perspective. A study was excluded from the review if it (i) did not focus on access to health care for NCDs among women; (ii) was published in a language other than English; or (iii) was conducted outside SA. Some primary literature explored the perception of women in addition to those of men. Publications were included in the review if the authors distinguished between the findings that were specific to women to those from men.\n\nThe authors searched for primary literature from the following databases: Scopus, Web of Science, and PubMed, based on the criteria described above and the search strategy described in Table 1. The reference lists of included studies were also hand-searched for other relevant studies. All retrieved articles were uploaded into EndNote to remove the duplicates. The articles were then uploaded to Rayyan QCRI (Copenhagen: The Nordic Cochrane Centre, Cochrane),22 where titles and abstracts were assessed independently against the inclusion criteria by three reviewers. Disagreements on selected studies were discussed and resolved by consensus or the intervention of a fourth reviewer when necessary. Thereafter, full texts of studies were screened to verify their conformance with the inclusion criteria. Details of excluded studies at this stage and reasons for their exclusion are presented in Figure 2.\n\nData from eligible studies was charted using a standardised data abstraction tool designed for this study. Macro descriptive data included: Author (s); Title-; Publication year-; study type and the microdata included: Study location; Aim of the study; Study population/sample size; Study design; Duration of the study; type of data analysis used; Study intervention/s; NCD studied; Outcome measured; barriers. Three reviewers independently charted the data from each eligible article. Any disagreements were resolved through discussion between the reviewers or further adjudication by a fourth reviewer.\n\nQuantitative data extracted were presented in tables or charts (as appropriate) in line with the review questions. The studies were grouped by the specific NCD, and summarised by the type of settings, populations, interventions, study designs, outcome measured, women’s life stage of focus. Identified barriers were mapped onto Levesque’s framework1 (five supply-side/health system dimensions and five demand-side/population dimensions) on access to health care to determine which points along the chain to accessing NCD-related health care among women are mostly adversely impacted (Figure 1). No additional quantitative analysis was conducted, other than that which was reported in the included source of evidence.\n\n\nResults\n\nOverall, the search yielded a total of 139 articles, and nine articles were duplicates. 134 articles were screened based on titles and abstracts, and 59 articles were excluded as they did not meet the inclusion criteria. The full texts of 75 articles were retrieved and 68 articles were excluded for the following reasons: studies involving both men and women where results for women were not reported separately (24 articles); studies that did not explore barriers of access to NCD-related health care (40 articles); the study was not conducted in SA (one article); the manuscript was either a published protocol or a case report (three articles) (Figure 2). The remaining seven articles were included in the review.\n\nOf the included studies, two were conducted in Western Cape (WC) province, one study was conducted in Gauteng (GA) province, one was conducted in Mpumalanga, Gauteng, and Limpopo, one study was conducted in Northern Cape (NC) and KwaZulu-Natal, one study was conducted in Eastern Cape (EC) province only, and one study was conducted in all nine provinces of SA. Of the seven included studies, six were published between 2011 and 2021 and one was published in 1997 (Table 2). For primary result articles, two studies included only women, while five studies also included men, but the proportion of women was significantly higher than that of men. Three studies reported barriers of access to T2D-related health care, two studies reported barriers of access to HPT-related health care, while two studies reported barriers of access to both HPT and T2D related health care. No studies reported barriers of access to obesity health care. A descriptive summary of the included studies is presented in Table 2.\n\nThe first dimension of accessibility from a health system perspective in the Levesque’s framework is the approachability dimension, relating to the fact that health care services are identifiable and visible to people facing health needs (Figure 1). In this review, two studies reported barriers that impacted the notion of approachability to services (Table 3). The barriers included women lacking knowledge about services available related to HPT and T2D care23; a communication problem was identified as a health administration issue in management of maternal HPT.24\n\nComplementary to the dimension of approachability is the demand-side dimension; the person’s or population’s ability to perceive need for care (Figure 1). One study reported barriers impacting the ability to perceive dimension (Table 3). In this study, it was reported that women’s self-awareness of their HPT status was low.25\n\nThe second dimension of accessibility from a health system perspective in the Levesque’s framework is acceptability (Figure 1). Acceptability relates to cultural and social factors that impact the person’s possibility to accept different aspects of NCD-related health care services. The barrier related to the acceptability dimension was reported in one study (Table 3). The barrier reported was mistrust of physicians at private hospitals where diabetes care is provided arising from treatment fee charges.26\n\nThe corollary dimension of acceptability is ability to seek health care, relating to the concepts of individual autonomy, personal capacity to choose to seek NCD-related health care (Figure 1). One study reported barriers that affected this dimension of access to NCDs health care (Table 3), and these included: concerns about confidentiality and perceived discrimination hindering one’s ability to seek health care.27\n\nThe third dimension of accessibility from the health system perspective in the Levesque’s framework is availability and accommodation (Figure 1). The dimension relates to the fact that health care services, either the physical space or health care personnel, are reachable both physically and in a timely manner. Six studies reported barriers that impacted on the availability and accommodation dimension of accessibility (Table 3). Physicians’ heavy workloads, and travelling longer distances to reach health facilities23; medicine and pharmaceutical stock-outs27,28; poor health facilities in public hospitals24,26; limited availability of testing equipment, inadequate staffing, and lack of transportation to physically reach service providers,27 transport and safety issues29 are the barriers that impacted availability and accommodation dimension. No barriers were reported to be impacting the demand-side dimension of ability to reach health care.\n\nAffordability is the fourth supply-side dimension of accessibility, and it relates to people’s capacity to spend resources and time to use appropriate services (Figure 1). The dimension captures the direct costs of services and opportunity costs. The barriers related to affordability dimension were presented in two studies (Table 3) and they included: unaffordable transport costs28; and the cost of transport and services being borne by women.23 The corollary dimension for affordability dimension is the ability to pay for health care, and it describes the capacity of a person to generate economic resources to pay for health care services (Figure 1). One study presented poverty as a barrier to ability to pay for diabetes health care services.28\n\nThe fifth supply-side dimension of accessibility is appropriateness, relating to alignment of health care services with patients’ needs, the timeliness and quality of services provided (Figure 1). Three studies presented barriers that impacted appropriateness dimension of access to HPT and T2D care (Table 3). Inefficiently longer waiting times26,27; and delayed referral and management at an inappropriate level of health care are the factors that adversely affected the appropriateness dimension of access to T2D and HPT care. No barriers were reported to be impacting the demand-side dimension of ability to engage health care.\n\n\nDiscussion\n\nThis scoping review of seven studies expounded on the barriers of access to health care for HPT and T2D from the perspective of both the women and the health care providers. The identified barriers were mapped onto the Levesque et al.,1 framework of access to health care in order to identify which points along the chain to accessing health care are critically impacted by the identified impediments in the review. Mapping of the barriers on the framework highlight the weak points along the chain to accessing NCD care and allow for targeted intervention and effects to alleviate barriers to accessing NCD care in SA.\n\nSix out of the seven studies included in this review impacted the availability and accommodation dimension (supply-side). This dimension of accessibility of services is on the Levesque’s framework of access to health care (Figure 1) hence suggesting that access to HPT and T2D care is likely to be impeded right in the middle of the access to care process. The findings from this review indicate that from the health system and provider perspective, there are challenges related to pharmaceutical stock-outs, inadequate staffing, limited availability of testing and screening equipment and poor health facilities.24,26–28 These factors have been highlighted as key barriers to management and control of NCDs in SSA and globally.30–34 Efforts have been made to increase the number of health care workers (HCWs) and improve their capacity to deliver NCD care in SA; however, there are still inadequacies in HCW’s and health system’s capacity to cater for the increasing burden of NCDs.35,36 Inadequacy and overstretched staff could benefit from community health workers’ (CHW) engagement in health programmes since CHWs’ support has been reported to be effective in low- and middle-income countries (LMICs) in HPT and diabetes control.36–38 Further, integration of NCDs care services with existing HIV programmes have been reported to be effective in increasing the availability of NCDs care at primary and community health centers.37\n\nTravelling longer distances and limited availability of means of transportation to reach health facilities were also reported as supply-side barriers to access of HPT and T2D care. This is similar to findings from related studies that have been conducted in LMICs.39,40 It has being reported in SA that the poorest tend to reside furthest from the nearest clinic and their inability to bear travel costs constrains them to lower quality health care facilities.41 Since distance plays a significant role in mediating health care utilisation behaviour, more research is needed to quantify the relationship between the growing need for NCD care and access to this care nationally among women to support implementation decisions.\n\nFurther, two studies cited barriers related to the affordability dimension of access to health care which included unaffordable transport fares incurred by the women during the process of accessing services and all the costs are borne by the patient.23,28 In a bid to promote equitable financial access to health care services, SA has implemented different health financing policies such as user fee abolitions. Indirect costs such as transport, however, have continued to be highlighted as significant barriers for the poor. Poverty remains a constraint in accessing NCD care, mainly due to the inability to afford transport fares, and recommended medication.28,42 Similar findings have been reported in other LMICs which have implemented different forms of user fee abolition.34,39\n\nWomen’s lack of information about available HPT and T2D services was highlighted as a barrier impacting the approachability dimension of access to health care.23 Inadequate knowledge about health care services available limits women’s choice and directly impacts utilisation of the services. Availability of clear, correct, and timely information about NCD services increases women’s abilities to perceive need for care and seeking out for services. This demands more efforts to raise user awareness about HPT and T2D health care services available through use of mass media like radio and television, which has been associated with better use of health services in other LMICs.43,44\n\nFurthermore, one study reported a low self-awareness of HPT status among women, which negatively impacted their ability to perceive a need for care.25 People’s lack of awareness about NCDs and risk factors especially HPT and T2D is not uncommon in SA and globally.6,30,45 The lack of knowledge about NCDs and their risk factors among the women and the general population makes it challenging to reduce the burden of NCDs. Adopting of a multisectoral approach such as CHW raising NCD awareness through health education, and integration of NCD education in school curriculum could assist in behaviour change, increased knowledge about NCD risk factors and care available among women.37,46\n\nLonger waiting times and delayed referral were cited as barriers that impacted the appropriateness dimension of access to HPT and T2D care.26,27 Longer waiting periods are largely influenced by the large number of people seeking a specific service and the number of HCWs available to offer the service.47,48 Given the scale of NCDs burden, integration of the management of diabetes, and HPT into primary health care (PHC) represents a feasible, affordable, and equitable option for addressing women’s needs for NCDs care in a timely manner.49 This is because PHC is the most frequent entry point for the general population to the health system, hence offers a great opportunity for early detection and management of high-risk women visiting health services for other reasons such as antenatal care.50\n\nThe concept of health care access is comprehensive, and its definition and influencing factors are still evolving globally. Firstly, since this was a scoping review, the quality of the methodology used in the selected studies was not assessed. The summary findings should be interpreted cautiously, though the barriers reported in the reviewed studies are well corroborated, giving our findings some degree of credibility. Secondly, although three reviewers examined all articles, given the ambiguity and overlap of the dimensions of access to health care in the Levesque’s framework, it is possible that we missed or incorrectly categorised pertinent findings, potentially altering the results. Thirdly, only studies published in English were included in this review, therefore this may have led to omission of other relevant studies not published in English. Despite these limitations, this scoping review highlights the complexity of access to HPT and T2D care in SA and shows that limited studies have been conducted on access of health care services related to HPT, T2D, and obesity in SA and in women particularly.\n\n\nConclusion\n\nThis scoping review highlights barriers to accessing HPT and T2D health care in SA, preventing women from achieving the full extent of their health. Access to HPT and T2D services is impacted all along the chain of access, from perception of need to benefitting from care, though most of the barriers to accessing HPT and T2D health care that were reported in this review originated from supply-side (health system perspective) dimensions of access. This information underlines the need for more and better-quality research about access to NCD health care in SA especially among women who have a disproportionately high burden of obesity, T2D, and HPT.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: Review protocol for “Women’s access to health care for non-communicable diseases in South Africa: A scoping review”. https://doi.org/10.6084/m9.figshare.20292480.v1.51\n\nThis project contains the following extended data:\n\n• Scoping review Protocol.pdf (Review protocol for this study).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReporting guidelines\n\nFigshare: PRISMA-Scr checklist for “Women’s access to health care for non-communicable diseases in South Africa: A scoping review”. https://doi.org/10.6084/m9.figshare.20280327.v1.52\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
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}
|
[
{
"id": "151458",
"date": "09 Jan 2023",
"name": "Dorothy Lall",
"expertise": [
"Reviewer Expertise Health systems research",
"Health care organisation",
"health services",
"Primary health career",
"NCD care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study is a scoping review of literature to identify reported barriers for women to utilise health care services for NCDs in South Africa. The method reported is a scoping review and the findings of the primary research studies were mapped onto an a priori identified framework. The main findings were related to access from supply side.\nWhile the question is relevant, the need to assess only barriers for women as opposed to people is not well justified. The findings too are not discussed in the light of these being barriers for women... for example is it any different for men and if so how? There is an opportunity to discuss deeper how gender equity in health service organisation can be achieved.\nMethodologically - it is a clear that a systematic approach was taken however, mixing quantitative and qualitative studies requires more clarification as the fundamental assumptions underlying these studies is different... perhaps to have conducted this a mixed methods review - analysing both types of studies separately and make interpretations by combining findings would have been more appropriate.\nPresentation of findings is not clear and potentially misleading - how many studies reported a dimension of the framework is presented however is this the same study or different studies is not clear. Suggestion to redo the table 3 with references to the articles cited.\n\nThe discussion can be strengthened and does not do justice to the research question nor provides direction for applying these findings.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "11622",
"date": "28 Jun 2024",
"name": "Lara Dugas",
"role": "Author Response",
"response": "We are grateful for your time in reading our manuscript and providing detailed constructive feedback. The revised manuscript addresses the suggestions and concerns raised. Below is a summary of our response to some of the comments and suggestions not extensively addressed in the revised version. While the question is relevant, the need to assess only barriers for women as opposed to people is not well justified. The findings too are not discussed in the light of these being barriers for women... for example is it any different for men and if so how? There is an opportunity to discuss deeper how gender equity in health service organisation can be achieved. Sentences and paragraphs in the introduction and discussion have been rephrased and edited to highlight the justification for exploring barriers to women's access. Methodologically - it is a clear that a systematic approach was taken however, mixing quantitative and qualitative studies requires more clarification as the fundamental assumptions underlying these studies is different... perhaps to have conducted this a mixed methods review - analysing both types of studies separately and make interpretations by combining findings would have been more appropriate. The findings from both quantitative and qualitative studies were combined because only a few studies were included in this review. The goal of the review was to summarize barriers to access as reported in the included studies, regardless of any quantitative analyses conducted. However, this issue has been highlighted in the limitation section. Presentation of findings is not clear and potentially misleading - how many studies reported a dimension of the framework is presented however is this the same study or different studies is not clear. Suggestion to redo the table 3 with references to the articles cited. In the interpretation of the findings in Table 3, we provide a detailed description and citation of the studies that explored specific barriers to access. Additionally, Table 2 extensively summarizes all the barriers to access in each study separately. The discussion can be strengthened and does not do justice to the research question nor provides direction for applying these findings. Certain sections in the discussion have been revised to emphasize suggestions and recommendations."
}
]
},
{
"id": "266104",
"date": "14 May 2024",
"name": "Selene Valerino-Perea",
"expertise": [
"Reviewer Expertise Public health",
"policy",
"nutrition",
"non-communicable diseases",
"physical activity",
"health determinants."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSUMMARY The article summarises the literature exploring barriers to healthcare for obesity, hypertension and diabetes in women in South Africa. The authors use Levesque’s framework to organise these barriers and provide a clear picture of the specific points where access to healthcare is affected. The findings are relevant as country-specific information about these barriers is generally needed to guide policies. In addition, the authors highlight why women might need specific healthcare needs and, therefore, why this research is needed.\nGeneral comments The authors use frameworks both to conduct the review and to map results according to access to healthcare. This adds value to the research.\nOverall, the article is well-written and clear. However, I add a few suggestions to ease readability for readers. For instance, re-arranging the introduction’s information, using simpler terms and adding subheadings.\nSpecific comments\nABSTRACT\nConsider rephrasing “travelling longer distances” to “travelling long distances” and “inefficiently longer waiting times” to simply “long waiting times”. Could the authors explain in their response why the lack of knowledge about available services is on the supply-side rather than on the demand-side? Thanks. “unaffordable transport costs”. What does this refer to? Please clarify in the manuscript. Overall, the abstract's conclusion needs to be rephrased to improve readability. Conclusions could state that more research is needed on obesity as the authors did not find evidence on this aspect. The abstract does not mention a result/conclusion to the research question c). Please add it.\n\nINTRODUCTION\nThe introduction mostly covers all the information needed to justify why this research was conducted. However, the information is presented in a format that makes it difficult to understand which gap in the literature this research addresses. For example, the first paragraph discusses why healthcare systems need to be effective/efficient and then talks about women having specific healthcare needs. The next paragraph specifies NCD rates (but does not specify if these rates refer to women or all adults) and then again mentions why women might have specific healthcare needs. Then authors go back to talk about the need for efficient healthcare needs. -- It would be better to present the information in a more structured way. For example, 1) NCD rates in SA, particularly in women, 2) reasons why authors focus on women specifically (e.g. higher obesity rates, specialist needs around pregnancy, gender bias, disparities), 3) the need for efficient healthcare needs and any specific needs for women, 4) Levesque’s dimensions. The introduction could use some rephrasing to improve readability. For example: “The ultimate focus of any health care system is effective and efficient provision of evidence-based health care services fulfilling the needs of the clients and satisfying their expectation for receiving better quality services.” – This sentence could simply be “The main goal of any health care system is to provide effective, efficient and evidence-based services fulfilling the client's needs and satisfying their expectation for quality services”.\n\nOther sentences like “The concept of access is better explained as an interaction between characteristics of persons, social and physical environments and the characteristics of health systems and providers” could also be rephrased. Terms like “necessitating” or “impediments” can also be simply substituted as ‘needing’ or ‘barriers’. –- Please rephrase complex sentences to simpler ones. “possibly more in sub-Saharan Africa (SSA)”. – what do authors mean by this? Specifically, by the term “possibly”, please expand on the manuscript. “Driving this increased risk among women is persistent exposure to the leading modifiable risk factors for NCDs, coupled with other health conditions such as reproductive, maternal, child, and adolescent health” – Which modifiable risk factors do authors refer to? What do authors mean by “other health conditions such as reproductive, maternal, child, and adolescent health”. Hormonal changes? Please expand on the manuscript. The introduction includes claims aspects such as “The burden of NCDs among women in SSA has doubled in the recent years” or “T2D is the second leading cause of death in the country and the leading cause of death among women” –- Have these increases and rates are larger in women compared to men? Overall, it is fine if the rates of NCDs in women in SA are not largely different to those in men, as the authors have identified other reasons why the research focuses on women, but it is important to clarify these aspects if these are mentioned as reasons to focus on women. In addition, these sentences could use adding some numbers to provide detail on certain claims. \"Specifically, there has been dramatic increase in the prevalence of NCDs such as type II diabetes (T2D) and hypertension (HPT)\" – please specify if this claim refers to all adults or women only. Overall, the introduction explains really well why using Levesque’s frameworks adds value to this research.\n\n“The aim of this scoping review was to systematically map the evidence available regarding barriers to women’s access to health care for NCDs, focusing on obesity, HPT and T2D, over their life course in SA” –- please consider deleting the word “systematically” as this is not a systematic review\n\nMETHODS\nApologies, I do not understand what the authors mean by the sentence, “Given the complexity of research on access to health care for NCDs, a scoping review was deemed appropriate for collating and synthesizing the available literature on the topic” – why would complex research indicate a scoping review vs a systematic one? Please indicate so in the manuscript. “and (v) the study explored perceptions from a provider or patient perspective” – could authors explain what this means? I.e., perceptions from a provider or patient perspective as opposed to what? Please explain in the manuscript. Consider moving Table 1 to supplementary materials and, in the text, simply examples of used terms. Also please consider providing the specific search strategy in each database. “Thereafter, full texts of studies were screened to verify their conformance with the inclusion criteria”. – was this step also conducted by 2 reviewers independently? Please explain so in the manuscript. Apologies—I can’t see the footnote in Figure 2. Could the authors make sure it is visible? Thank you. (There are 2 asterisks in the figure but no footnotes.) “Quantitative data extracted were presented in tables or charts (as appropriate) in line with the review questions” – as some qualitative studies were also included, could authors describe how they extracted qualitative data as well? Thank you.\n\nRESULTS\nThe first paragraph and Figure 2 state that 9 articles were removed as duplicates, but that would leave 130 articles in the records screened. Please edit as appropriate. Why was the case report excluded? This is not mentioned in either inclusion or exclusion criteria. Please explain in the manuscript. “but the proportion of women was significantly higher than that of men” – not sure if this sentence is needed as the results of women are reported separately to those of men in these studies (according to the methods section). Table 2: overall, I find that the results are not reported consistently across the table. E.g., using the term ‘client’ in some rows vs. using the term ‘patient’ in others. Some studies also report total sample sizes and subgroups; others do not present total sample sizes; others provide characteristics of the sample (socially disadvantaged women) while others don’t; the study objectives are presented using different sentence structures, etc. I see this across the table - please ensure results are presented consistently and using the same terms. Table 2: Not sure why the column ‘barriers’ is presented here as this information is already contained in Table 3. Please consider deleting. Table 3 presents supply-side and demand-side dimensions separately, while the text presents the same dimension together. Please consider presenting the table with more columns to compare the supply and demand aspects side by side (as these are presented together in both the Framework in Figure 1 and in the text. Approachability dimension – should the word “approachability” be the word in bold font (rather than the word “dimension”)? \"A communication problem was identified as a health administration issue in the management of maternal HPT\". – could authors explain what they mean by this sentence? Not currently clear. The supply-side and demand-side barriers related to the first two dimensions (e.g. approachability and acceptability) are presented in different paragraphs, which can limit readability. Could the authors use subheadings or present all information relating to the same dimension in the same paragraph? Thank you. “The barrier reported was mistrust of physicians at private hospitals where diabetes care is provided arising from treatment fee charges” – Please clarify is this refers to T2D or HPT or both. Same in the barriers reported that do not specify this aspect. Thank you.\n\nDISCUSSION\n“This scoping review of seven studies expounded on the barriers of access to health care for HPT and T2D from the perspective of both the women and the health care providers” – The aim was also to review the barriers for obesity care. It can be mentioned here that the results focus on HPT and T2D given the lack of evidence on obesity. Overall, the discussion could use subheadings to ease readability. “The identified barriers were mapped onto the Levesque et al.,1 framework of access to health care in order to identify which points along the chain to accessing health care are critically impacted by the identified impediments in the review” – consider deleting “by the identified impediments in the review” as the sentence stands on its own. \"Mapping of the barriers on the framework highlight the weak points along the chain to accessing NCD care and allow for targeted intervention and effects to alleviate barriers to accessing NCD care in SA\". – Please indicate that authors refer specifically to T2D and HPT rather than all NCDs. \"Six out of the seven studies included in this review impacted the availability and accommodation dimension (supply-side).\" – do authors mean “explored” instead of “impacted” in this sentence? “however, there are still inadequacies in HCW’s and health system’s capacity to cater for the increasing burden of NCDs” – please indicate which inadequacies persist. The ‘health care workers’ (HCWs) and ‘community health workers’ (CHW) – abbreviations are not needed as these are not used frequently in text – please use full terms. The discussion should mention (perhaps in limitations) that these findings could represent only the barriers perceived by patients/providers. That is, given that the reviewed studies did not use Levesque’s framework themselves, it is plausible that the studies did not capture all the barriers or that some might have been over/underrepresented. The fact that no studies explored barriers to obesity should be discussed more thoroughly in the discussion. “The summary findings should be interpreted cautiously, though the barriers reported in the reviewed studies are well corroborated” – how are these corroborated? Please explain in the manuscript. “Secondly, although three reviewers examined all articles, given the ambiguity and overlap of the dimensions of access to health care in the Levesque’s framework, it is possible that we missed or incorrectly categorised pertinent findings, potentially altering the results.” What implication for research does this have? Perhaps authors could suggest specific alterations to Levesque’s framework?\n\nCONCLUSION\n“This information underlines the need for more and better-quality research about access to NCD health care in SA especially among women who have a disproportionately high burden of obesity, T2D, and HPT.” - The authors also suggest in the discussion some interventions or policies that could address some barriers. Please add that suggestion here as well.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": [
{
"c_id": "11620",
"date": "29 Jun 2024",
"name": "Lara Dugas",
"role": "Author Response",
"response": "We appreciate your time and effort in reading and providing extensive constructive feedback on our manuscript. The suggestions and concerns raised have been addressed in the revised manuscript. Below is a summary of our response to some comments and suggestions that were not extensively addressed in the revised version. ABSTRACT • All comments are addressed in the revised manuscript. • Comment 2: According to Levesque’s framework of access to health care, there is a thin line between Approachability (supply-side) and Ability to perceive need for care (demand-side). In the framework, Approachability relates to the fact that people facing health needs can identify that some form of service exists, can be reached, and impacts the individual's health. Based on this conceptualization, we considered Knowledge about available services on the supply side. INTRODUCTION • We considered all suggested changes, and they are reflected in the revised manuscript. • Subheadings were not included, but the paragraphs were edited, and some sentences were re-written according to reviewers' suggestions. METHODS • All suggestions made by the reviews are considered in the revised manuscript • Table 1 was included in the main text because it reflects the key terms used in each database and how they were combined during the search. Since it contains such important information related to the search strategy, we thought having it in the main text would be better. • Figure 2 has been edited. RESULTS • All suggestions by the reviewer have been included in the revised manuscript. • “but the proportion of women was significantly higher than that of men” – not sure if this sentence is needed as the results of women are reported separately to those of men in these studies (according to the methods section). The reason for adding this statement was to highlight to the reader that while some studies included men as participants, their representation was notably lower compared to women. Therefore, the reported barriers may primarily reflect those faced by women. • Table 2: - please ensure results are presented consistently and using the same terms. Addressed, some information that is missing was not explicitly reported in the included articles. • Table 2: Not sure why the column ‘barriers’ is presented here as this information is already contained in Table 3. Please consider deleting it. In Table 2, we aimed to summarise the barriers directly, as reported in the respective articles. Table 3 categorizes and presents the barriers according to the Levesque framework. • Table 3 presents supply-side and demand-side dimensions separately, while the text presents the same dimension together. Please consider presenting the table with more columns to compare the supply and demand aspects side by side (as these are presented together in both the Framework in Figure 1 and in the text. Presenting the supply and demand side by side offers a more comprehensive view of the results. However, we chose to summarize the findings in the format depicted in Table 3 due to variations in the barriers explored across different studies and the diversity of NCDs examined. Nevertheless, we described and interpreted the results by delineating a supply domain alongside its corresponding demand domain. This approach offers readers a comprehensive understanding of the interplay between supply and demand factors, as illustrated by the Levesque framework. DISCUSSION • All suggestions by the reviewer are addressed in the revised manuscript. CONCLUSION • All suggestions by the reviewer are addressed in the revised manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/11-990
|
https://f1000research.com/articles/13-600/v1
|
07 Jun 24
|
{
"type": "Study Protocol",
"title": "Occupation-related antecedents, job-related outcomes, and intervening factors of mental health disorders among food handlers: A scoping review protocol",
"authors": [
"Harshit Singh",
"Senthilkumaran Piramanayagam",
"K Thirugnanasambantham",
"Harshit Singh",
"K Thirugnanasambantham"
],
"abstract": "Background Mental health and work are closely interlinked. Evidence suggests that food handlers suffer from poor mental health across the globe. A job in the food service sector is emotionally demanding as employees directly interact with customers who insist on impeccable services and real-time responses. The causes of mental health conditions among food handlers are multifactorial. Studies on the antecedents, outcomes, and intervening factors of foodservice employees’ mental health are fragmented and sparse.\n\nObjective We aimed to explore the existing literature describing the antecedents and outcomes of mental health disorders among food handlers. Moreover, we also aimed to explore various contextual factors that directly or indirectly influence the relationship between multiple antecedents and outcomes of food handlers’ mental health.\n\nInclusion criteria Studies that focus on identifying the antecedents, outcomes, and contextual factors that influence the relationship between the antecedents and consequences of food handlers’ mental health will be included in the scoping review.\n\nMethods This scoping review will follow Arksey and O'Malley's (2005) framework: 1) identifying the research question; 2) identifying relevant studies; 3) study selection; 4) charting the data; and 5) collating, summarizing, and reporting results. Comprehensive searches will be conducted in databases such as PubMed, PsycINFO, and CINAHL using relevant keywords. Studies meeting the inclusion criteria that focused on antecedents, outcomes, and contextual factors influencing the mental health of food handlers will be selected. Data will be extracted and charted in electronic form. The findings will be narratively summarized and thematically analyzed to answer the research questions.",
"keywords": [
"Food handlers",
"Mental health disorders",
"Pathogenesis",
"Intervening variables",
"Occupational outcomes"
],
"content": "Introduction\n\nThe prevalence of mental health disorders is high worldwide. The World Health Organization (WHO) report on Global Mental Health 2022 indicates that one in eight individuals in the world is living with mental disorders (World Health Organisation, 2022). The WHO defines mental health as “A state of mental well-being that enables people to cope with the stresses of life, to realize their abilities, to learn well and work well, and to contribute to their communities. Mental health is an integral component of health and well-being and is more than the absence of mental disorder.” The WHO emphasizes that mental health is a basic human right and an integral element of our general health and well-being (World Health Organisation, 2022). The prevalence of mental health conditions and their socioeconomic consequences is enormous. A health condition is a broad term that generally covers mental and psychological disorders.\n\nThe cost of mental condition to the world economy, which stood at approximately US$ 2.5 trillion in 2010, is expected to reach US$ 6 trillion by 2030, alongside an increase in social cost. Low- and middle-income countries (LMIC) alone need to bear 35 per cent of the total cost of healthcare for mental health conditions. In addition to the direct costs involved in the treatment of mental health conditions, countries also face indirect costs, such as reduced economic productivity, unemployment, societal inequality, suicides, and substance use. In most societies, mental health is neglected and fails to provide care and support to people (World Health Organisation, 2022). Although mental health conditions are common across the globe, millions of individuals suffer from silence, which has a significant negative impact on their daily lives. The World Mental Health Report published by the WHO in 2022 indicates that even after publishing its landmark health report in 2001, the recommendations remain valid today (World Health Organisation, 2022).\n\nMental health and work are also highly interlinked. Employees’ mental health is a ubiquitous concern in the workplace. While most employees report at least one symptom of poor mental health, approximately 20 per cent of employees have mental illness (Rosado-Solomon et al., 2023). Employees’ mental health has a huge impact on organizations and, subsequently, on global society. A collective policy brief on mental health by the WHO and the International Labour Organization (ILO) indicates that 12 billion working days are lost every year due to anxiety and depression (World Health Organisation & International Labour Organisation, 2022). Poor mental health can influence an individual employee’s physical health, which further increases the risk of accidents, poor quality of work, and higher levels of absenteeism. Good mental health among employees enables them to be more productive, and vice versa, in unhealthy work environments. Individuals are able to function, cope, connect, and thrive better because of their good mental health (World Health Organisation & International Labour Organisation, 2022).\n\nFood handlers can be anyone who directly or indirectly handles unpackaged and packaged food, food equipment, and utensils used to serve or prepare food (Food and Agriculture Organization of the United Nations, 2017). Food handling is the most common occupation and is exposed to many stress factors. The management expectation of dedication and commitment, which ultimately leads to a long working hours culture, makes food service employees have a higher average risk of exposure to depression, stress, anxiety, and chronic pain (Cerasa et al., 2020). Moreover, studies have shown that verbal aggression, bullying, physical aggression, screams, and threats are common in the food service workplace (Cristina et al., 2021). The existing literature on mental health-related challenges among food handlers provides a diverse set of factors that are associated with mental health. Researchers have also highlighted that events such as global health emergencies like the COVID-19 pandemic have fuelled mental health challenges among food handlers. For example, perceived stress has been found to increase owing to occupation-related stressors among food service employees during the pandemic (Wilkesmann & Wilkesmann, 2021).\n\nResearch studies that attempt to identify the factors that are critical for mental health among food handlers are multifactor: job-related factors (Eburne & Eburne, 2010; Ishaque et al., 2021) person- or employee-related factors (Chuang et al., 2011; Harris & Giuffre, 2010; Hinterstoisser, 2011), organization-related factors (Chen & Wang, 2019; Chuang et al., 2011; Ishaque et al., 2021), contextual factors (Cerasa et al., 2020; Cristina et al., 2021; Harris & Giuffre, 2010; Hinterstoisser, 2011; Kohli & Mehta, 2022) and external environment-related factors (Chen & Wang, 2019; Wilkesmann & Wilkesmann, 2021). However, there is no synthesized evidence on the antecedents of mental health conditions among foodservice employees. In a similar manner, outcomes of mental health conditions also described in the literature. It is also multidimensional, as the mental health of food handlers has significant effects on individuals, organizations, family members, and society at a large (Cerasa et al., 2020; Chen & Wang, 2019; Chuang et al., 2011; Cristina et al., 2021; Harris & Giuffre, 2010; Hinterstoisser, 2011; Ishaque et al., 2021; Kohli & Mehta, 2022; Pidd et al., 2015). The most common outcome frequently highlighted in literature is employee turnover. The most common antecedents, outcomes, and contextual factors are presented in Figure 1.\n\nWhile employee mental health and well-being are crucial, there remains a dearth of research in this area, particularly among foodservice handlers (Cristina et al., 2021; Ishaque et al., 2021; Kohli & Mehta, 2022). Our objective was to fill this gap by conducting a thorough scoping review that delves into the antecedents, outcomes, and intervening factors associated with mental health disorders among food handlers, as detailed in this protocol.\n\n\n2. Methods\n\nThe researchers in the proposed scoping review will adopt the updated methodological guidelines of the JBI for the scoping review protocol (Peters et al., 2020). A preliminary search of PROSPERO, MEDLINE, JBI Evidence Synthesis, and Cochrane Database of Systematic Reviews was conducted to confirm that no current or scoping reviews or systematic reviews were underway.\n\nThis review aims to examine the factors that contribute to mental health conditions among food handlers worldwide. We will identify the factors associated with mental health conditions, including stress, depression, anxiety, and burnout, among food handlers. These factors are classified as individual- or person-related, occupation- or work-related, organizational-, and environment-related. We will also explore the outcomes of mental health conditions among food handlers in individuals, organizations, and society. We will look at potential mediators and moderators that may influence the complex relationship between the factors that influence foodservice employees’ mental well-being. Through a comprehensive review of the literature, we hope to highlight gaps, synthesize insights, and inform future research, practices, and policies to effectively address mental health concerns among food handlers, who are an overlooked occupational group. The research questions of the proposed scoping review were developed based on Population, Concept and Context (PCC framework). The framework is presented in Table 1.\n\nWith the above PCC framework, we aimed to address the following research questions: (1) What are the occupation-related factors that cause mental health conditions in food handlers? (2) What are the outcomes of food handlers’ mental health conditions for individuals, organizations, and society? (3) Do any intervening factors moderate or mediate the relationship between antecedents and outcomes of food handlers’ mental health? (4) What strategies have been adopted to address mental health conditions among food handlers?\n\nStudies that are considered potential to be included in the scoping review, if it: (i) associated with food handlers including chef, cook, waiter, gastronomes, and workers associated with food handling experiencing the metal health conditions and its impact on individuals, organizations, and society; (ii) published in English; (3) full text; (4) adopted quantitative, qualitative, or mixed-method study designs; and (5) grey literature including conference proceedings, presentations, and posters. The authors will be contacted if only the abstract of the study is available. Research works published in other languages and the non-availability of full text that studied mental health associated factors will be excluded.\n\nThe search approach aims to locate both published and unpublished studies. An initial limited search across Web of Science, Scopus, Google Scholar, PubMed, EMBACE, and CINAHL was conducted to identify key articles, extract relevant keywords, and index terms describing the topic. With guidance from a library specialist, a comprehensive search string was developed by combining these terms using Boolean operators. I). The search terms and string used in preliminary search strategy for PubMed is presented in Table 2.\n\nThis search will be adapted for each database/information source included: PubMed, EMBASE, CINAHL, Web of Science Core Collection, PsycINFO, and ProQuest Dissertation and Theses Global for unpublished literature. The reference lists of all the included evidence sources will also be handsearched to identify additional eligible studies. The search strategy utilized a combination of controlled vocabulary (e.g., MeSH, CINAHL Headings) and natural language terms related to the population (food handlers), concept (mental health), and context (workplace). Proximity and truncation operators were applied to capture the relevant variations in terminology.\n\nOur search will cover all relevant databases to generate a list of citations that will be organized and uploaded onto a systematic review platform. To ensure accuracy, duplicate records will be removed during the uploading process. After training with a pilot sample, two independent reviewers screen the titles and abstracts of the remaining citations to assess their eligibility. Citations that meet these criteria will be subjected to a full-text review. Both reviewers will evaluate the full text of these citations against the inclusion criteria, and any reasons for exclusion will be recorded in detail. In cases of disagreement between the reviewers, a third reviewer will be consulted to resolve the issue.\n\nTwo independent reviewers will extract data from all the studies included in the scoping review using a standardized electronic data extraction form. The form will be developed specifically for this review to capture relevant details about the participants, concepts, contexts, study methods, and key findings related to the research questions. The data to be extracted from the existing literature is presented in Table 3.\n\nPrior to commencing full data extraction, the two reviewers will independently pilot test the form of the three included studies to ensure clarity, comprehensiveness, and functionality. Based on their experiences during this pilot phase, the form will be revised and finalized as needed, with any modifications documented transparently. Throughout the data extraction process, the two reviewers will work independently and meet periodically to discuss and resolve any disagreements through a consensus. If disagreements persisted after discussion, a third reviewer will be consulted to achieve resolution. For any studies published within the last 24 years where critical data are missing or unclear, attempts will be made to contact the original study authors to request additional information. Online systematic review software (https://www.cadima.info/) will be utilized to manage and streamline the data-extraction process. This systematic approach to extracting and documenting relevant data elements aims to capture key evidence from the literature in a consistent and comprehensive manner.\n\nThe extracted data will be synthesized and presented using both narrative and visual formats. If sufficient studies are available, findings related to mental health factors among food handlers will be organized into relevant thematic categories. These may include individual-level factors (e.g., socio-demographics and coping strategies), job/task characteristics (e.g., workload and emotional demands), organizational aspects (e.g., workplace policies and support systems), and broader contextual influences (e.g., cultural norms and regulatory environment). The analysis aims to systematically map the range of determinants and consequences associated with mental health conditions, such as stress, burnout, depression, and anxiety, specifically among this workforce. Potential moderating and mediating variables that impact the complex interplay between antecedents and outcomes will also be examined where the data permits. Diagnostic approaches and assessment methods used to evaluate mental health in food handler populations across studies will be summarized, highlighting potential strengths, limitations, and research gaps. Impacts on quality of life and workplace aspects like absenteeism, productivity and turnover will be narratively synthesized. Wherever feasible, the findings will be visually depicted using tables, figures, and conceptual models to provide an integrated understanding. Differences in mental health factors across relevant subgroups (e.g., occupational roles, geographical regions, workplace settings) will also be analyzed and presented.\n\n\n3. Discussion\n\nWe plan to conduct the first scoping review that focuses on consolidating evidence across the intersecting issues of mental health conditions among food handlers, a vulnerable occupational population. This review aimed to provide a broad map of the available research landscape related to mental health status, associated factors, and relevant interventions among food handlers across diverse contexts. We will analyze the coverage, insights, and remaining knowledge gaps to guide future studies and organizational efforts to address this topic. We will use a systematic strategy to capture published and grey literature across several databases and search for citations. However, there are some limitations regarding the language (only English) and databases screened due to logistical constraints. We should note that scoping reviews do not assess the methodological quality or risk of bias in the included studies, and we will not do so either. Despite its limitations, this scoping review represents a crucial step in consolidating the current fragmented evidence on mental health among food handlers. By synthesizing available research across diverse contexts, this review will provide a comprehensive overview of the current state of knowledge, facilitating the identification of gaps and priorities for future investigations. These findings can inform the development of targeted interventions, workplace policies, and training programs tailored to the unique needs and challenges faced by food handlers, ultimately promoting their mental well-being and overall occupational health.\n\nFollowed PRISMA-ScR guidelines",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nMendeley: Occupation-related antecedents, job-related outcomes, and intervening factors of mental health disorders among food handlers: A scoping review protocol; https://doi.org/10.17632/9972jsjsrw.1 (Piramanayagam et al., 2024)\n\nData are available under the terms of the CC0 1.0 UNIVERSAL license (CC0).\n\n\nAcknowledgments\n\nNone to report.\n\n\nReferences\n\nCerasa A, Fabbricatore C, Ferraro G, et al.: Work-Related Stress Among Chefs: A Predictive Model of Health Complaints.2020; 8(March): 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen H, Wang C: Incivility, satisfaction and turnover intention of tourist hotel chefs Moderating effects of emotional intelligence. Int. J. Contemp. Hosp. Manag. 2019; 31(5): 2034–2053. Publisher Full Text\n\nChuang N, Lei SA, Lei SA: Job Stress Among Casino Hotel Chefs in a Top-Tier Tourism City. J. Hosp. Market. Manag. 2011; 20(5): 551–574. Publisher Full Text\n\nCristina I, Machado K, Wagner J, et al.: Stress, anxiety and depression among gastronomes: association with workplace mobbing and work – family interaction. Int. Arch. Occup. Environ. Health. 2021; 94(8): 1797–1807. PubMed Abstract | Publisher Full Text\n\nEburne JP, Eburne JP: The Chef Drive: Cooking Beyond the Pleasure Principle. Contemp. Fr. Francoph. Stud. 2010; 14(2): 169–177. Publisher Full Text\n\nFood and Agriculture Organization of the United Nations: Food Handlers Manual: Instructor.2017.\n\nHarris DA, Giuffre P: ‘“The Price You Pay”’: How Female Professional Chefs Negotiate Work and Family. Gend. Issues. 2010; 27: 27–52. Publisher Full Text\n\nHinterstoisser TM: An Investigation into the Relationship Between Conscientiousness, Self-Awareness, and Occupational Stress Outcomes in Culinary Chefs. University of Denver; 2011. Reference Source\n\nIshaque F, Id S, Amu H, et al.: Prevalence and predictors of work-related depression, anxiety, and stress among waiters: A cross-sectional study in upscale restaurants. PLoS ONE. 2021; 16(4): e0249597–e0249518. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKohli N, Mehta M: Occupational Stress: A Case Study among Chefs and Kitchen Workers. International Journal of Advnaces in Engineering and Management. 2022; 4(3): 970–977. Publisher Full Text\n\nPeters MDJ, Marnie C, Tricco AC, et al.: Updated methodological guidance for the conduct of scoping reviews. JBI Evidence Synthesis. 2020; 19: 3–10. PubMed Abstract | Publisher Full Text\n\nPidd K, Roche A, Fischer J, et al.: A recipe for good mental health: A pilot randomised controlled trial of a psychological wellbeing and substance use intervention targeting young chefs A recipe for good mental health: A pilot randomised controll. Drugs: Education, Prevention and Policy. 2015; 22(4): 352–361. Publisher Full Text\n\nPiramanayagam S, Singh H, Thirugananasambantham K: PRISMA-ScR - Checklist for Study Titled: Occupation-related antecedents, job-related outcomes, and intervening factors of mental health disorders among food handlers: A scoping review protocol. Mendeley Data. 2024; V1. Publisher Full Text\n\nRosado-Solomon EH, Koopmann J, Lee W, et al.: Mental Health and Mental Illness in Organizations: A Review, Comparison, and Extension. Acad. Manag. Ann. 2023; 17(2): 751–797. Publisher Full Text\n\nWilkesmann U, Wilkesmann M: Which factors are associated with the chefs’ perception of stress at the beginning of COVID-19 lockdown ?. Int. J. Hosp. Manag. 2021; 96(October 2020): 102945. Publisher Full Text\n\nWorld Health Organisation: World mental health report: Transforming mental health for all. World Health Organization; 2022. Publisher Full Text\n\nWorld Health Organisation, & International Labour Organisation: Mental health at work: Policy brief.2022."
}
|
[
{
"id": "348983",
"date": "02 Jan 2025",
"name": "Benta Mbare",
"expertise": [
"Reviewer Expertise qualitative research",
"occupational health",
"organizational psychology",
"inequalities and inclusions",
"minorities",
"health sciences"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis protocol is written concisely and is easy to follow and understand. However, the intended study appears to be very broad in scope which is too ambitious and may challenge the analysis process. Below are my reflections\nTitle: The current title of the study does not effectively convey the purpose or focus of the research. At present, it appears to be a collection of terminologies, some of which are repetitive and lack coherence. To improve clarity and impact, the title should be restructured to succinctly reflect the study's objectives and scope.\nBroader context: Mental health is a broad and multifaceted subject. Thus, the background part should emphasise on occupational mental health and also mention the global prevalence and burden of occupational mental health conditions.\nFocus of study: Food is handled by many professionals and consumers. It is my understanding that the authors aim to investigate food handlers specifically within professional settings. I think the title should explicitly reflect this distinction to avoid confusion as the term “food handlers” sound quite broad.\nFeasibility and scope: The aim to study mental health among food handlers worldwide may not be entirely feasible, especially given the significant differences in labour market profiles and occupational conditions across countries. These disparities are likely to influence the findings on \"mental health.\" Is there an intended comparative analysis regarding these distinctions, and what are the specific elements to be examined?\nStudy selection criteria: The scope of study selection is unclear. What types of studies are the authors intending to include? Will the review encompass qualitative, quantitative, or mixed-methods research? Are non-academic reports or grey literature (e.g., government publications, industry data) also considered, and if so, what criteria will be used to evaluate their inclusion? Providing more detail on the methodology and selection criteria would enhance the protocol’s transparency.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-600
|
https://f1000research.com/articles/13-598/v1
|
07 Jun 24
|
{
"type": "Study Protocol",
"title": "The effect of balanced energy-protein supplementation provided to lactating women on maternal and infant outcomes: study protocol for a prospectively planned individual patient data (IPD) meta-analysis",
"authors": [
"Mihaela Ciulei",
"Shouhao Zhou",
"Kelly Gallagher",
"Sunita Taneja",
"Nita Bhandari",
"Patrick Kolsteren",
"Ameer Muhammad",
"James Tielsch",
"Alemayehu Argaw",
"Ranadip Chowdhury",
"Parul Christian",
"Trenton Dailey-Chwalibóg",
"Brenda de Kok",
"Daniel Erchick",
"Fyezah Jehan",
"Joanne Katz",
"Subarna Khatry",
"Carl Lachat",
"Tsering Lama",
"Muhammad Nisar",
"Yasir Shafiq",
"Ravi Upadhyay",
"Alison Gernand",
"Maternal BEP Studies Harmonization Initiative",
"Mihaela Ciulei",
"Shouhao Zhou",
"Kelly Gallagher",
"Sunita Taneja",
"Nita Bhandari",
"Patrick Kolsteren",
"Ameer Muhammad",
"James Tielsch",
"Alemayehu Argaw",
"Ranadip Chowdhury",
"Parul Christian",
"Trenton Dailey-Chwalibóg",
"Brenda de Kok",
"Daniel Erchick",
"Fyezah Jehan",
"Joanne Katz",
"Subarna Khatry",
"Carl Lachat",
"Tsering Lama",
"Muhammad Nisar",
"Yasir Shafiq",
"Ravi Upadhyay"
],
"abstract": "Abstract*\nBackground The high prevalence of infant stunting and maternal undernutrition in low- and middle-income countries poses a significant public health threat. The World Health Organization recommends balanced energy-protein (BEP) supplementation to pregnant women from populations with a high prevalence of underweight (prepregnancy BMI <18.5 kg/m2), leaving a notable gap in guidance for lactating women. Therefore, we established the Maternal BEP Studies Harmonization Initiative (BEP Initiative) to investigate the impact of BEP supplementation given to pregnant and/or lactating women on maternal and infant outcomes by synthesizing data from multiple clinical trials. This is a study protocol for our prospective individual participant data (IPD) meta-analysis on BEP lactation trials.\n\nMethods Data from four randomized controlled trials that include mother-infant dyads in India (n=816), Pakistan (n=957), Burkina Faso (n=800), and Nepal (n=726) will be pooled and analysed. Women were randomized to BEP (one trial had a third arm with maternal BEP plus infants receiving azithromycin) or control groups at baseline (during the first week) and received the intervention through six months postpartum. A one-stage IPD meta-analysis will be done using mixed-effects linear and log-binomial regression models to account for between-trial heterogeneity. The primary outcome of infant length-for-age z scores (LAZ) and secondary outcomes of maternal and infant indicators of nutritional status, all at six months of age, will be examined. Also, we will assess baseline characteristics as covariates and effect modifiers for the BEP to outcome relationship.\n\nDiscussion This prospective IPD meta-analysis uses a one-stage IPD meta-analysis, which allows for higher statistical power to examine outcomes, more flexibility in defining variables, and can examine effect modifiers, which could inform which individuals or populations may benefit more from BEP given during lactation.",
"keywords": [
"IPD meta-analysis",
"prospective IPD meta-analysis",
"BEP supplementation",
"balanced energy-protein supplementation",
"lactation",
"women",
"low- and middle-income countries",
"LMIC"
],
"content": "Introduction\n\nPregnant and lactating women with undernutrition are at high risk of adverse maternal and infant health outcomes. Often, undernutrition is characterized by low body mass index (BMI), low mid-upper arm circumference (MUAC), short stature, and/or micronutrient deficiencies, which put pregnant women at risk for complications such as intrauterine growth restriction and preterm birth.1 The World Health Organization (WHO) recommends balanced energy-protein (BEP) supplementation in populations at risk of underweight (defined as more than 20% of pregnant women with a BMI <18.5 kg/m2) to reduce the risk of stillbirth and small for gestational age neonates.2 However, the consequences of undernutrition among lactating women have commonly been overlooked. Lactating women require additional calories to produce milk, and maternal weight status may impact the volume of milk produced and available for infant consumption.3 In food insecure settings, particularly in low- and middle-income settings, there is a high prevalence of infant stunting.4–6 Stunting, or impaired growth due to inadequate nutrition, can have serious long-term consequences for children's health and development. Meanwhile, breast milk is often the sole or main source of calories and nutrients for infants under six months of age in low-resource settings, and supplementing the diet of women who are breastfeeding could have a direct impact on infant growth and health.\n\nBEP supplementation products are ready-to-use or prepared foods that provide energy and protein (accounting for less or equal to 25% of the total energy content).7 When given during pregnancy, packaged BEP products are often fortified with multiple micronutrients or if BEP is in the form of locally-prepared food, it is often given along with a multiple micronutrient or iron and folic acid (IFA) tablet. The current evidence in systematic reviews and meta-analyses has focused on studies where BEP supplements are given during pregnancy, and synthesis is lacking for trials giving BEP during lactation.8–12\n\nTo align BEP product formulations, the Bill & Melinda Gates Foundation (BMGF) assembled an expert panel in 2017 to develop guidelines for the macro- and micronutrient content of BEP supplements for pregnancy and lactation.7 The panel also recommended that BEP products be developed and evaluated in both pregnant and lactating women in low-resource settings to assess health benefits. To further advance the evidence-based research, BMGF funded several independent randomized controlled trials (RCTs) and in 2020, convened the Maternal Nutrition Harmonization Workshop to harmonize key variables across these trials and prioritize outcomes for the IPD meta-analysis.13 This later led to the formation of the Maternal BEP Studies Harmonization Initiative (hereinafter BEP Initiative) to examine the pooled effect of BEP in pregnancy and lactation on maternal and child health.\n\nThe current protocol describes the objectives, data, and analysis plan of our prospective individual participant data (IPD) meta-analysis that focuses on the effect of BEP supplementation given during lactation in four trials with similar designs, outcome measures, and settings (i.e., low-and middle-income countries (LMIC)). The primary aim of this IPD meta-analysis is to assess the effect of BEP supplementation in lactating women on infant length-for-age z scores (LAZ) at six months of age. For secondary outcomes, we will assess maternal and infant weight and malnutrition indicators at six months postpartum. Last, we will examine maternal and infant characteristics that may modify the relationship between BEP intervention and outcomes.\n\n\nProtocol\n\nThis protocol was preregistered in Open Science Framework (https://osf.io/9nq7z) and all individual trials were prospectively registered online (Table 1). We followed The Preferred Reporting Items for Systematic Reviews and Meta-Analysis-Protocol framework, and the checklist is appended.14 The reporting of the IPD meta-analysis will use the PRISMA-IPD reporting checklist.15\n\na Intervention and control given for 6 months postpartum; all trials provided multiple micronutrients as part of BEP intervention; MumtaLW and MISAME-III gave iron-folic acid supplements to both intervention and control for 6 weeks; see Table 2 for details\n\nb French to English translation: Micronutrients for the health of the mother and infant\n\nc Factorial design for MISAME-III and MINT was random assignment for pregnancy and random assignment for postpartum. Only data on lactation will be used for this portion of the meta-analysis\n\nd Sample size for enrollment (final analytic sample size may be different)\n\ne The MINT trial had a break in enrollment\n\nFour BEP supplementation trials during lactation will be included in this prospective IPD meta-analysis located in: India (IMPRINT), Burkina Faso (MISAME-III), Pakistan (MumtaLW), and Nepal (MINT) (see Table 1 for study information and acronym definitions). All four studies are part of the BEP Initiative. Recruitment is complete for IMPRINT, MumtaLW, and MISAME-III, and sample sizes are as follows: IMPRINT (n=816), MumtaLW (n=957), MISAME-III (n=800), and MINT (n=726). The expected total sample size is 3,299 women. The sample size for some exploratory outcomes will be lower than the total enrollment sample size due to certain information (e.g., blood collection or analysis) being collected on a subset of participants (by design). Also, the sample size for the MISAME-III and MINT trials is lower than the sample size for the full trials because these trials have a factorial design to provide BEP during pregnancy and/or lactation. Groups receiving BEP supplementation during pregnancy are not included in this analysis. Risk of bias assessments will be carried out and reported for each of the individual trials using the Cochrane risk of bias tool (a publically available tool).16 There is no risk of duplicate data.\n\nFor this prospective meta-analysis, we assume the mean LAZ at six months of age to be -0.57 (standard deviation 1.10) in the control group.17 A total sample size of 3,299 (1,809 for BEP package group and 1,490 for control group) yields 88% power to detect a minimum LAZ difference of 0.10 between BEP and control at a significance level of 5% using mixed-effects linear regression, and assuming an intra-class correlation as low as 0.30. For secondary outcomes, we will have 89% power to detect a standardized mean difference of 0.10, assuming an intra-class correlation as low as 0.20. The PASS Software v22.0.4 was used for sample size calculation (NCSS, LLC, Kaysville, Utah).\n\nIn the IMPRINT trial, mother-infant dyads were included in the study if a participant-initiated breastfeeding within seven days postpartum. In the MumtaLW trial, lactating women with undernutrition (MUAC <23.0 cm), between 13-49 years of age, and their newborns (captured within seven days from birth) were included in the study. Additionally, lactating women had to intend to exclusively breastfeed the infant for the first six months of age. In the MISAME-III and MINT trials, women between 15-40 and 15-30 years, respectively, were enrolled in the study following a positive urine test if they were found to be missing menstruation in the prior five weeks and following an ultrasound examination that revealed an intrauterine pregnancy <21 completed weeks of gestation. They were in the trial from early gestation through 6 months postpartum and were counseled to exclusively breastfeed for 6 months. Additionally, in all trials, participants indicated that they were not allergic to BEP ingredients (e.g., peanuts).\n\nTable 1 summarizes the basic study information for the included maternal BEP lactation trials. Among them, IMPRINT followed an individual randomization, controlled efficacy trial design. MumtaLW followed a multi-arm, community-based randomized controlled, open-label, assessor-blinded superiority trial design with a treatment allocation ratio of 1:1:1. MISAME-III was an individual randomized 2x2 factorial efficacy design where participants are individually and randomly allocated to a prenatal intervention or control and a postnatal intervention or control group. Similarly, MINT followed a household randomized 2x2 factorial efficacy design where participants in the same household obtained the same prenatal and postnatal intervention or control. The current analyses will focus only on the postpartum intervention.\n\nThe intervention tested in each trial was a BEP supplement given to women from birth (or within a week of birth) to six months postpartum. The intervention groups also received what the control group received as the standard of care (see below) in addition to BEP. IMPRINT’s nutritional intervention was five different BEP snacks produced by a local company and a separate multiple micronutrient supplement (Table 2).18 The MumtaLW trial provided a BEP local product called Mumta that is fortified with multiple micronutrients; two sachets per day were provided.19 MumtaLW had a third intervention arm in which the women received BEP and the infants also received one dose of azithromycin at 42 days. The MISAME-III and MINT trials provided a micronutrient fortified BEP supplement produced by the Nutriset (Malaunay, France).20\n\na Groups in the intervention and control received the standard of care for maternal and infant clinical care. Trials also provided health-based counseling (e.g., on breastfeeding), which varied by study. Further details can be found in each trial’s published protocol.\n\nb Values for serving size, kcals, and protein represent two sachets of BEP (75 g each).\n\nAll four trials had a control arm that was intended to align with the standard of care for postpartum women in each country (Table 2). In the IMPRINT trial, women were encouraged to use IFA, calcium, and vitamin D supplements for six months postpartum from the national program in India (i.e., not provided by the trial).18 The national program also provides a food supplement that contains 600 kcals (18-20 g protein). In the MumtaLW trial, women received IFA from the government program or the trial (i.e., the trial ensured it was provided) for six weeks postpartum. In the MISAME-III trial, women also received IFA from the trial for six weeks postpartum. Finally, in the MINT trial, IFA was not provided as it was not part of the standard of care during lactation in Nepal.\n\nMost trials provided participants (intervention and control) with counseling for nutrition, breastfeeding, and infant care, or referred to services where counseling was available. Trials also encouraged women to use postnatal clinical care for themselves and their infants and referred to clinical services in the case of illness.\n\nThe primary outcome for this IPD meta-analysis is infant length-for-age z score (LAZ) at six months of age, which represents linear growth across that timeframe. Secondary outcomes include infant weight and malnutrition at six months of age (weight-for-length z score (WLZ) and weight-for-age z score (WAZ)), infant growth velocity (i.e., change in length and weight), infant stunting (LAZ <-2), wasting (WLZ <-2), and underweight (WAZ <-2)) at six months of age. All infant weight and nutrition status indices (LAZ, WAZ, WLZ) will be calculated based on WHO Growth Standards21 (or INTERGROWTH-21st for infants born preterm, when gestational age is available), which are sex-specific. We will also assess maternal anthropometry including mean BMI and MUAC, underweight (BMI <18.5 kg/m2) and low MUAC (<23.0 cm) at six months postpartum (Table 3).\n\nExploratory outcomes include infant head circumference-for-age and MUAC-for-age z scores (based on WHO Growth Standards, see above) at six months; maternal and infant biomarkers for iron deficiency, anemia, inflammation, and other micronutrients at six months of infant age (ferritin, transferrin receptor, hemoglobin, C-reactive protein (CRP), alpha-1-acid glycoprotein (AGP), other micronutrients (biomarkers to be determined)); and maternal mortality rate (per 100,000 live births) and infant mortality rate (per 1,000 live births; Table 3).\n\nIndividual-level variables collected by trials for women include maternal age, education, baseline weight and height, parity, adherence to BEP, health and pregnancy history, diet, breastfeeding type (exclusive, predominant, and partial), and household food insecurity. For infants, variables include sex, gestational age at birth, age at each measurement (calculated from birth date), weight, length, head circumference, and MUAC. Nutritional biomarkers are available for some maternal and infant blood samples (see list in exploratory outcomes). Study-level variables include nutritional content of BEP, geographic setting (Africa or South-East Asia), and prevalence of undernutrition in study population (e.g., infant stunting or maternal underweight).\n\nData for this meta-analysis will come from the four participating trials. The investigators of each trial have agreed to provide data and will send individual trial datasets to a data repository (hosted by the study sponsor). Trial investigators will remove personal identifiers, and the data repository analysts will further scan for and remove any identifiable information. Then, de-identified data will be shared with the meta-analysis research team at Penn State. After Penn State receives individual data sets, they will clean and merge them to create a pooled dataset for the IPD meta-analysis. While working with these data sets, only the Penn State IPD meta-analysis research team will have access to the individual and pooled datasets, which will be stored in a secure drive, password protected by the university.\n\nEach trial will share their original data to the data repository team, which will prepare de-identified datasets. First, we will review the dataset processed by the data repository team to see if it includes all variables needed for the meta-analysis. Although we will receive cleaned data, we will conduct additional examination of variables quantitatively and visually by checking distributions, frequencies, missingness, and outliers (biological or statistical). For instance, for the LAZ outcome and all other z-scores, we will use the WHO criteria in determining biologically implausible values using the recommended cutoffs (LAZ <-6 or >+6; WAZ <-6 or >+5, WLZ, MUAC z-score, and head circumference z-score <-5 or >+5).22,23 Next, we will complete initial transformations to normalize continuous distributions and categorize variables as appropriate. This step will include re-coding or creating new variables to align variable definitions for analysis with the proposed definitions from the prior harmonization work.13 Further, we will query any anomalies and compare the sample sizes and descriptive statistics with prior publications and study protocols. We will resolve any data issues or questions with the investigators for the corresponding trial. Then, we will be able to combine individual trial data sets into an analytic data set along with a variable to indicate which trial the data came from. The final product of this stage will be a merged dataset that is ready for the main analysis.\n\nData validation and merging will be conducted in Stata (StataCorp, College Station, Texas); data analysis and graphic presentation of the results will be run in Stata and R (R Core Team). To investigate the effects of the BEP intervention package on outcomes, a one-stage IPD approach will be implemented for all analyses.24 This approach is preferred over the conventional two-stage IPD approach, in which trial-level aggregated summary data are pooled in the first stage for a meta-analysis model in the second stage.25,26 Overall, the use of a one-stage IPD approach will allow us to adopt more appropriate likelihood functions, make fewer model assumptions, and incorporate more effective modelling of effect modifiers to accommodate the between-study heterogeneity while we quantify the effects of BEP on maternal and child outcomes.27\n\nFor the main analysis, the BEP intervention package will include all study arms that provided BEP to women (in the MumtaLW trial, BEP and BEP with infant azithromycin are combined; for the other trials, there is only one BEP arm). For continuous outcomes measured at six months of infant age, the effect of BEP on the outcome (e.g., LAZ) will be assessed with mixed-effects linear regression models. For dichotomous outcomes (e.g., stunting), the effect of BEP on the outcome will be assessed using relative risk estimates from mixed-effects log binomial models (or alternatively, Poisson regression if log-binomial models do not converge). We will perform both univariable analysis (BEP intervention and trial in model) and multivariable analysis (adding adjustment for baseline individual- and study-level characteristics) to examine the effect of BEP on outcomes. For multivariable models, we will include variables that are statistically significant predictors of the same outcome in the univariable analysis and variables that are unbalanced at baseline in randomized groups. In all models, intervention arm will be specified as a fixed effect, trial will be specified as a random effect (to account for heterogeneity between trials), and any other variables in multivariable models will be specified as fixed effects. Heterogeneity between trials will be assessed using I2 statistics. Risk of bias assessments will be carried out and reported for each of the individual trials using the Cochrane risk of bias tool.\n\nWe plan to examine effect modifiers because understanding which groups may benefit the most from BEP supplementation is an important goal of this initiative. An interaction term between the treatment and a potential effect modifier will be included in separate mixed-effects linear or log binomial (or Poisson) regression models. We will examine the following individual-level subgroups based on biological plausibility and prior literature: maternal age (<20 y, 20-29 y, ≥30 y), education (none vs ≥1 year), parity (1 child vs ≥2 children), maternal BMI (<18.5 kg/m2 vs ≥18.5 kg/m2), maternal height (<150 cm vs ≥150 cm), MUAC (<23 cm vs ≥23 cm),28 infant sex (male vs female), and infant malnutrition as defined by low birth weight (<2,500 g vs ≥ 2,500 g), stunting (LAZ <-2 vs ≥ -2), wasting (WLZ <-2 vs ≥ -2), and underweight (WAZ <-2 vs ≥ -2). Study-level variables we plan to examine are: prevalence of infant stunting at baseline, and prevalence of maternal underweight at baseline.\n\nIn a set of exploratory analyses, we will examine if breastfeeding types (exclusive, predominant, partial) mediate the effect of BEP on the outcomes at six months. We will also analyze differences in benefits to maternal outcomes by levels of BEP adherence (<80% vs ≥80%), which can be useful in planning future studies or dissemination efforts.\n\nWe will set an alpha cutoff of p <0.05 to determine if our results are significantly different from those expected if the null hypothesis was correct. For testing interactions, we will use a cutoff of p <0.10. The method of Benjamini and Hochberg29 will be applied to control for false discovery in multiple comparisons in the assessment of interaction effects in subgroup analyses.\n\nThe IPD meta-analysis will be analyzed based on an intent-to-treat protocol, which assumes that all randomized individuals will be included in the analyses. However, if we observe more than 20% of data missing per treatment arm, it will be flagged as potential bias (differential missingness), and we will consider two possible approaches, either performing multiple imputation assuming that data are missing-at-random,30,31 or modeling the missing data by building a Bayesian hierarchical modeling and test different missing data patterns.32 The robustness of the results will be tested in sensitivity analyses using complete cases. To estimate the missing values, the participant baseline characteristics (maternal age, maternal education, maternal BMI and height at baseline, parity, household food insecurity, baseline value of LAZ, and infant sex) will be summarized using descriptive statistics.\n\nWe will test a two-stage approach in sensitivity analyses to assess the robustness of our results to different approaches. Usually, both approaches provide similar results.25,26 We will also assess the effects of variations in interventions such as BEP alone vs BEP with azithromycin vs control; BEP given with vs. without an IFA tablet; and differences in nutrient content (e.g., total calories (400 vs 600 vs 800 kcals)) in BEP products.\n\nThe results of this work will seek peer-review and publication in fully open-access journals. Further, a centralized data repository will provide pooled and de-identified datasets for data analysis. This is the first prospective IPD meta-analysis that tests the effect of BEP given during lactation on maternal and infant outcomes. The results from this work will aid in expanding the WHO recommendation of BEP given to pregnant to also lactating women, if proven beneficial.\n\nProtocol version 2. The project began on October 15, 2020. It is funded by the BMGF. We preregistered the lactation meta-analysis on Open Science Framework (https://osf.io/9nq7z) on October 4, 2022. This protocol manuscript mirrors our preregistration but expands and adds important details for the included trials and data analysis methods. We have received data from three out of four participating trials via an external data repository. The data collection is on-going for the fourth trial and will conclude in 2024, when we anticipate having the complete pooled dataset.\n\n\nDiscussion\n\nSince 2016, the WHO has recommended BEP supplementation for pregnant women in settings with high rates of undernourishment to reduce incidence of small for gestational age and stillbirth. However, there are no current BEP recommendations for lactating women, and similar to pregnancy, more energy and nutrients are required in this life stage. In response, this prospective IPD meta-analysis aims to fill in that gap and investigate the effects of BEP supplementation given to lactating women. We will assess infant and maternal outcomes and identify subgroups that may benefit the most from this intervention. Prior systematic reviews and meta-analysis studies have suggested that BEP supplementation given to pregnant women may improve low birth weight, birth weight, small for gestational age, and stillbirth outcomes8–12; improvements to maternal and child health from BEP in lactation are expected.\n\nThe four BEP trials included in our meta-analysis are conducted in low- and middle-income countries among women at risk of or with undernutrition. The BEP intervention is administered either in the form of a packaged supplement or snack, with all studies providing ≤25% of energy from protein. Unlike prior BEP research, the proposed IPD meta-analysis study has harmonized definitions for key variables of interest, and we will use concurrently conducted RCTs, which should improve the quality of data and the reliability of our estimates.\n\nThis study protocol has several strengths. Generally speaking, prospectively planned IPD meta-analysis is superior to retrospective IPD meta-analysis or aggregate meta-analysis because it is the least biased and most reliable in producing quality results. Additionally, this approach allows the combination of study- and individual-level variables from multiple trials into one dataset, thereby improving the power to assess overall effect estimates and effect modifiers. The effect modifiers can identify which groups of lactating women benefit the most from BEP supplementation (if any). We will also be able to include study-specific random effects into the analyses and investigate the influence of covariates on heterogeneity of treatment effects. These aspects will strengthen the current but limited evidence on BEP interventions and help generalize the findings in food insecure settings.\n\nThis study has a few limitations that should be considered when interpreting results. Although all studies provided BEP to lactating women, there are variations in the form and quantity of the BEP. For instance, in the IMPRINT and MumtaLW trials, BEP provides 600 and 800 kcals, respectively, which is a higher amount than the recommended range of 250-500 kcals.7 Further, the control group varies, which may impact our results. For example, IFA is not the standard of care in lactation in all settings, such as in Nepal. Also, compliance is not measured in all trials for the control group, especially when this group is advised to take advantage of the national standard of care available. Furthermore, the included trials have some differences in study design, data definitions, and data collection methods. Substantial efforts were made later to harmonize the primary and secondary outcome measures, in our case, through the BEP Initiative.13 Last, studies also differ in eligibility criteria, and one study only enrolled women that were undernourished. However, we will test in subgroup analyses if maternal undernourishment status is an important factor in the BEP treatment effect.\n\nUltimately, this prospective IPD meta-analysis protocol will extend our knowledge on the effectiveness of giving BEP supplementation to lactating women on infant growth and other important maternal and infant outcomes. Thus, this work aims to overcome prior challenges and clarify the benefits of BEP in dyads from low-and middle-income settings. The results of this study will be disseminated through publication in fully open-access peer-reviewed journals.\n\nFor each individual trial, local ethical approval was obtained. This IPD meta-analysis uses de-identified data (deemed exempt from ethical approval by the Institutional Review Board at Penn State). The de-identified and harmonized IPD meta-analysis dataset will be stored in a data repository. The research findings will be disseminated in peer-reviewed, open-access journals.",
"appendix": "Data availability\n\nNo data is associated with this article.\n\nmedRxiv, ‘PRISMA-P’-checklist under Supplementary material for ‘The effect of balanced energy-protein supplementation provided to lactating women on maternal and infant outcomes: study protocol for a prospectively planned individual patient data (IPD) meta-analysis,’ doi: https://doi.org/10.1101/2023.11.06.23298006 Data are available under the terms of CC-BY-NC-ND 4.0 International license.\n\n\nAcknowledgements\n\nWe would like to thank all members of each research team for the studies included in the BEP Initiative. Our Technical Advisory Group, Drs. Martha Mwangome, Wafaie Fawzi, Sant-Rayn Pasricha, Parul Christian, and Rajiv Bahl served as scientific advisors, and we are grateful for their important guidance.\n\nCollaborators listed under Maternal BEP Studies Harmonization Initiative: Eleonor Zavala, Steven C. LeClerq (Johns Hopkins Bloomberg School of Public Health), Benazir Baloch (Aga Khan University), Lieven Huybregts (International Food Policy Research Institute), Laeticia C Toe (Institut de Recherche en Sciences de la Santé Burkina Faso), Giles Hanley-Cook (Ghent University), Grace J Chan (Boston Children’s Hospital), Mulatu M Derebe (Amhara Public Health Institute), Fred van Dyk, Luke C Mullany, Daniel Erchick (Johns Hopkins Bloomberg School of Public Health), Michelle S Eglovitch, Chunling Lu, Krysten North, Ingrid E Olson (Brigham and Women's Hospital), Nebiyou Fasil, Workagenehu T Kidane, Fisseha Shiferie, Tigest Shifraw, Fitsum Tsegaye, Sitota Tsegaye (Addis Continental Institute of Public Health), Sheila Isanaka (Harvard TH Chan School of Public Health), Rose Molina, Michele Stojanov, Blair Wylie, (Beth Israel Deaconess Medical Center), Amare W Tadesse (London School of Hygiene and Tropical Medicine and Addis Continental Institute of Public Health)\n\n\nReferences\n\nKozuki N, et al.: Short Maternal Stature Increases Risk of Small-for-Gestational-Age and Preterm Births in Low- and Middle-Income Countries: Individual Participant Data Meta-Analysis and Population Attributable Fraction. J. Nutr. 2015; 145: 2542–2550. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: WHO recommendations on antenatal care for a positive pregnancy experience.2016. Reference Source\n\nNommsen LA, Lovelady CA, Heinig MJ, et al.: Determinants of energy, protein, lipid, and lactose concentrations in human milk during the first 12 mo of lactation: the DARLING Study. Am. J. Clin. Nutr. 1991; 53: 457–465. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Joint child malnutrition estimates-levels and trends (2019 edition). Geneva: WHO; 2018. Reference Source\n\nLocal Burden of Disease Child Growth Failure Collaborators: Mapping child growth failure across low-and middle-income countries. Nature. 2020; 577: 231–234. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUNICEF/WHO/World Bank Group: Levels and trends in child malnutrition: UNICEF/WHO/World Bank Group joint child malnutrition estimates: key findings of the 2023 edition.2023; 32. Reference Source\n\nReport of an Expert Consultation held at the Bill & Melinda Gates Foundation: Framework and specifications for the nutritional composition of a food supplement for pregnant and lactating women (PLW) in undernourished and low income settings. Gates Open Research. 2017; 3: 1498.\n\nImdad A, Bhutta ZA: Maternal nutrition and birth outcomes: effect of balanced protein-energy supplementation. Paediatr. Perinat. Epidemiol. 2012; 26 Suppl 1: 178–190. PubMed Abstract | Publisher Full Text\n\nOta E, Hori H, Mori R, et al.: Antenatal dietary education and supplementation to increase energy and protein intake. Cochrane Database Syst. Rev. 2015; 2015: CD000032. PubMed Abstract | Publisher Full Text\n\nStevens B, et al.: The effect of balanced protein energy supplementation in undernourished pregnant women and child physical growth in low- and middle-income countries: a systematic review and meta-analysis. Matern. Child Nutr. 2015; 11: 415–432. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLassi ZS, et al.: Effects of nutritional interventions during pregnancy on birth, child health and development outcomes: A systematic review of evidence from low- and middle-income countries. Campbell Syst. Rev. 2021; 17.\n\nPerumal N, et al.: Impact of scaling up prenatal nutrition interventions on human capital outcomes in low- and middle-income countries: a modeling analysis. Am. J. Clin. Nutr. 2021; 114: 1708–1718. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGernand AD, et al.: Harmonization of maternal balanced energy-protein supplementation studies for individual participant data (IPD) meta-analyses – finding and creating similarities in variables and data collection. BMC Pregnancy Childbirth. 2023; 23: 107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoher D, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst. Rev. 2015; 4: 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStewart LA, et al.: Preferred Reporting Items for a Systematic Review and Meta-analysis of Individual Participant Data: The PRISMA-IPD Statement. JAMA. 2015; 313: 1657–1665. Publisher Full Text\n\nSterne JAC, et al.: RoB 2: a revised tool for assessing risk of bias in randomised trials. BMJ. 2019; 366: l4898.\n\nBecquey E, et al.: Impact on child acute malnutrition of integrating a preventive nutrition package into facility-based screening for acute malnutrition during well-baby consultation: A cluster-randomized controlled trial in Burkina Faso. PLoS Med. 2019; 16: e1002877. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaneja S, et al.: Impact of nutritional interventions among lactating mothers on the growth of their infants in the first 6 months of life: a randomized controlled trial in Delhi. India. Am J Clin Nutr. 2021; 113: 884–894. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMuhammad A, et al.: Nutritional support for lactating women with or without azithromycin for infants compared to breastfeeding counseling alone in improving the 6-month growth outcomes among infants of peri-urban slums in Karachi, Pakistan—the protocol for a multiarm assessor-blinded randomized controlled trial (Mumta LW trial). Trials. 2020; 21: 756.\n\nVanslambrouck K, et al.: Effect of balanced energy-protein supplementation during pregnancy and lactation on birth outcomes and infant growth in rural Burkina Faso: study protocol for a randomised controlled trial. BMJ Open. 2021; 11: e038393. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: 2018 Global reference list of 100 core health indicators (plus health-related SDGs).2018.\n\nWHO Multicentre Growth Reference Study Group: WHO Child Growth Standards based on length/height, weight and age. Acta Paediatr. Suppl. 2006; 450: 76–85.\n\nWorld Health Organization: WHO Anthro Survey Analyser; Quick guide.2019.\n\nRiley RD, et al.: One-stage individual participant data meta-analysis models for continuous and binary outcomes: Comparison of treatment coding options and estimation methods. Stat. Med. 2020; 39: 2536–2555. PubMed Abstract | Publisher Full Text\n\nRiley RD, Lambert PC, Abo-Zaid G: Meta-analysis of individual participant data: rationale, conduct, and reporting. BMJ. 2010; 340: c221. Publisher Full Text\n\nDebray TPA, Moons KGM, Abo-Zaid GMA, et al.: Individual Participant Data Meta-Analysis for a Binary Outcome: One-Stage or Two-Stage?. PLOS ONE. 2013; 8: e60650. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKontopantelis E: A comparison of one-stage vs two-stage individual patient data meta-analysis methods: A simulation study. Res. Synth. Methods. 2018; 9: 417–430. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVervers M, Antierens A, Sackl A, et al.: Which Anthropometric Indicators Identify a Pregnant Woman as Acutely Malnourished and Predict Adverse Birth Outcomes in the Humanitarian Context?. PLoS Currents. 5.\n\nBenjamini Y, Hochberg Y: Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological). 1995; 57: 289–300. Publisher Full Text\n\nWhite IR, Royston P, Wood AM: Multiple imputation using chained equations: Issues and guidance for practice. Stat. Med. 2011; 30: 377–399. PubMed Abstract | Publisher Full Text\n\nBell ML, Fiero M, Horton NJ, et al.: Handling missing data in RCTs; a review of the top medical journals. BMC Med. Res. Methodol. 2014; 14: 118. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHong H, Chu H, Zhang J, et al.: A Bayesian missing data framework for generalized multiple outcome mixed treatment comparisons. Res. Synth. Methods. 2016; 7: 6–22. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "335482",
"date": "27 Nov 2024",
"name": "Maureen Makama",
"expertise": [
"Reviewer Expertise Maternal health",
"Evidence Synthesis and Guideline Development",
"Nutrition"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well-written protocol for an individual participant data meta-analysis of randomised trials of BEP supplementation in lactating women. I have some comments for the authors to consider: 1) Why was the protocol not registered on PROSPERO? 2) Did the authors consider assessing the research integrity of the included trials using a research integrity assessment tool? 3) Are there other eligible RCTs that are not part of the BEP Initiative? If yes, have the authors considered including them? If not justify not including those studies.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-598
|
https://f1000research.com/articles/13-596/v1
|
07 Jun 24
|
{
"type": "Systematic Review",
"title": "Digital health intervention in patients undergoing cardiac rehabilitation: systematic review and meta-analysis",
"authors": [
"Ali Suleiman Harbi",
"Kim Lam Soh",
"Putri Binti Yubbu",
"Kim Geok Soh",
"Ali Suleiman Harbi",
"Putri Binti Yubbu",
"Kim Geok Soh"
],
"abstract": "Background Cardiovascular disease (CVD) continues to be the foremost mortality internationally. Cardiac rehabilitation has proven as an effective program in reducing CVD burden. Participation in cardiac rehabilitation programs is very low. Digital health intervention emerged as an alternative method to deliver Cardiac rehabilitation. This review aimed to investigate the impact of digital health intervention on the outcomes of interest\n\nMethods the following databases: PubMed, CINAHL, Scopus, and Cochrane Library have been searched to retrieve randomized controlled trials that examine the impact of digital health intervention on blood pressure, body mass index, lipid profile, blood glucose, Six-Minute Walk Test, and peak oxygen consumption. filters were set to include studies published in English between 2000-2023.\n\nResults Nineteen studies were included in this review. Six-Minute Walk Test (MD = 16.70; 95% CI: 6.00 to 27.39, p = 0.000) and maximal oxygen consumption (SMD = 0.27; 95% CI: 0.08 to 0.45, p = 0.004) significantly improved following digital health intervention, after employing the sensitivity analysis significant improvement was observed in systolic (MD = -2.54; 95% CI: -4.98 to -0.11, p = 0.04) and diastolic blood pressure (SMD = -2.0182; 95% CI: -3.9436 to -0.0928, p = 0.04) favoring experimental groups. Subgroup analysis revealed significant improvement in quality of life after three months of follow-up (SMD = 0.18; 95% CI: 0.05 to 0.31, p = 0.00), no significant differences have been observed in body mass index, lipid profile, and blood glucose.\n\nConclusion The findings emphasize the significant impact of digital vs CBCR or usual care on physical capacity, blood pressure, and quality of life. Despite the non-statistically significant differences in body mass index and lipid profile, the comparable effect between the two methods suggests the superiority of digital over CBCR or usual care due to its convenient nature, accessibility, and cost-effectiveness.",
"keywords": [
"Digital",
"virtual",
"telerehabilitation",
"mhealth",
"wearable devices",
"cardiac rehabilitation"
],
"content": "Introduction\n\nCardiovascular disease (CVD) continues to be the foremost cause of morbidity and mortality internationally,1,2 contributing to a substantial health challenge and economic burden in all global regions.3 In 2020, nearly 19 million deaths were linked to CVD, representing an 18.7% increase from 2010, and over half a billion individuals around the world are struggling with CVDs.4 Despite the evolution of various technologies used in the treatment of CVD over recent decades, patients still commonly experience subsequent cardiovascular events, such as stroke and myocardial infarction, leading to recurrent hospital admissions, and raising the personal, social, and economic burden of the disease.5 Therefore, presence of continuous management after diagnosed with CVD is very important.\n\nCardiac rehabilitation (CR) has proven as an effective program in reducing CVD burden.6 A growing body of evidence highlights the positive impact of CR in controlling the modifiable risk factors, such as obesity, smoking, sedentary lifestyle, hyperglycemia, and hypertension.7 Unfortunately, participation in CR programs (CRPs) is very low globally, less than 20% of eligible patients refer to CRPs.8,9 Common barriers that prevent enrollment in and adherence to CRPs include a lack of transportation, the nature of the disease, and personal and job responsibilities.10,11 Moreover, such programs were profoundly affected during COVID-19 lockdowns, entailing escalating healthcare costs due to reduced healthcare service provision, including detection of CVD problems, long-term management, and increased risk due to sedentary behaviors during the period 2020-2022.12\n\nIn order to overcome these existential barriers, healthcare systems have started thinking about alternative methods to deliver CRPs, including using digital health intervention (DHI) as a medium to deliver CRPs.13–16 Different types of DHI have been used, such as, smartphone applications, internet websites and platforms, virtual reality, short messages, and wearable and sensor devices.16,17 Innovative ideas were applied using these technologies to monitor, coach, and track patients remotely during CRPs. The spread of smartphones and the availability of low-price internet in many contexts enables healthcare providers to design several types of CRPs.13\n\nRecently, the World Heart Federation Roadmap for Digital Health in Cardiology emphasized the capacity of digital health technologies to realize optimal and universal health coverage. It seeks to encourage both patients and healthcare providers, endorsing universal health coverage, improving long-term patient outcomes and care experiences, and mitigating healthcare costs.18\n\nThe nonstop advancement in technology has introduced novel DHI interventions, that warrant a comprehensive assessment of their effect on the outcomes for patients undergoing CR. the presence of new studies in this field, providing an opportunity to consolidate and analyze the expanding body of literature. Moreover, the presence of varying results in previous works emphasizes the necessity for a rigorous meta-analysis to clarify consistent patterns, recognize potential sources of heterogeneity, and offer valuable perspectives into refining DHI strategies for CR. By synthesizing these elements, this review aims to contribute a deep understanding of the role of digital health intervention (DHI) in enhancing cardiometabolic risk factors, physical capacity, and quality of life (QoL), guiding both researchers and healthcare providers toward evidence-based interventions and optimizing patient outcomes in the context of CR.\n\n\nMethods\n\nThis systematic review and meta-analysis followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines.19 Two authors (ASH and PY) independently searched the following databases: PubMed, CINAHL, Scopus, and Cochrane Library. References of included studies also were searched manually for studies not included in primary search. The time filter was set to retrieve studies between 2000-2023, and the language filter was set to include only studies published in English. The two authors used Medical Subject Headings (MeSH) to determine the relevant alternative keywords used in the search process. The retrieved papers were initially checked by titles for potential inclusion in this systematic review and meta-analysis, and those which passed this stage were sequentially checked for eligibility by reading their abstracts and then full texts. Any conflict was resolved by discussion until consensus was reached among the authors, and the final decision about the included and excluded studies was made by the senior author (SKL).\n\nThe inclusion criteria of this systematic review and meta-analysis entailed that included studies: (1) were randomized controlled trials; (2) studied populations of patients with CVD; (3) studied populations aged ≥ 18 years; (4) employed interventions using digital technology; (5) investigated the impact of DHI on one or more of the outcomes of interest; and (6) had follow-up periods of at least four weeks. Any study did not meet these criteria was excluded. In addition, studies with mixed populations (i.e., patients with CVD and patients with non-CVD) were excluded. Duplicate retrieved studies were removed using. The EndNote software (Endnote X9), and then by manual checking.\n\nData were extracted and recorded in a preset Microsoft Excel spreadsheet independently by one reviewer (ASH), and were then checked by another reviewer (PY). The extracted data included: first author’s name; year of publication; sample size and number of participants in each group; type of population; type of DHI; outcomes included in the review; change in mean, standard deviation, for experimental and control groups for each outcome; country where the study was conducted; mean participants’ age; and percentage of each gender. Units were converted when necessary. For example, if a study presented cholesterol in mg/dl, this was converted into mmol/L.\n\nThe intended population for this review and meta-analysis comprised patients with CVD, including those who were diagnosed with heart failure, myocardial infarction, and those who had undergone percutaneous intervention, coronary artery bypass graft, or valvular surgery. The considered DHIs included special applications delivered via smartphone, social media, and the web, using wearable devices and sensors, and using virtual technology. The comparator is the control group who revived center-based CR (CBCR) or usual care. The outcomes of interest for this study are cardiometabolic risk factors, physical capacity and QoL, specifically: systolic blood pressure (SBP), diastolic blood pressure (DBP), body mass index (BMI), total cholesterol (TC), low density lipoprotein (LDL), high density lipoprotein (HDL), triglyceride (TG), blood glucose (BG), Six-Minute Walk Test (6-MWT), and peak oxygen consumption (VO2 peak).\n\nData analysis was performed in accordance with Cochrane handbook for systematic reviews of interventions.20 Using Jamovi software (Jamovi 24.11). Random effect statistical model was applied. To estimate the effect of DHI versus CBCR or usual care, change in means from baseline (change score) and standard deviations were used. Heterogeneity was tested using I2, whereby values of 25%, 50%, and 75% indicate low, moderate, and high heterogeneity, respectively. Hypothesis testing was performed at a two-tailed 0.05 level and a 95% CI.\n\nIf I2 values showed high heterogeneity (I2 > 50%), sensitivity analysis was performed by removing the study(s) that caused heterogeneity. Publication bias was assessed visually by a funnel plot and statistically by the Egger test. Subgroup analysis was performed based on duration of follow-up (≥ 3 months vs ˂ 3 months), population average age (≥ 60 vs ˂ 60 years) and medium of delivery (smartphone vs other methods).\n\nthe Cochrane risk-of-bias tool for randomized trials (RoB 2)21 was used to assay risk of bias. Two authors (ASH and PY) independently evaluated the included studies based on the following domains: (1) random sequence generation (selection bias); (2) allocation concealment (selection bias); (3) blinding of outcome assessment (detection bias); (4) incomplete outcome data (attrition bias); and (5) selective reporting (reporting bias). RoB 2 provides signal questions for each domain, which the evaluator should use to make an overall Risk of bias judgement (which can be low, high, or unclear). Blinding of participants and personnel is impossible due to the intrinsic nature of rehabilitation studies, so this domain was not assessed.\n\nThe certainty of evidences was assessed using Grading of Recommendation Assessment, Development and Evaluation (GRADE) approach, GRADE is a systematic approach to rating the certainty of evidence in systematic reviews, the users rate the quality of evidence for each outcome of interest based on five criteria (i.e. risk of bias, inconsistency, indirectness, imprecision, and publication bias) in all studies that reported that particular outcome. according to which the quality of evidence could be high, moderate, low, or very low.22 RCTs are considered by the tool to be generally high quality evidence, but they may be downgraded due to the assessment of Risk of bias, inconsistency, indirectness, imprecision, and publication bias.\n\n\nResults\n\nThe selected databases (PubMed, Cochrane Library, CINHAL, and Scopus) were last searched on 3rd October 2023, and the bibliographies of included studies were also reviewed to identify other related works. The searching process revealed 3673 studies, 2656 of which remained after removing duplicates. Subsequently, 254 remained after reviewing titles, and 173 after reviewing abstracts. Consequently, 81 were eligible for full-text reviewing, and the final number of studies included in this systematic review and meta-analysis was 19. Figure 1 illustrates the searching process.\n\nThis systematic review and meta-analysis of 19 RCTs published between 2014 and 2023 encompassed 1740 participants. The included studies were conducted in 11 countries (Australia, China, Czech Republic, Finland, Japan, the Netherlands, New Zealand, Poland, Portugal, Spain, and the USA). Sample sizes ranged from 22 to 312, and duration of follow-up ranged from 6 weeks to 12 months. The outcomes reported in the studies were SBP (n = 12), DBP (n = 10), BMI (n = 10), TC (n = 9), LDL (n = 9), HDL (n = 7), TC (n = 6), Qol (n = 10), BG (n = 3), VO2 peak (n = 7), and 6-MWT (n = 5). Participants were diagnosed with CHD, myocardial infarction, having undergone percutaneous intervention, valve surgery, or coronary artery bypass graft. Table 1 demonstrates the studies’ characteristics.\n\nStudies included in this review reported different types of CR. Five studies employed only exercise CR,23–27 while others employed comprehensive multicomponent forms. Six studies applied DHI plus CBCR.25,28–32\n\nDifferent devices were used to deliver DHI in the included studies, of which the smartphone was the most widely used, through special applications or platforms equipped with instructional features.28,30,33–37 Patients could use these programs independently, while healthcare professionals could also use and monitor them to determine participants’ status and performance. They could also interact, provide coaching, and give instant or scheduled feedback to patients, and use text messages, emails, and common social media messaging formats to interact with participants.\n\nSmartphones were also used in combination with wearable devices in many studies, such as step trackers, wrist heart rate monitors, biometric vests, and wearable belts.24–27,31,38–42 The wearable devices had sensors providing information about heart and respiratory rates, ECG, time, training mode, duration, and distance of training physical activity. Some of the devices were connected to participants’ smartphones, computers, or landlines,29 enabling researchers to monitor participants. Educational information about patients’ healthy lifestyles and dietary habits was also provided through technology used in some studies, in which participants were asked to enter their values for metrics such as BP, lipids, glucose, and weight.30,31\n\nTwo studies,23,43 used virtual reality technology to provide DHI. Virtual reality is a unique technology fitted to fulfill many requirements for effective rehabilitation.44 It can create a fully virtual and three-dimensional setting, where the user interacts through different sensory stimuluses, forming as much of the reality as possible, for the purpose of encouraging participants to increase their physical activity levels, using various materials like videos and games.45\n\nAll 19 included studies were assessed for Risk of bias; none of them had high Risk of bias for the random sequence generation domain; six (30%) had unclear Risk of bias, since they did not report the method of randomization; and the remaining 13 studies (70%) were assessed as having low Risk of bias. Five studies did not report sufficient information about allocation concealment and were assessed as having unclear bias, while the remaining 14 mentioned that they used concealed opaque envelopes to allocate participants. For the blinding outcome assessment domain, 10 (50%) studies did not provide sufficient information on whether the data was analyzed blindly or not so, they were assessed as unclear Risk of bias, while the remaining 9 studies mentioned that the data was analyzed by a blinded statistician.\n\nFor incomplete outcome data, 3 (15%) studies were assessed as high Risk of bias because of the high dropout rate during the intervention, and they did not report how they treated the missing data; and 2 (10%) studies were assessed as unclear Risk of bias, with attrition rates >10%. The remaining 14 (75%) reported the use of intention-to-treat (ITT) analysis and detailed the methods to treat the missing data. All studies were assessed as low Risk of bias regarding selective reporting bias. (Figure 2) and (Figure 3) summarize the outcomes of bias testing.\n\nThe certainty of evidence was assessed using the GRADE approach. Downgrading was undertaken in some cases, mainly due to imprecision, because some included studies had small sample sizes. Of the eleven outcomes examined in this review, nine outcomes were judged as having moderate quality of evidence (SBP, DBP, TC, LDL, HDL, TG, VO2 peak, 6-MWT, and QoL); one outcome (BMI) was judged as a low quality of evidence, and another (BG) was judged as very low quality of evidence. Details of assessing the certainty of evidence are presented in Table 2.\n\nThe pooled effect siize was calculated using mean difference in case that all studies used the same scale and using hedge’s g in case different scales were used based on the following formulas\n\nWhere g^ is the pooled effect size, K is the number of studies, gi is the effect size of study i, and Wi is the weight for study i\n\nWhere MD is the pooled mean difference, K is the number of studies, MDi is the weight for study i, and Wi is the effect size of study i\n\nBlood pressure\n\nSystolic blood pressure: 12 studies evaluated the effects of DHI on SBP, and meta-analysis showed no statistically significant difference (MD = -2.16; 95% CI: -5.41 to 1.08), with high heterogeneity (Q (11) = 40.05, p < 0.0001, tau2 = 0.09, I2 = 71.53%). After employing the sensitivity analysis, by removing the studies by Skobel et al. (2017) and Dorje et al. (2019), the result became statistically significant (MD = -2.54; 95% CI: -4.98 to -0.11) (z = -2.05, p = 0.04), with moderate heterogeneity (Q (9) = 12.67, p = 0.18, tau2 = 5.18, I2 = 34.69%). Figure 4 shows the forest plot of the impact of DHI vs CBCR/usual care on SBP.\n\nDiastolic blood pressure: 10 studies evaluated the effects of DHI on DBP. Meta-analysis showed no statistically significant difference (SMD = -1.16; 95% CI: -3.69 to 1.37) (z = -0.90, p = 0.3681), with high heterogeneity (Q (9) = 29.51, p = 0.0005, tau2 = 11.45, I2 = 71.96%). After employing the sensitivity analysis, by removing the study by Skobel et al. (2017), the result became statistically significant, with moderate heterogeneity (SMD = -2.0182; 95% CI: -3.9436 to -0.0928) (z = -2.05, p = 0.04) (Q (8) = 14.91, p = 0.0608, tau2 = 3.83, I2 = 46.29%). Figure 5 shows the forest plot of the impact of DHI vs CBCR/usual care on DBP.\n\nLipid profile\n\nTotal cholesterol: Nine studies reported the impact of DHI on TC. Meta-analysis revealed no statistically significant difference (SMD = 0.09; 95% CI: -0.05 to 0.23) (z = 1.23, p = 0.22). Moderate heterogeneity was observed (Q (9) = 13.73, p = 0.13, tau2 = 0.02, I2 = 39.16%). Employing sensitivity analysis by removing the study by Dorje et al. (2019) made the heterogeneity null (Q (7) = 2.77, p = 0.9054, tau2 = 0.0000, I2 = 0.0000%), but without statistical significance. Figure 6 shows the forest plot of the impact of DHI vs CBCR/usual care on TC.\n\nLow density lipoprotein: Nine studies reported the impact of DHI on LDL. Meta-analysis revealed no statistically significant difference (SMD = -0.01; 95% CI: -0.26 to 0.24) (z = -0.12, p = 0.91). A high amount of heterogeneity was noted among the results (Q (8) = 28.04, p = 0.0005, tau2 = 0.10, I2 = 71.09%). Employing sensitivity analysis by removing the studies by Dorje et al. (2019) and Johnston et al. (2016) made the heterogeneity null (Q (6) = 5.4898, p = 0.48, tau2 = 0.0000, I2 = 0.0000%), but without statistical significance (z = 1.61, p = 0.11). Figure 7 shows the forest plot of the impact of DHI vs CBCR/usual care on LDL.\n\nHigh density lipoprotein: Seven studies evaluated the impact of DHI on HDL. Meta-analysis showed no statistically significant difference (SMD = 0.01; 95% CI: -0.04 to 0.05) (z = 0.25, p = 0.81), and the heterogeneity was null (Q (6) = 3.68, p = 0.7205, tau2 = 0.0000, I2 = 0.0000%). Figure 8 shows the forest plot of the impact of DHI vs CBCR/usual care on HDL.\n\nTriglyceride: Six studies evaluated the impact of DHI on TG. Meta- analysis showed no statistically significant difference (SMD = -0.05; 95% CI: -0.14 to 0.05) (z = -0.95, p = 0.34). However, there was no significant heterogeneity Q (5) = 6.89, p = 0.23, tau2 = 0.0000, I2 = 0.00%). Figure 9 shows the forest plot of the impact of DHI vs CBCR/usual care on TG.\n\nBlood glucose\n\nOnly three studies evaluated the impact of DHI on BG compared to control. Meta-analysis showed no statistically significant difference (SMD = -0.48; 95% CI: -1.14 to 0.19) (z = -1.41, p = 0.16), with high heterogeneity (Q (2) = 7.92, p = 0.0190, tau2 = 0.2506, I2 = 73.07%). Figure 10 shows the forest plot of the impact of DHI vs CBCR/usual care on BG.\n\nPhysical capacity\n\nSix-Minute Walk Test (6-MWT): Five studies examined the effect of DHI on 6-MWT. Meta-analysis showed statistically significant differences (MD = 16.70; 95% CI: 6.00 to 27.39) (z = 3.06, p = 0.00), with null heterogeneity (Q (4) = 6.25, p = 0.18, tau2 = 0.0000, I2 = 0.0000%). Figure 11 shows the forest plot of the impact of DHI vs CBCR/usual care on 6-MWT.\n\nMaximum oxygen consumption: Seven studies examined the impact of DHI on VO2 peak. Meta-analysis showed statistically significant differences (SMD = 0.27; 95% CI: 0.08 to 0.45) (z = 2.85, p = 0.0044), with low heterogeneity in the true outcomes (Q (6) = 6.02, p = 0.42, tau2 = 0.01, I2 = 15.27%). Figure 12 shows the forest plot of the impact of DHI vs CBCR/usual care on VO2 peak.\n\nBody mass index\n\nTen studies evaluated the impact of DHI on BMI. Despite the non-significant difference (MD = -0.05; 95% CI: -0.17 to 0.07) (z = -0.77, p = 0.44), the results showed a trend toward experimental groups with neglected heterogeneity (Q (9) = 9.77, p = 0.37, tau2 = 0.0001, I2 = 0.34%). Figure 13 shows the forest plot of the impact of DHI vs CBCR/usual care on BMI.\n\nQuality of life\n\nTen studies examined the impact of DHI on QoL versus control. Although the results revealed no statistically significant difference (SMD = 0.10; 95% CI: -0.02 to 0.23) (z = 1.62, p = 0.11), a trend favoring intervention was observed. Subgroup analysis based on duration of follow-up (≤ 3 months vs > 3 months) was conducted, and a statistically significant difference was observed in the subgroup with duration of follow-up >3months (SMD = 0.18; 95% CI: 0.05 to 0.31) (z = 2.71, p = 0.00), and the heterogeneity was null (Q (7) = 0.84, p = 0.9970, tau2 = 0.0000, I2 = 0.0000%). while the studies with duration of follow-up ≤ 3 months did not demonstrate any significant difference. Figure 14 shows the forest plot of the impact of DHI vs CBCR/usual care on QoL. (Figure 15) and (Figure 16) show the forest plots of the subgroup analysis of the impact of DHI vs CBCR/usual care on QoL\n\n\nDiscussion\n\nIndividuals living with CVD face constant vulnerability to adverse events. The presence of uncontrolled risk factors significantly heightens the likelihood of experiencing major adverse cardiac and cerebrovascular events (MACCE). To address preventable factors (e.g., overweight, hyperlipidemia, hyperglycemia, and hypertension), CR has emerged as a well-established traditional intervention. However, despite its documented effectiveness in reducing mortality and readmission rates, conventional center-based CR (CBCR) experiences challenges in terms of adherence. Studies reveal a concerning statistic, with less than 20% of patients actively participating in CBCR. Various reasons have been cited for this diminished participation, including logistical factors such as distance and transportation, as well as motivational issues.8,9\n\nRecognizing these barriers, DHI has emerged as an innovative method to overcome these challenges. By leveraging digital technologies, this approach aims to enhance accessibility, convenience, and motivation, thereby offering a promising solution to improve adherence rates and optimize the overall impact of CR for individuals with CVD.\n\nMaximal oxygen consumption is a pivotal physiological metric gauging an individual’s upper limit for oxygen utilization during intense physical exertion.46 VO2 peak serves as a vital indicator of cardiovascular endurance and fitness.47,48 This parameter holds noteworthy importance in exercise physiology, managing exercise prescription, and weighing the efficiency of intervention programs.49 The strong opposite relationship between VO2 peak and CVD mortality has been documented in many large-scale studies.50\n\nIn a large prospective study conducted in the UK, physical capacity emerged as a robust predictor of mortality, surpassing traditional cardiac risk factors.51 Consequently, the findings of the current review confirm these contemporary conclusions, stressing the need for intervention programs aimed at increasing physical capacity, and providing valuable insights into strategies that can positively enhance overall health.\n\nIn conjunction with VO2 peak, the 6-MWT offers a practical and insightful assessment of functional capacity and endurance, tasking individuals with covering as much distance as possible in a six-minute timeframe.52 Notably, the effect estimate in all included studies evaluated the impact of DHI on VO2 peak and 6-MWT outcomes favored the experimental groups. Despite the variation in the nature and duration of the interventions, it has been observed that the heterogeneity among studies evaluating VO2 peak was minimal, and null among the studies that evaluated 6-MWT. This finding underscores the efficacy and consistency of DHI in enhancing cardiovascular fitness, showcasing their potential to surpass conventional modalities.\n\nThe superiority of DHIs over conventional programs may be interpreted by the frequent reminder and feedback features available in the former. These features serve as warning signs for the patient to increase adherence to the program, and devices such as pedometers, ECG, and HR monitoring directly transfer patients’ data to the healthcare provider, whereby they can instantly (or rapidly) intervene, encourage, and provide required instructions. Similarly, a recent literature review revealed that a statistically significant improvement in physical capacity was observed when using DHI compared with traditional care approaches.53 This finding contradicts the result of another meta-analysis which did not find a significant impact on VO2 peak, the forest plot in that study indicated improvement in intervention groups, but the result may be due to the small number of included studies (n = 4).54\n\nWhile the majority (7/10) of the studies investigating the influence of DHI on BMI demonstrated favor toward the experimental groups, the pooled effect did not yield statistically significant differences. Similarly, non-significant effects of DHI on BMI have been observed in previous studies.54,55 Nevertheless, the comparable effects observed between DHI and CBCR or usual care on BMI with very low heterogeneity (I2 = 0.34%) could be attributed to the influence of other factors not adequately addressed in both types of interventions, such as metabolic rate and sleeping pattern.56 Therefore, it is crucial to consider these multifaceted influences when evaluating the effectiveness of DHI in the context of BMI outcomes.\n\nThe meta-analysis results indicate a non-significant difference between DHI and CBCR or usual care in TC, LDL, HDL, and TG levels. Various factors, such as diverse modalities within DHI, patient adherence, uptake, duration and intensity of interventions, average age, and percentages of males and females in each study, may be instrumental in the lack of statistically significant results. Moreover, the limited positive effects on lipid profile may be because DHIs might not effectively address symptoms and medication management.57 Improving these aspects in the intervention could lead to better physiological outcomes.37\n\nAt initial analysis, this review showed no significant differences between the two types of intervention on SBP and DBP, marked by high heterogeneity among the included studies. After conducting the sensitivity analysis by removing two studies (Dorje et al., 2019; Skobel et al., 2017) from SBP outcomes, and one study from diastolic outcomes (Skobel et al., 2017), the results became statistically significant, with moderate heterogeneity, favoring the experimental group.\n\nHypertension is a known cardiometabolic risk factor associated with increased morbidity and mortality.58–61 According to a study by Pan, H., et al (2020) there was a two-fold increase in risk for sudden cardiac death with prevalent hypertension, and a 28% increase in risk for sudden cardiac death per 20 mmHg increment in SBP.62 The comprehensive nature of DHI extends beyond exercise routines, encompassing dietary guidance, stress management, and adherence to a healthy lifestyle. This holistic approach addresses various contributors to blood pressure control, promoting a more effective and tailored intervention. Additionally, direct monitoring and instant feedback enhance the patients’ adherence and enable early professionals’ intervention. However, controversial results have been demonstrated in previous studies, for instance, one study observed a significant reduction in blood pressure for those who received DHI compared to those who did not,63 and another study demonstrated no statistically significant differences for these variables.54\n\nHigh blood glucose level is a risk factor leading to CVD, and is associated with all-cause mortality.64 Only three studies evaluated the impact of DHI on glucose level, and the meta-analysis revealed no significant differences, with high heterogeneity. However, the three studies favored the experimental groups. Similarly, no significant difference was observed in a previous meta-analysis of three studies.65 The scarce number of studies examining the impact of DHI on blood glucose warrants more future investigation.\n\nThe pooled intervention effect on QoL showed no significant differences, with low heterogeneity. Subgroup analysis based on the duration of follow-up (> 3 months vs ≤ 3 months) yielded a statistically significant pooled effect favoring the experimental groups in studies with follow-up duration > 3 months, with null heterogeneity, while the studies with duration of follow-up ≤ 3 months did not demonstrate any significant difference. This result indicated that DHIs were more effective with longer periods. Notably, there was consistent agreement among these studies, as evidenced by the absence of heterogeneity, and the finding that patient adherence and engagement with a new intervention is a gradual process, often taking some time.66 Additionally, the integration of DHI necessitates adaptation and technology familiarity that may take more time, particularly with patients with advanced age.67 Inconsistent findings have been observed in the previous studies, one of which found a positive impact of using DHI on QoL,68 while another did not observe superiority of DHI on QoL compared to CBCR or usual care.54 However, a small number of included studies were analyzed in both of these previous reviews.\n\nThese results strongly suggest that DHI is a potential feasible solution for certain rehabilitation program participants who experience certain difficulties of access. For instance, in conventional formats are not accessible or realistic for such participants, DHI can achieve better outcomes in terms of physical activity, blood pressure and QoL on the long term. Additionally, similar outcomes can be achieved in terms of BMI and lipid profile indicators, highlighting the potential effectiveness of an efficient potential healthcare service augmented by modern technologies, to optimize the achievement of clinical targets. This is in alignment with the emerging healthcare service paradigmatic context, seeking to maximize patient satisfaction and outcomes in particular (and important) areas such as CVD.\n\nSome limitations have been encountered in this review. Firstly, the small number of participants in some included studies limited the statistical power and increased the amount of heterogeneity in particular outcomes. Secondly, the DHIs were vary in terms of intensity and duration so the results should be interpreted with caution in this context. Thirdly, the generalizability of the result may be affected by the higher proportional representation of males than females in included studies. However, this may refer to CVD prevalence rather than study design.\n\n\nConclusion\n\nThe findings emphasize the significant impact of DHI vs CBCR or usual care methods on physical capacity, as evidenced by improvement in VO2 peak and the 6-MWT. Significant differences have been observed favored DHI in systolic and diastolic BP employing sensitivity analysis. Despite the non-statistically significant differences in BMI and lipid profile, the comparable effect between the two methods suggests the superiority of DHI over CBCR or usual care due to its convenient nature, accessibility, and cost-effectiveness. The positive effects on QoL, especially with extended engagement, highlight the gradual yet meaningful impact of DHI compared with CBCR or usual care methods. No statistically significant difference was observed in relation to the impact on blood glucose.",
"appendix": "Data availability\n\nNo data associated with this article.\n\nThe Endnote reference manager available from: https://endnote.com/downloads/ alternative free access reference manager available from: https://www.mendeley.com/download-reference-manager/windows.\n\nMeta-analysis statistical spreadsheet available from: https://www.jamovi.org/download.html.\n\nRisk of bias assessment available from: https://sites.google.com/site/riskofbiastool/welcome/rob-2-0-tool/current-version-of-rob-2?authuser=0.\n\nZenodo: Data set for article “Digital health intervention in patients undergoing cardiac rehabilitation: systematic review and meta-analysis”, https://doi.org/10.5281/zenodo.11360997. 69\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: PRISMA Checklist for Article “Digital Health Intervention in Patients Undergoing Cardiac Rehabilitation: Systematic Review and Meta-Analysis. https://doi.org/10.5281/zenodo.11288634 . 70\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: PRISMA flow chart for Article “Digital Health Intervention in Patients Undergoing Cardiac Rehabilitation: Systematic Review and Meta-Analysis”. https://doi.org/10.5281/zenodo.11288735 . 71\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nRoth GA, et al.: Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the Global Burden of Disease Study 2017. 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JMIR Mhealth Uhealth. 2022; 10(12): e39593. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nBallesteros J, et al.: Evolving dynamic self-adaptation policies of mhealth systems for long-term monitoring. J. Biomed. Inform. 2020; 108: 103494. PubMed Abstract | Publisher Full Text\n\nChangizi M, Kaveh MH: Effectiveness of the mHealth technology in improvement of healthy behaviors in an elderly population-a systematic review. Mhealth. 2017; 3: 51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKleinpell RM, Avitall B: Telemanagement in chronic heart failure: a review. Dis. Manag. Health Out. 2005; 13: 43–52. Publisher Full Text\n\nZenodo: Data set for article “Digital health intervention in patients undergoing cardiac rehabilitation: systematic review and meta-analysis”. [Data set]. Zenodo. Publisher Full Text\n\nZenodo: PRISMA Checklist for Article “Digital Health Intervention in Patients Undergoing Cardiac Rehabilitation: Systematic Review and Meta-Analysis” [PRISMA Checklist]. yesZenodo. . DOI: 10.5281/zenodo.11288634\n\nZenodo: PRISMA flow chart for Article “Digital Health Intervention in Patients Undergoing Cardiac Rehabilitation: Systematic Review and Meta-Analysis” [PRISMA flow chart.]. yesZenodo. . DOI: 10.5281/zenodo.11288735"
}
|
[
{
"id": "292601",
"date": "26 Jun 2024",
"name": "Abedalmajeed Methqal Shajrawi",
"expertise": [
"Reviewer Expertise my interest areas are Cardiovascular disease",
"risk factors",
"psychological variables and physical activity."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript is well written, organized and well structured. The abstract well written, clear and informative.\n\nIntroduction: Write more about why cardiac patients do not engage in CR. what are the other solutions. give a brief about digital health. benefits and disadvantages. etc.\nMethod: Clear and well-written.\n\nResults: Perfect, this section is concise and informative.\nDiscussion: you need to mention which stage in CR that used in each study. Also, the difference in cultural impacts on the health lifestyle .\n\nConclusion: need to be revised.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No",
"responses": []
},
{
"id": "292594",
"date": "08 Jul 2024",
"name": "Issa Hweidi",
"expertise": [
"Reviewer Expertise Cardiac Nutsing"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nVery-well written paper that needs some additional improvements to get it ready for indexing. The following are my general comments to the authors: ABSTRACT -A structured summary has been written. -Done between 2000 and 2023. -Keywords should be checked according to MESH guidelines. INTRODUCTION -There seems to be a connection problem between Paragraph 1 and Paragraph 2. -References could be more up-to-date. There are current sources where the same statements are written. It also needs to be revised grammatically. METHODS -Inclusion and exclusion criteria determined according to PICO stages -In the -Study selection section, it is necessary to indicate who selected the studies. Was there any bias or not? The reader should get clear answers to these questions in this section. -There are semantic problems in English up to this point. English language editing is required. -Meta-analysis part done very well. -Please describe the results of the critical appraisal of the quality of the selected studies. -Please provide more detail regarding the intervention protocols and their effectiveness DISCUSSION - What is expressed in the method section should not be rewritten in this section. - p values should be written in a standardized way. - More recent references should be used. - Please discuss the clinical implications of the study results in clinical practice.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-596
|
https://f1000research.com/articles/12-1571/v1
|
08 Dec 23
|
{
"type": "Research Article",
"title": "Evaluation of the merit of ethanolic extract of Annona reticulata as an anti-cancer agent in human colon cancer cell lines (HCT-116)",
"authors": [
"Pooja Prakash Rao",
"Vijetha Shenoy Belle",
"Akshatha G Nayak",
"Nitesh Kumar",
"Vanishree Rao",
"Sri Pragnya Cheruku",
"Krishnananda Prabhu",
"Pooja Prakash Rao",
"Akshatha G Nayak",
"Nitesh Kumar",
"Vanishree Rao",
"Sri Pragnya Cheruku"
],
"abstract": "Background Colon cancer is the fourth most common cancer type worldwide. Novel alternative therapeutic anti-cancer drugs against colon cancer with less toxicity are to be explored . This study was aimed to explore the anti-proliferative and anti-migratory activity of various fractions of Annona reticulata ethanolic leaf extract on human colon cancer cell lines (HCT-116) and to explore the potential molecular targets from the most potent plant extract fraction.\n\nMethods After obtaining ethical clearance from the institutional ethics committee, the extract and fractions were prepared and a preliminary analysis of the phytochemical was done qualitatively. Total phenolic and flavonoids were determined. Ethanolic leaf extract and its fractions were subjected to cytotoxicity analysis using the sulforhodamine B assay and the most promising fraction which showed the highest viability was selected to study anti-migratory activity. The anti-migratory effect was studied using a scratch wound healing assay. Gas chromatography-mass spectrometry (GC-MS) was done to identify the major phytocompounds present in the fraction. The major five phytocompounds identified from the GC-MS were subjected to bioinformatics analysis.\n\nResult Among the four fractions, the petroleum ether fraction exhibited the highest anti-proliferative activity. The migration of colon cancer cells was significantly inhibited by the extract and petroleum ether fraction. The major phytocompounds identified from GC-MS were phytol (13.03%), 2,6-bis (3,4-methylenedioxyphenyl)-3,7-dioxabicyclo (3.3.0) octane (11.95%), gamma.-sitosterol (10.45%), alpha.-tocopherol-beta.-D-mannoside (7.50%) and 3-amino-4-piperonyl-5-pyrazolone (5.84%). The bioinformatics analysis of these phytochemicals showed a high potential to affect the levels of key proteins driving colon cancer progression, inhibiting the enzymes and proteins overexpressed in cancer.\n\nConclusion The outcome of this study endorses the potential of phytochemicals of the petroleum ether fraction of ethanolic leaf extract of Annona reticulata for the development of a new chemotherapeutic agent in the treatment of colon cancer.",
"keywords": [
"Anti-cancer",
"anti-migratory",
"colon cancer",
"Annona reticulata",
"Phytocompounds",
"Gas Chromatography-Mass Spectrometry",
"Bioinformatics",
"Fractionation"
],
"content": "Introduction\n\nColon cancer is the fourth most commonly diagnosed malignancy and the fifth leading cause of deaths due to cancer worldwide.1 About 85% of the patients diagnosed with colon cancer undergo surgery with a curative intent. Even so, it is seen that the cancer recurs in about 50% of these patients even after the optimal resection of the primary tumor.2 Most of the conventional chemotherapeutic treatments make use of a combination of cytotoxic drugs. However, these are usually associated with chemoresistance and side effects.3 The failure of established therapies to influence the natural history of colon cancer has led the scientist to seek for new therapies based on the principles derived from cancer biology.\n\nHerbal plants have been used extensively by the traditional healers for the treatments of several ailments, including many cancers and have been associated with fewer side effects, effective in treatment, affordable and easily available compared to the conventional chemotherapeutic drugs.4 Out of 175 molecules that were approved for the treatment of cancer from the year 1940 to 2017, 49% were natural or modified natural products, which indicates the significant contribution of the natural phytochemicals towards the development of the anticancer agents.5\n\nPrevious studies have shown that alcoholic leaf extract of Annona reticulata exhibits anticancer activity against various cancers such as hepatoma, melanoma, colon cancer, cervical cancer, lung cancer and breast cancer.6 Previous studies using ethanolic leaf extract of Annona reticulata have significantly inhibited 1,2-dimethylhydrazine (DMH) induced colon cancer in rats.7\n\nThe present study was carried out to identify the phytocomponents and to explore the anticancer activity of ethanolic leaf extract Annona reticulata and its fractions on its anti-proliferative and anti-migratory activities on HCT-116 colon cancer (adenocarcinoma) cell lines.\n\n\nMethods\n\nThe study was carried out after getting approval from the Institutional ethics committee (IEC - 723/2019) between 1st November 2019 to 25th May 2021.\n\nHCT-116 colon cancer cell lines were purchased from NCCS (National Centre for Cell Science), Pune, India and cultured on Dulbecco’s Modified Eagle Medium (procured from Invitrogen, Thermo Fisher Scientific, India) containing penicillin (100 units/mL), streptomycin (100 μg/mL) and 10% fetal bovine serum (FBS) in a humidified incubator (Rivotech Incubator, India) maintained at 37°C and 5% CO2 for 24-48 hours. The plates can be stored for 6 months at -80°C for future use.\n\nThe leaves of Annona reticulata were procured from the herbal garden of Dhanya Nursary, Koteshwara, Karnataka, India. The authentication of the plant was performed by the Department of Plant Sciences, Bangalore Central University, Karnataka, India.\n\nPreparation of ethanolic leaf extract of Annona reticulata\n\nFresh leaves of Annona reticulata (1 kg) were cleaned using water and air dried for 20 days. Then the leaves were homogenized and subjected to grinding using a blender (Panasonic MX-AC400 1000-Watt Mixer Grinder) to obtain a fine powder. This leaf powder was macerated in a Soxhlet apparatus (Borosil, India) with ethanol (1L) until the solvent became colorless. After the extraction was complete, using a rotary vacuum evaporator (EPS Biosolutions, India), the solvent was evaporated until semisolid crude extract was obtained. This ethanolic leaf extract was stored at -20°C until use.8\n\nFractionation of ethanolic leaf extract of Annona reticulata\n\nThe ethanolic leaf extract (100 g) was sequentially fractionated using a series of organic solvents starting with petroleum ether followed by diethyl ether, chloroform, and ethyl acetate in a fractionating column (Borosil, India). The extract obtained with each solvent was filtered using a rotary vacuum evaporator (EPS Biosolutions, India) at 250-280 rpm. The evaporation of the solvent was carried out at a temperature below 35°C.9\n\nPreliminary phytochemical analysis of ethanolic leaf extract and its fractions\n\nAnnona reticulata ethanolic leaf extract and its fractions were evaluated for the presence of various classes of phytocomponents using specific biochemical tests mentioned below.10,11\n\nTest for Terpenoids\n\n2 mL of Chloroform was added with the 5 mL of alcohol leaf extract. Then 2 mL of concentrated sulphuric acid was added to the solution. If a reddish-brown color formed this would indicate the presence of terpenoids.\n\nTest for Flavonoids\n\nTo test for flavonoids, 2 mL of 20% NaOH mixture was mixed with 2 mL of alcohol leaf extract for the development of the yellow color. If the solution turns colorless after the addition of 2 drops of diluted acid confirms the presence of flavonoid in the given sample.\n\nTest for Phenols/polyphenols\n\n2 mL of test solution in alcohol was added with one drop of neutral ferric chloride 5% solution. The formation of an intense blue color indicates the presence of phenols.\n\nTest for Saponins/fatty acids\n\n5 mL of distilled water was mixed with 1 mL alcohol leaf extract in test tube and it was mixed vigorously using vortex mixer. The upper froth layer was separated and mixed with few drops of olive oil and mixed vigorously and the foam appearance showed the presence of saponins.\n\nTest for Tannins\n\n2 mL of test solution was added with bromine water and acetate. Decoloration of bromine water indicates the presence of tannins.\n\nTest for steroids/polysterols\n\n2 mL of chloroform and concentrated sulphuric acid were added with the 5 mL leaf extract. In the lower chloroform layer red color would appear to indicated the presence of steroids.\n\nTest for Alkaloids - Drangendroff’s test\n\n2 mL of the extract was mixed with 1 mL of Dragendroff’s reagent. The formation of orange or orange red precipitate indicates the presence of alkaloids.\n\nTest for carbohydrates\n\nThe Anthrone test was used in this study. 2 mg of ethanolic extract was shaken with 10 mL of water, and the filtrate was concentrated. To this 2 mL of anthrone reagent solution was added. Formation of green or blue color indicates the presence of carbohydrates.\n\nAnalysis of total phenolic and flavonoid content of ethanolic leaf extract and its fractions\n\nTotal phenolic content (TPC) and total flavonoid content (TFC) of ethanolic leaf extract and its fractions were determined using the Folin-Ciocalteu method and aluminum chloride colorimetric assay respectively.12 In brief, to analyze TPC, 12.5 μl of Annona reticulata ethanolic leaf extract and its fractions (1 mg/mL) was added to a 96-well microplate [Thermo Fisher Scientific, India] and mixed with 125 μL of Folin–Ciocalteu reagent and the mixture was incubated for 5 minutes at room temperature. This was followed by the addition of 12.5 μL of 7% Na2CO3 and the plate was placed in the dark for 90 min. With the help of a microplate reader (Thermo Fisher Scientific, India) the absorbance was measured at 760 nm. Further, utilizing the standard curve of gallic acid, TPC was determined, and the results were expressed as mg of gallic acid equivalent per gram (mg GAE/g) of dry plant material.\n\nFor the analysis of TFC, briefly, 100 μL of Annona reticulata ethanolic leaf extract and its fractions (1 mg/mL) was added to a 96-well microplate (Thermo Fisher Scientific, India) and mixed with 100 μL of 2% aluminum chloride, and the final mixture was incubated for 10 min. The absorbance was measured using a microplate reader (Thermo Fisher Scientific, India) at 368 nm. Drawing upon the curve of quercetin, the TFC was determined, and the result was expressed as mg quercetin equivalent per gram (mg QE/g) of dry plant material.\n\nGas chromatography-mass spectrometry (GC-MS) analysis of petroleum ether fraction of ethanolic leaf extract of Annona reticulata13,14\n\nThe GC-MS analysis of the petroleum ether fraction was performed using a gas chromatography-mass spectrometer equipped with an RTX5 capillary column (length: 30 m×0.25 mm; film thickness: 0.25 micron) (RESTEK, PA, USA). An aliquot of 1 μl of the petroleum ether fraction of Annona reticulata ethanolic leaf extract was injected into the capillary column. Helium gas was used as a carrier gas at a flow rate of 1.0 ml/min. Initially, the temperature of the column was set at 60°C for 2 minutes and then was raised to 150°C and maintained at that temperature for 5 minutes. Then the temperature of the oven was increased and maintained at 280°C for 10 min. The ion source temperature was fixed at 200°C and the interface temperature was set at 280°C. Mass spectral scan range of 40-500 m/z was attained. The relative percent quantity of each phytocomponent in the petroleum ether fraction was evaluated by comparing the average peak area of each component to the total area of the chromatogram. The components present in the extract based on the GC-MS result were identified using Wiley-8 library and National Institute of Standard and Technology Mass Spectral Library (NIST). This analysis was carried out at Analytical Research & Metallurgical Laboratories Pvt. Ltd. (ARML), Bengaluru, India.\n\nGrowth conditions and Subculture of HCT116 colon carcinoma cells\n\nHCT116 is an adherent human colorectal carcinoma cell line and has an epithelial morphology. The cells were cultured in T-25 (Eppendorf, India) flasks in DMEM, high glucose consisting of 10% Fetal Bovine Serum [FBS]. The cells are grown until 60 to 70% confluency is achieved upon which, the cells are trypsinized by addition of 1ml of 0.2% Trypsin-EDTA solution ((GibcoTM, ThermoFischer Scientific, India). The detached cells were collected and counted using conventional neubaur chamber for seeding. The seeding density was dependent on the surface area of the well.\n\nSulforhodamine B assay\n\nSulforhodamine B (SRB) assay was carried out to determine the effect of the ethanolic leaf extract and its fractions on the viability of the HCT-116 cell line.15 HCT116 cells were seeded in a 96-well plate at a density of 5000 cells/well. The cells were given a 24h window to adhere to the well surface, after which, the cells were treated with compounds of interest at different concentration ranges. The ethanolic leaf extract and its fractions were added at a concentration range of 500 μg/mL - 7.81 μg/mL for a period of 48h to evaluate cytotoxic effect. 0.1% DMSO was used as control as the stock was prepared in DMSO such that, the highest concentration added to the well contains ≤0.1% DMSO. The standard anticancer drug, doxorubicin was added to the wells at concentration range of 24 μM - 0.046 μMand was used as positive control in the assay. Measurement of absorbance was carried out at 510 nm with the help of a microplate reader (Thermo Fisher Scientific, India), and the dose-response curve was used to calculate the half maximal inhibitory concentration (IC50) of each fraction. The most promising fraction was then chosen for further studies.\n\nScratch wound healing assay for migration of HTC-116 cell lines\n\nScratch wound assay was performed to evaluated the migratory properties of cancer cells in response to treatment with our prepared extracts. A monolayer of cells were prepared by seeding 2×105 HCT-116 cells/mL in a 6-well plate and allowed to adhere to the well surface during a 24 hr window. Following this, Dulbecco’s phosphate buffered saline (DPBS) was used to wash the cells and then using a sterile 200 μl micropipette tip, a linear wound was created in the cell monolayer. DPBS was used to remove any detached cells and cellular debris.16 Annona reticulata ethanolic leaf extract (30.16 μg/mL) and petroleum ether fraction (29.07 μg/mL) prepared by appropriate dilution with serum-free DMEM was added to the wells in duplicates To evaluate their ability to inhibit the migration of the cells. The concentrations of the ethanolic leaf extract and petroleum ether fraction used were based on the IC50 values of these fractions as obtained from the sulforhodamine B cytotoxicity assay. Wound areas were photographed at 0 and 24 hr in 4× magnification using an Labomed (USA, Model -TCM 400) inverted tissue culture microscope with a digital camera. The cells treated with 0.1% DMSO served as control and cells treated with doxorubicin (0.75 μM) served as a positive control. The images were analyzed and photographed at two time points that is at ‘0’ hr (zero) and after 24 hr of treatment using ImageJ software (NIH, USA) RRID:SCR_003070 version 1.53j. The healing of the wound was considered as closure of the wound and rate of migration of the cells was represented as percentage (%) migration for each group and compared with DMSO control\n\nWhere, Ai is the initial wound area at ‘0’ (zero) hr and A24hr is the wound area after 24 hr of extract/drug administration.\n\nBioinformatics analysis was carried out to determine the potential molecular targets of the major phytocompounds of the most potent fraction. The structures of the top five phytocompounds from GC-MS data of the petroleum ether fraction were retrieved from the NCBI PubChem database. These structures were then uploaded to the prediction of activity spectra for substances (PASS) online server (Version 2.0) to analyze the potential anticancer activities of active compounds using target fishing screening. This screening was based on the chemical similarity between various molecules and on the utilization of current knowledge of the biological activity of small molecules. “Chemical similarity principle” stating that similar molecules are likely to possess equivalent properties form the basis of this methodology. The potential anticancer activity of a phytocomponent using the PASS online server was determined on the basis of the probability activity (Pa) values of the pharmacological properties in the range of 0.03 to 0.99. The results were then filtered for anticancer activity, analyzed and recorded.17\n\nAll the assays were carried out in triplicate (n=3). The data was analyzed using graph pad prism (V.8.4.3) software with a perpetual license and the data from all the assays are expressed as mean ± standard deviation. One way-Analysis of Variance (ANOVA) followed by Duncan’s multiple range post hoc test was used to determine the statistical significance within various fractions. Student t-test was used to analyze the statistical significance between the treatment and control groups and Duncan’s multiple range test was used to analyze the statistical significance within various groups. p<0.05 was considered statistically significant.\n\n\nResults\n\nThe final dried ethanolic leaf extract yield was 170.3 g and was stored at -20°C until use. Fractionation of ethanolic leaf extract produced dried petroleum ether fraction (0.5 g), diethyl ether fraction (15.06 g), chloroform fraction (47.07 g) and ethyl acetate fraction (35.1 g).\n\nResults of the phytochemical analysis of ethanolic leaf extract of Annona reticulata and its fractions are summarized in Table 1. The presence of terpenoids, flavonoids, polyphenols, tannins, steroids and poly-sterols were reported in the extract, whereas alkaloids and saponins were absent.\n\nTPC was expressed as mg of gallic acid equivalent per gram of dry plant material (mg GAE/g) and TFC was expressed as mg of quercetin equivalent per gram of dry plant material (mg QE/g). Ethanolic leaf extract was found to contain highest TPC (46 ± 0.26 mg GAE/g of plant extract) and TFC (19.9 ± 0.3 mg QE/g of plant extract) compared to its fractions. The TPC and TFC of all the fractions were mentioned in Table 2.\n\nThe GC-MS analysis of the petroleum ether fraction revealed the presence of 56 volatile compounds (Figure 1). The most predominant phytocompounds present in the petroleum ether fraction were phytol (13.03%), 2,6-bis (3,4-methylenedioxyphenyl)-3,7-dioxabicyclo (3.3.0) octane (11.95%), gamma.-sitosterol (10.45%), alpha.-tocopherol-beta.-D-mannoside (7.50%) and 3-amino-4-piperonyl-5-pyrazolone (5.84%) were labeled and indicated in Figure 1.\n\nThe dose-dependent curve equations were used to determine the IC50 for ethanolic leaf extract and its fractions. Annona reticulata ethanolic leaf extract and its fractions significantly (p<0.05) inhibited the proliferation of HCT-116 cells in a dose-dependent manner (Table 3). The ethanolic leaf extract demonstrated a potent anti-proliferative activity with an IC50 of 30.16 ± 0.56 μg/mL. Among the fractions tested, petroleum ether fraction exhibited the highest anti-proliferative activity (IC50-29.07 ± 0.83 μg/mL) followed by diethyl ether fraction (IC50-32.03 ± 0.78 μg/mL), ethyl acetate fraction (IC50-33.66 ± 1.20 μg/mL) and chloroform fraction (IC50-43.0 ± 1.64 μg/mL).\n\n$ represent IC50 values at which maximum anti-proliferative effect was observed.\n\nBased on the results of the anti-proliferative assay, ethanolic leaf extract and petroleum ether fraction were chosen for further studies.\n\nThere was significant reduction in the migration of HCT-116 colon cancer cells into the wound area upon the treatment with Annona reticulata ethanolic leaf extract (p<0.05, Figure 2B) and its petroleum ether fraction (p<0.01, Figure 2C) when compared to standard drug doxorubicin (Figure 2D) at the end of 24 h.\n\nLegends: The images demonstrate the inhibition of cell migration of HCT-116 cells where A represents DMSO control (0.1%), B represents ethanolic leaf extract at its IC50 (30.16 μg/mL), C represents petroleum ether fraction at its IC50 (29.07 μg/mL) and D represents Doxorubicin at its IC50 (0.75 μM). The images are captured under 40x magnification at ‘0’ hour and 24 hours of treatment with ethanolic leaf extract, petroleum ether fraction, standard drug (doxorubicin), where * represent percentage of inhibition of migration after 24 hours of treatment.\n\nThe migration rate of HCT-116 cells was 15.6 ± 2.9% and 9.34 ± 1.6% at 24 h post treatment with ethanolic leaf extract (30.16 μg/mL) and petroleum ether fraction (29.07 μg/mL) respectively. The petroleum ether fraction demonstrated highest anti-migratory activity on HCT-116 cells compared to ethanolic leaf extract and standard drug doxorubicin (Figure 2).\n\nThe bioinformatics analysis of the five major phytocompounds of the petroleum ether fraction using the PASS online server tool revealed the potential pharmacological activities and molecular targets, indicating the possible interactions of these compounds in cancer signaling pathways. A higher Pa value indicates greater probability of the pharmacological activity. Based on the chemical similarity principle it was seen that the phytocompounds of the petroleum ether fraction have the ability to inhibit enzymes and proteins overexpressed in cancers such as EIF4E, B-Raf, NOS2, ICAM, caspase 3, caspase 8, and MMP-9, demonstrating their potential to inhibit various processes in cancer such as proliferation, migration, invasion, angiogenesis and immune invasion. The phytochemicals also showed a high potential to affect the levels of key proteins driving colon cancer progression such as c-Myc, MMP-9, p53 and B-Raf indicating their potential to be developed as promising anticancer agents for colon cancer. The predicted anticancer activity and the possible molecular targets of these compounds are given in supplementary file.\n\n\nDiscussion\n\nOne of the major causes of colon cancer mortality is metastasis and it involves multiple sequential and integrated cellular processes.18 Given the importance of cell migration and angiogenesis in tumor metastasis, the development of chemotherapeutic agents targeting the pathways and proteins involved in these processes can prove to be effective for the treatment of metastatic cancers.19 Natural phytocompounds are an important source of emerging chemo-preventive, chemotherapeutic and chemo-sensitizing agents for the treatment of cancer.20\n\nPlant polyphenols and flavonoids were reported to have numerous biological effects including anti-inflammatory, antioxidant, antiproliferative, and anticarcinogenic properties and have shown to possess the potential to be developed into relatively safe and effective chemotherapeutic agents.21 It was seen that the amount of total phenolic and flavonoid content of the fractions increased with the increase in polarity of the solvent reported in this study. These findings were supported by previous studies which have shown that the solubility of polyphenolic compounds is higher in organic solvents with polarity lower than that of water.22,23 Further, the polar properties of the polyphenols determine their solubility and the relative lipophilicity.24 The total phenolic content of Annona reticulata ethanolic leaf extract and its fractions was higher than that of previously reported for other members of the Annonaceae family such as ethanolic leaf extracts of Annona muracata and Monodora tenuifolia.25\n\nOne of the most important properties of the chemotherapeutic agents is the ability to inhibit the proliferation of cancer cells and induce apoptosis.26 All the fractions of Annona reticulata ethanolic leaf extract exhibited anti-proliferative activity towards HCT-116 cell line in a dose-dependent manner. In the in-vitro SRB assay, the least polar solvent fraction, i.e., petroleum ether fraction showed the highest anti-proliferative effect towards HCT-116 cells as evidenced by its lowest IC50 value amongst other solvent fractions, despite of containing the lowest TPC and TFC among others. This indicates that relatively non-polar phytocompounds present in the petroleum ether fraction such as alpha-tocopherol-beta-D-mannoside and gamma-sitosterol contribute significantly to the anticancer activity. As per the American National Cancer Institute, a crude extract’s IC50 value of less than 30g/mL is regarded promising,27 signifying the potential of the petroleum ether fraction and its phytocompounds for the treatment of colon cancer. At IC50 concentration, the cytotoxicity induced by Annona reticulata ethanolic leaf extract and its petroleum ether fraction on HCT-116 colon cancer cell line was significantly higher than that induced by its ethanolic root extract on A-549, K-562, HeLa, and MDA-MB cell lines.28 Based on previous studies it was observed that HCT-116 colon cancer exhibited higher sensitivity for ethanolic leaf extract of Annona reticulata than that for ethanolic extract of Zingiber officinale, essential oils of Illicium verum and methanolic branch extract of Anacardium occidentale.29 The high anti-proliferative property exhibited by the petroleum ether fraction of Annona reticulata ethanolic leaf extract towards the colon cancer cells could be attributed to the presence of a diverse class of phytochemicals in it, as demonstrated by the GC-MS analysis carried out in this study. Based on the chemical similarity principle, phytocompounds like phytol, 2,6-bis(3,4-methylenedioxyphenyl)-3,7-dioxabicyclo (3.3.0) octane, and gamma-sitosterol have the potential to function as JAK2 expression inhibitor and B-Raf inhibitor thereby inhibiting STAT activity through the JAK/STAT pathway and inhibit the signaling through the RAS/RAF/MEK/ERK pathway respectively, reducing the expression of genes intricated in cancer cell proliferation thereby inducing the anti-proliferative effect.30,31 The ability of these phytocomponents to act as potent antioxidants also contributes to the inhibition of proliferation of cancer cells.32\n\nThe process of cell migration and invasion through the extracellular matrix (ECM) is an important step in cancer metastasis and is a hallmark of cancer.33 For metastasis, cancer cells have to migrate and invade the basement membrane, ECM and the endothelial cell layer in order to reach the blood or lymphatic vessels.34 Hence, complementation of colon cancer treatment with drugs that can inhibit the ability of the cancer cells to migrate and invade the ECM would aid in inhibiting the establishment of secondary tumors through metastasis.35 In this study, Annona reticulata ethanolic leaf extract and its petroleum ether fraction significantly inhibited the migration of the HCT-116 cells, which was observed as a decrease in the rate of cell migration. The anti-migratory activity exhibited by the extract and its fraction on colon adenocarcinoma cell lines was found to be higher than that observed by previous studies for the compounds thymol, kaempferol and wogonin.36 The phytoconstituents in petroleum ether fraction, 2,6-bis (3,4 methylenedioxyphenyl)-3,7- dioxabicyclo (3.3.0) octane can modulate the expression of cell cycle regulators and suppress the expression of eukaryotic translational initiation factor 4E (EIF4E). This mechanism is responsible for inhibition of expression of an ECM degrading enzyme, matrix metalloprotease-9 (MMP-9), thereby preventing cancer cell metastasis.35 Besides this, inhibition of nitric oxide synthase-2 (NOS2) expression by the phytochemicals of the petroleum ether fraction could also be one of the possible mechanisms involved in its anticancer property by preventing cancer cell migration.37\n\nGC–MS analysis was performed for the petroleum ether fraction showed the highest anti-proliferative and anti-migratory activity amongst the other fractions tested. The most abundant phytochemical of the petroleum ether fraction was phytol, an acyclic diterpene alcohol and has proven to possess cytotoxic activity against several cancers.38,39 The other two phytocompounds found in high quantities were 2,6-bis(3,4-methylenedioxyphenyl)-3,7-dioxabicyclo(3.3.0) octane and gamma.-sitosterol. Studies have proven that these compounds inhibit tumorigenesis, tumor cell proliferation, growth and survival, thereby inhibiting various cancers.40 3-Amino-4-piperonyl-5-pyrazolone is a compound that contains a piperonyl ring and previous studies have shown that the compounds containing piperonyl ring were known to possess anti-cancer properties.41 Proteins like p53 and NF-κB are involved in colon cancer progression42 and docking studies have shown that alpha.-tocopherol-.beta.-D-mannoside interact with these compounds and inhibit their action, thereby prevent cancer cell progression.43 Hence the potent anticancer activity exhibited by the petroleum ether fraction can be attributed to the presence of these phytocompounds independently or to their synergistic effects.\n\nThe plant phytocompounds derived tumor-targeting complexes provide hope for synthesizing natural anti-cancer agents that are more effective and that exhibit specific toxicity towards tumors but remain relatively non-toxic to healthy tissues in the body.44 Once the proteins involved in tumor growth, proliferation and metastasis of colon cancer were identified using the NCBI PubMed database, based on the structure of the major compounds found from GC-MS analysis and the chemical similarity principle, we have identified that the phytocompounds from the petroleum ether fraction of Annona reticulata ethanolic leaf extract can potentially target specific genes, regulatory proteins and enzymes involved in colon cancer progression such as c-MYC, TP53, JAK2, caspase 3, caspase 8, NOS2 etc. These results indicate the ability of phytocompounds in the petroleum ether fraction of Annona reticulata ethanolic leaf extract to inhibit various steps of colon cancer progression and metastasis such as cell migration, invasion and angiogenesis, thus signifying their potential to be developed into novel anticancer agents. These targets can further be studied using in-vitro and in-vivo studies for the development of novel targeted therapies.\n\n\nConclusions\n\nAnnona reticulata ethanolic leaf extract and its fractions exhibited potent anticancer activity against colon cancer as evidenced by their significant anti-proliferative and anti-migratory HCT-116 colon cancer cells. Based on the observations from the in-vitro studies it appears that the phytocompounds in the petroleum ether fraction of Annona reticulata ethanolic leaf extract may have potential anti-cancer properties which should be further explored and experimented for its possibility to be developed as a novel anti-cancer/neo adjuvant chemotherapeutic agent. Further studies can be carried out to study the mechanism of cell death.\n\nThe study was carried out after getting approval from the Institutional ethics committee (IEC - 723/2019).",
"appendix": "Data availability\n\nFigshare: Data files, https://doi.org/10.6084/m9.figshare.24124425.v1. 45\n\nThis project contains the following underlying data:\n\n- Plant sample-GC MS data.pdf\n\n- 9,12 octadecadienoic acid.docx\n\n- 9,12octadecadienoic acid,dihydroxypropyl ester.docx\n\n- Ethyl alpha d glucopyranoside.docx\n\n- Hexadecanoic acid.docx\n\n- linoleic acid ethyl ester.docx\n\n- SRB data of extract.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank the Manipal Academy of Higher Education for funding (Research Seed Money grant) and infrastructural Support.\n\n\nReferences\n\nSung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 2021; 71(3): 209–249. PubMed Abstract | Publisher Full Text\n\nRodríguez-Moranta F, Saló J, Arcusa À, et al.: Postoperative surveillance in patients with colorectal cancer who have undergone curative resection: a prospective, multicenter, randomized, controlled trial. J. Clin. Oncol. 2006 Jan 20 [cited 2022 Mar 18]; 24(3): 386–393. PubMed Abstract | Publisher Full Text\n\nOkem A, Henstra C, Lambert M, et al.: A review of the pharmacodynamic effect of chemo-herbal drug combinations therapy for cancer treatment. Med. Drug Discov. 2023; 17(November 2022): 100147. Publisher Full Text\n\nAiello P, Sharghi M, Mansourkhani SM, et al.: Medicinal plants in the prevention and treatment of colon cancer. Oxidative Med. Cell. Longev. 2019 Dec 4; 2019: 1–51. Publisher Full Text Reference Source\n\nSeca AML, Pinto DCGA: Plant Secondary Metabolites as Anticancer Agents: Successes in Clinical Trials and Therapeutic Application. Int. J. Mol. Sci. 2018 Jan 16 [cited 2022 Mar 18]; 19(1). 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Reference Source\n\nVichai V, Kirtikara K: Sulforhodamine B colorimetric assay for cytotoxicity screening. Nat. Protoc. 2006 Aug 17; 1(3): 1112–1116. Publisher Full Text Reference Source\n\nRamos-Silva A, Tavares-Carreón F, Figueroa M, et al.: Anticancer potential of Thevetia peruviana fruit methanolic extract. BMC Complement. Altern. Med. 2017 May 2 [cited 2022 Mar 18]; 17(1): 241. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChávez-Fumagalli MA, Schneider MS, Lage DP, et al.: A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. Evidence-based Complement. Altern. Med. 2018; 2018: 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartin T, Ye L, Sanders A, et al.: Cancer Invasion and Metastasis: Molecular and Cellular Perspective Cancer Invasion and Metastasis: The Role of Cell Adhesion Molecules. Cancer Invasion Metastasis Mol. Cell. Perspect. 2014; 9: 1–28.\n\nRajabi M, Mousa SA: The Role of Angiogenesis in Cancer Treatment. Biomedicines. 2017 Jun 1 [cited 2022 Mar 18]; 5(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nAhmed MB, Islam SU, Alghamdi AAA, et al.: Phytochemicals as Chemo-Preventive Agents and Signaling Molecule Modulators: Current Role in Cancer Therapeutics and Inflammation. Int. J. Mol. Sci. 2022; 23(24). Publisher Full Text\n\nTungmunnithum D, Thongboonyou A, Pholboon A, et al.: Flavonoids and Other Phenolic Compounds from Medicinal Plants for Pharmaceutical and Medical Aspects: An Overview. Medicines. 2018 Aug 25 [cited 2022 Mar 18]; 5(3): 93. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaminiuk CWI, Plata-Oviedo MSV, de Mattos G , et al.: Extraction and quantification of phenolic acids and flavonols from Eugenia pyriformis using different solvents. J. Food Sci. Technol. 2014; 51(10): 2862–2866. Publisher Full Text\n\nSepahpour S, Selamat J, Manap MYA, et al.: Comparative analysis of chemical composition, antioxidant activity and quantitative characterization of some phenolic compounds in selected herbs and spices in different solvent extraction systems. Molecules. 2018; 23(2): 1–17. Publisher Full Text\n\nNg ZX, Samsuri SN, Yong PH: The antioxidant index and chemometric analysis of tannin, flavonoid, and total phenolic extracted from medicinal plant foods with the solvents of different polarities. J. Food Process. Preserv. 2020 Sep 25; 44(9): e14680. Publisher Full Text\n\nSimo MK, Nguepi MD, Sameza ML, et al.: Cameroonian medicinal plants belonging to Annonaceae family: radical scavenging and antifungal activities. Nat. Prod. Res. 2018 Sep 2; 32(17): 2092–2095. Publisher Full Text\n\nZhong L, Li Y, Xiong L, et al.: Small molecules in targeted cancer therapy: advances, challenges, and future perspectives. Signal Transduct. Target. Ther. 2021; 6(1): 201. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndriani H, Aminah H, Dewayani BM, et al.: Cytotoxic Effect of Extract Aaptos suberitoides Marine Sponge in MDA-MB 231 Triple Negative Breast Cancer Cell Line. J. Pharm. Sci. Res. 2020; 12(9): 1188–1191.\n\nSuresh HM, Shivakumar B, Hemalatha K, et al.: In vitro antiproliferativeactivity of Annona reticulata roots on human cancer cell lines. Pharm. Res. 2011 Jan; 3(1): 9–12. Publisher Full Text Reference Source\n\nAbdullah S, Siti Amalina ZA, Murad NA, et al.: Ginger extract (Zingiber officinale) triggers apoptosis and G0/G1 cells arrest in HCT 116 and HT 29 colon cancer cell lines. Adv J Microbiol Res. 2018; 12(12): 001–009.\n\nBose S, Banerjee S, Mondal A, et al.: Targeting the JAK/STAT Signaling Pathway Using Phytocompounds for Cancer Prevention and Therapy. Cells. 2020 Jun 11; 9(6). PubMed Abstract | Publisher Full Text | Free Full Text\n\nMolina-Cerrillo J, San Román M, Pozas J, et al.: BRAF Mutated Colorectal Cancer: New Treatment Approaches. Cancers (Basel). 2020 Jun 14; 12(6): 1571. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu X, Cheng J, Wang X: Dietary Antioxidants: Potential Anticancer Agents. Nutr. Cancer. 2017 May 19 [cited 2022 Mar 18]; 69(4): 521–533. Publisher Full Text Reference Source\n\nWinkler J, Abisoye-Ogunniyan A, Metcalf KJ, et al.: Concepts of extracellular matrix remodelling in tumour progression and metastasis. Nat. Commun. 2020 Oct 9; 11(1): 5120. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohnson SM, Wang X, Evers BM: Triptolide Inhibits Proliferation and Migration of Colon Cancer Cells by Inhibition of Cell Cycle Regulators and Cytokine Receptors. J. Surg. Res. 2011 Jun; 168(2): 197–205. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nGandalovičová A, Rosel D, Fernandes M, et al.: Migrastatics-Anti-metastatic and Anti-invasion Drugs: Promises and Challenges. Trends Cancer. 2017 Jun 1 [cited 2022 Mar 18]; 3(6): 391–406. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nOgasawara M, Matsubara T, Suzuki H: Screening of natural compounds for inhibitory activity on colon cancer cell migration. Biol. Pharm. Bull. 2001 [cited 2022 Mar 18]; 24(6): 720–723. PubMed Abstract | Publisher Full Text\n\nVannini F, Kashfi K, Nath N: The dual role of iNOS in cancer. Redox Biol. 2015 Dec; 6: 334–343. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nde Alencar MVOB , Islam MT, de Lima RMT , et al.: Phytol as an anticarcinogenic and antitumoral agent: An in vivo study in swiss mice with DMBA-Induced breast cancer. IUBMB Life. 2019 Feb; 71(2): 200–212. PubMed Abstract | Publisher Full Text\n\nSakthivel R, Malar DS, Devi KP: Phytol shows anti-angiogenic activity and induces apoptosis in A549 cells by depolarizing the mitochondrial membrane potential. Biomed. Pharmacother. 2018 Sep; 105: 742–752. PubMed Abstract | Publisher Full Text\n\nAnifowose SO, Alqahtani WSN, Al-Dahmash BA, et al.: Efforts in Bioprospecting Research: A Survey of Novel Anticancer Phytochemicals Reported in the Last Decade. Molecules. 2022 Nov 28; 27(23): 8307. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nArshad M, Bhat AR, Pokharel S, et al.: Synthesis, characterization and anticancer screening of some novel piperonyl-tetrazole derivatives. Eur. J. Med. Chem. 2014 Jan 7 [cited 2022 Mar 18]; 71: 229–236. PubMed Abstract | Publisher Full Text\n\nHoesel B, Schmid JA: The complexity of NF-κB signaling in inflammation and cancer. Mol. Cancer. 2013; 12(1): 86. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrishna Kumar AK, Krishnamurthi V, Moorthy S, et al.: Studies on NF-κB Docking with Common Bioactive Compounds in Punica granatum peel and Vitis vinifera Seeds. J. Exp. Biol. Agric. Sci. 2022 Aug 30; 10(4): 886–893. Publisher Full Text Reference Source\n\nWang H, Oo Khor T, Shu L, et al.: Plants vs. Cancer: A Review on Natural Phytochemicals in Preventing and Treating Cancers and Their Druggability. Anti Cancer Agents Med. Chem. 2012 Nov 1; 12(10): 1281–1305. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBelle VS: Data files. Dataset. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "254403",
"date": "30 Apr 2024",
"name": "Veronique Seidel",
"expertise": [
"Reviewer Expertise Natural Products Research"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript describes the phytochemical analysis and anticancer potential of the ethanolic extract of Annona reticulata (AR). Major comments:\nIn the introduction, the authors should indicate if AR is used in traditional medicine. Several other references reporting on the anticancer activity of AR )and its phytoconstituents) should have been mentionned (eg: Ref-1; Ref-2; Ref-3; Ref-4; Ref-5. The authors should detail when the plant was collected (month/year) and include where a voucher specimen has been deposited (including its code number) GC-MS alone only putatively identifies compounds within a plant extract. A more reliable methodology would have been to use MS/MS. The anticancer potential of the ethanolic extract of AR leaves has previously been reported using HCT-116 cells. (Ref-6\nMinor comments:\nReferences 1, 2 and 5 are too old and must be updated. The authors should quote GLOBOCAN 2022 for reference 1 The preliminary phytochemical tests are standard tests. Please provide references for these testsThis manuscript describes the phytochemical analysis and anticancer potential of the ethanolic extract of Annona reticulata (AR).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11692",
"date": "10 Jun 2024",
"name": "Vijetha Shenoy Belle",
"role": "Author Response",
"response": "Major comments: 1. In the introduction, the authors should indicate if AR is used in traditional medicine. Response to reviewer’s comments: The ‘Introduction’ section of the manuscript has been modified as per the suggestions provided by the reviewer. 2. Several other references reporting on the anticancer activity of AR) and its phytoconstituents) should have been mentioned (eg: Ref-1; Ref-2; Ref-3; Ref-4; Ref-5. Response to reviewer’s comments: The references are cited in the introduction about Annona reticulata. 3. The authors should detail when the plant was collected (month/year) and include where a voucher specimen has been deposited (including its code number) Response to reviewer’s comments: The plant was collected in May 2020 and it was authenticated by Dr. Padma S, Department of Plant Science, Bangalore Central University, Bangaluru. The specimen voucher number was not provided by the authenticator. So we are attaching the certificate provided by her. https://f1000research.s3.amazonaws.com/linked/653415.141542_Referee_Veronique_Seidel_v1.pdf 4. GC-MS alone only putatively identifies compounds within a plant extract. A more reliable methodology would have been to use MS/MS. Response to reviewer’s comments: Due to constrain in the funds only GC-MS was done to identify the phytoconstituents in the extract. 5. The anticancer potential of the ethanolic extract of AR leaves has previously been reported using HCT-116 cells. (Ref-6 Response to reviewer’s comments: This study (Ref 6) was conducted by the same corresponding author. Reference 6 was an in-vivo study. The current in-vitro study used ethanolic extract along with its fractions for its anticancer properties on HCT-116 cell lines along with details on bioinformatic analysis. Minor comments: 1.References 1, 2 and 5 are too old and must be updated. The authors should quote GLOBOCAN 2022 for reference 1. Change the references which are older. Response to reviewer’s comments: New reference has been updated in the manuscript. 2. The preliminary phytochemical tests are standard tests. Please provide references for these tests. This manuscript describes the phytochemical analysis and anticancer potential of the ethanolic extract of Annona reticulata (AR). Response to reviewer’s comments: Reference 10, 11 are for all the preliminary phytochemical standard tests."
}
]
},
{
"id": "232442",
"date": "25 May 2024",
"name": "Dr Shivashankara AR",
"expertise": [
"Reviewer Expertise Antioxidants and oxidants in health and disease",
"biochemical analysis of biological samples"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a novel work on anticancer agents. The petroleum ether fraction of ethanolic leaf extract of Annona reticulata was found to have most potent anticancer effect. This study followed sound methodology and the conclusions drawn are adequately supported by the results. Data analysis is done properly. Suggestions : 1) Authors can include papers published in 2023 for citing 2) Quality assurance method for the qualitative and quantitative analysis needs to be mentioned\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-1571
|
https://f1000research.com/articles/13-590/v1
|
07 Jun 24
|
{
"type": "Systematic Review",
"title": "Systematic Review of the Epidemiology, disease severity and preventive measures of Mpox disease: A public health guideline for densely-populated countries",
"authors": [
"Mohammad Meshbahur Rahman"
],
"abstract": "Background Research on Mpox is essential to protect public health, develop effective interventions, and enhance global preparedness for infectious disease outbreaks. Owing to the scarcity of any specific treatment for Mpox disease, public health guidelines are important for patient care and management. Therefore, this systematic review suggests a public health policy guidelines to control Mpox diseases, especially in densely populated countries.\n\nMethods In this systematic review study, the databases and search engines PubMed, Scopus, BanglaJol, WHO, and Google Scholar were searched, and related literature was retrieved for further investigation. Articles describing monkeypox epidemiology, clinical symptoms, and preventive strategies, and published in English language were the core inclusion criteria; articles published in other languages were excluded. All records in the literature were managed through Mendeley (version 1.19.4) reference manager and summarized for further investigation.\n\nResults Mpox severity is prevalent in America and Europe. Male (96.3%) and young adults aged 18-44 years (mean: 34 years) were the most vulnerable population due to the virus. Among the patients, rash and fever were the most frequent symptoms, with cough, vomiting, anogenital pain and/or bleeding, conjunctivitis, diarrhea, and genital edema being the least prevalent symptoms in less than 5% of the patients. As there is no specific treatment for the disease, infection control in densely populated countries require early detection, isolation of infected individuals, strict infection control measures, mass vaccination campaigns, education, public awareness campaigns, and continued investment in research.\n\nConclusions This study underscores the urgent need for comprehensive infection control strategies, including early detection, strict isolation protocols, mass vaccination initiatives, and ongoing research investment given the absence of specific treatment options for the disease.",
"keywords": [
"Monkeypox",
"Virus",
"Control strategies",
"Guidelines"
],
"content": "Introduction\n\nThroughout history, the world has been shaken by various pandemics and epidemics, such as plague, cholera, influenza, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), Dengue, and COVID-19, which have affected humanity and resulted in millions of deaths.1–7 Rare diseases, also known as orphan diseases, affect a relatively small number of individuals in a population.8 However, these conditions often pose significant challenges in terms of diagnosis, treatment, management, and research, owing to their limited prevalence and scarcity of available information.9 While each rare disease may affect only a few people, it collectively affects a substantial portion of the global population.8,9\n\nMpox (formerly known as monkeypox) is a rare viral disease closely related to the human smallpox virus.10 The disease was first identified in 1958 in monkeys kept for research purposes in Denmark, and subsequently found to be present in a range of animals, including rodents, squirrels, and other small mammals, and in humans in central and western African countries.11 Mpox has also been reported in other parts of the world including Asia.12 The virus that causes Mpox is a member of the Orthopoxvirus genus, which also includes the variola virus that causes smallpox.13 Mpox is a zoonotic disease, meaning it is transmitted from animals to humans. The primary route of transmission is contact with infected animals or humans.14,15 The virus can spread through contact with body fluids or contaminated objects such as bedding or clothing.16 On September 27, 2022, over 66,000 cases were confirmed in more than 100 non-endemic countries, with fluctuating epidemiological foot printing from retrospective epidemics.11\n\nThis narrative review study was undertaken to address the urgent need for comprehensive patient care and management guidelines as well as to provide crucial insights for informing policy and practices regarding the Mpox disease outbreak. The primary objective of this study was to assess the epidemiology, clinical symptoms, and severity of Mpox and develop a meticulously crafted guideline that would effectively address the various aspects of patient care and management in the context of Mpox. Given the significant public health implications of Mpox in densely populated countries, this study holds immense importance for informing and shaping future policies, guidelines, and practices to effectively mitigate the impact of this infectious disease.\n\nAs a new viral disease, research on Mpox is limited, and its scarcity is highly visible in developing countries, including Bangladesh. Due to the unavailability of specific treatments for the disease, preventive guidelines are necessary to control the disease. Considering this, the current study aimed to assess the epidemiology, symptoms, and severity of the disease by reviewing the current literature and suggesting a preventive guideline for controlling Mpox disease in densely populated countries.\n\n\nMethods\n\nA systematic literature search was performed on the current epidemiology, symptoms, severity, and possible preventive guidelines for controlling Mpox disease. This study followed the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA PRISMA-P) 2020.17\n\nInitially, various databases and search engines including PubMed, BanglaJol, WHO and Google Scholar were searched, and related literatures were retrieved by incorporating keywords such as “Mpox,” “Monkeypox,” “Monkeypox Outbreak,” “Control of Monkeypox,” “Prevention of monkeypox,” “Epidemiology of Monkeypox,” “Symptoms of Monkeypox,” “Densely Populated Countries,” and “Preventive Guidelines for Monkeypox.” A snowball technique was then applied to search for relevant articles for further investigation. We also searched the websites of national and international health organizations to retrieve recent statistics.\n\nThe inclusion criteria were as follows: (i) articles and webpage describing the current epidemiology, clinical symptoms, and preventive strategies, and (ii) articles published in English. The exclusion criteria were as follows: (i) studies describing other parameters that were not of interest and (ii) studies published in other languages.\n\nAll records in the literature were managed using the Mendeley (version 1.19.4) reference manager, and duplications were eliminated. The epidemiology of MPOX has been reported in graphs. The severity of MPOX disease has been reported using a bar diagram. Six preventive guidelines for controlling Mpox were incorporated into the reviewed literature.\n\n\nResults and discussion\n\nSystematic research was conducted in which a total of 55 and four webpage reports articles were identified via an initial search removing duplicates. Of these, 10 studies including eight articles with two websites of WHO met the eligibility criteria and were included for further assessment. The details search strategies are presented in supplementary Figure S1.18\n\nThe global numbers of confirmed cases and deaths due to Mpox disease are presented in Figure 1. Most cases were reported in different regions of America and Europe (Figure 1a). In Asia, the number of MPOX cases was comparatively lower. The number of deaths due to the disease was also the highest in the American region (Figure 1b). The second highest level was in Africa. South Asia was the least affected region by Mpox. Most of the affected patients were male (96.3%) and 3.65% were female. Males between 18-44 years old were disproportionately affected by this outbreak and accounted for 79.0% of cases, with a median age of 34 years.10 Households were the most common exposure setting (45%), and the most common form of transmission was sexual encounters (51%).19\n\n(a) Cases from January 1, 2022 to July 2024, 2023; (b) Deaths due from March 1, 2022 to June 1, 2023. This figure has been reproduced based on the dataset retrieved from the website of the World Health Organization.19\n\nRash and fever were the most frequent symptoms of Mpox diseases (Figure 2). More than 90% of MPOX-affected patients suffered from any rash. Systemic and Genital rashes were the most common symptoms in the affected patients. The second most frequent symptom was fever, affecting more than 50% of the patients suffered by fever. Literature suggests that the symptoms of Mpox are similar to those of smallpox, but the disease is generally milder. The mean incubation period for the virus is usually 9.1 (95% CI 6.5–10.9) days, with 5th and 95th percentiles of the distribution being 2–20 days.20 Initial symptoms include fever, headache, muscle aches, and fatigue.10 A rash then develops, starting on the face and spreading to other parts of the body. The rash usually progresses to the blister stage before crusting and healing over several weeks.10 Mpox is generally a self-limiting disease; however, severe cases can occur, particularly in people with weakened immune systems. The disease can be fatal in some cases, with mortality rates ranging from 1% to 10%, depending on the outbreak and the population affected.21\n\nThis figure has been reproduced based on the dataset retrieved from the website of the World Health Organization.19\n\nMPOX is a viral disease that poses a significant threat to public health, particularly in highly populated countries. The virus is primarily transmitted from animals to humans and can spread rapidly in areas with dense populations. There is no specific treatment for MPOX, but the disease can be managed through supportive care, including the use of antiviral medications, antibiotics to prevent secondary infections, and pain relief. In some cases, vaccination with the smallpox vaccine may provide protection against Mpox.22 As there is no specific treatment for MPOX, effective control strategies are essential to prevent outbreaks and minimize the impact of the disease.\n\nStrategy 1: The first step in controlling MPOX is the identification and isolation of infected individuals.23 Rapid detection and reporting of cases are critical for preventing the spread of the virus. Public health agencies should establish effective surveillance systems to monitor outbreaks and ensure that all suspected cases are investigated promptly. Early diagnosis and treatment can help reduce the severity of the disease and limit its spread.22\n\nStrategy 2: Another key control strategy is the implementation of strict infection control measures in healthcare settings.24 Healthcare workers should take precautions to avoid contact with infected individuals and wear appropriate protective equipment such as gloves and masks. Patients with suspected Mpox should be isolated to prevent the spread of the virus to others.\n\nStrategy 3: Vaccination is another important control strategy for MPOX. The smallpox vaccine, which provides protection against Mpox, has been successfully used in some outbreaks. In highly populated countries, mass vaccination campaigns are necessary to prevent outbreaks.22 The effectiveness of the vaccine may vary depending on the population being vaccinated and the specific strain of virus involved.\n\nStrategy 4: Healthcare professionals play a vital role in controlling the spread of MPOX in highly populated countries.25 They take steps to improve the infection control measures in healthcare settings. Healthcare workers should wear appropriate protective equipment, such as gloves and masks, and implement effective disinfection procedures to prevent the spread of the virus. Patients with suspected Mpox should be isolated to prevent the spread of the virus to others.26\n\nStrategy 5: Education and public awareness campaigns are also critical for controlling the spread of Mpox.22 Public health agencies should educate the public about the disease, its mode of transmission, and the importance of promptly seeking medical attention if they suspect that they may have been exposed to the virus. Individuals should be encouraged to practice good hygiene, such as regular hand washing, to prevent the spread of the virus.22\n\nStrategy 6: Finally, it is essential to invest in research to better understand the virus and to develop more effective prevention and treatment strategies. These include studying the transmission of the virus from animals to humans, developing improved diagnostic tests, and developing new therapies and vaccines.27,28\n\n\nConclusions\n\nThis systematic review assessed the epidemiology and severity of Mpox disease, and suggested six control strategies as a guidelines for patient care in densely populated countries. The findings require a multifaceted approach that includes early detection and isolation of infected patients, harsh infection control measures in healthcare settings, mass vaccination campaigns, public education and awareness campaigns, and continued investment in research to control and manage the disease in densely populated countries.\n\n\nEthics approval and consent to participate\n\nEthical approval and participant consent were not applicable due to the nature of the study.\n\n\nAuthors contribution\n\nMMR conceived the idea of the study, conducted systematic searches, screened, and finalized the articles included in the review study, analyzed, drafted, edited the manuscript, and approved the final manuscript for submission.\n\n\nAuthors’ information\n\nMohammad Meshbahur Rahman serves as an Assistant Professor of the Department of Biostatistics of the National Institute of Preventive and Social Medicine (NIPSOM), Mohakhali, Dhaka-1212 under the Directorate General of Health Services of the Ministry of Health and Family Welfare of Bangladesh. His research focuses broadly on public health, healthcare policy, epidemiology, and biostatistics. In addition, Mr. Rahman involves to the global and regional public health policy research.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: PRISMA Checklist and Flow chart for Systematic Review of the Epidemiology, disease severity and preventive measures of Mpox disease: A public health guideline for densely-populated countries, DOI: https://doi.org/10.6084/m9.figshare.25919971. 18\n\nThis study contains the following extended data:\n\n• Supplementary Figure S1. (PRISMA Flow chart)\n\n• Supplementary Table S2. PRISMA_2020_checklist (PRISMA Checklist)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe author is grateful to Mr. Sadhan Kumar Das, Senior Staff Nurse, Directorate General of Nursing, Ministry of Health and Family Welfare, Bangladesh, for his support with the manuscript.\n\n\nReferences\n\nPiret J, Boivin G: Pandemics Throughout History. Front. Microbiol. 2021; 11: 11. Publisher Full Text\n\nAl Noman A, Das D, Nesa Z, et al.: Importance of Wolbachia-mediated biocontrol to reduce dengue in Bangladesh and other dengue-endemic developing countries. Biosaf. Health. 2023; 5: 69–77. Publisher Full Text Reference Source\n\nPaul GK, Rahman MM, Naznin S, et al.: Depression and Anxiety among University Students: A Comparison between COVID-19 Pandemic Panic Period and Post-panic Period in Bangladesh. Open Access Maced. J. Med. Sci. 2022 Jan 2; 10(E SE-Public Health Epidemiology): 52–59. Publisher Full Text Reference Source\n\nHossain MS, Tasnim S, Chowdhury MA, et al.: Under-five children’s acute respiratory infection dropped significantly in Bangladesh: An evidence from Bangladesh demographic and health survey, 1996–2018. Acta Paediatr. 2022; 111(10): 1981–1994. PubMed Abstract | Publisher Full Text\n\nRahman MM, Al NA, Islam ANMS, et al.: Bangladesh striving against double burden: Dengue outbreak surges amid COVID-19 pandemic. J. Glob. Health Econ. Policy. 2021; 1: e2021015. Publisher Full Text\n\nHaque MF, Rahman MM, Alif SM, et al.: Estimation and prediction of doubling time for COVID-19 epidemic in Bangladesh: a modelling study of first 14 month’s daily confirmed new cases and deaths. Glob. Secur. 2021; 3(2). Publisher Full Text\n\nRahman MM, Bhattacharjee B, Farhana Z, et al.: Age-related Risk Factors and Severity of SARS-CoV-2 Infection: a systematic review and meta-analysis. J. Prev. Med. Hyg. 2021 Jul 30 [cited 2021 Oct 4]; 62(2): E329–E371. PubMed Abstract | Publisher Full Text Reference Source\n\nShafie AA, Chaiyakunapruk N, Supian A, et al.: State of rare disease management in Southeast Asia. Orphanet J. Rare Dis. 2016; 11(1): 107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMitani AA, Haneuse S: Small Data Challenges of Studying Rare Diseases. JAMA Netw. Open. 2020 Mar 23; 3(3): e201965–e201965. Publisher Full Text\n\nWorld Health Organization: Mpox (monkeypox). World Health Organization; 2023 [cited 2023 Aug 1]. Reference Source\n\nUllah M, Li Y, Munib K, et al.: Epidemiology, host range, and associated risk factors of monkeypox: an emerging global public health threat. Front. Microbiol. 2023; 14: 14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParker S, Schultz DA, Meyer H, et al.: Smallpox and Monkeypox Viruses. Reference Module in Biomedical Sciences. Elsevier; 2014; pp. 639–644.\n\nPayne S: Chapter 35 - Family Poxviridae.Payne S, editor. Viruses. Academic Press; 2017; pp. 279–285. Publisher Full Text\n\nFleischauer AT, Kile JC, Davidson M, et al.: Evaluation of Human-to-Human Transmission of Monkeypox from Infected Patients to Health Care Workers. Clin. Infect. Dis. 2005 Mar 1; 40(5): 689–694. PubMed Abstract | Publisher Full Text\n\nMutombo M, Jezek Z, Arita I, et al.: HUMAN MONKEYPOX TRANSMITTED BY A CHIMPANZEE IN A TROPICAL RAIN-FOREST AREA OF ZAIRE. Lancet. 1983 Apr 2; 321(8327): 735–737. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCenters for Disease Control and Prevention: Mpox in Animals|Mpox|Poxvirus|CDC.2023 [cited 2023 Feb 16]. Reference Source\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021 Mar 29; 372: n71. Publisher Full Text Reference Source\n\nRahman MM: PRISMA Checklist and Flow chart for Systematic Review of the Epidemiology, disease severity and preventive measures of Mpox disease: A public health guideline for densely-populated countries. figshare. 2024. Publisher Full Text\n\nWorld Health Organization: 2022-23 Mpox (Monkeypox) Outbreak: Global Trends. World Health Organization; 2023 [cited 2023 Aug 1]. Reference Source\n\nGuzzetta G, Mammone A, Ferraro F, et al.: Early Estimates of Monkeypox Incubation Period, Generation Time, and Reproduction Number, Italy, May–June 2022. Emerg. Infect. Dis. 2022; 28(10): 2078–2081. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBeer EM, Bhargavi RV: A systematic review of the epidemiology of human monkeypox outbreaks and implications for outbreak strategy. PLoS Negl. Trop. Dis. 2019; 13(10): 1–20.\n\nIslam MR, Haque MA, Ahamed B, et al.: Assessment of vaccine perception and vaccination intention of Mpox infection among the adult males in Bangladesh: A cross-sectional study findings. PLoS One. 2023 Jun 8; 18(6): e0286322. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHasan S, Saeed S: Monkeypox Disease: An Emerging Public Health Concern in the Shadow of COVID-19 Pandemic: An Update. Trop. Med. Infect. Dis. 2022 Oct 3; 7(10): 283. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEdmond MB, Wenzel RP: 300 - Infection Prevention in the Health Care Setting.Bennett JE, Dolin R, Blaser MJ, editors. Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases. Philadelphia: W.B. Saunders; Eighth Edition. 2015; pp. 3286–3293.e1.\n\nTitanji BK, Tegomoh B, Nematollahi S, et al.: Monkeypox: A Contemporary Review for Healthcare Professionals. Open Forum Infect. Dis. 2022 Jul 1; 9(7). PubMed Abstract | Publisher Full Text | Free Full Text\n\nKuehn R, Fox T, Guyatt G, et al.: Infection prevention and control measures to reduce the transmission of mpox: A systematic review. PLOS Glob. Public Health. 2024 Jan 18; 4(1): e0002731. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPoland GA, Kennedy RB, Tosh PK: Prevention of monkeypox with vaccines: a rapid review. Lancet Infect. Dis. 2022 Dec 1; 22(12): e349–e358. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDsouza VS, Pattanshetty S, Raj R, et al.: Rapid review on monkeypox policies among the G20 nations: relevance to policy and practitioner. F1000Res. 2022; 11(1360): 1360. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "288581",
"date": "27 Jun 2024",
"name": "Jason Kindrachuk",
"expertise": [
"Reviewer Expertise monkeypox virus",
"mpox",
"outbreak response",
"emerging infectious diseases",
"zoonosis",
"One Health",
"filoviruses"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author has provided an overall review regarding mpox mitigation and containment strategies that focuses primarily on clade IIb-associated mpox cases. This is interesting but becomes extremely difficult to interpret within the context of non-clade IIb MPXV infections, in particular within regions where clade I MPXV predominates. Major criticisms are provided below: Major Comments: The major criticism of this review is it never quite addresses the overrepresentation of data accrued for the review from clade IIb-associated mpox cases during the 2022 global epidemic. This is a really important consideration given the diverse disease presentation between these cases as compared to historic mpox such as that driven by clade I virus infections. This becomes confusing when discussing primary mechanisms of transmission (e.g. 2022 epidemic was driven by human-to-human transmission and no zoonosis; historic mpox/clade I-associated mpox is overrepresented by zoonotic transmission), primary affected populations (e.g. clade IIb cases overrepresented among men aged 18-49; clade I cases highly overrepresented among children), and disease presentation. This was problematic throughout the review and many of the comments below will address this topic directly: - mpox is the disease (not known as mpox disease). Also, is the scarcity here referring to the considerable supply issues of TPOXX or MVA-BN for endemic regions or a lack in the diversity of treatment options available? - The results appear to focus overall on total mpox cases. What should be considered here is the difference between non-endemic and endemic impacts. For example, mpox in Central Africa (clade I monkeypox virus-associated) has had ongoing public health impacts that include case fatality rates of 5-10% and severe disease with the greatest impacts on those <15 years of age (including in the ongoing mpox outbreak within the DRC). This contrasts strongly from what has been seen with clade II virus infections, most notably during the 2022 epidemic across non-endemic settings. - What is meant here is unclear. Is this referring to the prevalence of mpox in the Americas and Europe (for which the PHEIC has been removed and cases have been limited as compared to 2022) or the disease itself for which most cases were typified by mild illness? - Could be argued that mentioning the impacts of variola virus here would be pertinent given that this review highlights another orthopoxvirus species - smallpox was the disease; virus is called variola virus - It would be beneficial to mention here that transmission has also been strongly linked to dense sexual networks such as seen during the 2022 epidemic and with a growing number of cases in the ongoing outbreak in DRC - in reference to “…policy and practices regarding the Mpox disease outbreak”, Which outbreak? Is this referring to the global epidemic, the DRC outbreak, etc? -in reference to “…As a new viral disease, research on Mpox is limited, and its scarcity is highly visible in developing countries”, This is not a new disease though given that mpox was first described in humans in 1970. Also, scarcity of what exactly though? There is undoubtedly a lot of clinical information available from the 2022 epidemic - Lymphadenopathy as a hallmark of mpox as compared to smallpox should be mentioned here. Same with the clinical presentation for cases linked to sexual transmission (e.g. anogenital lesion presentation) compared to the characteristic 'classical' mpox or smallpox presentation -in reference to “Mpox is generally a self-limiting disease; however, severe cases can occur, particularly in people with weakened immune systems. The disease can be fatal in some cases”, Is this generally true for all mpox or only for clade IIb? For clade I virus this would be most predominant within those <15 years of age. Also, if considering clade IIb case fatality rates, the lower number would be <1% -on Page 5, why is this switched from Mpox (which is generally not capitalized) to MPOX? -Also on Page 5, and in reference to “The virus is primarily transmitted from animals to humans and can spread rapidly in areas with dense populations.”, This again highlights the difficulty in interpretation of this review. Clade IIb-associated cases appear to be overrepresented among many of the comments made about mpox; however, here it refers to zoonosis as the primary driver of MPXV transmission. Technically, if one looks at all data in combination, the driver would be sexual (intimate) contacts given how many cases were recorded during the 2022 epidemic. Zoonosis has been (and continues to be) the primary driver of clade I MPXV transmission in Central Africa, where DRC has borne the greatest burden of disease among endemic countries. -And also on Page 5, “As there is no specific treatment for MPOX…”. How does TPOXX or therapeutic application of Jynneos (Imvamune) factor into this? -Figure 2 is really applicable to clade IIb-associated cases at this point in time given the overrepresentation of data from the 2022 epidemic.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
},
{
"id": "301426",
"date": "16 Jul 2024",
"name": "Chandrakant Lahariya",
"expertise": [
"Reviewer Expertise Public health",
"Infectious diseases",
"non communicable diseases",
"Epidemiology",
"Primary healthcare",
"Global health."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe third paragraph of the background can be deleted and combined with the last paragraph. Objective/aim of the review should be mentioned at the end of the section. In fact, this section can be edited and re-written with a shorter and crisper format. A small flow diagram of each stage of article search can be included in the methodology section. The article seems like a simple narrative review hence can be thought about the nomenclature. The authors can mention the added knowledge that the systematic review is adding to public health. Results and discussion section can be separated into two separate sections. This is one of the weakest section. The discussion and policy implications should be mentioned. Similarly, There is an ongoing outbreak of mPox going on in DRC in Western Africa. Yet, this is not getting the global attention. The vaccines are available in USA which does not have cases but very limited stock is available in African countries where the cases are so widespread. These are the health equity issues which should be discussed in the paper.\nThere is need for citing the relevant review articles on the topic during the discussion (1-2)\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
},
{
"id": "301421",
"date": "22 Jul 2024",
"name": "Charles Grose",
"expertise": [
"Reviewer Expertise Varicella",
"Herpes Zoster",
"Herpes Simplex",
"Monkeypox."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis review of monkeypox focuses on a public health guideline for densely populated countries. Obviously monkeypox is a disease of current interest. Nevertheless, there are serious reservations about this review that are listed below. Major points.\nEpidemiology section. The title suggests a focus on densely populated countries. But the first section of Results describes the worldwide spread of monkeypox, with much more data about monkeypox in Europe and North America. There have already been numerous systematic reviews of monkeypox in Europe and North America. The author of this review is a professor at the National Institute of Preventive and Social Medicine in Dhaka, Bangladesh. He notes that the number of monkeypox cases is comparatively low in S.E. Asia. But that is exactly the point of great interest. Strongly suggest a major re-focus of this manuscript to monkeypox in S.E. Asian countries, for example, Bangladesh, India, and Pakistan. Cite all the important articles written about monkeypox in S. E. Asia. Interpret these articles and provide an explanation about why S.E. Asia has escaped major outbreaks of monkeypox. Perhaps provide a map to inform us about the regions of S.E. Asia that have reported any cases of monkeypox. Figures 1 and 2. Remove these figures that report primarily about monkeypox in Europe and North America. Substitute figures that report about the disease that occurred in countries in S. E. Asia. Include a map of locations. Section on treatment and control strategies. The current description is very general. Substitute a discussion about control strategies that are currently available in countries such as Bangladesh and India. What was done when cases of monkeypox occurred in recent years to protect the general population possibly exposed? What do the authors advise for the future? Likewise, for strategies 1 to 6, focus on what is available in Bangladesh and other countries in S. E. Asia. Do not try to provide strategies for Europe and North America..\nSmaller points.\nVaricella (Chickenpox) in S.E. Asia. Outbreaks of varicella have been confused with outbreak of monkeypox. In other reports from Africa, outbreaks of varicella have proceeded outbreak of monkeypox. The physicians thought that the damage to skin caused by varicella skin lesions may have facilitated the subsequent spread of monkeypox among the same population. Have there been any reports of dual varicella and monkeypox outbreaks in S. E. Asia? Write answer in the text. Table. Perhaps provide a table that lists the most important articles about monkeypox that occurred in S. E. Asian countries.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-590
|
https://f1000research.com/articles/11-538/v1
|
18 May 22
|
{
"type": "Research Article",
"title": "Delta-Aminolevulinic acid dehydratase enzyme activity and susceptibility to lead toxicity in Uganda’s urban children",
"authors": [
"Ambrose mukisa",
"Denis Kasozi",
"Claire Aguttu",
"Joseph Kyambadde",
"Ambrose mukisa",
"Denis Kasozi",
"Claire Aguttu"
],
"abstract": "Background: Rapid industrialization, urbanization, and population explosion in sub-Saharan Africa escalate environmental lead levels and subsequently blood lead levels in children. Its levels in one’s environment account for their blood lead levels. One’s susceptibility to lead toxicity is governed by nutrition status, age and genetics. This study aimed at expounding susceptibility to lead toxicity by relating blood lead levels, delta-aminolevulinic acid dehydratase (ALAD) enzyme activity, and genetic variations of proteins that code for ALAD in urban children of Uganda. Methods: A total of 198 blood samples were spectrophotometrically analysed for blood lead levels (BLL), hemoglobin (Hb) levels, and ALAD enzyme activity before DNA extraction, polymerase chain reaction, and restriction fragment length digestion for ALAD polymorphism. Results: Up to 99.5% of the total samples analyzed coded for ALAD1 allele compared to 0.05% that coded for ALAD2. There was a significant relationship between BLL, Hb status and ALAD enzyme activity in the three isozymes (ALAD1-1, ALAD1-2 and ALAD2-2) in strength of ALAD1-1 (r = 0.42, p -value = 0.02) ˂ ALAD1-2 (r = 0.62, p -value = ˂ 0.001) ˂ ALAD2-2 (r = 0.67, p -value = ˂ 0.001). Conclusions: Majority of children in Uganda code for the ALAD1 allele, which is important for blood lead ions hoarding during lead toxicity. Hoarding of blood lead not only delays exposure effects but also accumulates its levels in deposit tissues and this poses adverse effects later in their lives",
"keywords": [
"Blood Lead levels",
"Lead toxicity susceptibility",
"d-aminolevulinic acid dehydratase enzyme activity",
"d-aminolevulinic acid dehydratase gene polymorphism."
],
"content": "Introduction\n\nUganda, like many other African countries, is faced with numerous simultaneous transitions that include economic development, industrialization, population explosion, and urbanization.\n\nThese transitions are coming with both environmental and health changes. Population explosion is putting pressure on the environment through increased anthropogenic activities, elevated volumes of electronic wastes and this has resulted in increased volumes of toxic pollutants like lead in both air and water bodies. Because lead is an accumulative toxin, its increased concentration in the environment continues to cause health challenges, especially to the children.1–4 Elevated environmental lead levels correlate with the blood lead levels in exposed individuals.5 Childhood lead exposure is associated with various health challenges that include lung, stomach, and bladder cancers, anemia, neurocognitive disorders, intelligent quotient (IQ) lowering, and stunted growth.4,6 Although environmental lead pollution is preventable, little attention is accorded to this preventable problem in many African countries including Uganda. Recent studies conducted in different parts of Kampala slums report elevated blood lead levels, especially among children.3,7 One’s susceptibility to lead toxicity is modulated by age, genetics, nutritional and malaria infection status.3,8,9 The rate of lead ion absorption, especially in the intestines, is further shown to increase with a decrease in hemoglobin levels. Following its absorption, lead sinks in red blood cells (RBCs) where it specifically binds the delta-aminolevulinic acid dehydratase (ALAD) enzyme. This enzyme (ALAD) is second and important in the heme biosynthetic pathway and it is involved in the condensation of glycine and succinyl CoA, decarboxylation into delta-aminolevulinic acid (ALA).\n\nIt specifically catalyses the heme formation reaction where two molecules of ALA are converted into monopyrrole porphobilinogen.\n\nThe enzyme ALAD is rich with thiol groups and zinc ions, that have a high affinity for lead ions and this renders the enzyme more sensitive to attack by circulating lead ions.10,11 It is a tetramer homodimer with eight identical subunits and is located in the cytoplasm. In each of its subunits, it binds eight zinc atoms, where four zinc molecules act as catalysts, whereas the remainder serve as tertiary structural stabilizers. In times of lead burden, lead ions displace zinc from the enzyme’s active site and inhibit its activity, resulting in the accumulation of ALA.12 Accumulated levels of ALA trigger the production of reactive oxygen species (ROS), which are associated with oxidative stress.\n\nSeveral studies from different regions indicate varying blood lead levels, biological markers, and even symptoms among people in the same locality. This observation is attributed to the polymorphic nature of the gene that codes for the ALAD enzyme. Polymorphism of the ALAD gene is reported to modulate one’s susceptibility to lead toxicity.13,14 The ALAD enzyme is encoded by a single gene on chromosome 9q34 region.15 This gene codes for two alleles i.e., ALAD-1 and ALAD-2,16 which are codominant (Single Nucleotide Polymorphism database (dbSNP) ID: rs1800435 [http://www.ncbi.nlm.nih.gov/SNP/index.html]). Their expression results in a polymorphic enzyme system consisting of three different isozymes: ALAD1-1, ALAD1-2, and ALAD2-2. Individuals dominantly expressing ALAD1-2 and ALAD2-2 have a higher susceptibility to lead toxicity than those expressing the ALAD1-1 isozyme. The prevalence of the ALAD-2 allele is race-specific and usually ranges from 0 to 20 percent.13 Therefore, the ALAD polymorphism affects and modifies lead metabolism and delivery to target organs.17 To date, no study regarding ALAD enzyme activity and polymorphism distribution in the Ugandan population has been conducted. The present study, therefore, aimed at expounding on the ALAD enzyme activity, and the distribution of ALAD genotypes in relation to lead exposure susceptibility in Ugandan children. Thus, this is the first study to address lead exposure susceptibility, ALAD enzyme activity, and polymorphism in Ugandan children.\n\n\nMethods\n\nThis study was approved by Gulu University Research Ethics Committee No. (GUREC-048) dated 31/05/2019. Intentions of the study were first clearly explained in both English and a local language to the participant’s parents/guardians before signing informed consent forms.\n\nThis was a cross-sectional study that involved randomly selected children that resided in Katanga slum of Kampala Uganda (00°18′49″N 32°34′52″E, coordinates) for at least a year. The area has approximately 7000 inhabitants and 15.2% of these are under 5 years of age [http:/www.askyourgov.ug].\n\nThe sample size for the study was derived from the expression\n\nThrough their local leaders, homes of study participants were visited and explained the purpose of the study prior to signing of consent forms by their parents/guardians. Visibly malnourished children and those with a history of blood transfusion were excluded from this study. Duplicate samples of venous blood (5 ml; n = 198) were drawn from each study participants by qualified nurses and technicians. One tube contained heparin and this was used for hematocrit determination, while the other tube containing ethylenediamine tetra acetic acid (EDTA) was used for other assays. The samples were transported on ice to Makerere University Biochemistry Department laboratory for analysis.\n\nBlood lead levels were determined on an atomic absorption spectrophotometer (Agilent MY17180002 200 series) equipped with a graphite tube atomizer (GTA 120), a hollow-cathode lead lamp with a working current of 5 mA, 283.3 nm spectral line, and 0.5 nm bandwidth as described elsewhere.18 Five hundred microliter (500 μl) aliquots of blood samples were mixed with 1.2 ml of a solution that was prepared by mixing equal volumes of 0.5% Triton X-100 and 1% di-ammonium phosphate ((NH4)2HPO4). A total volume of 1.8 ml of deionized water was added to each sample in the tube and followed by the addition of 1.5 ml of 20% trichloroacetic acid (TCA) before vortex mixing. The samples were centrifuged at 5000 rpm for 20 min and 10 μl of the supernatant from each was collected and injected into the graphite tube. Lead standard concentrations ranged from 2 μg/dL to 50 μg/dL. Samples were analyzed in duplicate, and their mean values were determined with occasional blanking with deionized/distilled water. The equipment had a detection limit of 2 μg/dL.\n\nHemoglobin levels were determined following a cyanmethemoglobin reaction method described elsewhere.19 Blood samples were processed and analyzed as described in our previous study.5 Briefly, 100 μl of each sample were reacted with cyanide reagent and incubated at room temperature for 15min. Hemoglobin concentration was then determined using Jen way 6051 colorimeter at 540 nm against a reagent blank.\n\nThe hematocrit levels of the study blood samples were assayed as described elsewhere.20 Whole blood samples in heparinized tubes were forced into narrow diameter glass capillary tubes to two-third levels. The capillary tubes had a self-sealing compound from one end. The capillaries together with the blood were loaded onto a microhematocrit centrifuge and ran at a relative centrifugal force of 14,000 ×g for five minutes. Following centrifugation, hematocrit levels of each sample were measured within 10 min while the tubes were kept in a horizontal position to avoid merging of the layers. Hematocrit levels were estimated by calculating the ratio of the column of packed erythrocytes to the total length of the sample in the capillary tube.\n\nThe blood δ−ALAD enzyme activity in all the samples collected was measured following a method described by.21 The ALAD enzyme activity of each sample in duplicate was determined by incubating 0.20 ml of the sample with 1.30 ml of Triton X-100 reagent in disposable plastic tubes and thereafter adding 1 ml of buffered ALA substrate (0.01M). The buffered ALA substrate was prepared by dissolving 0.1676 g of ALA-HCL in 100 ml of phosphate-citrate buffer pH 6.65. The buffer was previously prepared by dissolving 6.703 g/dL Na2HPO4 (0.25 M) and citric acid 5.25 g/dL (0.25 M). Aliquots equivalent to 1ml of Trichloroacetic acid (TCA) reagent were added to each sample and the blank (plain distilled water).\n\nTo both test and blank aliquots, 1.0 ml of the modified Ehrlich’s reagent was added. This was previously prepared by dissolving 10 g of p-dimethylaminobenzaldehyde (DMBA) in 420 ml of acetic acid and diluted to 1 L with distilled water. Before storing the reagent at 40°C a working solution was prepared by mixing 50 ml of DMBA-acetic acid with 8 ml of 70% perchloric acid. Following the addition of the modified Ehrlich’s working reagent, the mixtures were allowed to stand for 13 min for color development before measurement at 555 nm on a spectrophotometer.\n\nThe corrected absorbance A = (Test absorbance – the blank absorbance) was used to calculate the activity of the enzyme.\n\nWhere 12500 is the blood dilution factor.\n\nBlood samples were analyzed for polymorphism as described elsewhere,22,23 Genomic DNA from each blood sample was extracted using a Qiagen genomic DNA purification kit (DNeasy, Catalogue no. 69506) following the manufacturer’s instruction. The resultant DNA products were purified before polymerase chain reaction (PCR) amplification. The PCR reaction mixture equivalent to 50 μL contained 1× buffer (10 mM Tris-HCl, pH 8.8; 50 mM KCl), 2 mM MgCl2, 0.2 mM dNTPs, 20 pmol each primer and 3U Taq DNA polymerase.\n\nForward primer, 5′-AGACAGACATTAGCTCAGTA-3′,\n\nand reverse primer, 5′GGCAAAGACCACGTCCATTC-3′\n\nThe running conditions on a Gene Amp PCR system 9700 were; pre-denaturation at 94°C for 5 min, followed by 35 cycles of denaturation at 94°C for 30 s, annealing at 58°C for 30 s, synthesis at 72°C for 1min and final extension at 72°C for 5min. The amplified products (916-bp region of genomic DNA) in volumes of 10 μL were digested overnight with MspI restriction enzyme (2.5 units) in a 20 μL reaction mixture containing 50 mM sodium chloride, 10 mM Tris-HCl, 10 mM magnesium chloride, 1mM dithiothreitol (pH 7.9) at 37°C. The fragments were separated by electrophoresis on a 2% agarose gel stained with ethidium bromide and visualized under a UV illumination system. ALAD1-2 samples had both a 583- and a 512-bp fragment, whereas ALAD1-1 individuals had a single 583-bp fragment.\n\nResults were expressed as means, correlations and the statistical significance was evaluated by one-way analysis of variance (ANOVA) using Minitab 19 statistical software, an equivalent open access alternative is Scilab-6.1.1 statistical software. In addition to maximizing data collection, missing data cases were completely omitted (listwise) from the data set prior to statistical analysis.\n\n\nResults\n\nFollowing genotyping of the samples for ALAD alleles, the outcome is shown in Table 1 with corresponding BLL, Hb levels, hematocrit, and ALAD enzyme activities. The results indicate that the ALAD1-1 isozyme was the most predominant with moderately high hemoglobin levels and seemingly normally functioning ALAD enzyme. The frequency of the ALAD2-2 isozyme is shown to be the least predominant as compared to the ALAD1-1 and ALAD1-2 isozymes. Comparing the hemoglobin levels across all the groups, it is apparent that members with ALAD2 allele have lower Hb levels compared to members coding for ALAD1.\n\n\n\nThe results further indicate that members with isozyme ALAD1-1 had their ALAD enzyme activity functioning moderately normal as compared to the rest. Correlational analysis revealed that ALAD enzyme activity and hemoglobin levels strongly correlated with blood lead levels across all the genotypes ( Table 2).\n\n\nDiscussion\n\nVarious factors including duration (time) of exposure,24 levels of the environmental lead pollutant in the area, nutritional status, age, and genetics modulate one’s lead poisoning susceptibility.25,26 Even with similar environmental settings and confounding factors, variations in susceptibility to lead poisoning among individuals exist.27,28\n\nThis study therefore aimed at expounding on the relationship between genetic variations of proteins that code for ALAD enzyme and lead susceptibility among individuals (children aged 6–60 months) living in the same geographical area (Katanga Uganda). Based on the available literature about the stoichiometric inhibitory effect of blood lead ions on ALAD activity,29 we hypothesized that ALAD allele frequency distribution account for one’s blood lead levels. The extent of this ALAD enzyme inhibition is dependent on one’s ALAD protein genetics.13 From the fact that this enzyme (ALAD) is polymorphic with a G-to-C transversion at position 177 (db SNP ID: rs1800435) and two alleles (ALAD1 and ALAD2) and three isozymes; ALAD1-1, ALAD1-2, and ALAD2-2, dominating ALAD allele accounts for lead toxicity susceptibility. It is reported that delta-aminolevulinic dehydratase enzyme polymorphism differs by race, and geographical location. From the current study findings, we report significant correlations between ALAD genotype and Hb level, ALAD genotype and ALAD enzyme activity, and blood lead levels in magnitudes of ALAD1-1 (r = 0.42, p-value = 0.02) ˂ ALAD1-2 (r = 0.62, p-value ≤ 0.001) ˂ ALAD2-2 (r = 0.67, p-value ≤ 0.001) see (Table 2). Blood lead levels were significantly elevated in carriers of ALAD 2-2 isozyme than those of both ALAD1-2 and ALAD1-1 isozyme carriers (Table 1). The variations in lead burden among these three groups observed in Table 1 are attributed to the difference in the electronegativity of the amino-acids lysine and asparagine that code for these isozymes. From this study’s findings, we concur with reports of various previous studies from different regions that indicate a low prevalence of ALAD1-2 and ALA2-2 as compared to the ALAD1-1 genotype. Based on the study results in (Table 1), it is acceptable that having ALAD1-2 and ALAD2-2 isozymes as the less predominant phenotypes delay lead poisoning symptoms, like ALAD enzyme inhibition, than individuals who have ALAD1-1 as the dominating isozyme. We statistically analyzed data groups (ALAD1-1 vs ALAD1-2 and 2-2 individuals) using one-way analysis of variance (ANOVA). Stepwise regression and multiple analyses of variance were used to assess the contribution effect of different ALAD genotypes towards blood lead levels, ALAD enzyme activity, and hemoglobin levels of the study participants (Table 1). Compared to other isozymes, ALAD1-1 genotype, which is encoded by the less electronegative protein lysine, was the most dominant, and because of this, it binds fewer lead ions hence more susceptibility to lead poisoning. This is owed to the fact that lead ions bind ALAD with high electronegative charge tightly, hence reducing the number of bioavailable lead ions in circulation. Then, unbound lead ions circulating freely in the body systems end up affecting many vital organs. However, in times of oxidative and nutritional challenges, this tightly bound lead is released back into circulation resulting in manifestations like anemia, impaired intelligent quotient (IQ), etc.\n\nThese findings, therefore, reveal that ALAD polymorphism modifies lead kinetics by, for example, making ALAD2-2 isozyme predominant carriers lower the uptake of lead ions into cortical bones.\n\nThis study, therefore, concludes that ALAD polymorphism is of great importance in modulating the toxicokinetics of lead toxicity and therefore recommends a more detailed study on ALAD genotyping involving a bigger Uganda population.\n\n\nData availability\n\nThis study’s participants were minors, whose data public sharing is ethically restricted. However, the data that support these study findings are available from the corresponding author [J.K., joseph.kyambadde@gmail.com], upon presenting a clear written statement on the purpose of data requested for.\n\nDryad: A representative gel of ALAD following a restriction fragment length digestion, https://doi.org/10.5061/dryad.vt4b8gttz.30\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nShen XM, Yan CH, Guo D, et al.: Low-level prenatal lead exposure and neurobehavioral development in children in the 7rst year of life: A prospective study in Shanghai. Environ. Res. 1998; 79: 1–8. Publisher Full Text\n\nShen XM, Yan CH, Guo D, et al.: Prevalence of elevated blood lead levels of children in Shanghai. Chinese J. Preventive Med. 1997; 31: 9–12. [Chinese]\n\nShen XM, Guo D, Wu SM, Xu JD: Resilience of children to lead poisoning: A pilot study. J. Clin. Pediatr. 1990; 8: 105–106. [Chinese]\n\nCenters for Disease Control and Prevention (CDC): Preventing Lead Poisoning in Young Children. U. S. Department of Health and Human Services, Public Health Service, CDC; 1991.\n\nMukisa A, Kasozi D, Aguttu C, et al.: Relationship between blood Lead status and anemia in Ugandan children with malaria infection. BMC Pediatr. 2020; 20(1): 1–7. Publisher Full Text\n\nSteenland K, Boffetta P: Lead and cancer in humans: where are we now?. Am. J. Ind. Med. 2000; 38(3): 295–299. Publisher Full Text\n\nCusick SE, Jaramillo EG, Moody EC, et al.: Assessment of blood levels of heavy metals including Lead and manganese in healthy children living in the Katanga settlement of Kampala, Uganda. BMC Public Health. 2018; 18(1): 717. PubMed Abstract | Publisher Full Text\n\nDesai MR, Terlouw DJ, Kwena AM, et al.: Factors associated with hemoglobin concentrations in pre-school children in Western Kenya: cross-sectional studies. Am. J. Trop. Med. Hyg. 2005; 72(1): 47–59. Publisher Full Text\n\nKwena AM, Terlouw DJ, De Vlas SJ, et al.: Prevalence and severity of malnutrition in pre-school children in a rural area of western Kenya. Am. J. Trop. Med. Hyg. 2003; 68(4_suppl): 94–99. Publisher Full Text\n\nPapanikolaou NC, Hatzidaki EG, Belivanis S, et al.: Lead toxicity update. A brief review. Med. Sci. Monit. 2005; 11(10): RA329–RA336. PubMed Abstract\n\nChia SE, Yap E, Chia KS: δ-Aminolevulinic acid dehydratase (ALAD) polymorphism and susceptibility of workers exposed to inorganic lead and its effects on neurobehavioral functions. Neurotoxicology. 2004; 25(6): 1041–1047. PubMed Abstract | Publisher Full Text\n\nYang Y, Wu J, Sun P: Effects of delta-aminolevulinic acid dehydratase polymorphisms on susceptibility to lead in Han subjects from southwestern China. Int. J. Environ. Res. Public Health. 2012; 9(7): 2326–2338. PubMed Abstract | Publisher Full Text\n\nKelada SN, Shelton E, Kaufmann RB, et al.: δ-Aminolevulinic acid dehydratase genotype and lead toxicity: a HuGE review. Am. J. Epidemiol. 2001; 154(1): 1–13. PubMed Abstract | Publisher Full Text\n\nZiemsen B, Angerer J, Lehnert G, et al.: Polymorphism of delta-aminolevulinic acid dehydratase in lead exposed workers. Int. Arch. Occup. Environ. Health. 1986; 58: 245–247. PubMed Abstract | Publisher Full Text\n\nPotluri VR, Astrin KH, Wetmur JG, et al.: Human δ-aminolevulinate dehydratase: Chromosomal localization to 9q34 by in situ hybridization. Hum. Genet. 1987; 76(3): 236–239. PubMed Abstract | Publisher Full Text\n\nBattistuzzi G, Petrucci R, Silvagni L, et al.: Delta aminolevulinate dehydrase: A new genetic polymorphism in man. Ann. Human Genet. 1981; 45: 223–229. PubMed Abstract | Publisher Full Text\n\nFleming DE, Chettle DR, Wetmur JG, et al.: Effect of the delta-aminolevulinate dehydratase polymorphism on the accumulation of lead in bone and blood in lead smelter workers. Environ. Res. 1998; 77: 49–61. PubMed Abstract | Publisher Full Text\n\nNavarro JA, Granadillo VA, Parra OE, et al.: Determination of lead in whole blood by graphite furnace atomic absorption spectrometry with matrix modification. J. Anal. At. Spectrom. 1989; 4(5): 401–406. Publisher Full Text\n\nBalasubramaniam P, Malathi A: Comparative study of hemoglobin estimated by Drabkin’s and Sahli’s methods. J. Postgrad. Med. 1992; 38(1): 8–9. PubMed Abstract\n\nAdeleye QA, Oniyangi O, Audu LI, et al.: The optimal time for haematocrit check after packed red blood cell transfusion among children with anaemia. S. Afr. J. Child Health. 2021; 15(3).\n\nBurch HB, Siegel AL: Improved method for measurement of delta-aminolevulinic acid dehydratase activity of human erythrocytes. Clin. Chem. 1971; 17(10): 1038–1041. PubMed Abstract | Publisher Full Text\n\nWetmur JG, Kaya AH, Plewinska M, et al.: Molecular characterization of the human deltaaminolevulinate dehydratase 2 (ALAD) allele: Implications for molecular screening of individuals for genetic susceptibility to lead poisoning. Am. J. Human Genet. 1991; 49: 757–763.\n\nWetmur JG, Bishop DF, Cantelmo C, et al.: Human delta-aminolevulinate dehydratase: Nucleotide sequence of a full-length cDNA clone. Proc. Natl. Acad. Sci. USA. 1986; 83: 7703–7707. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchwartz BB, Lee BK, Stewart W, et al.: Associations of ALAD genotype with plant, exposure duration, and blood lead and zinc protoporphyrin levels in Korean lead workers. Am. J. Epidemiol. 1995; 142: 738–745.\n\nMahaffey KR: Nutritional factors and susceptibility to lead toxicity. Environ. Health Perspect. 1974; 7: 107–112. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoyer RA, Mahaffey KR: Susceptibility to lead toxicity. Environ. Health Perspect. 1972; 2: 73–80. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNeedleman HL, Bellinger D: The health effects of low-level exposure to lead. Annu. Rev. Public Health. 1991; 12(1): 111–140. Publisher Full Text\n\nBenkmann HG, Bogdanski P, Goedde HW: Polymorphism of delta-aminolevulinate acid dehydratase in various populations. Human Hered. 1983; 33: 62–64. Publisher Full Text\n\nWarren MJ, Cooper JB, Wood SP, et al.: Lead poisoning, haem synthesis and 5-aminolaevulinic acid dehydratase. Trends Biochem. Sci. 1998; 23(6): 217–221. Publisher Full Text\n\nMukisa A: A representative gel of ALAD following a restriction fragment length digestion. Dryad. 2022. Publisher Full Text"
}
|
[
{
"id": "138566",
"date": "09 Jun 2022",
"name": "Muhammad Sajid Hamid Akash",
"expertise": [
"Reviewer Expertise EDCs-induced cardiometabolic disorders",
"Biochemical Genetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript describes in detail the role of ALAD (delta-aminolevulinic acid dehydratase) in enzymatic activity and its susceptibility to lead toxicity in urban children of Uganda. This study seems interesting, but there are certain flaws and shortcomings that need careful attention of the authors to revise their manuscript on the basis of the following comments:\nWhat are the toxic values of lead? Give the ratio of exposure to lead globally as well as in Uganda. Furthermore, introduction section of this article needs some major revisions to add more data about the role of exposure of lead on various enzymes notably delta aminolevulinic acid by considering the latest studies conducted on the role of lead on ALAD and various other metabolizing enzymes. Following references (Environ Sci Pollut Res. 2022; https://doi.org/10.1007/s11356-022-20069-5 and Environ Sci Pollut Res. 2021; https://doi.org/10.1007/s11356-021-15323-1) may help the authors in this regards.\n\nFormatting, spacing and grammatical mistakes should be corrected.\n\nHave you taken socio-demographic information of the patients?\n\nWhat were the inclusion and exclusion criteria of your study?\n\nIn result section, a table related to susceptibility (increased or decreased) population is missing. Add this data as your title and aim is related to susceptibility also.\n\nDiscuss your findings with the recent previous studies under the discussion section, only 7 references are supporting your discussion, of whom no study was related to your findings.\n\nWhat are the limitations of your study?\n\nConclude your findings comprehensively under a separate heading.\n\nCitations are missing in most of the sentences of introduction (especially first 3 to 4 sentences). Try to add most recent citations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "184451",
"date": "09 Aug 2023",
"name": "Lorenz S. Neuwirth",
"expertise": [
"Reviewer Expertise Developmental behavioral neurotoxicology of lead exposures with over 20 years experience in basic research/pre-clinical models of childhood lead expsosures."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the abstract the language is unclear in the following:\nBackground: it should read \"in sub-Saharan Africa the population of Uganda has experienced increased environmental exposures to lead as a contaminant that subsequently has caused elevated blood lead levels in children as a neurotoxicant within these areas.\" The sentences that follows...\"Its levels in one's environment account for their blood lead levels.\"...is confusing and unclear. Eliminate and replace with a range of blood lead levels that were previously observed in this area prior to the population explosion and how it impacts the lives of children when exposed to a neurotoxin like lead.\n\nMethods: A statement of how many children, their age range, and gender proportion should be included to help the reader obtain a sense of what this study did methodologically. Also, the measurements for BLL, Hb, and ALAD should be noted in parentheses following each term (i.e., BBL measured in ug/dL). The method of spectrophotometry should be changed to atomic absorption spectrophotometry with graphite furnace analysis.\n\nResults: No indication of the mean and standard deviation of the BLLs and Hb by age and gender are noted, which is problematic. Moreover, the correlations that are noted which state a relationship is too general and needs to be more explicit. Indicate whether a positive linear, negative linear, non-linear, or curvilinear (i.e., U-shaped or inverted-U-shaped) relationships are observed for each comparisons. Further, the correlations should be additionally supported by an effect size using a Cohen's d or ds to fully allow the reader to understand the impacts of these findings and their potential generalization into work being done on a similar level in other countries.\nKey words: I would suggest only keep Blood lead levels, then add d-aminolevulinc acid dehydratase enzyme, hemoglobin, childhood lead exposure,\n\nIntroduction: The writing has too many split infinitives and/or awkward phrasing and should be proof read to ensure clarity before submitting (i.e., first sentence...\"numerous simultaneous transitions...).\nLead is an environmental contaminant at high- and low-exposure levels. However, levels that are deems low enough to be safe are still detrimental to the developing central nervous system in children as lead is a neurotoxin with no safe level of exposure. This should be somehow added in the first paragraph to establish a stronger problem statement. Also, this would avoid the ambiguities presented by stating lead is an accumulative toxin as this suggests low levels are safe and tolerable, which they are not.\nThe following sentence on the impacts of lead exposures in children should have clear blood lead levels noted as to which organ systems are disrupted at what lead exposure levels (i.e., low-levels reduce IQ, alter hormones, and stunt growth, but to not harm the lung, stomach, and etc.).\nThe sentence should be re-written...\"Lead ion absorption in the intestines has been reported to exhibit a negative linear relationship between increased intestinal absorption and decreased hemoglobin (Hb) levels.\" This sentence also needs an in-text citation to support its claim.\nPlease define and/or elaborate...\"lead sinks in read blood cells\"... do you mean its ability to absorb into and bind?\n\nThe sentence that \"ALA triggers the production of ROS...\" should be followed by another sentence on the functional significance in why this pathway is activated. The increased lead body/brain burden is activating oxidative stress and ALA is mobilized as a defensive or counteractive mechanisms to trigger ROS to try to protect the brain and body from lead (neuro)toxic exposures at the physiological levels.\nOverall, the introduction needs to be tighter, better framed, and more information on the clinical impacts of children. Additionally, from where exactly are they obtaining such exposures? A few sentences should address this issue. Then when are children identified to be lead poisoned (i.e., birth, age 1-5, once they start school, or when emergency hospitalization is required). This needs to be clear for the reader as different countries may have different proactive measures or reactive measures for treating children for lead poisoning in clinics. The pharmacokinetics for how long the children are exposed set up a government and policy susceptibility measure for these children that appears to be overlooked and would be important to include here. Identifying biomarkers (ALAD polymorphisms) and BLLs are measures of the lead insult already harming children, but at what ages are these biomarkers being reported and proactively assessed for in the population?\nAdditionally, the ALAD-1 and ALAD-2 allele should be explained in terms of their significance, what each allele is associated with in terms of medical or neurological risk factors or susceptibility factors for conditions (i.e., including lead poisoning), and how other populations prevalence are similar and different from Uganda.\nMethods Section: How long did the transportation of samples take (i.e, hours)? And were they on dry or wet ice? The lead standard concentrations should all be reported as it is unclear the step-wise increases used and this would help the reader understand the sensitivity range of the samples measured. What was the margin of error for the samples detection accuracy? This ought to be reported. Note: ml and ul should be changed to mL and uL and made consistent throughout the manuscript.\nRemove words like ours and we to prevent author bias throughout the manuscript. Write in the third person.\nData Analysis section: The statistical formulas used for each dataset should be described separately. Each test should include its alpha level for the significance threshold, the confidence interval, and the post hoc comparisons along with the effect sizes. Correlations should then be described after these methods to understand how the data were treated to draw the inferences that are reported in the manuscript.\nResults section: The results should be describe in clear statistical reporting formats including the degrees of freedom, and what each finding means. The way the statistics are reported is too brief and under informing and should not just point to the tables without further explanation.\n\nIn the Tables, the mean should be accompanied by the standard deviation, and the standard error of the mean. Also, the data should be broken down by males vs. females as well as combined genders as there are differences reported in the literature as a function of gender/sex.\nIt would be helpful to show a figure of the BLL differences as a a bar graph with means and standard error of the means for males, females, and combined gender and split into age groups dependent upon how the spread of the demographics sampled. Another figure should be similarly constructed on hemoglobin levels, and a third on the ALAD-1 and ALAD-2 molecular work. Then from here, the data should be explained and the rationale put forth as to why then correlations were employed and in what ways to explore which relationships. This would strengthen the manuscripts methodology significantly.\nIt would be helpful to include correlation scatterplots of each of the relationships noted for the reader to visualize and gain a sense of what was done and what the data offer as new information and findings.\nDiscussion section:\nIt is again too brief and does not link back to the original problem statement, the hypothesis under study, and the need for an improved understanding of ALAD-1 vs ALAD-2 in general then as it relates to lead poisoning. This should then be further compared to ALAD-1 and ALAD-2 in the literature, how lead poisoning may be both a risk for changes in ALAD genotype polymorphisms/alleles, and how lead poisoning may potentially compound or exacerbate ALAD-1 and ALAD-2 medical and neurological risk factors. It is plausible that multiple-generations of people living in lead exposed environments may become less or more susceptible to such exposures and epigenetic modifications of the ALAD alleles may be commensurate with such experiences. This should be approached and described in this section.\n\nLastly, what are the conclusions and takeaways for the reader? What should they be made more aware of publicly regarding both lead exposures in Uganda due to industrialization, urbanization, economic development, e-waste sites, etc. and how can an educational outreach of this information coupled with ALAD-1 and ALAD-2 genotype help to alert the public of their lived risks when residing in such an environment? This seems to be overlooked and would be important to add mean and purpose for the public regarding the work done. Also, what are the economic impacts of these 15.2% of children from the 7,000 inhabitants screened in this study over the lifespan? This would be a nice closure point to address and bring attention to the need for more research and support in this area.\nReferences: It seems to be too light for a manuscript of this type and I would suggest consulting the literature more and developing it to have at least 50-70 references.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-538
|
https://f1000research.com/articles/13-588/v1
|
06 Jun 24
|
{
"type": "Research Article",
"title": "The gap that Matilda will bridge: a look at the Colombian case",
"authors": [
"Isabel Cristina Rivera-Lozada",
"Andrés Mauricio Gómez-Sánchez",
"Oriana Rivera-Lozada",
"Andrés Mauricio Gómez-Sánchez"
],
"abstract": "Objective To determine gender gaps in Emeritus researchers in Colombia.\n\nMethods Oaxaca-Blinder-Kitakagwa decomposition model, correcting the sample selection bias with the inclusion of Mills’ inverse ratio (Heckman’s Lambda) through an ordered probit model. Data: Information available in the ScienTI Platform – Colombia during the period 2015-2021.\n\nResults The results show that the gender gap between female and male researchers is 5.8%. To achieve Emeritus status, one must be over 65 years old, and the possibility of achieving Emeritus status is 5.1% higher for female researchers than for their male counterparts. These differences can be explained by the time constraints that female researchers face in being productive, as they spend more time than male researchers on caregiving responsibilities, either due to motherhood or the care of other dependent family members.\n\nConclusions The results obtained allow us to affirm that there is a gender gap in scientific research in Colombia in the Emeritus research category in the calls for proposals for the period 2015-2021. Moreover, the existing gap cannot be explained by factors associated with attributes of education and academic productivity that are part of the regulatory requirements, insofar as not being explained by them, it evidences the existence of discrimination against women researchers to access the highest research category.",
"keywords": [
"Gender gap",
"segregation",
"discrimination",
"scientific research",
"STEM."
],
"content": "Introduction\n\nGender equality, beyond being a fundamental human right proclaimed by the United Nations in the Sustainable Development Goals, is a decisive factor for justice and social progress (Naciones Unidas, s/f, 2020). In the context of the fourth industrial revolution, the participation of women in science, research and technology is one of the lowest in the world and in Latin America. In Colombia, 33.2% of the total number of people employed in these sectors are women (Chiarella et al., 2023).\n\nGender gaps in science, research and technology respond to multiple factors that include low participation in the sector, caused by segregation processes resulting from the traditional assignment of roles that lead to broken ladders and sticky floors (Rivera-Lozada et al., 2023a), as well as phenomena such as the Matilda effect where sexism in science has been a source of invisibilisation and exclusion of women (Saborit-Rodríguez et al., 2022) or the Curie effect that has intimidated female scientists in the face of such a high figure to emulate (Des Jardins, 2010).\n\nRecently, several research have sought to identify the existence of gender differences in research authorship (Pinho-Gomes et al., 2020) or research productivity linked to gender (Mayer & Rathmann, 2018). In general, it is possible to document the gender disparity in science in terms of productivity and the recognition derived from it (Sá et al., 2020).\n\nIn the Colombian case, studies related to gender gaps in research (Ávila-Toscano et al., 2019; Gutiérrez, 2012; Tovar Rojas, 2008) have not explored yet the existence of gaps in access to research rankings granted by the Ministry of Science, Technology and Innovation (MinCiencias): Junior, Associate, Senior and Emeritus. The requirements for classification in the aforementioned categories respond to strictly academic criteria previously stipulated (MinCiencias, 2021) and therefore the consideration of discriminatory elements of gender or any other kind is not pertinent. As a result, female researchers have the same possibility of accessing the Emeritus category as male researchers. Therefore, if the above is not met, we are faced with phenomena such as the Matilda effect or the Curie effect as a possible explanation for the results.\n\nIn this perspective, this research has the objective to identify the existence of gender gaps in the Emeritus category as it is the most demanding, with the highest research level and with a small number of male and female researchers nationwide. This allows filling an analytical gap by determining the possible existence of gender gaps to achieve the Emeritus research category, taking into account the profile of the group of researchers of MinCiencias for the 2015-2021 period attributable to gender discrimination identified in the scientific field.\n\nThis research brings for the first time the analysis of gender discrimination in the highest research category, at least for Colombia, and the inclusion of Heckman’s Lambda to deal with the sample selection problem through an ordered Probit model and not with a Probit model, as is the tradition to capture the different hierarchies in the categories of researchers. The overall results reveal a gap of 5.1%, whose difference in the coefficients attributable to gender discrimination phenomena is increasing from 4% in 2015 to 4.6% in 2017, remains the same for 2019 and reaches 4.8% in 2021.\n\n\nLiterature review\n\nThe gender gap is the form used to represent the disparity between men and women in terms of resources, opportunities, access and rights (CEPAL, s/f; Sebastiá, 2020). In the case of Science, Technology and Innovation (STI), these gaps are difficult to measure because there is little available internationally data and indicators to study these phenomena (López-Bassols et al., 2018) that some find associated with career choice by men and women. In the case of women, it may be related to stereotyped occupations (Morales Inga & Morales Tristán, 2020) as a consequence of what appears to be a natural extension of the traditional roles of patriarchal societies where women choose occupations related to care, such as nursing, education, childcare, while men choose professions related to authority such as military, judicial, legislative and engineering careers, among others (Rivera-Lozada et al., 2023a).\n\nTo understand the issue of the status of women in science, technology, engineering and mathematics (STEM), research in the United States identified factors such as motivation, self-concept, self-efficacy and identity, biases, stereotypes, university culture and lived experiences, barriers to tenure, promotion, work-life balance and administrative advancement (Blackburn y Heppler, 2020) in an effort to capture environmental and personal factors attributable to the profile.\n\nThe literature review showed that the determining factors of scientific production include geographical location (Luna Morales y Luna Morales, 2018; Pinho-Gomes et al., 2020), position (Castro, 2018; Pons Peregort et al., 2013), time commitment (Maceira Ochoa, 2017; Pinho-Gomes et al., 2020) research classification or ranking (Mayer y Rathmann, 2018), marital status (Aiston y Jung, 2016; Sougou et al., 2022), number and age of children (Pons Peregort et al., 2013), inclusive funding programmes (López Belloso y Díez Sanz, 2017; Montané y Carvalho, 2012) institutional determinant (Gomez, 2019; Moreno Cubillos et al., 2012; Ortega Ayala, 2019), sexist bias (Guil Bozal, 2016; Sougou et al., 2022), gender stereotypes and roles (Bordons et al., 2013; García-Jiménez y Herrero, 2022), discrimination (Truffa, 2012), income level (Churba, 2023; Jabbaz et al., 2019), segregation (López Montes y Morón Gallego, 2017; Vargas et al., 2016), glass ceiling (Cárdenas Tapia, 2015; García, 2014; Rivera Lozada et al., 2020) and recognition (Matilla Quiza y Mo Romero, 2014; Sá et al., 2020).\n\nFrom this review emerges the classification of research barriers that contribute to gender gaps in four categories: i) Academic offer in terms of fields of knowledge, access, participation and presence of women, ii) Research policy as a guarantor or not of inclusion through funding strategies, participation and promotion of relevant research lines with a female perspective, iii) Scientific production as a result of the increase in the academic offer, the increase in female enrolment in higher education, specifically in STEM, the strengthening of research groups and the increase in scientific collaborations, and finally, iv) Profile based on characteristics, motivations and distinctive features of female and male researchers (Rivera-Lozada, et al., 2023b; UNESCO, 2019).\n\nThis research addresses the factors associated with the fourth category, Profile, abandoning the diversity of factors proposed in the other categories, not because they are considered less important, but because of the difficulty in measuring them and the availability of the corresponding information. Thus, the study incorporates age, classification of the researcher, place of birth, affiliation, level of education and gender, in order to show, based on them, the existing gaps in the probability of a male or female researcher reaching the highest research category in Colombia.\n\n\nMethods\n\nThe research has a quantitative approach developed through stochastics models. Specifically, Oaxaca-Blinder-Kitakagwa decomposition modelling is implemented, correcting the sample selection bias with the inclusion of Mills’ inverse ratio (Hackman’s Lambda) through an ordered probit model. The population of the study includes all university professors and/or researchers registered in the Ministry of Science, Technology and Innovation in Colombia.\n\nThe data used in this study are drawn from MinCiencias database spanning in four waves (2015, 2017, 2019, and 2021) with 77,168 observations. It is worth mentioning that waves in previous periods are not taken into account, given that the Emeritus category had not been achieved by any researcher presented to that date, probably due to the requirement that this implied. The data is openly accessible in the ScienTI Platform.1\n\nThe stochastic model used explains the differences in the probability of achieving the Emeritus research category between men and women, and specifically how much of this gap comes from observable and unobservable variables attributable to gender discrimination.\n\nFor this purpose, an Oaxaca-Blinder-Kitakawa decomposition model (Blinder-Kitakawa, 1973; Oaxaca, 1973) is implemented within the variant of Fairlie (1999), 2005 and Yun (2004), including for the first time in gender studies, dichotomous variables to capture gaps in different research categories, using therefore a discrete choice Probit model. It is worth mentioning that this model also introduces Heckman’s Lambda (1979), also known as Mills’ inverse ratio, to deal with possible of sample selection bias problems, since possibly not all researchers in Colombia are registered with MinCiencias and therefore the sample would not be random. The novelty with this sample selection correction is that the model used is an ordered Probit, to capture the hierarchy of the different research categories.\n\nSince this study uses data from 2015 onwards, it is not possible to implement panel data models as there are so few years (T=4 periods) and an increasing number of individual units (N); then (N>T): and according to Pesaran (2015), the estimators of fixed and random effects, instrumental variables and the generalised method of moments (GMM), will be biased. For this reason, this study has conducted a cross-sectional analysis for each period and compares the results over time.2\n\nIn formal terms, the model assumes that the dependent variable (the differentials in the probability of obtaining the Emeritus status between men and women) is a dichotomous variable explained non-linearly for a set of covariates. In this sense, following Fairlie, (1999) and Vicéns-Otero (2012), the model in general is as follows:\n\nWhere Y¯H and Y¯Mare the average probabilities of achieving the emeritus status for men and women respectively. On the other hand, F(∙) denotes the cumulative distribution function of the normal distribution evaluated at Xβ̂ for both groups. The first bracket on the right side captures the observable factors that explain the probability differentials in both groups. The second bracket also explains the differentials, but due to unobservable factors, attributable to discrimination phenomena. Lastly, NM and NH are the number of observations for men and women, respectively.\n\nAs an example, the existence of a 10% probability differential between men and women to achieve the highest category, and in addition, 7% of this percentage is attributable to observable characteristics (such as level of education or university of origin, among others), the remaining 3% is attributed to gender discrimination because it is not explained by any other observable factor.\n\nFor this study, the stochastic model is based on human capital models (Schultz, 1959) and on Mincer’s (1974) extended income model, where education and experience/age are key determinants of the phenomenon to be explained, but also another set of covariates associated with the individual. In this sense, it is assumed that the probability differentials in achieving the maximum category are attained according to a set of observable characteristics, where most of them come from the researcher’s background and a few others are of an institutional and statistical nature (Heckman’s Lambda).\n\nSpecifically, the explanatory variables X (equation 1), the age of the person is considered as a proxy variable for work experience. This happens because the database used does not have this information, but fundamentally because, as stated by (Zveglich et al., 2019), when calculating experience in the traditional way by subtracting the years of education minus five from age (assuming that most children start primary education at that age), this value is the same for all individuals of the same age and educational level, regardless of gender. Therefore, age is included in this study with the understanding that the older the age, the more experience, but also because the Emeritus category is only available for researchers who are 65 years of age or older according to current regulations. It is worth noting that age squared is also considered to capture the concavity of the function in this variable, that is, to check if the probability differentials of being an Emeritus researcher between the two groups grow at decreasing rates with age (Gómez-Sanchez y Ramírez-Gutiérrez, 2021).\n\nOn the other hand, the Mincer equations include the level of academic education because the higher the level of study, the higher the salary earned. However, they are included here due to current regulations, since the highest categories require more advanced qualification levels; thus, the Emeritus category requires, but not limited to, a doctoral level of academic education. At this point it is worth noting that the levels of postdoctoral education are not academically recognised by MinCiencias, as they are international professorial stays whose objective is to carry out academic research. Therefore, according to Resolution 1764-2013 of MinCiencias they are not study programmes and do not lead to a degree. In this sense, only doctoral studies will be taken into account.\n\nThe stochastic model assumes that other characteristics also explain the possibility of obtaining the highest category, such as the area of academic education, the university of origin and nationality. These variables are, in this study, part of the extension of Mincer’s (1974) traditional model.\n\nThe area of training is important because depending on the availability of financial resources, evolution of technology, innovations and culture, some fields of science have a greater amount of research than others (Ríos Gómez & Herrero Solana, 2005), as is the case in the last decade of research on artificial intelligence, biotechnology, renewable energies and neuroscience leading research worldwide (Banich & Compton, 2018; Clark & Pazdernik, 2015; Russell et al., 2015). Therefore, belonging or not to these areas has an impact on the possibility, quantity, and quality of research and thus on obtaining the highest category. For this reason, the stochastic model controls this situation by introducing the researcher’s area of knowledge.\n\nThe affiliation of researchers is also relevant, and, in the case of Colombia, it is concentrated in the universities in the centre rather than in the periphery of the country. This is due, as mentioned above, to the academic quality of the universities and the financial resources available or accessible to them, or, as stated by Ríos Gómez and Herrero Solana (2005), to the industrial, economic and political development of some regions compared to others. In this sense, the most important universities in the country are located in the golden triangle of Colombia, which corresponds to the cities of Bogota, Medellin and Cali, where the most important universities in the country are located (Universidad Nacional, Javeriana, Andes, Antioquia and Valle).\n\nOn the other hand, the nationality of the researcher could also explain the phenomenon analysed, since the possibility of having a doctorate, speaking a foreign language, or having authored articles published in international journals, among others, is high. Some of these researchers have been hired directly, others have arrived under the figure of visiting professors in the context of international academic mobility at universities, but they have stayed in the country and have become part of MinCiencias’ calls for proposals.\n\nFurthermore, to account for the possibility that the area of education is related to the university of origin, a dichotomous interaction variable is also included. Finally, as the sample may not be random, the estimators will be biased and inconsistent if estimated using the Ordinary Least Squares (OLS) method. Therefore, Heckman’s Lambda is included within the explanatory variables X in equation 1, as a way to avoid endogeneity due to omitted variable. However, this process involves implementing a stochastic model prior to equation (1) to obtain the variable in question.\n\nHeckman’s Lambda is traditionally obtained through a Probit model to capture the participation of the individual, in this case, of the Colciencias ranking. Nevertheless, because in this case the variable analysed has four categories with a hierarchical order (Emeritus, Senior, Associate and Junior), then the dependent variable is ordinal, and therefore an ordered Probit model must be used. In this sense, the model allows finding the probability of observing the result i corresponding to the probability that the estimated linear function plus the random error is within the critical points that separate the research categories:\n\nWhere kare the critical points; i refers to the four research categories, αk are the parameters to be estimated; xkj are the variables that explain participation. This includes age, an interaction variable between age and university of origin, and another interaction variable between area of training and university of origin. The variable uj are the stochastic errors which follow a normal distribution.\n\nOnce the model is estimated (equation 2), the default value of ẑj, is obtained, which is replaced in the normal density function ϕ(ẑj) and in the cumulative distribution function Φ(ẑj); and finally, its division is the Heckman’s Lambda or Mills’ inverse ratio:\n\nWith all the above, and taking into account equations (1) and (3); the stochastic model specifically to determine the gender gaps in the Emeritus category has the following structure:\n\nThe variable Y is dichotomous and takes the value of 1 if the researcher is in the Emeritus category and 0 otherwise. The explanatory variables are age (age), age squared (age2); academic level (level), area of knowledge (area), nationality (nat), and university of origin (univ). Moreover, d2 is the dichotomous variable that captures the interaction between the area of education and university of origin; and λ̂H is the Heckman’s Lambda estimated in equation 3. Finally, εi are the random errors that are assumed to follow a normal distribution and are well-behaved; for example, εi∼N(0,1).3\n\nSince this study attempts to show gender gaps between men and women in terms of research categories, Figure 1 shows the proportion of people who applied to MinCiencias’ call for proposals in the analysed period, broken down by men and women.\n\nSource: Own elaboration.\n\nThe figures reveal that the number of women who have applied to the calls for proposals has always been lower compared to the group of men. Even though the participation of women is increasing, from 35.5% in 2015 to 39.4% in 2021, this change has been very subtle. On the other hand, men participation has been decreasing, but also only slightly, from 64.5% in 2015 to 60.6% in 2021. This allows us to affirm two things. First, there are still gaps that are stable over time, at least for researchers who apply to these calls. Second, while these figures do not reveal any kind of ex ante discrimination, they could indicate in some way that the number of female researchers in Colombia is lower than that of men, although it must be borne in mind that possibly not all researchers are included in the calls for proposals.\n\nAs the objective of the study links gender with the highest research category, Table 1 shows the evolution of the Emeritus category, classified by gender over the years in which the calls were made.\n\nThe figures show that in the Emeritus category (Figure 2), it is historically men and not women who can achieve this recognition. In fact, in 2015 the number of women who obtained this category out of the total represented 25.39% and by 2021 it was only 28.90%, that is, an absolute increase of 3.3%, while in the case of men, the proportion has decreased almost imperceptibly, from 74.6%1 in 2015 to 71.1% in 2021. This indicates that the gap remains in Colombia, and for every three men in this category there is only one woman.\n\nSource: Own elaboration.\n\nIt is worth noting that in the remaining categories below the maximum (Senior, Associate and Junior), the pattern is also repeated. As Figure 3 shows, in the Senior category, the proportion of men exceeds that of women, regardless of the period or call for applications, at around 60%, while for women it is only 40% on average. In the case of the Associate category, the situation is similar, with men accounting for 63% and women for 37% on average. Finally, in the Junior category, the most recurrent of all, but at the same time the lowest or least demanding, 75% of the people in this category are men and the remaining 25% are women.\n\nSource: Own elaboration.\n\nWith all of the above, it can be inferred that female participation in the different research categories in Colombia is less than half compared to that of men. In this order of ideas, it does not seem to be a simple coincidence that there are such high differences across the categories, because there are regulations defined by MinCiencias to obtain them. In this sense, it is necessary to know what determines these gaps, whether they are observable factors (such as academic education levels or university of origin, for example), or whether there are unobservable factors associated with discriminatory phenomena, especially in the highest category (Emeritus), given that it is the most demanding to achieve among all.\n\nOther relevant aspects that could help to investigate this phenomenon are listed in Table 1. Given that the highest research categories require higher levels of academic education (specifically doctoral education), the figures show that the participation of researchers with PhD degrees in the different calls for applications has been similar between men and women, although it has always been slightly higher for men. It is also worth noting that this participation has been decreasing for both genders. Indeed, between 2017 and 2021 it has decreased by approximately 4% and 3% for women and men, respectively.\n\nFrom the classification of sciences: natural, engineering and technology, medical and health, agricultural, social and humanities (OECD, 2007), the majority of researchers in Colombia (around 30%) come from the social sciences. In this area, female participation has been slowly increasing from 30.93% in 2015 to 33.68% in 2021. It should be noted that participation has always been higher for women than for men, where the average differential has remained below 7% in the period analysed.\n\nThe knowledge society also marks a direction in which new gender gaps are opening up, and this is what is happening with research in STEM (science, technology, engineering and mathematics) areas, Figure 4 shows the recent evolution of gender gaps in this area for Colombia.\n\nSource: Own elaboration.\n\nThe figures reveal that, in research areas such as mathematics and engineering, the gap between men and women is too wide (close to 60% on average in both cases) and remains almost constant over the period under analysis. In the case of science and technology, the gap is less marked, close to 25% on average for both cases; however, it also tends to remain unchanged over time.\n\nThe above indicates that in all STEM research areas for Colombia in its recent academic history there is male hegemony. However, there are some fields of knowledge where this phenomenon is more recalcitrant, such as mathematics or engineering, where approximately for every four men there is only one woman doing research, and others where this ratio is 2:1.\n\nTo achieve Emeritus status, the requirements include, but are not limited to, being over 65 years of age. The information in Table 1 shows that the average age between men and women is very similar (men around 44 and women around 43). The histograms of age by gender and year (not shown) reveal a distribution similar to a Chi-square for each call. In this sense, there are few cases of people under 40 years of age; however, from this age up to 60 years of age there is a large number of researchers; finally, after this age range, the proportion is decreasing.\n\nOn the other hand, if the university of origin is Universidad Nacional de Colombia, Los Andes, Javeriana, Antioquia or Valle, the figures show that participation is higher for women than for men at the beginning of the sample period (in 2025 it was 11.71% for men and 14.15% for women) but in the last call for applications in 2021 the gap is much smaller (9.04% versus 9.50%, respectively). It is also evident that the origin of these universities has been decreasing regardless of gender, which reveals that other universities have begun to gain prominence in research in Colombia, as is the case of some universities on the Colombian Atlantic coast, such as the Universidad de la Costa, Universidad Del Norte and Universidad de Cartagena.\n\nIn terms of nationality, as might be expected, the majority of the participants in the call for applications are of Colombian origin (around 95%). It is also worth noting that there is a very subtle differential in foreign nationality between men and women, as overall 6% of men are non-Colombian, while for women it is 5%. Unfortunately, the database does not provide exact information on the country of origin, only whether they are Colombian or foreign.\n\nSTATA Version 17.0 (StataCorp. 2021, StataCorp LLC.) (RRID: SCR_012763) software is used for the data statistical analysis.\n\nTable 2 shows the estimates of the stochastic model (equation 4). The first column corresponds to the results for the 2015 call, the second for the 2017 call and so on. The last column shows the results for all calls together. In general, the results show that the parameters are positive and statistically significant, regardless of the year and group analysed.\n\nSpecifically, the first column (year 2015) reveals that the probability of men achieving the Emeritus category is 13.4% on average, while for women it is lower and equal to 8.3%; therefore, the average gap is 5.1% as shown in the third row (Difference). This differential in the probability of success is decomposed into the sum of three parts; one attributable to observable variables or more precisely those included in the stochastic model as explanatory variables (Endowment) and one to unobservable variables (Coefficients). The last row is a mixture of the last two (Interaction).\n\nIn this order of considerations, the decomposition of the gap of 5.1% reveals that a very low part corresponds to the differences in the observable characteristics (0.7%); while a very high part corresponds to the unobservable variables (4.0%) and another very low part equal to 0.4% is attributable to the interaction. With the above, it can be affirmed that for the year 2015, there are gender gaps that are minimally explained by observable reasons and largely by gender discrimination.\n\nThe following calls (2017, 2019, 2021) repeat the previous pattern, as the possibility of reaching the highest category is always higher for men than for women, so the gap is always positive. Again, the part corresponding to the differences in the observable variables is minimal (all less than 1%); however, the difference in the coefficients that are indexed to gender discrimination phenomena is increasing, as they go from 4% in 2015 to 4.6% in 2017, remains the same for 2019; and by 2021 they reach 4.8%. This means that gender discrimination is increasing in order to reach the highest category of research in Colombia.\n\n\nDiscussion\n\nThe results show that the breakdown of the gender gap between male and female researchers is 5.8%. This figure is minimally explained by observable reasons and is largely attributable to gender discrimination. This occurs in Ibero-America, where gender gaps are marked not only by the Matilda effect, which accounts for the systematic discrimination of women in science whose contributions are made invisible and assumed by their male counterparts (Rossiter, 1993), but also by the Curie complex that exposes women scientists to an almost mythical Marie Curie benchmark of excellence, to the point of making them feel inferior and unable to reach and equal (Des Jardins, 2010); or by the impostor syndrome (Rose Clance & Ament Imes, 1978) where the situation has become so internalised that they believe their achievements are exaggerated and therefore normalise discrimination to the point where they feel it does not exist.\n\nAchieving the Emeritus status requires an age of over 65 years and the chance of being Emeritus is 5.1% higher for female researchers than for their male counterparts. These differences can be explained by the time limitations that women researchers have to be productive in that they spend more time than male researchers on care work, either due to maternity or caring for other dependent family members because women are traditionally responsible for these activities, low male co-responsibility, deficiencies in the system to promote conciliation mechanisms (Ayala del Pino, 2015) that facilitate the insertion of a new model of productivity and in Colombia is certified as family-responsible companies (Ministerio de trabajo, 2018).\n\nLikewise, the late or slow start of women’s research careers due to motherhood, the use of time for care work, and the fact that men retire five years later than women (Ley 100 de 1993-Gestor normativo, 1993) contribute to the gap for women researchers to reach the Emeritus category in Colombia. The results show that for every three men in the Emeritus research category there is only one woman, and this pattern of participation is repeated in all research categories, a situation that calls for actions to support the funding of research projects and agendas led by women researchers as a gender balance strategy (Tacsir et al., 2014).\n\nThe growth trend of researchers with doctoral education in calls for proposals is growing at decreasing rates and in regions such as Chile and Colombia the gap is 33% and 37% respectively; this situation ends up being reflected in the productivity of female researchers, where Colombia also stands out with marked gender gaps (Albornoz et al., 2018). In this regard, the results of (Muñoz-Ñúngo et al., 2022) indicate that in 2019, women sign 48.52% of scientific production and reinforce the trend that delays and female researchers from achieving the highest research category, Emeritus.\n\nThe results also showed that most of the researchers in Colombia are concentrated in the Social Sciences, around 30% and female participation here is the highest among the disciplinary fields 33.68% in the call for 2021, in accordance with the results of research that also show that in Colombia, the number of female researchers with similar productivity to male researchers is growing (Ávila-Toscano et al., 2019) which reinforces the idea that women are concentrated in areas of knowledge considered not very significant (Gaceta UNAM, 2021).\n\nIn the field of STEM, gender gaps in mathematics and engineering are around 60% and in science and technology around 25%, a situation that is worrying because the skills and knowledge of today and the future are forged in these fields, in particular, information and communication technologies (ICT) are strongly masculinised and vertical and horizontal barriers persist (López-Bassols et al., 2018) which makes it necessary to deconstruct the stereotypes of the professions as well as to rethink the mechanisms of access, participation, promotion and advancement in these disciplines, given that they were formulated under patriarchal and masculinising perspectives (Monroy, 2019) in consideration of the fact that these professions are better paid and the absence or low participation of women in them widens social gaps and increases the feminisation of poverty (Goldin & Katz, 2009; Palacios Riaño, 2019).\n\nThe most relevant universities in the country reflect a greater participation of women researchers, a situation that is beginning to change with the emergence of regional universities, but, as Gutiérrez (2012) points out, the research groups led by women are classified in the lowest categories and are mainly concentrated in Bogota, Antioquia and Valle del Cauca.\n\n\nConclusions\n\nThe results obtained allow us to affirm that there is a gender gap in scientific research in Colombia in the Emeritus research category in the calls for proposals for the period 2015-2021. Moreover, the existing gap cannot be explained by factors associated with attributes of education and academic productivity that are part of the regulatory requirements, insofar as not being explained by them, it evidences the existence of discrimination against women researchers to access the highest research category.\n\nThe present research has received approval from the Ethics and Scientific Integrity Committee of Norbert Wiener University, under file number 298 of January 25, 2022 (298-2022). It is important to highlight that this study falls under the category of minimal risk, as it does not involve the participation of human subjects but is instead based on the collection and analysis of data from sources available online. The use of secondary information has been carried out with strict adherence to confidentiality, through the implementation of rigorous analysis codes. Due to this methodology and the nature of the data employed, it has not been necessary to obtain informed consent from individuals, as previously established. It is worth emphasizing that, despite the absence of direct interaction with participants, the study has undergone thorough ethical scrutiny by the relevant committee, which has determined that it presents minimal risk. Therefore, informed consent was not required, as mentioned earlier, given that it originates from secondary sources. However, it is important to note that the study has been approved by an ethics committee and has been deemed to pose minimal risk, as detailed in the ethical considerations.",
"appendix": "Data availability\n\nZenodo: The Gap that Matilda will bridge: a look at the Colombian case [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10806352 (Rivera-Lozada et al., 2024)\n\nThis project contains the following underlying data:\n\n• The Gap that Matilda will bridge.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAiston SJ, Jung J: Women academics and research productivity: an international comparison. Globalised re/gendering of the academy and leadership. Routledge; 2016; pp. 17–32. Publisher Full Text\n\nAlbornoz M, Barrere R, Matas L, et al.: 2.1 Las brechas de género en la producción científica iberoamericana.2018. Retrieved November, 28. Reference Source\n\nÁvila-Toscano JH, Marenco-Escuderos AD, Romero-Pérez IK: Redes de cooperación entre autores e instituciones en Ciencias Sociales dentro del modelo científico colombiano: comparación por género y área del conocimiento. Revista General de Información y Documentación. 2019; 29(1): 209–227. Publisher Full Text\n\nAyala del Pino C: La conciliación de la vida familiar y laboral en España y Colombia. Revista de Trabajo y Seguridad Social. 2015; 385: 93–130. Publisher Full Text\n\nBanich MT, Compton RJ: Cognitive Neuroscience.2018. Reference Source\n\nBlackburn H, Heppler J: Who Is Writing About Women in STEM in Higher Education in the United States? A Citation Analysis of Gendered Authorship. Front. Psychol. 2020; 10: 491183. Publisher Full Text\n\nBlinder AS: Wage Discrimination: Reduced Form and Structural Estimates. J. Hum. Resour. 1973; 8(4): 436. Publisher Full Text\n\nBordons M, Gómez Caridad I, Hillán L, et al.: Indicadores de género en las publicaciones científicas: “gate-keepers” y autores.2013. Reference Source\n\nCárdenas Tapia M: La Participación De Las Mujeres Investigadoras En México. Investigación Administrativa. 2015; 44: 64–80. Reference Source\n\nCastro M d F: Procesos socio-ambientales de tecnología e innovación: De las brujas alquimistas de ayer a las científicas ambientales de hoy. Nodo: Arquitectura. Ciudad. Medio Ambiente. 2018; 13(25): 34–43. Publisher Full Text Reference Source\n\nCEPAL: >Brechas de género.s/f. Recuperado el 20 de diciembre de 2023 de. Reference Source\n\nChiarella A, Lacunza A, Camisassa J, et al.: Mujeres en ciencia y tecnología: cómo derribar las paredes de cristal en América Latina.2023. Reference Source\n\nChurba MJ: Brecha salarial de género/2021 en la universitat de valencia.2023. Reference Source\n\nClark DP, Pazdernik NJ: Biotechnology. Elsevier; 2015. Publisher Full Text\n\nDes Jardins J: The Madame Curie Complex: The Hidden History of Women in Science.2010. Reference Source\n\nFairlie RW: The absence of the African-American owned business: An analysis of the dynamics of self-employment. J. Labor Econ. 1999; 17(1): 80–108. Publisher Full Text\n\nFairlie RW: An extension of the Blinder-Oaxaca decomposition technique to logit and probit models. J. Econ. Soc. Meas. 2005; 30(4): 305–316. Publisher Full Text\n\nGaceta UNAM: El rol de la mujer en las ciencias sociales.2021. Reference Source\n\nGarcía-Jiménez L, Herrero E: “Nunca lo lograrás, eres demasiado guapa”: Voces de mujeres investigadoras en comunicación. IC Revista Científica de Información y Comunicación. 2022; 19(19): 385–410. Publisher Full Text\n\nGarcía M: Reflexiones sobre los retos que enfrentan las mujeres en el ingreso, la permanencia y la promoción en el Sistema Nacional de Investigadores. Revista de Comunicación de la SEECI. 2014; (35E): 18–25. Publisher Full Text\n\nGoldin C, Katz LF: The Race between Education and Technology.2009. Reference Source\n\nGómez-Sanchez AM, Ramírez-Gutiérrez Z: Tasa de crecimiento salarial real a la educación privada para profesores universitarios: un análisis por género con datos panel en el suroccidente colombiano. Dimensión Empresarial. 2021; 19(1): 1–23. Publisher Full Text\n\nGomez CE: “Las condiciones de mi sexo”: Mujeres científicas argentinas frente a la memoria masculinizada. Revista de Investigación del Departamento de Humanidades y Ciencias Sociales. 2019; 16: 47–58. Publisher Full Text Reference Source\n\nGuil Bozal A: Gender and construction of scientific knowledge. Revista Historia de la Educación Latinoamericana. 2016; 18(27): 263–288. Publisher Full Text\n\nGutiérrez JP: Análisis de los grupos de investigación colombianos en ciencias económicas desde una perspectiva de género. Revista Facultad de Ciencias Económicas:Investigación y Reflexión. 2012; 20(2): 143–164. Publisher Full Text Reference Source\n\nHeckman JJ: Sample selection bias as a specification error. Econometrica. 1979; 47(3): 153–161. Publisher Full Text\n\nJabbaz M, Samper-Gras T, Díaz C: La brecha salarial de género en las instituciones científicas. Estudio de caso. Convergencia. Revista de Ciencias Sociales. 2019; 26(80): 1–27. Publisher Full Text\n\nLey 100 de 1993-Gestor normativo: 1993. Reference Source\n\nLópez-Bassols V, Grazzi M, Guillard C, et al.: Las brechas de género en ciencia, tecnología e innovación en América Latina y el Caribe: resultados de una recolección piloto y propuesta metodológica para la medición. Banco Interamericano de Desarrollo. Inter-American Development Bank; 2018. Publisher Full Text\n\nLópez Belloso M, Díez Sanz A: Aproximación a las resistencias de género en los procesos de cambio estructural en las Instituciones de Investigación europeas. REencuentro. Análisis de Problemas Universitarios. 2017; 28: 311–332. Reference Source\n\nLópez Montes E, Morón Gallego N: La segregación ocupacional del profesorado femenino en la universidad española. REencuentro. Análisis de Problemas Universitarios. 2017; 28: 214–236. Reference Source\n\nLuna Morales ME, Luna Morales E: Mujeres investigadoras en las primeras estructuras de organización en ciencias exactas e ingenierías en México de 1900-2000: Estudio Bibliométrico. Investigación Bibliotecológica: archivonomía, bibliotecología e información. 2018; 32(77): 193–215. Publisher Full Text\n\nMaceira Ochoa L: Agenda para la igualdad en las universidades europeas: consideraciones críticas y lecciones. REencuentro. Análisis de Problemas Universitarios. 2017; 28: 261–282. Reference Source\n\nMatilla Quiza MJ, Mo Romero E: De la excepción a la normalidad: Mujeres científicas en la Historia. Encuentros Multidisciplinares. 2014; 47: 1–10. Reference Source\n\nMayer SJ, Rathmann JMK: How does research productivity relate to gender? Analyzing gender differences for multiple publication dimensions. Scientometrics. 2018; 117(3): 1663–1693. Publisher Full Text\n\nMincer JA: Schooling, Experience, and Earnings. Schooling, Experience, and Earnings. NBER; 1974; Vol. 10(2). Reference Source\n\nMinCiencias: Anexo 1 convocatoria nacional para el reconocimiento y medición de grupos de investigación, desarrollo tecnológico o de innovación y para el reconocimiento de investigadores del sistema nacional de ciencia, tecnología e innovación -2021.2021. Reference Source\n\nMinisterio de trabajo: 12 nuevas empresas colombianas le apuestan a la conciliación laboral, familiar y personal.2018. Reference Source\n\nMonroy ML: La sociedad del conocimiento y las brechas de género en ciencia, tecnología e innovación. Cuadernos Latinoamericanos de Administración. 2019; 15(29). Publisher Full Text\n\nMontané A, de Carvalho MEP : Diálogo sobre género: justicia, equidad y políticas de igualdad en educación superior (Brasil y España). Revista Lusófona de Educação. 2012; 21: 97–120. Reference Source\n\nMorales Inga S, Morales Tristán O: ¿Por qué hay pocas mujeres científicas? Una revisión de literatura sobre la brecha de género en carreras STEM. J. Commun. Res. 2020; 22(22): 118–133. Publisher Full Text\n\nMoreno Cubillos C, Leonor C, Gallego S, et al.: Discriminación y violencia de género en la Universidad de Caldas. Revista Hacia la Promoción de la Salud. 2012; 17: 59–76. Reference Source\n\nMuñoz-Ñúngo B, Maz-Machado A, Rodríguez-Fanec C, et al.: La presencia de la mujer en las publicaciones de Educación en Colombia: un análisis en el Emerging Sources Citation Index. Biblios Journal of Librarianship and Information Science. 2022; (82): 41–50. Publisher Full Text\n\nNaciones Unidas: Igualdad de género: Por qué es importante.s/f. Recuperado el 19 de diciembre de 2023, de. Reference Source\n\nNaciones Unidas: Informe de los Objetivos de Desarrollo Sostenible 2020.2020. Reference Source\n\nOaxaca R: Male-Female Wage Differentials in Urban Labor Markets. Int. Econ. Rev. 1973; 14(3): 693. Publisher Full Text\n\nOrtega Ayala L: Proceso de transversalización de la perspectiva de género en la Universidad Autónoma de Ciudad Juárez. Avances y obstáculos. Universidades. 2019; 81: 33–43. Reference Source\n\nPalacios Riaño M: Feminización de las ocupaciones y diferencias salariales por género para Colombia urbana: 2008-2016. Ciencia Unisalle; 2019, enero 1. Reference Source\n\nPesaran MH: Short T Dynamic Panel Data Models. Time Series and Panel Data Econometrics. Oxford University Press; 2015; pp. 676–702. Publisher Full Text\n\nPinho-Gomes A, Peters S, Thompson K, et al.: Where are the women? Gender inequalities in COVID-19 research authorship. BMJ Glob. Health. 2020; 5(7). PubMed Abstract | Publisher Full Text | Free Full Text\n\nPons Peregort O, Calvet Puig M, Tura Solvas M, et al.: Analysis of equal gender opportunity in science and technology: The professional careers of women scientists and technologists. Intangible Capital. 2013; 9(1): 65–90. Publisher Full Text\n\nRíos Gómez C, Herrero Solana V: La producción científica latinoamericana y la ciencia mundial: una revisión bibliográfica (1989-2003). Rev. Interamericana de Bibliotecología. 2005; 28(1): 43–61. Reference Source\n\nRivera-Lozada IC, Gómez-Sánchez AM, Muñoz-Paz I: Segregación ocupacional femenina: El pegamento que enmascara la discriminación salarial en una universidad colombiana. Dermatol. Int. 2023a; 40(1): 227–245. Publisher Full Text\n\nRivera-Lozada IC, Gómez-Sánchez AM, Rivera-Lozada O: The gap to be bridged by Matilda: a look at the Colombian case. [Data]. Zenodo. 2024. Publisher Full Text\n\nRivera-Lozada IC, Rivera-Lozada O, Escobar-Perez C: Gender gaps in research: a systematic review [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Res. 2023b; 12: 1302. Publisher Full Text\n\nRivera Lozada IC, Muñoz Paz I, Gómez Sánchez AM: Visibilizando el techo de cristal en la Universidad del Cauca: un análisis de discriminación laboral de género. La Manzana de la Discordia. 2020; 15(2): 216–241. Publisher Full Text Reference Source\n\nRose Clance P, Ament Imes S: The impostor phenomenon in high achieving women: dynamics and therapeutic intervention. Psychother.: Theory Res. Pract. 1978; 15. Reference Source\n\nRossiter MW: The Matthew Matilda Effect in Science. Soc. Stud. Sci. 1993; 23(2): 325–341. Publisher Full Text\n\nRussell S, Dewey D, Tegmark M: Research Priorities for Robust and Beneficial Artificial Intelligence. AI Mag. 2015; 36(0738–4602): 105–114. Publisher Full Text Reference Source\n\nSá C, Cowley S, Martinez M, et al.: Gender gaps in research productivity and recognition among elite scientists in the U.S., Canada, and South Africa. PLoS One. 2020; 15(10): e0240903. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaborit-Rodríguez A, Morales-Pérez M, Macola-Ross D d l C, et al.: El sexismo en la historia de las ciencias: efecto Matilda. Revista Médica Electrónica. 2022; 44(4): 758–768. Reference Source\n\nSchultz TW: Investment in Man: An Economist’s View. Soc. Serv. Rev. 1959; 33(2): 109–117. Publisher Full Text\n\nSebastiá I: ¿Qué es la brecha de género?. El Orden Mundial - EOM; 2020. Reference Source\n\nSougou NM, Ndiaye O, Nabil F, et al.: Barriers of West African women scientists in their research and academic careers: A qualitative research. PLoS One. 2022; 17(3): e0265413. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTacsir E, Grazzi M, Castillo R: Women in Science and Technology: What Does the Literature Say? Inter-American Development Bank. 2014, febrero 11; 29. Reference Source\n\nTovar Rojas P: La mujer colombiana en la ciencia y la tecnología ¿Se está cerrando la brecha? ARBOR Ciencia, Pensamiento y Cultura. 2008; 184(733): 835–844. Publisher Full Text\n\nTruffa AC: Percepciones de la ciencia y estereotipos de género: Un proyecto de investigación con adolescentes de educación secundaria. Fundamentos en Humanidades. 2012; 13: 87–98. Reference Source\n\nUNESCO: Descifrar el código: la educación de las niñas y las mujeres en ciencias, tecnología, ingeniería y matemáticas (STEM). Unesco; 2019; 85. Reference Source\n\nVargas D, Requena J, Caputo C: Desvanecimiento de la brecha de género en la universidad venezolana. Interciencia. 2016; 41(3): 162–170. Reference Source\n\nVicéns Otero J: Descomposición Oaxaca-Blinder en modelos lineales y no lineales. Documento de trabajo No. 20.2012. Reference Source\n\nYun MS: Decomposing differences in the first moment. Econ. Lett. 2004; 82(2): 275–280. Publisher Full Text\n\nZveglich JE, Van der Meulen Rodgers Y, Laviña EA: Expected work experience and the gender wage gap: A new human capital measure. Econ. Model. 2019; 83: 372–383. Publisher Full Text\n\n\nFootnotes\n\n1 Data retrieved from: https://minciencias.gov.co/ciudadano/datosabiertos, last accessed February 13th, 2024.\n\n2 Despite this, the authors used panel data information but the results were inconclusive. These can be provided upon request to the authors.\n\n3 The definition of model variables are included in Appendix 1."
}
|
[
{
"id": "288265",
"date": "24 Jun 2024",
"name": "Ernesto Mesa-Vázquez",
"expertise": [
"Reviewer Expertise Intensive agriculture",
"'Gender differences in overplacement",
"water management",
"ecosystem services",
"sustainability",
"farmer attitudes",
"experimental and behavioural economics",
"social preferences",
"herding behaviour"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAfter reading the aforementioned article, I would say that: I confirm that the literature review is sufficient to deal with the research problem. Besides, I completely agree with the authors' chosen approach. Due to the nature of the data and the research question, given the limited number of years, the Oaxaca-Blinder-Kitagawa decomposition model is the right choice. The reasons why other approaches aren't feasible are clearly explained: \"Since this study uses data from 2015 onwards, it is not possible to implement panel data models as there are so few years (T=4 periods) and an increasing number of individual units (N); then (N>T): and according to Pesaran (2015), the estimators of fixed and random effects, instrumental variables and the generalised method of moments (GMM), will be biased.\" This is crystal clear. I'm quite sure the authors also conducted other estimations, such as OLS regression or multinomial regression, but these techniques wouldn't be accurate for this purpose. Finally, I think this paper is necessary to understand the underlying issues at Colombian universities regarding the gender gap at the top researcher level. Nevertheless, I have some minor comments that could be revised before indexing: \"The overall results reveal a gap of 5.1%, whose difference in the coefficients attributable to gender discrimination phenomena is increasing from 4% in 2015 to 4.6% in 2017, remains the same for 2019 and reaches 4.8% in 2021.\" I consider this statement should be written as \"... starts from 5.1% in 2015, increases to 6.0% in 2017, then decreases to 5.8% in 2019, and finally reaches 4.3% in 2021.\" In addition, I think the last column (\"All\") could confuse the reader. My suggestion is to delete it or provide a better explanation of its meaning. In equation 1, I would recommend changing the prefixes \"H\" and \"M\" throughout the article to \"M\" and \"W\" when referring to men and women. In Figure 3, authors should include a chart legend for better understanding. In addition, they should also include year 2021. Lastly, the authors could consider including the \"Emeritus\" category in the same chart as the other categories.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "288264",
"date": "24 Jun 2024",
"name": "Yenny Naranjo Tuesta",
"expertise": [
"Reviewer Expertise My research has been focused on the field of accounting and finance. In particular sustainable accounting",
"accounting education",
"management control and sustainability."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article raised the problem of women in research and especially that of achieving Emeritus status in Colombia. Although it focuses on showing the aspects related to the Matilda and/or Curie effect, the research evidence that not only that is relevant, but it also evidences that public policies also influence and do not reflect support to improve the competences and participation of women in the STEM field itself.\n\nThe article in general is very good and reflects this problem that not only occurs in Colombia but surely extends to other contexts. I consider that in the conclusion it falls very short and should be more emphatic in the way forward and the importance of this research for different parties.Authors are encouraged to review citations prior to indexing.\n\nThe article is interesting, complete and pertinent. For minor suggestions, it is recommended to review the citations before indexing, just to confirm that the cross-reference works and is correct.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "288271",
"date": "25 Jun 2024",
"name": "Yolvi Javier Ocaña Fernandez",
"expertise": [
"Reviewer Expertise Education",
"innovation",
"education and research policies"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript titled \"The Gap that Matilda Will Bridge: A Look at the Colombian Case\" is a highly interesting article that seeks to identify the gaps among researchers in a country emerging in the field of research. The introduction is well-structured, fulfilling all essential elements, and clearly presents the situation of researchers in Colombia. The knowledge gap is precisely defined. Additionally, a detailed literature review is included, which helps the reader understand the issues faced by researchers in the Colombian context. Regarding methodological aspects, the appropriate Oaxaca-Blinder-Kitakagwa model has been used. This model corrects the sample selection bias by including the inverse Mills ratio (Heckman's Lambda) in an ordered probit model, ensuring the validity, reliability, and generalizability of the data. Including data from 2015 to 2021 allowed for a robust analysis. The results met the research objectives, particularly in identifying the gender gap between male and female researchers. It is highlighted that one needs to be over 65 years old to achieve emeritus status. Additionally, the research explains the time constraints faced by female researchers, as they dedicate more time to family responsibilities. The conclusions are well-formulated and align with the research objectives. It is mentioned that the existing gap cannot be explained by factors associated with education and academic productivity attributes, which are part of normative requirements. This indicates discrimination against female researchers in achieving the highest research category. Finally, the bibliographic references are relevant and updated concerning the topic addressed. In terms of form, the writing is clear, concise, and coherent. I consider this research to be a valuable contribution to gender studies, and as a reviewer, I would APPROVE it.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-588
|
https://f1000research.com/articles/11-972/v1
|
23 Aug 22
|
{
"type": "Research Article",
"title": "A potential role of arcadia in conditioned media - umbilical cord derived mesenchymal stem cell on cartilage repair",
"authors": [
"Bintang Soetjahjo",
"Denny Adriansyah",
"Wibi Riawan",
"Denny Adriansyah",
"Wibi Riawan"
],
"abstract": "Background. Certain conditions can stimulate stem cells to produce secretory factors that differ from each condition, such as hypoxia. Umbilical Cord-derived Mesenchymal Stem Cells have been known to have higher proliferation rates, plasticity, and better self-improvement ability than MSCs from other sources. The objective was to analyze the secreting proteins in the Conditioned Medium - Umbilical cord-derived Mesenchymal Stem Cells (CM-UCMSCs) which potentially has a role in the chondrogenesis of cartilage defect. Methods. We used SDS PAGE combined with electrospray ionization mass spectrometry using mass spectrometer to perform a proteomic analysis of CM-UCMSCs which conditioned in a state of fasting (without serum albumin). Then, we continue to analyze to identify proteins of interest using Mascot sequence matching software. Then Analyzed using in silico / molecular docking to know the interaction of each protein with the cartilage repair factor. Results. SDS PAGE performed on all secreted products in CM-UCMSCs. We found one dominant band, then we used Mass Spectrometry continued Mascot sequencing protein that band, conclude that the protein was a D4A9T1/ RNF-111/ Arkadia Protein. And then using in silico/ molecular docking method analyzed that Arkadia Protein worked synergistically with TGF-β1 Protein through activation of TGF-β1 receptors to induce the chondrogenesis. Conclusions. Our results show that the fasting state on CM-UCMSCs promoted secreted Arkadia protein. From in silico model prediction, this protein suspects to have an important role in the process of repairing cartilage defects. However, further research is needed before feasible and safe for the clinical application of CM-UCMSCs in cartilage repair.",
"keywords": [
"Conditioned Medium - Mesenchymal Stem Cells",
"Mass Spectrometry",
"Chondrogenesis",
"Arkadia",
"Molecular Docking"
],
"content": "Introduction\n\nCurrently, stem cells had provided promising potential as a substitute for cells, tissues, and organs, as well as for studying the biomolecular pathogenesis of the disease. Stem cell therapy in cartilage disease has been widely reported to have a good result in animal studies to clinical trials.1 Our previous research, in vivo application of Conditioned Medium - Umbilical cord-derived Mesenchymal Stem Cells (CM-UCMSCs) on white mouse cartilage defects, was found to increase significantly in the immunohistochemical examination of several proteins known to be markers in the process of chondrogenesis: Transforming growth factor-beta 1 (TGF-β1), SRY (sex-determining region y) box 9 (SOX9), Aggrecan, and Collagen Type II2 and also seen as significant in histological assessment using O’driscoll scoring.3\n\nMesenchymal Stem Cells or Mesenchymal stromal cells (MSCs) was understood could differentiate into regenerating tissue producing cells, but in recent research, MSCs has changed the name to Medicinal Signaling Cells (MSC) to more accurately reflect the fact that these cells secrete bioactive factors that are immunomodulatory and trophic (regenerative) meaning which home in on sites of injury or disease.4 MSCs also have an immunomodulatory effect, they can secrete anti-inflammatory cytokines which can be a pathway for the therapeutic mechanism in several immune and chronic diseases.5 MSCs isolated from the umbilical cord have been known to have higher proliferation rates, plasticity, and better self-improvement ability than MSCs from other sources.6 Wharton's jelly-derived stem cell-conditioned medium (WJ-SCs-CM) can increase the expression of cartilage-specific genes (aggrecan, Sox9, and collagen type II) by Chondrocytes and can be introduced as a promoting factor for cartilage regeneration.7 The derivatives of the stem cell are soluble factors that are secreted into the conditioned medium (CM).6 Certain conditions can stimulate stem cells to produce secretory factors that differ from each condition, such as hypoxia, hyperoxia, hypoglycemia, hyperglycemia, etc.8\n\nA meta-analysis compared between secretome based therapy and stem cell therapy in articular cartilage regeneration, and the result is the secretome has a slightly higher potential than cell-based therapy.9 We assume that the free cell therapy approach will be safer and easier in the production and distribution process in the future. Therefore, this study aims to determine the components of the CM-UCMSCs in the state of fasting, which has suspected to play a role in the process of cartilage defect repair.\n\n\nMethods\n\nThis research was conducted at the physiology laboratory of the veterinary medicine faculty. This study was experimental laboratory design with post-test only control group. There were thirty-six male Wistar rats aged 3-months, which were obtained from Gajah Mada University Yogyakarta, Indonesia (Letter number: 263/KEC-LPPT/V/2015). The sample size was calculated using Federer Formula:\n\nn = sample size\n\nt = number of experimental groups\n\nThere were 6 groups (t = 6), so we calculated the sample size were 4 for each groups. The homogeneity was confirmed through the balanced body weight (150-250 grams). All experimental procedures involving animals were carried out in keeping with guidelines from the National Institutes of Health Guide for the Care and Use of Laboratory Animals to ameliorate any suffering of animals.10 The animal models were acclimatized for a week at a temperature of 21-23 °C with controlled humidity (50 ± 5%) in a 12-hour artificial light cycle (8 am to 8 pm) to help them to adapt to the same conditions as they various origins. All rates were located individually in polycarbonate cages (0.90 × 0.60 × 0.60 m). Every animal model was fed with standard pellet and water was provided ad libitum with the husk replaced every three days. All animal models were routinely inspected and observed regarding their food consumption and fecal characteristics. Expected and unexpected adverse event were recorded to identify the deficiencies in procedures or study design,\n\nThe sample in each group was randomly chosen by giving each trial animal a tag number. Following that, the researcher randomly chose the tag numbers. They were divided into 6 groups, including control group receiving treatment for 2 months (C2), control group receiving treatment for 3 months (C3), and control group receiving treatment for 4 months (C4). Treatment group, receiving treatment for 2 months (T2), receiving treatment for 3 months (T3), and receiving treatment for 4 months (T4). Rats in treatment groups were injected with 1 mL/Kg body weight (BW) conditioned medium of UCMSCs 5 times with interval a week after creating cartilage defect. However, cartilage defect was created by surgery on the medial condyle area, followed by the destruction of cartilage through manual mechanical technique by drilling (750 rpm) using Kirschner Wire (D = 1.0 mm; h = 1.0 mm). There was no exclusion of animal during the experiment. The researchers also collaborate with veterinarian for group allocation in each stage of experiment, outcome assessment, and analysis.\n\nSuffering and pain is minimized using appropriate anesthesia of 0.1 ml/10 grams body weight (BW) (Kepro, Netherlands), and xylazine 5 mg/kg BW (Xyla, Netherlands) were administered. General observations for signs of pain or suffering in the animal were conducted daily as needed. Moribund condition was used as a humane endpoint.10 However, because of the experiment using minimal invasive procedure and single treatment was used, there was no animal reached humane endpoint. Outcome measure was the histological changes of cartilage healing using O’driscoll scoring.11 Also the immunohistochemistry analysis for TGFβ-1, SOX-9, Aggrecan, and Collagen type II as a hallmark biomarker of cartilage regeneration. The results of this experiment are shown in previous study.3,12\n\nThis study has been approved by Ethical Clearance Commission of Gajah Mada University, Yogyakarta (Number: 263/KEC-LPPT/V/2015).\n\nStem cell culture was obtained from the umbilical cord of the Wistar rat (Rattus novergicus) aged 19 days washed in povidone-iodine 10% and normal saline in media transport (Dulbelco’s Eagle Modified Medium (DMEM) contained 200ug/ml penicillin, 200ug/ml streptomycin, dan 200u/ml fungizone). Then small pieces of the umbilical cord (around 20mm3) were dissolved with 0.25% EDTA collagenase and trypsin enzyme, then incubated for 30 minutes at 37 °C; added 2cc complete medium DMEM one time, 10% fetal bovine serum (FBS), 50ug / ml penicillin-streptomycin, and 2.5ug/ml fungizone), and then centrifuged at a speed of 3000 rpm for 10 minutes at 4 °C; then incubated again at 37 °C and 5% CO2, after 24 hours changed the medium. The culture was continued until approximately 80% of the confluence was achieved utilizing of the last suspension of each passage spread on the flask and cultured in an incubator, the medium was replaced every three days. This process was carried out consecutively until it reaches four passages. Morphologically, MSCs showed their spindle shape and fibroblast-like appearance using H&E and Giemsa staining. Cells exhibited a high nucleus to the cytoplasmic ratio on Giemsa staining. The adhered MSCs showed spindle-shaped morphology on H&E staining. The heterogeneity of the different MSC samples was demonstrated with Giemsa staining.\n\nMesenchymal stem cells that have reached 80% confluence were harvested using the warm trypsinization method. After the deneutralization of trypsin, the cell suspension was centrifuged at 3000 rpm for ten minutes; The supernatant was removed, the cell deposit is washed with PBS three times. Subsequent cell deposition was resuspended with a new medium with a concentration of 10,000 cells/ml. Subsequently, validated mesenchymal stem cells placed on culture plates were added with 10 ml of complete medium without serum or under fasting state with 5% CO2 levels during 48 hours and thereafter resupplied with serum FBS again. After fasting state, UCMSCs observed were in the normal-looking cell morphology, CM-UCMSCs produced metabolites or secretome in the secreted conditioned media and were harvested then processed to analyze.\n\nThe conditioned medium was analyzed by a mass spectrometer (MS). Protein samples were trypsin digested and peptides extracted according to standard techniques. Peptides were analyzed using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS PAGE) then continue electrospray ionization MS. In SDS-PAGE, the use of sodium dodecyl sulfate (SDS, also known as sodium lauryl sulfate) and polyacrylamide gel largely separated solely based on polypeptide chain length and eliminates the influence of the structure and charge, and proteins. The conditioned medium was then collected, and cell residues were removed using centrifugation, then added sample buffer to samples, and mixed by flicking the tube. Heated the samples at 100 °C for three minutes in a heat block, then centrifuged at 15,000 rpm for one minute at 4 °C, and used the supernatant for SDS-PAGE.\n\nMass spectrometry using the Shimadzu Prominence nano HPLC system [Shimadzu] coupled to a 5600 TripleTOF mass spectrometer [Sciex]. Tryptic peptides were loaded onto an Agilent Zorbax 300SB-C18, 3.5 μm [Agilent Technologies] and separated with a linear gradient of water/acetonitrile/0.1% formic acid (v/v). Spectra were analyzed to identify proteins of interest using Mascot sequence matching software [Matrix Science] with MSPnr100 database by Proteomics International, Western Australia. And then protein found was analyzed using molecular docking or in silico model to visualized and tracked protein interactions with chondrogenesis markers used PyMol V.1 and webserver FireDock (http://bioinfo3d.cs.tau.ac.il/FireDock/), and the interaction between amino acid used LigPlot V.1. by Indonesian Bioinformatics and Biomolecular INBIO, Indonesia.\n\n\nResults\n\nPeptides were analysed using SDS PAGE in eight tubes. The following results were obtained in Figure 1. Furthermore, the SDS PAGE results found dominant bands performed MS using the Shimadzu Prominence nano HPLC system [Shimadzu] coupled to a 5600 TripleTOF mass spectrometer, and identified proteins of interest using Mascot sequence matching software [Matrix Science] with MSPnr100 database found protein suitability as in Figure 2.\n\nBased on our previous studies, we found to increased significantly in TGF- β1, SOX9, Aggrecan, and Collagen Type II.2 Therefore, after found D4A9T1/Rnf111/Arkadia Protein we analyzed interaction among these proteins using molecular docking or in silico. The docking process is carried out to predict the interaction of two molecules. This prediction is useful for knowing the potential interaction among molecules. We found there were interaction among Rnf-111, TGF-β1R, and TGF-β1 (Figure 3). The bond between TGF-β1R and RNF-111 has an affinity value (-27.52) while the interaction between TGF-β1R and TGF-β1 has an affinity value (-26.33).\n\nThe bond between TGF-β1R and RNF-111 ligand is at a different site (Figure 3). The interaction of TGF-β1R and RNF-111 could trigger the process of chondrogenesis through the TGF-β1R pathways. This can be seen from the activation patterns that tend to be the same when viewed from binding amino acids were THR18 and ILE42 (Table 1).\n\n\nDiscussion\n\nIn the present study, we found that one of the most dominant bands of CM-UCMSCs in the fasting state is Rnf-111. Rnf111 (ring finger 111) also known as Arkadia, is an E3 ubiquitin ligase degrade the negative TGF-b signal regulators, i.e. Smad7, c-Ski, and SnoN to amplify transforming growth factor (TGF)-b family signaling.13 TGF-β1 is one of the ligand proteins known to play a role in inducing the process of chondrogenesis.14 This is the basis for our hypothesis that the Arkadia/Rnf-111 protein suggests has a role in the process of chondrogenesis.\n\nCM applied intraarticular knee of OA rats, it means this protein is in outside of chondrocytes, therefore, we assume this protein has an involvement in the process of chondrogenesis through the receptor-ligand pathway. From the result of in silico (Figure 3), the increasingly negative affinity value means that the higher the affinity which means the bond between the ligand and receptor is getting stronger. Based on these results, RNF-111 has a slightly higher activity than TGF-β1 in activating TGF-β1 receptors. The difference in binding position between TGF-β1 and RNF-111 on the TGF-β1R side shows that there is no competition in the activation process or there is no competitive binding, but rather the synergy process mechanism for activation affinity. Therefore, we suspect that RNF-111 as a part of CM-MSCs plays a synergistic role in the process of chondrogenesis through the TGF-β1R pathway.\n\nChen et al, shown that CM-MSCs had a satisfying effect on reducing the progression of OA in mice, by protecting microarchitecture from subchondral bones, balancing the MMP-13 and TIMP-1 ratios in cartilage, and promoting autophagy.15 CM-MSCs decreased matrix metalloproteinase (MMP) activity in cell supernatants as well as the levels of MMP-3 and MMP-13 proteins and mRNA while enhanced type II collagen expression in OA chondrocytes stimulated with IL-1𝛽.16 Another study, found that CM produced by MSC possess a well therapeutic effect on inflammatory chondrocyte, and the 10-fold concentrated MSC-conditioned medium could down-regulated chondrocyte synthesis inflammation-associated, and free-radical-related genes, such as TNF-α, IL-1β, IL-6, and iNOS even treated for 72 h OA.17 More specific research, found the exosomes from Embryonic MSCs has an effect on OA by balancing the synthesis and degradation of chondrocyte extracellular matrix (ECM), which in turn provides a new target for OA drug and potential drug-delivery system development.\n\nAlthough TGFβ1 has been widely known to play a role in the process of chondrogenesis, in animal studies of mice and rabbits, there are reported side effects of growth factor-based therapy, such as supplementation of TGF-β1 which can trigger synovial proliferation and fibrosis, an attraction in pro-inflammatory lymphocytes, and induce the formation of osteophytes.18 This is the answer to why single growth factor supplementation is not recommended to treat articular abnormalities.19 We suspect those components and the environmental factors in CM-MSCs as whole support, especially in our study, to induce the process of chondrogenesis and repairing process of the cartilage defect completely.\n\nA limitation of the study is that we did not analyze the concentration of every protein in CM-UCMSCs using immunoassay such as ELISA, and we cannot provide data of interaction with every single protein with the process of chondrogenesis. A further important weakness of this study is that we did not do the empirical methods (in knock out models), to verify the result of in silico analysis.\n\n\nConclusion\n\nThe conditioning medium has been demonstrated could promote MSCs secreting soluble protein in culture media. Using SDS-PAGE combined Mass Spectrometry we found the dominant protein in our CM-UCMSCs is Arkadia/RNF-111 protein. From in silico methods, we conclude that this protein as a dominant protein of CM-UCMSCs. However, we need further research to find out the important role of Arkadia/RNF-111 protein in the process of chondrogenesis through the TGF-β1R pathway and all of the secreted products in CM-UCMSCs, using knock out models to be feasible and safe for clinical application of CM-UCMSCs in cartilage repair. Then specific dose, duration, and technique of administration should be an attention in the future.\n\n\nAuthor contributions\n\nBintang Soetjahjo: Conception and design, financial support, administrative support, provision of study material, collection and assembly of data, manuscript writing\n\nDenny A: Data analysis and interpretation, manuscript writing, final approval of manuscript\n\nWibi Riawan: Data analysis and interpretation, manuscript writing, final approval of manuscript\n\n\nData availability\n\nAll data underlying the results are available as part of the article.\n\n\nReporting guidelines\n\nDryad. ARRIVE checklist and flowchart. DOI: https://doi.org/10.5061/dryad.zw3r228b6",
"appendix": "References\n\nPaschos NK, Sennett ML: Update on mesenchymal stem cell therapies for cartilage disorders. World J Orthop. 2017; 8(12): 853–860. PubMed Abstract | Publisher Full Text\n\nSoetjahjo B, Hidayat M, Sujuti H, et al.: Immunohistochemistry Evaluation of TGF-β1, SOX-9, Type II Collagen and Aggrecan in Cartilage Lesions Treated with Conditioned Medium of Umbilical Cord Mesencyhmal Stem Cells in Wistar Mice (Rattus novergicus). J Trop Life Sci. 2018; 8(1): 21–27. Publisher Full Text\n\nSoetjahjo B, Hidayat M, Sujuti H, et al.: The significant effect of conditioned medium of umbilical cord mesenchymal stem cells in histological improvement of cartilage defect in Wistar rats. Turkish J Immunol. 2018; 6(2): 57–64. Publisher Full Text\n\nCaplan AI: Mesenchymal Stem Cells: Time to Change the Name !. STEMCELLS Transl Med. 2017; 6(6): 1445–1451. Publisher Full Text\n\nUllah I, Subbarao RB, Rho GJ: Human mesenchymal stem cells - current trends and future prospective. Biosci Rep. 2015; 35(2): 1–18. PubMed Abstract | Publisher Full Text\n\nSriramulu S, Banerjee A, Di Liddo R, et al.: Concise review on clinical applications of conditioned medium derived from human umbilical cord-mesenchymal stem cells (UC-MSCS). Int J Hematol Stem Cell Res. 2018; 12(3): 229–233.\n\nFamian MH, Saheb SM, Montaseri A: Conditioned Medium of Wharton’s jelly derived stem cells can enhance the cartilage specific genes expression by chondrocytes in monolayer and mass culture systems. Adv Pharm Bull. 2017; 7(1): 123–130. PubMed Abstract | Publisher Full Text\n\nPawitan JA: Prospect of stem cell conditioned medium in regenerative medicine. Biomed Res Int. 2014; 2014: 7–9. PubMed Abstract | Publisher Full Text\n\nMuhammad SA, Nordin N, Mehat MZ, et al.: Comparative efficacy of stem cells and secretome in articular cartilage regeneration: a systematic review and meta-analysis. Cell Tissue Res. 2019; 375(2): 329–344. PubMed Abstract | Publisher Full Text\n\nTan B: Guidelines on the Care and Use of Animals for Scientific Purposes. Naional Advis Comm Lab Anim. 2004; Reference Source\n\nRutgers M, van Pelt MJP , Dhert WJA, et al.: Evaluation of histological scoring systems for tissue-engineered, repaired and osteoarthritic cartilage. Osteoarthr Cartil. 2010; 18(1): 12–23. Publisher Full Text\n\nSoetjahjo B, Hidayat M, Sujuti H, et al.: The significant effect of conditioned medium of umbilical cord mesenchymal stem cells in histological improvement of cartilage defect in Wistar rats. Turkish J Immunol. 2018; 6(2): 57–64. Publisher Full Text\n\nMiyazono K, Koinuma D: Arkadia-beyond the TGF-β pathway. J Biochem. 2011; 149(1): 1–3. PubMed Abstract | Publisher Full Text\n\nFukumoto T, Sperling JW, Sanyal A, et al.: Combined effects of insulin-like growth factor-1 and transforming growth factor-β1 on periosteal mesenchymal cells during chondrogenesis in vitro. Osteoarthr Cartil. 2003; 11(1): 55–64. PubMed Abstract | Publisher Full Text\n\nChen W, Sun Y, Gu X, et al.: Conditioned Medium of mesenchymal stem cells Delays Osteoarthritis Progression in a Rat Model by Protecting Subchondral Bone, Maintaining Matrix Homeostasis and Enhancing Autophagy. J Tissue Eng Regen Med. 2019; 13(January): 1618–1628. Publisher Full Text\n\nPlatas J, Guillén MI, Del Caz MDP, et al.: Conditioned media from adipose-tissue-derived mesenchymal stem cells downregulate degradative mediators induced by interleukin-1 β in osteoarthritic chondrocytes. Mediat Inflamm. 2013; 2013: 1–10. PubMed Abstract | Publisher Full Text\n\nChen Y-C, Tan KP, Shen Y-S, et al.: Can mesenchymal stem cells and their conditioned medium assist inflammatory chondrocytes recovery? PLoS One. 2018; 13(11): e0205563. PubMed Abstract | Publisher Full Text\n\nBlaney Davidson EN, van der Kraan PM , van den Berg WB : TGF-β and osteoarthritis. Osteoarthr Cartil. 2007; 15(6): 597–604. Publisher Full Text\n\nFortier LA, Barker JU, Strauss EJ, et al.: The role of growth factors in cartilage repair. Clin Orthop Relat Res. 2011; 469(10): 2706–2715. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "167437",
"date": "28 Mar 2023",
"name": "William Mark Erwin",
"expertise": [
"Reviewer Expertise molecular biology",
"mass spectroscopy",
"intervertebral disc biology",
"stem cell biology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI struggle with the methods and subsequent mass spec analysis due largely to errors/lack of specifics in the methods section. I have no way of knowing if the bands on the SDS PAGE gel are from the MSCs or held over from the FBS that was in the media originally. DMEM (unless specifically produced to be FBS deficient commonly has FBS contaminants and will provide spurious results on SDS PAGE gels. I do not see any attempts to demonstrate that the bands observed are solely from the conditioned medium. The SDS PAGE gel containing the conditioned medium clearly has multiple bands (although more faint), how is this explained? Subsequent conclusions are difficult to accept without more details verifying that there are no artifacts in the proteins analyzed by SDS PAGE and mass spec.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11699",
"date": "05 Jun 2024",
"name": "Bintang Soetjahjo",
"role": "Author Response",
"response": "Thank you for the review, we will revised the picture of SDS PAGE gel"
}
]
},
{
"id": "187986",
"date": "07 Sep 2023",
"name": "Girish Pattappa",
"expertise": [
"Reviewer Expertise Meniscus",
"Cartilage",
"Regenerative Medicine",
"Osteoarthritis",
"Animal models",
"Hypoxia",
"Mechanobiology."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors of the article have investigated the role of secretomic factors that could influence chondrogenic differentiation of mesenchymal stem cells (MSCs). In this particular case, umbilical cord MSCs secretome was analysed using combined SDS-Page/mass spectroscopy and Mascot sequencing. The dominant band correlated with the Arcadia protein and in silico/docking showed that this interacted with TGF-β1 and its receptors.\nThe authors need to consider the following in their revision.\nIn agreement with the previous reviewer, the methodology for the mass spectroscopy and subsequent gel is difficult to ascertain the particular band corresponding to Arkadia. What were the specific peptides evaluated in the mass spectroscopy analysis and how was the Arkadia band shown in the present figure ?\n\nThe conditioned media used in the experiments was from monolayer culture and rat umbilical cord MSCs. How is this comparable to human cell secretome and pellet or micromass culture that are nominally used for MSC chondrogenesis ? An independent analysis of human MSC secretome should be conducted to show that these are comparable.\n\nThe authors should perform a MSC chondrogenesis study to understand the expression of Arkadia protein in these cultures to show that its expressed during this process.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11700",
"date": "05 Jun 2024",
"name": "Bintang Soetjahjo",
"role": "Author Response",
"response": "Thank you for the review, we will revised the picture of SDS PAGE gel"
}
]
}
] | 1
|
https://f1000research.com/articles/11-972
|
https://f1000research.com/articles/13-36/v1
|
08 Jan 24
|
{
"type": "Research Article",
"title": "Evaluation of role of Tigecycline among clinically significant multidrug resistant pathogens from a tertiary care hospital",
"authors": [
"Annapoorna Remash",
"Pooja Rao",
"Suchitra Shenoy",
"Shrikala Baliga",
"Shafir Kassim",
"Annapoorna Remash",
"Suchitra Shenoy",
"Shrikala Baliga",
"Shafir Kassim"
],
"abstract": "Background Tigecycline, a glycylcycline antibiotic is a promising option for the treatment of single or multidrug resistant pathogens. The aim of the study was to evaluate the in-vitro Tigecycline susceptibility of various pathogens from clinical samples received at the tertiary care hospitals in South India.\n\nMethods The analysis of specimens from patients admitted were carried out in this prospective cross sectional study. The identification and antimicrobial susceptibility testing was performed by semi-automated Vitek 2 systems and Kirby Bauer method. Pattern of data analysis was done by descriptive statistics.\n\nResults Among 2574 isolates, 812 isolates were gram positive pathogens and 1762 isolates were gram negative pathogens. Resistance to Tigecycline was more common among gram negative pathogens (18.62%) in comparison to the gram positive pathogens (0.49%). Among 740 Extended Spectrum Beta Lactamases (ESBL) producers such as Klebsiella species & E coli, 629 isolates were susceptible, and 93 isolates were resistant to the tigecycline. All the methicillin resistant Staphylococcus aureus (MRSA) isolates were susceptible to tigecycline.\n\nConclusion Multidrug resistant (MDR) pathogens like Acinetobacter species, and Klebsiella species were found to be highly effective in vitro to tigecycline for elimination of infections caused by both gram positive and gram negative pathogens. The use of combination therapy becomes crucial to prevent the development of Pan Drug resistance.",
"keywords": [
"Tigecycline",
"MRSA treatment",
"Extended Spectrum Beta Lactamases",
"Multi Drug Resistant treatment"
],
"content": "Introduction\n\nTigecycline is the first novel broad spectrum glycylcycline antibiotic. It belongs to the class of protein synthesis inhibitor and is bacteriostatic in its action.1 Although tigecycline is structurally related to minocycline, alterations to the molecule resulted in its expanded spectrum of activity and decreased susceptibility to the development of resistance when compared to other tetracycline antibiotics.2 They are administered intravenously. The vast increase in the rate of antibiotic resistant bacteria such as Staphylococcus aureus, Acinetobacter baumannii, and Escherichia coli has led to the development of tigecycline.2 Being a tetracycline derivative the therapeutic activity of tigecycline has been expanded to include both gram positive and gram negative organisms including multidrug resistant organisms.1–3 It exhibits strong in vitro activity against gram positive, gram negative, aerobic, anaerobic and atypical bacterial species including antibiotic resistant strains.4 Due to the limited therapeutic options, the treatment of life threatening infections caused by multidrug resistant pathogens becomes a challenge.4–6 The drug has its niche in therapy of pan drug resistant (PDR) organisms due to minimum drug-drug interactions, organ toxicity, handy twice daily dosing and absence of monitoring renal functions tests.7\n\nResistance-nodulation-cell division (RND)-type transporters and other efflux pump systems has been observed as mechanism for development of resistance in E. coli and Klebsiella spp.8 In this retrospective study, we analyzed the antibiotic susceptibility pattern of all the clinically significant gram positive and gram negative aerobic bacteria towards tigecycline. The study was designed to warrant the surveillance of tigecycline susceptibility among diverse species of bacteria from the clinical samples.\n\n\nMethods\n\nThis was a retrospective study conducted at Department of Microbiology, Kasturba Medical College Hospitals, Mangalore. The data of all clinically significant isolates from specimen such as pus, wound tissue, respiratory samples, blood and body fluids from consecutive patients over a period of one year from January 2021 to December 2021 were included in the study. Urine samples have been excluded from the study due to poor drug urine concentration of tigecycline.\n\nThe study began after the approval from Institutional Ethics Committee (IEC), KMC, Mangaluru (Reg No: IEC KMC MLR02-2020/107). The IEC has waved off the patient informed consent as it is a retrospective lab based study and also granted permission to share the data in an open repository system. The study is in agreement with Helsinki declaration, and Laboratory Information System (LIS) and microbiology records were accessed with written permission from the microbiology department incharge.\n\nThe comprehensive data which includes 2574 clinically significant isolates were retrieved from readily available data in the Laboratory Information System and microbiology records and analyzed during a two month period. The data information was collected from medical records and the experiments which were already conducted in the laboratory. The antibiotic susceptibility pattern data records which were carried out by The VITEK® 2 Compact (biomerieux, USA), a semi-automated method and Kirby-Baurer disk diffusion method and interpreted as sensitive, intermediate and resistant as per the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Food and drug administration guidelines respectively were compiled and analyzed. EUCAST criteria with the interpretation of minimum inhibitory concentration (MIC) which ranged from 0.06 to 64 μg /ml where MIC of tigecycline for Enterobacteriaciae <2 μg /ml is sensitive and >8 μg/ml was considered resistant.9 For the Kirby-Baurer disk diffusion method with Tigecycline disk 15 μg (Hi-Media, India), the isolates with >19 mm zone diameter were considered sensitive while <14 mm as resistant strains.10 Data records of all the Staphylococcus aureus isolates for Methicillin resistance using the cefoxitin disk method or by Vitek 2 compact system and gram negative Enterobacterales data for ESBL production using ceftazidime and ceftazidime clavulunic acid or Vitek 2 compact systems were analysed. Descriptive statistics data analysis was done by entering the data into an Excel version 2308 (RRID:SCR_016137) sheet and analyzed using IBM SPSS (RRID:SCR_002865) version 25. The continuous and categorical variables have been represented as mean ± standard deviation and frequency percentages respectively.\n\n\nResults\n\nOut of 2574 patient’s data analyzed, 64% were males and 36% were females. The tigecycline susceptibility was similar among both of these groups approximating to 85%. Resistance to tigecycline was more common among males (13.58%) than females (11.67%) where the difference is not significant.\n\nIsolates from children in the age group 0-10 were more susceptible to tigecycline (95.38%), as the age increases there is trend for decreasing susceptibility to tigecycline (Figure 1). Among the samples, resistance to tigecycline was most common in isolates from cerebrospinal fluid (CSF) samples (44.44%) and high susceptibility was seen in blood, body fluids (93%) and pus (91%) (Table 1).11\n\nTigecycline demonstrates potent in vitro activity against most relevant pathogens. The gram negatives and gram positives such as E. coli (n=471, 99.5%) and S. aureus (n=480, 100%) displayed potent activity to tigecyclines respectively followed by Enterococcus spp. (n=77, 98.7%), Acinetobacter spp. (n=296, 88%) and Klebsiella spp. (n=401, 74.5%) with exceptions to Pseudomonas species & Proteus species (Table 2).11\n\nAmongst 740 ESBL producers, which includes 368 Klebsiell species and 363 Escherichia coli, 99.72% of ESBL producing E.coli had higher susceptibility to tigecycline. Resistance to tigecycline was more common among ESBL Klebsiella species (25%), than in E.coli (0.28%). In 481 isolates of Staphylococcus aureus, 212 isolates were methicillin resistant Staphylococcus aureus (MRSA) and 269 isolates were methicillin sensitive Staphylococcus aureus (MSSA). All of the 212 MRSA isolates (100%) were susceptible to tigecycline.11\n\nSusceptibility to tigecycline was higher in gram positive (99.5%) with MIC (≤ 0.12 μg) in comparison to gram negative pathogens (78%) (Table 3). The MIC for tigecycline ranged from ≤ 0.12 to 2 μg/ml for 91% of isolates which were in the susceptible range, while 8% gram negatives isolates had MIC ≥ 8 μg which were resistant and among them 3% of them were Klebsiella species.11\n\n\nDiscussion\n\nTigecycline is an effective alternative drug of choice for the treatment of infections caused by MDR gram negative pathogens and MRSA.12 The susceptibility trend changed as the age increased probably due to use of antimicrobial agents and previous exposure over the years to antibiotics such as Carbepenems.13 In our study, out of 481 Staphylococcus aureus isolates all (100%) were susceptible to tigecycline. Among these 212 (44.07%) isolates were MRSA which has shown 100% susceptibility to tigecycline. This is consistent with studies conducted by Bijayini Behera et al., in an Indian tertiary care hospital.12 In their study, 21 MRSA isolates were analyzed to detect tigecycline susceptibility pattern. All the 21 isolates were suscetible to tigecycline. In a study conducted by Manisha et al., to analyze tigecycline susceptibility pattern among MDR bacteria in a tertiary care hospital, 35 MRSA isolates were subjected to assay of which all isolates had shown susceptibility to tigecycline which is also consistent with the results from this study.14 Hence, this indicates that tigecycline can be used as a therapeutic alternative for treating infections caused by MRSA and ESBL producing MDR pathogens especially in intraabdominal skin & soft tissue infections where the penetration of the drug is high at these sites when compared to blood and respiratory tract. Though the susceptibility is high in blood but the usage of tigecycline is questionable as the volume of distribution of the drug in blood is low.10\n\nThe most common antibiotic resistance mechanism evolving among the family Enterobacterales is through the development of ESBL production.15 In our study, the 538 Klebsiella isolates which includes 476 (88.48%) Klebsiella pneumoniae, 6 (1.12%) Klebsiella oxytoca and 56 (10.40%) isolates were identified as Klebsiella spp. Among the Klebsiella pneumoniae isolates, 350 (73.53%) were found to be susceptible to tigecycline, 13 (2.73%) isolates were found to show intermediate sensitivity and 113 (23.74%) isolates were resistant to tigecycline. Anand Manoharan et al., conducted a study to evaluate tigecycline activity in clinical isolates among Indian medical centers in which 120 Klebsiella spp. were analyzed.16 In their study all the isolates were found to be susceptible to tigecycline which is not consistent with our study. In studies conducted by Simit Kumar et al., 100%, Bijayini Behera et al., 97% and Soham Gupta et al., 85.7%, Kusuma GR et al., 97.14% sensitivity towards tigecycline while reduced susceptibility was noted in this study.12,17–19 Over a decade, reduced susceptibility towards tigecycline has been noted. It was also noted that in a study performed by Subhash C Arya et al 66% isolates were found to be susceptible to tigecycline.20\n\nAmong the Enterobacterales, Klebsiella species showed higher resistance with MIC>2 ug/ml in 25% of the isolates. In studies conducted by Nandi P et al., 21 isolates were ESBL producers out of which only 1 (4.76%) was resistant to tigecycline which is not consistent with the present study.2\n\nIn our study, out of the 473 E. coli isolates, 471 showed good susceptibility to tigecycline with 99.58% being sensitive and having MIC between ≤0.5 to 2 μg/ml. The data of higher E. coli susceptibility than Klebsiella spp. was similar in another study.20 Out of these, 363 (76.74%) isolates were ESBL producers of which only 1 (0.28%) isolate was resistant to tigecycline and 362 (99.72%) isolates were found to be sensitive to tigecycline. Tigecycline has decreased in vitro activity or intrinsically resistant to Pseudomonas spp., Morganella spp., Proteus spp. and Providencia spp.21\n\n\nConclusions\n\nTigecycline is a newly introduced antibiotic used mainly in the treatment of infections caused by multidrug resistant organisms. Tigecycline is active against the most frequently encountered pathogens including Klebsiella species, E.coli, Staphylococcus aureus, Acinetobacter species, CONS, Enterobacter species and Streptococcus species. Tigecycline has shown excellent in vitro activity against ESBL producing pathogens and MRSA isolates. The usage of tigecycline should be monitored routinely so as to track the development of resistance. It should be used as a reserve antibiotic to treat life threatening infections as a combination regimen with other antibiotics and also in infections caused by MDR bacteria.",
"appendix": "Data availability\n\nDryad: Tigecycline among clinically significant multidrug resistant pathogens. https://doi.org/10.5061/dryad.sqv9s4n6z. 11\n\nThis project contains the following underlying data:\n\n- Dryad_Data_Collection.xlsx\n\nDryad: Tigecycline among clinically significant multidrug resistant pathogens. https://doi.org/10.5061/dryad.sqv9s4n6z. 11\n\nThis project contains the following underlying data:\n\n- README_file.txt.txt (The file includes the title with the authors who have made contributions to the study, duration, location, funding and sharing and access information)\n\nData are available under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.\n\n\nReferences\n\nRose WE, Rybak MJ: Tigecycline: first of a new class of antimicrobial agents. Pharmacotherapy. Aug 2006; 26(8): 1099–1110. Publisher Full Text\n\nNandi P, Sk C: Original article In vitro susceptibility pattern of Tigecycline against MRSA, ESBL producing Escherichia coli, Klebsiella species and Acinetobacter isolates in a rural tertiary care hospital. Int. J. Med. Dent. Sci. 2021; 4: 607–617. Publisher Full Text\n\nSohail M, Rashid A, Aslam B, et al.: Antimicrobial susceptibility of Acinetobacter clinical isolates and emerging antibiogram trends for nosocomial infection management. Rev. Soc. Bras. Med. Trop. May-Jun 2016; 49(3): 300–304. PubMed Abstract | Publisher Full Text\n\nMuralidharan G, Micalizzi M, Speth J, et al.: Pharmacokinetics of tigecycline after single and multiple doses in healthy subjects. Antimicrob. Agents Chemother. May-Jun 2016; 49(1): 220–229.\n\nShanthi M, Sekar U: Multi-drug resistant Pseudomonas aeruginosa and Acinetobacter baumannii infections among hospitalized patients: risk factors and outcomes. J. Assoc. Physicians India. 2009; 57: 636. 638-40, 645. PubMed Abstract\n\nBlondeau JM: Tigecycline an overview and update. Therapy. 2009; 6: 851–870. Publisher Full Text\n\nNabarro LE, Veeraraghavan B: Combination therapy for carbapenem-resistant Enterobacteriaceae: increasing evidence, unanswered questions, potential solutions. Eur. J. Clin. Microbiol. Infect. Dis. 2015; 34(12): 2307–2311. PubMed Abstract | Publisher Full Text\n\nRoy S, Datta S, Viswanathan R, et al.: Tigecycline susceptibility in Klebsiella pneumoniae and Escherichia coli causing neonatal septicaemia (2007–10) and role of an efflux pump in tigecycline non-susceptibility. J. Antimicrob. Chemother. 2013; 68(5): 1036–1042. PubMed Abstract | Publisher Full Text\n\nBreakpoint Tables for Interpretation of MICs and Zone Diameters, The European Committee on Antimicrobial Susceptibility Testing (EUCAST) Version 7.1.2017.\n\nUS FDA approved guidelines for use of Tigecycline 2019.\n\nRao P: Tigecycline among clinically significant multidrug resistant pathogens. Dataset. Dryad. 2023. Publisher Full Text\n\nBehera B, Das A, Mathur P, et al.: Tigecycline susceptibility report from an Indian tertiary care hospital. Indian J. Med. Res. April 2009; 129: 446–450. PubMed Abstract\n\nPark GE, Kang CI, Cha MK, et al.: Bloodstream infections caused by Acinetobacter species with reduced susceptibility to tigecycline: clinical features and risk factors. Int. J. Infect. Dis. 2017; 62: 26–31. PubMed Abstract | Publisher Full Text\n\nManisha M, Nita G: In vitro activity of tigecycline against MRSA and Vancomycin resistant Enterococci as evaluated by disc diffusion method and E-test. Int. J. Collab. Res. Intern. Med. Public. Health. 2013; 5(8): 567.\n\nSouli M, Kontopidou FV, Koratzanis E, et al.: In vitro activity of tigecycline against multiple-drug-resistant, including pan-resistant, Gram-negative and Gram-positive clinical isolate from Greek hospitals. Antimicrob. Agents Chemother. 2006; 50: 3166–3169. PubMed Abstract | Publisher Full Text | Free Full Text\n\nManoharan A, Chatterjee S, Madhan S, et al.: Evaluation of tigecycline activity in clinical isolates among Indian medical centers. Indian J. Pathol. Microbiol. 2010; 53: 734–737. PubMed Abstract | Publisher Full Text\n\nKumar S, Bandyopadhyay M, Mondal S, et al.: Tigecycline activity against metallo-β-lactamase-producing bacteria. Avicenna J. Med. Oct-Dec 2013; 3(4): 92–96. PubMed Abstract | Publisher Full Text\n\nGupta S, Aruna C, Nagaraj S, et al.: In vitro activity of tigecycline against multidrug-resistant Gram-negative blood culture isolates from critically ill patients. J. Antimicrob. Chemother. May 2012; 67(5): 1293–1295. PubMed Abstract | Publisher Full Text\n\nKusuma GR, Tejasree A, Vijay Kumar GS: In vitro susceptibility to tigecycline in multidrug resistant bacteria isolates from a tertiary care hospital. Int. J. Cur. Res. Rev. Oct 2016; 8(19).\n\nArya SC, Nirmala A: Tigecycline in vitro susceptibility and antibiotics fitness for Gram negative pathogens. Saudi Med. J. 01 Nov 2008; 29(11): 1558–1560. PubMed Abstract\n\nKhare V, Gupta P, Haider F, et al.: Study on MICs of Tigecycline in Clinical Isolates of Carbapenem Resistant Enterobacteriaceae (CRE) at a Tertiary Care Centre in North India. J. Clin. Diagn. Res. Mar 2017; 11(3): DC18–DC21. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "275521",
"date": "10 May 2024",
"name": "Gamal Wareth",
"expertise": [
"Reviewer Expertise AMR"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article by Remash et al. stands out for its unique approach to evaluating the role of Tigecycline among clinically significant MDR pathogens from a tertiary care hospital in India. The article included a large number of pathogens collected from different clinical samples. It is well-organized and suitable for publication in this journal. However, a few minor comments are necessary before publication.\nPlease change the gram to Gram all over the text. The manuscript needs little English editing Do you have an explanation for why isolates from children in the age group 0-10 were more susceptible to tigecycline? Please discuss this point. Resistance to Tigecycline is uncommon as it is a new drug and not widely used in developing countries. Several studies showed that even MDR pathogens were susceptible, for example, antibiotic susceptibility testing of the 19 K. pneumoniae strains from patients in Vietnam revealed that all isolates were susceptible to Tigecycline despite they were MDR; Please discuss this paper in discussion (https://doi.org/10.51585/gjm.2024.1.0030)ref 1 , please include more studies from other countries\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11624",
"date": "28 Jun 2024",
"name": "Pooja Rao",
"role": "Author Response",
"response": "The changes on few grammar additions and inclusion of few other articles in the discussion has been made as per the requirements of the reviewer."
}
]
},
{
"id": "252069",
"date": "12 Jun 2024",
"name": "Richa Sinha",
"expertise": [
"Reviewer Expertise Diagnostics",
"Infectious disease",
"Hospital surveillance"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article highlights today's most common problem of Multi-drug resistant bugs. As Tigecycline is active against both Gram positive and Gram negative bacteria's, it's importance lies in it's use against MRSA, VRE and ESBLs. Though antibiogram is given for various isolates recovered and identified from the clinical samples, in the result section, the table does not highlight the percentage of staphylococcus which were identified to be MRSA, same with VRE and ESBLs. The authors are requested to represent the same in tabulated form.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-36
|
https://f1000research.com/articles/13-319/v1
|
23 Apr 24
|
{
"type": "Research Article",
"title": "Effect of different surface treatments on repair bond strength of alkasite based restorative material",
"authors": [
"Tina Puthen Purayil",
"Kishore Ginjupalli",
"Kalyana Pentapati",
"Aastha Dureja",
"Rashmi Nayak",
"Tina Puthen Purayil",
"Kalyana Pentapati",
"Aastha Dureja",
"Rashmi Nayak"
],
"abstract": "Background This study investigates various surface treatment methods to assess shear bond strength between set Cention N (alkasite-based restorative material) and fresh alkasite based restorative material. Assessing different surface treatments provide insights in optimizing repair procedure that enables durability of the restoration, thus potentially benefitting clinical outcomes.\n\nMethods A total of 48 alkasite based restorative material blocks, measuring 4 mm in depth and 8 mm in diameter, were prepared. The samples were randomly divided into 8 groups (n = 6) according to the surface treatment done. Group I: Surface preparation by bur; Group II: Surface treatment by laser; Group III: Application of 2-step etch and rinse adhesive (Adper Single Bond 2 adhesive),Group IV: Application of single step self-etch adhesive (Scotchbond Universal adhesive); Group V: Bur preparation followed by application of 2-step etch and rinse adhesive; Group VI: Bur preparation followed by application of single step self-etch adhesive; Group VII: Laser preparation followed by application of 2-step etch and rinse adhesive; and Group VIII: Laser preparation followed by application of single step self-etch adhesive. Post-surface preparation, all the specimens were restored with freshly mixed alkasite material. All samples were then subjected to repair bond strength measurements using a universal testing machine. ANOVA with post-hoc Games-Howell test and two-way ANOVA with post-hoc Bonferroni test was performed to evaluate the influence of surface preparation on the repair bond strength.\n\nResults Among the various surface treatments, use of a 2-step etch and rinse adhesive resulted in a higher repair bond strength compared to other surface treatments, whereas roughening of the surface using burs resulted in the lowest repair bond strength (P=0.02).\n\nConclusion Application of 2-step etch and rinse adhesive to the existing alkasite based restorative material provides superior bonding with the freshly added alkasite based restorative material.",
"keywords": [
"Alkasite",
"Bond strength",
"Repair",
"Surface treatment"
],
"content": "Introduction\n\nIn the past, complete replacement of restorations was the standard approach for eliminating small defects in restorations. However, complete removal of the restoration followed by preparation of the tooth to receive a fresh restoration weakens the tooth structure, resulting in unnecessary removal of tooth structure and, in some cases, irreversible injury to the dental pulp. Even in the absence of secondary caries or discoloration at the tooth-restoration interface, repair is suggested instead of complete replacement of the restoration, primarily because of its conservative approach. Thus, repair of the restoration is an effective approach to enhance the longevity of the restorations.1–4 In addition, durability of the repaired restorations is equivalent to that of replacement of the restorations.5 However, the success or failure of such a process is dependent on the bond strength between the old and the new restorative materials at their interface, which is affected by a myriad of parameters, including surface treatment of the old restoration before placement of new restorative material.\n\nVarious methods that alter the physical and chemical features of the surfaces of old restorative materials have been employed to improve the bond strength between the existing and new restorative materials. These include surface preparation using a bur, laser, air abrasion with aluminum oxide particles, pre-treatment of the surface with silane, and the use of resin-based adhesive systems along with different primers.6–8\n\nAlkasite is a tooth-colored restorative material (Cention® N, Ivoclar Vivadent Liechtenstein), widely used for deciduous and permanent restorations of Class I, II, and V carious lesions.9 Manufacturers and recent research indicate that it exhibits flexural strength comparable to that of silver amalgam, along with superior handling characteristics.9,10\n\nAs this material is recently introduced, data on the clinical performance and survival or clinical service life of the material along with the type of failure of the material in a variety of clinical conditions are not widely available. However, in the event of failure of such restorations, in the form of dislodgement or fracture of the material, it is important to establish a suitable repair method.\n\nMost surface treatment methods aim to increase surface area of the bonding between the two materials to promote the interaction between the aged and fresh restorative materials thus improving the bond strength. However, literature on the effect of surface treatment on the bond strength between the old and new alkasite based restorative materials is not available. Hence, the main aim of this study was to evaluate the effect of various surface treatments on the repair bond strength between old and new alkasite based restorative materials.\n\n\nMethods\n\nA total of 48 acrylic blocks (4 cm height × 2 cm width) were prepared using a self-cure acrylic resin. After the polymerization and aging of the acrylic blocks for 24 h, a cylindrical hole of 4 mm × 4 mm was drilled on one side of the acrylic block.\n\nAlkasite based material powder was weighed using an electronic balance and added to a pre-weighed quantity of liquid at a ratio of 4.6:1, as recommended by the manufacturer. Both the powder and liquid were mixed with a plastic spatula for 30 s to obtain a thick putty-like consistency suitable for packing. The material was packed into the holes in the acrylic block, and curing was performed for 20 s using a Light Emitting Diode (LED) light curing unit at 850 mW/cm2 (3M ESPE Elipar, St Paul, USA). The specimens were then stored in distilled water at 37°C for one month.\n\nAfter the aging process, the acrylic blocks containing alkasite based material were randomly divided into eight groups (n=6) and subjected to either of the following surface treatments: Table 1 describes the various methods used for surface preparation across the different groups.\n\nGroup I (Bur): The surface of alkasite based material was roughened using a TR 11 diamond bur (Mani, Tochigi, Japan) with a high-speed handpiece under water spray. Bur was replaced after surface preparation of five specimens.\n\nGroup II (Laser): The alkasite based material surface was irradiated by an Er;Cr:YSGG laser (Waterlase, Biolase Technology, Sanclemente, CA, USA) at 2780 nm wavelength at 3 W output power and 20 Hz frequency of 60μsec duration. A laser tip was used with a gentle sweeping motion at a working length of 1 mm with a spot size of 800μm (MZ-8 Ziptip, Biolase) under a water spray.\n\nGroup III (ASB2): The surface of alkasite based material was treated with 2 step etch and rinse adhesive where the specimen was first etched with 37% phosphoric acid (Ivoclar Vivadent, USA) for 15 s, followed by rinsing for 10 s with water and air drying. Subsequently, two coats of adhesive (Adper Single Bond 2, 3M ESPE St Paul MN, USA) were applied to the etched surfaces of alkasite based material with gentle agitation, followed by air blowing of the excess adhesive to leave a thin film. This was followed by light-curing of the adhesive for 10 s using an LED light-curing unit.\n\nGroup IV (SBUA): The surface of alkasite based material was treated with a single step self etch adhesive (Scotchbond Universal Adhesive, 3M ESPE, St Paul, MN, USA) using a microbrush for 20s, thinned by mild air pressure for 5 s, followed by light-curing of the adhesive for 10 s using an LED light-curing unit.\n\nGroup V (Bur+ASB2): The alkasite based material surface was roughened as described for Group I, followed by application of 2-step etch and rinse adhesive as described for Group III.\n\nGroup VI (Bur+SBUA): The alkasite based material surface was roughened as described for Group I, followed by application of a single step self-etch adhesive as described for Group IV.\n\nGroup VII (Laser+ASB2): The alkasite based material surface was laser-irradiated as described for Group II, followed by application of 2-step etch and rinse adhesive as described for Group III.\n\nGroup VIII (Laser+SBUA): The alkasite based material surface was laser-irradiated as described for Group II, followed by application of a single step self-etch adhesive as described for Group IV.\n\nAfter the completion of the surface preparation of alkasite based material as described above, a freshly mixed alkasite based material as per the manufacturer’s instructions was build up to a height of 4 mm. Subsequently, the material was cured using LED light curing for 40 s. After the curing, samples were stored in distilled water for 24 h.\n\nThe repair bond strength was evaluated in shear mode. The samples were fastened to the lower half of a universal testing machine (Model 3366; Instron Corp., USA). A compressive load was applied at a loading rate of 0.5 mm/min at the interface between the old and new alkasite based materials until debonding. The maximum load observed during the test, divided by the area of the specimen, was reported as the repair bond strength in MPa (n=6).\n\nData were analyzed using SPSS version 20. Statistical significance was set at P<0.05. Normality was tested using the Shapiro-Wilk test. Mean values were compared using ANOVA with post-hoc Games-Howell test. A two-way ANOVA with post-hoc Bonferroni test for inter-group comparisons was performed to evaluate the role of surface preparation and adhesive application on the repair bond strength. The data for this study are available in Figshare.11\n\n\nResults\n\nThere was a significant difference in the mean repair bond strength between the eight groups (P=0.02). Post-hoc tests showed that Group III (ASB2) and Group VII (Laser+ASB2) had significantly higher mean repair bond strengths than Group I (Bur). No other significant differences were observed between groups (Table 2). Two-way ANOVA was used to evaluate the role of surface preparation and adhesive application on repair bond strength. Levene’s test showed no significant differences in variance across groups (P=0.25). There was no significant interaction between the type of adhesive and surface preparation (P=0.121). The main effects showed that the type of adhesives showed a significant difference on the repair bond strength (P=0.01), whereas no significant difference was observed with respect to the surface preparation. The estimated marginal means for Group III (ASB2) were significantly higher than compared to those without adhesives (P=0.003), whereas no other significant differences were observed with respect to adhesives on the repair bond strength.\n\n\nDiscussion\n\nFailure of dental restorations or the need for retreatment is not uncommon in routine dental practice. In such cases, re-restoration is a standard procedure aimed at repairing and restoring the tooth to its natural form and function. The surface of the existing restoration is prepared using a variety of methods to enhance its bonding with freshly placed restoration material, which can influence the bond strength between the two materials, impacting the longevity of the repair.12,13\n\nAlkasite restorative material is a new category of filling materials based on urethane dimethacrylate (UDMA) resin. It is supplied as a self-curing powder/liquid formulation, along with optional light curing. Its ability to effectively polymerize to complete depth of the restoration leads to a high polymer network density in the material. This could be attributed to the sole use of the cross-linking methacrylate monomer, along with a stable, efficient self-cure initiator.9 The existing literature is scarce in terms of the methods to be followed to achieve superior bonding between the existing restorative material and fresh material in case of repair. Thus, the present study aimed to investigate the effect of different surface treatments on the repair bond strength between existing and new alkasite based restorative materials.\n\nThe results of the present study indicate that the use of adhesive results in a superior repair bond strength. This was in accordance with a study conducted on composites14 where the use of adhesive proved to be a conservative and effective treatment approach for the repair of restorative materials. Among the two adhesive systems, the highest repair bond strength was observed with the application of 2-step etch and rinse adhesive. Among the various surface treatments evaluated in the present study, surface preparation using burs resulted in the lowest repair bond strength.\n\n2-step etch and rinse adhesive is a fifth generation bonding agent that employs a separate etching step prior to the application of adhesive. A separate etching process followed by rinsing would have helped in cleaning the surface of the restoration and increased its surface roughness, leading to an increase in the surface area of the bonding, better wettability of the adhesives, and leading to superior repair bond strength. A similar improvement in bond strength has been reported in previous investigations.15,16\n\nSingle step self-etch adhesive, a seventh generation dentin bonding agent, on the other hand, is a hydrophilic multipurpose and all-in-one adhesive that does not require an additional etching step. Despite its ease of use, it showed less favorable repair bond strength than 2-step etch and rinse adhesive. The absence of a separate etching step, which is generally followed by washing would not result in the exposure of a clean surface with an enhanced surface area needed for superior bonding. In addition, the hydrophilicity of the adhesive may interfere with the durability of the interfacial bond repair because hydrophilic adhesives tend to absorb more water over time, resulting in hydrolytic degradation. Secondly, when universal adhesives with etchant action are applied to enamel or dentin, the buffering capacity of the dental hard tissue neutralizes its acidity.17 In contrast, during the repair of alkasite based material, the acidic resin monomer was not neutralized because of the absence of apatite, which may have resulted in inadequate polymerization of the freshly prepared restorative material.18\n\nEr;Cr:YSGG laser was employed in this study because of its effectiveness in ablating restorative surfaces using highly energized water molecules.19 Despite its effectiveness over other lasers in restorative repair, the present study did not show superior repair bond strength. This could be due to the inability of the highly viscous alkasite based material to flow into irregularities created by the laser. Despite both etchant and laser rendering the surface of the restoration rough by varying degrees, the use of etchant followed by application of adhesive resulted in better repair bond strength. This could be due to the better flowability of the adhesive, which provided higher micromechanical retention of the restorative material.20\n\nThe use of burs resulted in the least favorable results in terms of the repair bond strength. To ensure a close adaptation of the aged and freshly mixed alkasite based material, there is a need for an intermediate material, as the freshly mixed material may not properly wet the aged alkasite based material, making it difficult to achieve the bond. The adhesives help in penetrating into the irregularities and optimizing the bond that would otherwise be difficult due to the high viscosity and low wetting potential of the restorative material.21,22 Though studies have shown that the use of burs for restorative repair is comparable to that of lasers,23 the smear layer produced after the use of burs could have also contributed to the poor repair bond strength.\n\n\nConclusions\n\nBased on the results of the present study, it can be concluded that repair of alkasite based restorative material with the use of 2-step etch and rinse adhesive resulted in superior bond strength. However, surface roughening techniques such as using a bur or laser irradiation did not show significant improvement in the bond strength.",
"appendix": "Data availability statement\n\nUnderlying data is available in Figshare at the following link:\n\nhttps://doi.org/10.6084/m9.figshare.25488814.v2. 11\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nThe authors extend their appreciation to Dr. Vasudev Ballal for his contribution in offering insights into shaping the study design.\n\n\nReferences\n\nÖzcan M, Barbosa SH, Melo RM, et al.: Effect of surface conditioning methods on the microtensile bond strength of resin composite to composite after aging conditions. Dent. Mater. 2007 Oct [cited 2024 Feb 7]; 23(10): 1276–1282. PubMed Abstract | Publisher Full Text\n\nFernández E, Martín J, Vildósola P, et al.: Can repair increase the longevity of composite resins? Results of a 10-year clinical trial. J. Dent. 2015 [cited 2024 Feb 7]; 43(2): 279–286. PubMed Abstract | Publisher Full Text\n\nGordan VV, Riley JL, Geraldeli S, et al.: Repair or replacement of defective restorations by dentists in the dental practice-based research network. J. Am. Dent. Assoc. 2012 [cited 2024 Feb 7]; 143(6): 593–601. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLucena-Martín C, González-López S, Navajas-Rodríguez De Mondelo JM: The effect of various surface treatments and bonding agents on the repaired strength of heat-treated composites. J. Prosthet. Dent. 2001 [cited 2024 Feb 7]; 86(5): 481–488. PubMed Abstract | Publisher Full Text\n\nKanzow P, Wiegand A: Retrospective analysis on the repair vs. replacement of composite restorations. Dent. Mater. 2020 Jan 1 [cited 2024 Feb 7]; 36(1): 108–118. PubMed Abstract | Publisher Full Text\n\nMartin J, Fernandez E, Estay J, et al.: Minimal invasive treatment for defective restorations: five-year results using sealants. Oper. Dent. 2013 Mar [cited 2024 Feb 7]; 38(2): 125–133. PubMed Abstract | Publisher Full Text\n\nBouschlicher MR, Reinhardt JW, Vargas MA: Surface treatment techniques for resin composite repair. Am. J. Dent. 1997 [cited 2024 Feb 7]; 10(6): 279–283. PubMed Abstract\n\nBonstein T, Garlapo D, Donarummo J, et al.: Evaluation of varied repair protocols applied to aged composite resin. J. Adhes. Dent. 2005 [cited 2024 Feb 7]; 7(1): 41–49. PubMed Abstract\n\nCention N (Powder-liquid filling material): Ivoclar Vivadent AG.[cited 2024 Feb 7]. Reference Source\n\nMishra A, Singh G, Singh S, et al.: Comparative Evaluation of Mechanical Properties of Cention N with Conventionally used Restorative Materials—An in vitro Study. Int. J. Prosthodont Restor. Dent. 2018 Dec [cited 2024 Feb 7]; 8(4): 120–124. Publisher Full Text\n\nPurayil TP, Ginjupalli K: Bond strength of Polyalkasite cements with various surface preparations.2024\n\nŞişmanoğlu S, Gürcan AT, Yıldırım-Bilmez Z, et al.: Efficacy of different surface treatments and universal adhesives on the microtensile bond strength of bulk-fill composite repair. J. Adhes. Sci. Technol. 2020 May 18 [cited 2024 Feb 7]; 34(10): 1–13. Publisher Full Text\n\nEliasson ST, Tibballs J, Dahl JE: Effect of different surface treatments and adhesives on repair bond strength of resin composites after one and 12 months of storage using an improved microtensile test method. Oper. Dent. 2014 Sep 1 [cited 2024 Feb 7]; 39(5): E206–E216. PubMed Abstract | Publisher Full Text\n\nBlum IR, Lynch CD, Wilson NHF: Factors influencing repair of dental restorations with resin composite. Clin. Cosmet. Investig. Dent. 2014 [cited 2024 Feb 7]; 6: 81–87. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPamir T, Şen BH, Evcin Ö: Effects of etching and adhesive applications on the bond strength between composite resin and glass-ionomer cements. J. Appl. Oral Sci. 2012 [cited 2024 Feb 7]; 20(6): 636–642. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFurtado MD, Immich F, da Rosa WL d O , et al.: Repair of aged restorations made in direct resin composite – A systematic review. Int. J. Adhes. Adhes. 2023; 124: 103367. Elsevier. Publisher Full Text\n\nCamps J, Pashley DH: Buffering action of human dentin in vitro. J. Adhes. Dent. 2000 [cited 2024 Feb 7]; 2(1): 39–50. PubMed Abstract\n\nSanares AME, Itthagarun A, King NM, et al.: Adverse surface interactions between one-bottle light-cured adhesives and chemical-cured composites. Dent. Mater. 2001 [cited 2024 Feb 7]; 17(6): 542–556. PubMed Abstract | Publisher Full Text\n\nIaria G: Clinical, morphological, and ultrastructural aspects with the use of Er:YAG and Er,Cr:YSGG lasers in restorative dentistry. Gen. Dent. 2008 [cited 2024 Feb 7]; 56(7): 636–639. PubMed Abstract\n\nHickel R, Brüshaver K, Ilie N: Repair of restorations - Criteria for decision making and clinical recommendations. Dent. Mater. 2013 [cited 2024 Feb 7]; 29: 28–50. PubMed Abstract | Publisher Full Text\n\nHannig C, Hahn P, Thiele PP, et al.: Influence of Different Repair Procedures on Bond Strength of Adhesive Filling Materials to Etched Enamel In Vitro. Oper. Dent. 2003 [cited 2024 Feb 7]; 28(6): 800–807. PubMed Abstract\n\nCavalcanti AN, De Lima AF, Peris AR, et al.: Effect of surface treatments and bonding agents on the bond strength of repaired composites. J. Esthet. Restor. Dent. 2007 Apr [cited 2024 Feb 7]; 19(2): 90–98. Publisher Full Text Reference Source\n\nKimyai S, Mohammadi N, Navimipour EJ, et al.: Comparison of the Effect of Three Mechanical Surface Treatments on the Repair Bond Strength of a Laboratory Composite. Photomed. Laser Surg. 2010 Oct 1 [cited 2024 Feb 7]; 28(S2): S-25–S-30. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "274360",
"date": "25 May 2024",
"name": "Emad Farhan Alkhalidi",
"expertise": [
"Reviewer Expertise conservative dentistry",
"endodontics",
"crown and bridge"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComments to author(s) Dear authors, The subject is of interest but there are some points should be corrected.\nTitle: Its better to be as \"Effect of different surface treatments on bond strength of repairing alkasite based restorative material\".\nAbstract: The background needs rephrasing for \"This study investigates various surface treatment methods to assess shear bond strength between set Cention N (alkasite-based restorative material) and fresh alkasite based restorative material.(mention N).\"\nMethod l: line 9; Please write the statistics test in sequential manner\n\nResults: Rephrase, \"this is conclusion\"\nMethodology Rephrase first 3 lines, remove \"aging to the acrylic block\". This is not your main work. It causes confusion to reader. Put \"aging\" in line 8, \"the specimens were aging (stored in distilled water at 37c for one month).\" Throughout the paper write manufacturing details for materials and devices. Rewrite statistical analysis tests in sequential manner. Reference 11 in statistical analysis referred to what results? Line 1- \"one way ANOVA showed that there was Levene’s test showed\" you don't write it before Please check the tests of statistical analysis. Table 2 needs more details and explanations.\nReferences: Ref 12, 13 not present in the article. Please check it.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11701",
"date": "06 Jun 2024",
"name": "Tina Purayil",
"role": "Author Response",
"response": "Thanks for the comments. The following edit was done in the manuscript Query1: Title: Its better to be as \"Effect of different surface treatments on bond strength of repairing alkasite based restorative material\". Response 1: Title has been updated accordingly to maintain clarity and integrity “Effect of different surface treatments on the repair bond strength between aged and new alkasite based restorative material” Query 2 Abstract: The background needs rephrasing for \"This study investigates various surface treatment methods to assess shear bond strength between set Cention N (alkasite-based restorative material) and fresh alkasite based restorative material. (mention N).\" Response 2: Abstract background has been rephrased as suggested. To avoid confusion, we have replaced the word “fresh” with “new” Revised text-This study investigates various surface treatment methods to assess shear bond strength between set Cention N (alkasite-based restorative material) and new alkasite based restorative material. Query 3 Method: line 9; Please write the statistics test in sequential manner. Response 3: Shapiro-Wilk and Levene's tests were used to check normality and Homogeneity of variance. Query 4 :Results: Rephrase, \"this is conclusion\" Response 4: The sentence has been edited to “Using a 2-step etch and rinse adhesive resulted in a higher repair bond strength (26.05±2.12) compared to other surface treatments. In contrast, roughening of the surface with burs led to lowest repair bond strength (17.06±3.29) (P=0.02)” Methodology Query 5: Rephrase first 3 lines, remove \"aging to the acrylic block\". This is not your main work. It causes confusion to reader. Put \"aging\" in line 8, \"the specimens were aging (stored in distilled water at 37c for one month).\" Response 5: First three lines has been rephrased and aging repositioned as suggested. Revised text-One-day after the polymerization of the acrylic blocks, a cylindrical hole of 4 mm × 4 mm was drilled on one side of the acrylic block. The specimens were then stored in distilled water at 37°C for one month for aging. Query 6: Throughout the paper write manufacturing details for materials and devices. Response 6: Manufacturing details for materials and devices have been added Self-cure acrylic resin (DPI-RR Cold Cure, DPI, Mumbai, India) High speed handpiece (NSK M25, Nakanishi Inc, Kanuma City, Japan) Query 7: Rewrite statistical analysis tests in sequential manner. Response 7: We have edited it as follows: “Data were analyzed using SPSS version 20 (IBM Corp. Released 2011. IBM SPSS Statistics for Windows, Version 20.0. Armonk, NY: IBM Corp.). Statistical significance was set at P<0.05. Normality was tested using the Shapiro-Wilk test. Based on the normality, and test of homogeneity of the variances (Levene statistic) mean were compared using ANOVA with post-hoc Games-Howell test. Subsequently, a two-way ANOVA with post-hoc Bonferroni test for inter-group comparisons was performed to evaluate the role of surface preparation and adhesive application on the repair bond strength.” Query 8: Reference 11 in statistical analysis referred to what results? Response 8: Reference 11 is the underlying raw data of this research as per journal guidelines. Query 9: Line 1- \"one way ANOVA showed that there was Levene’s test showed\" you don't write it before. Please check the tests of statistical analysis. Response 9: This has been edited as per the comment in Query7. Query 10: Table 2 needs more details and explanations. Response 10: Table 2 has been revised with more details and explanation References: Query 11: Ref 12, 13 not present in the article. Please check it. Response 11: Reference 12 and 13 were cited in the first paragraph of the discussion"
}
]
},
{
"id": "274359",
"date": "30 May 2024",
"name": "Nazmiye Donmez",
"expertise": [
"Reviewer Expertise dental restorative materials",
"fiber-reinforced composite restorations"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this manuscript. This present study provides useful information about the repair protocol of alkasite restorative material. However, there are several points that need to be corrected in this manuscript. Some of the changes are defined below.\nMethods section:\n“A total of 48 acrylic blocks (4 cm height _ 2 cm width) were prepared using a self-cure acrylic resin.” Sample sizes are written incorrectly in the method section.\n\n“The specimens were then stored in distilled water at 37°C for one month.” Please add a reference to this sentence.\n\n“Group III (ASB2): The surface of alkasite based material was treated with 2 step etch and rinse adhesive where the...” Please write the brand of the adhesive.\n\n“Specimen preparation”: After the completion of the surface preparation of alkasite based material as described above, a freshly mixed alkasite based material as per the manufacturer’s instructions was built up to a height of 4 mm. Subsequently, the material was cured using LED light curing for 40 s.\n\nThe second paragraph of the Method section states that the samples were polymerized for 20 seconds. In this sentence, it is stated that it was polymerized for 40 seconds. Polymerization times were used differently in the preparation of the samples. Write the reason.\n\nAdd a table where the contents of the adhesives used and the alkasite material, which is the filling material, are written.\n\nAfter the bonding test, fracture-type analysis of the sample surfaces should be performed and supported by SEM.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11702",
"date": "06 Jun 2024",
"name": "Tina Purayil",
"role": "Author Response",
"response": "Methods section: Query 1“A total of 48 acrylic blocks (4 cm height _ 2 cm width) were prepared using a self-cure acrylic resin.” Sample sizes are written incorrectly in the method section. Response1: A total of 48 acrylic blocks (4 cm height × 2 cm width) were prepared using a self-cure acrylic resin. One-day after the polymerization of the acrylic blocks, a cylindrical hole of 4 mm × 4 mm was drilled on one side of the acrylic block. These holes were restored with alkasite based material. Hence, sample size was 48 alkasite based material blocks. These 48 blocks underwent surface preparation followed by restoration with newly added alkasite based material and were subsequently subjected to repair bond strength assessment. Query 2: The specimens were then stored in distilled water at 37°C for one month.” Please add a reference to this sentence. Response 2: The following reference was added Padipatvuthikul P, Mair LH. Bonding of composite to water aged composite with surface treatments. Dent Mater. 2007 Apr;23(4):519-25. Query 3: Group III (ASB2): The surface of alkasite based material was treated with 2 step etch and rinse adhesive where the...” Please write the brand of the adhesive. Response 3: Manufacturing details have been added to the article; Adper Single Bond 2, 3M ESPE St Paul MN, USA Query 4: “Specimen preparation”: After the completion of the surface preparation of alkasite based material as described above, a freshly mixed alkasite based material as per the manufacturer’s instructions was built up to a height of 4 mm. Subsequently, the material was cured using LED light curing for 40 s. The second paragraph of the Method section states that the samples were polymerized for 20 seconds. In this sentence, it is stated that it was polymerized for 40 seconds. Polymerization times were used differently in the preparation of the samples. Write the reason. Response 4: Apologies for the error. This was due to an oversight. All samples were polymerised for 20 seconds. The manuscript has been edited to reflect this. Query 5: Add a table where the contents of the adhesives used and the alkasite material, which is the filling material, are written. Response 5: Added a table with materials used in the study along with their compositions Query 6: After the bonding test, fracture-type analysis of the sample surfaces should be performed and supported by SEM. Response 6: Thank you for your insight. We acknowledge this as a limitation of our study. As these methods were resource intensive and expensive, we could not perform the same. We will plan future experiments including SEM."
}
]
}
] | 1
|
https://f1000research.com/articles/13-319
|
https://f1000research.com/articles/13-586/v1
|
06 Jun 24
|
{
"type": "Case Report",
"title": "Case Report: A case of metastasis to branchial cleft cyst from papillary thyroid cancer",
"authors": [
"Sheetal Shelar",
"Roohi Gupta",
"Rajasbala Dhande",
"P. H. Parihar",
"Roohi Gupta",
"Rajasbala Dhande",
"P. H. Parihar"
],
"abstract": "Branchial cleft cysts are frequently encountered congenital anomalies, arising from the first to fourth pharyngeal clefts and second branchial cleft anomalies are the most common. These anomalies, even though present from birth, become symptomatic only later in life. Majority of them are benign in nature. However, these cysts can get secondarily infected or can harbour secondary metastases and sometimes even primary malignancy in very rare cases. Here we discuss a case of a middle-aged female presenting with a gradually increasing branchial cleft cyst with incidental thyroid lesion on ultrasonography, later proven to be papillary thyroid carcinoma with metastatic spread to the brachial cleft cyst.",
"keywords": [
"Branchial cleft cyst",
"ultrasonography",
"thyroid gland",
"papillary carcinoma",
"metastases"
],
"content": "Introduction\n\nIncomplete obliteration of the first four pharyngeal arches gives rise to branchial cleft anomalies in the form of cysts, sinus or fistulae formation depending on the degree of obliteration during embryonic development.1,2 The most common branchial cleft anomaly is the branchial cleft cyst arising from the second pharyngeal cleft.1,3 Their most common location is below the mandible just anterior to sternocleidomastoid but can occur at any location along the path of second branchial apparatus.4 Since most of them are benign, their presentation to a clinician is usually when it increases in size or post-infection when it becomes tender with or without surrounding inflammatory skin changes.5,6 Investigating a symptomatic branchial cleft cyst becomes important to rule out neoplastic etiology and for early management.\n\n\nCase Presentation\n\nA 35-year-old female presented to the surgery OPD with a 2-3 cm swelling on the left side of the neck along the middle third of sternocleidomastoid muscle (Figure 1). The patient said that the swelling was present since many years. However, in the past three months there was gradual increase in the size of the swelling. It was round to oval in shape, soft in consistency, non-tender and freely movable over the underlying muscle. There was no evidence of adjacent skin changes or any other neck swelling on physical examination.\n\nThe patient had no complains of difficulty in breathing or deglutition and no restriction in movement of the neck. She had no history of trauma, fever or any event of tuberculosis. Her routine blood investigations as well as thyroid profile was within normal ranges.\n\nOn ultrasound of the neck, the lesion measured 2 x 1.5 cm, was thin walled solid-cystic (cystic component> solid) with echogenic debris and abutting sternocleidomastoid muscle (Figure 2a). The solid component showed internal vascularity on color doppler (Figure 2b).\n\nThyroid gland was further examined on ultrasonography and appeared normal in maximum dimensions. The isthmus and right lobe were normal in echotexture (Figure 3).\n\nHowever, the left lobe of thyroid revealed an ill-defined round (1 x 1 cm) hypoechoic solid lesion with punctate microcalcifications and increased vascularity within (Figure 4a). Rest of the left lobe appeared normal in echotexture as well as vascularity (Figure 4b). The lesion was graded BIRADS-4 on ultrasound indicating moderate suspicion for malignancy.\n\nThe patient was then further evaluated on computed tomography before subjecting the patient to FNAC (fine needle aspiration cytology) of the neck lesion. On contrast enhanced CT of the neck, there is a well-defined round solid-cystic lesion lying posterior to middle one-third of the left sternocleidomastoid muscle and focally abutting the left jugular vein. The lesion has thin enhancing wall and enhancing internal solid component (Figure 5).\n\nAfter these radiological investigations, the patient was then taken for FNAC of the swelling. The first sample that was fluid aspirate came out to be indeterminate in nature. However, in the next sampling, the solid component was targeted and it came out to be positive for malignant cytology. Since the patient had concurrent BIRADS-4 thyroid lesion, there was suspicion of thyroid malignancy with metastasis to the branchial cleft cyst. The thyroid lesion was then taken up for aspiration and was proven to be papillary thyroid carcinoma.\n\n\nDiscussion\n\nBranchial cleft cysts are one of the most commonly encountered lateral neck masses.6,7 These are embryological remnants that occur due of failure of closure of the pharyngeal arches before birth.8 Metastases to the branchial cleft cyst is rare and identifying, differentiating it from cystic metastatic lymph nodes is important to plan treatment.9,10 Papillary thyroid carcinoma frequently metastasizes and therefore it is necessary to evaluate the thyroid gland in such instances to narrow down the diagnoses.11,12\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.",
"appendix": "Data Availability\n\nNo data associated with this article.\n\n\nReferences\n\nAdams A, Mankad K, Offiah C, et al.: Branchial cleft anomalies: a pictorial review of embryological development and spectrum of imaging findings. Insights Imaging. 2016 Feb; 7(1): 69–76. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBenson MT, Dalen K, Mancuso A, et al.: Congenital anomalies of the branchial apparatus: embryology and pathologic anatomy. Radiographics. 1992 Sep; 12(5): 943–960. PubMed Abstract | Publisher Full Text\n\nPrasad SC, Azeez A, Thada ND, et al.: Branchial anomalies: diagnosis and management. Int. J. Otolaryngol. 2014 Mar 4; 2014: 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPanchbhai AS, Choudhary MS: Branchial cleft cyst at an unusual location: a rare case with a brief review. Dentomaxillofac. Radiol. 2012 Dec; 41(8): 696–702. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcCormack SM, Nicewicz MJ: Complications and Diagnosis of Branchial Cleft Cysts: A Case Report. Cureus. 2022 Dec 18; 14(12). Publisher Full Text\n\nValentino M, Quiligotti C, Carone L: Branchial cleft cyst. J. Ultrasound. 2013 Mar; 16: 17–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPapadogeorgakis N, Petsinis V, Parara E, et al.: Branchial cleft cysts in adults. Diagnostic procedures and treatment in a series of 18 cases. Oral Maxillofac. Surg. 2009 Jun; 13: 79–85.\n\nBagchi A, Hira P, Mittal K, et al.: Branchial cleft cysts: a pictorial review. Pol. J. Radiol. 2018 May 11; 83: 204–209. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWaldhausen JH: Branchial cleft and arch anomalies in children. Seminars in pediatric surgery. WB Saunders; 2006 May 1; 15(2): pp. 64–69). Publisher Full Text\n\nChi HS, Wang LF, Chiang FY, et al.: Branchial cleft cyst as the initial impression of a metastatic thyroid papillary carcinoma: two case reports. Kaohsiung J. Med. Sci. 2007 Dec 1; 23(12): 634–638. PubMed Abstract | Publisher Full Text\n\nBriggs RD, Pou AM, Schnadig VJ: Cystic metastasis versus branchial cleft carcinoma: a diagnostic challenge. Laryngoscope. 2002 Jun; 112(6): 1010–1014. PubMed Abstract | Publisher Full Text\n\nNoguchi S, Noguchi A, Murakami N: Papillary carcinoma of the thyroid I. Developing pattern of metastasis. Cancer. 1970 Nov; 26(5): 1053–1060. Publisher Full Text"
}
|
[
{
"id": "307444",
"date": "12 Aug 2024",
"name": "Nor Azirah Salahuddin",
"expertise": [
"Reviewer Expertise Otorhinolaryngology",
"head and neck surgery"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comment\nThe discussion is too short. As we know branchial cyst can represent primary malignancy or secondary mets. How the author differentiates the initial diagnosis of branchial cystic vs malignant cystic swelling/secondary metastasis cystic neck swelling (ref 1). Is there any cytology diagnosis which suggests the swelling is a branchial cyst e,g cholesterol crystal. Suggest to elaborate the discussion how this case is differ from reported cases and ass learning points to others so that it will be more valuable for the indexing.\n\nRef: Mc Loughlin L, Elsafty N, Kavanagh F, Gillanders S, et al.: AB087. 192. Branchial cleft cyst— really?. Mesentery and Peritoneum. 2018; 2.\n\nMinor comment\nThe case presentation was presented well but the author did not highlight the management and outcome of the case. We would like to know further the management eg surgical intervention, oncology treatment etc The second FNAC was done to target the solid component. Is the repeated FNAC done under ultrasound guided? References -some of the references cited was too old (>20 years).\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-586
|
https://f1000research.com/articles/13-585/v1
|
06 Jun 24
|
{
"type": "Research Article",
"title": "Attribution clause as a tool for addressing contractual imbalances and applicability in civil contracts",
"authors": [
"Mamooa Al-Samadi",
"Hashim Balas"
],
"abstract": "Abstract* Attribution rules act as a tool to modify the terms of a contract by accepting pre-specified terms and conditions. This methodology ensures that the contractual relationship is protected while addressing potentially complex scenarios that may arise during contract execution due to evolving circumstances. To maintain the binding force of the contract, Parties expedite dispute resolution and protect the integrity of their contracts by choosing recourse and prior agreeing to remedies, which encourages continuity in enforcement. These clauses are intended to automatically amend the terms of the contract without requiring the parties to participate in the amendment process. These items adjust the amount of funds subject to the obligation according to changes observed by external indicators associated with the obligation. This is done by comparing the price of a particular currency with the price of a different commodity. In the case of payment in gold or foreign currency, it represents an assault on the binding legal force of the national currency by competing with it as a means of payment and considering it as one of them. Terms of payment in gold and foreign currency are excluded from the attribution requirement, which replaces legal means of payment with new means of payment. It does not constitute a basis for determining the extent of fulfillment of the obligation, and we conclude that the attribution clause is a distinct legal system that deals with amending contractual terms and the contractual imbalance they cause. Amendment is permitted in the event of circumstances occurring that would upset the balance throughout the contract implementation period, and we recommend adopting the attribution clause as an automatic adjustment tool.",
"keywords": [
"contract",
"amendment",
"agreement",
"attribution clause",
"contractual balance"
],
"content": "Introduction\n\nEntering into a binding contract that effectively produces its legal effects is typically based on the parties' freedom of will. This implies that the contracting parties are free to define their contractual relationships to best serve their purposes and interests. Therefore, including an amendment clause pertaining to contractual obligations in the contract can be regarded as a helpful tool for protecting the parties' interest, particularly when confronting any change in circumstances during the implementation stage.\n\nThis approach typically creates a state of balance in the performances of the contractual parties. However, implementing the amendment of the obligations is not so easy, as several obstacles may arise that affect the result that the contracting parties hope to reach. Nevertheless, this approach has been found helpful because having the ability to review the terms of a contract maintains its continuity. These contract mechanisms are gaining increasing prominence for their influential role in providing swift and radical solutions to disputes that may arise between contracting parties, in addition to providing a guarantee of optimal implementation of obligations and achieving the contractual goal (Khater, 1998).\n\nSome circumstances surrounding the implementation of the terms of the contract may potentially change in the future, jeopardizing the contract's economic viability. These conditions come within the framework of the parties to the contract, protecting against the financial and monetary fluctuations that may hinder the implementation of the contract, which is an objective condition in the contract that includes linking the value of the contractual obligations to an indicator, element, or an external economic or monetary standard characterized by relative consistency and stability, which allows predicting the value of contractual performances in terms of this agreed-upon indicator, and then distributing the consequences of financial risks between the parties to the contract by including automatic amendment clauses (La Clauses de Variation Automatique) for the value of the obligation if circumstances arise. Exceptionally, in a way that reduces the possibility of a dispute arising between the parties to the contract over how to deal with a change in the circumstances of contract implementation, one of whose applications is the attribution clause.\n\nThe general norms of the contract's amendment were the only things covered by the Jordanian Civil Law in Article 164 and Article 147 of the Egyptian Civil Code, which did not touch its specifics or forms. To the best of our knowledge, no studies have addressed this problem in-depth in the Jordanian legislation, so we attempted to clarify the attribution provision. As a result, this topic did not acquire a significant position. And the civil legislator's stance on it. Our research aims to provide insight into the civil legislator's stance regarding the attribution clause and the degree to which it is utilized to amend contracts to fulfill obligations.\n\nIn this paper, we have adopted the comparative approach by analyzing the legal texts directly related to the subject, comparing provisions with Egyptian and Jordanian legislation, guided in particular by the rulings of the French judiciary, and attempting to present a legislative model that can be relied upon to solve the problem of this research. (DALLOZ, 2009) The attribution clause is a new, widespread, pronounced mechanism regulating agreement. It enables the contracting parties to freely enter contracts and choose the provisions that best fit their interests. Furthermore, they gained increasing importance because they provide a rapid and radical solution to disputes, ensure the optimal implementation of obligations, and achieve the goal of the contract. The next chapter presents the subject of attributions in detail.\n\n\nMethods\n\nScientific analysis methods were used in this study in the form of document analysis and analysis of legal studies. Data were obtained using the Boolean search engine to comb through the Scopus database between the years 1951 and 2023. The search was conducted on May 1, 2023. The researcher used R, R-Studio, VoSviewer, and Microsoft Excel tools to analyze the documents and data. networks. The steps taken by the researcher are as follows:\n\nFirst, the researcher will conduct a literature review on relevant topics to ensure that research relevant to the scientific topics is being conducted. In addition, a literature review is useful for identifying appropriate keywords and is considered to represent the scope of the research.\n\nIn the second stage, the researcher used analysis and criticism through inductive and deductive methods, which is necessary for a correct understanding of the attribution clause as a tool for addressing contractual imbalances and applicability in civil contracts. A search in Scopus resulted in several documents. Furthermore, filtering was performed using the Boolean operators (LIMIT-TO (DOCTYPE, “ar”)) and (LIMIT-TO (LANGUAGE, “English”)) to limit the use of English documents and articles as document types, which narrowed the result For final documents.\n\nIn the third stage, the final documents were analyzed using Scopus, R, and R-Radio analyzer to determine the number of documents per year and the number of documents by journal, author, affiliation, country, and topic/field. Furthermore, analysis was performed at the document network level through visualization.\n\nThe attribution clause is a distinct legal system addressing the amendment of contractual conditions and the contractual imbalance they cause. It permits amendment in the event of circumstances that would disturb the balance throughout contract implementation. The attribution clause typically echoes the desire of the contractual parties to maintain the contract. It is a good and effective method for amendment that is far from traditional methods. It combines the pursuit and confirmation of contractual justice with cooperation between the parties to the contract.\n\nEven though the attribution clause with a specific text is not included in the French Civil Code, it is adopted by the French judicial and jurisprudential tendency. Its success in achieving its established purpose depends on its excellent structuring to ensure the ease of carrying out the amendment process without the parties intervening.\n\nBased on the results above, we suggest adopting the attribution clause as an automatic amendment tool. We propose that the chambers of industry and commerce and the appropriate professional unions work together to establish guidelines for the most significant standards the contracting parties may use to amend their agreement automatically. This approach avoids court intervention and promotes and supports the automatic agreement method for contract amendment.\n\nThe attribution clause is included in the form of automatic amendment conditions (La Clauses de Variation) to adapt to changing circumstances threatening the financial balance and dynamically respond to changes in the market, such as fluctuations in market conditions during the implementation of the contract. The attribution clause simply provides flexible automatic amendments to the original contract terms and conditions previously agreed upon (Ghannam, 1982; Sentence, 1985) without the intervention of the contracting parties or constant renegotiation of the entire contract. Generally, the amended conditions must be enforceable, not violate the public order, or be unlawful. Otherwise, the contract becomes invalid or voidable.\n\nThis clause upholds a value external to the contract as an indicator or standard for the obligation's genuine content. Generally, individuals resort to amending their contracts by including amendment conditions (Al-Basha, 1992; Al-Najjar, Badawi, & Shalala, 1983; Ommeslagehe, 2020) based on a moving average indicator which was adopted in 1957 (Benabent, 2004) to maintain the continuity of their agreement (Al-Shawabkeh, 2005; Benabent, 2004).\n\nThis amendment strategy, also known as mobile scale (l'échelle mobile), is based on connecting the value of contractual obligations to an external economic or fiscal indicator, element, or standard that is characterized by relative consistency and stability, allowing the value of contractual performances to be expected in terms of this agreed-upon indicator. This leads to the distribution of the consequences of financial risks between the two parties to the contract through automatic adjustment of the value of the obligation if exceptional circumstances arise and in a way that reduces the possibility of a dispute arising between the parties to the contract over how to deal with changing circumstances of contract implementation.\n\nHowever, when including the attribution clause, the contracting parties maintain a contractual balance by achieving equality in mutual obligations and establishing justice to satisfy their interests. Furthermore, these kinds of clauses typically deepen trust between individuals by avoiding currency smuggling, protecting the national economy from inflation, and leading to the maintenance of the contractual balance despite the decline in the value of the currency by anticipating the value of the contractual payments in terms of an economic or monetary standard (Doucet, 1965, Sultan, 1963). It addresses the impact of the conditions that can be expected upon concluding the contract by distributing the consequences of financial risks between parties to the contract based on anticipating in advance through a contractual condition that a debt, which is generally monetary, increases automatically and is proportional to an element chosen by the parties, called an indicator, controlling the effects of changing circumstances by the parties when concluding the contract, they can include it; To approve the amendments they must make upon its implementation, then this mechanism is suspended (Alachkar, 2010).\n\nThis element is described as an objective, quantitative component used as a guide to adjust the increase or decrease of the obligation's value. It also measures the impact of changing circumstances on the subject matter of the contract in a way that ends disputes between parties regarding the actual value of obligations under the contract owing to shifting economic conditions without the need for a new agreement to deal with new contractual data and conditions.\n\nThere are two steps involved in adding an attribution clause. Firstly, when the contract is being finalized, it is necessary to decide on an external indicator, which is the basis for calculating the rate of inflation or deflation and the amount of the contractual obligation that will increase or decrease. The second step is deciding how this indicator will be applied, which is done on predetermined periodic dates yearly, every two or three years, or the amendment is linked whenever a crisis or modification in the contractual terms occurs. This will determine the price level for the modified contractual obligation.\n\nAn automatic nature characterizes this amendment method, and parties are prohibited from intervening after the expected events occur. This is represented by replacing a new contractual obligation or performance with the original performance stipulated in the contract, reducing the possibility of a dispute arising between the parties to the contract over how to deal with the change in the circumstances of contract implementation. (Lambertrie, 1987; Chavance, 2013).\n\nThis method of amendment has been criticized for only responding to the risks associated with the anticipated economic conditions related to price and exchange rates, which limits its efficacy in confronting the development of obligations and eliminates the circumstances surrounding the contract upon implementation from the two parties' circle of expectations because of unrelated political and legal circumstances. Directly related to the contract's topic, and while it is not anticipated, it might impact it (Alachkar, 2010; Al-Jamal, 2002; Marraud & Akyurek, 2009).\n\nThe attribution clause can be defined as an objective condition included in the contract to link the value of contractual obligations to an indicator or external element that is usually characterized by consistency and stability, such as a price index, the cost of living, or the average price of a specific commodity during a particular period, such as oil, gold, or any of the precious metals (Chavance, 2013).\n\nIt is also known as the indexation clause (clause d'indexation) or the variable scale clause (clause d'échelle mobile). These clauses, as mentioned previously, deal with any change that may result from a change in the situations under which the contract was concluded, which threatens the financial stability of the contract. Additionally, it can be adopted to protect both the creditor and debtor; therefore, the contracting parties tend to link their obligations to another element characterized by relative stability (Muhammad, 2008).\n\nTerre' Simler and Lequette (1993) confirmed that these clauses aim to automatically modify the contract terms without the parties intervening during the modification procedure. These clauses adjust the amount of money subject to the obligation according to the changes recorded by the external indicators to which the obligation is linked, as stated by the decision of the French Court Cassation DP 1920.1.137. The indicator is the basis for inferring, through the calculation method and rules, the amount of obligation imposed on the contractor by measuring the price of a specific currency or a specific commodity or other commodity (Muhammad, 2008; Rashwan, 1994). By incorporating a clause in the contract that links the obligations emanating from it to a specific index that mitigates the impacts of economic inflation, it counteracts the damage caused by changes in the currency's value.\n\nThese requirements fall under the contracting parties' protection framework against challenges and monetary and economic fluctuations (Terre', Simler & Lequette, 1993) that might make it more challenging to carry out the terms of the agreement and look for ways to deal with them. This method works well for selecting the contracting parties, aligning their interests with the agreement (Doucet, 1965; Tallon, 1986), keeping the contractual balance, and allowing the contractual payments to be expected in terms of a predetermined monetary or economic standard (Alachkar, 2010; Lambertrie, 1987).\n\nThe attribution clause does not apply to payments made in gold or foreign currencies because their values can fluctuate significantly concerning local currency. Nonetheless, the contractual parties may try to keep their payment arrangements stable and avoid the risks related to changes in currency exchange rates. Furthermore, in particular countries or for specific transactions, the usage of gold and foreign currencies may be subject to regulatory prohibitions or regulations. Hence, including them in the attribution clause may constitute an assault on the binding and legal force of the national currency (Muhammad, 2008; Madani, 1952; Rashwan, 1994).\n\nThe conditions of the attribution clause have been criticized for their rigidity. Given their relationship to price and exchange rates, it is predicted to react to risks and economic situations. However, its efficacy in tackling developments and broad changes surrounding the contract's implementation is limited by political and legal variables unrelated to the contract's subject and yet has the potential to impact it (Accaoui, 2008; Alachkar, 2010; Camelbeke, 1984).\n\nArticles L112-1 to L112-4 of the French Monetary and Financial Law Code\" monétaire et financier\" (Cornu, 1988) contained the rules for automatic amendment. It should be noted that, in contrast to the laws of Egypt and Jordan, the French Monetary and Exchange Law regulated the amendment process. It should be noted that the French legislator prohibited dealing with some indicators because they do not reduce the burden of the obligation on the debtor and are not suitable as a basis for amendment.\n\nThe external indicator is linked to the activity or performance of one of the parties to the contract by linking the percentage of change to this activity, but what activity can be linked? Is it a professional activity or related to another activity?\n\nThe nature of the activity does not matter as long as it ensures the continuation of the contractual relationship between its parties (Fadel, 2001; Abdel Rahman, 2000). The French Legislative Decree of 1958, Article 79, stipulates that the chosen indicator must be directly associated with an activity carried out by one of the parties, even if it is not their primary job. Estimating the existing link between the indicator's nature and the contract's subject is considered a matter of fact. For instance, the court ruled that since the free will contract for a commercial establishment deals with intangible movable property. Not built real estate, the judges of the matter cannot declare without violating the text of Article 79 of the Legislative Decree of 1958 amended by the Law of July 9, 1970, Monetary and Financial Law, Article 112-2, the validity of the clause that it stipulates the adoption of an index for the royalty payable by the managing tenant, linking it to the national building cost index. Also, all clauses stipulating the adoption of index clauses based on the French progressive minimum wage among professions (SMIC) are prohibited, except for what is related to alimony debts, and it is not permissible.\n\nThe employer may automatically approve the employee's request to reconsider the wage based on the French minimum wage. It ruled that choosing a wage index for a specific occupational category is not prohibited, as it is not considered a reference to the general level of wages. It also ruled the validity of adopting a particular index based on the general level of wages in France, which includes all activities practiced in France, - while in “the Brothers” decision, it was considered that the indicator adopted on the general level of inflation is illegal based on Article 79 of the Legislative Decree (Social Cassation December 13, 2006: Civil Bulletin V, No. 374). Estimating the validity of the indicator approved at the time of concluding the contract cannot be affected by a subsequent modification of the activity practiced by the debtor.\n\nOne of the contractors' primary professional activities is directly tied to the external indicator. Only those professional components directly related to and necessary for the primary activity are considered for something to be deemed effective. The professional activity practiced at the contract conclusion and initially regarded must be considered in the event of a change in professional activity. However, the professional activity performed throughout the contract's conclusion may alter; thus, we wonder if the condition is still in place or has been changed.\n\nThe parties must carefully consider their options when finalizing the terms of the contract, even if they are allowed to include any condition that best serves their interests. Suppose the attribution condition is necessary and constitutes a fundamental component of the contract structure. In that case, the contract is considered void entirely because this condition constitutes an essential component. On the other hand, if the condition is not crucial to the contract and the entirety of the agreement is not contingent upon it, the result is to effectively suspend or maintain this condition without any active influence on the contract.\n\nIt is crucial that this condition represents the parties' intents and is the basis of their mutual agreement; removing it would disrupt the delicate balance of the contract. However, if the condition is judged non-essential and its nullification does not affect the balance of the contract—as long as the contractor can still examine the condition—then the nullification only relates to the condition attached to the contract. It should be noted that French civil law considered the fraudulent nature of the illegal clause a decisive clause.\n\nIf the professional activity is altered, the condition is frozen instead of void along with the contract. The main goal of the revision is to preserve the contract, not to make it void. It is unimaginable that the contract and this paragraph would become void automatically due to a change in professional activity. Therefore, the condition is frozen to guarantee contract stability. Although there are obstacles to modifying the phrase and attempts to protect against currency depreciation, the selected external indicator's function in validating the clause is still linked to the professional activity of one party.\n\nThe subject of a contract, the obligation, and the goal of the contractual procedure are all considered part of the subject matter of the contract. The selected external indicator is regarded as a part of the contract if there is a clear relationship between it and the contract's subject matter and if it is an effective tool for protecting the stability of the contractual obligations (Benabent, 2004; Qasim, 2018).\n\nFurthermore, to be valid, the external indicator must have a direct link to the contract subject as required by the interests of the contracting parties. In the loan contract agreed upon for building or purchasing a house, the external indicator of the building price included in the loan contract must directly relate to the subject of the loan. Its scope can be expanded if there is a proportionality between the value of the thing subject to the condition and the external indicator if the agreement relates to professional requirements, such as a restaurant owner.\n\nHowever, if it is related to personal needs, it is difficult to find a relationship between it and the subject of the contract. Finding a direct relationship between the rent, the price of the raw construction materials, and the construction wage is complex. There is no direct relationship between rent and building rent (Tallon, 1986).\n\nAt the very least, the external indicator must be related to one of the contracting parties' activities. The contractor's professional activity is the intended activity; however, the professional activity need not be the primary activity of the contractor. Any component of this activity is legitimate so long as it is connected to the selected basis in a way that guarantees the change clause's effectiveness.\n\nThe French judiciary provided further details regarding the attribution conditions and the connection between the external indicator, the contract's subject matter, and individual activity. The contract is not deemed invalid; the condition is considered invalid and non-existent. This is because the activity was not required to be particular or significant, and flexibility was required in addressing the amount of the invalidity resulting from it.\n\nMultiple complications may face the implementation of the attribution clause; namely, the parties fail to choose the suitable external indicator, replace the existing indicator with an ineffective one, or remove it, which leads to obstructing its application as the basis relied upon to address the balance of contractual performances. This typically limits its effectiveness in considering the interests of the contracting parties and threatens the stability of transactions and fairness.\n\nThe structure of the attribution clause and the linked external indicator considerably affect the contract. The external indicator can be simple and be applied quickly and clearly, or it can be complex, containing multiple elements, such as the cost of raw materials locally compared to the cost of raw materials and their international prices.\n\nThe external indicator is approved by resorting to standards based on the standards of professional and commercial institutions and norms, statistics and metrology institutions, such as the Jordanian Standards and Metrology Institution, the National Statistics Organization in France, the Egyptian General Authority for Standardization and Quality and the Chambers of Commerce and Industry in these countries, without specifying the basis on which these organizations publish them. (Fabre, 1983)\n\nHowever, in some cases, the indicator is adopted as a criterion for alteration. It is changed periodically, given that the value is variable and not fixed, which leads to difficulty in calculating the value of the subject of the contract, especially when compared to the first automatic amendment if the approved external indicator is multiple and repetitive. In the event of a second automatic amendment to the contract, the first reference number is not used, but the new reference number that has changed is relied upon. Therefore, both parties to the contract must stipulate that the last value of the subject matter of the contract has been fulfilled so that it can be used to make the new amendment.\n\nBased on Article 112-1 of the French Monetary and Exchange Code, frequent amendment of the attribution condition is unnecessary. Otherwise, the condition is invalid due to the refusal of French law to have a discrepancy or irregularity in adopting the calculation of the external indicator in repeated amendments.\n\nReciprocity is a term adopted by the French Court of Cassation to amend the terms of the contract in a way that achieves the interests of both parties to the contract to prevent the enrichment of one party at the expense of another.\n\nBut what is the solution if the two parties to the contract agree to exclude the attribution clause if the value decreases, and it cannot be amended except if the value increases?\n\nThis problem was raised before the French judiciary, and the amendment that limited its effect to increasing the obligation was considered invalid, as it does not provide for reciprocity and stipulates an amendment to the higher value, as it relates to the basic rules of lease contracts. Because it conflicts with these rules, which are part of the public order, and because it will enable the beneficiary to evade the decrease in rent, it conflicts with the purposes of the Monetary and Exchange Law in France regulating these conditions (Desouki, 1995).\n\nReciprocity is a term adopted by the French Court of Cassation in Cass.3e civ.,14 janv.2016, to amend the terms of the contract in a way that achieves the interests of both parties to the contract to prevent the enrichment of one party at the expense of another. However, what is the solution if the two parties to the contract agree to exclude the attribution clause if the value decreases, and it can not be amended except if the value increases?\n\nThis problem was raised before the French judiciary, and the amendment that limited its effect to increasing the obligation was considered invalid, as it does not provide for reciprocity and stipulates an amendment to the higher value, as it relates to the basic rules of lease contracts. Because it conflicts with these rules, which are part of the public order, and because it will enable the beneficiary to evade the decrease in rent, it conflicts with the purposes of the Monetary and Exchange Law in France regulating these conditions.\n\nHowever, in 2010, the Douai Court of Appeal held that adopting the annual standard for rent in the event of a rise was a legal loss and consistent with contractual freedom. Given the disparity in judicial rulings concerning the terms of exchange for amendments under the automatic amendment clause, I believe the French Court of Cassation's decision to be valid. This is because the exchange ensures that the creditor party doesn't arbitrarily use the automatic amendment in the contract, which states that the amendment can only be made for its benefit.\n\nEven when the contracting parties have agreed to use an external indicator, this figure may change illegally while the contract is executed. In this case, the attribution condition is nullified if the state suspends trading or limits the use of this indication and it does not meet the legal requirements to be valid (Arabi, 1999; Al-Otaibi, 2009). This is taken into account with the intention behind this condition. The criterion is entirely void if legislative limitations on the external indicator are intended to safeguard national currency for reasons of public interest. Any interested party may defend it, and the court may bring it up on its own if it violates public policy because it is illegal, as in the case of this external indicator on minimum wages or the general price level, which is one instance where it is forbidden by law. French Civil Code specifies that the legally prohibited indicator is invalid and cannot be supported or ratified.\n\nOn the other hand, we encounter relative invalidity unrelated to public purpose if legislative limitations seek to balance contractual performances, which results in outlawing such conditions. Contracting parties may agree to continue utilizing the external indicator concerning their interests if it does not relate to public policy.\n\nFor instance, the Court of Appeal, which clarified the parties' mutual intention, ruled by its absolute authority that the parties' intent fundamentally leaned towards adopting the indicator principle. This decision was made based on the interpretation of the parties' intent by the subject judges, based on one party's initiative at the contract's inception to propose the indicator, which was adopted as an alternative indicator (Oppet, 1979; Sama'ah, 2015). Since the indicator choice provision translated this intention, replacing the invalidated indicator with one that complies with the law is necessary.\n\nHowever, does the condition's invalidity render the contract entirely void, or does it just render the condition invalid?\n\nThe French judiciary resolved this issue by considering that the contractual obligation was null and void because it was impacted by the stated condition driving the contract. Eliminating the condition also invalidates the contract's rationale, making it completely void. The contract is void due to the specific and essential condition impacting the agreement. It is possible to isolate the contract's illegal element, symbolized by the external indicator leading to nullity. If this unlawful section, a secondary and ambiguous clause, is not the agreement's primary purpose and is not necessary as specified in Article 143 of The Egyptian Civil Law and the Jordanian Civil Code in Article 169. However, what recourse does one have if the purpose of the non-severability is to evade legal requirements?\n\nThis can be explained by the fact that violating the law ruins everything. If the non-severability clause is meant to evade legal requirements, the clause is null and void, and the contract is still in effect. As long as the contract is in effect, the reference condition is void since it is deemed unwritten. Considering the potential benefits the contracting parties may receive from the unlawful condition, what would happen if they said nothing about it?\n\nThe French Civil Code states that the invalidation must only address the clause adopting the indicator related to a commercial lease since it is a secondary clause whose invalidation does not disturb the balance of the contract as long as the owner reserves the right to legal reconsideration, even if a description such as This clause in the contract is considered a decisive clause. At the same time, there is nothing in it that makes it essential; it does not give the lessor the right to waive the tenant's rights by completely nullifying the contract, and in the same sense, another decision came that the nature of fraud that characterizes the clause that declares the illegal clause is decisive (Al-Khasawneh, 2014).\n\nEven if the condition helps the contracting parties, it must not contradict the public interest. If it is, the condition should be void for illegality. The private interests of the contracting parties are subordinated to the public interest attained by nullifying the requirement (Fadel, 2001). Finding an alternative method to prevent nullity can be accomplished by swapping out the external indication.\n\nSince both parties to the contract are free to choose any indicator or more, we suggest selecting a reserve indicator as a solution to the nullity of the external indicator. This will help the parties overcome any obstacles preventing the amendment's implementation. When the contract is concluded, and the initial external indicator is determined, there should be agreement on the indicator. The validity of the external indicator is unaffected, and its impact is restricted to the future and does not go back into the past should an agreement on the indicator not be achieved at the end of the contract (Brik & Faisal, 2008; Qandil, 2009).\n\nIn two situations, the external indicator is typically changed: first, when the parties agree upon a reserve indicator number, and second, when a reserve indicator number is not agreed upon. The parties may or may not agree on a reference number if a reserve indicator number is not agreed upon in advance. What should be done in these situations?\n\nContracting parties utilize the procedure of replacing the external indicator to protect the contract during drafting in case of issues that could prevent it from being carried out. This allows for automatic modifications by rearranging the contract in response to changes in the external indicator (Abdel Latif, 2016; Fadel, 2001).\n\nThe parties may address the issues brought about by the original external indicator's nullity by pre-agreement on its automatic replacement with the reserve external indicator. In that case, the reserve indicator replaces the void one retroactively following the requirements of the contracting parties. Contracting parties might use it to keep the contract in place and continue with it. The parties may select a new external indicator if they cannot agree on a reserve indicator, but it will not automatically replace the void one (Doucet, 1965; Aradimus, 1988), If the parties to the contract cannot agree upon a reserve external indicator in advance or cannot agree upon an indicator, may they ask the court to step in and replace the void indicator? If so, does the judge have the power to act in place of the parties?\n\nWith the assumption that the parties' will was essentially focused on adopting an indicator, the court, in this case, can substitute it based on his absolute assessment of the parties' joint intention. A legally permissible indicator must be used in its place; hence, the void indicator must be changed. The rate of the indicator to be applied when required can also be determined by knowledge (Jassim, 2011). The accomplishment of the contract's goal and its continuation is reflected in the interpretation of the contracting parties' intention to achieve the true purpose and their understanding of the intended standard in conformity with the referral requirement and their shared intention (Doucet, 1958). Consequently, the contract may be terminated, and the imbalance in the contract may not be addressed if the judge finds that the external index is null and void without the parties' consent.\n\nIt should be noted that in French Civil Law, judges could exclude the application of the indicator specified in the contract if they considered, in their absolute appreciation of the common intention of the parties, that the inclusion of this indicator in the contract was the result of an error resulting from hasty and reckless writing. In another decision, it was stated that the subject judges could decide regarding the mere application of the clause Approval of the indicator stipulated in the contract (Mansour, 1987). It may be resolved, in the event of non-publication to which this indicator is referred, not to determine the rate of the indicator to be applied utilizing expertise when necessary.\n\nSome contend that examining a contract's provisions using the attribution clause does not require halting the contract's execution (Gustan, Jaman, & Pino, 2008). However, this point of view is challenged because it contradicts the idea of contract review, which holds that suspension of contract execution is a necessary consequence of review commitment. This trend is supported by Article 1135 of the French Civil Code (Abdelal, 1998).\n\nThe parties' agreement determines the contract's continuity decision when its terms fail to be revised. The parties may decide to execute the original contract under the same terms, or they may choose to cease contract execution for a while before deciding how to proceed. This could include ending the contract thoroughly, going back to regular execution, terminating automatically, or using another strategy to help each party overcome their current struggles (Al-Salmani, 2010; Hammoud, 2001; Toulemon, 1951). The contract must be upheld without an agreement regarding what will happen to it in the event of failure; only the clause that does not relate to a core component of the original contract should be canceled (Abu Zaid, 1995).\n\nHowever, if the review is successful and results in an amendment that covers every aspect of the original contract, it will be considered a renewal. The new agreement is considered a modification to the previous agreement in this scenario and not a renewal if the amendment simply resolves a few of the contract's supporting issues.\n\nThe attribution clause cannot be exhaustively defined, but examples can be cited from practical applications such as the Clause of Renegotiation, Hardship Clause, and Safeguard Clause. The parties should outline the circumstances that give rise to these clauses, the degree of instability in the relationship between the parties, and what happens to the contract when these events occur (Al-Khasawneh, 2014). These are contract terms whose contents are determined by the agreements reached by the parties. These comprise the parties' obligations to restructure the contract in light of any imbalance in its economic stability (Gustan et al., 2008; Reinecher, 1982). The parties may include in their contracts any terms they think fit to distribute and share risks between them through review provisions that can be reviewed in whole or in part when specific events specified in the contract or clause occur.\n\nNotably, Article 1134 is a French civil, and Articles 88, 213, and 214 of a Jordanian civil include clauses on the hardship clause, a most favorable customer clause, and a force majeure clause that allows the financial terms of the contract to be reviewed in the event of changes in raw material costs.\n\nNumerous civil laws and the Jordanian Civil Law stipulate the attribution clause in general rules without addressing its details. All contracts are subject to the principle of contractual freedom, so the contract has its effect and becomes binding on the contracting parties. They must adhere to what is stated in the contract in application of the principle of 'Pacta sunt servanda.' The attribution clause is subject to the same rule, which also aims to resolve any dispute expected by the parties that may arise due to changing circumstances.\n\nThe Jordanian lawmaker has provided an explicit text in Articles 87-102, considering the contract a private law whose provisions are bound by the parties out of their own free will, and neither of them can alone dissolve or amend it (the Jordanian Court of Cassation No. 6337/2018 and Decision of the Jordanian Court of Cassation. No. 5534/2016).\n\nIt has been emphasized through these texts that the contract is considered the binding law for the contracting parties' Pacta sunt servanda', so it is not permissible. It can be annulled or amended except by agreement of both parties and for reasons determined by law. The Jordanian Court of Cassation confirmed this in its decision, “The contract is as a binding the law of the contracting parties “Pacta sunt servanda,” and its parties must abide by the terms of this contract and the rights it entails for the two parties unless they are prohibited by law or in violation of public order.” The judge does not have the power to amend the contract terms, and his role is limited to determining the rights arising from it. Additionally, he has no authority to amend the rights and obligations except in the cases determined by the law. This is also the case with the attribution clause. Once the parties agree on this, the contract becomes a binding law, and no party can amend or dissolve its conditions because it becomes an integral part of the contract (Raad, 1993).\n\nArticle 164 of the Jordanian Civil Code declares the permissibility of a contract being associated with a condition or contractual clause that benefits one of the contracting parties or a third party unless the law prohibits it or violates public order or public morals. The Article permitted the parties to the contract to include any conditions as long as they didn't violate public order and morals. These conditions, as stated by the decisions of the Jordanian Court of Cassation in its legal capacity No. 1102/1999, on 2000 No. 2141/1999, are conditions that alter the effects of the contract and are related to the contracted party. They often come in the form of contractual clauses.\n\nIndividuals are considered legislators within the scope of their contract, but they have the power to regulate their contractual relationship without prejudice to the freedom of others. Therefore, it is not permissible for a judge or legislator to act based on the sanctity of this bond if these agreements are compatible with the law. Consequently, it is said that the contract is the binding law of contracting parties (Shanab, 1977; Malkawi, 2003).\n\nGiven that the conditions are limitless and unbounded, it is noteworthy that the Jordanian lawmakers have categorized these conditions rather than identifying each one. But since the lawmaker permitted the inclusion of certain situations in the contract for the contract, its suitability, or customary conditions, it can be said that he has established standards for the validity of the condition, and the clause (attribution) is subject to them.\n\nA few of the amendment's terms and conditions clarify the agreement's subject matter and forbid its cancellation by severing the potential dispute from the altered contractual circumstances. From a different perspective, the condition is also appropriate for the contract. Some contracts, such as deferment periods, incorporate conditions to maintain the parties' financial balances intact.\n\nSpecific attribution clauses are customary, mainly when part of an international contract or a commercial agreement where the parties employ the provision frequently. Insofar as they don't break the rules, the parties can be considered legislators for themselves regarding the attribution clause. Insofar as they don't break the rules, the parties can be regarded as legislators regarding the attribution clause: public law and the violation of other people's rights. The judge doesn't have the power to intervene in the amendment of conditions the parties agreed upon since what the parties agree to is regarded as binding on them and the judiciary as long as it is within the limits of the law.\n\n\nConclusion\n\nThe primary goal of this research is to clarify the nature of the attribution clause and offer a practical model that the parties to a contract may use to organize their contractual obligations and govern their agreements.",
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Dar Al-Nahda Al-Arabiya, Cairo: Their Forms and Provisions; 1995.\n\nAlachkar R: Clause de hardship et clause d amiable composition, doctoral thesis, Paris.2010; II: 2010.\n\nArabi S: Addressing the imbalance in international contracts in international trade law.1999.\n\nAradimus A: The impact of the depreciation of the currency and its effect on the rights of contractors and litigants, the Justice Magazine. Beirut Bar Association; 1988; vol. v22. .\n\nAl-Basha M: Al-Kafi: A modern Arabic reference. Beirut: Publications Company for Distribution and Publishing; 1992; 223.\n\nBenabent A: Civil Law and Obligations, ed: Mansour Al-Qadi. Lebanon: Al-Majd University Foundation for Studies and Publishing, Beirut; 2004: 115.\n\nBrik D, Faisal H: The power of the parties and the judge to amend the contract. Algeria: Research obtaining a license from the Higher School of the Judiciary; 2008.\n\nCamelbeke M: l’adaptation du contrat international aux circonstances nouvelles. Paris: ' sous la direction de R.RODIERE et les reflexions comparatives de D.TALLON.Ed.A.Pedon; 1984.\n\nChavance E: le novueau regime des clauses d indexation' actes pratiques & ingenierie immobiliere' lexisnexs jurisclasseur. octobre. novembre.2013.\n\nCode monétaire et financier/Livre Ier: La monnaie/TitreIer: Dispositions générales/Chapitre II: Règlesd'usage de la monnaie/Section 1: L'indexation (Articles L112-1 à L112-4).\n\nCornu G: Legal Terminology Glossary, ed: Mansour Al-Qadi: Legal Terminology Glossary. Beirut: University Establishment for Studies, Publishing, and Distribution; 1988; 1998.\n\nDALLOZ: French Civil Code, (in Arabic) Saint Joseph University in Beirut, 118th Edition in Arabic, 2009.2009.\n\nDesouki M: Legal aspects of managing negotiations and concluding contracts. Saudi Arabia: General Will Institute; 1995.\n\nDoucet V: Les Clauses d indexation et les ordonnances du 30 decembre 1958 et du 4 fevrer 1959.L.G.D.J: Paris.1958.\n\nDoucet JP: Les Clauses d indexation et les ordonnances du 30 décembre 1958 et du 4 févrer 1959. Paris: LGDJ; 1965.\n\nFabre F: Les clauses d’adapation dans les contats. R.T.D Com; 1983.\n\nFadel K: Amending the contract during implementation. Faculty of Law, University of Algiers; 2001. Master's thesis.\n\nGhannam S: The impact of changing circumstances on international trade contracts. Cairo University; 1982. PhD thesis.\n\nGustan J, Jaman C, Pino M: Al-Mutawil in Civil Law, Formation of the Contract, ed: Mansour Al-Qadi. Beirut: Majd University Foundation for Studies and Publishing; 2008.\n\nHammoud A: Legal aspects of the negotiation stage of a contractual nature. Journal of Legal and Economic Research. 2001; 10(20). Menoufia University.\n\nAl-Jamal M: The Quest for Contracting. Beirut: Al-Halabi Legal Publications; 2002; 136.\n\nJassim A: The legal system of the renegotiation clause, a study in international trade contracts. Al-Muhaqqiq Al-Hilli Journal of Legal and Political Sciences. Iraq: University of Babylon; 2011; Volume 11(1).\n\nAl-Khasawneh A: Legal Aspects of the Commitment to Renegotiate and Review Contracts. Journal of Law. 2014; (1): 2014. Kuwait University, Kuwait.\n\nKhater S: Adapting the contract in light of price fluctuations, a comparative study in civil law. Saddam University Journal. 1998; 2(3).\n\nLambertrie, I.DE: Rapportfrancais,in “lecontrataujourdhu: comparaison Franco.anglaise”, sous la direction de D.TALLON et D.HARRIS,LGDJ,Paris.1987.\n\nMadani S: The state's responsibility for its legitimate actions, doctoral dissertation, International Press.1952; p. 165.167.\n\nMalkawi B: The impact of the principles of the contract when a political crisis occurs (e.g., the Middle East since 1945), Dar Wael for Printing. Amman: Publishing and Distribution; 2003.\n\nMansour S: The element of stability and the factor of change in the civil contract. Dar Al-Fikr Al-Lubani; 1987.\n\nMarraud C, Akyurek M-LO: Crise economique et revision des contrat. Gaz. Pal; 2009.\n\nMuhammad A: Provisions for estimating compensation and the effect of changing the purchasing power of money on its estimation, a comparative study. Cairo: Dar Al-Nahda Al-Arabiya; 2008; vol. 2008. : 414.\n\nAl-Najjar I, Badawi A, Shalala Y: French-Arabic Legal Dictionary. Lebanon: Library of Lebanon; 1983; 85.\n\nOmmeslagehe PV: Clauses de force majeure et d’imprevision (hardship) dans les contrats internationaux. Rev.Int. Dr Com. 2020. ' P' 7 et s.\n\nAl-Otaibi S: The idea of the jewel in the contractual relationship, a comparative study. Alexandria: University Press House; 2009.\n\nQandil M: The role of parties in settling contractual disputes. Alexandria: New University Publishing House; 2009.\n\nQasim M: Civil Law Obligations, Contract. Lebanon: Al-Halabi Legal Publications; 2018; V(1): p. 316.\n\nRaad N: The decline in cash value and monetary obligations' fate in Lebanese law. Al-Adl Magazine. 1993; V 28. Beirut Bar Association.\n\nRashwan R: The impact of economic conditions on the binding force of a contract. Cairo University; 1994. PhD thesis.\n\nReinecher H: L’influence de la dépreciation monetaire sur droit des obligations. II.Paris.1982.\n\ns.; N. GRAS; Essai sur les clauses contractuelles' thèse' de Lille2'.2014.\n\nAl-Salmani A: Renegotiation Clause in International Trade Contracts. Moroccan Law Journal. 2010; 2010: 231. Dar Al-Salam Printing and Publishing, Morocco, No. 16.\n\nSama'ah K: The legitimacy of agreeing based on estimating the value of the obligation in light of the change in the purchasing power of money in Jordanian civil law. Jordanian Journal of Law and Political Science. 2015; Volume 7(1): 2015. Jordanian University, Amman.\n\nSentence V: CCI N 3344/1981,Rec.sen.arb.CC1 1974.1985.1985.\n\nShanab M: Lessons in the Theory of Commitment. Dar Al Nahda Al Arabiya, Cairo: Sources of Commitment; 1977.\n\nAl-Shawabkeh H: The impact of the deterioration of the value of money on contractual obligations, a comparative study of Islamic jurisprudence. 200, Jordan: Faculty of Law, Mutah University; 2005; 91. Master's thesis.\n\nSultan A: The Summary of the General Theory of Commitment. Cairo: Dar Al-Maaref; 1963.\n\nTallon D: Réflexions comparatives' les modifications du contrat au cours de son execution en raison des circonstances nouvelles. Rev. Int. Dr. Comp; 1986.\n\nTerre F, Simler P, Lequette Y: Droit civil, les obligations' 5èmeéd.' DALLOZ' Paris.1993.\n\nToulemon A: Évolution de la jurisprudence en matiere de clauses d’échelle mobile et de clauses de variation suivnt indices. R.T.D. com; 1951."
}
|
[
{
"id": "316148",
"date": "26 Aug 2024",
"name": "Xavier Nugraha",
"expertise": [
"Reviewer Expertise Civil Law",
"Criminal Law"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. This research idea is very interesting and provides a breakthrough in the event that there are parties to the contract who cannot sign changes to the contract, then the attribution clause can automatically modify the existing contract. This is very useful especially associated with smart contracts that are developing today. 2. In the background of this research can be described real case examples related to the importance of the Attribution clause. 3. In the background of this research, the formulation of problems and differences with several related studies can be described (even though the researcher has said that this research is new research). 4. In the recommendation, the form of regulation (law) related to attribution clause can be added. 5. The existence of regulatory descriptions and case examples in several countries regarding attribution clauses makes the analysis of the author varied 6. It could be described in a table of concrete examples of automatic contract changes based on attribution clauses, so that readers can understand more easily the urgency and examples of attribution clauses. 7. Examples of circumstances can be outlined, so that this attribution clause can occur, so that the contract is changed automatically\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "313451",
"date": "03 Sep 2024",
"name": "Tze Chin Ong",
"expertise": [
"Reviewer Expertise Commercial law",
"Consumer Protection Law and International commercial law."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article discussed the attribution clause in civil contracts which means it applies to all contracts. However, the attribution clause can only apply to insurance contracts or certain financial contracts under the law. There are no clear examples of how the attribution clause is used and the implication of contract certainty is reversing. The attribution clause can only be applied in the circumstances that one of the parties to the contract breaches the obligations of the contract. The suggestion of using such an attribution clause altered the contractual nature and sanctity of the contract. The attribution clause could not be applied to all civil contracts, it is only of limited use for specific contracts such as insurance, financial services, investments, etc. Hence the findings of the research are problematic. Besides, the methodology used for the paper is unclear whether it is qualitative or quantitative research, and how the method is used to achieve the finding. There is no clear problem statement, no clear objectives and literature reviews are inadequate.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "316154",
"date": "11 Sep 2024",
"name": "Radosveta Vassileva",
"expertise": [
"Reviewer Expertise Comparative Private Law (with a focus on obligations)",
"Legal History",
"EU Law",
"Constitutional Law"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article focuses on the feasibility of what it calls an \"attribution clause\" - a provision in the contract that prescribes certain modifications when a change of circumstances takes place. Such clauses may promote efficiency by helping parties to avoid lengthy disputes and litigation while respecting the principles of freedom of contract and the binding force of contract. After surveying some of the available literature and offering some insights into how French law approaches the question, the article analyses if and how such clauses can be recognized under Jordanian law.\n\nThe article makes a scholarly contribution - its discussion on Jordanian law is particularly interesting since this is a jurisdiction that is often ignored in foreign literature. Since the article is written in English, it is accessible to a wider audience that can learn more about Jordanian law.\n\nThere are some areas, however, that could be improved.\n1. The scope of the paper can be defined better, so that its contribution is more distinct. Namely, in the introduction, the authors mention a provision from Jordanian law and a provision from the Egyptian Civil Code, without quoting them and without clarifying why they are interested in these two jurisdictions (why they put them together to begin with). Subsequently, the relevant discussion at the end of the article concerns only Jordanian law, which creates the impression that something is missing (where is the discussion on Egyptian law?). 2. It is recommended that the authors explain better why they analyse French law in such detail before discussing the developments in Jordan - is there a connection between French law and Jordanian law that the foreign reader should know in advance? Any reference to literature on this question will be helpful. 3. At multiple places, the article refers to 'the balance of the contract' without defining what this means in the jurisdictions they discuss. It should be noted that not only this notion does not exist everywhere, but its definition varies. 4. Sadly, at several places, the article is thin on references. a. For instance, in the section titled 'The connection between the external indicator and the parties' activity', the authors refer to court rulings without referencing them properly. The reader would expect to see the name of the court, the date on which the decision was handed down, the number of the court decision, the number of proceedings, etc., so that he/she can find this decision. b. In the section titled 'The relationship between the external indicator and the subject of the contract', the authors discuss the approach of the 'French judiciary' without including a proper reference - either court decisions or at least a reference to an academic article/book is necessary. c. In the section titled 'Amendment for parties’ reciprocity', the decision by the French Court of Cassation is not referenced properly. Idem for the decision by the court of appeal. d. In the section titled 'Invalidity of the External Indicator', the claim that 'French Civil Code specifies that the legally prohibited indicator is invalid and cannot be supported or ratified' is not supported by any literature. One expects at least a reference to the concrete article/articles from the civil code that have been taken into consideration to make this claim. In the same section the authors refer to 'the Court of Appeal', without specifying which one and without giving any details about the court decision/decisions they have in mind. In the same section, the sentence starting with 'The French Civil Code states that the invalidation must only address the clause adopting...' does not refer to the relevant articles. e. Overall, it is recommended that the authors make sure that each court decision they discuss is referenced properly and that each time they make claims about the approach of the French judiciary/French law, they cite a proper source. 4. In the bibliography at the end, many of the references in French have been misspelled. It is recommended that this be remedied.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-585
|
https://f1000research.com/articles/13-4/v1
|
03 Jan 24
|
{
"type": "Systematic Review",
"title": "The safety and efficacy of spray cryotherapy after endoscopic sinus surgery in chronic rhinosinusitis: A systematic review of randomized controlled trials",
"authors": [
"Mohammad J. J. Taha",
"Obaida Falah",
"Mohammad T. Abuawwad",
"Ayham R. Sara",
"Adham A. Aljariri",
"Abdulqadir J. Nashwan",
"Ibrahim T. Abuawwad",
"Ahmad J. Taha",
"Abdullah A. Elhakim",
"Majed Akili",
"Mohammad J. J. Taha",
"Obaida Falah",
"Mohammad T. Abuawwad",
"Ayham R. Sara",
"Adham A. Aljariri",
"Ibrahim T. Abuawwad",
"Ahmad J. Taha",
"Abdullah A. Elhakim",
"Majed Akili"
],
"abstract": "Background Chronic rhinosinusitis (CRS) is a condition that affects 5–12% of the general population. Endoscopic sinus surgery (ESS) is the preferred treatment because of its few adverse effects. The most common post-operative consequences include synechia, nasal blockage, and disease recurrence. Spray cryotherapy is a novel therapeutic approach with promising outcomes for the treatment of upper airway disorders. This review aimed to investigate the effects of spray cryotherapy (SCT) following ESS in patients with chronic rhinosinusitis.\n\nMethods Six electronic databases were searched for randomized clinical trials (RCTs). The selected trials were evaluated for methodological quality, and data were extracted by two independent reviewers. The Cochrane risk-of-bias tool was used to assess the quality of evidence.\n\nResults Three RCTs with 85 patients were included in the final analysis. SCT was related to -16 and -77 reductions in Lund-McKay and SNOT-22 scores after 36 weeks of follow-up, in contrast to a placebo, which showed -10.4, -65. Regarding the side effects of SCT, no adverse effects were reported, and visual assessments showed no pain, visual field loss, or any other ocular complications.\n\nConclusions SCT is a new treatment modality after endoscopic sinus surgery that shows an effective post-operative management strategy with better post-operative scales (Lund-McKay, SNOT-22, POSE, and Lund-Kennedy) and less edema, obstruction, crusting, and inflammation with minimal or no side effects. However, further research with longer follow-ups, a larger sample size, and subjective assessment is needed to assess any possible long-term side effects.",
"keywords": [
"chronic rhinosinusitis",
"functional endoscopic sinus surgery",
"middle meatus antrostomy",
"nasal polyposis",
"spray cryotherapy"
],
"content": "Introduction\n\nChronic rhinosinusitis (CRS) is a name describing a family of clinical conditions that affect 5–12% of the general population, disturbing their quality of life and adding a financial burden to the healthcare system.1 Chronic rhinosinusitis in adults was defined in the European position paper on rhinosinusitis and nasal polyps 2020 as “the presence of two or more symptoms, one of which should be either nasal blockage, obstruction, congestion, or nasal discharge (anterior or posterior nasal drip), with or without facial pain/pressure, and with or without a reduction or loss of smell; for 12 weeks; with validation by telephone or interview.”.1 CRS can occur with or without polyps, and there appears to be a significant overlap between the two forms of chronic rhinosinusitis in terms of the inflammatory profile, clinical presentation, and treatment effect. Despite these differences in etiology and phenotype, many treatments for chronic rhinosinusitis are initiated in clinical practice without knowledge of a patient’s “polyp status,” despite the fact that 25–30% of CRS cases present with nasal polyps (NP).2 CRS has many variations in terms of histology and clinical presentation, making its management controversial. Medically, many options are available, including corticosteroids, antibiotics, antihistamines, anti-leukotrienes, decongestants, saline, and aspirin, while surgical options include primary sinus surgery, revision endoscopic surgery, and many other techniques.1,3 In the present study, the surgery of interest is endoscopic sinus surgery (ESS) for CRS. Despite being widely utilized with over 250,000 sinus surgeries per year in the US,4 it is usually associated with synechia, obstruction, and stenosis of the maxillary or frontal ostium, which is caused by the apposition of two mucosal surfaces. Excessive scar formation, adhesions, and sinus osteomeatal stenosis are considered the main causes of disease recurrence and the need for revision surgery.5\n\nSpray cryotherapy (SCT) is a technique that involves treating mucosal lesions with liquid nitrogen at -90°C to freeze cellular water content and impose cellular necrosis for a few minutes to prevent mucosal surface adhesion, resulting in faster healing, less obstruction, and stenosis.6 It was previously adapted for the treatment of esophageal lesions, including esophageal cancer and Barrett’s esophagus.7–9 In 2010, SCT was first used by Krimsky et al. for the treatment of glottic and subglottic stenosis, and was the first application of SCT in airway surgery.10 Subsequently, SCT was successfully used in cases of benign and malignant airway diseases.11,12 In this systematic review of randomized controlled trials, we summarized and analyzed the available evidence regarding the impact of SCT after ESS for CRS with or without polyps. To our knowledge, this is the first systematic review to address the effects of SCT on healing after ESS surgery.\n\n\nMethods\n\nThis systematic review of randomized controlled trials was performed in accordance with the PRISMA checklist.13,14 The filtration phases were carried out according to the Cochrane criteria.15\n\nWe included studies that examined the effectiveness of post-operative SCT in patients with chronic rhinosinusitis of either sex, regardless of age, from any healthcare context. The main outcome of interest was investigating the main impact of SCT after endoscopic sinus surgery for chronic rhinosinusitis with or without nasal polyposis. According to our inclusion criteria, the studies included satisfied the following criteria: 1) randomized control trials (RCT); 2) SCT was used following endoscopic sinus surgery; and 3) Only in English.\n\nThe PubMed, Scopus, ClinicalTrails.gov, Cochrane Library, Web of Science, and Google Scholar databases were used for the searches, which had a date range from inception until 1/8/2023 for all databases. Randomized controlled trials, endoscopic sinus surgery (mesh terms), and spray cryotherapy (mesh terms) were used as search terms. For Google Scholar, Web of Science and ClinicalTrials.gov we used the simplest of keywords “spray cryotherapy and chronic rhinosinusitis” without filter. For PubMed and Scopus “(((spray cryotherapy) or (SCT)) and ((chronic rhinosinusitis) or (chronic rhinitis)) and ((endoscopic sinus surgery) or (endoscopic sinus surgery (MESH)))” were used. We also manually searched the entire text of the recognized systematic reviews that had been published in the area for potentially relevant details. Following the searches, references were located and exported to an Endnote X9 file after duplicates were eliminated. Filtration and extraction were performed by two independent reviewers, and any disagreement was resolved by a third reviewer.\n\nThe Cochrane Handbook for Systematic Reviews of Interventions was used to evaluate the quality of the retrieved RCTs. The following areas were covered by the Cochrane risk-of-bias assessment tool: sequence generation (selection bias), allocation sequence concealment (selection bias), blinding of participants and staff (performance bias), blinding of outcome assessment (detection bias), incomplete outcome data (attrition bias), selective outcome reporting (reporting bias), and other possible sources of bias.\n\nTo prevent bias, each publication was extracted separately by two randomized authors, and any disagreements were resolved by a third reviewer. The study design, participant country, participant age, description of cryotherapy, control groups, outcomes, and time points were among the characteristics extracted from the studies. Each process followed the suggested techniques in Higgins & Cochrane (2020).15,16\n\nBecause of the small number of included trials, a planned meta-analysis using a random effects model was not possible. Mean differences and 95% confidence intervals are shown. RevMan 5.4 software (Cochrane Collaboration) was used for all analyses. Arguments between the reviewers were handled by a third reviewer (MJJT). We planned subgroup analyses to examine the effects of different types and doses of cryotherapy, as well as the two forms of CRS (one with polyposis and one without). Furthermore, sensitivity analyses were performed to determine whether a significant risk of bias affected the estimates. We aimed to use meta-regression for subgroup and sensitivity analyses if feasible (i.e., at least 10 trials were analyzed); otherwise, qualitative analysis might have been performed in accordance with the guidelines.17\n\nFor <10 pooled studies, publication bias evaluation is unreliable according to Egger et al. As a result, we were unable to use Egger’s test for funnel plot asymmetry to evaluate publication bias in the current review.18,19\n\n\nResults\n\nOur search yielded 322 results; 206 duplicates were eliminated, and the remaining 83 abstracts were reviewed. Three randomized controlled trials were incorporated after 10 prospective full texts were evaluated. Figure 1 in this review provides an illustration of the filtration procedures. According to the Cochrane risk-of-bias tool, all included studies were scored as low risk (Figures 2 and 3).\n\nThree of the articles met the inclusion criteria. Table 1 summarizes the characteristics of the included studies. There were 85 chronic rhinosinusitis patients in the entire study population among all papers that were chosen, with approximately equal representation of men and women (54 males and 57 females). In all studies, the average age of the study population was 42.65±14 years.\n\nRegarding the operative technique, devices, and post-operative management, the Brymill (Ellington, CT) CRY-AC-3 Cryogenic System was used in all included studies, and all patients received post-operative antibiotics as part of different post-operative protocols. The characteristics of the surgical and post-operative protocols are summarized in Table 2.\n\nOwing to the heterogeneity of the data regarding the measurements of post-operative improvement, conducting a meta-analysis was inappropriate. However, spray cryotherapy, according to Rezaeian (2018), was related to -16 and -77 reductions in Lund-McKay and SNOT-22 scores after 36 weeks of follow-up, in contrast to the placebo, which showed -10.4, -65. This outcome was also demonstrated by the POSE and Lund-Kennedy scores. Additionally, adhesions were more frequent on the control side than on the cryotherapy side. One middle meatus with a decreased dimension was reported in an SCT patient, compared to eight middle meatal antrostomies with stenoses in the control group at the final follow-up. In the Trombitas study, post-operative stenosis is defined as when the MMA diameter is less than 6 mm.\n\nAccording to Trombitaș et al.,20 the spray cryotherapy (SC) group significantly outperformed the control group in terms of nasal obstruction and discharge. Furthermore, the placebo side was linked to mononuclear cell infiltration, edema with collagen fiber dislocation, epithelial hyperplasia, goblet cells, and persistent squamous metaplasia on top of the epithelial hyperplasia, whereas the SC side was linked to superior collagen fiber organization. Similarly, according to Albu et al.21 throughout the entire follow-up period, the side that had received cryotherapy showed considerably less edema of the mucosa, polypoid alterations, adhesions, and ostia narrowing. However, both treatments had identical distributions of discharge and crusting.\n\nAccording to Albu et al.,21 there were no adverse effects (for example, hemorrhage or infection) in either group during the trial period, and this conclusion was also demonstrated by Rezaeian.22 Furthermore, Trombitas et al.20 investigated the visual assessments as SCT was sprayed around the orbit and found no pain, visual field loss, visual acuity, color perception, diplopia, ocular motility, visual acuity, globe displacement, or swelling.\n\n\nDiscussion\n\nThe main goal of this study was to investigate the role and impact of SCT in chronic rhinosinusitis with or without nasal polyps following endoscopic sinus surgery. The most obvious finding to emerge from this study was that the overall effects of SCT are favorable, promising, and associated with good outcomes and better healing. SCT is a new post-operative modality that began with Dr. Albu and his team,21 who used SCT following ESS based on a previous study conducted by Krimsky et al.,23 who used SCT to treat glottic and subglottic narrowing. However, Albu et al.21 reported some limitations, such as a lack of subjective outcomes in the post-operative assessment, a short follow-up period, and the need to divide patients into two groups, with and without polyposis, to evaluate the overall impact of SCT on the healing of different diseases. Following the Albu study, Rezaeian22 and Trombitas et al.20 Three studies used the same SCT protocols. However, Rezaeian’s study had a 36-week follow-up period and only included patients with CRS with nasal polyposis. In addition, Trombitas’ study showed a longer follow-up period of 12 months (52 weeks), and it also measured mucosal histology pre- and post-operatively, which provided cellular evidence besides the clinical evidence regarding the healing outcome.\n\nThe present study investigated chronic rhinosinusitis with and without nasal polyposis. Despite differences in etiology and phenotype, many therapies for chronic rhinosinusitis are initiated in clinical practice without knowing a patient’s “polyp status.” Determining the type of CRS does not necessarily recommend therapy modifications. Lee-Yee et al. examined patients with and without polyps together in the first examination of treatment results, followed by a subgroup analysis, as we did.24\n\nThe main symptoms of CRS are nasal blockage/obstruction/congestion and nasal discharge (anterior/posterior nasal drip)25 and SCT shows a great reduction in all rhinosinusitis scores, lesser post-operative adhesions, discharge, side effects, inflammatory cell infiltration, and better collagen fiber arrangements in comparison with placebo, which could be explained by the fact that cryotherapy induces disruption of endothelial damage, thrombosis, and ischemia, and improves mucosal healing and decreases granulation tissue formation.26 On the histological level, it resulted in better collagen organization and reduced keratinization, and long-term observation documented the absence of scarring and stricture formation.27\n\nGreenwald et al.28 studied the safety and efficacy of endoscopic sinus surgery in the treatment of esophageal cancer and found no adverse effects, which is comparable to our findings. Using SCT in airway surgery, on the other hand, has been linked to problems such as barotrauma, pneumomediastinum, nitrogen gas embolism, and pneumothorax.29 However, none of these side effects were reported in the trials included in the present study. As a result, SCT as a post-ESS treatment appears to be safe. However, further studies with longer follow-up periods are required to determine the safety of SCT.\n\nOne of the main post-operative complications of ESS in CRS is recurrence, which was not reported in any of the included trials for a 12-month follow-up period. However, in a study conducted on the recurrence of nasal polyposis, six-months after ESS recurrence was 35% and after 18-months it was 40%.30 In other studies, the recurrence rate reached up to 60% after 18 months of follow-up, indicating that the percentage of recurrence increased over time; therefore, longer follow-up is needed to determine the recurrence ratio after SCT.\n\nIn accordance with the present results, a previous study conducted by Gorelik et al. demonstrated that both cryotherapy and radiofrequency had better outcomes than a placebo.29 Moreover, SCT has been shown to improve post-operative outcomes in different ENT surgeries, including those for malignant airway disease, as demonstrated by a study conducted by Browning et al.31 Browning et al. showed that SCT is safe and demonstrated better outcomes in post-operative respiratory complications from malignancies, such as dyspnea/hypoxia, granulation tissue, and bleeding tissue. Other advantages of using SCT in the management of airway diseases have been reported in many other studies.23,32,33\n\nOne of the limitations of this study was the lack of data on the clinical history of the included patients, which could alter the patients’ results and outcomes. For example, diabetes can slow down the healing process. Furthermore, the Global Allergy and Asthma Network of Excellence epidemiological study found a strong link between asthma and CRS,34 which raises two concerns: What was the prevalence of asthma in the included studies? How does cryotherapy affect the symptoms of asthma?\n\n\nConclusions\n\nThe present systematic review was designed to determine the impact of SCT on ESS following chronic rhinitis; the results of this investigation show that SCT is associated with better healing and fewer negative complications such as synechia, edema, obstruction, crusting, and inflammation. Moreover, the findings of this study contribute to existing knowledge on the advantages of using cryotherapy in medicine in general, and specifically in post-operative airway surgery. Nevertheless, more research on this topic needs to be undertaken with osteitis, osteogenesis, and visual side effects, with a suitable assessment to reveal any adverse consequences associated with endoscopic SCT.",
"appendix": "Data availability\n\nAll underlying data are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA checklist for ‘The safety and efficacy of spray cryotherapy after endoscopic sinus surgery in chronic rhinosinusitis: A systematic review of randomized controlled trials’, https://www.doi.org/10.6084/m9.figshare.24661968. 14\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAcknowledgements\n\nThe authors would like to express great appreciation to Dr. Usama Abdelnaseer for his valuable and constructive suggestions during the development of this research. Open Access funding was provided by the Qatar National Library.\n\n\nReferences\n\nFokkens WJ, et al.: European Position Paper on Rhinosinusitis and Nasal Polyps 2020. Rhinology. 2020; 58(Suppl S29): 1–464. Publisher Full Text\n\nStevens WW, Schleimer RP, Kern RC: Chronic Rhinosinusitis with Nasal Polyps. J. Allergy Clin. Immunol. Pract. 2016; 4(4): 565–572. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTa NH: Will we ever cure nasal polyps? Ann. R. Coll. Surg. Engl. 2019; 101(1): 35–39. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBhattacharyya N: Ambulatory sinus and nasal surgery in the United States: demographics and perioperative outcomes. Laryngoscope. 2010; 120(3): 635–638. PubMed Abstract | Publisher Full Text\n\nManciula L-G, et al.: The effects of postoperative astaxanthin administration on nasal mucosa wound healing.2019; 8(11): 1941.\n\nMoore RF, Lile DJ, Abbas AE: Current status of spray cryotherapy for airway disease. J. Thorac. Dis. 2017; 9(Suppl 2): S122–s129. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGreenwald BD, et al.: Endoscopic spray cryotherapy for esophageal cancer: safety and efficacy. Gastrointest. Endosc. 2010; 71(4): 686–693. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShaheen NJ, et al.: Safety and efficacy of endoscopic spray cryotherapy for Barrett’s esophagus with high-grade dysplasia. Gastrointest. Endosc. 2010; 71(4): 680–685. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohnston MH, et al.: Cryoablation of Barrett’s esophagus: a pilot study. Gastrointest. Endosc. 2005; 62(6): 842–848. PubMed Abstract | Publisher Full Text\n\nKrimsky WS, et al.: Spray cryotherapy for the treatment of glottic and subglottic stenosis. Laryngoscope. 2010; 120(3): 473–477. PubMed Abstract | Publisher Full Text\n\nFinley DJ, et al.: Airway spray cryotherapy: initial outcomes from a multiinstitutional registry. Ann. Thorac. Surg. 2012; 94(1): 199–204. discussion 203-4. PubMed Abstract | Publisher Full Text\n\nFernando HC, et al.: Feasibility of spray cryotherapy and balloon dilation for non-malignant strictures of the airway. Eur. J. Cardiothorac. Surg. 2011; 40(5): 1177–1180.\n\nLiberati A, et al.: The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration. J. Clin. Epidemiol. 2009; 62(10): e1–e34. PubMed Abstract | Publisher Full Text\n\nAbuawwad M: PRISMA 2020 checklist for The safety and efficacy of spray cryotherapy after endoscopic sinus surgery in chronic rhinosinusitis: A systematic review of randomized controlled trials. [Dataset]. figshare. Publisher Full Text\n\nHiggins JPT, Cochrane C: Cochrane handbook for systematic reviews of interventions. Cochrane book series. Hoboken, NJ: Wiley-Blackwell; Second ed.2020; 15. : 123–125. Publisher Full Text\n\nWan X, et al.: Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Med. Res. Methodol. 2014; 14: 135. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHiggins J, et al.: Cochrane Handbook for systematic reviews of interventions version 6.2, 2021.2021.\n\nEgger M, et al.: Bias in meta-analysis detected by a simple, graphical test. BMJ. 1997; 315(7109): 629–634. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTerrin N, et al.: Adjusting for publication bias in the presence of heterogeneity. Stat. Med. 2003; 22(13): 2113–2126. Publisher Full Text\n\nTrombitaș V, et al.: Maxillary antrostomy patency following intraoperative use of spray cryotherapy. J. Clin. Med. 2019; 9(1): 88. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlbu S, et al.: The influence of spray cryotherapy on wound healing following endoscopic sinus surgery in chronic rhinosinusitis. Laryngoscope. 2016; 126(1): 25–32. PubMed Abstract | Publisher Full Text\n\nRezaeian A: Outcome of spray cryotherapy plus functional endoscopic sinus surgery on management of healing in nasal polyposis. Am. J. Otolaryngol. 2018; 39(1): 10–13. PubMed Abstract | Publisher Full Text\n\nKrimsky WS, et al.: Spray cryotherapy for the treatment of glottic and subglottic stenosis. Laryngoscope. 2010; 120(3): 473–477. PubMed Abstract | Publisher Full Text\n\nChong L-Y, Piromchai P, Sharp S, et al.: Biologics for chronic rhinosinusitis. Cochrane Database Syst. Rev. 2021; 3(3): CD013513. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu Z, et al.: Chinese society of allergy and Chinese society of otorhinolaryngology-head and neck surgery guideline for chronic rhinosinusitis.Allergy Asthma Immunol. Res.2020; 12(2): 176–237.PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrimsky WS, et al.: Bronchoscopic spray cryotherapy: assessment of safety and depth of airway injury.J. Thorac. Cardiovasc. Surg.2010; 139(3): 781–782.PubMed Abstract | Publisher Full Text\n\nKrimsky WS, et al.: Spray cryotherapy for the treatment of glottic and subglottic stenosis.Laryngoscope.2010; 120(3): 473–477. PubMed Abstract | Publisher Full Text\n\nGreenwald BD, et al.: Endoscopic spray cryotherapy for esophageal cancer: safety and efficacy.Gastrointest. Endosc.2010; 71(4): 686–693.PubMed Abstract | Publisher Full Text | Free Full Text\n\nGorelik D, et al.: Indirect comparison of the efficacy of radiofrequency neurolysis and cryotherapy in the treatment of chronic rhinitis. Int. Forum Allergy Rhinol. n/a(n/a).\n\nDeConde AS, et al.: Prevalence of polyp recurrence after endoscopic sinus surgery for chronic rhinosinusitis with nasal polyposis.Laryngoscope.2017; 127(3): 550–555. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrowning R, Turner JF Jr, Parrish S: Spray cryotherapy (SCT): institutional evolution of techniques and clinical practice from early experience in the treatment of malignant airway disease. J. Thorac. Dis. 2015; 7(Suppl 4): S405–S414.\n\nFinley DJ, et al.: Airway spray cryotherapy: initial outcomes from a multiinstitutional registry. Ann. Thorac. Surg. 2012; 94(1): 199–204. PubMed Abstract | Publisher Full Text\n\nBhora FY, et al.: Treatment of benign tracheal stenosis using endoluminal spray cryotherapy. JAMA Otolaryngology–Head & Neck Surgery. 2016; 142(11): 1082–1087. PubMed Abstract | Publisher Full Text\n\nJarvis D, et al.: Asthma in adults and its association with chronic rhinosinusitis: the GA2LEN survey in Europe.Allergy.2012; 67(1): 91–98. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "261156",
"date": "18 Apr 2024",
"name": "Sergei Karpischenko",
"expertise": [
"Reviewer Expertise Clinical and scientific interests: endoscopic sinus sugery",
"laser surgery in otorhinolaryngology",
"laryngeal and tracheal microsurgery",
"otosurgery",
"oncology",
"dacryology."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMohammad J. J. Taha et al. present an important and interesting systematic review to analyse data from randomised clinical trials on the outcomes of spray cryotherapy (SCT) after endoscopic sinus surgery (ESS) in patients with chronic rhinosinusitis with and without polyps. Functional endoscopic surgery of the nasal cavity and paranasal sinuses is currently the leading method of surgical treatment of chronic rhinosinusitis. In the postoperative period it is necessary to correct inflammatory and regenerative processes to reduce postoperative reactive phenomena, prompt healing, reduce the risk of complications. The accumulated clinical and scientific data show that despite the diversified preventive measures after ESS local complications in the nasal cavity remain an urgent problem. Spray cryotherapy is a possible treatment method that can reduce complications after ESS. Abstract Covers the aims, methodology, overall results and conclusions. Introduction Aspects of endoscopic sinus surgery and the relevance of adjunctive postoperative care are covered in detail and convincingly. The authors provide information on the place of the problem in otorhinolaryngology and the health care system, and recall the impact of chronic rhinosinusitis on quality of life. At the same time, general information about chronic rhinosinusitis seems somewhat redundant. It may be worth adding information about the difficulties and challenges of postoperative care of the nasal mucosa after ESS, postoperative access to prevent scarring and synechiae formation. It is probably worth presenting information about the existing possible solutions to these problems, emphasising that this issue has no unambiguous solution. Methodology A systematic review of randomised controlled trials was conducted according to the PRISMA checklist. The filtering stages of the studies were carried out according to Cochrane criteria. Which indicates the compliance of the publication with international standards. The inclusion criteria are relevant to the research objectives. The process of material collection is described in an accessible and consistent manner and provides insight into the sample obtained. Each publication was extracted separately by two independent authors and any disagreements were resolved by a third reviewer. The size of the sample obtained influenced the planned statistical processing methods, which did not affect the quality of the article or its informative value in any way. Results As a first figure, a PRISMA flow chart of included and excluded studies is presented, which allows to assess the amount of work undertaken in the process of selecting studies for the systematic review. Subsequently, the risks of bias for each included study are given graphically. A table of studies provides a comprehensive overview of the patient groups, participant characteristics, outcomes and time periods of follow-up. The effects of cryotherapy administered after endoscopic sinus surgery are systematically analysed based on the SNOT-22, Lund-McKay, POSE and Lund-Kennedy scoring scales. Discussion An extended review of the literature on the above topic was performed and references to similar studies are provided. The paragraph beginning \"Greenwald et al.\" is most likely a misspell: replace endoscopic sinus surgery with spray cryotherapy. Given the researchers' stated goal, it seems rational to replace chronic rhinitis with chronic rhinosinusitis in the conclusion section. In summary, this is a systematic review that is an important addition to the literature. As the authors correctly note, cryotherapy after endoscopic sinus surgery is a promising method that requires follow-up RCTs.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": []
},
{
"id": "275424",
"date": "29 May 2024",
"name": "Serafín Sánchez-Gómez",
"expertise": [
"Reviewer Expertise Rhinology",
"cochlear implants"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a systematic review study that evaluated the effects of spray cryotherapy (SCT) following endoscopic surgery for chronic rhinosinusitis. Three randomized clinical trials including a total of 85 patients were selected.\nSeveral decades after the introduction of endonasal endoscopic techniques for the treatment of CRS, adverse events and complications in the surgical field continue to occur despite technical and instrumental improvements. Therefore, it is pertinent to investigate new ways to reduce these events and complications that deteriorate the quality of life of patients, requiring meticulous postoperative care and sometimes leading to reoperations.\nThe authors present a study that compiles the experience of using spray cryotherapy on the surgical bed after endonasal endoscopic surgery, selecting three clinical trials that met the inclusion and exclusion criteria. The authors applied an extremely rigorous selection criterion for articles, including only those containing randomized and blinded clinical trials. This design is not well-suited for surgical procedures and introduces significant uncertainties about the reliability of the data included in the clinical trials. The inclusion of other well-designed prospective studies would have been acceptable.\nThe methodology of the systematic review is pertinent and correct. It would have been desirable for the authors to submit their project to be included in the PROSPERO database of systematic reviews. Nevertheless, the use of the PRISMA statement and Cochrane methodology ensures that the authors have used the best methods to adequately conduct a systematic literature review. The presentation of results in the PRISMA flowchart and tables is appropriate and sufficient.\nGiven the novelty of spray cryotherapy in the field of ESS, the authors could have provided more information about this therapy in the Introduction, as adverse events and complications are well-known.\nThe results of their systematic review showed that SCT was associated with better outcomes in Lund-McKay, SNOT-22, POSE, and Lund-Kennedy scales compared to placebo. It was also associated with less edema, obstruction, crusting, and inflammation. No adverse effects of SCT were reported. These are perfectly suitable outcome variables for the review's objective.\nThe authors have identified the main five weaknesses of the study:\n1. The sample size was small (only 3 studies with a total of 85 patients). Larger studies are needed.\n2. Follow-up periods were relatively short, up to a maximum of 12 months. Longer follow-up studies are needed.\n3. No information was provided on the clinical history of the included patients, which could have affected the results.\n4. Potential long-term side effects of SCT, such as osteitis or other ocular complications, were not evaluated.\n5. Only English articles were included, which could have introduced language bias. Studies in other languages should also be considered.\nThroughout the draft, a series of errors have been detected that should be resolved:\na.\n\nIn the Abstract, a consideration needs improvement: The phrase \"Endoscopic sinus surgery (ESS) is the preferred treatment because of its few adverse effects\" significantly limits the objective of the surgery if it is not stated that the reason for choosing this technique is due to achieving the best results, not only due to adverse effects. b.\n\nIn the 6th line of the Introduction, in the phrase \"...with validation by telephone or interview.\", there is an unnecessary period at the end of the phrase. c.\n\nThe third inclusion criterion in the Methodology section has \"Only in English\" capitalized, whereas the first criterion is in lowercase. The decision on capitalization should be consistent. d.\n\nIn the first paragraph of the Discussion, the phrase is incomplete or has punctuation errors: \"Following the Albu study, Rezaeian22 and Trombitas et al.20 Three studies...\" e.\n\nThe phrase in the Conclusion column of Table 1 contains English writing errors: \"SCT was associated with better outcomes in MMA diameter, histological analysis, nasal obstruction, and discharge, with no visual complications.\" f.\n\nThe phrase in the paragraph starting with Greenwald et al. should be corrected as the surgical technique does not correspond to the disease. g.\n\nIn the phrase \"Other advantages of using SCT in the management of airway diseases have been reported in many other studies,\" the word \"many\" is excessively emphatic and should be omitted. h.\n\nThe first sentence of the Conclusions, \"The present systematic review...\" could be better expressed as \"The present systematic review was designed to determine the impact of SCT on ESS in patients with chronic rhinosinusitis\" or “...following endoscopic surgery for chronic rhinosinusitis”\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": [
{
"c_id": "11695",
"date": "10 Jun 2024",
"name": "Abdulqadir Nashwan",
"role": "Author Response",
"response": "Comment (Lines 90-95): At the same time, general information about chronic rhinosinusitis seems somewhat redundant. It may be worth adding information about the difficulties and challenges of postoperative care of the nasal mucosa after ESS, postoperative access to prevent scarring and synechiae formation. Response: We appreciate the suggestion to provide more details on postoperative care. We will add information focusing on these challenges and how they can be managed effectively, as highlighted in references 5 and 6. Comment (Resolved Line 239): The paragraph beginning \"Greenwald et al.\" is most likely a misspell: replace endoscopic sinus surgery with spray cryotherapy. Given the researchers' stated goal, it seems rational to replace chronic rhinitis with chronic rhinosinusitis in the conclusion section. Response: The corrections have been made to accurately reflect the treatment discussed and the condition being addressed in the conclusion. Comment: The authors applied an extremely rigorous selection criterion for articles, including only those containing randomized and blinded clinical trials. This design is not well-suited for surgical procedures and introduces significant uncertainties about the reliability of the data included in the clinical trials. The inclusion of other well-designed prospective studies would have been acceptable. Response: We use randomized control trials as our inclusion criterion to ensure the highest quality data. Despite an extensive search for additional relevant studies, none met our rigorous standards, not even non-randomized clinical studies. Comment (Lines 99-101): Given the novelty of spray cryotherapy in the field of ESS, the authors could have provided more information about this therapy in the Introduction, as adverse events and complications are well-known. Response: We acknowledge this oversight and will revise the Introduction to include more comprehensive details about spray cryotherapy, especially regarding its adverse events and complications. Comment (Line 36): In the Abstract, a consideration needs improvement: The phrase \"Endoscopic sinus surgery (ESS) is the preferred treatment because of its few adverse effects\" significantly limits the objective of the surgery if it is not stated that the reason for choosing this technique is due to achieving the best results, not only due to adverse effects. Response: We will adjust the wording to clarify that the choice of ESS is based on its effectiveness in achieving the best outcomes, not merely its few adverse effects. Comment (Line 121): The third inclusion criterion in the Methodology section has \"Only in English\" capitalized, whereas the first criterion is in lowercase. The decision on capitalization should be consistent. Response: The capitalization will be corrected to maintain consistency throughout the document. Comment (Line 223): In the first paragraph of the Discussion, the phrase is incomplete or has punctuation errors: \"Following the Albu study, Rezaeian22 and Trombitas et al.20 Three studies...\" Response: This error will be rectified to ensure the sentence is complete and clear. Comment (Line 261): In the phrase \"Other advantages of using SCT in the management of airway diseases have been reported in many other studies,\" the word \"many\" is excessively emphatic and should be omitted. Response: The word \"many\" will be removed to avoid undue emphasis and maintain a neutral tone. Comment (Lines 270-271): The first sentence of the Conclusions, \"The present systematic review...\" could be better expressed as \"The present systematic review was designed to determine the impact of SCT on ESS in patients with chronic rhinosinusitis\" or “...following endoscopic surgery for chronic rhinosinusitis” Response: We will revise the conclusion to reflect these suggestions for greater clarity and precision in presenting the study’s objectives and outcomes."
}
]
}
] | 1
|
https://f1000research.com/articles/13-4
|
https://f1000research.com/articles/12-1419/v1
|
30 Oct 23
|
{
"type": "Research Article",
"title": "Relationship between benzene concentration, MDA levels and kidney function in car painting workshops in Surabaya: A cross-sectional observational study",
"authors": [
"Abdul Rohim Tualeka",
"Mohd Yusmaidie Aziz",
"Velu Perumal",
"Tamilanban Thamaraikani",
"Roslan Rosnon",
"Salsabila Novianti",
"Pudji Rahmawati",
"Ahsan Ahsan",
"Mohd Yusmaidie Aziz",
"Velu Perumal",
"Tamilanban Thamaraikani",
"Roslan Rosnon",
"Salsabila Novianti",
"Pudji Rahmawati",
"Ahsan Ahsan"
],
"abstract": "Background Car painting workers are at risk because of the use of solvents containing benzene as the main ingredient in the car painting process. One of the clinical effects of systemic benzene is kidney disorders. Therefore, the purpose of this study is to analyze the relationship between benzene and Risk Quotient (RQ) benzene concentrations with Malondialdehyde (MDA), Blood Urea Nitrogen (BUN), and creatinine levels in workers exposed to benzene in car painting workshops in Surabaya.\n\nMethods This is an observational, cross-sectional study conducted at two car painting workshops in Surabaya that use benzene as a solvent in their production process, namely in industries in Kalijudan and Jemursari. The research sample was taken using the accidental sampling method and as many as 30 respondents were involved in this study. The variables studied included benzene concentration, RQ benzene, MDA levels, and kidney function (BUN and creatinine levels). Analysis of the data used is a descriptive and bivariate analysis using the Pearson correlation test.\n\nResults There was no significant relationship between concentrations, RQ benzene, and MDA levels in workers in painting in Surabaya (p> 0.05). There was no significant relationship between benzene concentration, BUN levels, and creatinine levels in paint workers in Surabaya (p> 0.05). There was no significant relationship between benzene RQ and BUN and creatinine levels in paint workers in Surabaya (p> 0.05).\n\nConclusions The results of this study indicate that the effects of benzene do not lead to impaired kidney function. The benzene RQ variable in this study did not become a determining factor in BUN and creatinine levels in workers.",
"keywords": [
"Benzene",
"malondialdehyde",
"kidney function",
"car painting workshops",
"safe work"
],
"content": "Introduction\n\nBenzene is a carcinogenic unsaturated closed-chain aromatic hydrocarbon compound (ATSDR, 2007). Benzene has been known as a good organic solvent for various processes in the industry such as the rubber industry, shoes, paint solvents, components in motor fuels, components in detergents, pesticides, and pharmaceutical manufacturing (Paustenbach et al., 1992; Wijaya, 1993). One informal sector that is often exposed to benzene is the car paint shop. The car painting work area is one of the areas that requires attention due to its increasing number with a large risk of occupational diseases. The car painting process uses solvents containing benzene as the main ingredient in the work process which can have a detrimental effect on health. These materials enter the body through absorption with more presentation through inhalation due to exposure to steam in the process of spray painting (Coresh et al., 2007).\n\nContinuous benzene exposure can cause health effects. The body is continually exposed to benzene which causes symptoms and signs of chronic poisoning such as headaches, dizziness, nausea to vomiting, and slow-in-pale reactions due to anemia which is often accompanied by bleeding under the skin and mucosa. The clinical effects of benzene systemically cause cardiovascular, respiratory, neurological, gastrointestinal, liver, kidney, endocrine and reproductive systems, dermatology, local effects, hematological, immunological, metabolic, and allergic reactions (ATSDR, 2007; Cronkite et al., 1989; McHale et al., 2012; Tunsaringkarn et al., 2013).\n\nIn 2007 the (American Conference of Governmental Industrial Hygienists (ACGIH), 2007) issued a benzene chemical threshold of 0.5 ppm and since 1997 benzene has been confirmed to have carcinogenic properties in humans (Al = confirmed human carcinogen). The National Institute for Occupational Health and Safety (NIOSH) in 2010 set a recommended exposure limit or REL (Recommended Exposure Limit) of 0.1 ppm for 8 working hours (NIOSH, 2010). The threshold value of chemical factors at work according to Minister of Manpower and Transmigration number 13 in 2011 is 0.5 ppm. The benzene exposure pathway enters the human body in three ways, namely absorption through the skin, inhalation, and ingestion. Inhalation is a very important route to consider because benzene has volatile properties (ATSDR, 2007).\n\nBenzene which enters the body oxidizes to proteins, lipids and produces Malondialdehyde (MDA). An increase in MDA levels is a sign of an increase in free radicals in the blood. Increased MDA levels even become a benchmark to determine the risk of cancer that will occur in workers exposed to benzene. Exposure to benzene in high content causes narcotic effects and irritation to the eyes and airways (Ho et al., 2006). Long-term exposure to low content can result in bone marrow suppression and can be associated with leukemia events or other blood cell disorders. The population of workers who work in the car painting industry or use benzene can be exposed to the highest exposure levels. For this reason, special attention needs to be paid to workers for occupational safety and health.\n\nExposure to benzene and alkyl benzene has been linked to kidney and liver injury and kidney cancer (Brautbar et al., 2006; Henderson, 2001). Other research conducted in Indonesia also stated that as many as 256 child workers in the Cibaduyut Bandung slipper and shoe industry were listed as being threatened by various types of diseases such as liver and/or kidney damage and even leukemia (ILO, 2004). That is due to bad habits and an unhealthy work environment so workers in the Cibaduyut Bandung sandal and shoe industry inhale and ingest benzene compounds contained in the glue they use to make sandals.\n\nExamination of creatinine level in the blood is one of the parameters used to assess kidney function, because the concentration in plasma and its excretion in urine in 24 hours is relatively constant (Soedaman, 1995). This serum creatinine reflects the most sensitive kidney damage because it is produced constantly by the body (Lewis et al., 2014). In addition, high Blood Urea Nitrogen (BUN) levels have been associated with adverse kidney effects suggesting that BUN is a useful marker for predicting the development of kidney disease (Seki et al., 2019). Therefore, the purpose of this study is to analyze the relationship between benzene concentration and RQ benzene with MDA, BUN, and creatinine levels in workers exposed to benzene in a car painting workshop in Surabaya.\n\n\nMethods\n\nThis is an observational, cross-sectional study conducted at 2 car painting workshops in Surabaya that uses benzene as a solvent in its production process, namely in Kalijudan and Jemursari. The population in this study were all 90 workers exposed to benzene in two car painting workshops in Surabaya aged between 20-65 years in 2019. The research sample was taken using accidental sampling method involving 30 respondents. The variables studied were benzene concentration, RQ benzene, MDA levels and kidney function (BUN and creatinine levels). Analysis of the data used is a descriptive and bivariate analysis using Pearson correlation test.\n\nIn this study, the variables under investigation encompassed benzene concentration, RQ benzene (benzene metabolite), levels of malondialdehyde (MDA) as a marker of oxidative stress, and indicators of kidney function such as blood urea nitrogen (BUN) and creatinine levels. Benzene concentration and RQ benzene were considered exposures, representing the extent of exposure to benzene and its metabolic byproduct, respectively. MDA levels were examined as an outcome, reflecting oxidative stress status. Kidney function parameters (BUN and creatinine levels) were outcomes, indicating potential renal effects. To account for potential influences on the relationships, age and duration of exposure were treated as potential confounders, while smoking status was considered an effect modifier due to its potential interaction with benzene exposure.\n\nBenzene concentration and RQ benzene data were collected through air sampling in the workplace, utilizing gas chromatography as the assessment method. MDA levels, indicative of oxidative stress, were measured using spectrophotometric assays on blood samples. Kidney function markers, BUN, and creatinine levels, were assessed through blood tests conducted at a clinical laboratory. Efforts were made to address participant selection bias through the accidental sampling method. While this method might introduce some bias due to its non-random nature, its pragmatic approach allowed for data collection from the available workforce, considering practical constraints. The sample size, comprising 30 respondents, was determined based on available resources while aiming to capture a representative subset of the population.\n\nThe study employed a comparative approach between the two workshops to explore potential differences in variables of interest and their interactions. This approach facilitated a more nuanced understanding of the relationship between benzene exposure, MDA levels, and kidney function within the specific context of the car painting workshops in Surabaya.\n\n\nResults\n\nRespondent characteristics include age, sex, level of education, and work area. Table 1 presents the distribution of characteristics of workers exposed to Benzene in a car painting workshop in Surabaya.\n\nMost (33.3%) industrial workers aged 36-45 years and the majority (96.3%) was male with the highest level of education being SMA/SMK (44.4%). Most (63%) workers work in the Kalijudan area.\n\nBased on Table 2 of 27 respondents there were 21 respondents (77.8%) with benzene concentrations above the Threshold Value (> 0.5 ppm) and 6 respondents (22.2%) with benzene concentrations below the Threshold Value (≤ 0.5 ppm).\n\nHealth risk characteristics are stated as Risk Quotient (RQ, Risk Level), shown in Table 3 and are calculated by dividing the intake or intake (Ink) by reference (RfC). The calculation results of Risk Quotients (RQ) can indicate the level of health risks of workers due to exposure to benzene in the work environment. If the RQ value is more than or equal to 1 (RQ> 1) then workers exposed to benzene have health risks due to benzene exposure. If the RQ value is less than 1 (RQ <1), then workers exposed to benzene are safe from health risks due to benzene exposure. Based on the RQ calculation in Table 4, the majority of workers (92.6%) have RQ≥1 values for benzene exposure, which means the majority of them have health risk impacts due to benzene exposure.\n\nBased on the test results in Table 5 there is no significant relationship between Benzene concentration and MDA levels in workers exposed to benzene in a car painting workshop in Surabaya with a P value> 0.05.\n\nBased on the test results in Table 6 there is no relationship between RQ Benzene and MDA levels of workers exposed to benzene in a car painting workshop in Surabaya (P> 0.05).\n\nBased on the test results in Table 7 there was no significant relationship between Benzene concentrations, BUN levels and creatinine exposure of workers exposed to benzene in car painting workshops in Surabaya (P> 0.05).\n\nBased on the test results in Table 8 there was no significant relationship between Benzene concentrations, BUN levels, and creatinine exposure of workers exposed to benzene at a car painting workshop in Surabaya (P> 0.05).\n\n\nDiscussion\n\nThe results showed that there was no significant relationship between concentration, RQ benzene, and MDA levels in workers in a car painting workshop in Surabaya (p> 0.05). This is in line with research conducted on workers in shoe factories that benzene concentrations do not have a significant relationship with MDA levels (Tualeka et al., 2019). However, according to research conducted by (Odewabi et al., 2014) in Nigeria, exposure to free radicals especially benzene in gas station workers can increase MDA levels in workers. Research by (Suparno et al., 2018) also stated that high plasma malondialdehyde (MDA) levels are markers of oxidative stress that will cause DNA and RNA disturbances. Previous research suggests that oxidative stress might be related to pathogenesis and the dev1elopment of kidney disease, where it is suspected that malondialdehyde might play an important role in the pathogenesis of glomerulosclerosis (Kuo et al., 2005). In other studies, oxidative stress has progressively increased and is associated with the degree of kidney dysfunction in patients with chronic kidney failure (Dounousi et al., 2006; Terawaki et al., 2004).\n\nThere was no significant relationship between benzene exposure, BUN levels and creatinine in painting workers in Surabaya (p> 0.05). Research conducted by (D’Andrea & Reddy, 2018) in children showed no significant differences in serum creatinine levels between groups exposed to benzene and those not exposed. Although BUN levels were found to be significantly reduced in groups exposed to benzene compared with unexposed group (P = 0.001). Although studies related to the effects of benzene exposure specifically on kidney function (creatinine and BUN) are limited, previous studies related to the exposure of organic solvents to kidney function have been conducted to support this study. Research conducted by (Elfar et al., 1998) found no statistically significant differences between the groups exposed to organic solvents and the control group regarding kidney function and there was no significant relationship between the two and the length of exposure to organic solvents. This opinion is also strengthened by research conducted by (Kaukiainen et al., 2004) who found a negative relationship between serum creatinine levels and exposure to organic solvents.\n\n(Hoek et al., 2003) did not find any effect from exposure to organic solvents on effects to the kidneys. The lack of an association between kidney effects and the intensity or duration of exposure can be associated with individual vulnerability. Vulnerability to benzene can vary due to its effects which arise, in part, from genetic variations in metabolism, DNA repair, genome stability, and immune function (D’Andrea & Reddy, 2018). In the present study, the effects of benzene have not led to impaired kidney function, yet limited to acute exposure. In addition, the presence of toluene exposure inhaled by labor (measured at the same time as the measurement of benzene exposure using the OVM method) has antagonistic properties against benzene toxicity. According to (Inoue et al., 1988) workers exposed to a combination of benzene and toluene will experience decreased levels of phenol in the urine compared to those exposed to benzene or toluene separately. Therefore, further research can find out whether there is an antagonistic effect between benzene and toluene on creatinine and BUN levels.\n\nThere was no significant relationship between benzene RQ, BUN levels and creatinine levels in paint workers in Surabaya (p> 0.05). RQ calculation is calculated by dividing the intake or intake (ink) by reference (RfC). Therefore, one factor that influences the value of RQ is the amount of benzene intake. Based on the theory of (Louvar & Louvar, 1998) in determining the assessment of exposure (exposure assessment) regarding the amount of chemical intake received by individuals, the exposure time factor, duration of exposure, body weight and frequency of exposure have a significant contribution in determining the intake of xenobiotic material intake at body to cause health effects. Other factors such as duration of exposure, time of exposure, frequency of exposure, nutritional status, etc. can contribute in the event that there is no effect of the benzene RQ variable on kidney function. In this study, benzene intake in workers was relatively small and the work period of the worker was also not long at 8.2 years (<10 years). In sum, the benzene RQ variable in this study was not a determining factor in its effect on the results of BUN and creatinine levels.\n\nCross-sectional design restricts the ability to establish causal relationships between variables, which means that it captures data at a single point in time. Longitudinal studies would provide more robust evidence of the relationship between these variables. The study is conducted in only two car painting workshops in Surabaya, potentially limiting generalizability to other settings. The utilization of the accidental sampling method might introduce selection bias, as workers with greater awareness of health risks might be more inclined to participate, affecting the external validity of findings. Furthermore, age range selection (20-65 years) might lead to varying susceptibility levels and differences in exposure duration, potentially influencing the direction and magnitude of associations observed. The limited sample size (30 respondents) might hinder the ability to detect small but significant effects, impacting the study's statistical power. As the study relies on self-reported data for certain variables and uses laboratory assessments for others, measurement bias and misclassification could occur. Despite these limitations, the study's findings contribute to the existing understanding of the complex interplay between benzene exposure, oxidative stress, and kidney function in car painting workshops.\n\n\nConclusion\n\nIn this study, the majority of respondents (77.8%) were exposed to benzene concentrations above the Threshold Value (>0.5 ppm). The majority of workers (92.6%) had RQ≥1 against benzene exposure, which means the majority of workers were affected by benzene exposure. There was no significant relationship between benzene concentration and RQ on MDA level in workers (p>0.05). There was no significant relationship between benzene concentration, BUN level, and creatinine level in workers (p>0.05). There was no significant relationship between benzene RQ, BUN level, and creatinine level in workers (p>0.05).\n\nEthical approval was obtained from the Universitas Airlangga, Faculty of Dental Medicine ethics committee (605/HRECC.FODM/IX/2019).\n\nThe objectives and protocols of the study were explained to the participants and obtained written informed consent from each subject before participation in the study.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgments\n\nThe authors would like thank to the rector of Airlangga University. The authors would like to acknowledge Relationship between Benzene Concentration, MDA Levels and Kidney Function in Car Painting Workshops in Surabaya.\n\n\nReference\n\nAmerican Conference of Governmental Industrial Hygienists (ACGIH): Threshold Limit Values and Biological Indices. Cincinnati: 2007.\n\nATSDR: Benzene: Relevance to Public Health. ATSDR; 2007. Publisher Full Text\n\nBrautbar N, Wu MP, Gabel E, et al.: Occupational kidney cancer: exposure to industrial solvents. Annals of the New York Academy of Sciences. 2006; 1076: 753–764. Publisher Full Text\n\nCoresh J, Selvin E, Stevens LA, et al.: Prevalence of chronic kidney disease in the United States. JAMA. 2007; 298(17): 2038–2047. Publisher Full Text\n\nCronkite EP, Drew RT, Inoue T, et al.: Hematotoxicity and carcinogenicity of inhaled benzene. Environmental Health Perspectives. 1989; 82: 97–108. PubMed Abstract | Publisher Full Text | Free Full Text\n\nD’Andrea MA, Reddy GK: Health Risks Associated With Benzene Exposure in Children: A Systematic Review. Global. Pediatric Health. 2018; 5: 2333794X18789275. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDounousi E, Papavasiliou E, Makedou A, et al.: Oxidative stress is progressively enhanced with advancing stages of CKD. American Journal of Kidney Diseases: The Official Journal of the National Kidney Foundation. 2006; 48(5): 752–760. PubMed Abstract | Publisher Full Text\n\nElfar H, El Taless A, El-Abd A: Health hazards and biochemical changes due to exposure to petroleum hydrocarbons among workers in petrol filling stations. Egyptian Journal of Occupational Medicine. 1998; 22(2): 241–252.\n\nHenderson RF: Aromatic Hydrocarbons—Benzene and Other Alkylbenzenes. Patty’s Toxicology. 2001. Publisher Full Text\n\nHo TL, Fieser M, Fieser LF: Benzyl chloromethyl ether. Fieser and Fieser’s Reagents for Organic Synthesis. 2006. Publisher Full Text Reference Source\n\nHoek FJ, Kemperman FAW, Krediet RT: A comparison between cystatin C, plasma creatinine and the Cockcroft and Gault formula for the estimation of glomerular filtration rate. Nephrology, Dialysis, Transplantation: Official Publication of the European Dialysis and Transplant Association - European Renal Association. 2003; 18(10): 2024–2031. PubMed Abstract | Publisher Full Text\n\nILO: Pekerja Anak di Industri Sepatu Informal di Jawa Barat (Sebuah Kajian Cepat).2004.\n\nInoue O, Seiji K, Watanabe T, et al.: Mutual metabolic suppression between benzene and toluene in man. International Archives of Occupational and Environmental Health. 1988; 60(1): 15–20. PubMed Abstract | Publisher Full Text\n\nKaukiainen A, Vehmas T, Rantala K, et al.: Results of common laboratory tests in solvent-exposed workers. International Archives of Occupational and Environmental Health. 2004; 77(1): 39–46. PubMed Abstract | Publisher Full Text\n\nKuo H-T, Kuo M-C, Chiu Y-W, et al.: Increased glomerular and extracellular malondialdehyde levels in patients and rats with focal segmental glomerulosclerosis. European Journal of Clinical Investigation. 2005; 35(4): 245–250. PubMed Abstract | Publisher Full Text\n\nLewis SL, Dirksen SR, Bucher L: Study Guide for Medical-Surgical Nursing: Assessment and Management of Clinical Problems. Study Guide for Medical-Surgical Nursing: Assessment and Management of Clinical Problems. 9th ed.Elsevier Inc; 2014. Reference Source\n\nLouvar JF, Louvar BD: Health and environmental risk analysis: fundamentals with applications. (No Title). 1998.\n\nMcHale CM, Zhang L, Smith MT: Current understanding of the mechanism of benzene-induced leukemia in humans: implications for risk assessment. Carcinogenesis. 2012; 33(2): 240–252. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNIOSH: NIOSH pocket guide to chemical hazards. DHHS (NIOSH) Publication No. 2010-168 (Issue 2005). 2010. Publisher Full Text\n\nOdewabi AO, Ogundahunsi OA, Oyalowo M: Effect of Exposure to Petroleum Fumes on Plasma Antioxidant Defense System in Petrol Attendants. British Journal of Pharmacology and Toxicology. 2014; 5(2): 83–87. Publisher Full Text\n\nPaustenbach DJ, Price PS, Ollison W, et al.: Reevaluation of benzene exposure for the Pliofilm (rubberworker) cohort (1936-1976). Journal of Toxicology and Environmental Health. 1992; 36(3): 177–231. Publisher Full Text\n\nSeki M, Nakayama M, Sakoh T, et al.: Blood urea nitrogen is independently associated with renal outcomes in Japanese patients with stage 3-5 chronic kidney disease: a prospective observational study. BMC Nephrology. 2019; 20(1): 115. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSoedaman: Patofisiologi Soedaman: Mekanisme Penyakit. Hipocrates; 1995.\n\nSuparno S, Suhartono S, Sofro MAU, et al.: Kadar seng dan kadar malondialdehyde pada penderita multi drug resistant tuberculosis dan tuberkulosis sensitif. Jurnal Gizi Indonesia (The Indonesian Journal of Nutrition). 2018; 7(1): 8–14. Publisher Full Text\n\nTerawaki H, Yoshimura K, Hasegawa T, et al.: Oxidative stress is enhanced in correlation with renal dysfunction: examination with the redox state of albumin. Kidney International. 2004; 66(5): 1988–1993. PubMed Abstract | Publisher Full Text\n\nTualeka AR, Martiana T, Ahsan A, et al.: Association between Malondialdehyde and Glutathione (L-gamma-Glutamyl-Cysteinyl-Glycine/GSH) Levels on Workers Exposed to Benzene in Indonesia. Open Access Macedonian Journal of Medical Sciences. 2019; 7(7): 1198–1202. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTunsaringkarn T, Ketkaew P, Siriwong W, et al.: Benzene exposure and its association with sickness exhibited in gasoline station workers. Int. J. Environ. Pollut. Solutions. 2013; 1: 1–8. Publisher Full Text\n\nWijaya C: Deteksi Dini Penyakit Akibat Kerja.1993."
}
|
[
{
"id": "241777",
"date": "14 May 2024",
"name": "Said Moselhy",
"expertise": [
"Reviewer Expertise Biochemistry"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear editor - Subjects groups, sampling, exclusion and inclusion criteria , parameters, not clear. - What is the role of CYP450 for detoxification. - GFR and clearance should be done. - What about antioxidant activity? - How doses of exposure determined\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "11704",
"date": "19 Jun 2024",
"name": "Abdul Rohim Tualeka",
"role": "Author Response",
"response": "GFR and clearance should be done --- However, in this study, GFR and clearance measurements were not performed."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1419
|
https://f1000research.com/articles/11-131/v1
|
01 Feb 22
|
{
"type": "Research Article",
"title": "HIF-1α regulated pathomechanism of low birth weight through angiogenesis factors in placental Plasmodium vivax infection",
"authors": [
"Nugrahanti Prasetyorini",
"Nabila Erina Erwan",
"Teguh Wahju Sardjono",
"Tatit Nurseta",
"Rudi Priyo Utomo",
"Rivo Yudhinata Brian Nugraha",
"Wike Astrid Cahayani",
"Ettie Rukmigarsari",
"Latania Naufa Arinugraha",
"Loeki Enggar Fitri",
"Nugrahanti Prasetyorini",
"Nabila Erina Erwan",
"Teguh Wahju Sardjono",
"Tatit Nurseta",
"Rudi Priyo Utomo",
"Rivo Yudhinata Brian Nugraha",
"Wike Astrid Cahayani",
"Ettie Rukmigarsari",
"Latania Naufa Arinugraha"
],
"abstract": "Background: Malaria in pregnancy leading to placental malaria. The main pathogenesis of the complex foetal implications in placental malaria is tissue hypoxia, due to sequestrations of Plasmodium falciparum infected erythrocytes in the placenta, but the pathomechanism of placental Plasmodium vivax infection have not been studied in detail. Hypoxia inducible factor-1α (HIF-1α) is a key transcriptional mediator of the response to hypoxic conditions which interacts with the change and imbalances of many chemical mediators including angiogenic factors, leading to abnormality of foetal growth. Methods: This study was conducted cross sectionally in Maumere, Sikka Regency, East Nusa Tenggara Province, that previously known as one of malaria endemic area with high incidence of low birth weight (LBW) cases. In this study the peripheral and umbilical blood samples as well as placental tissues were collected from mother delivered their babies with LBW at the TC Hiller Regional Hospital. All of the blood samples were examined for the presence of parasites by microscopic and PCR technique, while the plasma levels of VEGF, PlGF, and VEGFR-1, VEGFR-2, and HIF-1α were determined using ELISA. The sequestration of infected erythrocytes and hemozoin were determined from placental histological slides and the expression of placenta angiogenic factors were observed by immunofluorescent technique. Results: In this study there were 33 cases had complete data to be analysed. Of them, there were 19 diagnosed as vivax malaria and no one of falciparum malaria. There were significant differences of Δ 10th percentile growth curve of baby’s body weights and also all angiogenic factors in placental tissues {VEGF, PlGF, and VEGFR-1, VEGFR-2, and HIF-1α} between those infected and not infected cases (p<0.05), but not for VEGF and VEGFR-2 in the plasma. Conclusion: This study found Plasmodium vivax sequestration may cause LBW through the changes and imbalances of angiogenic factors leaded by HIF-1α.",
"keywords": [
"Placental malaria",
"Plasmodium vivax",
"LBW",
"HIF1-α",
"angiogenesis factors"
],
"content": "Introduction\n\nMalaria is still a major public health problem and the main cause of disease and death in developing countries1. Young children and pregnant women, especially in the 1st and 2nd trimesters, are the population most vulnerable to malaria infection1. In malaria-endemic areas, at least 25% of pregnant women are infected with malaria, which accounts for 20% of maternal deaths2,3. In 2019, for 33 countries in the World Health Organisation (WHO) African Region with moderate to high malaria transmission it was estimated that 12 million (35%) of 33 million pregnancies were exposed to Plasmodium falciparum malaria4. Rijken et al. reported that around 75 million pregnant women in the Asia-Pacific region were exposed to Plasmodium vivax in 20072. Globally, malaria causes more than 10,000 maternal deaths and 200,000 neonatal deaths annually, most of which are due to low birth weight (LBW)4–6. Pregnant women living in stable transmission areas are at risk for placental malaria, and pregnant women living in unstable areas have three times the risk of developing severe malaria than non-pregnant adult women living in the same areas2,3.\n\nIndonesia is one of the countries in Southeast Asia that has a fairly high malaria case. In 2016 there were 218,480 positive cases of malaria, this condition decreased by almost half of the positive cases of malaria in 20127. The malaria parasites found were Plasmodium falciparum (62%) and Plasmodium vivax (37%). Reports by health facilities in Indonesia (2016) stated that there were 218,450 confirmed cases of malaria with a death rate of 161 cases8. The three high malaria-endemic provinces are Papua, West Papua, and East Nusa Tenggara (NTT). Three regencies in NTT which are high endemic areas for malaria are Sikka Regency, Lembata Regency, and Ngada Regency. Sikka Regency is located on Flores Island, bordered by East Flores Regency and Ende Regency, has an area of 7,436.10 km2 and a population based on a survey population in 2010 was 315,477 people9. In 2008, 87,622 clinical malaria cases were reported in Sikka Regency10. A previous study conducted on 92 babies born with low birth weight in T.C. Hillers Regional Hospital, Maumere, Sikka Regency between December 2012 to December 2013, reported that 39 (42.4%) infants had congenital malaria of which 19 (48.7%) infants were asymptomatic, while the rest had sepsis, jaundice, and prematurity11.\n\nPlacental malaria is characterized by the accumulation of parasite-infected erythrocytes, mononuclear cells and malaria pigment (hemozoin) in the placental blood vessels12. Most reports of placental malaria are caused by infection with Plasmodium falciparum, which sequesters in the syncytiotrophoblast. This sequestration occurs by expressing the surface protein Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) which specifically mediates the cytoadhesion of Plasmodium falciparum infected erythrocytes to placental chondroitin sulfate A (CSA) located in the syncytiotrophoblast6,13,14. This cytoadhesion and sequestration prevent the escape of circulating adult parasites thereby avoiding the mechanism of clearance by complement and spleen. During the occurrence of placenta malaria, the Th1/Th2 balance shifts to the Th1 pathway and there is an increase in the production of the pro-inflammatory cytokines, interferon-ϒ (IFN-ϒ) and tumour necrosis factor-α (TNF-α). This inflammatory response causes changes in the structure and function of the placenta which are associated with poor pregnancy outcomes such as maternal anemia, prematurity, stunted fetal growth and LBW15. Placental malaria is a major cause of stunted fetal growth with poor pregnancy outcomes in the form of babies born with LBW16.\n\nPlacenta malaria will evoke complement activation, both systemically and at the maternal-fetal interface in the placenta17. There is an increase in complement of anaphylatoxin C5a in circulating blood and in placental tissue in mothers with placental malaria5. Previous in vitro studies showed that Plasmodium falciparum glycosylphosphatidylinositol (PfGPI) together with C5a increased pro-inflammatory milieu at the maternal-fetal interface, in the form of increased cytokines and chemokines derived from monocytes18. One of the consequences is the occurrence of dysregulation of angiogenic factors19 which causes stunted fetal growth5,6,20,21. The local oxygen environment during pregnancy is one of the important regulatory factors of angiogenesis. The main pathway of oxygen regulation of gene expression is hypoxia inducible factor-1α (HIF-1α). Under hypoxic conditions, HIF-1α accumulation upregulates VEGF which is a major proangiogenic factor directly. VEGF activity will induce the expression of vascular endothelial growth factor receptor-1 (VEGFR-1/Flt-1) and vascular endothelial growth factor receptor-2 (VEGFR-2/KDR). During hypoxia, VEGF will bind to receptors and stimulate capillary growth. Hypoxia inducible factor-1α (HIF-1α) also induces an increase in the soluble anti-angiogenic factor Flt-1 (sFlt-1)22,23. High placental HIF-1α expression after the 1st trimester of pregnancy is an abnormal condition that describes the occurrence of placental hypoxia due to inadequate placentation. Increased placental HIF-1α expression will cause an increase in placental sFlt-1 levels which will be released into the maternal circulation. Soluble Flt-1 (sFlt-1) strongly binds free VEGF and free PlGF, decreased placental angiogenic activity. This condition is found in pregnancies with preeclampsia and IUGR24–26, and in placental malaria27. Increased placental HIF-1α expression is also found in maternal anemia28.\n\nCarvalho et al. for the first time demonstrated that Plasmodium vivax-infected erythrocytes (Pv-iEs) can perform ex vivo cytoadhesion on human lung endothelial cells (HLECs), Saimiri brain endothelial cells (SBECs), and placental cryosections both under static and flow conditions. This cytoadhesion is smaller than that of Plasmodium falciparum-infected erythrocytes (Pf-iEs), and is partly mediated by the VIR protein encoded by the Plasmodium vivax variant (vir) gene29. Fernandez-Becerra et al. showed in his study that spleen-dependent Plasmodium vivax genes encode immunogenic proteins during the course of infection, so it can be said that the spleen is an organ that plays a major role in expressing parasitic proteins involved in cytoadhesion30. Pv-iEs binding to endothelial cells is mediated by glycosaminoglycans, namely chondroitin sulfate A (CSA) and hyaluronic acid (HA)29,31. Although all stages of the Plasmodium vivax were found in peripheral blood, only a few of the mature forms of schizonts were found. It is not yet possible to establish whether the disproportionate Plasmodium vivax parasitaemia results from its sequestration in specific organs32.\n\nData on the number of pregnancies infected with Plasmodium vivax have not been widely published. The mechanism and clinical implications of Plasmodium vivax infection in pregnancy are still not clearly known, possibly because it is considered to cause a milder clinical effect than Plasmodium falciparum infection33. However, many studies have reported that vivax malaria in pregnancy is more associated with low birth weight and maternal anemia34,35 and may not be affected by parity because women living in areas with low malaria endemicity have low immunity to malaria36. In this study, an in vivo study was conducted on pregnant women infected with malaria, with an emphasis on placental malaria, to determine the effect of placental angiogenesis factors and maternal plasma angiogenesis factors on the pathomechanism of LBW through HIF-1α regulation. This study is the first study of placental malaria angiogenesis factors in Indonesia using human placenta samples.\n\n\nMethods\n\nThis research was conducted according to the guidelines of the Declaration of Helsinki and approved by the Faculty of Medicine Universitas Brawijaya Ethics Committee number 307/EC/KEPK/11/2018. Written informed consent, including for the baby's data to be used, was obtained from all subjects before participating in this study.\n\nThis study used a cross-sectional research design and took place in T.C. Hillers Regional Hospital, Maumere, Sikka Regency, East Nusa Tenggara Province; a malaria-endemic area in Indonesia. This study used a purposive sampling technique in managing research participants. Thus, all of the subjects which met the inclusion criteria were included. The study subjects were pregnant women who came to T.C. Hillers Regional Hospital during 2018 and met the inclusion criteria. The inclusion criteria were pregnant women who gave birth to babies with low birth weight (LBW) and small for gestational age (SGA). Subjects were divided into two groups, they were (i) case group, pregnant women who met the inclusion criteria and the malaria diagnosis criteria and (ii) control group, pregnant women who met the inclusion criteria and did not meet the malaria diagnosis criteria. Malaria cases were determined based on the discovery of Plasmodium parasites on examination of thin or thick blood smears and or the discovery of Plasmodium DNA in maternal blood and or umbilical cord blood by polymerase chain reaction (PCR) examination, and or the discovery of Plasmodium parasites or hemozoin in the placenta.\n\nThe diagnosis of malaria case in this study was confirmed by discovery of either the asexual form of Plasmodium on examination of thick or thin blood smears derived from maternal blood and or umbilical cord blood, and/or Plasmodium DNA obtained by polymerase chain reaction (PCR) examination, and/ finding of placental malaria. Hemozoin is a brown pigment crystal that forms in the digestive vacuole of Plasmodium as a product of hemoglobin catabolism37. Hemozoin was seen as greenish-black or yellowish-brown granules using a light microscope and sequestered intra or extra erythrocytes. Observations were made using a light microscope with 1000x magnification in 100 fields of view. Identification of infected erythrocytes was carried out by observing 100 fields of view. Identification of hemozoin sequestration was carried out by observing 100 fields, then the total number of hemozoin was calculated by dividing all fields by 100. The count includes hemozoin found in and outside infected (free) erythrocytes, attached to connective tissue, on white blood cells in the intervillous space, or macrophages covered by fibrin in the intervillous space.\n\nLow birth weight is defined as a birth weight of less than 2500 g38. In this study, what is meant by low birth weight is the difference between birth weight and the 10th percentile of the mean birth weight curve for boys and girls by gestational age from the reference curves of birth weight, length, and head circumference for gestational ages in Yogyakarta, Indonesia39.\n\nIn total, 10 milliliters of maternal venous blood were drawn from the median vein and put into a vacutainer containing anticoagulant (BD Vacutainer EDTA Tubes, 366643) for making blood smear preparations, plasma and dried blood spots on filter paper. Microscopic examination was carried out on blood smear preparations. Dried blood spots then were used for PCR examination to confirm the diagnosis of malaria. Plasma was stored at 20°C and sent to Malang city (in collaboration with the Prodia Laboratory) in less than 48 hours. These samples were then used to examine plasma levels of VEGF, PlGF, and VEGFR-1 (sFlt-1), VEGFR-2, and HIF-1α using ELISA method.\n\nIn total, five milliliters of blood were taken from the umbilical artery of the newborns and put into a blood collection tube containing anticoagulant (BD Vacutainer EDTA Tubes, 367863) to make blood smears for malaria parasites identification and make dried blood spots on filter paper for PCR examination, and for hemoglobin and leucocyte test.\n\nThe blood sample was dropped on an object-glass where a thin smear was made and dried. Furthermore, the smears were fixed evenly using absolute methanol and dried. The smears were stained with Giemsa solution (a mixture of Giemsa stain (Merck, HX612241) and Giemsa buffer (Bioanalytica, Indonesia) with a ratio of 1:9), then rinsed and dried. The thin smear slides were examined microscopically at 100 times magnification under the objective lens with immersion oil, on at least 100 visual fields for each examination. To calculate the degree of parasitemia, 1000x magnification was carried out using a light microscope (Olympus Biological Microscope, CX23), counting the number of erythrocytes infected with malaria parasites per 1000 erythrocytes40.\n\nSamples obtained from the central part of the gross placental anatomy with a size of 2 cm and fixation with 10% neutral buffer formalin, were then embedded into paraffin for immunofluorescence examination to determine the expression of VEGF, PlGF, VEGFR-1, VEGFR-2, and HIF-1α, the sequestration of infected erythrocytes and or hemozoin, as well as placental parasitemia. Placental histology preparations were made by cutting tissue that had previously been fixed with 10% neutral buffer formalin and inserted into a tissue cassette. Then, the samples were put into a basket and processed using tissue processor tool (Thermo Scientific Microm STP 120 Spin Tissue Processor). The process of casting into paraffin blocks was done by using tissue embedding tool (Sakura Tissue-Tek TEC 5 Embedding Station). The paraffin blocks were cooled in a freezer before cutting with a microtome (Leica, RM2245). Then, the tissue was put into an incubator (Memmert, UN30) for 30 minutes in a 70-80oC temperature setting to maximize further deparaffination. Furthermore, after the tissue was removed from the incubator, deparaffination and Hematoxylin-Eosin staining were performed using the Tissue Tex DRS 2000 Multiple Slide Stainer tool.\n\nImmunofluorescence examination procedure on placental tissue was used to measure placental expression of variables VEGF (anti-VEGFA antibody, SC 7269 FITC), PlGF (anti-PLGF antibody, SC 518003), VEGFR-1 (anti VEGFR-1 antibody, SC 271789 PE), VEGFR-2 (anti VEGFR-2 antibody, SC 6251 FITC), and HIF-1α (anti HIF-1α antibody (SC 13515 PE). The immunofluorescence procedure was performed by single staining for HIF-1α and double staining for other variables. The results of the immunofluorescence images were then quantified using ImageJ 1.52p Fiji software.\n\nDNA samples were obtained from blood sample extraction using PureLinkTM Genomic DNA Kits (Invitrogen, Carlsbad, California, USA) according to the manufacturer's instructions. After purification, all samples were stored at -20◦C till ready for the nested PCR. For the amplification of Plasmodium genus sequences, outer primer pairs (rPLU1 and rPLU5) were used. In the second reaction, two pairs of inner primers were used to detect P. falciparum (rFal1-rFal2) and P. vivax (rVIV1-rVIV2). PCR was performed using a Go Tag® Green Master Mix (Promega, Madison, Wisconsin, USA). 1 l template was treated with the following conditions: 1 l of each primer (10 M), 12.5 l of PCR master mix, and 9.5 l of double-distilled H2O2. The second nest reactions were carried out in a similar way using different primers. Sterile distilled water was used as a control11.\n\nELISA examination was performed to measure plasma levels of VEGF (human VEGF ELISA kit, Biolegend, Catalog No. 446507), PlGF (human PGF ELISA kit, bt-Lab, Catalog No. EO138Hu), VEGFR-1(sFlit1) (human VEGFR-1 ELISA kit, Invitrogen, REF#BMS268-3), VEGFR-2 (human VEGFR-1 ELISA kit, Invitrogen, REF#BMS2019), and HIF-1α (human HIF-1α ELISA kit, Invitrogen, REF#EHIF1A). The technique used was a quantitative sandwich enzyme immunoassay with the following procedure. The ELISA's standard was pipetted into a microplate that had been pre-coated with a specific antibody to the antigen according to the manufactured ELISA Kit. Each sample was pipetted into each well so the antigen would be bound to the immobilized antibody. Unbound materials were discarded. Then biotin-conjugated antibody specific for antigen was added into the wells, then washed. Afterward, avidin-conjugated Horseradish Peroxidase (HRP) was added, then washed to remove any unbound materials. Staining was done by adding a solution substrate, incubated for 30 minutes, and added a stop solution to stop the reaction. The preparations were read with a microplate reader (ZENIX-320).\n\nNewborns were examined by the obstetrician for the birth weight, length, head circumference, mid-upper arm circumference, chest circumference, Apgar score, placental size, and placental weight. The birth weight was measured immediately after birth using calibrated weighing scales. The birth length, head circumference, mid-upper arm circumference, and chest circumference were measured using a measuring tape. Apgar score was noted at the first minute of birth. The placental size was measured using a ruler, and the weight was measured using calibrated weighing scales.\n\nAll statistical analyses were conducted using SPSS 23 Statistic Program for Windows. The techniques for analyzing data include the normality test using the Shapiro Wilk test to determine the normal data distribution. Comparative analysis between the case and control groups was carried out using a one-way ANOVA test for normally distributed data and the Kruskal Wallis test for non-normally distributed data to assess dysregulation of angiogenesis in the pathomechanism of low birth weight due to malaria-inhibited fetal growth in the placenta. The correlation test used was a Pearson test for normally distributed data and the Spearman's rho test for non-normally distributed data to assess the correlation between the variables observed in the study. Path analysis was used to assess the conceptual research framework, i.e. whether the authors' concepts are relevant to the research findings. Data analysis was carried out with a confidence level of 95% and a degree of significance by p≤0.05.\n\n\nResults\n\nA total of 33 subjects met the inclusion criteria of this study. Then laboratory tests were carried out to identify the control group and the case group, as shown in Table 141.\n\nNotes: IE: infected erythrocytes; PCR=polymerase chain reaction.\n\nPlasmodium vivax was identified in all subjects of the case group, and no Plasmodium falciparum nor mixed infection was found. Histopathological examination of placental tissue from the case group showed sequestration of infected erythrocytes and/or hemozoin, followed by monocytes infiltration in the intervillous space in all samples. Two of the 19 malaria cases were identified from cord blood PCR. Examination of maternal peripheral blood smear can at least identify parasites compared to PCR and histopathological examination of the placenta, which is about 36.84%. The blood smears from the malaria case group showed in Figure 1.\n\nIn panel A, the arrow indicates the amoeboid form of Plasmodium vivax, panel B shows young schizonts of Plasmodium vivax, and panel C displays the mature schizont of Plasmodium vivax. The image size is the only modification made; no changes to brightness or contrast have been done.\n\nThis study showed no statistically significant differences in maternal age, gestational age, and maternal leukocyte count between the case and control groups. It can be seen that in the case group, the age distribution of pregnant women is slightly lower than the age distribution of pregnant women in the control group, but this is not statistically different. Statistically significant differences were only found in maternal hemoglobin levels in the case group (p=0,000<α), lower than in the control group. The subject characteristics and distributions showed in Table 2.\n\nNotes: All of the data were analyzed with the Mann-Whitney test. The case group was pregnant mothers who were diagnosed with malaria (+); The control group was normal pregnant mother/malaria (-) SD=standard deviation.\n\nThe characteristics of the babies in this study were recorded as shown in Table 3. There was a significant difference (p=0,000<α) in the mean Δ 10th percentile growth curve of birth weight between the case group (413.16±460,33 g) and the control group (-42.86±129.88 g). However, there was no significant difference (p=0.325>α) in the mean birth weight (g) between the case group (2189.47 ±182.06 g) and the control group (2239.29 ±190.85 g). It appears that the mean value of birth weight in the case group is significantly smaller than the mean in the control group. It can be said that pregnant women with malaria are likely to give birth to a baby with a smaller birth weight than a baby born to a non-malaria pregnant woman.\n\nNote: *) comparative results on the free sample t-test\n\n**) comparative results on the Mann-Whitney test\n\nVEGF in the placenta of the case group was lower (64,404±28,942) than the control group (226,693±39,025). In both the case and control groups, VEGF expression was more abundant in the trophoblast cells of the placental villi than in the intervillous space. PlGF expression in the placenta of the case group was lower (22,814,440±9,497,663) than the control group (84,693,238±29,981,727). PlGF expression in the case group was abundant in trophoblast cells of the placental villi, whereas it was mostly found in the intervillous space in the control group. PlGF expression in the placenta of the case group was significantly lower than that of the control group.\n\nThe expression of VEGFR-1 in the placenta of the case group was lower (107,444±46,696) than the control group (213,410±35,251). VEGFR-1 expression was more abundant in trophoblast cells in the placental villi than in the intervillous space in the case and control groups. The expression of VEGFR-1 in the case group's placenta was significantly lower than that of the control group. VEGFR-2 expression in the placenta of the case group was lower (96,968,870±24,300,623) than the control group (167,673,566±90,824,566). VEGFR-2 expression was abundant in trophoblast cells in the placental villi in the case and control groups. The expression of VEGFR-2 in the case group's placenta was significantly lower than that of the control group. The expression of HIF-1α in the placenta of the case group was higher (80,375,094±40,647,360) than the control group (25,286,646±27,238,953). In the case and control groups, HIF-1α expression was more commonly found in the trophoblast cells of the placental villi. HIF-1α expression in the placenta of the case group was significantly higher than that of the control group, as seen in the Figure 2. The quantification of angiogenic factor expression in the case and control groups are presented in Figure 3.\n\nPanel A to E shows the angiogenic expression in the placenta using immunofluorescence staining of VEGF, PlGF, VEGFR-1, VEGFR-2, and HIF-1α, respectively; VEGF: vascular endothelial growth factor; PlGF: placental growth factor; VEGFR-1: vascular endothelial growth factor receptor-1; VEGFR-2: vascular endothelial growth factor receptor-2; HIF-1α: hypoxia-inducible factor-1α.\n\nPanel A to E shows semiquantitative analysis of VEGF, PlGF, VEGFR-1, VEGFR-2, and HIF-1α expression in placenta, respectively; VEGF: vascular endothelial growth factor; PlGF: placental growth factor; VEGFR-1: vascular endothelial growth factor receptor-1; VEGFR-2: vascular endothelial growth factor receptor-2; HIF-1α: hypoxia-inducible factor-1α.\n\nThe results of the path analysis test showed that there was a significant direct effect (p=0.035) HIF-1α expression on VEGF expression with an effect coefficient of -0.545. Likewise, there was a significant direct effect (p=0.026) of HIF-1α expression on PlGF expression with an effect coefficient of -0.603. VEGF expression had no direct effect on VEGFR-1 expression (p=0.886), but had a direct effect on VEGFR-2 expression (p=0.000) with a coefficient of effect of 0.748. There was a significant direct effect (p=0.000) PlGF expression on VEGFR-1 expression with an effect coefficient of 0.937 shown. VEGFR-1 expression had no direct effect on birth weight (p=0.464), but VEGFR-2 expression had a significant direct effect (p=0.020) on birth weight with an effect coefficient of 0.743.\n\nThe mean maternal plasma VEGF levels in the case and control groups were almost the same; statistical results showed no statistically significant difference (p=0.769). The mean maternal plasma PlGF, VEGFR-1, VEGFR-2 level in the case group was lower than those in the control group. Statistically, there is a significant difference (p=0.026; 0.044; 0.042, respectively). Similar to VEGF plasma level, the HIF-1α plasma levels in the case and control groups had values that were not much different, which showed no significant difference (p=0.402). The angiogenic factor level in the case and control group are presented in Figure 4.\n\nPanel A to E shows the angiogenic factors level in the maternal plasma using ELISA of VEGF, PlGF, VEGFR-1, VEGFR-2, and HIF-1α, respectively; VEGF: vascular endothelial growth factor; PlGF: placental growth factor; VEGFR-1: vascular endothelial growth factor receptor-1; VEGFR-2: vascular endothelial growth factor receptor-2; HIF-1α: hypoxia-inducible factor-1α.\n\nThere was a significant difference in the mean expression of VEGF, PlGF, VEGFR-1, and VEGFR-2 placenta between the case and control groups. The mean value of placental VEGF, PlGF, VEGFR-1 and VEGFR-2 expression in the case group was lower than the mean in the control group. In addition, there was a significant difference in the mean placental HIF-1α expression between the case and the control groups. However, in contrast to other angiogenic factors, the mean placental HIF-1α expression in the case group was higher than the mean placental HIF-1α expression in the control group. The comparison of angiogenic factor expression in the placenta is shown in Table 4.\n\nNotes: *) T-test\n\n**) Mann-Whitney test\n\nSD=standard deviation.\n\nThere was no significant difference in the mean VEGF plasma levels between the case group and the control group. The mean value of VEGF plasma levels in the case group was slightly higher than the average VEGF level in the control group. However, this increase was not statistically significant. Similar to VEGF, the mean plasma levels of HIF-1α between case and control groups did not show a significant difference. However, HIF-1α in the case group was slightly lower than the mean HIF-1α expression in the control group. The plasma levels of PlGF, VEGFR-1, and VEGFR-2 between the case group and the control group showed significant differences. The mean levels of PlGF, VEGFR-1, and VEGFR-2 in the case group were lower than in the control group. The comparison of maternal plasma angiogenic factor levels is shown in Table 4.\n\n\nDiscussion\n\nAll malaria-positive samples in this study were identified either using maternal peripheral blood smear examination or PCR examination caused by Plasmodium vivax (Table 1). Microscopic examination of blood smears only detected 7 of the 19 positive samples (36.84%). On the other hand, 12 blood samples were detected positively by PCR examination (63.16%). The results showed that PCR is more sensitive than blood smear examination. Malaria detection using microscopic examination was only able to detect Plasmodium at levels of 20 parasites/μL and was influenced by the experience of the observer and the quality of staining blood smears. PCR is the most sensitive method because it can detect 2-6 parasites/μL42–45. It was surprising that all the histopathological preparations of 19 samples showed pigment/hemozoin depositions with or without infected erythrocytes or monocytes accumulation, indicated that all of the samples had already been infected as active acute, active chronic, and past infection46–49. In this study, all positive samples did not show signs and symptoms of malaria, so all positive samples were subclinical infections.\n\nInvestigation of acute infection through maternal peripheral blood smear examination cannot fully describe the history of maternal exposure to malaria during pregnancy. The absence of parasitemia on peripheral blood smear examination does not always represent a malaria-free placental infection48. In this study, acute, chronic, and past malaria infection in pregnancy may be related to placental histopathological changes' adverse consequences. In cases of subclinical malaria, placental histopathological changes might be found due to most of the sub-populations of parasites sequestered in several organs that serve as reservoirs of the parasite, such as the spleen and placenta, cause other inflammatory reactions43,48,50,51.\n\nCharacteristics of mothers. In this study, there were significant differences in the mean hemoglobin levels in women infected with Plasmodium vivax during pregnancy compared to the group of women who were not infected. At the same time, gestational age, maternal age, and leukocyte count showed no significant difference. The average hemoglobin level of pregnant women infected with malaria was 1.22 g/dL lower than the control group (mean ± standard deviation [SD]; 9.88±0.62 vs. 11.10±1.20, p=0.000). This finding aligned with several previous studies, which also shown that vivax malaria infection is associated with maternal anemia, abortion, premature birth, congenital malaria, and other severe complications36,52–56. Single Plasmodium vivax infection during pregnancy had a significant association with a twofold increased risk of maternal anemia compared to the group of mothers who did not experience malaria infection36,57. The occurrence of maternal anemia is closely correlated with nutritional status36. However, one of the other risk factors that can increase anemia in pregnant women with Plasmodium vivax infection is young age pregnancy58. In this study, the mean age of pregnant women in the case group was lower than the control group (mean ± SD; 27.68 ± 7.21 vs. 32.21 ± 6.25, p = 0.076); there was no significant difference. This factor may be considered one of the critical risk factors in the subsequent study involving many subjects.\n\nThe parity distribution in the case group was mainly primiparity (11/19; 57.9%), while in the control group, the highest number was mothers with third parity (6/14; 42.9%). This result has a distribution pattern similar to Bardaji et al. In their study, most malaria pregnant women were primigravida, and there was a tendency to decrease malaria prevalence as gravidity increased35. In a study of Karen women in Thailand involving a comparable number of participants, Plasmodium vivax was more common in primigravidas than in multigravida, and this was associated with anemia and an increased risk of low birth weight/LBW53.\n\nBoth case and control groups showed no significant difference (mean ± SD: 39.47±1.39 vs. 38.64±0.84, p=0.078) in gestational age, but all participants gave birth at term. In the study of Bardaji et al., it was found that the average gestational age was 38.6 weeks, with 12.6% of all participants giving birth prematurely (<37 weeks)35. From the results of their study, it cannot be concluded that there is a related relationship because it requires a joint analysis with other factors such as the severity of malaria infection, the onset of malaria infection, and pregnancy outcomes, which in this case includes the baby's birth weight. As in this study, all infants were born at term but had a significant effect of small for gestational age with malaria infection status in the form of the chronic active or previous history of malaria.\n\nCharacteristics of babies. This study showed a significant difference in the mean Δ 10th percentile growth curve of birth weight between the case group. However, there were no significant differences in the average birth weight of the baby, the length of the baby's birth weight, head circumference, upper arm circumference, chest circumference, Apgar score, placental weight, placenta size, and hemoglobin levels. However, the baby's mean hemoglobin level of the case group was 1.39 g/dL lower than the control group. The result was consistent with a previous study, which reported that single-episode of P. vivax infection during pregnancy was associated with a significant reduction in neonatal birth weight and maternal hemoglobin levels33. The results of the meta-analysis study also stated that there was an increased risk of 1-2 times the occurrence of LBW in pregnant women infected with malaria compared to those who were not infected59.\n\nMeanwhile, babies in both the case and control groups were included in LBW criteria, so it is not yet known whether the leading cause of LBW in the case group is influenced by the main factor of Plasmodium vivax infection, as in the previous studies33,58. While according to Bardaji et al., no direct relationship between Plasmodium vivax infection and an increased risk of LBW but stated that Plasmodium vivax infection during pregnancy is closely associated with maternal anemia, where this condition may harm the health of the newborn35. In addition, maternal anemia is a risk factor for the occurrence of LBW with an odds ratio (OR) value of 1.23 (95% confidence interval [CI]: 1.06–1.43)60.\n\nThe results showed significant differences in the LBW leukocyte count parameters in the case and control groups (mean ± SD: 12.70 x 103±2.81/μL vs. 10.24 x 103±2.11/μL, p<0.05). In general, the range of leukocyte count values in newborns can range from 10,000-26,000/μL, which is also highly dependent on the time of sampling61. Meanwhile, the results of the leukocyte count in newborns at Bantul Hospital, Indonesia, in 195 infants showed an average leukocyte count of 14.62 x 103±3.49/μL62. The leukocyte count in newborns in the case and control groups showed values within normal limits, with the leukocyte count in the case group significantly higher than the control group. Several factors can increase the leukocyte count in newborns, including infection, inflammation, medication history, and stress63–65.\n\nSequestration is the attachment of infected erythrocytes to host cells associated with severe malaria, such as cerebral malaria and malaria in pregnancy. Sequestration occurs in the capillaries and post-capillary venules of specific organs such as the brain, lungs, and placenta. Sequestration correlates with mechanical obstruction of blood flow in the microvasculature and the activation of vascular endothelial cells, leading to pathological outcomes. Some parasitic and host proteins as ligands and receptors for sequestration have been identified and explored further66.\n\nHeretofore, the sequestration phenomenon only occurred in Plasmodium falciparum infection46,67,68. Interestingly, none of the subjects in this study were infected with Plasmodium falciparum, but instead, hemozoin depositions were found in all 19 positive samples, while Plasmodium vivax infected erythrocyte sequestrations were found in some samples. The result indicates that the Plasmodium vivax could cause sequestration of infected erythrocytes. Submicroscopic placental infection of Plasmodium vivax confirmed by placental histopathology indicates that the Plasmodium vivax can be selectively sequestered in the placenta even at low densities in peripheral blood69. The finding of Plasmodium vivax-infected erythrocytes sequestration was also mentioned by Carvalho et al. through an ex vivo study, which found that Plasmodium vivax-infected erythrocytes could adhere to the placental tissue. This study also demonstrated the cytoadherence of Plasmodium vivax-infected erythrocytes on endothelial cells by in vitro approach and was known to have the same strength as cytoadherence of Plasmodium falciparum-infected erythrocytes29. Toda et al. found that Plasmodium vivax-infected reticulocytes could bind to human spleen fibroblasts (hSF). The binding involves the NF-kB signaling pathway transcription factor by plasma-derived extracellular vesicles that act as cargo for the Plasmodium vivax parasite. This process facilitates the expression of ICAM-1 on the surface of hSF as a receptor for Plasmodium vivax sequestration51. Other evidence supporting placental malaria due to other non-falciparum Plasmodium species is a submicroscopic infection of Plasmodium malariae and Plasmodium ovale in the placenta confirmed by PCR of placental blood samples. Detection of Plasmodium malariae infection was higher in placental blood samples than in peripheral blood samples, indicating a possibility of Plasmodium malariae binding affinity to the placenta. However, the study of non-falciparum placental infection was not supported by histopathological examination of the placenta70.\n\nMalaria infection causes changes in the placenta structure in the form of hemozoin deposition and an increase in monocyte infiltration in the intervillous space, which interferes with maternal-fetal circulation48. Sequestration of infected erythrocytes, hemozoin deposition, and monocyte infiltration in placental histopathology are the main signs of placental malaria12,71,72. The pathomechanism of sequestration of infected erythrocytes in the placenta is clearly described in Plasmodium falciparum infection. However, Plasmodium vivax, which has been considered to cause a mild latent infection than Plasmodium falciparum, has also been reported to cause placental malaria. Histopathological changes of placental malaria due to Plasmodium falciparum can show a different representation of placental malaria due to Plasmodium vivax. However, these differences are not delineated yet48. The histopathological appearance of the placenta due to Plasmodium vivax infection is similar to that of Plasmodium falciparum. Plasmodium vivax had also demonstrated the sequestration mechanism of infected erythrocytes in placental tissue structures49,73. These findings are consistent with the results of this study.\n\nSeveral mechanisms can explain the Plasmodium vivax-infected erythrocytes sequestration phenomenon. First, the Plasmodium vivax-infected erythrocytes sequestration can occur under low shear stress conditions in the placental intervillous space and causes a local inflammatory process of the placenta31. Second, Plasmodium vivax lacks surface proteins, such as Plasmodium falciparum Erythrocyte Membrane Protein-1 (PfEMP-1) called Variant Surface Antigen-2-CSA (VAR2CSA) for adhesion and sequestration of CSA in the placental intervillous space74,75. However, the Plasmodium vivax genome contains a subtelomeric multigene family called VIR proteins. VIR proteins can mediate the adhesion of infected erythrocytes to ICAM-1 by VIR14 and the CSA by VIR2 and VIR24. The bindings are speculative and require further research73,74,76. The discovery of VIR binding in ICAM-1 and CSA proved the presence of Plasmodium vivax sequestration in the previous study29. The third mechanism that can explain the sequestration of Plasmodium vivax is the formation of rosettes by interacting with the Glycophorin C receptor present on normal erythrocytes, which has the adhesive power as in Plasmodium falciparum. However, further research is needed to determine the specific mechanism of rosette formation73,77,78.\n\nOn histopathological examination of the placenta, it was found that pigment/hemozoin depositions were trapped in the fibrin or freely circulating in the intervillous space and monocyte infiltration in all 19 positive samples. This finding indicates that the mother had experienced malaria infection during her pregnancy46,79. The presence of pigment/hemozoin and monocyte depositions in the placenta indicates that malaria infection does not occur in late pregnancy. The infection process has occurred long enough to cause deposition and accumulation of inflammatory cells in the placenta acquired early in pregnancy or before pregnancy69,70. However, the time required for the appearance of placental malaria is not known and requires further research.\n\nVascular endothelial growth factor (VEGF). In this study, VEGF expression in the placenta of the case group was lower than in the control group. In the case and control groups, VEGF expression was more abundant in trophoblast cells in the placental villi than in the intervillous space. VEGF expression in the case group placenta was significantly lower than in the control group (p=0.00). Expression of VEGF placental IUGR was inconsistent between several studies that have been carried out. The results of this study are consistent with several studies, which reported a decrease in VEGF expression accompanied by increased placental PlGF expression of IUGR80,81. Several studies reported an increase in the expression of VEGF, VEGFA, bFGF, and eNOS in the IUGR placenta due to placental hypoxia82–84. However, another study concluded that there was no decrease in VEGF expression of IUGR compared to normal placentas85,86. In addition, VEGF expression and plasma VEGF levels could not predict late-onset preeclampsia, small gestational age (SGA), or premature delivery87.\n\nPlasma VEGF levels in the case group were lower and not significantly different from the control group in this study (p=0.769). The findings were consistent with several studies, which found that maternal plasma VEGF levels of IUGR and SGA did not show significant differences compared to preeclampsia88 or normal pregnancy89. Moreover, Tang et al. reported that maternal plasma VEGF levels in pregnancies with preeclampsia were lower than normal pregnancies and were associated with impaired fetal growth90. However, Boras et al. found that maternal free plasma levels of VEGF and sFlt-1 were higher in IUGR than in normal pregnancies91.\n\nBesides being involved in the regulation of development and vascular remodeling during placentation, VEGF, PlGF, and Angiopoietin are also involved in trophoblast invasion. Failure of trophoblast invasion and remodeling of the spiral arteries causes placental hypoxia, which involves pregnancy complications such as preeclampsia and IUGR92, causing the fetus to experience hypoxia. At low oxygen concentrations, there should be an increase in VEGF expression. The mechanism that can explain the decrease in placental VEGF expression in this study is increased soluble VEGFR-1 (sFlt-1) in the placental intervillous space. sFlt-1 is a form of the VEGFR-1 gene that is physiologically secreted by the placenta. sFlt-1 physiologically binds to free VEGF and PlGF with strong affinity and inhibits their binding to VEGFR-1 and VEGFR-2 receptors, thereby decreasing placental VEGF and PlGF expression. HIF-1α regulates placental sFlt-1 expression; under conditions of placental hypoxia, there will be an increase in placental sFlt-1 expression93,94. The sFlt-1 expression was also reported to increase in IUGR placentas95,96. An in vivo study in transgenic mice by Vogtmann et al. found that an increase in placental sFlt1 would disrupt the vascular endothelial growth factor signalling pathway, resulting in decreased expression of VEGFA, VEGFB, PlGF, and increased the expression of band and mRNA of Caspase-997. Placental hypoxia will increase placental VEGF expression92,93, but the source of circulating VEGF is not only from the placenta but also from another organs98, then those can explain why the plasma levels of VEGF in the case group and the control group were not different.\n\nThe finding of decreased placental VEGF expression in this study can describe early-onset IUGR because of placental hypoxia, correlated with placental HIF-1α expression. However, histo-morphological studies of placental villi were not performed to confirm the dominance of branching angiogenesis in placental villi. Early-onset IUGR in this study can be caused by malaria infection before pregnancy or early pregnancy46, as evidenced in this study.\n\nPlacental growth factor (PlGF). The placenta is the only organ that produces PlGF98. PlGF has a significant function in the activation, proliferation, and migration of endothelial cells and trophoblast invasion into the maternal spiral arteries99. In this study, the expression of PlGF in the placenta in the case group was lower than the control group (p=0.00). In the case group, PlGF expression was more abundant in trophoblast cells in the placental villi, whereas in the control group, it was primarily found in the intervillous space. Studies on PlGF expression in placental IUGR had also shown inconsistent results. The results of this study support previous studies which reported that placental PlGF expression in severe IUGR was significantly lower than in controls and inhibition of PlGF/Flt-1 signalling will interfere with trophoblast proliferation and migration99–101. However, Alahakoon et al. found an increase in PlGF and KDR expression in IUGR and preeclampsia placentas86. It explained that hyperoxia conditions in IUGR due to impaired oxygen extraction to the fetus increase PlGF expression and decrease placental VEGF expression, with the consequence of reduced capillary branching and terminal villi resulting in placental dysfunction92,93,102,103.\n\nPlacental hypoxia conditions that occur early in pregnancy result in a decrease in placental PlGF production by the syncytiotrophoblast, so PlGF expression and PlGF levels in maternal circulation decreases92,93,100. In this study, the plasma levels of PlGF in the case group were significantly lower than in the control group (p=0.026). Previous studies have also shown that plasma or plasma PlGF levels are lower in pregnancies with IUGR95,104,105 in pregnancies with preeclampsia97,106–108 and pregnancies with preeclampsia and IUGR88,90,96,109–115. Decreased maternal plasma PlGF levels in pregnancy complications due to defective placentation are associated with increased production of sFlt-1 in the ischemic placenta, which is then secreted into the maternal circulation104,106. Furthermore, significantly lower PlGF levels in the case group indicate that the causes of IUGR in the two groups may be different. Malaria infection in the placenta causes the activation of complement C5a, which will stimulate the accumulation of monocytes to release sFlt-118, explaining that the plasma levels of PlGF in the case group were significantly lower than the control group.\n\nVascular endothelial growth factor receptor (VEGFR)-1 and VEGFR-2. This study showed that VEGFR-1 expression in the placenta was lower in the case group than in the control group (p=0.00). VEGFR-1 expression was more abundant in trophoblast cells in the placental villi than in the intervillous space, both in the case and control group. VEGFR-1 is a receptor for VEGF and PlGF. Helske et al. found that VEGFR-1 expression was increased in preeclamptic and IUGR placentas compared with normal placentas. The up-regulated expression is not exactly found on all preeclamptic samples but may be associated with hypoxia and abnormal function of the placenta116. However, down-regulation of both receptors was also reported during mid-pregnancy with IUGR117.\n\nIn line with VEGFR-1, the expression of VEGFR-2 in the placenta of the case group was lower than the control group (p=0.015). In the case group and the control group, VEGFR-2 expression was more abundant in trophoblast cells in the placental villi. VEGFR-2 is a significant receptor for VEGF, plays a role in endothelial proliferation and normal vascular formation. In the placenta, the role of VEGFR-2 is to change trophoblasts into intravascular trophoblasts and form spiral arteries. VEGFR-2 is expressed in low amounts under hypoxic conditions because oxygen levels regulate VEGFR-2 expression. Placental VEGFR-2 and sFlt-1 expression was also reported to decrease in cases of preeclampsia95,118.\n\nIn this study, plasma levels of VEGFR-1 in the case group were lower and significantly different with the control group (p=0.044) Anna et al. found that serum VEGFR-1 concentrations in women with IUGR were decreased, along with a decrease in PlGF. At low oxygen concentrations, PlGF and VEGFR-1 levels decrease119. Besides that, serum levels of VEGFR-2 in the case group were lower and significantly different with the control group (p=0.042). Chaiworapongsa et al. found soluble VEGFR-2 (sVEGFR2) concentration increased in women with preeclamptic pregnancies and interpreted that sVEGFR-2 in maternal plasma could reflect endothelial cell function120.\n\nHypoxia-inducible factor-1α (HIF-1α). This study revealed that the expression of HIF-1α in the placenta of the case group was higher than the control group (p=0.001). In the case group and the control group, HIF-1α expression was more commonly found in trophoblast cells in the placental villi. There are not many studies in humans examining HIF-1α expression in the placenta of pregnancies with complications such as preeclampsia, IUGR, and SGA. The results of this study support an in vivo study on the IUGR mice model conducted by Robb et al., who found an increase in HIF-1α expression in the placenta121.\n\nIn this study, plasma levels of HIF-1α in the case group were lower and not significantly different with the control group (p=0.402). So far, studies of HIF-1α have been mainly carried out in placental tissue, as in the discussion on placental HIF-1α expression above. Azhur-Fabian et al. found elevated HIF-1α and p21 mRNA expression in all pregnancy plasma samples with hypoxia and IUGR and recommended them as markers for hypoxic pregnancy and/or IUGR122. In pregnancy, HIF-1α is expressed in the placenta early in normal pregnancy and throughout pregnancy under hypoxic conditions123. Those explain no statistically significant difference in plasma HIF-1α levels in the case and control groups.\n\nUnder normoxic conditions, HIF-1α will undergo rapid degradation so that it is considered inactive. At low oxygen levels, HIF-1α will regulate genes that control cell growth, differentiation, and metabolism. The active form of HIF-1α that was continuously exposed to cultured cells was shown to inhibit trophoblast differentiation. In placental IUGR, impaired invasion and remodelling of the spiral arteries result in placental ischemia throughout pregnancy because of the increased expression of HIF-1α. The increase in placental HIF-1α expression in this study represents early-onset IUGR. However, this study has not determined whether placental hypoperfusion causes hypoxia as the main factor causing the increase in HIF-1α because other factors such as reactive oxygen species (ROS) and inflammation induced by nuclear factor kappa (NF-κB) can also modulate HIF-1α accumulation.\n\nPath analysis revealed the effect of placental angiogenesis and HIF-1α transcription factors on LBW. From this analysis, it was seen that the signalling pathway from HIF-1α to placental VEGF expression, then from placental VEGF expression to placental VEGFR-2 expression, and from placental VEGFR-2 expression to LBW showed statistically significant results. In contrast, HIF-1α could not cause a direct effect on LBW (p=0.881). Placental VEGF expression significantly affected placental VEGFR-1 expression. The signalling pathway of HIF-1α significantly affected placental PlGF expression, then placental PlGF expression significantly affected placental VEGFR-1 expression, but this pathway did not significantly affect the incidence of LBW (p=0.504).\n\nVEGF and VEGFR regulate vasculogenesis during early embryogenesis and angiogenesis in later stages of pregnancy. VEGF bind to VEGFR-1/Flt-1 and VEGFR-2/KDR, playing an essential role in physiological and pathological angiogenesis124. PlGF binds to the VEGFR-1 receptor, plays a role in angiogenesis in the later stages of pregnancy125. VEGFR-2 is the primary receptor mediating the pro-angiogenic effects of VEGF126. sFlt1, the free form of Flt-1, has a strong ability to bind to VEGFA, PlGF, and VEGFB. Because the trophoblast lies between the maternal and fetal vascular systems, it is thought that sFlt1 functions as a separator between the maternal and fetal circulations in the placenta by suppressing both excessive angiogenesis and abnormal vascular permeability. Therefore, under physiological conditions, sFlt1 levels are maintained in the suitable range. The increased expression of sFLT-1, triggered by hypoxic conditions, will bind to VEGF, causing disturbances in vasculogenesis and angiogenesis, leading to obstetric complications. Several studies have reported overexpression of sFlt1 and decreased expression of VEGFA in preeclamptic patients127.\n\nIn placental malaria infection, there is an accumulation of Plasmodium-infected erythrocytes in the intervillous space of the placenta. Several histopathological characteristics of placental malaria, including thickening of the basement membrane and infiltration of monocytes in the intervillous space of the placenta (intervillositis), can increase the resistance to oxygen transport across the placenta. Accumulation of inflammatory cells and infected erythrocytes can cause placental hypoxia due to oxygen consumption by these cells, in addition to decreased blood perfusion due to reduced effective surface area for feto-maternal exchange. Such placental dysfunction can result in stunted fetal growth, characterized by low birth weight babies27.\n\nIncreased expression of HIF-1α is a marker of placental hypoxia, which should increase the expression of VEGF, VEGFR-1, and VEGFR-2. Decreased expression of VEGFR, VEGFR-1, and VEGFR-2 is possible through increased sFlt-1 binding to VEGF with strong affinity. sFlt-1 of the placenta increases its expression under hypoxic conditions93,94. Further studies are needed to prove this.\n\nThe pathway analysis results indicate a dysregulation of the angiogenic factor VEGF and its receptor VEGFR-2 due to the regulation of HIF-1α in placental malaria on the incidence of LBW. It can be interpreted that the occurrence of LBW in placental malaria due to the influence of angiogenesis factors VEGF and VEGFR-2, which are regulated by HIF-1α and are more significant than LBW in non-malaria cases.\n\nThe effect of plasma angiogenesis and HIF-1α transcription factors on the incidence of LBW was observed using binary logistic regression as bivariate analysis. Based on the results of the observational test of data in maternal plasma, four parameters were significantly different between the case group and the control group, namely: haemoglobin, PlGF levels, VEGFR-1 levels, and VEGFR-2 levels. It showed that haemoglobin levels were the most significant (p=0.010) in influencing the incidence of LBW, followed by plasma levels of PlGF (p=0.021) and plasma levels of VEGFR-1 (p=0.056). The plasma levels of VEGFR-2 did not affect the incidence of LBW (p=0.131).\n\nThe haematological effect of Plasmodium vivax malaria is anaemia with its consequent increased morbidity and mortality and more frequent in blood transfusions. Although the parasitemia of Plasmodium vivax malaria is lower than that of Plasmodium falciparum malaria, it can cause severe anaemia, as in Plasmodium falciparum malaria. Anaemia in Plasmodium vivax malaria can be explained by two mechanisms. First, production/transfer of infected and uninfected erythrocytes are more in Plasmodium vivax malaria, 34 uninfected erythrocytes for one infected erythrocyte (in Plasmodium falciparum malaria, the ratio is 8:1). Second, Plasmodium vivax-infected erythrocytes undergo more rapid deformity limiting erythrocytes that are expelled through the microvessels of the spleen during the 'spleen clearance' phase. In addition to these two mechanisms, activation of the immune system due to Plasmodium vivax infection increases the detection and removal of abnormal infected and uninfected erythrocytes57.\n\nIn this study, maternal anaemia significantly affected the incidence of LBW. Several publications also reported the same thing. Plasmodium vivax malaria infection in pregnant women in Bolivia was more at risk of anaemia and giving birth to low birth weight babies than pregnant women who were not infected36 as well as in a multicenter study in an area of low malaria transmission35 and Mangaluru, India128.\n\nBased on the above discussion, in this study, it can be concluded that angiogenesis factors and HIF-1α transcription factors in placenta or in local environment play a more important role in the incidence of low birth weight than those in systemic. Those indicated that there is dysregulation of placental angiogenesis factors VEGF, PlGF, and their receptors VEGFR-1 and VEGFR-2, which is triggered by placental hypoxia conditions (marked by increased placental HIF-1α expression) during placental Plasmodium vivax infection.\n\n\nData availability\n\nFigshare: HIF-1α REGULATED PATHOMECHANISM OF LOW BIRTH WEIGHT THROUGH ANGIOGENESIS FACTORS IN PLACENTAL Plasmodium vivax INFECTION. https://doi.org/10.6084/m9.figshare.1657746841.\n\nThis project contains the following underlying data:\n\n- Raw Data.xlsx (ELISA Graph and Raw Data, Immunofluorescence Graph and Raw Data, Subject Characteristics, and Baby’s Characteristics Data)\n\n- Figure 1A (Blood Smear Figure 1A)\n\n- Figure 1B (Blood Smear Figure 1B)\n\n- Figure 1C (Blood Smear Figure 1C)\n\n- Figure 2A (VEGF immunofluorescence)\n\n- Figure 2B (PlGF immunofluorescence)\n\n- Figure 2C (VEGFR-1 immunofluorescence)\n\n- Figure 2D (VEGFR-2 immunofluorescence)\n\n- Figure 2E (HIF-α immunofluorescence)\n\n- Figure 3 (Angiogenic Factor Expression Graph)\n\n- Figure 4 (Angiogenic Factor Level in Maternal Plasma Graph)\n\n- PCR Images 1-4 (Raw Gel Images of PCR test from maternal (1-3) and cord (4) blood samples)\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe authors would like to acknowledge and thank the Chairman of dr. T.C. Hiller Regional Hospital, Public Health Office of Sikka Regency, and Public Health Office of Nusa Tenggara Timur (NTT), Indonesia, for the permission and substantial support to this research. We also thanks to Tarina Widaningrum S.Si., MP. Ami Maghfironi, S.Si., and Wahyuda Ngatiril Lady S.Si., for their assistance in carrying out laboratory work.\n\n\nReferences\n\nCenters for Disease Control and Prevention (CDC): Malaria's Impact Worldwide. CDC. 2021. Reference Source\n\nRijken MJ, McGready R, Boel ME, et al.: Malaria in pregnancy in the Asia-Pacific region. Lancet Infect Dis. 2012; 12(1): 75–88. PubMed Abstract | Publisher Full Text\n\nKovacs SD, Rijken MJ, Stergachis A: Treating severe malaria in pregnancy: a review of the evidence. Drug Saf. 2015; 38(2): 165–81. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: World Malaria Report 2020. WHO. 2020; 73: 1–4. 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PubMed Abstract | Publisher Full Text\n\nNevo O, Many A, Xu J, et al.: Placental expression of soluble fms-like tyrosine kinase 1 is increased in singletons and twin pregnancies with intrauterine growth restriction. J Clin Endocrinol Metab. 2008; 93(1): 285–92. PubMed Abstract | Publisher Full Text\n\nTsatsaris V, Goffin F, Munaut C, et al.: Overexpression of the soluble vascular endothelial growth factor receptor in preeclamptic patients: pathophysiological consequences. J Clin Endocrinol Metab. 2003; 88(11): 5555–63. PubMed Abstract | Publisher Full Text\n\nVogtmann R, Kühnel E, Dicke N, et al.: Human sFLT1 leads to severe changes in placental differentiation and vascularization in a transgenic hsFLT1/rtTA FGR mouse model. Front Endocrinol (Lausanne). 2019; 10: 165. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCerdeira AS, Karumanchi SA: Angiogenic factors in preeclampsia and related disorders. Cold Spring Harb Perspect Med. 2012; 2(11): a006585. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJoó JG, Rigó J Jr, Börzsönyi B, et al.: Placental gene expression of the placental growth factor (PlGF) in intrauterine growth restriction. J Matern Neonatal Med. 2017; 30(12): 1471–5. PubMed Abstract | Publisher Full Text\n\nWu WB, Xu YY, Cheng WW, et al.: Decreased PGF may contribute to trophoblast dysfunction in fetal growth restriction. Reproduction. 2017; 154(3): 319–29. PubMed Abstract\n\nRavikumar G, Mukhopadhyay A, Mani C, et al.: Placental expression of angiogenesis-related genes and their receptors in IUGR pregnancies: correlation with fetoplacental and maternal parameters. J Matern Neonatal Med. 2020; 33(23): 3954–61. Publisher Full Text\n\nAhmed A, Perkins J: Angiogenesis and intrauterine growth restriction. Baillieres Best Pract Res Clin Obstet Gynaecol. 2000; 14(6): 981–98. PubMed Abstract | Publisher Full Text\n\nBurton GJ, Charnock-Jones DS, Jauniaux E: Regulation of vascular growth and function in the human placenta. Reproduction. 2009; 138(6): 895–902. PubMed Abstract | Publisher Full Text\n\nBenton SJ, McCowan LM, Heazell AEP, et al.: Placental growth factor as a marker of fetal growth restriction caused by placental dysfunction. Placenta. 2016; 42: 1–8. PubMed Abstract | Publisher Full Text\n\nKomwilaisak R, Tangkiratichai P: Maternal serum angiogenic growth factors in intrauterine growth restriction versus normal pregnancies. J Med Assoc Thai. 2017; 100(2): 119–24. PubMed Abstract\n\nMaynard SE, Venkatesha S, Thadhani R, et al.: Soluble Fms-like Tyrosine Kinase 1 and Endothelial Dysfunction in the Pathogenesis of Preeclampsia. Pediatr Res. 2005; 57(5 Pt 2): 1R–7R. PubMed Abstract | Publisher Full Text\n\nVrachnis N, Kalampokas E, Sifakis S, et al.: Placental growth factor (PlGF): A key to optimizing fetal growth. J Matern Neonatal Med. 2013; 26(10): 995–1002. PubMed Abstract | Publisher Full Text\n\nRădulescu C, Bacârea A, Huțanu A, et al.: Placental Growth Factor, Soluble fms-Like Tyrosine Kinase 1, Soluble Endoglin, IL-6, and IL-16 as Biomarkers in Preeclampsia. Mediators Inflamm. 2016; 2016: 3027363. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBersinger NA, Ødegård RA: Serum levels of macrophage colony stimulating, vascular endothelial, and placenta growth factor in relation to later clinical onset of pre-eclampsia and a small-for-gestational age birth. Am J Reprod Immunol. 2005; 54(2): 77–83. PubMed Abstract | Publisher Full Text\n\nKarumanchi SA, Epstein FH: Placental ischemia and soluble fms-like tyrosine kinase 1: Cause or consequence of preeclampsia? Kidney Int. 2007; 71(10): 959–61. PubMed Abstract | Publisher Full Text\n\nRomero R, Nien JK, Espinoza J, et al.: A longitudinal study of angiogenic (placental growth factor) and anti-angiogenic (soluble endoglin and soluble vascular endothelial growth factor receptor-1) factors in normal pregnancy and patients destined to develop preeclampsia and deliver a small for gestational age neonate. J Matern Neonatal Med. 2008; 21(1): 9–23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGhosh SK, Raheja S, Tuli A, et al.: Can maternal serum placental growth factor estimation in early second trimester predict the occurrence of early onset preeclampsia and/or early onset intrauterine growth restriction? A prospective cohort study. J Obstet Gynaecol Res. 2013; 39(5): 881–90. PubMed Abstract | Publisher Full Text\n\nLaskowska M, Laskowska K, Oleszczuk J: aVEGF-A and its Soluble Receptor Type 1 (sVEGFR-1, sFlt-1) Concentrations in Pregnancies with Intrauterine Growth Restriction in the Presence or Absence of Preeclampsia. Res J Pharm Biol Chem Sci. 2015; 6(2): 319–25. Reference Source\n\nChang YS, Chen CN, Jeng SF, et al.: The sFlt-1/PlGF ratio as a predictor for poor pregnancy and neonatal outcomes. Pediatr Neonatol. 2017; 58(6): 529–33. PubMed Abstract | Publisher Full Text\n\nNaimi AA, Schmidt-fittschen M, Herzeg A, et al.: Is There Any Association Between the Angiogenic Factors Sflt-1 / Plgf And Intrauterine Growth Restriction in Patients with Preeclamsia? J Womens Health Gyn. 2019; 6(3): 1–7. Reference Source\n\nHelske S, Vuorela P, Carpén O, et al.: Expression of vascular endothelial growth factor receptors 1, 2 and 3 in placentas from normal and complicated pregnancies. Mol Hum Reprod. 2001; 7(2): 205–10. PubMed Abstract | Publisher Full Text\n\nRegnault TR, de Vrijer B, Galan HL, et al.: The relationship between transplacental O2 diffusion and placental expression of PlGF, VEGF and their receptors in a placental insufficiency model of fetal growth restriction. J Physiol. 2003; 550(Pt 2): 641–56. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNevo O, Lee DK, Caniggia I: Attenuation of VEGFR-2 expression by sFlt-1 and low oxygen in human placenta. PLoS One. 2013; 8(11): e81176. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSemczuk-Sikora A, Krzyzanowski A, Stachowicz N, et al.: [Maternal serum concentration of angiogenic factors: PIGF, VEGF and VEGFR-1 and placental volume in pregnancies complicated by intrauterine growth restriction]. Ginekol Pol. 2007; 78(10): 783–6. PubMed Abstract\n\nChaiworapongsa T, Romero R, Gotsch F, et al.: Low maternal concentrations of soluble vascular endothelial growth factor receptor-2 in preeclampsia and small for gestational age. J Matern Fetal Neonatal Med. 2008; 21(1): 41–52. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRobb KP, Cotechini T, Allaire C, et al.: Inflammation-induced fetal growth restriction in rats is associated with increased placental HIF-1α accumulation. PLoS One. 2017; 12(4): e0175805. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAshur-Fabian O, Yerushalmi GM, Mazaki-Tovi S, et al.: Cell free expression of hif1α and p21 in maternal peripheral blood as a marker for preeclampsia and fetal growth restriction. PLoS One. 2012; 7(5): e37273. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPringle KG, Kind KL, Sferruzzi-Perri AN, et al.: Beyond oxygen: complex regulation and activity of hypoxia inducible factors in pregnancy. Hum Reprod Update. 2010; 16(4): 415–31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShibuya M: Vascular Endothelial Growth Factor (VEGF) and Its Receptor (VEGFR) Signaling in Angiogenesis: A Crucial Target for Anti- and Pro-Angiogenic Therapies. Genes Cancer. 2011; 2(12): 1097–105. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang Y, Zhao S: Vascular biology of the placenta. In: Colloquium Series on Integrated Systems Physiology: From Molecule to Function. Morgan & Claypool Life Sciences. 2010; 1–98. PubMed Abstract | Publisher Full Text\n\nOtrock ZK, Mahfouz RA, Makarem JA, et al.: Understanding the biology of angiogenesis: review of the most important molecular mechanisms. Blood Cells Mol Dis. 2007; 39(2): 212–20. PubMed Abstract | Publisher Full Text\n\nKappou D, Sifakis S, Konstantinidou A, et al.: Role of the angiopoietin/Tie system in pregnancy (Review). Exp Ther Med. 2015; 9(4): 1091–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChandrashekar VN, Punnath K, Dayanand KK, et al.: Malarial anemia among pregnant women in the south-western coastal city of Mangaluru in India. Informatics Med Unlocked. 2019; 15: 100159. Publisher Full Text"
}
|
[
{
"id": "192254",
"date": "24 Aug 2023",
"name": "Alberto Tobón-Castaño",
"expertise": [
"Reviewer Expertise Malaria Clinical and epidemiological aspects. Malaria immunology and molecular diagnosis."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral recommendations\nIntroduction:\nOrganize the epidemiological information to create a stronger narrative thread for conveying the intended message. For instance, consider presenting the findings of P. falciparum and P. vivax cases by year to avoid jumping between different years or locations without a specific order.\n\nUpon concluding the epidemiological figures, it is worthwhile to include a conclusion, which could be positioned at the end of the second paragraph. This conclusion could emphasize that, just as P. falciparum has been implicated in cases of gestational malaria and low birth weight, it is important to underscore that P. vivax also leads to similar outcomes. Moreover, cases among pregnant women might vary in frequency based on the specific study area or endemic region being referred to.\n\nIt is crucial to begin reinforcing the significance of P. vivax and its implications for infected pregnant women, as well as its association with the discovery of low birth weight, right from these initial two paragraphs.\nInclusion Criteria:\n\nTerm pregnancies? The gestational weeks of the included women are not specified.\n\nOnly reference is made to infants born with low birth weight and small for gestational age.\n\nRecommendation for Definitions: Similar to the definition of placental malaria, it would be beneficial to first define gestational malaria and congenital malaria. This clarification would elucidate the reason for discussing analyses of peripheral blood and cord blood samples, respectively.\n\nTerminology Recommendation: Clarify terms when referring to the presence of HZ in tissue; it's not about sequestration, but rather about its presence or absence. It can be found inside or outside the erythrocyte, either in a free or intraleukocytic form.\n\nReference Modification: Reference 40, which relates to the count of parasitized erythrocytes and addresses parasitemia, might not be the most suitable. We suggest finding a reference related to parasitemia in humans, considering the study's context, rather than using one related to mice.\nResults Recommendation:\nRegarding the diagnosis, all samples tested positive for P. vivax, and no positive samples were found for P. falciparum. Could a brief explanation be provided for this? Was it due to the endemic zone of the pregnant women? Did these results align with the diagnoses the pregnant women had at the time of inclusion?\n\nBased on the histological analysis of the placentas, was the parasitemia detected in tissue exclusively from P. vivax? Were the infected erythrocytes located in the intervillous space or adhered to the villi? Do you have images that can illustrate how the parasitized erythrocytes were observed in the tissue? It might be beneficial to include a panel of parasites and/or hemozoin seen in the tissue in Figure 1.\n\nWere the two cases of malaria diagnosed through cord blood classified as congenital malaria?\nRecommendations: Table 1:\nIt is suggested to change the order in which the data is presented, beginning with Controls and then Cases. This order aligns with how the rest of the results are shown from (Fig 2, Fig 3, Fig 4).\n\nIt is recommended to standardize the table presentation. In Table 2, consider displaying Controls (N=14) and Cases (N=19), and remove the last row that shows the total number of cases.\nRecommendation: Figure 1:\nFor Panel A, consider selecting a more representative and clear image of an amoeboid trophozoite of P. vivax.\n\nIn Panel B, the schizont appears truncated. Display a complete schizont instead.\n\nIn Panel C, if feasible, improve the photo quality. The current image seems to have a flash glare. It should be taken without flash and with improved focus, ideally using a microscope equipped with a camera.\nRecommendation: Table 2:\nIt is recommended to change the order in which the data is presented, starting with Controls and then Cases, to maintain consistency with how the rest of the results are shown from (Fig 2, Fig 3, Fig 4).\n\nBold significant P-value data. Although more of a stylistic suggestion, it helps draw the reader's attention and focuses on those key points.\n\nIt is suggested to show the sociodemographic characteristics first, describing from the general features of the study population to the specific aspects centered around the molecular results. This approach moves from general to specific. Consider using this table as Table 1 and organizing the information based on the results section.\nRecommendation: Table 3:\nIt is recommended to change the order in which the data is presented, starting with Controls and then Cases, to maintain the consistency shown in the rest of the results from (Fig 2, Fig 3, Fig 4).\n\nBold the data with significant P-values.\n\nNote that the P-value for the t-test and the Mann-Whitney test is significant at a level below 0.05%, only for the parameters of leukocytes and the percentile growth curve. While the results make reference to the growth curve, there is no mention of the increase in leukocytes in the cases. This should also be mentioned, as it allows for further discussion later on. This effect is expected and aligns with what has been reported for P. falciparum infections or previous reports on P. vivax.\nRecommendation: Table 4:\nWe recommend changing the order in which the data is presented, starting with Controls and then Cases, to maintain consistency with how the rest of the results are shown from (Fig 2, Fig 3, Fig 4).\n\nBold the data with significant P-values.\nSubject Characteristics and Distribution:\n\nWe suggest placing this section first, before presenting other results related to molecular parameters such as angiogenic or hypoxia factors. It is important to describe the population characteristics of the subjects to whom various molecular parameters will be measured.\nGeneral Recommendations for Results:\nEnsure consistency in the presentation of decimal figures. If you are using two decimal places in tables, maintain the same format in the text and avoid using three decimal places.\n\nIncorporate these suggestions into the structure and formatting of your results section to enhance clarity and coherence.\nRecommendation:\nFor the section \"Association of Angiogenic Factors Expression with Birth Weight\": Clarify the meaning of the expression values such as VEGF (64,404±28,942), PIGF (22,814,440±9,497,663), and others like VEGFR-1 (107,444±46,696). To understand the origin of these values, specify which parameter of the ImageJ software you are using. If you are using Pixel2, explain why you chose that parameter and not the mean fluorescence intensity (IntDent) as the expression value. This question applies to other sections where expression is discussed based on an Image analysis of photos.\n\nThe analyzes related to Low Birth Weight are not presented in detail; since all neonates had LBW, analyzes related to this outcome must be interpreted with care; it is not clear how these P values were obtained. For example: In relation to this :”VEGFR-1 expression had no direct effect on birth weight (p=0.464), but VEGFR-2 expression had a significant direct effect (p=0.020) on birth weight with an effect coefficient of 0.743”. It is not clear how this P values were obtained.\n\nFigure 2 and Figure 3: Since Figure 2 and Figure 3 stem from the same analysis, we recommend placing statistical analyses alongside the IFIs images. This layout would enhance clarity for the reader.\n\nWe suggest using a scale bar in the photographs or specifying if they were captured using a mobile device or cell phone, which could explain the absence of a scale bar. This will provide clarity to the readers regarding the visual representation of the images.\n\nIncorporate this recommendation into your article's image captions or descriptions to enhance the understanding of the visual content.\nSummary recommendations\nIntroduction: It's important to organize the epidemiological information coherently to effectively convey the message. It's suggested to present the findings of P. falciparum and P. vivax cases per year to avoid jumping around in time or space. After presenting the epidemiological figures, it could be concluded that, like P. falciparum, P. vivax also leads to consequences in pregnant women, influenced by the geographical zone.\nFocus on P. vivax and its Implications in Pregnant Women: From the initial paragraphs, emphasize the significance of P. vivax in pregnant women and its relation to low birth weight.\nInclusion Criteria: Specify the term of gestation. Clarify that the included women had babies with low birth weight and small for gestational age. Detail the case and control groups, diagnostic methods, and sources of blood samples.\nDefinitions and Terminology: Define \"gestational malaria\" and \"congenital malaria\" first. Clarify the term \"presence\" of HZ in tissue. Adjust reference 40 to make it relevant to the study context.\nResults: Explain why all samples tested positive for P. vivax and none for P. falciparum. Clarify if this is due to the endemic zone. Detail whether tissue parasitemia was exclusively from P. vivax and the location of infected erythrocytes in the placenta. Add clear photos of parasitized erythrocytes in tissue in Figure 1. Clarify if cases diagnosed through cord blood were classified as congenital malaria.\nTables and Figures: Change the presentation order in tables to start with Controls. Standardize data presentation and highlight significant P-value values. Enhance the image quality in Figure 1, specifically in panels A, B, and C. Include statistical analyses alongside IFIs images in Figure 2 and Figure 3. Use a scale bar on photographs or explain if they were taken from a mobile device.\nPresentation of Results: Highlight the sociodemographic characteristics of subjects initially and then address the molecular results. Organize information based on the study's focus.\nGeneral: Maintain consistency in presenting decimal figures in tables and text. Specify ImageJ analysis parameters in sections related to angiogenic factor expression.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10940",
"date": "22 Mar 2024",
"name": "Nabila Erina Erwan",
"role": "Author Response",
"response": "Introduction We will reorganize the epidemiological data of malaria in our manuscript. As suggested, we added the conclusion of the epidemiological data at the end of the second paragraph. The conclusion will be: \"This finding might emphasize that P. vivax also causes comparable effects, as P. falciparum has been linked to low birth weight and gestational malaria cases. Furthermore, the prevalence of instances among pregnant mothers may differ depending on the particular research location or endemic region in question.\" We mentioned the previous study in NTT, Indonesia, which showed evidence of P. vivax-associated low birth weight (LBW) in the second paragraph. Inclusion criteria All the participants were in term pregnancy, and the gestational age ranged from 37 to 42 weeks (ACOG, 2013). The characteristics of the subject are shown in Table 2. We will add the definition of the term pregnancies in the characteristic of the research participant subsection. The inclusion criteria were pregnant women who gave birth to babies with low birth weight (LBW) and small for gestational age (SGA). The research subjects were mothers who gave birth to babies with low birth weight (< 2500 g) and small gestational age (birth weight < 10th percentile for gestational age at birth) to describe the occurrence of stunted fetal growth. Our study used a peripheral blood sample to determine gestational malaria and a cord blood sample to determine placental malaria. However, we don’t identify the presence of congenital malaria. We also used placental samples to identify the placenta's pathological properties and diagnose placental malaria. We will change the term of hemozoin sequestration to hemozoin deposition (free hemozoin). Free hemozoin is found in extracellular form (outside the cell). We will change the reference with a more suitable reference for human parasitemia counting. Result Recommendation: In Nusa Tenggara Timur, the most common species of Plasmodium is P. vivax, which mostly affects women (Fitri et al., 2014). The results align with the diagnoses of the pregnant women, which met the inclusion criteria. The infected erythrocytes are located in the intervillous space, as in Figure 2. The two cases, which are the infected erythrocytes found in cord blood, might not become congenital malaria because the parasite might not developed due to the presence of the IgG of the mother and the kind of fetal hemoglobin (HbF). The definitive diagnosis of congenital malaria is defined by the presence of infected erythrocytes in the peripheral blood of the fetus. Recommendation: Table 1: We changed the order of the data presented in Table 1. We will edit the table presentation as suggested. Recommendation: Figure 1: For Panel A, this is the best figure among the blood slides. For Panel B, most parasite morphology is not intact; it might be because the patients/subjects have antibodies against Plasmodium, characterized by no clinical symptoms of all the subjects (pregnant mother). This is the best figure among the blood slides. For Panel C, this is the best figure among the blood slides. Recommendation: Table 2: We changed the order of the data in Table 2 and bolded the p-value data as suggested. We switched the data in Table 2 into Table 1 and vice versa to be presented in the text as suggested. Recommendation: Table 3: We changed the order of the data in Table 3 and bolded the p-value data as suggested. We added some discussion related to the laboratory findings of the baby in the discussion section. Recommendation: Table 4: We changed the order of the data in Table 4 and bolded the p-value data as suggested. Subject Characteristics and Distribution: We first presented the subject characteristics and distribution in the result and discussion section, followed by molecular parameters in the study. General Recommendations for Results: We will make sure of the consistency of decimal figures in the text. Recommendation: The meaning of expression values of angiogenic factors expression is a semi-quantification result of the immunofluorescence image using mean fluorescence intensity (IntDent) by Image J software. The relationship between HIF-1a, VEGFR1, and VEGFR2 expression and birth weight was analyzed using path analysis, which describes the causal-effect relationship and the residual coefficient (e). From the model, an equation was obtained, which explained that there was no significant direct effect (p=0.99) between HIF-1∝ expression on the baby's birth weight, nor did VEGFR1 expression directly affect the baby's birth weight (p=0.46 ). However, the expression of VEGFR2 had a significant direct effect (p=0.02) on the baby's birth weight with an influence coefficient of 0.74. As suggested, we merged Figures 2 and 3 to place the statistical analysis alongside the IFI images. The figures were captured using a mobile device, which could explain the absence of a scale bar. Summary Recommendations: We have revised the manuscript as suggested by the reviewers, and a detailed response is explained in the above response points."
}
]
},
{
"id": "182970",
"date": "29 Aug 2023",
"name": "Jean Claude Djontu",
"expertise": [
"Reviewer Expertise Immunology and molecular epidemiology of malaria"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI enjoyed reading this manuscript (Nugrahanti Prasetyorini et al) examining the HIF-1α regulated pathomechanism of low birth weight through angiogenesis factors in placental Plasmodium vivax.\n\nI have no major concerns with the scientific approach, but the sample size is too small (n= 19), and cannot allow to drawn high evidence based conclusion. The results of the abstract are not clearly stated, thus do not support the conclusion.\nIn the method section, the authors should define the word “placental malaria” and add the the placental tissue histology as one of the tools for the placental malaria diagnosis.\nImportantly, the manuscript is in need of a linguistic revision to correct grammar, sentence structure and other language issues. I encourage the authors to engage a copyeditor, preferably with a science background.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10941",
"date": "22 Mar 2024",
"name": "Nabila Erina Erwan",
"role": "Author Response",
"response": "Thank you for the comments. Here are the responses for the reviewer: We acknowledge our limitation regarding the sample size, even though we conducted a total sampling collection for one year. We will increase the sample size in further research to reveal the conclusion. We will clearly state the definition of placental malaria in the method section, specifically in the diagnosis of placental malaria subsection, as shown by the phrase \"which is determined by placental tissue histopathological examination based on infected erythrocyte sequestration, monocyte infiltration, and hemozoin deposition (Rogerson et al., 2007)\". We will proofread our manuscript before it is resubmitted as the new version."
}
]
}
] | 1
|
https://f1000research.com/articles/11-131
|
https://f1000research.com/articles/12-1329/v1
|
13 Oct 23
|
{
"type": "Research Article",
"title": "Morphological study of the popliteus muscle-tendon complex in formalin embalmed adult cadavers",
"authors": [
"Rajanigandha Vadgaonkar",
"Mamatha Tonse",
"Vandana Blossom",
"P. Gopal Govind Kalluraya",
"B.V. Murlimanju",
"Rajanigandha Vadgaonkar",
"Mamatha Tonse",
"Vandana Blossom",
"P. Gopal Govind Kalluraya"
],
"abstract": "Background: The dimensions of popliteus muscle and its tendon are subjected to variability in the origin, mode of insertion, innervation patterns and vascular supply. The aim of this study was to measure the length, thickness and width of the popliteus muscle and its tendon at its different parts. The objectives were to study the topographic anatomy of the neurovascular structures of the popliteus and also to determine the dimensions of the popliteo-fibular ligament. Methods: This descriptive cross sectional institutional based study included 50 formalin embalmed adult lower limb specimens. The measurements were performed by using the digital Vernier caliper. Results: The length of the popliteus muscle belly along the upper and lower border were 44.2±6.63 mm and 89.26±14.41 mm, width of the muscle belly at midpoint, musculotendinous junction and insertion were 28.45±6.85 mm, 11.7±3.5 mm and 75.95±10.7 mm. The thickness of muscle belly at the midpoint was 2.55±0.55 mm. The length of popliteal tendon, width at origin and at musculotendinous junction were 24.85±2.15 mm, 7.55±1.55 mm and 8.5±1.15 mm. The thickness of tendon of popliteus was 2.6±0.75 mm. The length of nerve to popliteus was 50.44±8.66 mm and its origin was located 27.54±6.18 mm from the intercondylar line. The distance of origin of medial and lateral geniculate arteries from the intercondylar line were 26.26±10.47 mm and 20.76±5.19 mm. The distance of division of popliteal artery was 49.44±16.26 mm from the intercondylar line. The length and width of the popliteo-fibular ligament was 17.84±3.43 mm and 7.36±1.9 mm individually. Conclusions: This study offered detailed morphometric data of the popliteus and it is believed that the data of this anatomical research is enlightening to orthopedic surgeons particularly in the field of arthroscopic and plastic surgery. The data can be considered as the database from our population.",
"keywords": [
"Arthroscopic Surgery",
"Popliteus",
"Plastic Surgery"
],
"content": "Introduction\n\nThe popliteus is a muscle in the posterior compartment of the lower extremity, which is located at the leg and innervated by the tibial nerve. This is the only muscle in the back of leg, which acts on the knee joint and not over the ankle joint. This is considered as the unlocking muscle of the knee joint. It laterally rotates the femur over the tibia, while walking when one foot is on the ground. It helps in the knee stabilization along with the fibular collateral and popliteo-fibular ligaments.1 The popliteus has dual origin, one from the lateral femoral condyle and the other from the lateral meniscus. Its origin is tendinous and it is interesting to know that there exists variability in its origin like from the styloid process of the fibula.2 On few occasions, an accessory head of popliteus may originate from the sesamoid bone at the gastrocnemius lateral head. On rare occasions, there may be a popliteus minor muscle, which originates from the femur over the deep part of the plantaris muscle and its distal attachment is at the posterior aspect of knee joint. The popliteal tendon occupies a part of the knee joint capsule; however, it does not enter the synovial cavity. Hence it is intra-capsular, however extra-articular and extra-synovial. It runs underneath the fibular collateral ligament and biceps femoris tendon. The popliteus separates the lateral collateral ligament from the lateral meniscus and prevents its injury. The popliteus inserts at the dorsal aspect of the tibial upper end just over the soleal line. More clinical and basic anatomical studies are needed to understand the injuries and pathological involvement of popliteus in order to accomplish the better diagnosis and management.3 In this situation, the primary goal was to determine the dimensions of different parameters of popliteal muscle tendon complex at its various parts. The objectives were to measure the dimensions of popliteo-fibular ligament and to study the topographic anatomy of the neurovascular structures supplying the popliteus.\n\n\nMethods\n\nThis is a descriptive cross sectional institutional based study, which involved 25 formalin embalmed adult cadavers. The sample size is similar to the earlier study performed by Olewnik et al.1 The protocol of this anatomical research is available at dx.doi.org/10.17504/protocols.io.3byl4qqk8vo5/v1. Meticulous dissection was performed to expose the popliteus muscle, tendon and its neurovascular structures. In total, 50 popliteus muscles were analyzed based on the side. Gender based comparison was not performed. The inclusion criteria were adult embalmed cadavers, which were available at the department of anatomy. Cadavers showing pathological changes and congenital anomalies at the knee joint were excluded from this study. The exclusion criteria also included the previously dissected cadavers. The measurements were performed by using the digital Vernier caliper (Mitutoyo Digital Vernier Caliper 0-150 mm 500-196 made in Japan) and the analysis of the data was done by using the recent version of SPSS (version 27) software after applying the paired t-test. Single person, who is a coauthor in this study, performed all the measurements. This was followed to prevent the inter-observer bias and the measurements were taken on three consecutive times. The average of which was considered to prevent the intra-observer bias. The measurements of the popliteus muscle tendon complex are schematically represented in Figure 1 and tabulated in Table 1.\n\nThis anatomical research has received the approval from the ethics committee of our institution (Approval Committee Name: Institutional Ethics Committee, Kasturba Medical College, Mangalore, Approval Number: IEC KMC MLR: 09/2022/400, dated 21.09.2022). Since this is a study from the human cadavers, the consent from the participants is not applicable. This was waived by our institutional ethics committee. The consent was already given by the participant to perform the medical teaching and research, while donating his or her body. This present research is following the guidelines of the international ethical standards.\n\n\nResults\n\nThe length of the popliteus muscle belly along the upper and lower border were 44.2±6.63 mm and 89.26±14.41 mm, width of the muscle belly at midpoint, musculotendinous junction and insertion were 28.45±6.85 mm, 11.7±3.5 mm and 75.95±10.7 mm.15 The thickness of muscle belly at the midpoint was 2.55±0.55 mm. The morphometric data of the popliteus muscle belly are given in Table 2. The length of popliteal tendon, width at origin and at musculotendinous junction were 24.85±2.15 mm, 7.55±1.55 mm and 8.5±1.15 mm. The thickness of tendon of popliteus was 2.6±0.75 mm. Table 3 represents the dimensions of the tendon of popliteus of this study.\n\nThe length of nerve to popliteus was 50.44±8.66 mm and its origin was located 27.54±6.18 mm from the intercondylar line. The distance of origin of medial and lateral geniculate arteries from the intercondylar line were 26.26±10.47 mm and 20.76±5.19 mm. The distance of division of popliteal artery was 49.44±16.26 mm from the intercondylar line. Table 4 offers the topographic anatomy of the neurovascular structures of popliteus. The length and width of the popliteo-fibular ligament was 17.84±3.43 mm and 7.36±1.9 mm individually. They are summarized in Table 5 and the sidewise comparison of all the parameters, which are measured in this study are given in Table 6, Table 7, Table 8 and Table 9. The statistical significance was not there, when the right and left side comparison was considered (p>0.05). The only significant difference was observed for the width of the popliteal muscle at the insertion, which was higher for the left side (p<0.05).\n\n* (p<0.05).\n\nThe present study observed that, there was single twig (Figure 2) of nerve to popliteus in 17 lower limbs (34% cases), there were two twigs (Figure 3) in 42% cases (in 21 lower limbs) and the nerve to popliteus was giving 3 twigs (Figure 4) in 12 lower extremities (24%). The frequency of distribution of nerve to popliteus is represented in Figure 5.\n\n\nDiscussion\n\nThe popliteus muscle is the unlocking muscle of the knee and avoids the medial rotation of femur over tibia.4 It is known for variations and this is explained on the basis of phylogeny.5 In reptiles, fibula directly articulates with the lateral femoral condyle, so popliteus is more occupied between the proximal parts of tibia and fibula. In mammals, femur articulates with tibia, leading to the migration of popliteus muscle proximally until the lateral femoral condyle. In humans, attachment of popliteus to fibula is represented by the popliteo-fibular ligament. This is very important as it stabilizes the posterolateral aspect of the femoro-tibial articulation. According to Vani and Raveendranath,6 the length and width of tendon of popliteus was 35.12 mm and 9.52 mm, which was comparable to the dimensions by Jung et al.7 and Osti et al.8 LaPrade et al.9 reported that the length of popliteus tendon measures 54.5 mm. In our research, the same parameters were 24.85 ± 2.15 mm and the width at the musculotendinous junction was 8.5±1.15 mm. These dimensions are slightly lower in comparison to the data by Vani and Raveendranath.6 In their study, the distance of distal attachment of popliteus from its musculotendinous junction was 107.14±13.45 mm and widest part of popliteus measured 32.38±4.33 mm. Kurtoglu et al.10 reported in their study that popliteus muscle belly length and width were 107.14mm and 32.38mm. However, the mediolateral length of popliteus along the lower border was 89.26±14.41 mm in our study and the width of popliteus at the midpoint was 28.45±6.85 mm. These dimensions are small in comparison to Kurtoglu et al.,10 may be because of ancestral variations. Hwang et al.11 reported the popliteal length at its lateral border, which was 119±15 mm. This was almost parallel to the findings of Vani and Raveendranath.6 In the present study, this dimension was not performed and the morphometric data of the length and width of popliteus is different in our study in comparison to previous studies, as the different points were used for the measurements. The positive outcome of this anatomical research was we measured the length of the popliteus at both the upper and lower borders.\n\nVani and Raveendranath6 reported that, the distance of origin of nerve to popliteus from the intercondylar line ranged between 12.10±10.54 mm above the intercondylar line to 18.74±11.51 mm below the intercondylar line. In the present study, this distance was measuring 27.54±6.18 mm below the intercondylar line. In most of our specimens, it was observed that, nerve to popliteus was arising separately and was not giving the nerve to soleus or nerve to tibialis posterior. We could observe that; these nerves were separate branches coming from the tibial nerve. However, previous authors mentioned that, nerve to tibialis posterior originates from the nerve to popliteus.11\n\nIn the present study, it was observed that the nerve to popliteus along with the blood vessels, descend anterior to the popliteus muscle and enter at its anterior surface, which is obvious in Figure 2. The basic anatomical knowledge of these structures can enlighten the plastic surgeons during the reconstruction surgeries of popliteus. The anatomy and biomechanics of popliteus makes it an important structure, which keeps the knee stable. But its involvement is ignored in the complex injury of the knee joint.3 The isolated involvement of popliteus is seen in sports injuries and it may be misinterpreted as a tear of lateral meniscus. The sports like tennis, basketball and downhill running may put additional stress on the tendon of popliteus.3 The present study provided the data about the neurovascular structures in relation to the popliteus and it is believed that these details are clinically important for the effective treatment of the popliteus muscle spasticity.12 Popliteus muscle tendon complex is a landmark to the operating surgeon during the sling reconstruction of popliteus tendon.13 Popliteus is commonly injured in the posterolateral impact at the femoro-tibial articulation and gets torn. The muscular strains are also common in the sports injuries, which commonly affect the popliteus at its tendino-muscular junction.14 Due to all these implications, the present study was undertaken. The literature search did not reveal much studies about the morphometry of the popliteus and particularly, the dataset is not available from the Indian population. In this context, the data of the present study is enlightening to the orthopedic surgeons, particularly for the posterior knee approach procedures like baker’s cyst excision, fixation of tibial plateu fractures and meniscal tears. However, the present study has limitations like the smaller sample size, gender based comparison which was not made and the utilization of embalmed cadavers, where formalin alters the morphology.\n\n\nConclusion\n\nThe present study offered the detailed morphometric data about the dimensions of the popliteus muscle belly and its tendon along with the popliteo-fibular ligament. It is believed that, the data of popliteal muscle tendon complex of this study will be enlightening to the orthopedic surgeons particularly in the field of arthroscopic and plastic surgery like the reconstruction. The data can be considered as the database for our population.",
"appendix": "Data availability\n\nFigshare: Raw Data _Popliteus.xlsx, https://doi.org/10.6084/m9.figshare.23967018.v1. 15\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nOlewnik Ł, LaPrade RF, Paulsen F, et al.: A proposal for a new morphological classification of the popliteus muscle tendon with potential clinical and biomechanical significance. Sci. Rep. 2021; 11: 14434. Publisher Full Text\n\nHyland S, Varacallo M: Anatomy, Bony Pelvis and Lower Limb, Popliteus Muscle. [Updated 2020 Aug 15]. StatPearls. Treasure Island (FL): StatPearls Publishing; 2020.\n\nZabrzyński J, Huri G, Yataganbaba A, et al.: Current concepts on the morphology of popliteus tendon and its clinical implications. Folia Morphol. (Warsz). 2021; 80(3): 505–513. PubMed Abstract | Publisher Full Text\n\nStranding S, Borley NR, Gray H: Gray’s anatomy: the anatomical basis of clinical practice. 41st ed.Edinburgh: Churchill Livingstone/Elsevier; 2016; 1397.\n\nFu¨rst CM: Der Musculus Popliteus und seine Sehne. Acta Unversitatis Ludensis. 1903; 39: 1–134.\n\nVani PC, Raveendranath V: A morphometric study of the popliteus myotendinous complex with its clinical aspects. Muscles Lig. Tendons J. 2019; 09(1): 131–137. Publisher Full Text\n\nJung GH, Kim JD, Kim H: Location and classification of popliteus tendon’s origin: cadaveric study. Arch. Orthop. Trauma Surg. 2010; 130(8): 1027–1032. Publisher Full Text\n\nOsti M, Tschann P, Kunzel KH, et al.: Posterolateral corner of the knee: microsurgical analysis of anatomy and morphometry. Orthopedics. 2013; 36(9): e1114–e1120. Publisher Full Text\n\nLaPrade R, Ly T, Wentorf F, et al.: The posterolateral attachments of the knee. Am. J. Sports Med. 2017; 31(6): 854–860. Publisher Full Text\n\nKurtoglu Z, Elvan O, Aktekin M, et al.: Morphological features of the popliteus tendon, popliteo-fibular and lateral (fibular) collateral ligaments. Int. J. Morphol. 2017; 35(1): 62–71. Publisher Full Text\n\nHwang K, Lee KM, Han SH, et al.: Shape and innervation of popliteus muscle. Anat. Cell. Biol. 2010; 43(2): 165–168. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJeon A, Kim YG, Sohn Y, et al.: Nerve and arterial supply pattern of the popliteus muscle and clinical implications. Biomed. Res. Int. 2022; 2022: 6980471.\n\nFeng H, Hong L, Geng X, et al.: Posterolateral sling reconstruction of the popliteus tendon: an all-arthroscopic technique. Arthroscopy. 2009; 25(7): 800–805. PubMed Abstract | Publisher Full Text\n\nJadhav SP, More SR, Riascos RF, et al.: Comprehensive review of the anatomy, function, and imaging of the popliteus and associated pathologic conditions. RadioGraphics. 2014; 34(2): 496–513. PubMed Abstract | Publisher Full Text\n\nMurlimanju BV, Vadgaonkar R: Raw Data _Popliteus.xlsx. [Dataset]. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "215167",
"date": "16 Oct 2023",
"name": "Graham Louw",
"expertise": [
"Reviewer Expertise Medical Education",
"Clinical Anatomy",
"Embryology",
"Comparative Anatomy",
"Neurosciences",
"Gender-based studies in anatomical education."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for giving me the opportunity to read and comment on this submission.\nThis is an interesting study and the authors have done plenty of work to ensure that the research project was covered in depth.\nI have several suggestions for improvements which I hope will prove beneficial for the authors.\nThere are quite a few anatomical facts listed under the Introduction and I think that we need references for this information to be inserted.\nUnder Methods, the following is stated: \"Single person, who is a coauthor in this study, performed all the measurements. This was followed to prevent the inter-observer bias and the measurements were taken on three consecutive times. The average of which was considered to prevent the intra-observer bias.\" I do not follow this reasoning because it is far more reliable to have inter-observer participation for credible results - and I am not sure what this \"bias\" refers to.\nThe caption for Figure 1 needs to indicate what all of those letters mean. Alternatively, the journal may be happy to have the caption refer to the details in Table 1 as the explanation.\nUnder Methodology, we need to read how all of those anatomical points for the measurements were determined.\nThe authors state that \"The data can be considered as the database from our population.\" but I am unable to establish what this population is. Towards the end of their Discussion they state \"The literature search did not reveal much studies about the morphometry of the popliteus and particularly, the dataset is not available from the Indian population.\" but the details of the population need to be given under Materials.\nThe authors state that they did not explore \"gender\" differences but we do not know the gender identity of the bodies in the dissection hall - only their sex. the authors should state that sex differences were not explored.\nRegarding comparing left and right sides, we need to see the actual p values when deciding whether there was or was not statistical significance. Why was sidedness compared for some data and not for others?\nDid the authors consider making corrections for human variation, in other words a correction factor for overall height of the body? Or was the idea rather to report the averages of the data points used? If so, maybe the range (maximum / minimum) should be given and then the average for each one?\nFor the figures illustrating the dissections, the captions need to indicate what view this is (posterior) and whether it is a left or right leg, and then provide an indication of superior / inferior / lateral / medial.\nOne of the limitations is given as formalin altering the morphology of the structures - but in what way are they altered?\nThis article needs to be proofread for grammar - and I am not sure who will be doing that. It is no longer the role of a reviewer to address the language used by an author. Furthermore, does the journal check all of the referencing?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10781",
"date": "18 Jan 2024",
"name": "B.V. Murlimanju",
"role": "Author Response",
"response": "1. Reviewer comment: This is an interesting study and the authors have done plenty of work to ensure that the research project was covered in depth. Author Reply: We thank the reviewer for the kind words and appreciating our research. 2. Reviewer comment: There are quite a few anatomical facts listed under the Introduction and I think that we need references for this information to be inserted. Author Reply: We accept the reviewer opinion. As per the suggestion, citations are added for this literature. Three more references were added in the introduction section. 3. Reviewer comment: Under Methods, the following is stated: \"Single person, who is a coauthor in this study, performed all the measurements. This was followed to prevent the inter-observer bias and the measurements were taken on three consecutive times. The average of which was considered to prevent the intra-observer bias.\" I do not follow this reasoning because it is far more reliable to have inter-observer participation for credible results - and I am not sure what this \"bias\" refers to. Author Reply: In this study, repeatability of the measurements by asking a secondary observer was not performed. It would have been better if a subset of the sample was measured by a secondary observer and intraclass correlation was applied statistically. If the measurements are consistently taken by one observer incorrectly and then averaged to one value it still might not be representative of the 'true' dimensions of the vertebrae. Statistically confirming the agreement between these measurements would strengthen the quality of the research. If the intra-observer error is high, it might suggest the requirement for better measurement definitions or suggest using different tools for them in the field of vertebral morphometry in general. This information is added as a limitation of this study. 4. Reviewer comment: The caption for Figure 1 needs to indicate what all of those letters mean. Alternatively, the journal may be happy to have the caption refer to the details in Table 1 as the explanation. Author Reply: As per the reviewer suggestion, alternative option, refer to the details in Table 1 is added in the revised version. 5. Reviewer comment: Under Methodology, we need to read how all of those anatomical points for the measurements were determined. Author Reply: These anatomical points were approximately considered, which may not be the perfect morphometric assessment. This can be considered as another limitation of this manuscript and is added as a limitation in the revised version. . 6. Reviewer comment: The authors state that \"The data can be considered as the database from our population.\" but I am unable to establish what this population is. Towards the end of their Discussion they state \"The literature search did not reveal much studies about the morphometry of the popliteus and particularly, the dataset is not available from the Indian population.\" but the details of the population need to be given under Materials. Author Reply: As per the reviewer opinion, the details of the population is now given under the materials and methods. 7. Reviewer comment: The authors state that they did not explore \"gender\" differences but we do not know the gender identity of the bodies in the dissection hall - only their sex. the authors should state that sex differences were not explored. Author Reply: As per the opinion, it is now mentioned that the sex differences were not explored. 8. Reviewer comment: Regarding comparing left and right sides, we need to see the actual p values when deciding whether there was or was not statistical significance. Why was sidedness compared for some data and not for others? Author Reply: The study measured 17 parameters and all were compared over the right and left sides. They are given in tables 6, 7 and 8. Individual ‘p’ values are given in the raw data. 9. Reviewer comment: Regarding comparing left and right sides, we need to see the actual p values when deciding whether there was or was not statistical significance. Why was sidedness compared for some data and not for others? Author Reply: The study measured 17 parameters and all were compared over the right and left sides. They are given in tables 6, 7 and 8. Individual ‘p’ values are given in the raw data. 10. Reviewer comment: Did the authors consider making corrections for human variation, in other words a correction factor for overall height of the body? Or was the idea rather to report the averages of the data points used? If so, maybe the range (maximum / minimum) should be given and then the average for each one? Author Reply: The correction factor for overall height of the body is not given, which is a limitation of this study. Since we applied the paired ‘t’ test, the mean and standard deviation were considered instead of range and average. 11. Reviewer comment: For the figures illustrating the dissections, the captions need to indicate what view this is (posterior) and whether it is a left or right leg, and then provide an indication of superior / inferior / lateral / medial. Author Reply: As per the reviewer opinion, figures and figure legends were revised. The details of the view, side and the position were added. 12. Reviewer comment: For the figures illustrating the dissections, the captions need to indicate what view this is (posterior) and whether it is a left or right leg, and then provide an indication of superior / inferior / lateral / medial. Author Reply: As per the reviewer opinion, figures and figure legends were revised. The details of the view, side and the position were added. 13. Reviewer comment: One of the limitations is given as formalin altering the morphology of the structures - but in what way are they altered? Author Reply: We did not get the explanation for our writing. So, this limitation is removed in this revised version. We accept the reviewer opinion. 14. Reviewer comment: This article needs to be proofread for grammar – Author Reply: In this revised version, the manuscript was revised with respect to the written English. We utilized the online software www.gramarly.com. B.V. Murlimanju, MD Corresponding Author"
}
]
}
] | 1
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https://f1000research.com/articles/12-1329
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https://f1000research.com/articles/13-579/v1
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05 Jun 24
|
{
"type": "Opinion Article",
"title": "From ‘village tanks’ to ‘evaporating pans’: Colonial and Post-colonial responses to ancient village tanks in Sri Lanka",
"authors": [
"Chandana Jayawardana",
"H D Dilini Sadeepa",
"H D Dilini Sadeepa"
],
"abstract": "Village tanks, prevalent since ancient times, were an integrated part of the irrigation system in Sri Lanka (‘Ceylon’ till 1972). It was under these village tanks that paddy cultivation took place, and they were a part of the socially, technologically, and ecologically cohesive way of village life. The colonial authorities, who tried to renovate that ancient system, perceived village tanks as technically inefficient due to excessive evaporation and uneconomical land use. However, for several reasons, that perception could not be materialized during their renovation works. During the post-colonial period, with the implementation of the land colonization schemes in the 1930’s and the multipurpose river valley development schemes in the 1960’s, the scenario took a different shape. The technically perceived inferiority of the village tanks was brought into the new water management policies and the engineering designs. As a result, many of the village tanks were demolished, and those lands were converted to the farmlands. Instead of water availabilities assured through village tanks, canal irrigation became prominent. The socio-technical bondage between the village tanks and the village communities was not considered, presenting a classic case study for the consequences of neglecting social component of the technology. This paper discusses the social, political, and technical implications of these moves and their influence on shaping the present irrigation setup in the island.",
"keywords": [
"Ancient irrigation",
"Village tanks",
"Cascade systems",
"Colonial influences",
"Asian studies",
"Knowledge hegemony",
"Irrigation bureaucracy",
"Post-colonial politics"
],
"content": "Introduction\n\nWater harvesting strategies have been fundamental to the emergence and existence of human cultures and civilizations. The importance of technology and the social coordination necessary to establish those strategies is such that major schemes like ‘hydraulic civilization’ have been suggested in studying the social formations in historical perspective (Wittfogel, 1956, 1957). Those ancient irrigation systems have been subjected to many alterations in recent times, especially under the colonial occupations in the regions that accommodated them. The theoretical base used in such alterations differed from that of the original constructions, and concepts like ‘hydraulic bureaucracy’, ‘hydraulic solidarity’, ‘hydro-resilience’ and ‘colonial hydrology’ have been forwarded to discuss such discourses (Lansing, 1991; D’Souza, 2006; Beattie & Morgan, 2017). Various factors would have contributed to the differences between the ‘originals’ and ‘altered outputs’, among which the following played key roles. First, the authorities who were responsible for those alterations were not aware of the indigenous knowledge systems on which the ancient irrigation strategies emerged. Second, the concept of ‘modernization’ and taking Euro-centric knowledge as ‘universal’ for achieving that modernization, distanced the non-European irrigation strategies from their original footing.\n\nIn drawing on that broader context, this article examines the colonial (especially the British occupation from 1798 to 1948) and post-colonial (since 1948) influences on village tanks, a specific water storage typology, in Sri Lanka.1 Here, I argue that it is not the British occupation, but the Euro-centric knowledge that primarily contributed to the demolition of village tanks.2 To situate my findings within a techno-socio-political framework, I first examine the technical scheme represented by technocrats and engineers, and then the political scheme represented by colonial and post-colonial political elites.\n\n\nEarly colonial engagements\n\nThe power struggle of the west in the sixteenth century posed serious diplomatic and political challenges to the East. Sri Lanka was one of the countries affected by the consequences of three Western nations: the Portuguese (1594-1658), the Dutch (1640-1796), and the British (1798-1948) (de Silva, 2016). All of them occupied parts of the Island and, lastly, the British occupied the whole Island from 1815 to 1948. Since the Dutch occupation, the island’s ancient irrigation works have been a point of interest. However, it was the British influence that was most felt in irrigation related matters in the long run, and the term ‘colonial’ in this paper primarily refers to the occurrences during their tenure.\n\nToday, it is often said that some ancient irrigation works were restored during the colonial period. This is in the sense of the comment made by Henry G. Ward, Governor of the Island (1855-1860),\n\nI need not point out to you the immense advantages of these previous works. It is the restoration of an old system, not the commencement of a new [that is required] (Brohier, 1979c).\n\nLater, H.T.S. Ward, the first Director of the Irrigation Department (1900-1908), noted,\n\nAll the restoration work of ancient works, and although they will when restored irrigate immense tract of country, their restoration is but a step in the direction of the complete scheme that was worked out by the ancient engineers in their centuries of experience and industry (Kamaladasa, 2007).\n\nDespite the intention of returning to the previous system, the colonial authorities made their own decisions based on the system components they observed. This was basically because there were no information sources to ascertain what the original system would have been. As Kamaladasa correctly points:\n\nWhen the colonial rulers started exploring this complicated and comprehensive process of resuscitating the irrigation infrastructure in the mid-nineteenth century, there were neither written documents for them to refer to nor locally accepted or developed directions or guidance for them to follow. Except for the scattered physical evidence in the field, there was no record available, at least giving the basic location data, let alone the complicated engineering information (Kamaladasa, 2007).\n\nThis left the colonial authorities with many options in interpreting the ‘scattered physical evidence’, especially their original function and their contribution to the overall system. Naturally, and probably unknowingly, they went for the easiest option they could have. That is, they interpreted the evidence based on the knowledge and training they have received in the field of irrigation and water utilization technologies. One such interpretation was the sluice operation of large tanks, which resulted in converting ‘uncontrolled community water flows’ to ‘controlled and state-owned water flows’ by installing sluice gates (Jayawardana, 2013). Another example is survey measures of some parts of the ancient Yoda äla as six inches per mile, which resulted in taking ‘an ancient inter-basin elongated tank’ as an equivalent of the ‘modern water conveyance channel’ (Brohier, 1979b; Panapitiya, 2010). Adding to the list, resurrecting the ancient sluice sites of Kala wäwa and Maduruoya at locations complying with modern hydraulic engineering calculations was taken as an example of the superiority of then knowledge (Mendis, 2002; Jayawardana and Pieris, 2010). This is because of making colonial knowledge the yardstick for assessing ancient non-European knowledges.\n\nColonial misinterpretations and misrepresentations of the local irrigation history are not limited to the physical structures but transcend to the ideological sphere as well. The oft quoted visionary statement made by King Parakramabahu I (1153-1186 CE), as appears in the Cūḷavaṃsa, “[appakampīdise]-dese — salilaṃvuṭṭhisambavaṃ — vinālokopakarena — jātumāgañchi-sāgaraṃ” has been translated into German and then to English by W. Geiger (Cūḷavaṃsa 68:11, 1996).3 There, the Pali term ‘lokopakarena’ has been translated as ‘benefitting man’, which is an obvious misrepresentation of the relevant Pali term ‘lokopakarena’. The term ‘lokopakarena’ means ‘benefiting the world’, including living creatures, plants, and the entire ecological system. Limiting such a broader spectrum to a single term ‘man’ would have been the result of the anthropocentric worldview, illustrating the dichotomy between the European and non-European ways of human – nature interaction. Several scholars writing on the irrigation history of Sri Lanka, such as Brohier (1979a), Nicholas (1954), Weeramantry (2000) and Mendis (2002), used Geiger’s translation unchallenged, assimilating the colonial misrepresentations into the modern literature on the subject.4 Both the physical engagements and the ideological backgrounds necessitate revisiting the colonial encounters in local irrigation to understand how waterscapes were reshaped during colonial times.\n\n\nIdentifying ‘village tanks’ as a typology5\n\nIn modern irrigation, several parameters are used to categorize water storage utilities, and the criterion may depend on the purpose of the categorization. In the Sri Lankan context, the rainfall model, the water balance method, the hydrological endowment, and the physical state of the storage are some of the parameters used in such categorization (Witharana, 2004). This is in addition to criteria like the location of the storage, purpose of the storage, demographic features of the settlement, the command area, and water spread area, which are more or less general for the evaluation of any storage. However, no such technically based methodologies were used during the British period, and instead, more pragmatic factors such as water retention capacity, command area, and time consumed for repair work were used to categorize the tanks.\n\nMorgan classified irrigation works under three headings, based on the demographic features of the settlements; (1) tanks and water courses of magnitude in a ruinous condition remote from the population, (2) district irrigation works situated in or contiguous to population neighbourhoods, and (3) small village tanks, drains, and watercourses (Sessional Paper, 1867). Ievers (1899) noted that a better classification would be; (1) storage tanks, (2) village tanks, (3) dams or anicuts across streams, and (4) canals, usually called yoda-elas’.6\n\nDickson and Woodward anticipating the respective time periods needed for the restoration, divided the tanks into two broad categories; (1) the tanks which were too large to be restored by the shareholders themselves, even within a period of seven years, and (2) the tanks which could be restored by the shareholders within seven years provided the Government supplied the required masonry sluices and spills (Administration Report, 1873).\n\nLewis (1895), differentiating the water works based on the command area, noted, “In addition to the large irrigation reservoirs, there are hundreds of small tanks all over the country; some with villages attached to them, others under which cultivation is regularly carried on by people of the neighbouring villages, but without adjacent villages (called tāvadi tanks), and others wholly abandoned.”\n\nMurty, categorizing the tanks according to their contributory potential in restoration works, noted:\n\nThe steady restoration of abandoned village tanks is the best means of bringing back the ancient prosperity of the Wanni. …. There are some large tanks, however, which it is beyond the ability of the people themselves to restore unaided. Where such tanks are close to a considerable centre of population, I think it is the duty of the Government to restore them (Administrative Report, 1900).\n\nAccording to Kennedy (1934), “[The total area under paddy in Ceylon] may be divided into four main categories according to the system of irrigation in vogue in each: - major works, village tanks, village elas and direct rainfall.”7\n\nGoing through the above, it is evident that ‘village tank’ is a well identified tank typology as noted by the British.8 These are comparatively small in storage capacity as well as in command areas and cater only to the villages attached to them. Lewis notes that the villagers depended on the tank to irrigate their paddy fields, and no life was possible without a tank in the dry zone of the Island. The village and the tank are so bonded together and inseparable, that many of the villages were named after the tank attached to them (Lewis, 1896).\n\n\nCascade form of village tank distribution\n\nFurther to identifying ‘village tanks’ as a distinctive typology, British records note their multiplicity and also the standard character of their occurrence, in a chain form. Robert Knox (1673-1679), observed the frequent occurrence of village tanks and their contribution to food security, and noted:\n\nEvery town has one of these ponds [tanks], which if they can but get filled with water, they count their corn as good as in the barn. It was no small work to the ancient inhabitants to make all these banks, of which there is a great number, being some two, some three fathoms in height, and in length some above a mile, some less, not all of a size. They are now grown over with great trees, and so seem [like] natural hills (Knox, 2006).\n\nIevers (1899) also highlighted the contribution of land topology to the large number of small tanks. According to Ievers, “As the North Central Province, although apparently flat, is in reality undulating, the ancient tank builders took advantage of this conformation to make chains of tanks in the valleys.” Observing this character during his extensive travels in the southern part of the Island, Woolf made some diary entries, saying,\n\n…. Held meeting of proprietors of lands and then rode and walked right up these fields and chain of tanks as far as Ranesinge wewa” and again, “Water can get into this channel only when the water is a foot below spill level. The channel feeds a chain of village tanks, the water finding its way from one tank to another until it reaches Netolpitiya which is the southernmost and the last (Woolf, 1962).\n\nLater, Brohier (1979b) also subscribed to this identification, when noting the water distribution pattern adopted in Jaya Gaṅga scheme, “In each of the subsidiary valleys on its course the water is diverted by channels into little village tanks, or chains of tanks – the tanks lower down receiving the overflow from the tanks placed higher in each chain” (Brohier, 1979b)9. The physical occurrence of these ‘chains of tanks’ is illustrated by Modder, “The tank which bears the same name as the village [Vendakaduwa] is fed by the surplus water from the Madawakkulama tank, which draws the supply from Ihalagama tank, when in its turn is fed by the Ratambala-oya” (Modder, 1993).\n\nBoth these cascades are situated at Anuradhapura District, North Central Province (This figure has been reproduced from Panabokke et al., 2002 – Copyright owner IWMI).\n\n\nColonial reflections on the viability of village tanks\n\nAt this point, it is necessary to investigate the status of small tanks as perceived by British authorities, because such perceptions would have influenced policy decisions, technical designs, and subsequent restoration work implementation. One important observation in this direction is that the cultivation, mainly paddy, was provided from these village tanks and not from the large tanks occupying the major river water sheds. According to Nagel (1887-88), one of the functions fulfilled by the large tanks was, “when the small tanks are filled with rain and again become empty, either by the irrigation of the fields or by drying up-to afford the agriculture, the needful supply of water from this large tank by replenishing the small tanks near their fields and to save expenses” (Nagel, 1887-88). Later, Liesching noted,\n\nIt is not in the vicinity of these large tanks however, that, as a rule, any cultivation is carried on, but near the smaller and more manageable ones (Administrative Report, 1869).\n\nThis bondage between the village tank and the village community forced Government intervention to maintain those tanks in proper order. Several ordinances, such as the Irrigation Ordinance (No. 9 of 1856; No. 21 of 1861), the Paddy Cultivation Ordinance (No. 21 of 1867; No. 2 of 1873) and the Village Committees Ordinance (No. 26 of 1871) have either been introduced or amended to ensure the repair and maintenance of the village tanks (Karunananda, 2006; Kamaladasa, 2007).\n\nIn parallel with the above regulatory provisions, an officialdom that was exclusively dedicated to the maintenance of the village tanks, had also been formed. Karunananda summarizes this initiative, which was launched primarily to avoid delays and expenditure on the village tanks maintenance works (Karunananda, 2006). In this new setup, all proposals for the repair and restoration of village tanks were to be settled by the Government Agent and the Irrigation Assistant. The Director of Public Works, the technical authority on the subject, was to be consulted only in cases of any doubt or difficulty, or any permission needed. Under the command of the Irrigation Assistant, the posts of Superintendent of Village Tanks and Provincial Irrigation Assistant were established (Sri Lanka National Achieves, 6/3728 no. 51; 5/61 no. 34; 4/124 no. 122; 5/61 nos. 8 & 20). The office of Provincial Irrigation Assistant was subsequently changed to the Provincial Irrigation Engineer in 1886 (Sri Lanka National Achieves, 6/5046 no. 76; 41/3 no. 59). For districts such as Anuradhapura, the above cadre was not adequate to handle the increasing volume of repair and maintenance work, so the additional Irrigation Officers were recruited. They were formed into a separate branch within the Public Works Department, directly reporting to the Irrigation Assistant (Administrative Report, 1876). Under his command, Assistant Superintendents of Village Tanks, who were in charge of the earthwork, functioned. The Tank Overseers, who were commonly called kaṭṭikankānis, were subordinate to them (Sri Lanka National Achieves, 6/6909 no. 334).\n\nAs per the above discussion, it is obvious that a well-established official hierarchy, exclusively dedicated to the village tanks, was in place by the late 1800’s. Along with such institutional establishments, executable work schedules were also in practice. For instance, Governor Henry G. Ward (1855-1860) adopted a practice of villagers shifting the earth and the government providing the sluice and masonry without charge (de Silva, 2016). Governors such as William H. Gregory (1872-1877) also implemented the same policy to some extent and noted the progress, ‘work is now going on vigorously upon hundreds of tanks in the North-central province where the experiment began at the suggestion of Mr. Dickson [the first Government Agent of the North-central province] and now applications for similar assistance are coming in from the Western, North-western and Northern provinces’ (Sessional Paper, 1878).10 With the establishment of the new North-central province in 1873, the village tank repair works intensified, and the government revisited the financial and labour aspects. For the works within this province, Government Agent was entrusted to decide the most feasible option based on the paying abilities of the villages. Such options varied between either the entire cost of repair was passed to the villages, or half of the cost was passed to the villagers or providing the sluice free of charge by the government and villages to complete the earthwork (Sri Lanka National Achieves, 20/308 no. 185; Roberts, 1971; Bandarage, 2005; de Silva, 2016).11\n\nDespite all the above regulatory measures, exclusive officialdom, and executable schemes, the suitability of village tanks to fulfil their intended purpose, technically, was a matter of concern. Its roots transcend the British, going back to the Dutch period. Nagel notes to that effect, “These small tanks might be made smaller, and if it be possible to conduct the water from the large tanks into the fields by means of excavations, then these small tanks, though very good, will yet be unnecessary” (Nagel, 1887-88). When time passed by and the British authorities were regulating the irrigation policies for the Island, this idea of the un-productivity of the village tanks gathered further momentum. Presenting a paper about village tanks, Kennedy (1934), then the Deputy Director of Irrigation, said:\n\nThe suggestion to deliberately destroy a working tank may sound like rank heresy, but, as a matter of fact, the village tanks of Ceylon like the village cattle, are far too numerous for efficiency. Not only the evaporation losses enormously multiplied and maintenance costs increased, but potential paddy land is usurped to form the beds of the superfluous tanks. There are many cases where the total yield of the catchment could be efficiently and economically stored in one improved tank instead of in half a dozen or more, and used with scientifically guaranteed certainty of sufficiency for the irrigation of all the present fields and of all the beds of the superfluous tanks as well, if tradition would allow them to be turned into paddy fields (Kennedy, 1934).\n\nKennedy’s above-mentioned paper was to have a significant impact on the subsequent development of irrigation works. According to Mendis (1988), this paper was used as a Handbook in the Irrigation Department for the next 25 years. Another technical development that supplemented this move was the advances in the related technologies such as bund construction. Kennedy’s above statement should represent a combination of both the criticism of the village tanks as well as the appreciation of the potentials offered by the new technological developments to go for large reservoirs. Commenting on this trend by the mid-1930s, Brohier (1975) recorded:\n\nThe deep-water reservoir, achieved as a result of the advance in science of building gigantic earth or concrete bunds, which harnessed and helped to store millions of cubic feet of water at a depth of over a hundred feet at the dam site, naturally came to be considered much more beneficial. Giving credit where credit is due, it was J.S. Kennedy, a one-time Director of Irrigation, who first mooted the idea [of deep-water reservoirs] for Ceylon.\n\nCriticism of village tanks was aggravated by another factor, the mimicking of the same pattern in the fields fed by those tanks. This character was highlighted by Knox (1673-1679), “They [cultivators] all observe one time of reaping to prevent their corn being trampled or eaten up by the cattle. Thus they time their corn to their harvest; some sowing sooner, some later, but all reaping together, unless they be fields that are enclosed by themselves; and peculiar to one man” (Knox, 2006). Ievers (1899), observing ‘unproductive’ water utilization due to the scattered arrangement of fields, notes, “A great deal of wastage is unavoidable owing to the scattered position of the fields, and the impossibility of making all the cultivators begin work at the same time. These evils will only be remedied by the growth of the population and the extension of cultivated areas, which will force the people into economy of water” (Ievers, 1899).\n\nTo summarize, British authorities did not consider the patterns of occurring village tanks and village paddy fields in a technically favourable manner. The suggested strategy for higher efficiency was to concentrate on the large reservoirs and include the lands occupied by the village tanks in the command areas of those reservoirs. This criterion occupied colonial minds since the late 19th century. As Parker noted, “Two reasons are given for urging the abolishment of the village tanks: (1) a desire to void the present excessive waste of water in them by evaporation, (2) a wish to render possible the cultivation of the area of rich soil now forming their beds” (Sessional Paper, 1881).\n\n\nFrom perceptions to realities\n\nDespite highlighting the advantages of large tanks and the importance of converting village tanks into their command areas, such implementation was not feasible for several reasons. Firstly, the cost associated with such an initiative was prohibitively massive. After working out a detailed cost-benefit analysis of implementing this strategy for the village tanks fed by the Giant’s Tank (in Mannar district), Parker concludes that the eradication of the village tanks is not a financially feasible option, and noted;\n\nIf the larger project now recommended be adopted, the local rainfall caught in the tanks will probably not be needed, and so far as that is concerned the tanks might perhaps be dispensed with. But the 450 million of cubic feet of water which they impound must be stored somewhere, and the only other places for it are the two storage reservoirs. An additional expense must therefore be incurred for the purpose, and I quite fail to discover that the slightest benefit would be derived from the work. Undoubtedly no waste of water will be obviated, no additional cultivation will be provided for, not a rupee of additional revenue will accrue to Government. An excessive evaporation and absorption (in the tanks) will be prevented, and that is all; but the water which would have been drawn from the river, or the rainfall which would have been caught, to make good the loss, will simply be allowed to flow into the sea (Sessional Paper, 1881).\n\nAnother reason that prevented the demolition of village tanks was the claims made by the provincial administrative officers, who were more exposed to the ground level realities than their technical and policy making counterparts. Examining the attitudinal dichotomies among colonial officers, Warnapala (1974) identifies two major schemes between those who occupied the administrative centre (Colombo) and those who occupied the periphery (the Districts). The former believed that district officials were only concerned with local issues and not with the high-level colonial administration. The latter were more informed of the needs of the people and the environment in which they operated and wanted to address those needs through policy formation. There were constant clashes in attitudes between the two troupes, which frequently affected policymaking at the district level. This is well evident in the policy towards allowing villagers to continue chena cultivation.12 Despite the repeated attempts by the central government to abolish chena practice, some provincial officials acknowledge its importance for the subsistence of the peasantry. They pointed out that peasants turned to chena cultivation not out of indolence, but out of despair, particularly over the neglect of irrigation facilities necessary for paddy cultivation (Bandarage, 2005). Many provincial administrators emphasized the importance of village tanks and their proper maintenance, thus ensuring the peasantry’s access to irrigation water as much as possible. For example, Murty noted, “The steady restoration of abandoned village tanks is the best means of bringing back the ancient prosperity of the Wanni” (Administrative Report, 1900). Leonard Woolf, Assistant Government Agent and well known for his book Village in the Jungle, noted, “There are village tanks in these villages, and I am compelling the people to restore them, and the people are restoring them” (Woolf, 1962).\n\nThe inherent dislike of villagers for shifting to the new territories, leaving their traditional settlements, also contributed to the decision not to demolish the village tanks. Due to the lack of mobilization, the traditional villages had to sustain, so did the village tanks. As a result, Kennedy himself recommended that proper maintenance of village tanks, despite the fact that their command areas could not be expanded further, was an urgent and significant necessity (Brohier, 1975).\n\nThe Irrigation Department, the prime organization responsible for the irrigation development on the Island was declared a non-revenue organization in 1920, based on the recommendations made by the Food Supply Committee (de Silva, 2016). This could be considered a radical change as it allowed irrigation authorities to evaluate their projects without much weight on the financial returns to justify implementation. Further supplementing this move, all irrigation rates were waived off in 1926 with the view of encouraging paddy cultivation (Kamaladasa, 2007). The village tanks, on which the village level paddy cultivation depended and did not generate reasonable revenue for continuous maintenance, again proved their claim to existence.\n\nIt is with this background, that the Island’s irrigation works entered a new phase – the implementation of land colonization schemes. The Government has launched several land colonization projects in sparsely populated dry zone with the goal of increasing food supply and addressing the ever-increasing population density in wet zone regions. Starting from the Minneriya scheme (1933), major schemes like Minipe, Kagama, Elahera, Parakramasamudraya, Gal oya, and Udawalawe were implemented (Farmer, 1957, 1984; Amerasinghe, 1976; Peebles, 1990).13 These colonization schemes focused on the large ancient tanks, restored and feeding either village tanks or newly cleared forest areas, that had been converted to paddy fields and residential plots. These newly developed areas were designed in such a way that they were directly fed from the large tanks through canal irrigation. For example, the Gal Oya project (1949) implemented in this manner marked 124,140 acres fully allocated, 51,640 acres under village tanks serving the villages, and 72,500 acres under feeder canals serving the colonies (Brohier, 1975). This illustrates the fact that while acknowledging the relevance of village tanks for the sustenance of villages, the new developments were adopting the downstream development model based on canal irrigation. This was an obvious deviation from the ancient practice of feeding the settlements from a tank exclusively dedicated to them. Instead, the village level sustenance depends on a centrally controlled large tank, for which the maintenance and operation was well beyond the capabilities of the user community.\n\n\nPost-colonial designs — New waterscapes\n\nCeylon gained independence within the Commonwealth in February 1948. As discussed above, the general perception towards the village tanks by that time was that they were technically inefficient but could not be demolished due to the social, economical, and financial reasons. This dichotomy took a different shape during the early post-independence era. The budding thoughts of the newly formed independent state offered new hopes and challenges to the entire society. The irrigation sector, which took the challenge of marching towards self-sufficiency in food, derived new plans and policies towards that end (as naturally it should be). These initiatives were well supported by the modern developments in concrete technology, soil mechanics, and research on hydraulics, a worldwide trend after World War II. Sri Lankan achievements in the sphere of hydraulics and soil mechanics in the 1940’s were said to be the first of their kind in South East Asia, with new initiatives such as laboratories for hydraulic research (1936), soil mechanics (1943), material testing (1946) and divisions for river gauging (1942), hydrology measurements (1943) and forming models for new irrigation projects (1943) (Kamaladasa, 2007). All these factors would have contributed to the strategy adopted in new irrigation projects, which is well illustrated in a statement made by D.W.R. Kahavita;\n\nThere does not exist any doubt as to the need to achieve self-sufficiency in food. This is an achievement that cannot be realized by spending large sums of money on tiny village tanks which do not have the staying power in a drought, nor can a better standard of living be taken to a people depending on them. Vagaries of the monsoons and resulting destitution can be only fought by spending public funds on large schemes and not by creating little evaporating pans and relief works. The age of the village pond has passed away and the time has come to embark on large projects (Kahavita, 1950).\n\nKahavita, being the head of the design division of the Irrigation Department, should have represented not only his personal ideas but the vision and mission of the entire Department, as well as the technological insight of that time. Such insight would have been influenced by the global trends in hydraulic engineering at that time. The 1960s are regarded as the watershed decade of modernism, as well as the decade of major Third World dam and river regulation projects (Cosgrove, 1990). It was the decade of Kariba and Aswan, and of similar mega-structural projects in Mexico, Colombia, Ghana, Mozambique, and India, as well as in the wilderness regions of Canada and eastern Siberia. Engineering control of water would, it was argued, be the mechanism for leaping forward into the industrial future for developing countries, the status aimed at by the Sri Lankan irrigation technocrats, also.\n\nThe perceptions conceived during the colonial era regarding village tanks actually came to the reality during the post-colonial period. The new irrigation strategy adopted by the Irrigation Department was to avoid village tanks and promote downstream development through canal irrigation, fed from large reservoirs. Later, this trend transcended even to demolishing the functioning village tanks, if their location is not in line with the modern designs. Commenting on the general design criteria adopted in the Mahaweli Development Project (1970’s), the largest in the Island14, Panapitiya noted that:\n\nWhile we were developing lands under Yoda Ela in the 1970s, we also had to demolish most of the tanks in the area to suit our design criteria. Some tanks which were of bigger size had to be left mainly due to the pressure exerted from the original settlers of the traditional villagers of the area. In fact, J.R. Jayawardene, President at that time, had been summoned by the public to prevent the tank demolition activity launched by the Mahaweli Authority (Panapitiya, 2010).\n\n(This figure has been reproduced from Pfaffenberger, 1990).\n\nDiscussing the social dimension of Irrigation in general, Pfaffenberger points out that engineers’ involvement is limited to creating well designed and reliable irrigation structures (Pfaffenberger, 1990). The management of water, as engineers understand it, is a ‘people problem’ that lies beyond their professional responsibilities and competence. Pfaffenberger (1990) brings this scenario to the Sri Lankan post-colonial setup, in three schemes. First, the social design of irrigation was not by engineers but by administrative officers, the majority of whom were still British nationals, and local political elites. Second, engineers’ inattention to the social and cultural dimensions of technology, provided enormous opportunity and power to political elites to infiltrate irrigation-related matters. Third, engineers, for their part, continued to create the system that incorporated the British designs to which they had been trained in during their professional careers.\n\nThe first and second schemes in Pfaffenberger’s assertions could be directly aligned with Panapitiya’s comment, elaborating the involvement of political authorities in irrigation related engineering accomplishments. Pfaffenberger’s third point positions the Sri Lankan case within broader colonial knowledge transfer schemes in the sphere of water utilization. Goubert (1989) notes that the European engineers, whose skills had pushed the arteries of European trade across Asia, Africa, Australia, and America, came to be seen as the architects of a brave new world. Heffernan (1990) elaborates on the attempts to irrigate the northern Sahara, where the simpler technologies employed by indigenous communities in colonial territories were regarded as primitive by the European masters. Challenging the universal adaptation of Euro-centric irrigation techniques in a global context, Pacey (1991) questions the validity of replacing indigenous and ecologically sustainable irrigation practices in Africa, Meso-America, and Asia with the former, challenging the universal adaptation of Euro-centric irrigation techniques in a global context. Lansing (1991) discusses the Dutch engagement in Bali irrigation, and Horst (1998) discusses the inherent characteristics of British, Dutch, and French irrigation schools, both highlighting the misinterpretations and mishandling of non-European irrigation systems by European authorities.\n\nOnce the above comments by Panapitiya, Pfaffenberger, Goubert, Heffernan, Pacey, Lansing, and Horst are placed in an array, where does that lead us with regard topost-colonial irrigation practice in Sri Lanka? Panapitiya (2010) describes the ‘demolition of village tanks by engineering designs’ and the ‘saving village tanks by political elites’. Pfaffenberger describes how “engineers’ limitation to purely technical outcomes’ gave way to “politicians’ power to manage the water’. At face value, it appears that Panapitiya makes an example of Pfaffenberger’s assertion. However, the findings of Goubert and the rest reveal a hegemonic approach based on Euro-centric knowledge of irrigation and agriculture in non-European regions. As such, it is not the hegemony of British rule during colonial times, but the hegemony of British knowledge during post-colonial times that contributed to the demolition of village tanks, thus bringing the colonial equation of ‘village tanks = evaporating pans’ to materialization. Rather than an endeavour by a certain individual or institution, that is a result of evaluating an ancient local system using modern Euro-centric knowledge, thus creating a huge gap between perception and reality.\n\n\nConclusion\n\nAdopting proper water harvesting strategies is critical to preserving cultures and civilizations. The societies that have recently been subjected to colonial occupations have seen significant changes in those strategies, adopted by the colonial authorities. Such changes were based on the knowledge systems and worldviews possessed by the colonial authorities and were executed in the name of ‘modernization’, where the norms and definitions were again Euro-centric. This article tried to investigate the colonial and post-colonial engagements with a salient component of ancient Sri Lankan irrigation, the village tanks, positioning the discussion on this background.\n\nThe Dutch had the most influence in changing Sri Lanka’s ancient irrigation works in the eighteenth century, and the British had the most in the nineteenth and early twentieth centuries. Although those changes were implemented under the guise of ‘restoration of the ancient system’, ignorance of the physical character and the ideological background of the ancient system remove that cover, distancing the altered outputs from the original system. ‘Village tanks’ were one of the components of that ancient system, thus changed. The criterion for categorizing a particular body of water as a ‘village tank’ was based on several factors, but the basic one was that it should be coupled with a village. Village tanks were not occurring as isolated water bodies, but connected as clusters, leading to the identification of ‘chain of tanks’. During the colonial period, village tanks were treated as technically unproductive means of water usage. However, they had to be maintained as they were so bonded with village life and, without village tanks, village life would not be sustained. Several regulatory provisions, well established hierarchical officialdom, and executable schemes were in place to ensure the proper maintenance and functioning of village tanks under the British occupation.\n\nSince independence, this techno-social dichotomy has taken on a different shape. As the forerunners of a nation that earned its independence recently, the irrigation engineers were eager to march towards ‘modernity’ in faster steps. The colonial perception of village tanks as an unproductive water use strategy was fully acknowledged and the new irrigation schemes were designed based on the downstream development models with an emphasis on canal irrigation. Many of the village tanks were bulldozed and converted to the command areas of the canal irrigation schemes, totally neglecting the social bondage between the village tanks and the village communities. This post-colonial response could be attributed to two prime factors. First, the nature of technical education and professional training gained by engineers. Being Euro-centric in character, that education and training did not appreciate the relevance of the village tanks in broader irrigation network. Second, the attitude of the engineers, towards the social context of water harvesting. Leaving the responsibility to the political elites, engineers confined themselves to technical solutions, not accounting for the social component of technology. As such, it was not the colonial occupation that demolished the village tanks, but the Euro-centric knowledge that brought the equation ‘village tanks = evaporation pans’ to reality.\n\nEthical approval and written consent were not required.",
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Farm Power and Employment in Asia: Performance and Prospects. Colombo: 1984; pp. 224–238.\n\nFarmer BH: Pioneer Peasant Cultivation in Ceylon. Oxford: 1957.\n\nGoubert JP: The Conquest of Water: The Advent of Health in the Industrial Age. Polity Press; 1989.\n\nHeffernan MJ: Bringing the desert to bloom: French ambition in the Sahara desert during the late nineteenth century – the strange case of ‘la mer intérieure’.Cosgrove D, Petts G, editors. Water, Engineering and Landscape. Belhaven Press; 1990; pp. 94–114.\n\nHorst L: The Dilemma of Water Division; Conditions and Criteria for Irrigation System Design. International Water Management Institute; 1998.\n\nIevers RW: Manual of the North-Central Province: Ceylon. George J.A. Skeen, Government Printer; 1899.\n\nJayawardana C: A Mistaken Narrative: How the Ancient Biso-koṭuwa was Falsely Designated as a Valve-pit. Journal of Royal Asiatic Society of Sri Lanka. 2013; 58(2): 1–55. new series.\n\nJayawardana C, Pieris K: Peculiarities of Maduru Oya Ancient Sluice Inlet Structure. Sri Lanka: Annual Transactions of the Institution of Engineers; 2010; pp. 67–73.\n\nKahavita DWR: Reconnaissance Report on Heda Oya Project. Irrigation Department; 1950.\n\nKamaladasa B: Irrigation Development in Sri Lanka, Centenary Commemoration Publications 1906-2006. The Institution of Engineers; 2007.\n\nKarunananda UB: Nuwarakalaviya and the North Central Province under British Administration 1833-1900. Research Centre for Social Sciences, University of Kelaniya; 2006.\n\nKennedy JS: Evolution of Scientific Development of Village Irrigation Works. Transaction of the Engineering Association of Ceylon. 1934; pp. 233–234.\n\nKnox R: An Historical relation of Ceylon. Tisara Publishers; 1681/2006.\n\nLansing JS: Priests and programmers: technologies of power in the engineered landscape of Bali. Princeton University Press; 1991.\n\nLewis JP: Place Names in the Vanni. Journal of Royal Asiatic Society (Ceylon Branch). 1896; xiv(47): 203–222.\n\nLewis JP: Manual of the Vanni Districts (Vavuniya and Mullaittivu) of the Northern Province: Ceylon. H.C. Cottle, Acting Government Printer; 1895.\n\nMahāvaṃsa – vol 2: From 303CE to 1815 – Māgadhī text and Sinhaḷa Translation. Wikramagamage C, Thalagala A, trans. Buddhist Cultural Centre; 2015.\n\nMendis DLO: Lessons from Traditional Irrigation and Eco-systems.Sardar Z, editor. The Revenge of Athena: Science, Exploitation and the Third World. Manell Publishing; 1988; pp. 316–322.\n\nMendis DLO: Water Heritage of Sri Lanka. Sri Lanka Pugwash Group; 2002.\n\nModder F: Gazetteer of the Puttalam District of the North-Western Province of Ceylon. Lake House; 1908/1993.\n\nNagel T: Tanks and Irrigation in the Northern Province in the time of Dutch: To His Excellency W. J. Vande Graff in 1790 (George Lee, Trans.). Ceylon Literary Register. 1887-1888; vol II.\n\nNicholas CW: The Irrigation works of king Parakramabahu I. The Ceylon Historical Journal. 1954-1955; iv(1,2,3&4): 52–68.\n\nPacey A: Technology in World Civilization. MIT Press; 1991.\n\nPanabokke CR, Sakthivadivel R, Weerasinghe AD: Evolution, Present Status, and Issues Concerning Small Tank Systems in Sri Lanka. International Water Management Institute; 2002.\n\nPanapitiya M: Inconvenient Truth - behind Engineering Designs of Irrigation Projects Developed during the last Century. Economic Review. 2010; 36(1&2): 16–20.\n\nPeebles P: Colonization and ethnic conflict in the dry zone of Sri Lanka. Journal of Asian Studies. 1990; 49(9/1): 30–55. Publisher Full Text\n\nPfaffenberger B: The Harsh Facts of Hydraulics: Technology and Society in Sri Lanka’s Colonization Schemes. Technology and Culture. 1990; 31(3): 361–397.\n\nRoberts M: Irrigation policy in British Ceylon during the nineteenth century. South Asia. 1971; 2(1): 47–63.\n\nSessional Paper – IV: Report of the Committee appointed by the Legislative Council, on the 7th November 1866, to inquire into, and report upon Irrigation Works and Rice Cultivation in the Island of Ceylon with Appendices.1867.\n\nSessional Paper – XLI: Irrigation in the Northern Province: Report upon the Proposed Restoration of the Giant’s Tank.1881.\n\nSessional Paper – XXIV: Paper Relating to the Grain Tax.1878.\n\nSri Lanka National Achieves: File 20/308 no. 185, Letter from Irvings to Government Agent, Northern Province, dated 30 August 1873.\n\nSri Lanka National Achieves: File 4/124 no. 122, Letter from Carnavon to Gregory, dated 04 August 1874.\n\nSri Lanka National Achieves: File 5/61 nos. 8;20, Letters from Gregory to Carnavon, dated 29 August and 08 September 1874.\n\nSri Lanka National Achieves: File 6/3728 no. 51, Letter from Dickson to Colonial Secretary, dated 28 November 1873.\n\nSri Lanka National Achieves: File 6/5046 no. 76, Letter from Moir to Colonial Secretary, dated 22 April 1875.\n\nSri Lanka National Achieves: File 6/6909 no. 334, Letter from Ievers to Colonial Secretary, dated 28 November 1884.\n\nSri Lanka National Archives. File 41/3 no. 59, Letter from Swan to Government Agent, North Central Province dated 08 May 1875.\n\nSri Lanka National Archives: File 5/61 no. 34, Letter from Birch to Carnavon dated 10 June 1874.\n\nTennakoon MUA: Ellaṅgāva. Godage & Sons; 2005.\n\nTennakoon MUA: Towards sustainable management of chena: Unirrigated highland cultivation in Sri Lanka. Economic Review. 2010; 36(1&2): 10–15.\n\nWarnapala WAW: Civil Service Administration in Ceylon: A Study in Bureaucratic Adaptation. Godage International Publishers; 1974/2010.\n\nWeeramantry CG: Environmental Aspects of Sri Lanka’s Ancient Irrigation System. Sarvodaya Vishva Lekha; 2000.\n\nWitharana PDD: Village Tank Categorization.Aheeyar MMH, editor. Small Tank Settlements in Sri Lanka. Hector Kobbekaduwa Agrarian Research & Training Institute; 2004; pp.16–30.\n\nWittfogel KA: The hydraulic civilizations.Thomas WI Jr., editors. Man’s Role in Changing the Face of the Earth. University of Chicago Press; 1956; pp.152–164.\n\nWittfogel KA: Oriental Despotism: a Comparative Study of Total Power. Yale University Press; 1957.\n\nWoolf L: Diaries in Ceylon 1908-1911: Records of a Colonial Administrator. The Ceylon Historical Journal. 1962; ix(1-4): 1–286.\n\n\nFootnotes\n\n1 Although, major part of this article deals with the British colonial period of the Island’s history, its present name, Sri Lanka, rather than its colonial name, Ceylon, will be used throughout.\n\n2 It should be noted that only the techno-social responses during colonial times are considered here, rather than the vandalism displayed by British troops in suppressing military engagements against local insurgencies.\n\n3 Mahāvaṃsa and Cūḷavaṃsa are the chronicler texts elaborating the history of Sri Lanka, starting since the Buddha’s visit to the island (supposed to be circa. 6th century BCE) till the colonial occupation (early 19th century). They were originally written in Pali language and translated to English and Sinhala at various times by various parties.\n\n4 The Cūḷavaṃsa clause under the discussion could be translated as, “Truly in such a country, not even a little water that comes from the rain must flow into the sea without being made useful to the world”. This translation was based on the Pali version and the Sinhala translation of the relevant verse (Wikramagamage & Thalagala, 2015).\n\n5 The term ‘tank’ here stands as an equivalent to the Sinhala term ‘väwa’. However, the term väwa is embodied with broader social, cultural and ecological context which transcends much beyond the mere storage of water, hence the term ‘tank’ could not be taken as a direct translation of the Sinhala ‘väwa’. These details are not discussed here in detail and the term ‘tank’ is also used in the same context as the ‘väwa’.\n\n6 Yoda elas, literally meaning ‘giant canals’ are the canals conveying water from one river basin to another.\n\n7 The Sinhala term ‘elas’ stands for the ‘canals’.\n\n8 Since very early times, village tanks would have been considered a distinct typology. For example, the Jetavanārāma inscription of King Maḷu-Tisa (229-247 AD) indicates three types of water storage facilities; major tanks (maha vavi), gamika vavi (village tanks), and dana vavi (donor tanks) ( Epigraphia Zeylanica vol. I, pp.252-259). There, gamika vavi is generally identified as the Sinhala nomenclature for ‘village tanks’ as gamika = ‘village’ and vavi = ‘tank’. The other two typologies, maha vavi and gamika vaviare taken as ‘major tanks’ and ‘donor tanks’ respectively.\n\n9 With the introduction of exclusive studies on these village irrigation works in the 1980s, the need for specialized technical jargon became apparent. As a result, this particular pattern of ‘chains of tanks’ was re-named as ‘cascade systems’ by a pioneer of the studies, C.M Madduma Bandara, in the mid-1980s (Tennakoon, 2005).\n\n10 Creation of a new provincial unit under the name of North-central Province, by incorporating Nuvarakalaviya (from the Northern Province), Tamankaduwa (from the Eastern Province) and the Demala Hatpattu (from the North-western Province) in 1873 was of great importance in the initiation of large-scale irrigation works.\n\n11 It should be noted that the Government attempted to recover the costs incurred in repairing village tanks through indirect taxes.\n\n12 Chena cultivation is a slash and burn method of highland farming. Each chena is abandoned after a couple of years so that it may regain its fertility (Tennakoon, 2010).\n\n13 The social implications of these land colonization schemes have been discussed in length. Whether these studies discuss the occurrences in mid-20th century in proper historical perspectives may be a subject open for debate.\n\n14 The Multipurpose Mahaweli Development Program, first initiated in 1970 and later accelerated in 1977, covered nearly 349,920 hectares, including 91,100 hectares of new irrigable lands, electricity generation, infrastructure development, and many other socio-economic aspects of the country."
}
|
[
{
"id": "325851",
"date": "23 Dec 2024",
"name": "Maurits W Ertsen",
"expertise": [
"Reviewer Expertise Colonial water history"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper deals with an interesting topic and as such deserves to be considered for indexing. However, there are a few issues that might need some more attention first. First, I am not certain that the point made in the last paragraph of the Introduction that knowledge primarily contributed to anything. Obviously, knowledge is important, but people act upon that knowledge. Second, the colonial paragraphs are very dense in terms of information, citations and references, whereas the postcolonial text is very general and much less detailed. Perhaps some better balance can be attempted, either in writing style or in evidence used? Third, it may be acceptable that much of the reference material focuses on Sri Lanka, the contextualizing references are quite dated. There is much more written recently on dams, tanks, colonial-postcolonial connections and the like. Fourth, building on the third point, while the text may not need to put emphasis on it, the text does not really show how the Sri Lanka case is special or not in relation to other cases. I do not argue the case should not be shared, far from it, but its meaning could possibly be explored in more detail?\nSome smaller comments - The last paragraph of \"Early colonial\" (page 4) reads like an isolated part. Perhaps it could be removed or needs to be better integrated? - The paragraphs on \"Identifying\" and \"Cascade\" make use of colonial sources, which are then discussed and criticized in \"Colonial reflections\". I do not know the exact answer to this, but how can one use and criticize at the same time?\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-579
|
https://f1000research.com/articles/13-578/v1
|
05 Jun 24
|
{
"type": "Research Article",
"title": "Effectiveness of vestibular rehabilitation therapy and yoga in the management of chronic peripheral vertigo: A randomized controlled trial",
"authors": [
"K. Vaishali",
"Chandra Prasad Kishore",
"Chandra Prasasd Rao Sampath",
"Jeganathan P. S.",
"Chandra Prasad Kishore",
"Chandra Prasasd Rao Sampath",
"Jeganathan P. S."
],
"abstract": "Background The purpose of the study was to compare the effectiveness of yoga as a form of Vestibular Rehabilitation (VR) to standard VR for managing patients with symptoms such as dizziness, disequilibrium and gait instability.\n\nMethods 150 participants based on 18-point difference in the DHI score were randomly assigned to group 1- Yoga, group 2- VR and group 3- control group using block randomization. The intervention was provided for 12 weeks. The participants were assessed for Dizziness Handicap Inventory (DHI) at baseline, 4th, 8th and 12th week.\n\nResults The mean DHI for group 1(41.12±7.13) group 2 (42.96±10.54) group 3 (50.84±10.78), p<0.001 decreased significantly in group 1 and 2 when compared to baseline. There was no statistically significant difference in overall Dizziness Handicap Inventory (DHI) scores between the Yoga and Physiotherapy groups after one month; however, both groups resulted in a significant decrease in scores when compared to the control group. Similarly, by the end of the second and third months, there was no significant distinction between the Yoga and Physiotherapy groups, even though both had a considerable decrease in DHI scores when compared to the control group. Furthermore, an examination of the functional, emotional, and physical components of DHI demonstrated persistent trends of significant improvement in both the Yoga and Physiotherapy groups as compared to the control group over a three-month period.\n\nConclusions In addition to VR, Yoga and medications administered concurrently can provide effective therapeutic effects. Yoga has an advantage over VR since it offers a customized cure for giddiness in addition to symptom relief. Yoga might be a great alternative to the conventional VR because along with enhancing overall body relaxation, it is affordable and is easy to learn.",
"keywords": [
"Chronic Vertigo",
"Dizziness",
"Dizziness Handicap Inventory",
"Physiotherapy",
"Vestibular Rehabilitation",
"Vertigo",
"Yoga"
],
"content": "Introduction\n\nIndividuals suffering from vestibular diseases usually experience dizziness and difficulty with vision, balance, and mobility.1 Unilateral and peripheral vestibular diseases (UPVD) affect only one side of the vestibular system (unilateral) and only the portion of the system located outside the brain (peripheral, which is part of the inner ear).1,2\n\nEven though dizziness is a frequent complaint, clinicians typically have trouble diagnosing and treating it. They invest significantly on diagnostics but receive little in the way of conclusive results.2,3 Vertigo is the delusional feeling of motion that occurs while a person is motionless and can occur within the body or in the surroundings. It is frequently accompanied by a whirling sensation, nausea, emesis, and diaphoresis. Chronic vertigo is characterized as persistent vertigo.4–6 Recurrent episodes of vertigo are a hallmark of chronic vertigo. Recurrent spontaneous vertigo is frequently brought on by benign paroxysmal positional vertigo, Ménière’s syndrome, vertebra-basilar transient ischemic episodes, and migraine headaches. True labyrinthitis (sudden onset vertigo with hearing loss) and vestibular neuronitis (sudden onset vertigo without hearing loss) are monophasic illnesses that result in long-term disability.4 Treatment is symptomatic, with antivertiginous and antiemetic medications used to alleviate symptoms. However, according to numerous investigations of the treatment of vertigo, none of the conventional medications have a proven curative or preventative benefit or are suitable for long-term palliative usage.4\n\nFor the treatment of these conditions, the use of vestibular rehabilitation (VR), which combines various movement-based regimens, is growing. VR includes components such as intentionally inducing symptoms to “desensitize” the vestibular system, synchronizing eye and head movements, improving balance and walking abilities, and acquiring knowledge about the illness in order to cope better or engage in healthier lifestyles.7\n\nStudies, including double-blind placebo-controlled trials, have extensively validated the use of VR in a range of diseases linked with vertigo.8–11 Except in a few rare instances (like BPPV treatment), these interventions are not “powerful” in the sense that their impact is usually small yet essential.12 A well-known and frequently used method of VR in chronic vertigo brought on by central compensation is the Cawthorne Cooksey exercises.13–17 While consistent practice of these exercises delivers beneficial results in the long term, some patients find them tedious, leading to a lack of compliance.15–17 Balance activities like Yoga, Tai Chi, and martial arts are excellent alternatives to these occasionally dull exercises because they incorporate plenty of head movement and visual stimulation.18\n\nYoga is a popular kind of exercise that promotes a healthy lifestyle and relieves a variety of human ailments. It originated in India and has since expanded throughout the world. For thousands of years, people have practiced yoga. It is made up of old presumptions, observations, and concepts about the relationship between the mind and the body that have recently been validated by modern medicine. The health benefits of yoga have been thoroughly researched, including the Yoga Postures (Asanas), Yoga Breathing (Pranayama), and Meditation.6 Yoga includes relaxation, which may be beneficial to individuals who experience anxiety due to imbalance or dizziness. Yoga also has the advantage of being accessible to people of virtually any age. Even though yoga is less expensive than personalized therapy, its efficacy has not been directly compared to that of tailored therapy. The individuals who are most suitable for them are probably those who have “graduated” from individual therapy.19 The purpose of this study was to use Yoga Postures (Asanas) as part of VR by employing central compensation for peripheral vertigo. In addition to enhancing focus, concentration, and a general sense of well-being, some yoga positions may also aid with balance impairment and dizzy spells by offering VR, which may be helpful in the treatment of vertigo. The aim of this research has been to evaluate the effectiveness of yoga as a vestibular rehabilitation activity to traditional Vestibular Rehabilitation (VR).\n\n\nMethods\n\nWe conducted an observer-blinded, randomized controlled trial comparing Yoga, VR, and Pharmacotherapy in the academic department of Otolaryngology-Head & Neck Surgery, Kasturba Medical College, MAHE, Mangalore, Karnataka, between August 2009 and September 2012. The trial was reported in accordance with the guidelines of the Consolidated Standards of Reporting Trials (CONSORT) 201020 and is registered at the Clinical Trials Registry of India as CTRI/2019/03/017995 (Date of Registration: 08/03/2019; https://ctri.nic.in/Clinicaltrials/pmaindet2.php?EncHid=MjUxMTQ=&Enc=&userName=CTRI/2019/03/017995). This clinical trial was registered retrospectively because regulatory institutional policies related to trial registration had changed after the study was completed. In order to meet the new regulations and guarantee that the trial was carried out openly and in compliance with current standards, this retrospective registration was required. The research was carried out in compliance with the Helsinki Declaration and received approval from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee, Mangalore, MAHE (date of approval: 04/08/2009). This study adheres to the CONSORT guidelines.21 The Institutional Ethics Committee (IEC) at our institution did not have a registration number at the time of the ethical registration process. As a result, even though our study was approved, no ethical approval number was issued.\n\nThe inclusion of 150 participants in the study was based on an 18-point difference in the DHI score with a standard deviation of 21.9. Otolaryngologist diagnosed vertigo participants in the age group of 18 to 75 years were considered eligible. It was followed by a detailed examination and investigation procedure which included Electroneurography (ENG) to rule out pathologies other than peripheral vestibular disorders. Subjects with peripheral vestibular disorders were then referred to a vertigo clinic. Those subjects who fulfilled the research criteria were included in the study. The study included patients with BPPV, Labyrinthitis, Vestibular Neuronitis, Meniere’s disease, and local trauma who had chronic peripheral vestibular vertigo for at least a year and had not been recovered by treatments. Patients experiencing vertigo caused by middle ear conditions such as effusions, perilymphatic fistula, Otosclerosis, or Mastoiditis were excluded from the study. Patients with central vertigo, basilar artery insufficiency, or chronic unexplained vertigo were also excluded from participating.\n\nIndividuals suffering from vertigo are randomized 1:1 into three groups using sealed envelopes: yoga, VR, and control. The allocation sequence was produced by a computer in order to ensure fair recruitment throughout the research. The person recruiting the participants was not given the allocation sequence, and the randomization code was kept in sealed opaque envelopes. The allocation sequence was generated by a faculty member from the Department of Physiotherapy who was not involved in the study. After obtaining written informed consent and eligibility screening, 150 participants were randomly assigned into three groups: patients treated with yoga were categorized as Group I (n=50), physiotherapy as Group II (n=50), and those with medication as Group III (n=50) through block randomization (10 blocks of 15 subjects in each block) (Figure 1). Patients in Group I (Yoga) were subjected to a series of 20 asanas by the physiotherapist who was also a certified yoga trainer. Patients in Group II (Physiotherapy) were subjected to a series of established central compensatory exercises by the same physiotherapist. Patients in group III (Control) were treated for giddiness by medication alone by the Otolaryngologist. The outcome measures were assessed by another assessor who was not a part of the study intervention. The statistician who performed the data analysis was blinded to group allocation (Figure 1).\n\nAt baseline, participants were assessed for baseline information and DHI. Demographic data was obtained from the subjects. The blinded observer evaluated baseline evaluation for Dizziness Handicap Inventory (DHI). Reassessments of the outcome measures were conducted by the blinded observer 4 weeks, 8 weeks and 12 weeks. Data obtained during the research was kept absolutely confidential and was housed in a secure research server at MAHE’s Department of Physiotherapy, to which only the project investigators had access. Only de-identified data was evaluated after each participant was assigned an individual trial identification number. On the secure research server, the identifying key was kept in a separate file. The data set was only accessible to the project investigators.\n\nThe Dizziness Handicap Inventory (DHI) was used to assess the key outcome measures at baseline, 4 weeks, 8 weeks, and 12 weeks. DHI is made up of 25 self-perceived handicap components. A total score of 100 is generated, with higher scores indicating a greater level of self-perceived handicap. Individual scores for each of the three subscales (functional, emotional, and physical) are also computed.\n\nThe subjects in Group I were treated with 12 week course of yoga therapy. During the first week, patients attended a series of 30-45 minutes per session. Subsequently the patients were instructed to continue the prescribed yoga techniques once a day for 11 weeks at home independently. Subjects were provided with an audio cassette regarding the instructions for performing the asanas. Further written format of yoga techniques was provided to the subjects. Adherence to exercise was noted through telephone once in 15 days by the investigator. Yoga techniques employed were Svastikasana, Vajrasana, Sputavajrasana, Tadasana, Padahastasana, Trikonāsana, Parsvakonasana, Parshvottanasana, Virabhadrasana, Paschimothanasana, Pooravothanasana, Pavanamuktasana, Makarāsana, Bhujangasana, Navasana, Uttanapadasana, Ujjayi pranayama, Anuloma viloma pranayama, Trataka (concentrated gazing) and Savasana.13,14\n\nThe subjects in Group II were given a 12-week course of vestibular exercise. During the first week, the patient participated in a twenty-minute supervised vestibular training program in the morning and a twenty-minute unsupervised session in the evening. VR included vestibular adaptation by inducing retinal slip, eye-head exercise, remembering target exercise, resetting of VOR gain at various head speeds, ability to use somatosensory and vestibular input for postural control, ability to use vestibular and visual input for postural control, and improvement of dynamic postural control using all sensory input. Following that, the patients were instructed to complete the specified vestibular training regimen twice a day at home for 11 weeks on their own. Subjects were provided with an audio cassette regarding the instructions for performing the exercise. Further written formate of the exercises was provided to the subjects. Adherence to exercise was noted through telephone once in 15 days by the investigator.\n\nAll the subjects in Group III were treated with medicines alone. All patients were treated with Prochlorperazine (Stemetil MD) 5-10 mg three to four times daily starting from the least dose to increasing doses that were necessary to control the symptom.\n\nThe statistical analysis was carried out using Jamovi 2.2.5 software https://www.jamovi.org/. The demographic variables were computed using descriptive statistics. The outcome measure findings were described using the mean and standard deviation (SD). The Shapiro-Wilk test was used to determine the normality of the variable. The Dizziness Handicap Inventory (DHI) was analyzed using Repeated Measures ANOVA across the 3 timepoints for the 3 groups. Post-Hoc Analysis was used to assess multiple comparisons within and across groups. The Bonferroni test was used to examine multiple comparisons within and between groups. Statistical significance was determined when p<.05.\n\n\nResults\n\nFifty subjects were included in Group I (Yoga), fifty subjects in Group II (VRT), and fifty in group III (Control). The results were analyzed for 150 patients of the 85 (56.7%) were females 65 (43.3%) were males. In the yoga group 30 (60%) were females 20 (40%) were males in the VRT group 24 (48%) were females 26 (52%) were males and in the control group, 31 (62%) were females 19 (38%) were males respectively. The majority of the patients with giddiness were in the fourth to six decades of life. While most patients with the diagnosis of BPPV & Meniere’s were in the age group of 41-60 years, those with Labyrinthitis and Vestibular neuritis were in the age group of 21-40 years (Table 1a). Two patients lost to follow-up in each of the three groups. Two patients did not come after the first-month follow-up for unknown reasons. Four patients missed after two months follow up of exercise session (one due to transport difficulty, three had to be shifted their locality for their occupation).\n\nBPPV was the most common cause of peripheral vertigo (48.6%), followed by Meniere’s (35.1%) and Labyrinthitis or vestibular neuritis (13.2%) (Table 1b).22 The mean symptom duration was 15.76±7.67 months (12-72 months) for 150 patients.\n\nThe DHI-Physical at baseline mean±SD values between Yoga group (8.12±6.213), VRT group (6.96±4.802) and the control group (11.76±6.056), as shown in Table 2a, are observed to be different from each other. The DHI-Physical at 4 weeks mean±SD values between Yoga group (3.64±3.718), VRT group (3.6±3.747) and the control group (8.6±4.664), as shown in Table 3a. The DHI-Physical at 8 weeks mean±SD values between Yoga group (0.8±2.356), VRT group (0.42±0.906) and the control group (6.64±4.336), as shown in Table 4a. The DHI-Physical at 12 weeks mean±SD values between Yoga group (0.14±0.495), VRT group (0.1±0.505) and the control group (6±4.101), as shown in Table 5a. There was no statistical significance (mean difference, p value) between Yoga and VRT group (0.405, 1), statistical significance was noted between Yoga and Control group (-5.075, <.001) as well as VRT and Control group (-5.48, <.001). Based on the findings, all three groups were compared with each time point and it was found that there was a statistically significant difference (F=52, p<.001) between the 3 groups. When the groups were compared with each other, statistically significant difference (F=159.33, p<.001) were found throughout the time points. When the three groups were examined at various intervals, statistically insignificant (F=1.66, p=0.13) differences were found (Table 2b and Figure 2a).\n\nThe DHI-Functional at baseline mean±SD values between Yoga group (17.92±4.642), VRT group (16.72±3.326) and the control group (20.4±4.832), as shown in Table 3a, are observed to be different from each other. The DHI-Functional at 4 weeks mean±SD values between Yoga group (9.68±9.68), VRT group (10.08±4.198) and the control group (15.48±3.829), as shown in Table 3a. The DHI-Functional at 8 weeks mean±SD values between Yoga group (1.52±3.247), VRT group (2.16±3.203) and the control group (12.898±3.721), as shown in Table 4a. The DHI-Functional at 12 weeks mean±SD values between Yoga group (0.1±0.416), VRT group (0.72±1.97) and the control group (12.48±4.564), as shown in Table 5a. There was no statistical significance (mean difference, p value) between Yoga and VRT group (-0.115, 1), statistical significance was noted between Yoga and Control group (-7.945, <.001) as well as VRT and Control group (-7.83, <.001). Based on the findings, all three groups were compared with each time point and it was found that there was a statistically significant difference (F=156, p<.001) between the 3 groups. When the groups were compared with each other, statistically significant difference (F=641.3, p<.001) were found throughout the time points. When the three groups were examined at various intervals, statistically significant (F=32.1, p<.001) differences were found (Table 3b and Figure 2b).\n\nThe DHI-Emotional at baseline mean±SD values between Yoga group (17.96±3.928), VRT group (16.4±4.295) and the control group (18.68±4.688), as shown in Table 4a, are observed to be different from each other. The DHI-Emotional at 4 weeks mean±SD values between Yoga group (6.44±3.732), VRT group (6.92±4.375) and the control group (14.6±4.086), as shown in Table 3a. The DHI-Emotional at 8 weeks mean±SD values between Yoga group (0.8±2.65), VRT group (0.96±1.818) and the control group (12.0816±3.415), as shown in Table 4a. The DHI-Emotional at 12 weeks mean±SD values between Yoga group (0.08±0.566), VRT group (0.44±1.527) and the control group (11.6±3.681), as shown in Table 5a. There was no statistical significance (mean difference, p value) between Yoga and VRT group (0.14, 1), statistical significance was noted between Yoga and Control group (-7.86, <.001) as well as VRT and Control group (-8, <.001). Based on the findings, all three groups were compared with each time point and it was found that there was a statistically significant difference (F=189, p<.001) between the 3 groups. When the groups were compared with each other, statistically significant difference (F=674.2, p<.001) were found throughout the time points. When the three groups were examined at various intervals, statistically significant (F=40.1, p<.001) differences were found (Table 4b and Figure 2c).\n\nThe DHI-Total at baseline mean±SD values between Yoga group (44±10.482), VRT group (40.08±6.797) and the control group (50.84±10.782), as shown in Table 5a, are observed to be different from each other. The DHI-Total at 4 weeks mean±SD values between Yoga group (19.76±9.812), VRT group (20.6±10.461) and the control group (38.68±8.977), as shown in Table 3a. The DHI-Total at 8 weeks mean±SD values between Yoga group (3.12±7.774), VRT group (3.54±5.011) and the control group (31.7551±7.965), as shown in Table 4a. The DHI-Total at 12 weeks mean±SD values between Yoga group (0.32±1.096), VRT group (1.26±3.312) and the control group (30.08±9.026), as shown in Table 5a. There was no statistical significance (mean difference, p value) between Yoga and VRT group (0.43, 1), statistical significance was noted between Yoga and Control group (-20.88, <.001) as well as VRT and Control group (-21.31, <.001). Based on the findings, all three groups were compared with each time point and it was found that there was a statistically significant difference (F=245, p<.001) between the 3 groups. When the groups were compared with each other, statistically significant difference (F=743.9, p<.001) were found throughout the time points. When the three groups were examined at various intervals, statistically significant (F=30.9, p<.001) differences were found (Table 5b and Figure 2d).\n\n\nDiscussion\n\nThis study evaluated the effectiveness of yoga as a vestibular rehabilitation strategy to standard Vestibular Rehabilitation (VR) in treating persistent peripheral vertigo. Over time, the utility of vestibular exercises for managing patients with chronic symptoms of positional vertigo and disequilibrium has been established. A customized vestibular rehabilitation treatment (VRT) program was developed to match the unique demands of each individual, while taking into account a greater understanding of the vestibular system’s function and adaptation. VRT requires active patient participation and can be delivered through supervised outpatient workouts or home exercise regimens.9 Vestibular exercises are overseen and progressed by therapists, and suitable outcome measures are used to assess the patient’s progress. A VRT program typically lasts between four and ten weeks.\n\nThere is strong evidence that vestibular rehabilitation is both safe and effective in the treatment of unilateral peripheral vestibular impairment.10 Vestibular rehabilitation therapy (VRT) has shown significant benefit in individuals with a stable unilateral peripheral vestibular loss and partial central compensatory. Symptoms such as skew deviation, nystagmus, vertigo, oscillopsia, disequilibrium, nausea, and vomiting often disappear after an acute vestibular dysfunction, such as vestibular neuritis, as the central nervous system (CNS) achieves acute compensation during the first 24 to 72 hours. The cerebellum influences this compensation, which requires releasing cerebellar inhibition to establish symmetrical tonic firing rates in second-order neurons originating in the vestibular nuclei.7 While some patients recover quickly and spontaneously, individuals who have partial compensation or decompensation of the CNS to the vestibular system after the acute lesion may continue to have motion-induced vertigo, oscillopsia, and disequilibrium.11 Individuals in such instances may benefit from a personalized term of VRT guided by a skilled vestibular therapist.3\n\nHorak and colleagues found that after a 6-week intervention period involving treatment groups (vestibular rehabilitation therapy or VRT, general conditioning exercise, and medication), all three approaches led to a reduction in dizziness symptoms in individuals with chronic unilateral vestibular loss (UVL). However, only VRT demonstrated a significant increase in balance.12 According to Mira E’s review, improving the quality of life for individuals with peripheral vestibular diseases is a main goal of therapeutic therapies.11 Furthermore, Gottshall and colleagues determined that vestibular therapy in individuals with Meniere’s illness resulted in considerable improvements in balance function, as measured by objective and self-reported tests.13\n\nPersistent dizziness is commonly associated with considerable handicap, impairment, and psychological distress, and it frequently causes secondary concerns such as anxiety, hyperventilation, and neck pain as a result of keeping a stiff head position in order to avoid triggering head movements.8 Chronic dizziness requires a multimodal approach, with rehabilitation and simple counseling being required for all patients.14,15 Although exercises produce favorable outcomes when practiced consistently over time, some individuals may find them monotonous, leading to compliance concerns. Engaging in balance exercises such as Yoga, Tai Chi, martial arts, or games involving significant head movement and visual stimulation is another option worth investigating. Both Tai Chi and Yoga contain relaxing elements that might be beneficial, particularly for people with anxiety. Although their effectiveness has not been directly compared, these activities are often more cost-effective than individualized therapy. They are most likely appropriate for people who have finished personalized therapy.2\n\nYoga, which originated in India and is now extensively practiced worldwide, has become a popular type of exercise that provides a holistic approach to a healthy lifestyle as well as treatment from a variety of human ailments. Yoga, which has been practiced for over 5,000 years, incorporates breathing techniques, physical postures, and meditation. While yoga began as a spiritual practice inside Hinduism, a subset of the discipline known as Asana has grown in popularity in the Western world primarily as a physical fitness program. Yoga is frequently isolated from Hinduism or spirituality in Western contexts, serving only as a technique of preserving physical fitness and health. Clinical investigations are increasingly being conducted to determine the extent to which yoga helps psychological and emotional well-being. A PubMed search for “yoga and depression” yields 25 clinical trials concentrating on the association between yoga and emotional and psychological health published during 2007, 2008, and the first quarter of 2009. Moreover, three review articles and three systematic reviews were published over this time period to study the effects of various combinations of yoga, meditation, and yogic breathing on mental health.\n\nYoga incorporates ancient theories and principles concerning the relationship between the mind and body, which modern medicine is now proving through extensive research. Extensive research has been done to investigate the health benefits of many parts of yoga, such as yoga postures (asanas), yoga breathing (pranayama), and meditation. The material on the benefits of Yoga Poses is divided into three categories: physiological, psychological, and scientific comparisons to the benefits of regular exercise.16 Yoga’s physiological benefits include the establishment of stable autonomic nervous system equilibrium, a drop in pulse rate, a reduction in respiratory rate, improved eye-hand coordination, a reduction in reaction time, and good effects on posture and balance. Yoga is connected with increased somatic and kinesthetic awareness, mood enhancement, enhanced subjective well-being, improved concentration, better memory, heightened attention, and an overall rise in well-being. These findings have been objectively examined and compared to the advantages of regular exercise.17,18\n\nThe purpose of this study was to investigate the use of Yoga Postures (Asanas) as a component of vestibular therapy for central compensation in cases with peripheral vertigo. The hypothesis proposed that various Yoga postures could not only aid in vestibular rehabilitation but also reduce dizzy episodes while improving focus, concentration, and overall well-being, hence assisting in vertigo recovery. Another advantage of yoga is that it is appropriate for individuals of all ages. The study aimed to assess the efficacy of yoga vs physiotherapy (VRT), using yoga poses chosen to promote optimal movement of the head, balance, and body for vestibular rehabilitation and central compensation. In an observer-blinded randomized controlled study, the Dizziness Handicap Inventory (DHI) was used. The results showed that, as shown in the tables, yoga was comparable to VRT in all of the evaluated criteria.\n\n\nConclusion\n\nThe advantage of yoga over physiotherapy or VRT is that it provides a wholesome and customized cure for giddiness. That means, apart from providing symptomatic relief of giddiness by vestibular rehabilitation, yoga also brings in additional proven benefits like general body relaxation, increased blood oxygenation, detoxification, and an overall sense of well-being. Being cheap and easy to learn, yoga could be an excellent substitute for the traditional VRT.\n\n\nEthics and consent\n\nThe trial was registered at the Clinical Trials Registry of India as CTRI/2019/03/017995 (Date of Registration: 08/03/2019; https://ctri.nic.in/Clinicaltrials/pmaindet2.php?EncHid=MjUxMTQ=&Enc=&userName=CTRI/2019/03/017995). This clinical trial was registered retrospectively because regulatory institutional policies related to trial registration had changed after the study was completed. In order to meet the new regulations and guarantee that the trial was carried out openly and in compliance with current standards, this retrospective registration was required. The research was carried out in compliance with the Helsinki Declaration and received approval from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee, Mangalore, MAHE (date of approval: 04/08/2009). This study adheres to the CONSORT guidelines.21 The Institutional Ethics Committee (IEC) at our institution did not have a registration number at the time of the ethical registration process. As a result, even though our study was approved, no ethical approval number was issued. The participants provided their written informed consent to participate in the study. We confirm that we obtained written informed consent from all participants involved in our study to publish the study results and that all personal information will be kept confidential.",
"appendix": "Data availability\n\nHarvard Dataverse: Replication Data for: Datasheet. https://doi.org/10.7910/DVN/RUCLSQ. 22\n\nHarvard Dataverse: CONSORT checklist for ‘Effectiveness of vestibular rehabilitation therapy and yoga in the management of chronic peripheral vertigo: A randomized controlled trial’. https://doi.org/10.7910/DVN/QRMGP3. 21\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nThomas WB: Vestibular dysfunction. Vet. Clin. N. Am. Small Anim. Pract. 2000; 30(1): 227–249. Publisher Full Text\n\nAllum JH: Recovery of vestibular ocular reflex function and balance control after a unilateral peripheral vestibular deficit. Front. Neurol. 2012; 3: 83. Publisher Full Text\n\nHillier SL, McDonnell M: Vestibular rehabilitation for unilateral peripheral vestibular dysfunction. Cochrane Database Syst. Rev. 2007; 4. Publisher Full Text\n\nChu YT, Cheng L: Vertigo and dizziness. Acta Neurol. Taiwanica. 2007; 16: 50–60. PubMed Abstract\n\nKaratas M: Central vertigo and dizziness: epidemiology, differential diagnosis, and common causes. Neurologist. 2008; 14(6): 355–364. Publisher Full Text\n\nSloane PD, Coeytaux RR, Beck RS, et al.: Dizziness: state of the science. Ann. Intern. Med. 2001; 134(9, pt 2): 823–832. Publisher Full Text\n\nKonnur MK: Vertigo and vestibular rehabilitation. J. Postgrad. Med. 2000; 46(3): 222–223. PubMed Abstract\n\nJohansson M, Akerlund D, Larsen HC, et al.: Randomized controlled trial of vestibular rehabilitation combined with cognitive-behavioral therapy for dizziness in older people. Otolaryngol. Head Neck Surg. 2001; 125(3): 151–156. PubMed Abstract | Publisher Full Text\n\nPostema RJ, Kingma CM, Wit HP, et al.: Intratympanic gentamicin therapy for control of vertigo in unilateral Meniere’s disease: a prospective, double-blind, randomized, placebo-controlled trial. Acta Otolaryngol. 2008; 128(8): 876–880.\n\nBasta D, Rossi-Izquierdo M, Soto-Varela A, et al.: Efficacy of a vibrotactile neurofeedback training in stance and gait conditions for the treatment of balance deficits: a double-blind, placebo-controlled multicenter study. Otol. Neurotol. 2011; 32(9): 1492–1499. PubMed Abstract | Publisher Full Text\n\nHebert JR, Corboy JR, Manago MM, et al.: Effects of vestibular rehabilitation on multiple sclerosis–related fatigue and upright postural control: a randomized controlled trial. Phys. Ther. 2011; 91(8): 1166–1183. PubMed Abstract | Publisher Full Text\n\nKang CM, Tusa RJ: Vestibular rehabilitation: rationale and indications. Semin. Neurol. 2013; 33(03): 276–285. Thieme Medical Publishers. PubMed Abstract | Publisher Full Text\n\nCawthorne T: The physiological basis for head exercises. J. Chartered Soc. Physiother. 1944; 30: 106–107.\n\nCooksey FS: Rehabilitation in vestibular injuries. Proc. R. Soc. Med. 1946; 39: 273–278. Publisher Full Text\n\nKulcu DG, Yanik B, Boynukalin S, et al.: Efficacy of a home-based exercise program on benign paroxysmal positional vertigo compared with betahistine. J. Otolaryngol. Head Neck Surg. 2008; 37(3): 373–379. PubMed Abstract\n\nCorna S, Nardone A, Prestinari A, et al.: Comparison of Cawthorne-Cooksey exercises and sinusoidal support surface translations to improve balance in patients with unilateral vestibular deficit. Arch. Phys. Med. Rehabil. 2003; 84(8): 1173–1184. Publisher Full Text\n\nDal BT, Bumin G, Aksoy S, et al.: Comparison of Activity-Based Home Program and Cawthorne-Cooksey Exercises in Patients With Chronic Unilateral Peripheral Vestibular Disorders. Arch. Phy. Med. Rehabil. 2021; 102(7): 1300–1307. Publisher Full Text\n\nPrado ET, Raso V, Scharlach RC, et al.: Hatha yoga on body balance. Int. J. Yoga. 2014; 7(2): 133–137. PubMed Abstract | Publisher Full Text\n\nJacobson GP, Newman CW: The development of the dizziness handicap inventory. Arch. Otolaryngol. Head Neck Surg. 1990 Apr 1; 116(4): 424–427. Publisher Full Text\n\nSchulz KF, Altman DG, Moher D: CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials. J. Pharmacol. Pharmacother. 2010; 1(2): 100–107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVaishali K: CONSORT checklist for “Replication Data for: Reporting guidelines”. Harvard Dataverse. 2024; V1. Publisher Full Text\n\nVaishali K: Replication Data for: Datasheet. [Dataset]. Harvard Dataverse. 2024. Publisher Full Text"
}
|
[
{
"id": "298663",
"date": "22 Jul 2024",
"name": "Snehal Subrat Samal",
"expertise": [
"Reviewer Expertise Neurology and Neuro-rehabilitation"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is impeccably crafted and exhibits a high level of written proficiency. The elucidation provided for each of the three distinct groups is thorough and comprehensive, demonstrating a commendable attention to detail and accuracy in explication. One notable aspect deserving of further scrutiny pertains to the temporal parameters governing the administration of treatments across the groups. It is evident that the duration of treatment varies among the groups, posing a potential factor that may influence the outcomes observed. In addition, an intriguing proposition emerges from the author's perspective, suggesting the incorporation of audio cassette supplements alongside the medication regimen within the third group. This proposal warrants careful consideration and warrants a more in-depth exploration to assess its potential impact on treatment efficacy. Furthermore, the proposal to utilize the balance scale as an alternative outcome measure is a commendable suggestion, especially in light of the limitations associated with the exclusive reliance on the Dizziness Handicap Inventory (DHI) as a measure of Activities of Daily Living (ADL). The author's rationale for this recommendation is cogently articulated, underscoring the importance of incorporating a diverse array of metrics to capture the multifaceted nature of treatment outcomes. Lastly, the statistical analyses presented in the article are characterized by a high degree of clarity and precision, facilitating a comprehensive understanding of the data and findings. All the best., I appreciate your work and study\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "288113",
"date": "16 Sep 2024",
"name": "Jaya Shanker Tedla",
"expertise": [
"Reviewer Expertise Physical Therapy and Rehabilitation"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAn interdisciplinary study using Yoga for vestibular rehabilitation. The authors nicely executed it. However, answer a few of my comments so that readers will understand it more. Thank you\n1. We need to discuss the reliability and clinometric properties of the outcome measures you used in the outcome measures section. 2. Kindly mention clearly in the manuscript that these supervised sessions are part of familiarization and precisely what is taught in familiarization sessions should be implemented in unsupervised sessions. 3. The telephone call details should be described thoroughly in the methods section. Specify the motivational phrases used and explain if they were consistent for all participants or varied depending on their level of motivation. Additionally, specify the criteria used to measure and categorize the motivation levels. 4. How was adherence noted? Any tool used and at what intervals? 5. Highlighting its contribution to the field in the discussion would be beneficial.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-578
|
https://f1000research.com/articles/13-575/v1
|
05 Jun 24
|
{
"type": "Systematic Review",
"title": "The Impact of Cardiac Rehabilitation on Psychosocial Factors, Functional Capacity, and Left Ventricular Function in Patients with Coronary Artery Disease: Systematic Review and Meta-Analysis",
"authors": [
"Ali Suleiman Harbi",
"Dr Kim Lam Soh",
"Dr Putri Binti Yubbu",
"Kim Geok Soh",
"Ali Suleiman Harbi",
"Dr Putri Binti Yubbu",
"Kim Geok Soh"
],
"abstract": "Background Cardiac rehabilitation is a multifaceted program implemented after adverse events. It aims at facilitating the return to normal life. This review aimed to examine the impact of cardiac rehabilitation on psychosocial risk factors, functional capacity, and left ventricular function.\n\nMethods The following databases: CINAHL, Scopus, PubMed, and Cochrane Library have been searched to retrieve the randomized controlled trials that investigate the effectiveness of cardiac rehabilitation versus usual care on anxiety, depression, peak oxygen consumption, six-minute walk distance, left ventricular ejection fraction, and left ventricular end-systolic and diastolic dimensions. Filters were set to retrieve trials that were published in the English Language between 2000 and 2024. Risk of bias was assessed using the Cochrane risk-of-bias tool (Rob2). Data were analysed meta-analytically.\n\nResults Twenty two (22) trials were included, randomized 2283 participants. A significant improvement favouring intervention groups was observed in anxiety SMD = -0.3890 (95% CI: -0.5640 to -0.2140; p˂0.001), depression SMD = -0.4032 (95% CI: -0.7114 to -0.0950; p= 0.002), peak oxygen consumption MD = 1.2471 (95% CI: 0.3963 to 2.0979; p = 0.004), six-minute walk distance MD = 36.0290 (95% CI: 7.7497 to 64.3082; p = 0.013), and left ventricular ejection fraction MD = 3.0650 (95% CI: 1.1279 to 5.0022; p = 0.001), Although cardiac rehabilitation had no significant effect in decreasing left ventricular end-diastolic dimension MD = -0.0480 (95% CI: -0.2609 to 0.1648; p = 0.658) and left ventricular end-systolic and MD = -0.0670 (95% CI: -0.2829 to 0.1489; p = 0.543) a favourable trend toward intervention group was seen. Risk of bias was high in 1 study and unclear in 7 studies.\n\nConclusion For patients with Coronary Artery Disease, cardiac rehabilitation demonstrated effectiveness in improving psychological symptoms such as anxiety and depression, functional capacity as measured by peak oxygen consumption and six-minute walk test, and left ventricular function.",
"keywords": [
"Cardiac rehabilitation",
"Psychosocial factors",
"Functional capacity",
"Left ventricle"
],
"content": "Introduction\n\nCardiovascular disease (CVD) remains the main cause of morbidity and mortality internationally, contributing to a significant health burden worldwide. Nearly 19 million deaths were associated with CVD in 2020, representing an 18.7% growth from 2010, and over 500 million individuals globally are affected by CVD. Coronary artery disease (CAD) is the most frequently encountered CVD and is associated with a decline in quality of life.1,2 Despite technological progression in CAD treatment, patients still experience subsequent cardiovascular events,3,4 resulting in frequent readmissions, and escalating the personal and social burden of CAD.5 Hence, presence of ongoing management after being diagnosed with CAD is vital.\n\nCardiac rehabilitation (CR) is a multifaceted program implemented after an adverse event. It aims at facilitating the return to normal life and improving exercise capacity.6 Cardiac rehabilitation includes health education, behavioural counselling, lifestyle management and exercise training.6 It is recommended to start the program early in-hospital (phase I) and then continue with (phase II and III) either in-home or centre-based program.7\n\nThe Presence of psychosocial risk factors such as anxiety and depression disturb the prognosis of CAD.8–11 Studies showed that depression and anxiety increase the risk of frequent cardiac events and cardiac and all-cause mortality in patients with CAD.11–13 Conversely, psychosocial well-being has been described as a protective factor.14 Psychosocial risk factors adversely affect cardiac outcomes by encouraging an unhealthy lifestyle and by diminishing the likelihood of successful alteration of cardiac risk factors.15 They are also associated with decreased adherence to medical treatment and rehabilitation.15–17\n\nAs a principal clinical outcome of CR, Functional Capacity is a key factor in secondary prevention of CVD.18 it refers to the capability of an individual to undertake aerobic work.19 The collaborative performance of cardiovascular, pulmonary, and musculoskeletal systems determines an individual’s functional capacity.20 Several studies have reported that the evaluation of functional capacity offers essential diagnostic and prognostic information about patients with CVD.21 Therefore, it is imperative to assess the impact of CR on functional capacity. Functional capacity is frequently measured by exercise tests such as peak oxygen consumption (VO2peak) and 6-minute walk test (6-MWT).22,23\n\nThe left ventricle is a core component of the cardiovascular system. The primary function of the left ventricle is to provide other organs with blood flow. Maintaining sufficient blood supply needs effective contractility of the left ventricle. Patients with CAD may experience cardiac remodelling; a process defined as a group of alterations within the heart that lead to changes in the size, shape and function of the heart.24 The progression of cardiac remodelling may lead to severe left ventricle impairment and chronic heart failure.25 Therefore, the evaluation of cardiac rehabilitation on left ventricular function is very important.\n\nCardiac rehabilitation research is a dynamic field, and the presence of new research comparing the impact of CR vs usual care necessitates incorporating recent findings, analysing the growing body of literature, and recognizing the potential source of heterogeneity. The aim of this systematic review and meta-analysis was to examine the impact of CR on specific psychosocial risk factors functional capacity, and left ventricular function (i.e. anxiety and depression, 6-MWT, VO2peak, left ventricular ejection fraction (LVEF), left ventricular end-diastolic dimension (LVEDD), and left ventricular end-systolic dimension (LVESD)).\n\n\nMethods\n\nThe current systematic review and meta-analysis adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines.26 Two authors (ASH and PY) independently searched the following databases: PubMed, CINAHL, Scopus, Cochrane Library and EMBASE. Additionally, the references of included studies were manually searched to retrieve studies undetected in the primary search. Medical Subject Headings (MeSH) were used in the search process to retrieve the relevant studies. The filters were set to retrieve studies that were published in the English Language between 2000 and 2024. The retrieved studies were checked primarily by titles for potential inclusion in this review, subsequently, those potentially included papers were checked by abstract and then full text for eligibility. Any conflict was resolved by discussion until consensus was reached, and the final decision about the included and excluded paper was made by the senior author (KLS).\n\nThis systematic review and meta-analysis included studies that met the following criteria: 1) randomized controlled trial; 2) examined the impact of CR on at least one outcome of interest; 3) involving patients with CAD aged ≥ 18 years; 4) the minimum follow-up duration of four weeks. studies that did not meet these criteria were excluded. In addition, studies with mixed populations (i.e., patients with CAD and patients with non-CAD) were excluded. The EndNote software (Endnote X9) was used to remove the duplicated articles (alternatively many reference managers can be accessed and used freely such as Mendeley Reference Manager) then a manual check was done.\n\nA pre-set Microsoft Excel spreadsheet was prepared to record the extracted data. Two authors (ASH and PY) independently extracted the following data: first author’s name; year of publication; the location where the study was conducted; sample size and the number of participants in each group; percentage of each gender; intervention’s main components; duration of follow-up; populations’ diagnosis; the p-value for each compression; and post-intervention means and standard deviations for each group.\n\nThe population, intervention, comparator and outcomes (PICO) framework was used to guide this review. The intended population encompassed patients with CAD, including those who were diagnosed with, myocardial infarction, and those who had undergone percutaneous intervention, or coronary artery bypass graft, The considered intervention was the home-based CR (HBCR) or centre-based CR (CBCR); the comparator was those patients who received the usual or no care, the outcomes of interest are: 1) psychosocial risk factors measured by anxiety and depression; 2) functional capacity measured by VO2peak and 6-MWT; and 3) left ventricular function measured by left ventricular ejection fraction (LVEF), left ventricular end-diastolic dimension LVEDD, and left ventricular end-systolic dimension LVESD.\n\nData were analysed following the guidelines of the Cochrane Handbook for systematic reviews of interventions.27 Using Jamovi software (Jamovi 24.11). A random effect statistical model was applied. To estimate the effect of CR versus usual care, post-intervention between groups mean difference (MD) and standard deviations were used. Alternatively, standardized mean difference (SMD) was used in case the outcome was measured by different scales among the studies. Heterogeneity was tested using I2, whereby values of 25%, 50%, and 75% indicate low, moderate, and high heterogeneity, respectively. Hypothesis testing was performed at a two-tailed 0.05 level and a 95% CI. If I2 values showed high heterogeneity (I2 > 50%), sensitivity analysis was performed by using ‘leave-one-out approach, removing one study at a time and observing the impact on heterogeneity. Publication bias was assessed visually by a funnel plot and statistically by the Egger test. Subgroup analysis was performed based on the duration of follow-up (≥ 3 vs ˂ 3 months), and population average age (≥ 60 vs ˂ 60 years).\n\nTwo authors (ASH and PY) independently assessed the risk of bias in the included studies. Version 2 of the Cochrane risk-of-bias tool for randomized trials (RoB 2) was employed to assess the risk of bias in the included trials.28 RoB 2 is structured into a set of domains of bias: (1 bias arising from the randomization process; (2 bias due to deviations from intended interventions; (3 bias due to missing outcome data; (4 bias in the measurement of the outcome; (5 bias in the selection of the reported result. For each domain, a set of questions (signalling questions) is designed to guide the user in extracting information related to the risk of bias. Judgment regarding the risk of bias arising from each domain is made by an algorithm, based on answers to the signalling questions. Judgment can be ‘Low’ or ‘High’ risk of bias, or ‘Some concerns’. the final decision about the risk of bias Judgment was made by the senior author (KLS).\n\nThe quality of evidence across the outcomes was assessed using the Grading of Recommendation Assessment, Development and Evaluation (GRADE) approach.29 GRADE has four levels of evidence: high, moderate, low, or very low. Based on GRADE guidelines RCTs are considered high-quality evidence, then they may be downgraded 1 or 2 levels based on the assessment of Risk of bias, inconsistency, indirectness, imprecision, and publication bias for each outcome.\n\n\nResults\n\nThe preliminary search in the databases identified 3,357 studies. Duplicated articles were removed using the EndNote software. The remaining articles were screened by titles for potential inclusion. The retrieved articles were checked by reading the abstracts. After excluding the articles that did not meet the inclusion criteria. 95 articles were eligible for full-text reading. The final number of trials included in this review was 22 studies. The details of the search process are illustrated in Figure 1.\n\nThe present systematic review and meta-analysis includes 22 RCTs,22,30–50 conducted in 11 countries, 5 studies each in Iran and China, 2 studies each in Portugal, Japan, and Denmark, and 1 study each in USA, Brazil, Hong Kong, Turkey, Finland, and Indonesia. The included trials were published between 2003 and 2023. randomized 2283 participants 1196 in intervention groups and 1087 in control group. Sample sizes ranged from 29 to 310, and the mean of participants’ ages ranged from 40 to 85 years. One study reported a high percentage (71.2%) of female participants, while the rest of the studies exhibited low female representation, and the durations of follow-up ranged from 4 weeks to 12 months. Table 1 illustrates the studies’ characteristics.\n\n\n\n• Medication.\n\n• Diet.\n\n• Weight control.\n\n• Stress management.\n\n• Quitting smoking.\n\n• Light physical exercise\n\n• Relaxation.\n\n\n\n• Remote monitoring and coaching using a smartphone and Bluetooth-connected heart rate belt.\n\n• The device records training mode, training time and training intensity.\n\n• Participants were advised to exercise at least 30 min/day for 5 days/week.\n\n• participants had insight into their training history through an individual webpage.\n\n• A standard operating procedure, composed with a psychologist, was used for the individual coaching.\n\n• They were contacted weekly by telephone for supportive guidance.\n\n\n\n• Casual limb movements while in bed and simple walk training.\n\n• Energy expenditure estimated at 2 to 4 (METs).\n\n• Intensity targeted 4 and 5 perceived exertion Borg (PEB) scale rating.\n\n• Reach 60% (HRmax).\n\n\n\n• A 5-minute warm-up (stretching), 20-minute aerobic exercise (walking or jogging, gymnastics), and a 5-minute cool-down (stretching).\n\n• Brochure that included information about cardiac disease, risk factor management, the importance of exercise, dietary advice, psychological support, and compliance with medication.\n\n• Phone interview 1/week.\n\n\n\n• Three sessions/week, 1hour Each.\n\n• A warm-up (10 minutes), and 40 minutes of aerobic exercise training,10 minutes cooling down and finished by relaxation.\n\n• 40-60% of HRmax.\n\n• 2- Educated about risk factors, stress reduction methods, smoking cessation, body weight control, psychological, and nutritional.\n\n\n\n• Phase 1: inpatient ambulating program lasted for 7 to 14 days.\n\n• Phase 2: twice-weekly outpatient exercise and education program lasting for 8 weeks, 1 hour of education class followed by 2 hours of exercise training.\n\n• Phase 3: home exercise program lasted 6 months consisted of daily walking exercise for at least 60 minutes after warm-up exercise.\n\n\n\n• Three sessions/week 40-minute each (10 minutes of warm-up, 30 minutes of aerobic exercise on a cycle ergometer or treadmill).\n\n• 70%-85% of HRmax.\n\n• Regular appointments with a cardiologist.\n\n• medication optimization.\n\n\n\n• three sessions/week. 70-85 minutes each include warm-up and cool down.\n\n• 60-70 % of HRmax.\n\n• moderate-intensity workout.\n\n\n\n• Six to seven sessions/week, 40–60 minute each.\n\n• Included upper and lower extremities, breathing, self-massage, and whole-body exercises.\n\n• Moderate-intensity\n\n\n\n• Three sessions/week, 1 hour each.\n\n• Treadmill walking with adjusted speed and inclination.\n\n• 60-70 % of HRmax.\n\n• Every training session began and ended with 5 min warm-up cool-down periods.\n\n\n\n• Phase I: (Inpatient): Lasted 7-14 days, initiated after PCI.\n\n• Phase II (Outpatient Exercise and Education): Conducted three times weekly, lasting 2-3 months. each session comprised one hour of education followed by two hours of exercise training.\n\n• Electrocardiography (ECG) monitoring during exercise sessions.\n\n• Phase III (Community-based Home Exercise): Implemented between six and twelve months.\n\n• Phase IV (Long-term Follow-up): Extended until the end of the second post-PCI year. emphasized the importance of regular exercise and risk factor modification.\n\n\n\n• Three sessions/week, 30 minutes each.\n\n• Targeted intensity individually determined based on the HR recorded 1 minute before the threshold of anaerobic ventilation during CPET examination (70–80%) of HRmax.\n\n• 5 minutes warm-up, Gradual intensity increase over 20 minutes, 5 minutes cool down.\n\n\n\n• Physical exercise and educational components\n\n• Warm-Up Exercises (Approximately 20 Minutes)\n\n• Upright Aerobic and Dynamic Exercise (20–30 Minutes)\n\n• Cool-Down (Approximately 20 Minutes)\n\n• Dietary and Educational Program.\n\n\n\n• CAD-related health education (Once a week (2 months), each lasting about 60 minutes, covering basic CAD knowledge and post-discharge rehabilitation management.\n\n• Exercise guidance and surveillance (once a month for 10 months), 60 to 90 min each time; (3) frequency: 3 to 5 times per week; (4) intensity: fairly light to somewhat hard (11–13 on Borg scale).\n\n• Risk factor control (once a month for 10 months).\n\n• Psychological nursing (once a month for 10 months).\n\n\n\n• Three session/week, 60-90 minutes each and included 10-20 minutes of warm-up followed by 20-40 minutes of aerobic exercise and a final 10-minute cool-down. In addition, there was a 20-minute relaxation at the end of each session.\n\n• 60-85% of HRmax.\n\n• (HR) achieved on the exercise test.\n\n• Psychological, nutritional, and smoking cessation consultations.\n\n\n\n• Begins 12 hours after AMI, conducted twice daily during the inpatient phase.\n\n• Starts at 2 METs and progressively increases to 4 METs.\n\n• Educational Program covers information about cardiac diagnosis, sexual activity, exercise continuation, nutritional advice, and pharmacological regimen adherence.\n\n\n\n• 4 times a week for 4 weeks following hospital discharge.\n\n• Endurance Training Period:\n\n• First week: Starts with a walking time of 20 minutes.\n\n• Second week: Increases to 25 minutes.\n\n• Third week: increases to 30-35 minutes.\n\n• Fourth week: Reaches 35-40 minutes.\n\n• Cool-Down Period (5 minutes).\n\n\n\n• Health Education: once weekly focusing on topics such as post-CABG medicine management, risk factor management, and secondary prevention.\n\n• Rehabilitation Guidance: Includes aerobic, resistance, flexibility, and balance training guidance delivered weekly through video courses.\n\n• Exercise Supervision: Individualized exercise prescriptions based on pre-discharge evaluations\n\n• Psychological Care: twice weekly personal nurse-led counseling sessions via video call to address mental health and emotional support.\n\n\n\n• At admission: Included respiratory physiotherapy and aerobic training.\n\n• Post-hospital discharge (up to 4 weeks post-CABG): Involved continuous daily walking, muscle strengthening, and\n\n• endurance exercises.\n\n\n\n• Mindfulness practices were a key element, offered as a set of recorded meditation instructions.\n\n\n\n• Warm-Up: Begins with stretching exercises to prepare muscles and joints.\n\n• Aerobic Exercise: Includes cycling, treadmill walking, and in-room track walking for about 20 minutes.\n\n• Intensity tailored to individual anaerobic threshold or Borg’s scale rating.\n\n• Cool Down: Follows aerobic exercise to gradually lower heart rate.\n\n• Schedule: Conducted once daily in the hospital.\n\n• Additional Components:\n\n• Dietary Recommendations: Follow American Heart Association's phase II diet.\n\n• Educational Program: Provided by physicians, nurses, and dietitians, covering CAD and risk factors.\n\n\n\n• a combination of aerobic and resistance exercise training.\n\n• 24 supervised sessions, 90 minutes each,\n\n• intensity was set between 60-85% of maximum heart rate.\n\n• The program also offered nutritional and psychological consultations, along with risk factor management.\n\n• Center vs usual\n\n\n\n• two visits from a physiotherapist over 6 weeks with a follow-up call for any questions.\n\n• 6 sessions/week.30-minute each, with warm-up and cool-down, done Exercises matched personal abilities.\n\n• moderate effort (Borg scale 11–13).\n\n• Shorter exercises for very disabled patients, done more times a day.\n\n• physician visits at the start, 3, 6, and 12 months, plus follow-up calls at 4 and 5 months for monitoring and motivation.\n\n• dietary advice and help to quit smoking if needed.\n\n\n\n• Two types: activity messages and exercise planning messages.\n\n• Activity messages encouraged low-level physical activity\n\n• Exercise planning messages encouraged participants to exercise the next day\n\n• Mobile Application Features: Allowed participants to engage in activity self-monitoring and goal-setting.\n\n• Smartwatch data shared with exercise physiologists via email and a web-based dashboard.\n\nOf the 22 studies included in this review, 1 study (4.5%) was assessed as having a high risk of bias related to the randomization process. Because the participants were allocated based on the initial assessment. 32% (7 studies) were assessed as having unclear risk of bias since they did not provide information about allocation concealment, the remaining 63% (14 studies) detailed explicitly the allocation methods such as using an opaque envelope, coin flipping, computer-generated numbers and block size. There was no evidence indicating deviation from the intended intervention, therefore, all studies were assessed as having a low risk of bias regarding this domain. regarding missing outcome data, 1 study (4.5%) showed high risk of bias due to a substantial amount of missing data, 18% (4 studies) had an unclear risk of bias, and the remaining 17 studies (77%) reported handling missing data based on intention-to-treat (ITT) analysis. For measurement of the outcome domain, 55% (12 studies) did not provide sufficient information whether the data was analysed blindly or not, resulting in unclear risk of bias. On the other hand, a low risk of bias was observed in the remaining 45% (10 studies), either by reporting blind assessors or by showing a robust methodology. All studies showed low risk regarding reporting bias. Figures 2 and 3 summarize the outcomes of risk bias assessment.\n\nThe GRADE framework was used to evaluate the quality of the evidence in the included studies. Of the seven outcomes investigated in this review, five outcomes had moderate quality evidence (anxiety, depression, VO2peak, 6-MWT, and LVEF), and two had low-quality of evidence LVEDD and LVESD. Table 2 details the assessment of certainty of evidence.\n\n\nMeta-analysis of included studies\n\nAnxiety: Eight studies evaluated the effect of CR on anxiety levels. Meta-analysis showed a statistically significant reduction in anxiety levels in intervention groups compared with control SMD = -0.3890 (95% CI: -0.5640 to -0.2140). (z = -4.3577, p < 0.0001). There was a moderate amount of heterogeneity in the true outcomes, I2 = 41.62%, p = 0.0672. No indication of publication bias was observed (see Figure 4).\n\nDepression: Eight studies examined the effect of CR on depression. Meta-analysis revealed a statistically significant reduction in depression levels among intervention groups compared to control. SMD = -0.4032 (95% CI: -0.7114 to -0.0950). (z = -2.5638, p = 0.0018). However, a high amount of heterogeneity was observed I2 = 81.1861%, p = 0.0034. employing the sensitivity test by removing the study by Sharif et al. (2012)33 and the study by Kulcu et al. (2007)32 revealed statistically significant result without a significant amount of heterogeneity. SMD = -0.2663 (95% CI: -0.3948 to -0.1378), (z = -4.0626, p < 0.0001). I2 = 0.0000%, p = 0.4598. No indication of publication bias was observed (see Figure 5).\n\nPeak VO2peak: Eight studies investigated the impact of CR on VO2 peak. Meta-analysis showed a statistically significant improvement in Peak VO2 among participants in intervention groups compared to those in control groups. MD = 1.2471 (95% CI: 0.3963 to 2.0979). (z = 2.8728, p = 0.0041). There was no significant amount of heterogeneity in the true outcomes I2 = 0.0000%. p = 0.5604. No indication of publication bias was observed (see Figure 6).\n\n6-MWT: Five studies investigated the effect of CR vs usual care on 6-MWT. The pooled effect showed a statistically significant increase in 6-MWT among participants in intervention groups compared to those in control groups. MD = 54.7948 (95% CI: 15.6115 to 93.9782). (z = 2.1630, p = 0.0305). However, the true outcomes appear to be heterogeneous, I2 = 73.3622%, p = 0.0234. employing the sensitivity test by removing the study by Oerkild et al. (2012)36 and the study by Ghashghaei et al. (2012)35 revealed a statistically significant result MD = 36.0290 (95% CI: 7.7497 to 64.3082). (z = 2.4971, p = 0.0125) with moderate amount of heterogeneity, I2 = 45.3613%, p = 0.1670. No indication of publication bias was observed (see Figure 7).\n\nLVEF: Six studies examined the effect of CR vs usual care on LVEF. When compared to the control, participants in intervention groups demonstrated a statistically significant increase in LVEF. MD = 3.0650 (95% CI: 1.1279 to 5.0022). (z = 3.1011, p = 0.0019) with a moderate amount of heterogeneity, I2 = 39.10%, p = 0.0196. No indication of publication bias was observed (see Figure 8).\n\nLVEDD: Four studies evaluated the impact of CRP vs usual care on LVEDD. Meta-analysis demonstrated a non-statistically significant reduction in LVEDD in intervention groups compared to control, = -0.0480 (95% CI: -0.2609 to 0.1648). (z = -0.4422, p = 0.6583). and the heterogeneity was null I2 = 0.0000%, p = 0.6501. No indication of publication bias was observed (see Figure 9).\n\nLVESD: Five studies assessed the impact of CRP vs usual care on LVESD. Meta-analysis revealed that the intervention groups exhibited a non-statistically significant decrease in LVESD compared to control groups. MD = -0.0670 (95% CI: -0.2829 to 0.1489). (z = -0.6086, p = 0.5428). All studies appeared homogeneous I2 = 0.0000%, p = 0.6005. No indication of publication bias was observed (see Figure 10).\n\n\nDiscussion\n\nThe main findings for this systematic review and meta-analysis were that CR improved psychosocial risk factors, functional capacity, and left ventricular function, as indicated by the statistically significant improvement in (anxiety, depression, VO2peak, 6-MWT, and LVEF) in intervention groups as compared to control, and the favourable trend toward intervention groups in LVEDD and LVESD. There was no significant amount of heterogeneity among all outcomes, except for depression, 6-MWT, and LVEF. However, the heterogeneity could be handled by sensitivity analysis.\n\nConstant feelings of fear and worry about social and physical aspects of life influence the patient’s mental health.51 Anxiety and depression are common psychological disorders after cardiovascular events such as acute myocardial infarction and revascularization.51,52 Studies documented that the prevalence of anxiety and depression in patients diagnosed with CAD is very high compared to the general population.53,54 A recent meta-analysis aimed to estimate the prevalence of anxiety and depression in cardiac patients reported that the prevalence of anxiety was 32.9% (95% CI: 21.9-46.6%), while depression was noted at 31.3% (95% CI: 21.9-46.6%).55\n\nThose cardiac patients who are anxious and depressed are more susceptible to major adverse cardiac events and death.56–58 This creates the need for early assessment and treatment of anxiety and depressive symptoms. The findings of this review emphasize the ability of CR to alleviate anxiety and depression. By training the patients to adhere to a healthy lifestyle, CR aims to enhance patients’ satisfaction and return to normal life. Multidisciplinary CR that include physical training, psychological support, and health education appeared to be highly effective and have shown significant benefits in reducing anxiety and depression levels. The result of this review was in line with previous works. For instance, Yohannes and colleagues concluded that CR had a positive impact on particular psychological disorders, such as depression and anxiety and this impact was maintained at short and long follow-up.59 Escobar and colleagues also observed improvement in anxiety and depressive symptoms in patients experiencing CR.60\n\nFunctional capacity is a major outcome of CR, considered a key element in CAD secondary prevention.61 Functional capacity adversely affected by CAD results in a sedentary lifestyle.62,63 The inverse correlation between functional capacity and mortality rate has been reported in many studies. In a study conducted by Laukkanen and colleagues aimed to evaluate the relationship between functional capacity and cardiac and all-cause mortality rate, functional capacity appeared as a strong predictor of mortality beyond traditional risk factors.64\n\nFunctional capacity is frequently evaluated by VO2peak and 6-MWT.65 VO2peak is a vital physiological indicator determining an individual’s upper capability for oxygen utilization during strenuous physical exertion,66 as this metric reflects cardiovascular fitness and aerobic endurance it plays a crucial role in shaping exercise prescription and assessing the efficiency of therapeutic interventions such as CR.67 Additionally, the 6-MWT provides a practical and valuable evaluation of functional capacity. serves as a fundamental marker of cardiovascular fitness and aerobic endurance.65,68\n\nThe present review demonstrated significant improvement in functional capacity in CR groups compared to usual care. While the heterogeneity in the VO2peak outcome was low, it was high in the 6-MWT outcome, after employing the sensitivity test by removing the studies by Oerkild et al. (2012)36 and Ghashghaei et al. (2012)35 the result remained significant, with moderate heterogeneity. The relatively smaller sample sizes of these two studies compared to other studies in this outcome may contribute to the heterogeneous result observed. These significant results highlight the effectiveness of CR in enhancing patients’ functional capacity and overall health. These findings are supported by the findings of a recent scientific review, where the authors observed improvement in functional capacity after CR.69,70\n\nDespite the advancement in the contemporary treatment aimed at restoring coronary blood flow, the injury caused by myocardial ischemia leads to left ventricular remodelling; a transformative process that involves changes in the left ventricle’s dimensions, shape, and function.25 Therefore, the need for a treatment that enhances the left ventricular function without adversely affecting the ventricular remodelling is essential.\n\nThe findings of the present review demonstrated that CR significantly improved the left ventricular function. as evidenced by the significant increase in LVEF and the reduction in LVEDD and LVESV in intervention groups as compared with the control. Although the reduction in LVEDD and LVESD between the intervention and the control groups was not statistically significant, a favourable trend was observed in the participants in intervention groups without heterogeneity. These results emphasize that CR did not adversely affect the structure, shape, and function of the heart. These findings are consistence with the findings of previous studies which conclude that CR has favourable effects on LV function and remodelling in patients with CAD.71–73\n\nSome limitations in this review should be mentioned. Firstly, the variation of CR in terms of onset, duration, intensity and frequency among the included studies may influenced the outcomes differently, CR with higher does may produce better improvement. Secondly, the small sample size in some included studies diminished the statistical power and increased the heterogeneity in particular investigated outcomes. Thirdly, some studies lacked sufficient information to allow for judgment on the risk of bias, especially information about blinding of the data assessors. Finally, the limited number of available trials that met the inclusion criteria especially those that investigated the impact of CR on 6-MWT, LVEDD and LVESD. Future studies are recommended to explore the impact of CR on other physical, psychological, and cardiac outcomes, such studies may comprehensively clarify the beneficiary effect of CR and underscore the areas of improvement.\n\n\nConclusion\n\nFor patients with Coronary Artery Disease, including patients after PCI or CABG, cardiac rehabilitation effectively improved psychosocial risk factors such as anxiety and depression, functional capacity as measured by VO2peak and 6-MWT, and left ventricular ejection fraction. The findings underscore CR as a method that enhances patients’ overall health.\n\n\nData availability\n\n“All data underlying the results are available as part of the article and no additional source data are required.”\n\n\nSoftware and code\n\nThe Endnote reference manager available from: https://endnote.com/downloads/ alternative free access reference manager available from: https://www.mendeley.com/download-reference-manager/windows\n\nMeta-analysis statistical spreadsheet available from: https://www.jamovi.org/download.html\n\nRisk of bias assessment available from: https://sites.google.com/site/riskofbiastool/welcome/rob-2-0-tool/current-version-of-rob-2?authuser=0\n\n\nReporting guidelines\n\nZenodo: PRISMA Checklist for Article “The Impact of Cardiac Rehabilitation on Psychosocial Factors, Functional Capacity, and Left Ventricular Function in Patients with Coronary Artery Disease: Systematic Review and Meta-Analysis”. https://doi.org/10.5281/zenodo.11186070\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: PRISMA flow chart for Article “The Impact of Cardiac Rehabilitation on Psychosocial Factors, Functional Capacity, and Left Ventricular Function in Patients with Coronary Artery Disease: Systematic Review and Meta-Analysis”. https://doi.org/10.5281/zenodo.11186649\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
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PubMed Abstract | Publisher Full Text | Free Full Text\n\nOliveira NL, Ribeiro F, Teixeira M, et al.: Effect of 8-week exercise-based cardiac rehabilitation on cardiac autonomic function: A randomized controlled trial in myocardial infarction patients. Am. Heart J. 2014; 167(5): 753–61.e3. PubMed Abstract | Publisher Full Text\n\nSoleimannejad K, Nouzari Y, Ahsani A, et al.: Evaluation of the effect of cardiac rehabilitation on left ventricular diastolic and systolic function and cardiac chamber size in patients undergoing percutaneous coronary intervention. J. Tehran Heart Cent. 2014; 9(2): 54–58. PubMed Abstract Reference Source\n\nPeixoto TC, Begot I, Bolzan DW, et al.: Early exercise-based rehabilitation improves health-related quality of life and functional capacity after acute myocardial infarction: a randomized controlled trial. Can. J. Cardiol. 2015; 31(3): 308–313. PubMed Abstract | Publisher Full Text\n\nXu L, Cai Z, Xiong M, et al.: Efficacy of an early home-based cardiac rehabilitation program for patients after acute myocardial infarction: A three-dimensional speckle tracking echocardiography randomized trial. Medicine (Baltimore). 2016; 95(52): e5638. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbtahi F, Tahamtan M, Homayouni K, et al.: The Assessment of Cardiac Rehabilitation on Echocardiographic Parameters of Left Ventricular Systolic Function in Patients Treated by Primary Percutaneous Coronary Intervention due to Acute ST-Segment Elevation Myocardial Infarction: A Randomized Clinical Trial. Int. Cardiovasc. Res. J. 2017; 11(4): 130–136. Reference Source\n\nNoites A, Freitas CP, Pinto J, et al.: Effects of a Phase IV Home-Based Cardiac Rehabilitation Program on Cardiorespiratory Fitness and Physical Activity. Heart Lung Circ. 2017; 26(5): 455–462. PubMed Abstract | Publisher Full Text\n\nNishitani-Yokoyama M, Miyauchi K, Shimada K, et al.: Impact of Physical Activity on Coronary Plaque Volume and Components in Acute Coronary Syndrome Patients After Early Phase II Cardiac Rehabilitation. Circ. J. 2018; 83(1): 101–109. PubMed Abstract | Publisher Full Text\n\nHojskov IE, Moons P, Egerod I, et al.: Early physical and psycho-educational rehabilitation in patients with coronary artery bypass grafting: A randomized controlled trial. J. Rehabil. Med. 2019; 51(2): 136–143. PubMed Abstract | Publisher Full Text\n\nMa L, Deng L, Yu H: The effects of a comprehensive rehabilitation and intensive education program on anxiety, depression, quality of life, and major adverse cardiac and cerebrovascular events in unprotected left main coronary artery disease patients who underwent coronary artery bypass grafting. Ir. J. Med. Sci. 2020; 189(2): 477–488. PubMed Abstract | Publisher Full Text\n\nSnoek JA, Meindersma EP, Prins LF, et al.: The sustained effects of extending cardiac rehabilitation with a six-month telemonitoring and telecoaching programme on fitness, quality of life, cardiovascular risk factors and care utilisation in CAD patients: The TeleCaRe study. J. Telemed. Telecare. 2021; 27(8): 473–483. PubMed Abstract | Publisher Full Text\n\nMa C, Wang B, Zhao X, et al.: WeChat-based education and rehabilitation program in unprotected left main coronary artery disease patients after coronary artery bypass grafting: an effective approach in reducing anxiety, depression, loss to follow-up, and improving quality of life. Braz. J. Med. Biol. Res. 2021; 54: e10370. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCao RY, Zheng H, Hong Y, et al.: Cardiac Rehabilitation with Targeted Intensity Improves Cardiopulmonary Functions Accompanying with Reduced Copeptin Level in Patients with Coronary Artery Disease. J. Cardiovasc. Transl. Res. 2021; 14(2): 317–326. PubMed Abstract | Publisher Full Text\n\nZhao F, Liang C, John Zaslawski C, et al.: Effects of Qigong Therapy on the Anaerobic Threshold in Patients with Stable Coronary Artery Disease: A Randomized Controlled Trial. Evid. Based Complement. Alternat. Med. 2022; 2022: 5690568–5690569. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGolbus JR, Gupta K, Stevens R, et al.: A randomized trial of a mobile health intervention to augment cardiac rehabilitation. NPJ Digit. Med. 2023; 6(1): 173. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPogosova N, Saner H, Pedersen SS, et al.: Psychosocial Aspects in Cardiac Rehabilitation: From Theory to Practice. A Position Paper From the Cardiac Rehabilitation Section of The European Association of Cardiovascular Prevention and Rehabilitation of the European Society of Cardiology. Kardiologiia. 2015; 55(10): 96–108. PubMed Abstract | Publisher Full Text\n\nMurphy B, Le Grande M, Alvarenga M, et al.: Anxiety and Depression After a Cardiac Event: Prevalence and Predictors. Front. Psychol. 2019; 10: 3010. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBermudez T, Bierbauer W, Scholz U, et al.: Depression and anxiety in cardiac rehabilitation: differential associations with changes in exercise capacity and quality of life. Anxiety Stress Coping. 2022; 35(2): 204–218. PubMed Abstract | Publisher Full Text\n\nRao A, Zecchin R, Newton PJ, et al.: The prevalence and impact of depression and anxiety in cardiac rehabilitation: A longitudinal cohort study. Eur. J. Prev. Cardiol. 2020; 27(5): 478–489. PubMed Abstract | Publisher Full Text\n\nKarami N, Kazeminia M, Karami A, et al.: Global prevalence of depression, anxiety, and stress in cardiac patients: A systematic review and meta-analysis. J. Affect. Disord. 2023; 324: 175–189. PubMed Abstract | Publisher Full Text\n\nWorcester MU, Murphy BM, Elliott PC, et al.: Trajectories of recovery of quality of life in women after an acute cardiac event. Br. J. Health Psychol. 2007; 12(Pt 1): 1–15. PubMed Abstract | Publisher Full Text\n\nKim JM, Stewart R, Lee YS, et al.: Effect of Escitalopram vs Placebo Treatment for Depression on Long-term Cardiac Outcomes in Patients With Acute Coronary Syndrome: A Randomized Clinical Trial. JAMA. 2018; 320(4): 350–358. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou Y, Zhu XP, Shi JJ, et al.: Coronary Heart Disease and Depression or Anxiety: A Bibliometric Analysis. Front. Psychol. 2021; 12: 669000. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYohannes AM, Doherty P, Bundy C, et al.: The long-term benefits of cardiac rehabilitation on depression, anxiety, physical activity and quality of life. J. Clin. Nurs. 2010; 19(19-20): 2806–2813. PubMed Abstract | Publisher Full Text\n\nBravo-Escobar R, González-Represas A, Gómez-González AM, et al.: Effectiveness of e-Health cardiac rehabilitation program on quality of life associated with symptoms of anxiety and depression in moderate-risk patients. Sci. Rep. 2021; 11(1): 3760. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuidelines ECfSCorrà U, Piepoli MF, et al.: Secondary prevention through cardiac rehabilitation: physical activity counselling and exercise training: Key components of the position paper from the Cardiac Rehabilitation Section of the European Association of Cardiovascular Prevention and Rehabilitation. Eur. Heart J. 2010; 31(16): 1967–1974. PubMed Abstract | Publisher Full Text\n\nBeatty AL, Truong M, Schopfer DW, et al.: Geographic Variation in Cardiac Rehabilitation Participation in Medicare and Veterans Affairs Populations: Opportunity for Improvement. Circulation. 2018; 137(18): 1899–1908. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDouki ZE, Vaezzadeh N, Zakizad M, et al.: Changes in functional status and functional capacity following coronary artery bypass surgery. Pak. J. Biol. Sci. 2010; 13(7): 330–334. PubMed Abstract | Publisher Full Text\n\nLaukkanen JA, Kunutsor SK, Yates T, et al.: Prognostic Relevance of Cardiorespiratory Fitness as Assessed by Submaximal Exercise Testing for All-Cause Mortality: A UK Biobank Prospective Study. Mayo Clin. Proc. 2020; 95(5): 867–878. PubMed Abstract | Publisher Full Text\n\nNoonan V, Dean E: Submaximal exercise testing: clinical application and interpretation. Phys. Ther. 2000; 80(8): 782–807. PubMed Abstract | Publisher Full Text\n\nIbrahim A, Mat Ludin AF, Shahar S, et al.: Association between maximal oxygen consumption and physical performance tests among older adults with cognitive frailty. Exp. Gerontol. 2023; 184: 112326. PubMed Abstract | Publisher Full Text\n\nEkblom-Bak E, Ekblom B, Söderling J, et al.: Sex- and age-specific associations between cardiorespiratory fitness, CVD morbidity and all-cause mortality in 266.109 adults. Prev. Med. 2019; 127: 105799. PubMed Abstract | Publisher Full Text\n\nBudts W, Pieles GE, Roos-Hesselink JW, et al.: Recommendations for participation in competitive sport in adolescent and adult athletes with Congenital Heart Disease (CHD): position statement of the Sports Cardiology & Exercise Section of the European Association of Preventive Cardiology (EAPC), the European Society of Cardiology (ESC) Working Group on Adult Congenital Heart Disease and the Sports Cardiology, Physical Activity and Prevention Working Group of the Association for European Paediatric and Congenital Cardiology (AEPC). Eur. Heart J. 2020; 41(43): 4191–4199. PubMed Abstract | Publisher Full Text\n\nPrabhu NV, Maiya AG, Prabhu NS: Impact of Cardiac Rehabilitation on Functional Capacity and Physical Activity after Coronary Revascularization: A Scientific Review. Cardiol. Res. Pract. 2020; 2020: 1236968–1236969. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDibben GO, Dalal HM, Taylor RS, et al.: Cardiac rehabilitation and physical activity: systematic review and meta-analysis. Heart. 2018; 104(17): 1394–1402. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSadeghi M, Garakyaraghi M, Khosravi M, et al.: The impacts of cardiac rehabilitation program on echocardiographic parameters in coronary artery disease patients with left ventricular dysfunction. Cardiol. Res. Pract. 2013; 2013: 201713. Publisher Full Text\n\nWang Y, Chien CW, Xu Y, et al.: Effect of Exercise-Based Cardiac Rehabilitation on Left Ventricular Function in Asian Patients with Acute Myocardial Infarction after Percutaneous Coronary Intervention: A Meta-Analysis of Randomized Controlled Trials. Healthcare (Basel). 2021; 9(6). PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaykowsky M, Scott J, Esch B, et al.: A meta-analysis of the effects of exercise training on left ventricular remodeling following myocardial infarction: start early and go longer for greatest exercise benefits on remodeling. Trials. 2011; 12: 92. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "288105",
"date": "29 Jun 2024",
"name": "Thomas Maribo",
"expertise": [
"Reviewer Expertise Please make minor adjustments as suggested"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe systematic review and meta-analysis explores the impact of cardiac rehabilitation on psychosocial factors, functional capacity, and left ventricular function in patients with coronary artery disease. The study includes data from 22 randomized controlled trials involving 2283 participants, comparing cardiac rehabilitation to usual care. The findings indicate significant improvements in anxiety, depression, peak oxygen consumption, six-minute walk distance, and left ventricular ejection fraction among patients undergoing cardiac rehabilitation. The study underscores the importance of cardiac rehabilitation in enhancing psychological well-being and physical health in patients with coronary artery disease.\n\nThe results are highly interesting in relation to cardiac rehabilitation and care. So far, there has been a strong focus on the physical part of cardiac rehabilitation with an increasing interest in psychosocial factors. This article provides good evidence that there is a need to focus more on the psychosocial factors - without losing focus on the physical factors. The article is a good and solid contribution to this transformation\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-575
|
https://f1000research.com/articles/12-1444/v1
|
07 Nov 23
|
{
"type": "Review",
"title": "A review of ultrasound contrast media",
"authors": [
"Ammar A. Oglat"
],
"abstract": "There have been numerous attempts over the past 50 years to develop efficient ultrasound contrast media (UCM) for both cardiac and noncardiac uses. In other words, the first UCM was created in the 1980s as a result of early reports from the 1960s documenting the findings of ultrasound contrast enhancement by microscopic gaseous bubbles during echocardiographic tests. A nontoxic UCM (Definity, Optison, Sonazoid, and SonoVue are some of the current commercial contrast media for echography that have shown promise in a range of on- and off-label clinical purposes) that may be injected intravenously, travels through the pulmonary, cardiac, and capillary circulations, and is stable for recirculation would be ideal. Many potential UCMs have been developed or are currently being worked on. The understanding of the physical, chemical, and biological behavior of microbubbles has greatly advanced in increase tumor vascularity, highlight sites of ischemia, and improve the ability to see vascular stenosis. Future potential, like ultrasonic molecular imaging and therapeutic uses of microbubbles, are anticipated to benefit from new inventive advancements.",
"keywords": [
"contrast agents for ultrasound",
"Microbubbles",
"echocardiographic",
"M-mode"
],
"content": "Introduction\n\nIn obstetrics, cardiology, and radiology, ultrasound imaging is a common clinical tool for the morphological examination of soft tissues.1–7 As an ultrasonic wave—a longitudinal wave—travels through the body, tissue surfaces with various acoustic characteristics, such as speed of sound and density, produce reflections. The same transmitting transducer captures these scattered impulses and uses them to create an image. However, because to the size and characteristics of red blood cells, the intrinsic scattering from the blood pool is often several orders of magnitude lower than tissue at standard diagnostic frequencies (1–9 MHz). As a result, blood appears black on typical ultrasound images, making it difficult to determine the properties of blood flow. Doppler techniques can be used to measure blood velocity in bigger veins by comparing the relative motion of red blood cells to the surrounding tissue.8,9 This technique is frequently used in clinical settings (e.g., obstetrics,10 assessment of peripheral artery disease,11 cardiology12). However, this method has drawbacks when applied to areas with poor blood flow, significant tissue motion, and/or low hematocrit percentage.13–15\n\nThroughout the past few decades, ultrasound imaging’s diagnostic uses have greatly increased. The development of UCM has led to the provision of new useful physiologic and pathologic data, and the availability of perfusion imaging of cardiac or tumor tissue for everyday clinical decision-making.16,17 The early 1960s saw the first reports of the ultrasonic contrast effect was studies by Joyner. Further research revealed the existence of UCM made of saline, indocyanine green, hydrogen peroxide, dextrose, and renografin.16,18 UCM comprise of a suspension of small spheres of gas with a poor solubility in blood (e.g., perfluorocarbon), often ranging in size from below 10 μm in diameter. The relatively large size of UCMs guarantees that they remain strictly intravascular and function as red blood cell tracers, in contrast to contrast media employed in other modalities like (magnetic resonance imaging) MRI and computer tomography (CT).19\n\nAround 1980, achieving stability long enough for the UCM to reach the correct heart was one of the primary objectives in creating efficient UCMs. Left heart contrast was not possible until the 1990s because lung capillaries are effective filters. In 1995, contrast-enhancing substances with enhanced blood pool enhancement capabilities first surfaced. The next goal was to create bubbles that would allow for real-time imaging. In order to achieve this, air was substituted with weakly soluble gases, such as perfluorocarbons, which increased bubble endurance and allowed the development of software algorithms that could effectively distinguish UCM from tissue signals.20–23\n\nMicrobubbles vibrate about their equilibrium radius in an ultrasonic field due to the compressibility of their gas cores, and they have scattering cross-sections that are many orders of magnitude higher than a solid particle of the same size.16,24,25 A thin biocompatible encapsulation layer, often a phospholipid monolayer, stabilizes the bubbles by striking a balance between their ability to vibrate freely and their resistance to dissolving in-vivo during timeframes important for imaging, like half-lives of minutes.26,27\n\nContrast echocardiography has a virtually limitless potential. Contrast echocardiography is currently the subject of extensive interest and research, as this review demonstrates. The creation of novel contrast-producing chemicals is arguably the most intriguing component of this research. It will be fascinating to watch how these different agents grow. Ideally, one or more of these novel agents will be able to cross the capillaries, allowing for peripheral venous injection-based visualization of the left side of the heart.\n\n\nEmerging technique\n\nOver the world, contrast-enhanced ultrasound imaging is used in numerous medical and off-label applications. On multiple fronts, including the creation of novel pulse sequences and image processing techniques, the development of devices, and the creation of remote monitoring for ultrasonic therapies, this field is seeing cutting-edge breakthroughs at the same time.\n\nThe only UCM that has received clinical approval is microbubbles. These bubbles have the advantage of remaining intravascular because of their size, making it possible to perform diagnostic tests that would be challenging with diffusible tracers. The use of these “conventional” UCM is being expanded, though, to include molecular-based imaging, imaging of the extravascular space, and as a platform for both imaging and therapeutic administration.28–32\n\nExtensive study was done beginning in 1980 to establish contrast echocardiography as a recognized diagnostic method.33 Ophir and Parker (1989) provided a summary of UCM’s application in medical imaging.34 Free gas bubbles, encapsulated gas bubbles, colloidal suspensions, emulsions, and aqueous solutions were the five categories of agents that were categorized according to their physical characteristics. Producing the “perfect” contrast media that would satisfy the following requirements was still a major difficulty in those days. Such as, distribution of the substance inside the myocardial or heart chambers, which is indicative of regional blood flow; agent’s capacity to endure after an intravenous infusion during an imaging test; containing microbubbles with a diameter of less than 8 mm (smaller than red blood cells), allowing passage via the pulmonary system and the body’s smallest capillaries; good safety profile, physiological inert; and strong, regulated, and echogenic acoustic interaction.\n\nIn 1984 (Feinstein et al. 1984), cavitation was used to create microbubbles after inserting the tip of a sonicator horn into a solution of human serum albumin.17 This solved the problem of creating stable encapsulated microbubbles that could survive passage through the heart and the pulmonary capillary network. After a peripheral venous injection, these microbubbles could be seen in the left heart. Due to the creation of functionalized microbubbles,35 or microbubbles with one or more targeted moieties inserted into the phospholipid encapsulation,36 non-invasive imaging of pathophysiological events has recently been demonstrated to be viable with ultrasound. Target sites have focused on internal vasculature processes such inflammation,37 angiogenesis,38 and thrombus formation39 since microbubbles are purely intravascular. See Table 1.\n\nThe development of the first microbubbles that met the majority of the requirements for an intravenous UCM also sparked intense research by doctors, scientists, and the makers of ultrasound equipment to explain the physical phenomena and apply what they learned to therapeutic settings.\n\nThere were several technologies looked at to stabilize the microbubbles. For the purpose of lowering surface tension and stabilizing the gas core against quick dissolution, thin shells consisting of protein, polymer, or phospholipids were utilized. Unfortunately, due to the high solubility of air in water, the first-generation agents still had poor stability and relatively short circulation times. By substituting perfluorinated gases with low solubility in water, such as sulphur hexafluoride, perfluoropropane, or perfluorobutane for air during circulation, persistence during circulation was dramatically improved, resulting in sufficient persistence of the agent in the blood circulation for clinical use.41\n\nThere are many ultrasound-sensitive sub-micron agents currently being researched. This research is motivated by the enhanced-permeability and retention effect,42 whereby small nanometer sized particles locally extravasate from leaky blood vessels and accumulate in the perivascular space of solid tumors. Phase-shift droplets,43 nanobubbles,44 gas vesicles,45 echogenic liposomes,46 and polymeric nanoparticles47 are a few of the more common examples. Although research into the physics of acoustic droplet vaporization is still ongoing, it is most probable that both intrinsic and external elements play a role in the process.\n\n\nUltrasound imaging techniques using UCM\n\nVibrating microbubbles’ nonlinear nature is essential to their efficiency as an ultrasonic contrast agent. These emissions allow for the separation of bubble signals from the surrounding (about linear) tissue from those within tiny vessels. Thus, certain microbubble imaging modes were created concurrently with the advancements in UCM and as a result of a better knowledge of non-linear microbubble behavior; these are now used in the majority of clinical ultrasound systems.48–50 The first methods of bubble identification were harmonic imaging, which involved gathering and filtering energy from the receive signal at the second harmonic, which is twice the driving frequency. Because the second harmonic signal produced by microbubbles is substantially greater than the second harmonic signal produced by tissue, it has a higher signal-to-noise ratio than the fundamental energy. The success of low mechanical index (MI) (0.1) contrast-specific imaging, which is primarily employed for real-time perfusion and intra-cavitary measurements, is particularly explained by the non-linear shell behavior. Furthermore, a number of diagnostic imaging procedures and/or quantification strategies are founded on the distinct and extremely sensitive attribute of microbubble destruction.51 See Figure 1.\n\nDiagrammatic representation of the pulse inversion technique in (A). Two pulses that are 180 degrees out of phase will result in out-of-phase tissue echoes. On the other hand, this is not the case for microbubbles because of their nonlinear behavior. When an echo is produced by a microbubble, there is a significant signal, however when an echo is produced by linear tissue, the summed echo almost completely cancels out. (B) B-mode and (C) contrast-specific imaging of an 8 mm artery phantom show the enhanced vascular contrast caused by microbubble-specific imaging. This was recorded with a Philips iU22 scanner, a C5-2 probe, and the contrast medium Definity™. This number is taken from this source. Microbubble-specific imaging sequences capture nonlinear signal from contrast agent while rejecting linear scattering tissue, Yusefi, H., & Helfield, B. (2022), https://www.frontiersin.org/files/Articles/791145/fphy-10-791145-HTML/image_m/fphy-10-791145-g002.jpg, CC BY 4.0.28\n\nIn other words, the reflection pattern from the bubble to the ultrasound signal is significantly altered by UCM. They start by greatly boosting the backscattered signal.23 UCM resonate linearly in response to acoustic pressure. Acoustic pressure increases cause nonlinear vibrational patterns to manifest.52 Only at higher mechanical indices (MI) do tissues create harmonic resonances, making it easy to distinguish between the signal’s tissue or UCM origin. Multiples of the natural frequencies are received using filter devices, allowing for some background (non-UCM) signal reduction. Microbubbles are disrupted by high pressure levels, which results in strong signals and signals with various properties.\n\n\nM-mode echocardiograms using UCM\n\nUnderstanding the interaction between ultrasonic waves and gaseous microbubbles was made much easier by using the process utilized to explain the set of echoes first discovered on M-mode echocardiograms. The strong compressibility of the gas core appears to be particularly significant since it produces frequency-dependent volume pulsations with a clear maximum at the resonance frequency, which is inversely proportional to the size of the microbubbles.24,53 However, In the following circumstances, UCM is advised by cardiologic guidelines: if the left ventricular (LV) cavum does not have two continuous segments, If the original spectrum signals are insufficient, to enhance Doppler evaluations, when periodic evaluation of the ejection fraction is necessary given the reduced variability caused by UCM, and in the case of Takotsubo myopathy, left ventricular (LV) aneurysms, and intracavitary thrombi.52,54,55\n\n\nMicrobubbles-based color Doppler ultrasound\n\nAcoustic color Doppler is an imaging method that overlays color-coded maps of tissue velocity on grey-scale images of tissue anatomy. It combines anatomical information acquired from ultrasonic pulse-echo techniques with velocity information derived from ultrasonic Doppler techniques. The technique is most frequently used to visualize blood flow through the heart, arteries, and veins, but it can also be used to visualize the movements of solid tissues like the walls of the heart. vectors. Almost all commercial ultrasound equipment now provides color Doppler imaging, which has been proven to be very useful in determining blood flow in a variety of clinical circumstances. Although the technique for getting velocity information is quite similar to the technique for getting anatomical information, there are a number of reasons why it is technically more difficult. It also has a few flaws, the biggest of which is that, in conventional systems, the velocities measured and subsequently displayed are the components of the flow velocity directly towards or away from the transducer, whereas the method’s ideal output would provide data on the magnitude and direction of the three-dimensional flow vectors.56–61\n\nIn conjunction with color or power Doppler, stimulated acoustic emission is employed in high mechanical index (MI) imaging. A high MI ultrasound impulse is used to deflate the microbubbles, and the signal that is received is a complicated mixture of ultrasound waves that causes a Doppler shift.62 It is especially helpful when a UCM with tissue specificity, is in its late stages.20 Color Doppler imaging has been shown that despite the poor spatial resolution, real-time imaging was possible due to the tiny size of the picture window.63\n\nRecently, the use of ultrasound color Doppler has been shown to monitor bubbles during ultrasound therapy. An active ultrasound imaging method called color Doppler uses the phase shifts between the echoes of imaging pulses to measure velocities. In the aforementioned investigation, an increase in the color Doppler signal was connected with the formation of cavitation bubbles on their own under a high-pressure ultrasonic beam. The rise was utilized to evaluate tissue fractionation and was related to the mobility of the surrounding tissue brought on by cavitation within the focused location. Although this method is helpful for high-pressure therapy, it does not reveal how net bubbles flow through the field.64,65\n\n\nModern commercial UCM\n\nAll currently marketed UCM are made up of an inert gas enclosed in a shell. The gas determines solubility and most of the acoustic qualities of the bubbles, while the shell mostly affects the viscoelastic properties, such as stability and durability.66 Perfluorocarbon bubbles, which range in size almost 10 m and are real blood pool agents, allow transit through the pulmonary vascular system, which is necessary for entry to the systemic circulation.52 Soft shell materials have better nonlinear oscillations and are made of phospholipids or other surfactants.67 There are also protein-shelled microbubbles that contain an albumin shell around perfluoropropane gas.\n\n\nConclusion\n\nWe outlined the basics of contrast agent microbubble vibration and how it is used for common contrast-imaging applications in this paper. Throughout the past five decades, UCM imaging has made significant advancements. The main clinical focus in the past was echocardiography, with myocardial perfusion being referred to as the “holy grail” and being seen as a significant market for contrast echo. The main reason for echocardiography was LV opacification, which improves LV endocardial border delineation. UCM imaging is a safe and effective method for many clinical applications, and its use is growing. Due to increased clinical awareness of ultrasound’s advantages as well as collaborative research projects between physicists, chemists, engineers, and clinicians on the study of microbubble behavior, signal processing methods, contrast agent synthesis, and device development, this imaging technology has achieved tremendous success to date.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nOglat AA, et al.: A review of medical doppler ultrasonography of blood flow in general and especially in common carotid artery. J Med Ultrasound. 2018; 26(1): 3–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOglat AA, et al.: A new scatter particle and mixture fluid for preparing blood mimicking fluid for wall-less flow phantom. J Med Ultrasound. 2018; 26(3): 134–142. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmmar AO, et al.: Characterization and construction of a robust and elastic wall-less flow phantom for high pressure flow rate using Doppler ultrasound applications. Nat Eng Sci. 2018; 3(3): 359–377. Publisher Full Text\n\nOglat AA, et al.: Artifacts in diagnostic ultrasonography. Los Angeles, CA: SAGE Publications Sage CA; 2020.\n\nShalbi SM, et al.: A brief review for common doppler ultrasound flow phantoms. J Med Ultrasound. 2020; 28(3): 138–142. 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Publisher Full Text\n\nFeinstein SB, et al.: Microbubble dynamics visualized in the intact capillary circulation. J Am Coll Cardiol. 1984; 4(3): 595–600. PubMed Abstract | Publisher Full Text\n\nForsberg F, et al.: Effect of filling gases on the backscatter from contrast microbubbles: theory and in vivo measurements. Ultrasound Med Biol. 1999; 25(8): 1203–1211. Publisher Full Text\n\nBecher H, Burns PN: Handbook of contrast echocardiography: Left ventricular function and myocardial perfusion. Springer Science & Business Media; 2012.\n\nCosgrove D: Ultrasound contrast agents: an overview. Eur J Radiol. 2006; 60(3): 324–330. Publisher Full Text\n\nGoldberg BB, et al.: Ultrasound contrast agents: a review. Ultrasound Med Biol. 1994; 20(4): 319–333. Publisher Full Text\n\nIgnee A, et al.: Ultrasound contrast agents. Endosc Ultrasound. 2016; 5(6): 355–362. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCalliada F, et al.: Ultrasound contrast agents: basic principles. Eur J Radiol. 1998; 27: S157–S160. Publisher Full Text\n\nMedwin HJU: Counting bubbles acoustically: a review. Ultrasonics. 1977; 15(1): 7–13. Publisher Full Text\n\nCovella M, et al.: Echocardiographic aortic root dilatation in hypertensive patients: a systematic review and meta-analysis. J Hypertens. 2014; 32(10): 1928–1935. Publisher Full Text\n\nUnger EC, et al.: Therapeutic applications of lipid-coated microbubbles. Adv Drug Deliv Rev. 2004; 56(9): 1291–1314. PubMed Abstract | Publisher Full Text\n\nGarg S, Thomas A, Borden M: The Effect of Lipid Monolayer In-Plane Rigidity on. Vivo; 2013.\n\nYusefi H, Helfield B: Ultrasound contrast imaging: Fundamentals and emerging technology. Front Phys. 2022; 10: 100. Publisher Full Text\n\nFrinking PJ, et al.: Ultrasound contrast imaging: current and new potential methods. Ultrasound Med Biol. 2000; 26(6): 965–975. PubMed Abstract | Publisher Full Text\n\nAverkiou M, et al.: Ultrasound contrast imaging research. Ultrasound Q. 2003; 19(1): 27–37. Publisher Full Text\n\nCorreas J-M, et al.: Ultrasound contrast agents: properties, principles of action, tolerance, and artifacts. Eur Radiol. 2001; 11: 1316–1328. PubMed Abstract | Publisher Full Text\n\nSofuni A, et al.: Differential diagnosis of pancreatic tumors using ultrasound contrast imaging. J Gastroenterol. 2005; 40: 518–525. Publisher Full Text\n\nSenior R, et al.: Clinical practice of contrast echocardiography: recommendation by the European Association of Cardiovascular Imaging (EACVI) 2017. Eur Heart J Cardiovasc Imaging. 2017; 18(11): 1205–1205af. PubMed Abstract | Publisher Full Text\n\nOphir J, Parker KJ: Contrast agents in diagnostic ultrasound. Ultrasound Med Biol. 1989; 15(4): 319–333. Publisher Full Text\n\nLindner JR: Microbubbles in medical imaging: current applications and future directions. Nat Rev Drug Discov. 2004; 3(6): 527–533. PubMed Abstract | Publisher Full Text\n\nLangeveld SA, Meijlink B, Kooiman K: Phospholipid-coated targeted microbubbles for ultrasound molecular imaging and therapy. Curr Opin Chem Biol. 2021; 63: 171–179. PubMed Abstract | Publisher Full Text\n\nWang Y, et al.: Clopidogrel with aspirin in acute minor stroke or transient ischemic attack (CHANCE) trial: one-year outcomes. Circulation. 2015; 132(1): 40–46. Publisher Full Text\n\nWillmann JK, et al.: Targeted contrast-enhanced ultrasound imaging of tumor angiogenesis with contrast microbubbles conjugated to integrin-binding knottin peptides. J Nucl Med. 2010; 51(3): 433–440. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHamilton AJ, et al.: Intravascular ultrasound molecular imaging of atheroma components in vivo. J Am Coll Cardiol. 2004; 43(3): 453–460. PubMed Abstract | Publisher Full Text\n\nFrinking P, et al.: Three decades of ultrasound contrast agents: a review of the past, present and future improvements. Ultrasound Med Biol. 2020; 46(4): 892–908. PubMed Abstract | Publisher Full Text\n\nSchneider M, et al.: BR1: a new ultrasonographic contrast agent based on sulfur hexafluoride-filled microbubbles. Investig Radiol. 1995; 30(8): 451–457. PubMed Abstract | Publisher Full Text\n\nMatsumura Y, Maeda H: A new concept for macromolecular therapeutics in cancer chemotherapy: mechanism of tumoritropic accumulation of proteins and the antitumor agent smancs. Cancer Res. 1986; 46(12_Part_1): 6387–6392.\n\nSheeran PS, Dayton PA: Phase-change contrast agents for imaging and therapy. Curr Pharm Des. 2012; 18(15): 2152–2165. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHelfield B, Zou Y, Matsuura N: Acoustically-stimulated nanobubbles: opportunities in medical ultrasound imaging and therapy. Front Phys. 2021; 9: 654374. Publisher Full Text\n\nShapiro MG, et al.: Biogenic gas nanostructures as ultrasonic molecular reporters. Nat Nanotechnol. 2014; 9(4): 311–316. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKopechek JA, et al.: Acoustic characterization of echogenic liposomes: Frequency-dependent attenuation and backscatter. J Acoust Soc Am. 2011; 130(5): 3472–3481. Publisher Full Text\n\nKwan JJ, et al.: Ultrasound-propelled nanocups for drug delivery. Small. 2015; 11(39): 5305–5314. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBurns PJCR: Harmonic imaging: principles and preliminary results. Clin Radiol. 1996; 51: 50–55.\n\nWei K, et al.: Quantification of myocardial blood flow with ultrasound-induced destruction of microbubbles administered as a constant venous infusion. Circulation. 1998; 97(5): 473–483. PubMed Abstract | Publisher Full Text\n\nAverkiou MA, et al.: Imaging methods for ultrasound contrast agents. Ultrasound Med Biol. 2020; 46(3): 498–517. Publisher Full Text\n\nAlbrecht T, et al.: Improved detection of hepatic metastases with pulse-inversion US during the liver-specific phase of SHU 508A: multicenter study. Radiology. 2003; 227(2): 361–370. PubMed Abstract | Publisher Full Text\n\nAppis AW, et al.: Update on the safety and efficacy of commercial ultrasound contrast agents in cardiac applications. Echo Res Pract. 2015; 2(2): R55–R62. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu Y-Z, et al.: Ultrasound microbubble contrast agents: application to therapy for peripheral vascular disease. Adv Ther. 2009; 26: 425–434. PubMed Abstract | Publisher Full Text\n\nAlbrecht T, et al.: Comparison of bolus and infusion of the ultrasound contrast media levovist for color doppler ultrasound of renal arteries. Rofo. 2000; 172(10): 824–829. PubMed Abstract | Publisher Full Text\n\nPorter TR, et al.: Guidelines for the cardiac sonographer in the performance of contrast echocardiography: a focused update from the American Society of Echocardiography. J Am Soc Echocardiogr. 2014; 27(8): 797–810. PubMed Abstract | Publisher Full Text\n\nArning C, et al.: Revision of DEGUM ultrasound criteria for grading internal carotid artery stenoses and transfer to NASCET measurement. Ultraschall Med. 2010; 31(3): 251–257. Publisher Full Text\n\nUdesen J, et al.: Examples of in vivo blood vector velocity estimation. Ultrasound Med Biol. 2007; 33(4): 541–548. PubMed Abstract | Publisher Full Text\n\nThalhammer C, et al.: Colour-coded duplex sonography after renal transplantation. Ultraschall Med. 2007; 28(1): 6–27. quiz 25. Publisher Full Text\n\nParikh S, Shah R, Kapoor P: Portal vein thrombosis. Am J Med. 2010; 123(2): 111–119. Publisher Full Text\n\nBaik SKJLI: Haemodynamic evaluation by Doppler ultrasonography in patients with portal hypertension: a review. Liver Int. 2010; 30(10): 1403–1413. Publisher Full Text\n\nWhittingham TA: Medical diagnostic applications and sources. Prog Biophys Mol Biol. 2007; 93(1-3): 84–110. Publisher Full Text\n\nAlbrecht T, et al.: Stimulated acoustic emissions with the ultrasound contrast medium levovist: a clinically useful contrast effect with liver-specific properties. Rofo. 2000; 172(1): 61–67. PubMed Abstract | Publisher Full Text\n\nDietrich CF, et al.: Improved differentiation of pancreatic tumors using contrast-enhanced endoscopic ultrasound. Clin Gastroenterol Hepatol. 2008; 6(5): 590–597.e1. Publisher Full Text\n\nZhang X, et al.: Real-time feedback of histotripsy thrombolysis using bubble-induced color Doppler. Ultrasound Med Biol. 2015; 41(5): 1386–1401. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEvans DH, Jensen JA, Nielsen MB: Ultrasonic colour Doppler imaging. Interface Focus. 2011; 1(4): 490–502. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPaefgen V, Doleschel D, Kiessling F: Evolution of contrast agents for ultrasound imaging and ultrasound-mediated drug delivery. Front Pharmacol. 2015; 6: 197. Publisher Full Text\n\nLeong-Poi H, et al.: Influence of microbubble shell properties on ultrasound signal: Implications for low-power perfusion imaging. J Am Soc Echocardiogr. 2002; 15(10): 1269–1276. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "248551",
"date": "05 Mar 2024",
"name": "Hamad Yahia Abu Mhanna",
"expertise": [
"Reviewer Expertise Medical Imaging"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMinor comments:\n\nThe title is accurately representing the content of the article. Kindly make the contribution of this review clearer in the abstract section. In the abstract section, please rephrase most of the sentences using academic language. The introduction part is written in a thorough and complete manner. However, in the second paragraph, this is a run on sentence and hard to follow. “Throughout the past few decades, ultrasound imaging’s diagnostic uses have greatly increased. The development of UCM has led to the provision of new useful physiologic and pathologic data, and the availability of perfusion imaging of cardiac or tumor tissue for everyday clinical decision-making.” Recommend breaking it up for clarity. The caption of Figure (1) is too long and make the reader confused. Please rewrite it again in a brief way. Some of grammatical errors in the conclusion section need correction. Number of references is enough for this manuscript. Good Make sure that all sentences are linked together and all values in this study are true.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "11220",
"date": "04 Apr 2024",
"name": "Ammar A. Oglat",
"role": "Author Response",
"response": "Responses to Reviewer’s Comments Title: A review of ultrasound contrast media Dear Editor-in-Chief, The author sincerely appreciates the reviewers’ technical comments and the useful suggestions offered to us to revise our manuscript. My response to reviewers’ comments point by point are listed hereafter. Comments from Reviewer #1: The title is accurately representing the content of the article. Answer: Esteemed reviewer, Thank you for your helpful comments. Yes, I tried to make the title comprehensive to cover all the manuscript content. Kindly make the contribution of this review clearer in the abstract section. Answer: The mentioned comment is corrected. The whole abstract is modified and the contribution of this review is simplify and clarify. In the abstract section, please rephrase most of the sentences using academic language. Answer: The abstract section is modified and rephrased to be in a good scientific manner. The introduction part is written in a thorough and complete manner. However, in the second paragraph, this is a run on sentence and hard to follow. “Throughout the past few decades, ultrasound imaging’s diagnostic uses have greatly increased. The development of UCM has led to the provision of new useful physiologic and pathologic data, and the availability of perfusion imaging of cardiac or tumor tissue for everyday clinical decision-making.” Recommend breaking it up for clarity. Answer: Noted and done. The caption of Figure (1) is too long and make the reader confused. Please rewrite it again in a brief way. Answer: Yes. The caption is modified and shortened. Some of grammatical errors in the conclusion section need correction. Answer: Ok. Noted and the conclusion is edited. Number of references is enough for this manuscript. Good Answer: Thank you very much for your valuable comments and scientific support. Make sure that all sentences are linked together and all values in this study are true. Answer: I made a double check if all values in the manuscript again and there is no any error or mistake. Dear Respected reviewer. Thank you very much for your valuable comments which enhance the manuscript with scientific information. Appreciate"
}
]
}
] | 1
|
https://f1000research.com/articles/12-1444
|
https://f1000research.com/articles/12-423/v1
|
20 Apr 23
|
{
"type": "Brief Report",
"title": "Reliability of ankle dorsiflexor muscle strength, rate of force development, and tibialis anterior electromyography after stroke",
"authors": [
"Sharon Olsen",
"Denise Taylor",
"Imran Khan Niazi",
"Grant Mawston",
"Usman Rashid",
"Gemma Alder",
"Verna Stavric",
"Rasmus Bach Nedergaard",
"Nada Signal",
"Denise Taylor",
"Imran Khan Niazi",
"Grant Mawston",
"Usman Rashid",
"Gemma Alder",
"Verna Stavric",
"Rasmus Bach Nedergaard",
"Nada Signal"
],
"abstract": "Background: Measures of hemiparetic ankle dorsiflexor muscle strength and rate of force development (RFD) are often used to determine the efficacy of rehabilitation interventions after stroke. However, evidence supporting the reliability of these measures is limited. This brief report provides a secondary analysis investigating the between-session reliability of isometric ankle dorsiflexor muscle strength, rate of force development (RFD), and tibialis anterior electromyography (TA EMG), in people with chronic stroke. Method: Participants (n=15) completed three maximal isometric contractions of the ankle dorsiflexor muscles as fast as possible using a rigid dynamometer. Tests were repeated seven days later. Outcomes included ankle dorsiflexor isometric maximal voluntary contraction (MVC), RFD in the first 200ms (RFD200ms), time to reach 90% MVC, and peak TA EMG. Data were analysed for 13 participants using intra-class correlation coefficients (ICC) and standard error of the measure (SEM). Results: When the mean of three trials was analysed, there was excellent reliability for isometric dorsiflexor MVC (ICC 0.97 [95% CI 0.92-0.99]), moderate reliability for TA EMG (ICC 0.86 [0.60-0.96]) and time to reach 90% MVC (ICC 0.8 [0.53-0.93]) and poor reliability for dorsiflexor RFD200ms (ICC 0.79 [0.48-0.92]). Conclusion: Given the functional significance of the ankle dorsiflexors, future research should investigate more reliable methods for measuring rapid force production in the dorsiflexor muscles after stroke.",
"keywords": [
"muscle strength",
"maximal voluntary contraction",
"muscle power",
"rate of force development",
"electromyogram",
"outcome measure",
"reliability",
"stroke"
],
"content": "Introduction\n\nAnkle dorsiflexor impairments are common after stroke1 affecting both muscle strength, the force exerted during a single maximal effort, and muscle power, the ability to exert force over a short time.2 Impaired strength of the hemiparetic dorsiflexor muscles is associated with reduced walking endurance,3 walking speed,4 and functional mobility.1 Impaired dorsiflexor muscle power or rapid force production may limit the ability to react quickly during perturbations5,6 and contribute to falling.7 Measures of dorsiflexor strength, power, and rate of force development (RFD), are commonly used to determine the efficacy of rehabilitation interventions8,9 and thus, their reliability should be considered.\n\nMuscle strength can be measured isokinetically or isometrically through a maximal voluntary contraction (MVC) using rigid gold-standard dynamometry.10,11 Between-session reliability of isokinetic dorsiflexor MVCs in the hemiparetic limb ranges from moderate to excellent with ICCs ranging from 0.84 [95% CI (confidence interval) 0.52 to 0.96]12 to 0.98.13 However, isokinetic testing requires the ability to dorsiflex through full range at a given speed, thus excluding those with more severe stroke who are unable to do so.14 Isometric dorsiflexor MVCs, tested with rigid dynamometry, can be recorded in people with more severe hemiparesis, but have demonstrated only moderate between-session reliability (ICC 0.71).15 Alongside dorsiflexor MVC measures, it is common to concurrently record surface electromyography (EMG) of the tibialis anterior (TA) as a measure of motor unit activity. While TA EMG peak amplitude has been shown to be highly reliable in healthy adults within a session,16 it’s between-session reliability after stroke is only moderate (ICC 0.67).15\n\nRapid force production and muscle power in the hemiparetic limb has been measured using several outcomes6,17–19 including the RFD. The between-session reliability of dorsiflexor peak RFD measured with hand-held dynamometry (HHD) was good (ICC 0.92, 95% CI 0.83 to 0.96)20 in people with stroke who could walk unaided. However, this HHD method had poor concurrent validity against gold-standard dynamometry,21 suggesting the reliability of RFD should be assessed using a rigid dynamometry system.\n\nTo address these limitations, this brief report will provide a reliability analysis that was performed on a dataset from an experimental study, where baseline measures of ankle dorsiflexor strength and RFD were collected twice, seven days apart.9 This analysis aimed to determine the between-session reliability of isometric ankle dorsiflexor MVC, ankle dorsiflexor muscle RFD in the first 200ms (RFD200ms), time to reach 90% peak force, and TA EMG, in people with chronic stroke.\n\n\nMethods\n\nThis observational study utilised baseline measurement data that had been collected in an experimental study.9 Baseline measures were collected on two occasions, seven days apart.\n\nThe study was conducted in a research laboratory at the Auckland University of Technology, Auckland, New Zealand.\n\nThe 15 participants were adults, more than 6 months post stroke, with hemiparesis affecting ankle dorsiflexion. The sample size was based on that required for the broader experimental study.9 Exclusion criteria were significant cognitive/perceptual/communication deficits, cerebellar stroke, absent ankle dorsiflexor force, or medical conditions that would impact safety or protocol completion.9 Written informed consent, ethical approval (Health and Disability Ethics Committees 17/NTB/80), and trial registration were completed (ACTRN12617000838314).\n\nThe measurement outcomes were: isometric ankle dorsiflexor peak MVC, ankle dorsiflexor muscle RFD in the first 200ms (RFD200ms), time to reach 90% MVC (Time to 90% MVC), and peak TA EMG.\n\nDetailed procedures have been published elsewhere.9,22 Participants sat with their hemiparetic leg in a rigid purpose-built ankle dorsiflexion/plantarflexion dynamometer with the foot plate angled 25° into plantarflexion, knee flexion ≈50°, straps/guards at the hips, knee, ankle, metatarsals and toes,23 and EMG electrodes over the TA muscle in accordance with SENIAM guidelines (seniam.org). Following two submaximal practices, participants performed three 4-5 second isometric dorsiflexor MVCs (2 minutes between each). Participants were instructed to “pull as fast and hard as possible” and received loud verbal encouragement and real-time visual feedback. Force signals were amplified (×200, 500, or 1000 depending on amplitude) (Forza, OT Bioelettronica, Italy). EMG data was amplified (×500) (AMT-8, Bortec Biomedical, Canada). Force and EMG data were sampled at 1961Hz using a data acquisition board (Micro 1401, CED, UK) and Spike2 software (CED, UK). Procedures were replicated for the second session.\n\nMVC amplitudes15 were calculated as the difference between the mean baseline signal (500ms window) and the peak amplitude, in Spike2 software (CED, UK). For other measures, data was exported into LabVIEW 2017 software (National Instruments, United States) and the force data was filtered using a zero-phase shift 15 Hz low-pass 4th order filter.21,24 Movement onset was automatically identified where the signal exceeded the mean baseline signal by 3 SDs, and then confirmed visually. The baseline window and the onset threshold could be individualised to ensure the onset was identified correctly for each contraction. RFD200ms24,25 was determined by dividing force at 200ms by time. Time taken to reach 90% of peak force was also determined.18,26 TA EMG data was band-pass filtered (10–500 Hz). The root mean square (RMS) of the EMG signal was calculated 1-s either side of the peak force, and peak amplitude16 of the RMS signal was determined. All measures were calculated for each of the three contractions, then exported into Microsoft Excel (version 16.35, Microsoft Corporation, US) where the mean of three trials and the best of three trials were calculated.\n\nData were imported into R for reliability analysis (R version 4.1.127). Data normality was evaluated with the Shapiro-Wilk test. The intra-class correlation coefficient (ICC (2, 1), absolute agreement) from a 2-way random effects model was calculated, as were the standard error of measurement (SEM) and the SEM%. Correlation coefficients were interpreted as excellent (≥ 0.90), good (0.75–0.89), moderate (0.50–0.74) and poor (<0.50) based on their lower bound 95% CIs.28\n\n\nResults\n\nData for two participants were excluded due to failure to correctly complete the protocol. Therefore, the analysis included 13 participants (male n=6, mean age 68.5±10.6 years, mean 6.0±5.4 years post-stroke, left hemiparesis n=10). EMG data was missing for one further participant. Participants presented with a range of lower limb weakness.\n\nThe reliability analysis is reported in Table 1. MVC measures were the most reliable, with the mean of three trials displaying higher reliability than the best of three trials. TA EMG data demonstrated moderate reliability. For measures of rapid force production, when using the mean of three trials, the Time to 90% MVC had moderate reliability and RFD200ms had poor reliability; both measures demonstrated very low lower-bound CIs when only the best trial was analysed (Table 1).\n\n\nDiscussion\n\nThis is the first study to show excellent between-session reliability of isometric (rather than isokinetic) dorsiflexor MVCs in people with stroke (MVCMEAN ICC 0.97, 95% CI 0.92 to 0.99). Our results were comparable with those of Eng et al.13 using an isokinetic MVC. Importantly, the isometric method proposed here can be applied to people with more severe lower limb weakness. Our MVC reliability results were superior to the isometric MVC results of Klarner and colleagues who found moderate between-session reliability for hemiparetic dorsiflexor MVCs over three sessions (ICC 0.71).15 They analysed the best of only two trials, rather than the three trials used in this study, and did not describe any system to strap the toes as recommended to reduce measurement variability23; this may have lowered their ICC. Our reliability findings for TA EMG, which represent motor unit recruitment at the peak of the MVC, demonstrated only moderate reliability (TA EMGMEAN ICC 0.86, 95% CI 0.60 to 0.96), suggesting that EMG is prone to greater biological and/or measurement variability than force measures. As with the MVC data, our TA EMG data appeared more reliable than that previously reported (ICC 0.67).15\n\nThis study is also the first to report on the reliability of RFD or rapid force production of the hemiparetic dorsiflexor muscles using a rigid dynamometer. The ICCs were deemed moderate for Time to 90% MVCMEAN (ICC 0.80, 95% CI 0.53 to 0.93) and poor for RFD200msMEAN (ICC 0.79, 95% CI 0.48 to 0.92). These findings were inferior to those of Mentiplay and colleagues who used HHD to measure hemiparetic dorsiflexor RFD (ICC 0.92, 95% CI 0.83 to 0.96, n=28).20 Several factors may have contributed to these contrasting findings. Mentiplay et al’s participants could walk unaided, whereas our sample had variable lower limb impairment; they also measured the ankle in neutral,20 whereas we positioned the ankle in ≈25° plantarflexion based on the optimum position for producing dorsiflexion force29 and reducing the impact of antagonist muscle tone.24 Data processing methods also differed between the studies. Mentiplay and colleagues HHD method sampled force data at only 40 Hz,20,21 much lower than recommended,24,30 and then interpolated this to equate 1000 Hz, which may have increased reliability. Our study analysed RFD in the first 200ms, whereas Mentiplay et al.20 scanned successive 200ms windows to find the peak RFD, a method that excludes movement onset and any associated artefacts or issues with identifying onset.21 This very early force generation is particularly relevant for people with stroke who have lower motor unit discharge rates6,31 and may be more functionally important than maximal muscle strength or power, especially under circumstances where a rapid response is required (e.g., to prevent falling).32 Thus, while measuring RFD later in the movement may be more reliable,20,21 this measure lacks ecological validity. This concern is supported by the poor concurrent validity of the HHD RFD method against gold-standard dynamometry.21 Given our findings, further research is needed to explore more reliable methods for measuring hemiparetic RFD and muscle power that better account for sources of biological and measurement tool variability.\n\n\nConclusions\n\nThis analysis demonstrated excellent between-session reliability for hemiparetic dorsiflexor isometric MVC and moderate reliability for hemiparetic TA EMG. Dorsiflexor muscle RFD measures had poor to moderate reliability. Future research should investigate more reliable tools for measuring hemiparetic dorsiflexor muscle RFD and muscle power. Given the significance of dorsiflexor muscle function to lower limb recovery after stroke, it is vital this aspect of muscle function is better understood to enable more targeted rehabilitation.\n\nThe study was conducted in accordance with the Declaration of Helsinki, and approved by the Health and Disability Ethics Committees (17/NTB/80).",
"appendix": "Data availability\n\nEthical approval for data sharing has not been obtained. Requests for access to the data can be made to the corresponding author by providing the reason for the request and the benefits of data sharing, so that ethical approval can be sought.\n\n\nReferences\n\nNg SS, Hui-Chan CW: Ankle dorsiflexor, not plantarflexor strength, predicts the functional mobility of people with spastic hemiplegia. J. Rehabil. Med. 2013; 45: 541–545. Publisher Full Text\n\nBushman BA: Embracing Physical Activity: A Complete Exercise Program. ACSM's Complete Guide to Fitness & Health. 2nd ed.Bushman BA, editor. Human Kinetics: Champaign, Illinois; 2017; pp. 19–36.\n\nNg SS, Hui-Chan CW: Contribution of ankle dorsiflexor strength to walking endurance in people with spastic hemiplegia after stroke. Arch. Phys. Med. Rehabil. 2012; 93: 1046–1051. 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Brain Res. 2006; 171: 459–468. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSimpson D, Ehrensberger M, Horgan F, et al.: Unilateral dorsiflexor strengthening with mirror therapy to improve motor function after stroke: A pilot randomized study. Physiother. Res. Int. 2019; 24: e1792. PubMed Abstract | Publisher Full Text\n\nOlsen S, Signal N, Niazi IK, et al.: Peripheral electrical stimulation paired with movement-related cortical potentials improves isometric muscle strength and voluntary activation following stroke. Front. Hum. Neurosci. 2020; 14: 156. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStark T, Walker B, Phillips JK, et al.: Hand-held dynamometry correlation with the gold standard isokinetic dynamometry: a systematic review. PM&R. 2011; 3: 472–479. PubMed Abstract | Publisher Full Text\n\nHirano M, Katoh M, Gomi M, et al.: Validity and reliability of isometric knee extension muscle strength measurements using a belt-stabilized hand-held dynamometer: a comparison with the measurement using an isokinetic dynamometer in a sitting posture. J. Phys. Ther. Sci. 2020; 32: 120–124. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPohl PS, Startzell JK, Duncan PW, et al.: Reliability of lower extremity isokinetic strength testing in adults with stroke. Clin. Rehabil. 2000; 14: 601–607. PubMed Abstract | Publisher Full Text\n\nEng JJ, Kim CM, MacIntyre DL: Reliability of lower extremity strength measures in persons with chronic stroke. Arch. Phys. Med. Rehabil. 2002; 83: 322–328. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBohannon RW: Isokinetic testing of muscle strength of older individuals post-stroke: An integrative review. Isokinet. Exerc. Sci. 2020; 28: 303–316. Publisher Full Text\n\nKlarner T, Barss TS, Sun Y, et al.: Reliability of multiple baseline measures for locomotor retraining after stroke. Replace, Repair, Restore, Relieve: Bridging Clinical and Engineering Solutions in Neurorehabilitation. Proceedings of the 2nd International Conference on NeuroRehabilitation. Jensen W, Andersen OK, Akay M, editors. Aalborg, Denmark: Springer; 2014; pp. 479–486.\n\nRuiz Munoz M, Gonzalez-Sanchez M, Cuesta-Vargas AI: Tibialis anterior analysis from functional and architectural perspective during isometric foot dorsiflexion: A cross-sectional study of repeated measures. J. Foot Ankle Res. 2015; 8: 74. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFimland MS, Moen PM, Hill T, et al.: Neuromuscular performance of paretic versus non-paretic plantar flexors after stroke. Eur. J. Appl. Physiol. 2011; 111: 3041–3049. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCanning CG, Ada L, O’Dwyer N: Slowness to develop force contributes to weakness after stroke. Arch. Phys. Med. Rehabil. 1999; 80: 66–70. PubMed Abstract | Publisher Full Text\n\nStavric VA, McNair PJ: Optimizing muscle power after stroke: a cross-sectional study. J. Neuroeng. Rehabil. 2012; 9: 67. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMentiplay BF, Tan D, Williams G, et al.: Assessment of isometric muscle strength and rate of torque development with hand-held dynamometry: Test-retest reliability and relationship with gait velocity after stroke. J. Biomech. 2018; 75: 171–175. PubMed Abstract | Publisher Full Text\n\nMentiplay BF, Perraton LG, Bower KJ, et al.: Assessment of lower limb muscle strength and power using hand-held and fixed dynamometry: a reliability and validity study. PLoS One. 2015; 10: e0140822. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOlsen S, Signal N, Niazi IK, et al.: Reliability of tibialis anterior muscle voluntary activation using the interpolated twitch technique and the central activation ratio in people with stroke. Brain Sci. 2021; 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSiddiqi A, Arjunan SP, Kumar D: Improvement of isometric dorsiflexion protocol for assessment of tibialis anterior muscle strength. MethodsX. 2015; 2: 107–111. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaffiuletti NA, Aagaard P, Blazevich AJ, et al.: Rate of force development: Physiological and methodological considerations. Eur. J. Appl. Physiol. 2016; 116: 1091–1116. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPrieske O, Wick D, Granacher U: Intrasession and intersession reliability in maximal and explosive isometric torque production of the elbow flexors. J. Strength Cond. Res. 2014; 28: 1771–1777. PubMed Abstract | Publisher Full Text\n\nViitasalo JT, Komi PV: Force-time characteristics and fiber composition in human leg extensor muscles. Eur. J. Appl. Physiol. 1978; 40: 7–15. PubMed Abstract | Publisher Full Text\n\nR Core Team: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2018. Reference Source\n\nKoo TK, Li MY: A guideline of selecting and reporting intraclass correlation coefficients for reliability research. J. Chiropr. Med. 2016; 15: 155–163. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarsh E, Sale D, Mcomas AJ, et al.: Influence of joint position on ankle dorsiflexion in humans. J. Appl. Physiol. Respir. Environ. Exerc. Physiol. 1981; 51: 160–167. Publisher Full Text\n\nKozinc Ž, Smajla D, Šarabon N: The rate of force development scaling factor: a review of underlying factors, assessment methods and potential for practical applications. Eur. J. Appl. Physiol. 2022; 122: 861–873. PubMed Abstract | Publisher Full Text\n\nFreire B, Dias CP, Oliveira LS, et al.: Rate of force development and torque production assessment in spastic stroke survivors. Revista Brasileira de Cineantropometria e Desempenho Humano. 2015; 17: 328. Publisher Full Text\n\nSuetta C, Aagaard P, Rosted A, et al.: Training-induced changes in muscle CSA, muscle strength, EMG, and rate of force development in elderly subjects after long-term unilateral disuse. J. Appl. Physiol. 2004; 97: 1954–1961. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "191140",
"date": "11 Aug 2023",
"name": "George Koumantakis",
"expertise": [
"Reviewer Expertise Reliability",
"validity",
"questionnaires",
"musculoskeletal",
"physiotherapy",
"physical therapy",
"rehabilitation",
"EMG",
"functional assessment"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well-conducted test-retest reliability study. The authors know the correct statistical methods to report such a study. Minor issues are present, and these are highlighted to improve this work.\nThe authors should mention in their Abstract the respective SEM values as well.\nThe authors correctly make adequate links to the clinical utility of this study, as strength and rate of force development in the ankle dorsiflexors form part of participants’ gait improvement post-stroke.\nUnder ‘Participants’, the sample size (n=15), which eventually was n=13, is not adequately explained. Koo & Li (2016), pg. 158, suggest a sample of n=30 as adequate for a reliability study. The best you can do is add this to the limitations of your study.\nIt is unclear how many raters were in this study; please clarify.\nCorrect the characterization of ICCs, based not only on the lower limit of the ICC 95% CI but on the whole range of the CI, as suggested by Koo and Li (2016), pg. 161. Please correct throughout.\nThe EMG acquisition and analysis are correctly reported.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11644",
"date": "29 Aug 2024",
"name": "Sharon Olsen",
"role": "Author Response",
"response": "1.1 This is a well-conducted test-retest reliability study. The authors know the correct statistical methods to report such a study. Minor issues are present, and these are highlighted to improve this work Response: Thank you for your encouraging feedback. 1.2 The authors should mention in their Abstract the respective SEM values as well. Response: Thank you for this suggestion. We have added the SEM% values to the abstract results below. Abstract results: “Reliability was higher when analysing the mean of three trials rather than the best of three trials. There was excellent reliability for isometric dorsiflexor MVC (ICC 0.97 [95% CI 0.92, 0.99], SEM% 7%). However, for other outcomes, while the ICC indicated good reliability, the lower bound of the 95% confidence interval of the ICC fell in the moderate range for TA EMG (ICC 0.86 [95% CI 0.60, 0.96], SEM% 25%) and time to reach 90% MVC (ICC 0.8 [95% CI 0.53, 0.93], SEM% 23%) and in the poor range for dorsiflexor RFD200ms (ICC 0.79 [95% CI 0.48, 0.92], SEM% 24%).” 1.3 The authors correctly make adequate links to the clinical utility of this study, as strength and rate of force development in the ankle dorsiflexors form part of participants’ gait improvement post-stroke. Response: Thank you for this encouraging feedback. 1.4 Under ‘Participants’, the sample size (n=15), which eventually was n=13, is not adequately explained. Koo & Li (2016), pg. 158, suggest a sample of n=30 as adequate for a reliability study. The best you can do is add this to the limitations of your study. Response: Thank you for raising this concern. While other reliability studies in this field of stroke research have been conducted with similarly small samples (Eng et al., 2002; Klarner et al., 2014; Pohl et al., 2000), we agree that there is a risk of being underpowered. Therefore, we have amended the manuscript and discussed the sample size in the new limitations section copied below and made recommendations for further research in a larger sample. Strengths and limitations: Line 302 …\"The key limitation in this study was the sample size, which was below the n=30 recommended for reliability studies 28 but comparable with other studies in this field. 12, 13, 15 To address this limitation, we have been cautious with our interpretation of results, and considered both the ICC and its lower bound 95% CI (Koo & Li, 2016; Munro, 2005) and have provided SEMs to enable comparisons with other literature. However, due to this limitation, it is recommended that the findings generated in this study are confirmed with further research in a larger sample.” In addition, we have also provided sample sizes of other research in the discussion to aid in the interpretation. Line 262 \"... Our MVC reliability results were superior to the isometric MVC results of Klarner and colleagues who found moderate between-session reliability (ICC 0.71) for hemiparetic dorsiflexor MVCs over three sessions, with a similar sample size (n=12). 15 \" Line 267 \"...as with the MVC data, our TA EMG data appeared more reliable than that previously reported (ICC 0.67) in sample of 12 people with chronic stroke. 15 ” Furthermore, we have provided further explanation about the 2 dropouts in the results section. Line 156 \"Data for two participants were excluded due to failure to correctly complete the protocol; this was because one participant was not able to consistently follow the task instructions and another participant was observed falling asleep during the protocol.” In addition to these amendments related to the sample size and study power, we have revised our approach to the interpretation of the ICCs to take a more conservative approach – these amendments are detailed in question 1.6 which raised the issue of ICC interpretation. Please see 1.6. 1.5 It is unclear how many raters were in this study; please clarify. Response: Thank you for raising this question. This paper investigates between-session reliability, rather than inter-rater reliability. The aim of the paper is stated at the end of the introduction. “This analysis aimed to determine the between-session reliability of isometric ankle dorsiflexor MVC, ankle dorsiflexor muscle RFD in the first 200ms (RFD200ms), time to reach 90% peak force, and TA EMG, in people with chronic stroke.” In response to your question, we have clarified in the manuscript that the same researcher provided verbal instructions at the two measurement sessions, and that the visual inspection of data was completed by a single researcher. Line 119 “Participants were instructed to “pull as fast and hard as possible” and received loud verbal encouragement and real-time visual feedback. Instructions were provided by the same researcher at both sessions.” Line 131 “Movement onset was automatically identified where the signal exceeded the mean baseline signal by 3 SDs, and then confirmed visually by a single researcher. The baseline window and the onset threshold could be individualised by the researcher to ensure the onset was identified correctly for each contraction.” 1.6 Correct the characterization of ICCs, based not only on the lower limit of the ICC 95% CI but on the whole range of the CI, as suggested by Koo and Li (2016), pg. 161. Please correct throughout. Response: Thank you for raising this. We had chosen to interpret ICCs based on the lower bound of the 95% CI as a conservative approach which considers the sample is not a random sample of the population (Munro, 2005). However, given our sample was small (which we have discussed in 1.4 above), we agree that the full range should be considered and have amended the manuscript to take a more conservative approach to interpretation of the findings and clarified when we are interpreting the ICC or its lower bound 95% confidence interval. Relevant amendments to the abstract, discussion and conclusion are copied below. Abstract “Results: …There was excellent reliability for isometric dorsiflexor MVC (ICC 0.97 [95% CI 0.92-0.99], SEM% 7%). However, for other outcomes, while the ICC indicated good reliability, the lower bound of the 95% confidence interval of the ICC fell in the moderate range for TA EMG (ICC 0.86 [95% CI 0.60-0.96], SEM% 25%) and time to reach 90% MVC (ICC 0.8 [95% CI 0.53-0.93], SEM% 23%) and in the poor range for dorsiflexor RFD200ms (ICC 0.79 [95% CI 0.48-0.92], SEM% 24%). Conclusion: The findings raise concerns about the reliability of measures of rapid force production in the dorsiflexor muscles after stroke. Given the functional significance of the ankle dorsiflexors, larger studies should be conducted to further investigate these concerns and explore reliable methods for measuring rapid force production in the hemiparetic dorsiflexor muscles.” Results - Reliability analysis The reliability analysis is reported in Table 1. MVC measures demonstrated excellent reliability, with the mean of three trials displaying slightly higher reliability (ICC 0.97 [95% CI 0.92, 0.99]) than the best of three trials (ICC 0.97 [95% CI 0.90, 0.99]). For TA EMG data, the ICCs were in the good range but the lower bound 95% CIs were in the moderate range (ICC 0.86 [95% CI 0.60, 0.06]). For measures of rapid force production, when using the mean of three trials, the Time to 90% MVC and RFD200ms had ICCs in the good range, but the lower bound 95% CIs were in the moderate range for Time to 90% MVC (ICC 0.80 [95% CI 0.53, 0.93]) and in the poor range for RFD200ms (ICC 0.0.79 [95% CI 0.48, 0.92]). Both measures of rapid force production demonstrated very low lower-bound CIs when only the best trial was analysed (Table 1). Please note we have removed the interpretation column in Table 1, and instead provided this in the text to enable interpretation of both the ICC and its confidence interval. Discussion Line 267 “…Our reliability findings for TA EMG, which represent motor unit recruitment at the peak of the MVC, demonstrated lower reliability, with a good ICC and the lower bound 95% CI in the moderate range (TA EMG MEAN ICC 0.86 [95% CI 0.60, 0.96). Alongside an SEM% of 23-25%, this suggests that TA EMG is prone to greater biological and/or measurement variability than peak force measures.” Line 274 “…This study is also the first to report on the reliability of RFD or rapid force production of the hemiparetic dorsiflexor muscles using a rigid dynamometer. While the ICCs were in the good range when three trials were analysed, the lower bound of the 95% CI of the ICCs indicated reliability could be only moderate for Time to 90% MVC MEAN (ICC 0.80 [95% CI 0.53, 0.93]) and poor for RFD200ms MEAN (ICC 0.79 [95% CI 0.48, 0.92]).” Line 296 “Given our findings, further research is needed to investigate these concerns about the reliability of rapid force production measures in the hemiparetic dorsiflexor muscles. This research should explore alternative methods for data collection and processing (Maffiuletti et al., 2016) and seek to identify reliable methods for measuring hemiparetic RFD and muscle power that better account for sources of biological and measurement tool variability.” Conclusions “This analysis demonstrated excellent between-session reliability for hemiparetic dorsiflexor isometric MVCs. However, other measures of EMG and rapid force production were less reliable, with ICC 95% confidence intervals extending to the poor to moderate range, and SEM percentages between 23-25%. These findings, which utilise gold-standard dynamometry, raise concerns about the reliability of measures of rapid force production in the hemiparetic dorsiflexors muscles. Further research is required to examine reliability in a large sample of people stroke. In the meantime, researchers and clinicians should be cautious when interpreting rapid force production measures of the dorsiflexor muscles when determining the efficacy of stroke rehabilitation interventions. Given the significance of dorsiflexor muscle function to lower limb recovery after stroke, future research should investigate reliable tools for measuring hemiparetic dorsiflexor muscle RFD and muscle power. This will facilitate a greater understanding this aspect of muscle function and enable more targeted rehabilitation.” 1.7 The EMG acquisition and analysis are correctly reported. Response: Thank you. 1.8 Are the conclusions drawn adequately supported by the results? Partly Response: Thank you for indicating this. We have amended our conclusion with a more cautious approach to interpretation and based on Reviewer 2’s feedback, we have added implications for researchers and clinicians. The conclusions have been copied above in 1.6."
}
]
},
{
"id": "202687",
"date": "18 Sep 2023",
"name": "Vasilios Panoutsakopoulos",
"expertise": [
"Reviewer Expertise sports biomechanics",
"force measurements",
"range of motion measurements",
"aquatic therapy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe submitted manuscript comprises a test-retest reliability study. There are some topics that need to be addressed.\nGeneral comments:\nAddress the comments mentioned by Reviewer 1 (George Koumantakis).\n\nIt is recommended to provide, where appropriate, up-to-date references; only a quarter (8/32) of the cited literature was published in the last 5 years.\n\nState the hypothesis of the study.\n\nStudy Design: it would be of interest to provide results of the unaffected lower limb for comparison.\n\nCalculation of RFD200ms: what is the rationale to extract this parameter as the force at the time-instant 200 ms after the onset divided by 200? Could the time derivative of the force data provide an alternative insight regarding the RFD?\n\nFurther elaboration of the neuromuscular mechanisms tested in the study could provide additional context in the Discussion.\n\nProvide the strengths and the limitations of the study.\n\nThe conclusions partly replicate the final part of the Discussion. It is suggested to include recommendations for practical use.\n\nSpecific comments:\nIntroduction:\n“the ability to exert force over a short time”: this is the definition of power; it is proposed to delete this phrase.\n\n“Muscle strength can be measured isokinetically or isometrically”: Clarification is needed.\n\nMaterials and Methods:\nParticipants: elaborate on the inclusion criteria.\n\nMeasurement procedures: specify the duration of the 4-5 s isometric dorsiflexor MVCs.\n\nResults:\nTable 1: it is suggested to use subscript rather than superscript characters.\n\nDiscussion:\nSee the respective General Comments.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11646",
"date": "29 Aug 2024",
"name": "Sharon Olsen",
"role": "Author Response",
"response": "2.1 Address the comments mentioned by Reviewer 1 (George Koumantakis). Response: We have addressed Reviewer 1’s comments. 2.2 It is recommended to provide, where appropriate, up-to-date references; only a quarter (8/32) of the cited literature was published in the last 5 years. Response: Thank you for suggesting we review our reference list. We have reviewed the references and amended the manuscript to include some additional references and recent systematic reviews (Azzollini et al., 2021; Chamorro et al., 2017; Dorsch et al., 2021; Kwong et al., 2017; Lomborg et al., 2022; Mentiplay et al., 2015; Mentiplay et al., 2019; Noguchi et al., 2023). Whilst many references in the manuscript are older than 5 years, all references are relevant and representative of the small body of literature in this field. Such references are essential to our understanding of tibialis anterior muscle structure and function in healthy adults (Marsh et al., 1981; Ruiz Munoz et al., 2015; Siddiqi et al., 2015) and stroke populations (Fimland et al., 2011; Freire et al., 2015), and provide a review of previous studies investigating the reliability of hemiparetic muscle strength and rapid force production which began in the early 2000s (Eng et al., 2002; Pohl et al., 2000) and has not grown much since (Klarner et al., 2014; Mentiplay et al., 2018). 2.3 State the hypothesis of the study. Response: We have added the null hypothesis on line 95. “The null hypothesis was that the outcome measures are not reliable (intra-class correlation coefficient (ICC) < 0.5).” 2.4 Study Design: it would be of interest to provide results of the unaffected lower limb for comparison. Response: We agree this would be helpful. However, due to the time already allocation to complete the experimental protocol and the burden it put on people with chronic stroke, it was not deemed feasible to collect data for the unaffected limb in this clinical population. 2.5 Calculation of RFD200ms: what is the rationale to extract this parameter as the force at the time-instant 200 ms after the onset divided by 200? Could the time derivative of the force data provide an alternative insight regarding the RFD? Response: In response to the reviewer's query on the rationale for calculating RFD200ms, we chose this method to assess the initial burst of force generation capability, which is crucial for many functional movements in stroke survivors. We also investigated Time to 90% MVC. Both methods offer a straightforward comparison of early force development. Regarding the suggestion to use the time derivative of the force data as an alternative method. Calculating the time derivative of the force/time curve would provide information about the peak RFD in the early part of the contraction. However, peak RFD in small epochs is sensitive to unsystematic variations in the signal and provides peak RFD at an inconsistent time point which is considered a less comprehensive and less standardised approach to measuring RFD (Maffiuletti et al., 2016). We acknowledge that other methods for data processing may offer deeper insights into the rising force/time curve, for example, measuring RFD at multiple time points, or measuring the impulse of the force/time curve (Maffiuletti et al., 2016). However, these methods would require more complex data processing methods, which may be less feasible in clinical contexts. To acknowledge the need to explore alternative methods for data processing, we have made the following amendments to the discussion. Line 296 “Given our findings, further research is needed to investigate these concerns about the reliability of rapid force production measures in the hemiparetic dorsiflexor muscles. This research should explore alternative methods for data collection and processing (Maffiuletti et al., 2016) and seek to identify reliable methods for measuring hemiparetic RFD and muscle power that better account for sources of biological and measurement tool variability.” 2.6 Further elaboration of the neuromuscular mechanisms tested in the study could provide additional context in the Discussion. Response: To give greater context, we have added the following information to the introduction. Line 9 “Rapid force production requires recruitment of a large number of motor units as well as a high motor unit firing frequency, both of which are impaired in the hemiparetic dorsiflexor muscles after stroke.6 This results from central deficits, which reduce neural input to the motor neuron pool, but is also limited by peripheral changes, such as the reduction in the size of type 2a muscle fibres in the hemiparetic tibialis anterior (Noguchi et al., 2023) and soft tissue stiffness and spasticity in the antagonist plantarflexor muscles (Azzollini et al., 2021).” 2.7 Provide the strengths and the limitations of the study. Response: Thank you for this suggestion. We have added a section on strength and limitations to the discussion. Line 302 Strengths and limitations “A key strength of this study was the application of an isometric MVC procedure that could be completed by people with more severe stroke. This enabled enrolment of a broad sample with a range of lower limb weakness and functional walking ability, increasing the generalisability of findings to a wider stroke population. Other methodological strengths included positioning of the ankle to optimise dorsiflexion force 29 and fixation of the toes to reduce measurement variability. 23 In addition, our approach to measuring RFD enabled evaluation of the very early force production (0-200ms) which has not been evaluated previously in the hemiparetic dorsiflexor muscles. Further research could explore the reliability of other time windows. The key limitation in this study was the sample size, which was below the n=30 recommended for reliability studies 28 but comparable with other studies in this field. 12, 13, 15 To address this limitation, we have been cautious with our interpretation of results, and considered both the ICC and its lower bound 95% CI 28(Munro, 2005) and have provided SEMs to enable comparisons with other literature. However, due to this limitation, it is recommended that the findings generated in this study are confirmed with further research in a larger sample.” 2.8 The conclusions partly replicate the final part of the Discussion. It is suggested to include recommendations for practical use. Response: Thank you for this suggestion. Please find below our amended conclusion. Line 363 “This analysis demonstrated excellent between-session reliability for hemiparetic dorsiflexor isometric MVCs. However, other measures of EMG and rapid force production were less reliable, with ICC 95% confidence intervals extending to the poor to moderate range, and SEM percentages between 23-25%. These findings, which utilises gold-standard dynamometry, raise concerns about the reliability of measures of rapid force production in the hemiparetic dorsiflexors muscles. Further research is required to examine reliability in a large sample of people stroke. In the meantime, researchers and clinicians should be cautious when interpreting rapid force production measures of the dorsiflexor muscles when determining the efficacy of stroke rehabilitation interventions. Given the significance of dorsiflexor muscle function to lower limb recovery after stroke, future research should investigate reliable tools for measuring hemiparetic dorsiflexor muscle RFD and muscle power. This will facilitate a greater understanding this aspect of muscle function and enable more targeted rehabilitation.\" 2.9 Introduction: “the ability to exert force over a short time”: this is the definition of power; it is proposed to delete this phrase. Response: It was our intention to define muscle power to ensure this concept was clear at the outset. We have put the definition in brackets to make it clear that this sentence refers to only two concepts. Line 2 “Ankle dorsiflexor impairments are common after stroke 1 affecting both muscle strength (the force exerted during a single maximal effort) and muscle power (the ability to exert force over a short time).” 2.10 Introduction: “Muscle strength can be measured isokinetically or isometrically”: Clarification is needed. Response: Thank you for this prompt. We have provided clarification in the manuscript as follows. Line 65 “Isokinetic MVCs involve muscle contraction against accommodating resistance through the joints range of movement at a constant velocity, whereas isometric MVCs involve muscle contraction against stationary resistance at a set joint angle (Drouin et al., 2004).” 2.11 Participants: elaborate on the inclusion criteria. Response: The eligibility criteria have been provided below with some additional clarification. “The 15 participants were adults, more than 6 months post stroke, with hemiparesis affecting ankle dorsiflexion movement. The sample size was based on that required for the broader experimental study. 9 Exclusion criteria were significant cognitive/perceptual/communication deficits, cerebellar stroke, inability to produce ankle dorsiflexor force against the dynamometer, or medical conditions that would impact safety or protocol completion. 9” In addition, we have provided further information about the impairment and function of participants in the results section. “Participants presented with a range of lower limb weakness, from mild to severe, and used a variety of outdoor mobility aids (unaided n = 4, quad or walking stick n = 5, walking frame n = 2, wheelchair n = 2) suggesting a range of walking abilities.” 2.12 Measurement procedures: specify the duration of the 4-5 s isometric dorsiflexor MVCs. Response: The duration was 4 to 5 seconds. We have written this more clearly in the manuscript. Line 117 “Following two submaximal practices, participants performed three isometric dorsiflexor MVCs; each lasted a duration of 4 to 5 seconds and a 2-minute rest was given between each MVC.” 2.13 Results Table 1: it is suggested to use subscript rather than superscript characters. Response: We have changed these outcomes to subscript as suggested."
}
]
}
] | 1
|
https://f1000research.com/articles/12-423
|
https://f1000research.com/articles/13-569/v1
|
04 Jun 24
|
{
"type": "Case Study",
"title": "Management of blood thinning medications in elderly populations presenting with rectal bleeding: Are we doing right?",
"authors": [
"Akshay Bavikatte",
"Boby Sebastian",
"sade Uwaoma",
"Boby Sebastian",
"sade Uwaoma"
],
"abstract": "Introduction Rectal bleeding commonly occurs in elderly patients using blood thinners, posing management challenges due to limited guidance on reversal agents and medication restart criteria. This study aims to review the demographics and management of elderly patients with rectal bleeding while on blood thinners.\n\nMethods A retrospective analysis of patients aged 60 or older presenting with rectal bleeding at West Suffolk Hospital’s emergency department was conducted from January 2018 to December 2020. Data were extracted from electronic records, focusing on patients using blood thinners and adhering to British Society of Gastroenterology guidelines. All patients ceased blood-thinning medications upon admission. The hospital’s ethics committee approved the study, which focused on demographics, diagnosis, and management, particularly regarding re-initiation of blood-thinning medicines.\n\nResults During the study period, 170 patients were admitted to the emergency department of West Suffolk Hospital. 93 (54.71%) patients were included in the study. The average age of the participants was 82 years, and 62.3% were male. All patients were followed up for three months. Atrial fibrillation accounted for 52% of patients, while previous strokes accounted for 20%. The most typical pathology was diverticulosis. Regarding restarting of anticoagulants, Among patients on DOAC (Direct oral anticoagulant), 39% were restarted on discharge, 23% were switched to warfarin, and another 23% were not restarted; 15% planned to restart after seven days. For those on Warfarin, 62% were restarted on discharge, 22% stopped the medication, and the rest were switched to Dual Oral Anticoagulant. Among aspirin patients, 60% were restarted at discharge, while the remaining discontinued. All patients receiving clopidogrel and dual antiplatelet therapy were started at discharge. None of the patients were readmitted during the follow-up period of 3 months.\n\nConclusion Restarting of blood-thinning drugs in patients with rectal bleeding is subject to individual patient variation. Necessitates more extensive trials to achieve greater standardization.",
"keywords": [
"blood thinning medication",
"anticoagulants",
"per rectal bleed",
"reintiation of blood thinners"
],
"content": "Introduction\n\nRectal bleeding is a prevalent adverse effect in elderly patients taking blood thinners. Managing these patients can be challenging because of the scarcity of available guidance on the use of reversal agents and the decision to restart medication.1 Anticoagulant therapy is a major risk factor for rectal bleeding. It is estimated that over 6 million patients in the United States are treated with anticoagulants.2\n\nThe prevalence of blood thinning medications in the elderly population is a critical aspect of healthcare management. Studies have shown that the elderly often have a higher prevalence of chronic diseases, leading to the common use of multiple medications, a phenomenon known as polypharmacy, putting them at an increased risk of bleeding.3 The decision to restart anticoagulation therapy following an episode of rectal bleeding is a complex process that involves the assessment of individual patient risk factors and preferences. Factors such as the underlying indication for anticoagulation, severity of the bleeding episode, and overall risk of thrombosis must be carefully considered.4 Furthermore, patient demographics, such as age and comorbidities like rectal bleeding, can influence the decision-making process regarding anticoagulation therapy.5\n\nShared decision-making and a pragmatic approach are crucial in determining the restart of anticoagulants in patients with rectal bleeding, emphasizing the importance of considering additional clinical factors, individual physician experiences, and patient preferences in decision-making and advocating for shared decision-making.6\n\nWe performed a retrospective study to review patient demographics, pathology, and management of blood-thinning medications in elderly individuals admitted with rectal bleeding in our hospital and to assess the plan for restarting blood thinners.\n\n\nMethods\n\nA retrospective analysis of individuals aged 60 years or older who presented with rectal bleeding to the West Suffolk Hospital’s emergency department between January 2018 and December 2020 was conducted. The study enrolled patients receiving anticoagulant therapy presenting with per rectal bleed. Patient care followed the protocols outlined by the British Society of Gastroenterology,7 emphasizing prompt assessment, resuscitation, and endoscopic examination within 24 hours to identify the bleeding origin. Management options included endoscopic haemostasis, pharmaceutical intervention, or interventional radiology, with an emphasis on collaborative multidisciplinary care to optimize outcomes. Patients were stratified based on stability, with unstable cases undergoing post-resuscitation CT angiography for bleeding localization, while stable patients were admitted for observation. Bleeding etiology was determined during the same admission through gastroscopy and flexible sigmoidoscopy and all patients discontinued their blood thinning medications upon admission. The study focused on patient demographics, investigation, diagnosis, and management, particularly in relation to blood-thinning medications. Ethical approval for this study, conducted at West Suffolk Hospital, was obtained from the Ethics Committee of the hospital and the study was registered with the local audit committee (project number 5496) in January 2018. In consideration of the study design, which did not involve the collection of patient identification data, verbal consent was deemed appropriate and was approved by the Ethics Committee. All participants provided informed consent for the audit and subsequent publication of findings. To safeguard privacy and confidentiality, results were presented anonymously.\n\n\nResults\n\nA total of 170 patients were admitted to the emergency department of West Suffolk Hospital during the study period. 93 (54.71%) patients were included in the study, and the remaining patients were excluded because of age or not being on blood thinning medications. The average age of the participants was 82 years and 58 (62.3%) were male. Seven patients (8%) presented with a shock index less than one and had CT angiograms that did not reveal any active bleeding. All patients were followed up for three months. These patients were resuscitated using blood transfusions. Five patients were taking warfarin, which was reversed using a vitamin K (Phytomenadione) antagonist and fresh frozen plasma with consultation from the haematologist, while two patients on clopidogrel were managed with platelet transfusions.\n\nThe distribution of indications for blood-thinning medications among the study population is illustrated in Figure 1.8 Atrial fibrillation accounted for 59 (52%) patients, previous stroke accounted for 18 (20%), and cardiac comorbidities such as previous myocardial infarction accounted for 11(12%). Only five (6%) patients had a recent acute events: Cardiac co morbidity, cardiac intervention, deep vein thrombosis and pulmonary embolism within last 3 months within the last 3 months.\n\nIn the realm of anticoagulant therapy, 33 patients (35.4%) were administered direct oral anticoagulants (DOACs), while clopidogrel was prescribed for 16 patients (14.88%). Aspirin was the choice for 29 patients (32.5%), and 13 patients (14.2%) were on warfarin. Additionally, dual antiplatelet therapy was utilized by 2 patients (3.2%), as depicted in Figure 2.9\n\nDuring the same admission, patients underwent gastroscopy and flexible sigmoidoscopy to investigate the potential cause of rectal bleeding. Of the 97 patients, 52 (55.9%) were diagnosed with diverticulosis, 14 (15%) had acute colitis, and eight (8.60%) had no identified cause. Notably, none of the patients in this age group was diagnosed with malignancy. The distribution of the pathologies is provided in Figure 3.10 No patient required emergency surgery or radiological intervention, as the bleeding ceased with conservative management.\n\nIn terms of restarting the medication, all patients had a prolonged conversation in terms of the risks and benefits of restarting the medication as well as consultation with medical colleagues when required. There was a clear demonstration of a lack of uniformity in terms of plans for restarting blood-thinning medications.\n\nThe management of blood-thinning medications at discharge was meticulously tailored to individual patient needs. Among those prescribed DOACs, 14 patients (39%) were recommenced upon discharge, with 7 (23%) patients transitioning to alternative therapies such as warfarin, and a further 7 (23%) of them not resuming anticoagulation. Additionally, 5 (15%) patients were slated for delayed recommencement after seven days. Conversely, 8 (62%) patients on warfarin were reinstated upon discharge, while 3 (22%) of them ceased treatment and others were switched to direct oral anticoagulants. Notably, 18 (60%) patients of aspirin recipients were recommenced, while discontinuation was deemed appropriate for the remainder. However, all patients prescribed clopidogrel and dual antiplatelet therapy were promptly initiated on these agents upon discharge. This comprehensive management strategy is visualized in Figure 4,11 exemplifying the nuanced approach to optimizing patient outcomes.\n\nPatients were followed up for a period of 3 months, and readmission was mainly observed in patients on antiplatelet agents.\n\n\nDiscussion\n\nThe aging population in the UK, coupled with an increasing number of patients being initiated on blood thinners, has led to a significant increase in patients presenting with rectal bleeding. This trend is particularly notable in the elderly population, with individuals over 60 years of age constituting a substantial proportion of those affected.12 The incidence is higher in older patients and those taking multiple medications, and the incidence rate increases with age, with a greater than 200 -fold increase from the third to the ninth decades of life.13 The management of blood thinners in elderly patients with rectal bleeding presents a challenge due to the limited existing literature and lack of uniform guidelines, particularly regarding the recommendation of medications upon discharge. Current practices for handling lower gastrointestinal bleeding are influenced by local expertise and service availability, given the scarcity of high-quality evidence guiding such cases.14\n\nThe majority of elderly patients presenting with bleeding per rectum often consume blood thinners, which can have a significant impact on their management and outcomes due to the comorbidities that frequently require the use of multiple medications, including anticoagulants, to treat conditions such as atrial fibrillation and venous thromboembolism.15 In our study, 54.71% of the patients were blood thinners, which was a significant number, with the majority being male. In a study by Kim et al.,1612% of patients with rectal bleeding required ICU admission; similarly, our study showed that 8% of patients presented with severe shock and were managed conservatively according to the protocol.\n\nIn terms of indications for blood-thinning medications in elderly patients, a study by Russo et al.17 revealed that the most common indication is atrial fibrillation, followed by a history of stroke. Similarly, in our study, 52% of the patients had atrial fibrillation, followed by a history of stroke.\n\nIn the context of blood-thinning medications, a study by Afzal et al.18 analysed the prescription trends of oral anticoagulants in England over a decade. This study highlighted the use of Direct Oral Anticoagulants (DOACs), such as apixaban and rivaroxaban, along with warfarin, in managing conditions such as atrial fibrillation. A review by Minichelli et al.19 emphasized the significant impact of DOACs on anticoagulation therapy, providing a more convenient alternative to warfarin owing to factors such as reduced need for monitoring and fewer drug interactions, which is consistent with the finding that 35.4% of patients were prescribed DOACs in the context of blood-thinning medications. Lenz-Habijan et al.20 highlighted the importance of dual antiplatelet treatment (DAPT) involving aspirin and clopidogrel in reducing thromboembolic complications. This is relevant as 14.88% of patients were on clopidogrel and 32.5% were taking aspirin in the context of blood-thinning medications.\n\nDiverticulosis was the most common cause of lower GI bleeding in the very elderly population, accounting for 66.6% of cases.21 Similarly, in our study, 60% of patients were diagnosed with diverticulosis. This aligns with the notion that, in a significant proportion of elderly patients with lower GI bleeding, no specific cause may be identified, with diverticulosis being a common finding.\n\nStudies have shown that resuming anticoagulation therapy after a major bleeding event can induce anxiety for both clinicians and patients, as the decision to prevent thromboembolic events by restarting anticoagulation or reducing the risk of recurrent bleeding by discontinuing anticoagulation is challenging.22 The decision-making process often involves a multidisciplinary approach to ensure the best patient outcomes. While restarting oral anticoagulation alone has been associated with an increased risk of major bleeding compared to non-resumption of treatment, there is a difference in the risk of recurrent gastrointestinal bleeding between patients who restarted antithrombotic treatment and those who did not. This highlights the complexity of the decision-making process and the need for individualized treatment strategies.23 In our study, all patients on dual antiplatelet agents and the majority of patients on aspirin were reintroduced at the time of discharge. In terms of patients on DOAC, 39% of them were restarted, 23% switched to an alternative, and 5% stopped the medication completely; in terms of warfarin, the majority of them were restarted as soon as possible.\n\n\nConclusion\n\nThe management of blood-thinning drugs in patients with rectal bleeding is subject to individual patient variations, and a pragmatic approach is desired. This necessitates larger trials to achieve greater standardization.\n\nEthical approval for this study, conducted at West Suffolk Hospital, was obtained from the Ethics Committee of the hospital and the study was registered with the local audit committee (project number 5496) in January 2018. In consideration of the study design, which did not involve the collection of patient identification data, verbal consent was deemed appropriate and was approved by the Ethics Committee. All participants provided informed consent for the audit and subsequent publication of findings. To safeguard privacy and confidentiality, results were presented anonymously.",
"appendix": "Data availability statement\n\nUnderlying data Figshare: Management of Blood thinning medications in Elderly populations presenting with Rectal bleeding: Are we doing right?\n\n• Fig. 1: Graphical representation of indication of blood thinning medication in study population. (Version 1). figshare. https://doi.org/10.6084/m9.figshare.25705563.v1. 8\n\nThe Project contains following data:\n\nAtrial fibrillation was seen in 52% (n=59), previous stroke in 20% (n=18), and cardiac comorbidities, including myocardial infarction, in 12% (n=11). Recent acute events occurred in only 6% (n=5) within the last three months.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Management of Blood thinning medications in Elderly populations presenting with Rectal bleeding: Are we doing right?\n\n• Fig. 2: Illustration of the distribution of blood-thinning medications within the study population. (Version 1). figshare. https://doi.org/10.6084/m9.figshare.25705614.v1. 9\n\nThe Project contains following data:\n\nAmong the anticoagulant therapies, DOACs were administered to 35.4% (n=33) of patients, while 14.88% (n=16) received clopidogrel. Aspirin was prescribed for 32.5% (n=29) of patients, and warfarin for 14.2% (n=13). Dual antiplatelet therapy was used by 3.2% (n=2) of patients.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Management of Blood thinning medications in Elderly populations presenting with Rectal bleeding: Are we doing right?\n\n• Fig. 3: Illustration of the distribution of colorectal pathology among the study population. (Version 2). figshare. https://doi.org/10.6084/m9.figshare.25705638.v2. 10\n\nThe Project contains following data:\n\nDuring admission, 55.9% (n=52) were diagnosed with diverticulosis, 15% (n=14) with acute colitis, and 8.60% (n=8) had no identified cause for rectal bleeding. No malignancies were detected in this age group.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Management of Blood thinning medications in Elderly populations presenting with Rectal bleeding: Are we doing right?\n\n• Fig. 4: Illustration of the graphical representation of discharge advice regarding various blood-thinning medications among the study population (Version 1). figshare. https://doi.org/10.6084/m9.figshare.25705653.v1. 11\n\nThe Project contains following data:\n\nThe figure shows discharge management of blood-thinning medications: 39% of DOAC users resumed, 23% switched to warfarin, and 15% planned delayed restart. For warfarin, 62% resumed, 22% ceased, and others transitioned. Aspirin was recommenced in 60%, while clopidogrel and dual therapy were initiated universally.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nTanzi MG:New guidance for managing bleeding in patients on oral anticoagulants. Pharmacy Today. 2018; 24(2): 2. Publisher Full Text\n\nBae BK, Kim JE, Pyo H, et al.:Long-term findings of rectal endoscopy and rectal bleeding after moderately hypofractionated, intensity-modulated radiotherapy for prostate cancer.2023. Publisher Full Text\n\nMohammad G, Singh S, Singh P, et al.:Analysis of the prevalence and pattern of polypharmacy among elderly patients admitted in general medicine department of a rural tertiary care hospital in south india. Asian J. Med. Sci. 2023; 14(1): 146–150. Publisher Full Text\n\nKirchhof P, Benussi S, Kotecha D, et al.:2016 esc guidelines for the management of atrial fibrillation developed in collaboration with eacts. Eur. Heart J. 2016; 37(38): 2893–2962. PubMed Abstract | Publisher Full Text\n\nStærk L, Lip GY, Olesen JB, et al.:Stroke and recurrent haemorrhage associated with antithrombotic treatment after gastrointestinal bleeding in patients with atrial fibrillation: nationwide cohort study. BMJ. 2015; 351: h5876. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWitt DM:What to do after the bleed: resuming anticoagulation after major bleeding. Haematology. 2016; 2016(1): 620–624. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOakland K, Chadwick G, East JE, et al.:Diagnosis and management of acute lower gastrointestinal bleeding: guidelines from the British Society of Gastroenterology. Gut. 2019; 68(5): 776–789. PubMed Abstract | Publisher Full Text\n\nBavikatte A:Fig 1: Graphical representation of indication of blood thinning medication in study population. (Version 1). figshare. 2024. Publisher Full Text\n\nBavikatte A, Sebastian B, Uwaoma S:Fig 2: Illustration of the distribution of blood-thinning medications within the study population. (Version 1). figshare. 2024. Publisher Full Text\n\nBavikatte A, Sebastian B, Uwaoma S:Fig 3: Illustration of the distribution of colorectal pathology among the study population. (Version 2). figshare. 2024. Publisher Full Text\n\nBavikatte A, Sebastian B, Uwaoma S:Fig 4: Illustration of the graphical representation of discharge advice regarding various blood-thinning medications among the study population (Version 1). figshare. 2024. Publisher Full Text\n\nLawrenson R, Logie J, Marks CG:Risk of colorectal cancer in general practice patients presenting with rectal bleeding, change in bowel habit or anaemia. Eur. J. Cancer Care. 2006; 15(3): 267–271. Publisher Full Text\n\nDormann H, Krebs S, Muth-Selbach, et al.:Adverse drug reactions in patients with gastroenterological diseases: does age increase the risk? Aliment. Pharmacol. Ther. 2001; 15(2): 171–180. PubMed Abstract | Publisher Full Text\n\nAdenuga AT:Acute severe lower gastrointestinal bleeding in low- and medium-income countries: an approach to management of two cases and the need for local guidelines. Cureus. 2022; 14: e26169. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeutsch D, Romegoux P, Boustière C, et al.:Clinical and endoscopic features of severe acute gastrointestinal bleeding in elderly patients treated with direct oral anticoagulants: a multicentre study. Ther. Adv. Gastroenterol. 2019; 12: 175628481985167. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKim JH, Kim JH, Chun J, et al.:Early versus late bedside endoscopy for gastrointestinal bleeding in critically ill patients. Korean J. Intern. Med. 2018; 33(2): 304–312. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRusso V, Attena E, Maio MD, et al.:Non-vitamin k vs vitamin k oral anticoagulants in patients aged > 80 years with atrial fibrillation and low body weight. Eur. J. Clin. Investig. 2020; 50(11): e13335. PubMed Abstract | Publisher Full Text\n\nAfzal S, Zaidi STR, Merchant HA, et al.:Prescribing trends of oral anticoagulants in England over the last decade: a focus on new and old drugs and adverse events reporting. J. Thromb. Thrombolysis. 2021; 52(2): 646–653. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMenichelli D, Ronca V, Rocco AD, et al.:Direct oral anticoagulants and advanced liver disease: a systematic review and meta-analysis. Eur. J. Clin. Investig. 2020; 51(3): e13397. PubMed Abstract | Publisher Full Text\n\nLenz-Habijan T, Bhogal P, Peters M, et al.:Hydrophilic Stent Coating Inhibits Platelet Adhesion on Stent Surfaces: Initial Results In Vitro. Cardiovasc. Intervent. Radiol. 2018; 41(11): 1779–1785. PubMed Abstract | Publisher Full Text | Free Full Text\n\nÇelik M:Efficacy of early endoscopy and colonoscopy in very elderly patients with gastrointestinal bleeding. Pak. J. Med. Sci. 2017; 33(1): 187–190. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWitt DM:What to do after the bleed: resuming anticoagulation after major bleeding. Hematology. 2016; 2016(1): 620–624. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStærk L, Lip GY, Olesen JB, et al.:Stroke and recurrent haemorrhage associated with antithrombotic treatment after gastrointestinal bleeding in patients with atrial fibrillation: nationwide cohort study. BMJ. 2015; 351: h5876. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "289816",
"date": "21 Jun 2024",
"name": "Mohana Raj Thanpal",
"expertise": [
"Reviewer Expertise colorectal surgery"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic that was chosen is appropriate as managing this group of patients is complicated. This article clearly demonstrates the heterogeneity in management of these group of patients.\n\nThe presentation of the study is clear and straightforward. The results and figures are presented in easily understandable way. The discussion is also well structured.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes",
"responses": []
},
{
"id": "289819",
"date": "26 Jun 2024",
"name": "prakash krishnasamy",
"expertise": [
"Reviewer Expertise clinical management of similar group of patients included in the study"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study addresses on the day-to-day emergency clinical scenario that every health centre faces and very much relevant in everyday practice. It clearly depicts its data on the above question with relevant citations . Its results are much in concordance with day to day practice . This study has made a genuine effort in trying to study the current practices in the management of such patients.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-569
|
https://f1000research.com/articles/12-644/v1
|
12 Jun 23
|
{
"type": "Review",
"title": "A comprehensive review of energy efficient routing protocols for query driven wireless sensor networks",
"authors": [
"Punith Bekal",
"Pramod Kumar",
"Pallavi R Mane",
"Ghanshyam Prabhu",
"Punith Bekal",
"Ghanshyam Prabhu"
],
"abstract": "In this current era of communications and networking, The Internet of things plays the main role in the making of smart communication and networking. In this article, we have focused on the literature survey on wireless sensor networks which are energy efficient. Various standard protocols are reviewed along with some enhanced protocols which makes the network energy efficient. The comparison of the standard and enhanced protocols with respect to various applications in wireless sensor networks is thoroughly done in this article. The outcomes of the enhanced protocols are also briefly discussed. For easier analysis to future researchers, a comparative table which lists the enhanced protocols which are compared with standard counterparts along with the factors for energy efficiency of the protocols. This article also comments on the issues and challenges of the protocols which can be further analyzed for making the wireless sensor network more energy efficient.",
"keywords": [
"Energy efficient (EE)",
"Internet of Things (IoT)",
"Wireless sensor networks (WSNs)"
],
"content": "Introduction\n\nA wireless system is a type of data communication system that sends and receives data using radio frequency. It significantly decreased the requirement for wired connectivity. Ad hoc networks, on the other hand, operate without any infrastructure and hop between radio relays.1 The distributed mode, or the base station (BS), will assist in coordinating the node for efficient data transmission. Despite the availability of a variety of information services, wireless sector networks (WSNs) guarantee accurate data by localizing in time and place in response to user demand.2 A typical WSN functions better when it is under resource limitations like processor, bandwidth usage, storage capacity, etc. The sensor nodes (SNs) are randomly spread across the network area, efficiently managing the energy is a huge task. Due to vast developments taking place in wireless communication protocols, the sensor node internal components have become inexpensive, compact and more robust. A variety of services like routing, data processing, scheduling, key management, cryptography, etc. rely on sensor networks, which has attracted a lot of research attention. These services impose limitations on the network’s self-configurability, energy use, computing capacity, memory use, and other application-specific restrictions.3\n\nSNs, which might be few or many in number, make up sensor networks. These nodes come in different sizes; depending on their size, the SNs function well in various domains. As a result of their special design, SNs in WSNs frequently include a microcontroller that controls the monitoring, a transceiver for creating radio waves, and various types of devices for wireless communication in addition to a source of energy like a battery.4 The entire network functions simultaneously with sensors of different dimensions, and by using a routing mechanism, they are primarily concerned with getting the source data to the receiver node.4 The WSNs basic architecture is depicted in Figure. 1.\n\nThe basic components of a WSN architecture are power supply module, wireless communication module, processing module, and sensor module. An analog-to-digital converter (ADC) and a sensor make up the sensor module. A sensor and an ADC are also included in the processing module.4 The wireless module for communication has network layer and Mac layer protocols along with transceiver which helps in the data exchange between the nodes. The power supply module helps the nodes with the required energy for their operations.4\n\nTo attain a high level of efficiency in monitoring and control systems, importance is given to ensure the SNs are energy efficient (EE) and dependable data transfer in resource-constrained WSNs. A resource-constrained WSNs have nodes with less processing speed, limited data storage, limited bandwidth for communication, etc in comparison with wired sensor networks, where the sensor nodes are static which helps the user to upgrade the above-mentioned parameters as per the networks requirements. Extending network lifespan and boosting network dependability are two strategies to increase network reliability and decrease power usage of WSN nodes, respectively.5 In WSNs, proper monitoring of a phenomenon depends on the collective data provided by the target cluster of sensors, not on any individual node.5 Since WSNs are commonly used in many critical applications like territory tracking,6 military applications,6 health-monitoring systems,6 and so on, the major constraint here will be energy conservation of SNs. Different applications of WSNs are shown in Figure 2.\n\nMaking the SNs EE will always remain the highest priority in today’s WSNs scenario.7 Since the batteries of the SNs are not easily replaceable because of the deployment of the SNs in various terrains such as volcano detection in environmental applications, where the SNs are deployed which sometimes cannot be attended to. To maintain the energy of the sensors after their deployment in a sensor network, there are various energy-efficient protocols like “low energy adaptive clustering hierarchy (LEACH)”, “power efficient gathering in sensor information systems (PEGASIS)”, “threshold sensitive energy efficient sensor networks (TEEN)”, “adaptive threshold sensitive energy efficient sensor networks (APTEEN)” in WSNs. Such protocols would not only increase the sensor networks’ energy efficiency but also length of operation, throughput, and latency.\n\nWe have reviewed some enhanced EE protocols and a comparison is made with standard protocols in the article. These protocols have been categorized based on their application scenario. Even though the authors of the articles which have been reviewed here have made comparisons with standard protocols concerning lifetime enhancement, throughput, energy efficiency, packet delivery ratio (PDR), etc., our main concern here is the energy efficiency of these reviewed articles. The primary aim of this review article is to emphasize the outcomes and the limitations of each of the protocols so that researchers can get into the detail of these aspects and come up with algorithms which are more EE and also design more reliable WSNs protocols.\n\nTable 1 below gives the definitions of the factors that determine how EE the protocols under consideration are listed in this paper.\n\n\nLiterature review of energy efficient protocols for WSNs\n\nIn this section, previous review articles based on the energy-efficiency protocols for WSNs are discussed. The authors have thoroughly compared the EE techniques that are already in use. This section assists in understanding the various factors of the protocols which helps them in being EE by reviewing the already reviewed literatures. This review’s major objective is to inform readers about the current protocols that help WSNs.\n\nRecent developments in sensor network routing mechanisms are discussed in Ref. 8. Appropriate categories, like data-centric, location-based and hierarchical, are used to discuss each routing protocol are compared from earlier literatures. The main goal is to clarify WSN routing methods and identify unresolved problems that may be the focus of future studies. This research is distinguished from earlier studies on sensor networks as it focuses on data-centric routing approaches. The protocols for hierarchical routing are described which is again based on data-centric routing. The location-based routing in sensor networks is illustrated in Ref. 8.\n\nA strong emphasis on energy efficiency is considered in Ref. 9 and it provides a detailed discussion of topology control strategies so that battery-powered WSNs can extend their life comparing the already existing articles. Important topological control strategies are investigated in Ref. 9 to give light on how effectively energy efficiency is accomplished through these designs. The algorithms studied are further categorized based on the energy saving technique they implement and assessed by the disadvantages they provide so that designers can choose a better result that suits the applications. This article explains and examines the representative “atypical hierarchical routing protocols” and its benefits and disadvantages have been studied because the idea of “network lifespan” is frequently considered to study the algorithm’s overall outcome. Many research questions for attaining energy efficiency through protocol based on topology control on the findings are noted. The most recent advancements are discussed and update the data from earlier existing publications. Energy-saving clustering and mode scheduling techniques are included so that this work gives a more thorough survey. “Network lifetime”(NL) notion in the literature of protocols based on topology control exhibits notable variations. In contrast to past research, this work focuses on the factors that enable energy savings and increased network’s longevity for WSNs. Furthermore, unlike those that cover both centralized and distributed systems, the protocol based on topology control provided in this study are exclusively distributed approaches.9\n\nThe “cooperative diversity-enabled medium access control” (MAC) protocols for LANs and WSNs are studied in Ref. 10. With the help of the transceiver pair, adjacent nodes function as”virtual multiple input multiple output” (VMIMO) systems in cooperative diversity protocol, sending different iterations of a packet to the receiver over different fading channels. The wireless link’s spatial diversity can be used in conjunction with several replicas of same packet to recover the original one, increasing reliability. By successfully coordinating transmissions between parent, associate, and destination nodes, MAC protocols make a substantial contribution to making this concept a reality.”Channel state information“(CSI), which is supplied to a routing layer for partner selection, can be collected across neighboring nodes using cooperative MAC protocols. While the majority of the initial research focused on physical layer approaches, researchers have now looked into supporting cooperative diversity in top layer protocols, specifically in the MAC layer. The first focus was on creating cooperative MAC protocols based on the IEEE (Institute of Electrical and Electronics Engineers) 802.11 standard for Wireless LANs (WLANs). The application of cooperative diversity in a variety of technologies, such as WSNs and cellular networks, has recently been the focus of research. In this paper, advances in developing cooperative MAC protocols both to WLANs and WSNs are described.10 The outcome of this study show that the energy efficiency can be enhanced by having proper placement of relay between sink and source, distance among the sink source and in-between nodes can be made optimal. The drawbacks are that selection of optimal placement of a relay is a complex process and the trade-off between energy efficiency and reliability should be considered for the cost efficiency of the networks.\n\nArticle11 provides a complete review of”atypical hierarchical routing“(AHR) for the first time. In-depth evaluations of several existing logical topologies are provided together with the peculiar WSN hierarchical routing. The benefits and drawbacks of several AHR protocols are examined regarding their noteworthy performances and application scenarios. The remaining issues using hierarchical WSN structure are also presented. The goal of this study is to offer helpful advice to system developers on how to assess and choose the best logical topologies and hierarchical routing techniques for certain uses. A categorization approach for WSNs’ unusual hierarchical routing is provided. This offers readers a fresh viewpoint to comprehend this style of routing. This division of atypical hierarchical routing into four categories based on logical topologies is novel. This is the first attempt to give an in-depth analysis of WSNs’ unusual hierarchical routing methods. The characteristics, benefits, and drawbacks of many traditional and contemporary atypical hierarchical routing algorithms are discussed in this study. A thorough evaluation of the general performances and use cases of various atypical hierarchical routing technique is described. A few unresolved problems in this area of study are listed. This research topic continues to advance as new research directions for researchers.11\n\nThe study in Ref. 12 seeks to fill in the gaps and offers a current analysis of the sink mobility problem. Reviewing mobility management plans from an evolutionary standpoint by referring to already available literatures is its key contribution. “Unrestricted mobility” (UMM), “Uncontrollable mobility” (UMM), “Location-restricted mobility” (LRM), and “Path-restricted mobility” (PRM) are the four categories into which the related systems have been categorized. The proposed taxonomy is followed by an explanations of a number of typical solutions. To aid readers in comprehending the progression of growth within the category, the association between solutions is shown, along with extensive descriptions and in-depth analysis. By doing this, a few open issues that receive little attention or have not yet been thoroughly investigated are discovered, in addition to some prospective extensions based on recent research. It offers a comprehensive overview of mobility models that have also been often used in WSNs. It provides updates on current advancements in research and suggests that sink mobility management methods in WSNs should be viewed from an evolutionary perspective. By analyzing the advantages/defects of existing solutions and the relationship between them, it reveals potential extensions based on recent research and also several open areas which have gone unnoticed up to this point. The mobility concepts and features in WSNs are also described. The control of sink mobility is compared in this investigation. The conclusions and recommendations for additional study are outlined.12\n\nA detailed analysis of “Ant Colony Optimization” (ACO)-based routing protocols in WSNs” for the first time is considered in Ref. 13. Sorting different routing algorithms from earlier review articles into categories is the initial step. Second, one of most significant ACO-based routing methods are described, discussed, and qualitatively compared. Also highlighted are a number of outstanding WSN design issues. The primary goal of this survey is to critically review the most widely used ACO-based routing strategies developed for WSNs. This will assist in educating a huge audience about its existence. Various WSN ACO-based routing protocol types have also been listed. The ACO-based scheduling algorithms in WSNs are now categorized for the first time. It will be simpler for readers to comprehend these regulations as a result. Along with defining illustrative ACO-based routing protocols in WSNs, a summary of their benefits and drawbacks, and an evaluation of these protocols using a few metrics are also provided. This can be used by application developers to locate appropriate and additional solutions. Based on the most recent advancements in WSN technology, several research problems are highlighted and indicate some protocols based on ACO routing in future. This will advance the growth of this area of study. Finally, some unresolved problems and difficulties are also discussed.13\n\nThe article14 demonstrates the need for further focus on QoS-aware clustering. Furthermore, it is necessary to define how clustering can enhance user”quality of experience“(QoE). For intelligent systems to be able to support a variety of scenarios, it is crucial to understand the needs of the users. The implementation of clustering techniques for IoT systems in 5G networks is also discussed in this research. Numerous issues associated with using clustering techniques in a 5G setting for IoT are which are noted from the pre-existing articles are presented and talked about. One of the main strategies for green computing in WSNs is clustering, which may be used in a variety of systems. By just partially engaging the network’s sensors, such strategies can increase a WSN’s lifespan. Reviewing previous research from a QoS standpoint is necessary. Since the IoT concept was introduced, related techniques have been extensively used to assist people in their daily lives. IoT systems’ high diversity and usability set them apart from WSN systems. Examples of IoT systems include connected cars, smart homes buildings, etc. The trend toward wireless is the development of future networks (5G networks), and the migration of current IoT systems to such cutting-edge communication platforms. The distinctions between WSNs and IoT are studied in this paper, as well as the difficulties in integrating clustering algorithms into 5G-based IoT systems are investigated.14\n\nThe current advancements in WSNs are examined in Ref. 15, covering their applications, design restraints, and lifetime prediction approaches. NL maximization strategies is introduced, followed by the presentation of a collection of definitions for the NL design target used for WSNs. A few design guidelines with examples are then provided to illustrate the potential improvements of the various design criteria. Considering the most recent developments, a concise taxonomy of smart WSN applications is offered. A thorough list of the design restrictions for WSNs is given keeping mind the flaws faced by the earlier review articles. The definitions of NL are presented in general. The most current NL maximizing techniques are evaluated critically, and their efficiency, objective functions, and constraints functions are examined.15\n\nIn Ref. 16 the focus is on closely examining currently available communication standards and protocols to find any security flaws. The literature-available countermeasures to make sure the safety of protocols for communication against malignant activity have been studied, and they also present research problems and open research topics. The WSN routing protocol serves as the focal point of this paper’s study, but it also divides it into three categories according to the kinds of attacks each was created to withstand: There are three categories listed: “intrusion detection systems” (IDSs), “reactive solutions” (RSs) and “proactive solutions” (PSs). Finding the weak and strong countermeasure points, leads to the development of more secured protocols for WSNs. Developing a responsive system that could detect intruders, but also help the networks in intrusion recovery and avoid service disruptions is one of possible research routes in construction of safe WSN systems. An in-depth examination of network layer assaults launched against the protocol for “routing protocol for low-power and lossy networks” (RPL) routing concludes this study. The effect of specific assaults on a network’s performance is calculated by using Cooja network simulator. Lastly, new network layer security research possibilities are discussed, as well as how to use Cooja as a baseline to develop novel WSN system defenses.16\n\nDifferent EE routing protocols are taken into account in Ref. 17. This study aims to determines benefits and downsides of already reviewed articles. This study provides a suitable selection of an EE algorithm for various WSN applications by taking into consideration a number of variables. The decentralized hierarchical cluster-based routing algorithm makes use of both the routing based on cluster algorithm and the multi-criterion clustering algorithm. These algorithms run simultaneously. The “hierarchical energy efficient clustering” (HEEC), which improves high energy utilization and intends to prolong the life of sensor networks. In WSNs, the”clustering arrangement energy efficient routing protocol“(CAERP), that performs better than traditional clustering methods, intends to cut back on unnecessary energy use. The”centralized energy efficient distance“(CEED) routing protocol’s distributed CH selection mechanism is used to cluster and balance energy in SNs. The importance of this study is to discuss alternative routing algorithms while balancing energy usage and NL for WSNs.17\n\nHierarchical EE routing algorithms based on swarm intelligence and traditional methods are discussed in Ref. 18. The routing protocols belonging to both groups can be classed based on aggregation of data, energy efficiency, QoS, location awareness, fault tolerance, query-based, multipath, and scalability. A thorough study has been conducted on the hierarchical EE routing techniques disclosed from 2012 to 2017. A fundamental explanation and practical foundation are provided along with a taxonomy of protocols for routing. The protocols are analyzed in detail, including details on their objectives, classifications, methods, benefits, and potential uses in the future. Hierarchical routing algorithms, such as energy consumption, categorization location awareness,”quality of the service“(QoS), data aggregation, scaling, fault tolerance, query-based protocols, and multipath are thoroughly studied in this review. This work outlines a few of the unresolved problems in this field of study. Finally, fresh research avenues have been suggested to advance this field.18\n\nA comprehensive analysis of existing protocols that is suggested for energy consumption, PDR, NL, and route creation time is presented in Ref. 19. These tactics are derived from a variety of different games. It qualitatively contrast the major characteristics, advantages, and disadvantages. Three parameters were considered while choosing the articles to include in the survey. Along with the publications, seminars, and publishing year where the papers were published, the implication of the three different types of game theory are provided. The three subcategories of game theory are cooperative, non-cooperative, and evolutionary game theories. It doesn’t necessarily follow that a routing system will become considerably more appropriate over a certain application just because it adopts a new gaming style. Future research directions are also highlighted, along with a few significant unresolved issues.19\n\nIn addition to discussing the EE time synchronization over WSNs implementation problems,20 also looks at the features of the transmission state within the deafness as well as packet collision. It is specifically a thorough audit that includes tools, drawbacks and areas of interest from earlier related work inside the transmission state. The study assists researchers in three areas: (1) preventing packet collision during communication in WSNs, (2) preventing deafness that occurs during transmission in WSNs, and (3) increasing data collection throughout transmission states in WSNs. Additionally, it suggests a few pertinent open problems as ideas for ongoing investigation. An unusual center is offered to contain tools, points of interest, and downsides on related works in the transmission condition. The work contributed to research by identifying the primary problems and obstacles to energy efficiency in WSNs, classifying energy efficiency schemes according to the needs of the applications, and making general conclusions regarding all energy efficiency schemes.20\n\nThis is the initial offering of a complicated mathematical definition of EE in static WSNs. Attributes relating to the routing mechanism and pattern of traffic flow are displayed.21 The underlying cause of the “Hot Spot Problem” will be identified. “Hot Spot Problem” can be defined as draining of energy of the nodes closer to the sink more drastically because these nodes will be involved in communication within the network, and they get isolated. Additionally, based on the examination of the energy consumption characteristics, the concepts related to EE, such as the EE Tier, EE Perspective, and the EE Means are offered and described. The planned EE of WSN techniques from 2002 to 2019 is tracked and thoroughly examined. The “mobile node assistance scheme” (MNAS),”energy efficient MAC” (EEMAC) protocol, the “energy efficient routing scheme” (EERS), the “energy efficient clustering scheme” (EECS), and the “cluster-based compressive sensing data collection” (CSS), respectively, are divided into five main categories. The representatives that were frequently highlighted in recent years are presented in tables along with an analysis of each category’s design principle. The relationships between the five categories, as well as those between each one and the EE Tier, EE Perspective, and the EE Means are all carefully examined. Also specified is the context in which each of them should be used. A thorough statistical analysis is also done for each category. Finally, the potential and constraints that WSNs currently face in the context of new computing paradigms are highlighted, along with several workable research areas for EE of WSNs.21\n\nThe traditional and contemporary protocols are divided into categories based on the following factors in Ref. 22: (i) network structure; (ii) data exchange; (iii) usage of location information; and (iv) support for quality of service (QoS) or multiple pathways. This article’s goal is providing a comprehensive presentation of traditional protocols comes under each of above classifications, the traditional as well as modern ones, highlight their key attributes, providing a discussion about both specific and general issues raised, and pinpoint areas for further research. In comparison to earlier evaluations of a similar nature, the work described in this paper offers both an updated and a more thorough analysis of EE routing algorithms. Additionally, it both expands on the taxonomies that already exist and takes more performance factors into account for the analysis of the procedures under review. Comparisons based on performance measures and outcomes are also listed. The study’s findings are then examined, conclusions are taken, and unresolved research questions are listed.22\n\nAn in-depth examination of “WSN hierarchical routing protocols” is the main emphasis in Ref. 23. The hierarchical protocols are classified based upon their routing techniques. This research compares several hierarchical routing methods. As a consequence of routing in WSNs and its significance in the study, an effort is made to offer a complete analysis of various routing techniques and their implications on the performance of WSNs. These protocols are grouped under tree-based, chain-based, area-based, or grid-based networks. The main goal here is to serve as a guide for comparing the most pertinent baseline hierarchical routing systems. A more in-depth examination of the leader selection criteria, hierarchical structure, and cluster construction process. The consequences of energy load and the limitations of different routing methods are then carefully considered. In order to aid in subsequent research, this study examines alternative hierarchical routing methods for WSNs. These reviews and contrasts various parameters used in cluster construction for various updated LEACH versions in order to provide the criteria to be taken into account when creating a cluster and routing. The most significant state-of-the-art methods are carefully chosen to distinguish and emphasize the performance, advantages, disadvantages, and challenges of each routing technique. Finally, a thorough analysis of the most recent advancements in adaptive clustering for low-energy hierarchical routing is given, following the comparison of the many versions discussed in this study.23\n\nAn exhaustive survey of WSN clustering methods based on “hybrid energy efficient distributed” (HEED) is explored in Ref. 24. The advantages and disadvantages are listed and develop a novel understanding of the extended HEED-based WSNs protocols. Both the WSNs protocol rotated unequal HEED and energy-based rotated HEED are considered in this survey. For the next assessment and construction of protocol based on HEED, a fairway with the evaluation of every focused WSN algorithms is offered. The objectives of this survey were to highlight the benefits and drawbacks of each WSN protocol and its adaptability to various environments, provide extensive, well-explained variants protocols based on HEED new researchers in one place, and make it simple for network engineers to choose the best protocol for their needs.24\n\nVarious energy-saving techniques explored by various research communities in WSNs which reduce the node energy usage and enhance the network’s lifetime are examined in Ref. 25. Duty cycle, EE routing, EE medium access control (MAC), and error control code (ECC) are just a few of the energy-saving protocols covered. The duty cycle strategy uses the sleep/wake method to cut down on the nodes’ active time and preserve energy. The MAC protocols along with routing employs relevant energy-saving methods. This study also briefly discusses certain energy-saving approaches that are researched vastly for different ad-hoc networks, such as the use of topology management, transmission power control and directional antennas. The literature offers methods for reducing energy use and boosting a WSN’s lifespan. The many energy-saving strategies put forth by various researchers to lengthen the lifespan of WSNs are discussed in this paper. Energy-saving strategies used by other ad-hoc networks in addition to WSN are also discussed.25\n\nIn Ref. 26 WSNs EE routing strategies, its description and comparison of nine types of protocols, including network architecture, next-hop selection, network topology, protocol operation, delivery mode, initiator of communication, application type and path formation, according to a new proposed taxonomy has been explained. Each class is examined, talks about its representative routing protocols (benefits, drawbacks, mechanisms etc.), and then compare based on various factors for relevant classes. The main goal was to provide an overview of these methods using a fresh classification scheme that was previously discussed. A classification and comparison of current routing techniques under each category, highlighting their benefits and drawbacks are illustrated.26\n\nThe EE methods for WSNs that collect energy and an “environmental monitoring applications” (EMAs) is examined in Ref. 27. As a result of the dynamic deployment and communication problems related to EMAs, it covers the concentrating on the physical layer, WSN protocol stack, MAC, as well as network layer. The study looks at the data, network, and physical connection levels of WSNs for EMAs to see how new security flaws influence them. In order to comprehend security problems in EMAs, this study evaluates WSN network protocols, EE protocols, as well as energy recovery protocols. Additional discussions are made regarding the different simulation settings for EMA protocol designs, specifications of the design, QoS specifications, and network topology specifications. This study’s conclusion describes the safety problems with WSN for EMAs, including the risks just at network and nodal level as well as ways to mitigate and prevent them.27\n\nA variety of literature reviews on energy-optimized routing techniques are investigated in Ref. 28. According to the investigations, “fault tolerance with optimal relay node employing modified particle swarm optimization” (FTOR-ModPSO) and “fuzzy optimal clustering” approach have been taken into account.”Intra mobile agents“(IN-MA) are the foundation of the “particle swarm optimization with genetic algorithm” (PSO-GA). The goals are to reduce energy usage, boost packet delivery rates, and determine where SINK should be placed in a WSN. To use PSO-GA method based on the intracluster mobile agent to reduce power consumption and optimize the pathways between SNs and the sink node. Fuzzy logic can increase network existence without causing collisions. For WSNs, energy-aware QoS protocols are studied and existing energy optimization strategies for LEACH-based routing were covered.28\n\nStrategies for controlling the routing techniques and topology in WSNs are combined to study collectively in Ref. 29. Different parameters related to EE is studied from the earlier reviewed articles. To improve WSN performance at both the topology and routing levels, taxonomy of topology management approaches and routing strategies has been suggested. The fundamental tenet of providing a detailed analysis of each categorized category is to demonstrate how well-established and applicable its evolutionary methods are. In this review article, each technique or protocol was arranged according to the year it was reviewed, with a detailed description of the proposed work’s value to society, the particular approach or methodology chosen, and any shortcomings that might be fixed in subsequent research. Main focus is on analysis of never-before-reviewed graph-based techniques, specifically designed interference models, topology control in WSNs and associated algorithms. Insights on cutting-edge routing protocols, including traditional hierarchical routing, “particle swarm optimization” (PSO)-based, and “ant colony optimization” (ACO)-based routings, have also been offered. Quick comparison of solutions that have been suggested has been made, along with a discussion of the research gaps and unresolved problems, as well as new research directions for this area’s future advancement.29\n\n\nComparative study of enhanced energy efficient protocols for WSNs\n\nIn this section, we have listed suitable articles and their explanation based on the EE protocols and their outcomes. The comparison is based on the various factors defined earlier for the efficiency of the WSNs. Researchers can benefit from this paper as it lists many different enhanced protocols giving them a better understanding of these protocols along with their outcomes as compared to the standard protocols.\n\nA “3-Dimensional real-time geographic routing” (3DRTGP) was developed and analyzed.30 This offers three main features. First, the 3DRTGP, which offers a soft real-time capability, is suggested for 3D-deployed WSNs. To enable real-time operation, the protocol employs an adaptable “packet forwarding region” (PFR) and selects “fast-forwarding nodes” within the PFR. By restricting the number of forwarding nodes going down the path of the destination, PFR seeks to lessen channel contention and congestion. The delivery of an effective heuristic approach for such VNP in 3D WSNs is the second. This strategy makes it possible for the proposed protocol to function dependably even when there are vacant regions present. Thirdly, tweaking methods for 3DRTGP are offered so that the protocol can satisfy application requirements for latency and miss ratio. For instance, changing network density can satisfy an application’s requirement for a low miss ratio. Because 3DRTGP does not rely on beacon signals to gather data about neighbors, it uses less energy than the protocols compared in this article. The 3DRTGP is compared with”above below location aided routing” (ABLAR)31 and 3D Greedy protocol. For a WSN with 1000 nodes, 3DRTGP uses 31% lesser energy for every packet over ABLAR and 26% higher energy than for the 3D Greedy protocol.\n\nIn contrast to the other two techniques, 3D Greedy does have a high packet miss ratio, which might not be suitable for all real-time applications. Also, the proposed protocol is not applicable to mobile SNs within a network.\n\n“General self-organized tree-based energy-balance routing protocol” (GSTEB) is analyzed.32 A scenario where the network regularly gathers data from a landscape where each node continuously detects its surroundings and transmits the information back to BS is studied. There are typically two ways to define NL: a) the time span between the start of network activity as well as the initial node’s demise. b) The time frame covering the beginning of network activity and the death of the last node. The first definition is the one we use in this paper. In addition, it takes into account two extreme data fusion scenarios: case (1) it is possible to fully fuse the data between any two SNs. Regardless of the amount of data a node receives from its offspring, each node transmits the same amount of data; case (2) fusing the data is impossible. Each relay node transmits a message that is made up of the total of the data it has detected and received from its children. Another straightforward method for balancing network load is provided by GSTEB. In reality, it is challenging to uniformly spread the load over all nodes in such a situation. The proposed protocol is compared with LEACH,33 HEED,34 PEGASIS,35 “power efficient data gathering and aggregation” (PEDAP),36 “tree based energy efficient protocol for informtion systems” (TREEPSI),37 and “tree based clustering” (TBC).38\n\nEven though GSTEB requires BS to calculate the topography, which lengthens the delay and increases energy waste, these energy waste and delay characteristics are manageable while comparing the energy usage and transmission delay for data.\n\nAn enhanced “fault-tolerant clustering routing algorithm established on a gaussian network for WSNs” (FCGW) is proposed in Ref. 39. Here the “geographic adaptive fidelity” (GAF) technique will be used to partition the random sensors into virtual grids (clusters). To achieve precise energy usage and extend NL, each cluster will choose single operational node once at time as a CH node. Each CH node can be described as a Gaussian integer and interconnected to one another to construct a Gaussian network because WSN management must indeed be refined as a Gaussian network. A fault tolerance technique for CH nodes is suggested in this paper. Based on the Gaussian network’s symmetric link, redundant routing paths can readily take the place of the primary routing path in the event of failure, thereby improving data dependability and optimizing energy consumption. The studied protocol is evaluated with FT-LEACH, HEED34 and PSO-UFC protocols.40\n\nThis protocol gives high reliability in terms of data. Also, it has shown that the energy efficiency is high compared to the protocols considered here. i.e., it consumes 48% of energy whereas the other protocols consume 70% of its energy. It is difficult to join long-distance nodes in a wireless gaussian network because the packet latency would increase.\n\n“Robust and energy efficient multicast routing” (RE2MR) algorithm is studied.41 RE2MR is an enhanced multicast algorithm that addresses shortcomings of topology, geographic, and hierarchical multicast protocols while utilizing their benefits. It articulates the path search problem as the “capacitated concentrator location problem” (CCLP) but also determines the multicast topology which reduces path length’s sum of multicast base node to multicast members by substituting the existing concept of the “leader node” with the idea of the “facility node”. As a result, a system parameter may be used to restrain the number of subscribers that every facility node can manage. By using a “trajectory-based lightweight hole detection” (TLHD) method, RE2MR takes into account potential holes in realistic WSN installations. The knowledge of a hole found by TLHD and the combo of an application in iteration of CCLP enable RE2MR to adjust the multicast topology to be EE with respect to average path length. RE2MR enhances energy efficiency while utilizing wireless medium’s broadcast nature and precise packet header design. RE2MR is compared with “hierarchical geographic multicast routing” (HGMR), “robust and scalable geographic multicast protocol” (RSGM),42 and “multicast routing with branch information nodes” (MRBIN).43\n\nComparing RSGM and MRBIN, with RE2MR, the latter has an overall reduced total sum length, by up to 57%. One finding is that packet loss (PL) overall methods lower as node density (ND) rises. This can be explained by the fact that a node is more likely to find neighbors who are closer to its destination when the ND is greater. RE2MR does have an overall delay which is close to 8% and 50% lower than MRBIN and RSGM, respectively. The entire sum of path lengths will increase if the TLHD technique is not used because packets from a transmitter to a facility node from a facility node to multicast members pass across the face of the hole.\n\n“Range-based opportunistic routing” (ROR) is an enhanced version of “energy efficient opportunistic routing” (EEOR).44 A brand-new routing system named ROR is proposed, short for “Range-based Opportunistic Routing.” The opportunistic routing principle, which refers to the “option of nodes that have the least distance to the destination,” became a part of the EEOR protocol in new routing strategy ROR. ROR aims to decrease energy usage, extends lifespan of a SN, boost data transmission, and decrease the volume of control messages. Decreasing the number of forwarding lists from a different selection that only contains the nodes which are physically closest to the recipient and to have the maximum energy is the primary objective of ROR. The ROR protocol is compared with EEOR,45 “extremely opportunistic routing” (EXOR) protocol46 which are protocols for opportunistic routing.\n\nThe suggested protocol uses about 2500Mj of energy as opposed to the EEOR and ExOR protocols, which use about 3500Mj and 6500Mj of energy, respectively. When comparing performance in terms of dropped packets, the ROR protocol outperforms its competitors.\n\nAn “effective bypassing void routing protocol, which is based on a virtual routing circle” (BVR-VRC)47 is studied. An obstruction is encircled by edge nodes to form the framework of BVR-VRC. The BVR-VRC has two optimization modes: void and greedy. Where the greedy processing mode uses a greedy algorithm strategy to choose the relay node. The void processing mode is turned on when a void is found. Void region partition, virtual coordinate map, and void detecting are the three stages that help compensate for the void processing mode. The edge node’s virtual coordinates are established following introduction of the void processing mode. Then, the greedy mode is reinstated, allowing a greedy algorithm to choose these edge nodes that have virtual coordinates as the relay nodes.”greedy perimeter stateless routing“(GPSR)48 is compared with the proposed protocol and the following conclusion is made.\n\nDelivery ratios become less favorable in BVR-VRC but also GPSR when routing void size grows. Delivery ratio in BVR-VRC is greater than those in GPSR at all void sizes. Even though the first packet data meeting routing void has a substantial delivery delay, average delay both in BVR-VRC and GPSR rise as routing void expands, with GPSR’s delay rising more quickly than BVR- VRC. However, the advantage is to minimize the average hops and ensure that subsequent packets always use a greedy approach to choose the delay nodes. As a result, the overall working time’s average delay is decreased. Well after virtual coordinate mapping of BVR-VRC, the entire routing process adopts greedy forwarding. As a result, BVR-VRC uses less energy on average than GPSR does.\n\n“A more effective artificial bee colony (ABC) technique” is investigated.49 Fuzzy C-means clustering and a novel, updated ABC technique are used to tackle the initial-round EE clustering problem. The clustered WSN architecture is shown in Figure 3. The best CHs may be chosen and clustering may be maximized if every node has the same energy level. To address the clustering issue of later rounds, an improved ABC algorithm-based optimal clustering method is proposed. The ABC algorithm’s honey source update principle is joined with the WSN’s characterization of CH energy, cluster position, as well as CH density in order to maximize clustering.\n\nA routing approach based on an upgraded optimization of ant colonies is offered to find the best route out of each CH towards the BS. A busy/idle node based polling control scheme is created in the intracluster phase of communication to lower network energy usage and throughput of network will be increased. ABC-based clustered routing optimization is provided. According to results given by simulation process, the suggested method could effectively balance energy consumption, boost throughput, and extend lifespan of the network. The comparison of suggested techniques is made with “LEACH - centralized” (LEACH-C),33 “fitness-value-based Improved grey wolf optimization” (FIGWO)50 PSO51 and “Artificial Bee Colony - SD” (ABC-SD).52\n\nIn the metrics for total remaining energy, the suggested protocol performs well. This is due to the fact that by taking into account the energy component, both the recommended clustering and the ACO-based routing protocol discover the best result with respect to overall energy and energy balance. However, because the suggested method has only been investigated for stationary networks, it will need to be appropriately implemented for mobile WSNs.\n\nA “dynamic cluster-based static routing protocol” (DCBSRP) is proposed.53 With a superior E2E delay, lowest communication cost, maximum throughput, and lowest packet loss ratio, the recommended load balancing system is efficient and increases the lifespan of the installed WSNs. Additionally, the following measures have been adopted for the proposed scheme’s implementation: 1) Every SN is linked together. 2) A hybrid DCBSRP routing system is suggested and put into practice. 3) Static routing works for the duration of the specified time. 4) The studied method helps to sustain the life of the network with poor network communication and computation costs, and load balancing, very low packet loss ratio, rapid throughput and very low E2E delay. The “dynamic duty cycle (DDC) scheme”,54 “EE connected coverage scheme”,55 “optimal clustering in circular networks scheme” (OCCN)56 and “distributed optimal on-line task allocation algorithm”57 are compared with DCBSRP.\n\nThe suggested routing protocol minimizes network overhead and prolongs the network lifespan. It shows how long a single node may endure in the network when the suggested algorithm is in use. Furthermore, the observed regular node participation percentage was 95.9%. The effectiveness of the studied strategy in increasing the lifetime of network was astoundingly huge since the creation of micro clusters not only manages the network’s load but also appears to serve a promising function in enhancing the lifetime. Due to the clusters’ unicast communication, which reduces the possibility of network overhead, the latency was discovered to be relatively constant. The initial deployment of the DCBSRP routing system is difficult, however this is a one-time operation with long-term benefits.\n\n“An efficient 3D WSN routing scheme” (3D cluster protocol) is suggested.58 An innovative routing approach that combines SN scheduling with clustering routing in order to improve energy efficiency and lengthen NL n the 3D WSN is introduced. The set with fewest number of SNs using an”improved genetic algorithm“(I-GA) can be located, which makes use of unnecessary SNs of the 3D network to discover and switch them off. In order to find the optimum SNs to swap the energy-drained nodes, a node wake-up technique is also included. Due to the less-than-ideal wireless channel, the additional energy usage of the retransmission is also accounted for by this routing. This protocol is analyzed with main-3D59 Leach-3D.60\n\nFewer nodes are functioning at a time because of 3D-cluster protocol transfers data depending on the ideal node set, which significantly decreases energy usage. The authors modify the likelihood that SNs will turn into CH in the article, redesign intra-cluster and inter-cluster communication, and enable SNs surrounding BS to connect with BS directly without joining the cluster group. The network throughput decreases as the SNR threshold rises. This is because as the SNR threshold rises, channel quality requirements rise as well, increasing the likelihood that a link with relatively low quality may be disrupted. The frequency of data retransmission also will rise as a result, which consumes network energy and reduces NL. The network’s throughput will likewise be lowered proportionately at the same time.\n\nA new “distributed 2-hop cluster routing protocol” (D2CRP) is suggested.61 In order to balance energy usage on packet transmission and CH competition by minimizing the transmission distance, a distributed 2-hop clustering technique is developed. Employing 1-hop neighbor nodes as relays for transmitting data for each 2-hop cluster, a distributed intra-cluster routing approach is employed to achieve energy-efficient transmission in a cluster. To reduce overall transmission distance of each CH, a distributed inter-cluster routing technique is used to connect the CH nodes and send data to the BS in a chain-based manner. As a result, each CH can communicate with the BS using less energy. To decrease the amount of energy used for network transmission, the ideal cluster size of 2-hop clusters is proposed and discovered. This protocol is contrasted with LEACH,62 PEGASIS,35 R-LEACH,63 and TTDFP.64\n\nAfter RLEACH, PEGASIS, TTDFP, as well as the planned D2CRP, the LEACH protocol was the one to fully use the energy. Following the same cycles, the LEACH procedure uses the greatest energy and has the quickest curve growth. The D2CRP has a rate that is approximately 52% worse than LEACH, 27% worse than R-LEACH, 18% worse than PEGASIS, and 2% slower than TTDFP. The suggested D2CRP may be tested in mobile node settings. For practical applications, it is also recommended to investigate developing the routing scheme established on widely adopted standard like ZigBee and Bluetooth.\n\n“A delay-aware green routing protocol for virtual infrastructure” (DGRP) is analyzed.65 To lower the delay in transmission of data, a method for building the virtualized hierarchy of rings is proposed that enables each SN to communicate data toward a virtual sensor (VS) node in a 1-hop communication. A ring maintenance system is also suggested as an answer to the hotspot issue. Without initially acquiring the position of the mobile sink via VS nodes, SNs can transfer data to the sink using DGRP. Instead, Routing based on angle, which aids the VS node in choosing the path with the shortest length, is used to transport the information to the mobile sink through the virtual ring. Therefore, it is suitable for applications that require quick responses. Different experiments are carried out to assess and compare the suggested protocol with existing protocols of critical performance characteristics, such as energy consumption and latency. The ring routing protocol (RRP),66 and “grid-cycle routing protocol” (GCRP)67 are compared with the proposed protocol and their results are briefed as follows.\n\nEnergy utilization of RRP is higher than DGRP because of communication cost required to collect the sink position data prior to data transfers. However, using DGRP, source node sends information to the VS node, which then propagates farther toward the sink using routing based on angle within the ring. Because of its single-ring shape, RRP has the highest energy usage. This problem is solved by DGRP by building several rings. It thus relieves pressure upon SNs that frequently need to gather the sink location data for data transfers. Even though GCRP adheres to a set of guidelines to modify the sink position information, due to the mobility pattern of the sink, it uses a little bit more energy than DGRP. Dense sensor networks can use the suggested routing protocol. Future work will involve adapting DGRP to accommodate numerous mobile nodes to significantly enhance performance of data delivery.\n\n“Destination-oriented routing algorithm” (DORA) is a novel multichain routing technique that is put forth.68 In order to determine the appropriate cluster size of WSNs, DORA is built by taking into consideration both the actual communication distance and the packet forwarding direction in each node. This concept uses mathematical analysis to construct a cluster division that increases communication range and establishes the exact transmitting distance between any two nodes. DORA lowers the transmission energy needed for every routing channel by preventing the formation of the extended chains that might happen when using PEGASIS. It is compared with PEGASIS protocol35 and “random projection-polar coordinate-chain routing” (RPC).69\n\nThe average lifetime performance of DORA is over two times better than that of PEGASIS since PEGASIS’s energy consumption is greatly offset by its unexpected detours and unnecessarily lengthy chain routing pathways. With the polar routing architecture, RPC shortens the transmission path and outperforms PEGASIS in terms of lifespan performance. For different network sizes, DORA outperforms RPC in terms of lifetime by 60%, demonstrating that it can more efficiently shorten the routing path to the sink with a superior transmitting radius and polar angle.\n\nA routing protocol for “energy efficient heterogeneous ring clustering” (E2HRC) is proposed.70 This paradigm, nodes are grouped into various layers according to their relative placements. Additionally, different ring domains are split according to various levels. Figure 4 shows the ring communication topology. This lowers energy required for receiving and sending data by requiring the next node in one hop with the best direction angle to be chosen during interring domain communication. An energy balance-based routing protocol is provided, along with a clustering algorithm for it. The network is divided into various-sized heterogeneous clusters as according to node remaining energy and relative node location inside the cluster using a cluster probability model. Heterogeneous clustering and CH rotating processes are being used to balance node’s energy utilization and prevent the development of a network energy hole. Detailed explanations of the EE heterogeneous ring clustering-based E2HRC routing strategy are given, along with route creation, route maintenance, messages for clustering and clustering rotations.\n\nThe suggested E2HRC and RPL are contrasted.66 When the original RPL was utilized instead of the routing algorithm suggested in this paper, the fluctuation range of node energy usage curve with in WSN was higher. A few energy balanced E2HRC routing protocol phases, including CH ratio calculation, ring domain communication establishment, and probability factor determination, were examined. To maintain uniform in the CH distribution in the rings, CH selection and the probability factor adjustments method were implemented. The lifespan and energy usage of WSNs were properly balanced.\n\nA new routing protocol is proposed, called “energy efficient and reliable routing protocol for mobile WSN” (E2R2).71 A proposed protocol is hierarchical. Our top priorities are accessibility to the nodes and energy efficiency. Node mobility is considered during the routing decision-making process. This kind of routing seeks to maintain data packet transit over appropriate channels despite the mobility of nodes and eventual link failures. Mobility of the BS and the SNs in the routing considerations are considered. The network’s lifespan is extended by using the CH panel concept. The idea of BS feedback on data delivery in it is taken into consideration. This method makes sure that data is sent reliably to the BS; this is done by using various routes and switching between them as the BS sees fit. A modified probabilistic model is considered that can be utilized to choose the most effective path for data transfer. M-LEACH72 is compared with the proposed protocol.\n\nThe nodes move more quickly because of the high mobility environment. This protocol performs better than M-LEACH. However, as more nodes are placed in the field, the energy usage grows as well. The increase in energy usage is brought on by the evidence that as the node number rises, so does the quantity of packet exchanges, which results in a higher energy cost. Once more, average communication energy rises in tandem with network area expansion. This is as a result of the higher energy cost of long-distance communication. Even with the suggested protocol, throughput drops off dramatically while data rate rises.\n\nIt is suggested to use “signal to noise ratio-based dynamic clustering for WSNs” as an effective and safe routing algorithm.73 A hybrid “efficient and safe routing protocol developed using SNR-based dynamic clustering mechanisms” (ESRPSDC) is developed, which is a combination of SNR-based robustic clustering and routing pattern-based safety mechanisms.73 Threshold energy and node energy are the main criteria in this article. The node is chosen as the CH if its energy exceeds the threshold energy. The cluster list will then be modified. A quick comparison of ESRPSDC with two well-liked routing protocols: LEACH and PEGASIS is made.\n\nThe typical energy use, measured as mWh. Whenever the network size is changed with 30% of the nodes being malevolent, all three methods cut power consumption, demonstrating the strength of their clustering. However, ESRPSDC showed roughly 50% higher reductions when compared to LEACH and PEGASIS. The proposed algorithm has to be optimized for both heterogeneous WSNs and energy consumption.\n\nThe proposed protocol is a “biologically inspired secure autonomous routing (BIOSARP)” system.74 The layout of the suggested method is based on enhanced ACO. TelosB radio sensing board that are wireless SNs, also employ BIOSARP. TelosB is a low-power transceiver based on the CC2420 ChipCon chip. Ten TelosB nodes being deployed in the field to construct an extensive WSN testbed. TelosB’s lighting, built-in temperature, and humidity sensors are activated while conducting the experiment. The proposed protocol is compared with “Energy and delay model based on ant algorithms” (E&D ANTS)75 and “improved energy efficient ant-based routing (IEEABR)”.76\n\nWhen compared to E&D ANTS, BIOSARP acquires a lot less routing burden. This is because BIOSARP avoids using forward and backward agents and analyzes the data packets as needed. Additionally, BIOSARP outperforms SRTLD because it doesn’t run the broadcast operation on each hop. Comparing the results of BIOSARP and IEEABR reveals that BIOSARP uses less energy and also that the enhanced ACO algorithm used by BIOSARP is the sole cause of the better results.\n\nThe “efficient dual-path geographical routing” (EDGR) protocol is suggested.77 EDGR utilizes two node-disjoint anchored lists that travel via both sides of routing holes to achieve dual-path routing, which prevents data being transferred over the boundaries of routing holes. By sending every data packet to the destination across two paths, if possible, in greedy form rather than bypass mode, this shortens the routing time and balances the load. In the event of a node malfunction in relay area, EDGR offers an innovative alternative technique to choose an effective forwarder by including a random shift to the position of the sub-destination. Without additional communication overhead, such a strategy is practicable, reasonable, and EE. EDGR is expanded into 3D sensor networks and should provide energy-aware forwarding for routing hole detour. The performance of EDGR and its extension in a variety of communication contexts, including various communication durations, network densities, and routing hole widths is evaluated. “Energy-efficient beaconless geographic routing” (EBGR),78 “Energy-efficient Multicast Geographical Routing” (EMGR), and “Power Adjusted Greedy- Cordinate Face(1)” (PAG-CFace(1)-PAG)79 are compared with EDGR.\n\nThe energy utilization increases in all the protocols compared in this article. This is due to the routing hole which lengthens the data transmission path. The energy is less utilized by both EDGR and EMGR which is as per the EBGR standard. Despite this, the NL of EDGR and EMGR are increased which is more than EBGR by 12.8% and 6.5% respectively. Also the EDGR uses less energy in comparison with PAG-CFace(1)-PAG which is 10.5% below that of PAG-CFace(1)-PAG even though the communication time increases. For less communication duration also the suggested algorithm uses least energy.\n\nA suggested protocol for “enhanced balanced energy-efficient network-integrated super-heterogeneous” (E-BEENISH) routing is studied.80 A mechanism that took the distance between both the source and the destination nodes into consideration is created to circumvent the overly straightforward threshold setting of the suggested protocol. The problem of the node farther from the BS dying early due to its energy consumption is exacerbated worse when the node remote from the sink node serves as the CH. The suggested protocol chooses CHs when taking into consideration the distance factor, the average energy of the network, and the leftover energy to avoid the ping-pong effect. A normalized weighting constant is suggested to increase the NL and evenly distribute the energy and proportion of distance in the thresholds design more evenly. “Stable Election Protocol” (SEP),81 “Distributed Energy Efficient Clustering” (DEEC),82 and “Centralized Energy Efficient Clustering” (CEEC)83 are compared with this protocol.\n\nIt is clear that the SEP protocol performs well in the beginning, but as the number of rounds increases, performance rapidly declines. The network’s lifetime has increased by roughly 60%, 40%, 15%, and 25% compared to protocols for comparison, respectively. E-BEENISH also has more total leftover energy than other procedures. Although the suggested technique extends the lifespan of heterogeneous networks, it also makes the procedure more difficult. The technique, however, does not account for the network jitter and delay brought on by the latency in the data transmission phase.\n\n“Multi-threshold segmentation-based energy efficient routing” protocol (EERPMS) is suggested in Ref. 84. A connection among node clustering and multi-threshold image analysis transforms the difficulty of node clustering into the difficulty of choosing the right segmentation threshold. Combining the Otsu algorithm with node angle and number results in a cluster creation methodology based on the variation of node angle and numbers between clusters. Various communication models among nodes in various scenarios are addressed to prevent substantial energy consumption among nodes brought on by the multi - path fading model. To decrease node energy consumption and lengthen NL, a multi-threshold segmentation-based energy-efficient routing protocol is presented. It is merged with the multi-threshold segmentation-based node clustering technique and the CH selection method based on the optimal CH position. This protocol is compared with63 Residual energy based - LEACH\" (R-LEACH),63 FIGWO,50 and “Clustering Routing Protocol based on Fuzzy C Means” (CRPFCM).\n\nThe energy usage of our suggested EERPMS has consistently been maintained to a minimum. The number of loads carried by CHs in each cycle is essentially the same because the load balancing factor is considered during clustering. The highest residual energy is in the EERPMS network. The EERPMS protocol can also save up to 64.5%, 58.60%, and 56.15% of network energy when compared to the protocols taken for comparison.\n\nThe “energy-saving clustering by voronoi adaptive dividing (ESCVAD)” technique is suggested in Ref. 85. It is successful in realizing dynamic clustering of WSN. Additionally, it fixes two problems with the standard WSN routing protocol, namely the uneven distribution of cluster and SN node deaths. Based on thorough weighing of distance and energy, an optimization approach for CH selection is developed. By efficiently balancing the energy use between both the CH node and the cluster member (CM) node, this approach increases the NL In addition to accounting for the effect of the CH’s positioning on the transmitting energy consumption, it also takes into account the energy level of the cluster-own head. This proposed an approach for reliable working time optimization. From the CH election stage through the stable operation stage, the relation between control signaling and energy consumption via signaling are both optimized. Energy consumption may be made to be more stable and gradual by designing the operating stage appropriately. “Minimum Transmission Energy” (MTE86), LEACH,87 “Centralized-LEACH” (LEACH-C), “Stable Election Protocol” (SEP),88 and TEEN89 are compared with the protocol suggested.\n\nESCVAD uses a lot less energy during the first two phases of signaling contact than other protocols. The MTE Protocol does have the fastest energy consumption, and it is almost twice as much as ESCVAD. The residual energy of the ESCVAD protocol has the slowest declining trend and the least energy consumption rate. While signaling only uses 0.31 J, ESCVAD’s energy consumption for data transfer work is 199.69 J. First two stages of the other five regimens’ energy requirements range from 29.28 to 52.04J. This outcome may indicate that the ESCVAD significantly increases energy efficiency compared to the other five treatments. Sink node element can also be taken into account as a movable factor in the detailed analysis of ESCVAD in the future. WSN routing algorithm in a mobile environment with the aid of this architecture should be explained.\n\n“Multi-hop routing protocol is built on game theory and coverage optimization (MRP-GTCO)” is studied in Ref. 90. To prohibit the data of cluster members from not being transferred owing to the selfishness of nodes will not become the CH in the current network, a punishment mechanism depending on node residual energy and node degree is developed. In a clustering game with a punishment system, the likelihood of nodes becoming CHs is examined. An original CH selection strategy based upon that CH coverage rate and remaining energy is given in order to achieve the consistency of CHs and lower the transmission energy usage across nodes. The best multi-hop relay select theorem for clusters has the objective of transferring intra-cluster data to BSs whilst CHs consume the smallest amount of energy under a variety of circumstances. “Localized game theoretical clustering algorithm” (LGCA),91 R-LEACH,63 and “energy efficient clustering algorithm based on game theory” (ECAGT)92 are used for comparison of the proposed protocol.\n\nThe proposed MRP-GTCO protocol maintains a range of CHs between 6 and 10, and in most cases, this range can fluctuate around the ideal range of cluster - head (10 nodes), which will help to ensure that the proposed protocol can operate with minimal network energy usage and guarantee energy efficiency. The MRP-GTCO CHs are evenly distributed over the detection region, and the distances between them and other CHs or cluster members are reasonable. There are nine CHs, which is nearly the ideal number. However, MRP-GTCO can always send more data packets to the BS while the network uses the same amount of energy. As a result, MRP-remarkable GTCO’s energy efficiency is evident. There is still room for improvement in MRP-final GTCO’s node death rounds.\n\n“A hybrid method called energy and traffic aware sleep-awake (ETASA)” is proposed by Ref. 93. In heterogeneous WSN, a hybrid technique for load balancing and energy efficiency has been presented.\n\nFigure 5 demonstrates the clustering process. The possibility that a node will be chosen as CH is increased by the CH selection process, which favors highest enhancement of energy of node, the least amount of traffic, and also the most pairings. The load balance is enhanced by this CH selection technique. To decrease the number of permitted slots, idle monitoring in the network, and energy usage, the conventional “time division multiple access” (TDMA) scheduling by giving one slot to a group of pairs is broadened. Evaluation of the proposed method’s performance utilizing current cutting-edge baseline routing protocols. For that it is compared with the “Traffic and energy aware routing (TEAR)” protocol is presented in Ref. 94, and the “Sleep-awake energy efficient distributed“(SEED) algorithm.95\n\nComparing the ETASA algorithm to TEAR and SEED, it has more energy left over. The CH selection approach employed in ETASA improves load balancing since it avoids choosing isolated nodes for CH roles, in contrast to TEAR, where the CH selection procedure primarily focuses on choosing high energy and low traffic nodes. The outcome demonstrates that the suggested ETASA has lifespan improvement against TEAR and SEED of 16% and 15%, respectively. The same network takes into account the traffic variability within the context of various zones.\n\n“Mobile sink-based adaptive immune energy efficient clustering protocol (MSIEEP)” is studied.96 MSIEEP was created to increase WSN longevity and lessen the energy hole issue. The positions of the mobile sink, the optimum number of CHs, and their placements are determined by MSIEEP using the Adaptive Immune Algorithm (AIA), which aims to minimize the total energy deficit through effective communication and overhead control packets forwarded by all nodes in the network. LEACH,33 “Mobile sink improved energy efficient PEGASIS-based” routing protocol (MIEEPB)97 are compared with the protocol in discussion.\n\nIt is clear that mobile sink improves the network’s lifetime and stability. Additionally, it boosts the network’s throughput while lowering energy loss. Additionally, comparing to MIEEPB protocol and rendezvous protocol, the suggested three moving patterns increase lifespan of the network by 56.79, 62.43, and 103.35% and by 30.35, 35.04, and 69.06%, respectively. Regarding the static sink, it can be shown that the proposed technique extends the stability time by 1315, 888.5, and 878.65 rounds, respectively, when compared with other protocols. In contrast, the stability period in the mobile sink case increased by 1875.2, 1732.2, and 1722.2 rounds, respectively, in comparison to the LEACH.\n\n“Mode-switched grid-based routing (MSGR) protocol for WSN” is proposed.94 A grid head is selected from each virtual grid that covers the entire sensing region. The MSGR protocol is then used to send data packets to the mobile sink. In its concluding portion, it suggests a method for limiting sink mobility and grid head re-election. An “energy-aware grid-based routing technique” (EAGER) for WSN95 is compared with MSGR.\n\nMSGR has more active nodes than the current protocol EAGER throughout the time period specified. This is due to MSGR’s ability to conserve more energy in nodes by alternatively putting data-disseminating nodes in the active or sleeping state. Additionally, additional node energy is lost as a result of the overhead rerouting in EAGER.\n\nDue to the alternate switching of grid-head states, the proposed MSGR uses significantly less energy per node on average, avoids flooding of control packets for establishing routing paths (unlike EAGER), and doesn’t constantly reroute to find the shortest path. According to the methodology used, EAGER utilizes more energy per node than the way that was suggested. Future work on this project can be expanded by employing several mobile sinks.\n\n“An optimized protocol called straight-line routing” (SLR) is proposed.98 A unique random-walk routing system that we suggest is straight-line routing (SLR). This is really effective and easy to implement. Together, it considers low energy consumption and a high probability of successful path discovery. Monte Carlo simulations support the effectiveness of the strategy in this regard. Meandering pathways used by RR waste energy, and the packet payload contains a log of the nodes it has visited. RR does not choose visited nodes as a result, but it does not result in better searching directions. SLR, like RR, performs best when there are so few occurrences, as was already mentioned. In a WSN environment, this makes sense because nodes typically only form a small number of information requests (emergency events) when watching a region. By accounting for multiple beginning orientations, it also raises the baseline SLR. Then, it notes that reversing the initial direction might be a smart move if it goes away from the desired location. SLR expects a random-walk-style protocol to be more scalable and energy-efficient as a result. It is compared with “rumor routing” (RR).99\n\nThe overall energy cost with a transmitting range of 50 can be decreased for RR because of hop count for all SLR techniques is lower than those for RR. Notably, all ratios were below 50% for small networks (transmission range of 50). Due to the possibility of numerous unreachable cases, this performance is not regarded as satisfactory.\n\nWe discuss the Q-DAEER algorithm, “an innovative Q-learning-based data aggregation-aware EE routing protocol”.100\n\nFigure 6 shows the schematic for the system used in this paper. In order to locate a global best path, lower total energy consumption, and increase WSN lifespan, this work offers an energy-aware routing method. A node determines the potential levels of data aggregation from nearby nodes when it must select a routing path. Data from different sensor types (such as temperature and vibration measurement sensors) may not correlate strongly, therefore they cannot be combined. Utilizing the revised Q-values depending on the incentives, these SNs can select the best next node in the network in this way. This algorithm is compared with the “shortest path routing (SPR)” and “shortest path routing with data aggregation (SPRwDA)”.\n\nBecause the SPR and SPRwDA employ the shortest transmission path, which is only defined by the present network architecture, the energy usage at each time step is nearly constant. Since SPRwDA employs the suggested data aggregation technique prior to transmitting data at each node, it is clear that less energy is used than in SPR. The strategy dynamic reward update rule used in the proposed Q-DAEER technique causes each SN in the WSN utilizing this same proposed routing algorithm to have dynamic energy usage. Since data aggregation model 1 has the maximum efficiency, it uses the least energy on average compared to the other models. The suggested Q-DAEER can lower energy usage for 3 data aggregation models by 67%–32% compared to SPR and by 25%–5% compared to SPRwDA. The suggested Q-DAEER algorithm contains a data action selection algorithm and a Q-table updating technique, although the latter initially takes more time.\n\nQSDN-WISE is a “QoS-based routing strategy that combines local network upkeep, a routing algorithm, and a clustering method” is proposed.101 For software-defined WSNs, a brand-new QoS-based routing strategy based on SDN-WISE is suggested. A centralized architecture built on SDN-WISE is developed to allow complex network administration and boost system adaptability. It is advised to use a “double CH-based uneven clustering” (DCHUC) method to reduce the strain on CHs and avoid the energy hole problem. Built on SDN-WISE, QSDN-WISE is a QoS-based routing protocol that can support data with different QoS requirements. SDN-WISE framework,102 “Disjoint multipath routing protocol” based on SDN (SDN-DMRP),103 HEED,104 “Improved Routing Protocol for Low power and Lossy networks” (IRPL),104 and “Energy-efficient Unequal Clustering” (EEUC) are compared with the proposed protocol.\n\nThe network lives in suggested protocol and SDN-DMRP are greater than those in SDN-WISE under the assumption of the same number of nodes. As multi-path routing is used in SDN-DMRP, which distinguishes energy consumption, the NL is longer than in SDN-WISE. Due to clustering algorithm in QSDN-WISE takes into account the node remaining energy when selecting cluster-head nodes and employs the concept of non-uniform clustering to control the network energy consumption, the lifetime of the network in QSDN-WISE is significantly longer than in SDN-DMRP and SDN-WISE. In order to better balance the network’s energy usage, QSDN-WISE employs multi-path routing based on the double CHs and takes into consideration node residual energy.\n\n“A new distributed mobile sink routing technique” is proposed.66 In this study, a new hierarchical routing method for WSNs with a mobile sink called Ring Routing protocol is described. When using ring routing, a virtual ring structure is created that makes it simple to add new sink locations to the rings and for regular nodes to rapidly and effectively borrow sink locations from the rings as needed. The mobile sink selects the BS along sink’s path in order to relay sensor data to them. To avoid packet losses in the case that a SN’s sink position information becomes out-of-date, the sensor data is sent from the old BSs to the new BS. Ring Routing can be used with sensors which use asynchronously low-power MAC protocols designed for WSNs because it only necessitates a limited number of broadcasts. Ring routing just requires the MAC layer to be able to support broadcasts. It is suitable in situations when sink movement is unpredictable and will not depend on predicting the trajectory of the sink. Ring Routing’s performance is compared with “Line-Based Data Dissemination“(LBDD)105 and Railroad106 compared with the proposed protocol.\n\nThe typical energy usages of Ring Routing, LBDD, and Railroad for different sink speed values are compared. Ring routing provides optimum performance in every circumstance. Regarding values for sink speed, LBDD performs better than Railroad. There is a cost associated with the energy advantages of ring routing. In every scenario, Ring Routing results is better in terms of average energy consumption than LBDD and Railroad. Ring routing as well as LBDD both perform consistently across a range of network sizes, while Railroad’s performance suffers noticeably for bigger networks. By simply keeping the positions of each sink on the ring, it is simple to adapt the concept of Ring Routing to work with many mobile sinks. However, without considering the benefits of employing many sinks, this would merely be a change.\n\n“A distributed robust routing protocol” is presented.79 The contribution is the investigation of distributed EE stable routing for mobile WSNs. This suggested methodology only requires local knowledge because cooperative relay is carried out at each step. Lower layer coordination is required for multi-node cooperation. The dependable cooperative routing is centered on a cross-layer design that leverages the IEEE 802.11 scheduling scheme that has been proved to be efficient in past studies. After establishing a path between the source and destination nodes, robust cooperative routing may ensure delivery of packets both against temporary and permanent path breaking. Since more robust and dependable links are selected for routing, cooperation between nearby nodes also increased energy efficiency. Selecting dependable lines may lessen the need for retransmissions, conserving energy and cutting down on delays. Performance is significantly improved by the robust cooperative routing technique when mobility of nodes and connection error are present. “Destination Sequenced Distance Vector” (DSDV),107 and “Adhoc on Demand Distance Vector” (AOMDV)108 are compared here.\n\nThis efficient routing protocol uses more energy per bit as node mobility rises. Since control overhead experienced while path discovery does not change significantly with node mobility, the energy usage of AOMDV is only tangentially connected with node mobility. As anticipated, node mobility causes a dramatic increase in the energy usage of DSDV as frequent topology changes result in more overhead. Although at a far slower rate than DSDV, this resilient routing algorithm also requires more energy as mobility of nodes rises. Instead of creating a new E2E path, the best relay node with modest message exchange is chosen. When the maximal node mobility is low, RRP’s energy consumption is lower than AOMDV’s, but it gradually approaches it as the highest node mobility rises. The cause is that packets at high mobility must frequently go through the cooperative procedure. The freshly self-nominated node on the desired path also sends update messages more frequently to update path information, which explains the increase in energy usage. Due to the collaboration process and the longer back off delay, RRP transmits packets with a longer delay than DSDV.\n\n“A new energy efficient routing strategy for 3D WSNs based on a delicate ant colony algorithm” proposed.109 The causes behind the performance degradation of 2-D WSN routing protocol over 3-D WSNs is investigated.\n\nFigure 7 explains the proposed system model for the network. Sink node (SN) and ‘n’ regular nodes will be present in the network. The center of the sensor network is where the SN is located. Ordinary nodes (OD) cannot have their isomorphic energy raised and are randomly distributed in three dimensions. Every node has a unique ID on its own. The communication power of OD can be altered in accordance with the communication distance. CH nodes analyzes the information at the cluster nodes using the data fusion approach. Nodes regularly acquire data and continuously transfer data to SN. The nodes with lower overall distances from the nearby nodeshave a better probability of becoming CHs when the comparative distance among nodes and the neighboring nodes are taken into account. The SN assumes the OD role and utilizes the CH update mechanism to build a routing table unique to each CH. It is advised to use a novel path-finding method based on the ant colony method. The construction of wireless sensor networks is better suited for this technique. In addition to an overall length of the generated path, the algorithm also considers the energy of nodes that the path passes through. LEACH-3D,110 “Advanced Zonal Stable Election Protocol” (AZ-SEP),111 “Unequal clustering routing protocol” (UCNPD)112 considering energy balancing based on “network partition and distance” are compared with the proposed protocol.\n\nEven when the UCNPD-3D protocol, which is less successful than this protocol but still effective, loses half of its nodes, the average remaining energy of the nodes in this protocol is still higher than 50%. As a result, performance of the suggested algorithm is better than the other three protocols. This protocol utilizes the technique of SN route path generation and works in conjunction with the CH and SCH rotation mechanisms as well as the fragile collection ACO algorithm. This algorithm uses less energy throughout the clustering and route path construction processes, outperforming the other three protocols in terms of overall energy consumption.\n\nBased on an “improved Archimedes optimization method, a WSNs routing” protocol (IAOAR) is proposed.113 By improving the Archimedes optimization method, a fitness function is developed to identify the best CH location in relation to the distance between the virtual CH and the sink node as well as the energy is associated with the SN, which also controls energy usage between both the common node and the CH. The better position adjustments of CHs under the attraction of virtual force are researched in order to reduce the excessive energy loss caused by the near closeness of CHs. The augmented ACO algorithm is presented to find the minimal path among CHs for multi-hop data transfer. The improved ACO algorithm increases the ACO algorithms’ capability for global search by analyzing the ant scale, ant propagating direction, and changeover probability all through the entire search process. LEACH, “Energy consumption-based LEACH” (E-LEACH),114 “Maximum-LEACH” (MAXLEACH)115 are compared with the proposed protocol.\n\nThe protocol suggested in this study still has high energy compared to the other protocols that have virtually used up all of their energy. The primary explanation is that this algorithm, when choosing the CH, takes into account not just the node’s current energy but also its distance from the sink node and its location inside cluster. More crucially, the virtual force is employed to scatter the CHs equally as farther as possible, reduce transmission distances, and also consume less energy by repelling the CHs at close range. Even after the last remaining nodes of initial four algorithms have been exhausted, IAOAR nevertheless survives a significant number of nodes. This method contains fewer nodes during the same round than other algorithms. The reason is that this paper introduces multi-hop transmission along with balancing the consumption in the cluster. It uses an enhanced ACO algorithm to determine best route for transmitting information, which lowers the energy usage of CH nodes that are located far away from sink nodes and increases the network lifespan. However, the technique suggested in this research has to be further refined in heterogeneous WSNs whereas the effect of heterogeneous SNs on network’s energy usage is not taken into account.\n\n“RowBee, a new routing technology built on the cross-technology communication (CTC)” principle is proposed.116 To the best of our knowledge, the problem of a routing protocol based on CTC has never been studied in earlier literature. A simple but efficient routing method is described that use a WiFi gadget as a centralized coordinator to transmit the information to the neighboring ZigBee devices in order to reduce E2E delay. The ZigBee nodes will wakeup simultaneously in response to these beacons’ rendezvous in order to transmit data. The results of the investigation show how drastically RowBee’s simple architecture may reduce data transfer latency. Because it doesn’t require changing the node duty-cycle schedules, RowBee is very power-efficient.”Plant-Bioenergy MAC“(PB-MAC)117 is compared with the new protocol.\n\nThis algorithm uses less energy than PB-MAC for just any number of nodes, and the energy consumption rises gradually as the number of sensors rises. Particularly, the energy expenditure disparity rapidly widens when more sensors are added to the situation. As the number of sensors nodes rises, so does the energy usage. However, RowBee consistently consumes less energy than PB-MAC.\n\nWSN protocol for “secure and energy-conscious heuristic-based routing (SEHR)” is proposed.118 The goal of this study was to suggest a WSN heuristic routing technique that is secure and energy-conscious.\n\nFigure 8 depicts the architecture of SEHR protocol. It is classified into three modules as shown in the figure. Due of its limited resources, the SEHR protocol’s main objectives are effective utilization of energy, dependability, and secured information transfer performance. In this study, the beam heuristics-based SEHR protocol is used to achieve better data routing. It uses aggregate power, number of hop count, and integrity of link measurements to understand the decision of routing. The optimized results are produced by a beam-based heuristic algorithm, which was created in the recognized area of artificial intelligence. The processing and memory requirements on SNs are reduced by the proposed protocol, which also develops a graph-based solution is based on beam heuristics. The studied protocol also provides data authentication and encryption for inter-routing security using the cryptographic algorithm counter mode (CTR). Since the encryption of each datagram depends on the one before it, the proposed algorithm is more reliable and secure. The suggested work provides a method for route maintenance in addition to dynamic sensing and isolation of hostile nodes even during data security phase. The proposed protocol significantly enhances the network efficiency of low-powered sensor elements in terms of many network properties as compared to current cutting-edge alternatives. SecTrustRPL,119 “heuristic-based EE” routing,120 and PSO-based routing121 are compared with the proposed protocol.\n\nThe SEHR protocol’s performance evaluation in comparison to the current solution is shown in terms of a range of node counts and data processing rates. In the presence of faults nodes, the SEHR protocol reduces energy consumption by an average of 39% and 33%, respectively. Due to its smart and fault-tolerant routing method, the SEHR protocol has been successful in stabilizing the routing direction for considerable amount of time. As a result, nodes with greater energy levels are chosen as data forwarders, minimizing the proportion of extra energy usage in route request and responder packets. The goal will be to enhance the SEHR protocol in the future by utilizing some simple machine learning-based approaches to provide the network more intelligence and fault tolerance.\n\n“Sustainable multipath routing protocol” (SMRP) is proposed.122 For multi-sink WSNs, a multi-path routing strategy called SMRP is recommended. To validate the effectiveness of proposed protocol in regards of endurance, efficiency, and delay of delivery, extensive simulation studies have been carried out. In SMRP, SN routing decisions are based on the local environment, the remaining energy, as well as the depth information. Two distributed multi-path routing algorithms are contrasted with SMRP: “Information Potential Field” (IPF)123 and “Energy-aware dual-path geographical routing” (EDGR).77\n\nProposed method performs best in three routing protocols in terms of PDR and “portion of living node” (PLN). Due to the fact that, EDGR and IPF will not take the external environment into account during routing, its pathways are susceptible to environmental influences. Transmission of data will become even more concentrated as more channels are closed for environmental reasons, which worsens the network’s energy imbalance. In contrast, SMRP can utilize the benefits of multi-path for energy balance more effectively because of high path chance of survival in challenging conditions. The efficiency of static multi-sink WSNs’ routing is main topic of this paper. Future work can expand proposed method to mobile multi-sink WSNs.\n\n“Trust and energy aware routing protocol (TERP)” is proposed.124 The shortcomings of current trust-based routing protocols have been specifically addressed by the development of a TERP. Given the resource - constrained nature of WSN, TERP was designed with dependability and energy efficiency in mind. TERP has the capacity to proactively identify and exclude bad nodes during the trust evaluation phase. The routing protocol, in contrast, features an energy awareness element during the route setup phase that enhances load balancing among trusted nodes. In addition to methods that ensure E2E paths are selected while taking the current levels of energy of the intermediate nodes under consideration, the TERP protocol was designed with trust-based routing integrated. This is essential because some network nodes’ high energy consumption can lead to their death and impair the network’s capacity to function. Since it is always desirable to choose short routes that need fewer wireless broadcast and cause fewer disturbance with the wireless medium, TERP also takes into account the total path length of any best path. Compared to other cutting-edge protocols like “Lightweight trust based routing protocol “(LTB-AODV)”,125 and “Trust-aware secure routing framework” (TSRF),126 the TERP is briefed as follows.\n\nSince TERP’s architecture emphasizes reliability and energy efficiency, it keeps a significantly excellence in terms of computational time since the composite routing metric chooses reliable and EE nodes for routing. When nodes are chosen based on trust parameters, both LTB-AODV and TSRF don’t carry out any load balancing. Instead, they stay a part of effective routes until their energy runs out. As a result, existing systems perform inadequately in terms on network longevity under conditions of high network traffic. The TERP scheme provides a simple solution for SNs with limited resources, but its effectiveness on actual hardware platforms has to also be verified. Future work might be thought of as a modest testbed for the actual implementation of the suggested TERP method.\n\n“An energy and temperature-aware, weighted, QoS-based routing protocol” known as (WETRP) is proposed by Ref. 127. The two steps of the suggested method are route identification and route maintenance. Hotspots and energy-poor nodes are avoided during route discovery which determines the shortest path with the lesser amount of link lag among both the sender and the receiver node. The “thermal-aware routing algorithm” (TARA),128 and “Hotspot preventing routing” (HPR)129 are compared with the proposed work.\n\nThe network resource determines a network’s lifespan. The lifespan of network is increased via better resource management. In terms of network longevity, WETRP beats other systems because TARA and HPR concentrate on eliminating hotspot nodes and locating the coolest neighbors, respectively. This causes inefficient use of valuable resources, which causes network nodes to lose energy more quickly. WETRP, on the other hand, is thermal and energy-aware strategy that maximizes NLby making an intelligent choice about temperature and energy, giving both variables equal weight. Future versions of this study could be tailored to address the problems brought on by postural body movement. Additionally, the suggested approach can incorporate packet-level priority so that important data packets can be distinguished from non-critical data packets and routed according to priority.\n\n\nComparison of enhanced energy efficient protocols reviewed\n\nThe various EE protocols are listed in Table 2. Their comparison with the factors of energy efficiency are listed which could help researchers and academicians to understand the research gaps in WSNs. It help to understand the factors to improve lifetime of WSNs.\n\n\nIssues and challenges of energy-efficient protocols in WSNs\n\nWSN protocols must overcome many challenges so that it can be more EE and more precise. One of major factor which must be analyzed in WSNs is the mobility of nodes in the network which must be considered while designing a protocol. When the distance between the nodes in WSN is more, packet delay and sum of path length will be increased which further affects the efficiency of the network. Hence an efficient protocol should take care of this parameter. In some protocols the implementation will be very complex which will not be very effective for real time applications. The protocols must be optimized for both heterogeneous WSNs and energy consumption. The heterogeneous WSN’s lifespan can be improved, but care must be taken to reduce the complexity of the protocols. WSNs which involve large areas of network coverage, the protocols should be able to consider multiple clusters and CH selection becomes the most important factor which will help in reducing the energy utilization of nodes. The protocols should consider congestion and also data transmission due to clustering and multiple hops among the clusters. Asynchronous duty cycles between the SNs can also help to increase energy economy and routing performance.\n\n\nConclusions\n\nIn real life scenario, there are widespread applications of WSNs. The integration of the IoT with WSNs has been of great interest in recent times. This makes the WSN technology an open area for advancement in research and development. In the past years, more involvement is shown by a lot of researchers/academicians across the globe in this area where works have been carried out to make the WSNs more EE, improving the lifespan of the networks. Based on the above factors, in this work a sincere attempt is made to compare different protocols which make the WSNs more efficient with respect to utilization of energy, lifespan of the network, throughput and so on. Different protocols have been considered in this work, which are thoroughly compared with the standard protocols based on various factors which makes the protocols considered in this review more EE than the already existing ones. Apart from the various factors which have been considered in this article for making the WSNs more EE, there are many more parameters which can be still taken up or future study. This limitation can be overcome by researchers by studying the parameters not considered in this article. The work will help as a one stop check point for the researchers as it gives more insight into the factors that make the protocols understudy more EE and robust.",
"appendix": "Data and software availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe would like to thank the Department of Electronics and Communications, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal for providing us with the required resources which helped us a lot in completing our research work in a very smooth manner.\n\n\nReferences\n\nAgrawal R, et al.: Classification and comparison of ad hoc networks: A review. Egypt. Inform. J. Mar. 01, 2023; 24(1): 1–25. Elsevier B.V. Publisher Full Text\n\nAlkhatib AAA, Elbes MW, Maria EMA: Improving accuracy of wireless sensor networks localisation based on communication ranging. IET Commun. Nov. 2020; 14(18): 3184–3193. Publisher Full Text\n\nSinghal S, Gankotiya AK, Agarwal S, et al.: An investigation of wireless sensor network: A distributed approach in smart environment. 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Publisher Full Text\n\nZhang W, Han G, Feng Y, et al.: IRPL: An energy efficient routing protocol for wireless sensor networks. J. Syst. Archit. Apr. 2017; 75: 35–49. Publisher Full Text\n\nIEEE International Conference on Communications: proceedings. IEEE Xplore. 2008.\n\nShin J-H, Kim J, Park K, et al.: Railroad: Virtual Infrastructure for Data Dissemination in Wireless Sensor Networks.2005.\n\nPerkins CE: Highly Dynamic Destination-Sequenced Distance-Vector Routing (DSDV) for Mobile Computers.\n\nMarina MK, Das SR: On-demand multipath distance vector routing in ad hoc networks. International Conference on Network Protocols. 2001; pp. 14–23. Publisher Full Text\n\nZhang T, Chen G, Zeng Q, et al.: Routing Clustering Protocol for 3D Wireless Sensor Networks Based on Fragile Collection Ant Colony Algorithm. IEEE Access. 2020; 8: 58874–58888. Publisher Full Text\n\nRecent Advances in Communications.\n\nKhan FA, Khan M, Asif M, et al.: Hybrid and multi-hop advanced zonal-stable election protocol for wireless sensor networks. IEEE Access. 2019; 7: 25334–25346. Publisher Full Text\n\nZhang DG, Liu S, Zhang T, et al.: Novel unequal clustering routing protocol considering energy balancing based on network partition & distance for mobile education. J. Netw. Comput. Appl. Jun. 2017; 88: 1–9. Publisher Full Text\n\nYao Y, Xie D, Li Y, et al.: Routing Protocol for Wireless Sensor Networks Based on Archimedes Optimization Algorithm. IEEE Sens. J. Aug. 2022; 22(15): 15561–15573. Publisher Full Text\n\nInstitute of Electrical and Electronics Engineers and Shenyang Normal University: Proceedings of 2020 IEEE International Conference on Power, Intelligent Computing and Systems: ICPICS 2020: Shenyang, China, July 28-30.2020.\n\nSuman J, Shyamala K, Roja G: Improving network lifetime in WSN’s based on maximum residual energy. 2021 2nd International Conference for Emerging Technology, INCET 2021. Institute of Electrical and Electronics Engineers Inc; May 2021. Publisher Full Text\n\nGao D, Zhang S, Zhang F, et al.: RowBee: A Routing Protocol Based on Cross-Technology Communication for Energy-Harvesting Wireless Sensor Networks. IEEE Access. 2019; 7: 40663–40673. Publisher Full Text\n\nWu Y, Li B, Zhu Y, et al.: Energy-Neutral Communication Protocol for Living-Tree Bioenergy-Powered Wireless Sensor Network. Mob. Inf. Syst. 2018; 2018: 1–15. Publisher Full Text\n\nHaseeb K, Almustafa KM, Jan Z, et al.: Secure and energy-aware heuristic routing protocol for wireless sensor network. IEEE Access. 2020; 8: 163962–163974. Publisher Full Text\n\nAirehrour D, Gutierrez JA, Ray SK: SecTrust-RPL: A secure trust-aware RPL routing protocol for Internet of Things. Futur. Gener. Comput. Syst. Apr. 2019; 93: 860–876. Publisher Full Text\n\nBinu GS, Shajimohan B: A novel heuristic based energy efficient routing strategy in wireless sensor network. 2083. Publisher Full Text\n\nEdla DR, Kongara MC, Cheruku R: A PSO Based Routing with Novel Fitness Function for Improving Lifetime of WSNs. Wirel. Pers. Commun. Jan. 2019; 104(1): 73–89. Publisher Full Text\n\nFu X, Yang Y, Postolache O: Sustainable multipath routing protocol for multi-sink wireless sensor networks in harsh environments. IEEE Transactions on Sustainable Computing. Jan. 2021; 6(1): 168–181. Publisher Full Text\n\nLiu Y, Dong M, Ota K, et al.: ActiveTrust: Secure and Trustable Routing in Wireless Sensor Networks. IEEE Trans. Inf. Forensics Secur. Sep. 2016; 11(9): 2013–2027. Publisher Full Text\n\nAhmed A, Bakar KA, Channa MI, et al.: TERP: A Trust and Energy Aware Routing Protocol for Wireless Sensor Network. IEEE Sens. J. Dec. 2015; 15(12): 6962–6972. Publisher Full Text\n\nMarchang N, Datta R: Light-weight trust-based routing protocol for mobile ad hoc networks. IET Inf. Secur. Jun. 2012; 6(2): 77–83. Publisher Full Text\n\nDuan J, Yang D, Zhu H, et al.: TSRF: A trust-aware secure routing framework in wireless sensor networks. Int. J. Distrib. Sens. Netw. 2014; 2014. Publisher Full Text\n\nBhangwar AR, et al.: WETRP: Weight Based Energy Temperature Aware Routing Protocol for Wireless Body Sensor Networks. IEEE Access. 2019; 7: 87987–87995. Publisher Full Text\n\nTang Q, Tummala N, Gupta SKS, et al.: TARA: Thermal-Aware Routing Algorithm for implanted sensor networks. Lecture Notes in Computer Science. Springer Verlag; 2005; pp. 206–217. Publisher Full Text\n\nBag A, Bassiouni MA: Hotspot Preventing Routing algorithm for delay-sensitive applications of in vivo biomedical sensor networks. Inf. Fusion. Jul. 2008; 9(3): 389–398. Publisher Full Text"
}
|
[
{
"id": "226763",
"date": "14 Feb 2024",
"name": "Sarang Karim",
"expertise": [
"Reviewer Expertise IoT",
"WSN",
"UWSN",
"Routing Protocols",
"Smart Agriculture",
"Machine Learning",
"Water Quality Analysis"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors conduct a comprehensive survey on energy-efficient WSN routing protocols; however, there are major flaws in the article:\nThe work is updated and currently focused by the many researchers around the globe. So I validated their work, but the work must be comprehensive and compared with the latest existing survey papers\nThere are many survey articles on WSN; authors must compare their surveys with existing surveys in terms of table and descriptions.\nThe authors suggest future analysis to make WSN more energy-efficient without specifying how this analysis will be conducted or the expected outcomes. Providing more clarity on the proposed future work would strengthen the context.\nThe section \"Issues and challenges of energy-efficient protocols in WSNs\" needs more explanation and justification.\nThe section \"Issues and challenges of energy-efficient protocols in WSNs\" must also proposed new trends and solutions to tackle the challenges.\nAuthors are encouraged to cite the latest papers from 2023.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly",
"responses": [
{
"c_id": "11364",
"date": "16 Apr 2024",
"name": "Pramod Kumar",
"role": "Author Response",
"response": "We have updated article as per reviewer comments and incorporated all the changes in the article."
}
]
}
] | 1
|
https://f1000research.com/articles/12-644
|
https://f1000research.com/articles/12-1527/v1
|
28 Nov 23
|
{
"type": "Study Protocol",
"title": "Therapy of parapneumonic empyema in children: a protocol for a scoping review of the literature",
"authors": [
"Danilo Buonsenso",
"Francesca Cusenza",
"Lucrezia Passadore",
"Francesca Bonanno",
"Carolina Calanca",
"Sonia Rasmi",
"Francesco Mariani",
"Susanna Maria Roberta Esposito",
"Francesca Cusenza",
"Lucrezia Passadore",
"Francesca Bonanno",
"Carolina Calanca",
"Sonia Rasmi",
"Francesco Mariani",
"Susanna Maria Roberta Esposito"
],
"abstract": "Background: Empyema (the presence of pus in the pleural space) is a severe complication of community-acquired pneumonia and significant cause of morbidity, but, fortunately, not mortality in children. Between 0.6 and 2% of pneumonias are complicated by empyema and the three main pathogens involved are Streptococcus pneumoniae, Staphylococcus aureus and group A Streptococcus 1,2,3,4. Optimal management in children, especially the choice of antibiotics, method of administration and duration of therapy, are still matter of debate and currently, lack of strong specific recommendations. This paper displays the study protocol for a scoping review that aims to summarize the available literature on the microbiological epidemiology, the treatment options, and the outcomes of pleural empyema in pediatric population. Methods: Comprehensive research combining the terms pediatric (children aged 0 to 18 years) and pleural empyema will be performed on PubMed and SCOPUS to identify all eligible studies. At first, two reviewers will screen their abstract and then their full text to detecting the articles that meet the inclusion criteria. This work will be carried out independently, everyone on a different Excel spreadsheet and each researcher will be blinded to the decision of the other researcher. When the process will be completed, in case of discordance, any disagreement will be identified and resolved through discussion or with the help, when needed, of a third author. Dissemination: The findings of this review will be published in a peer-reviewed journal.",
"keywords": [
"Parapneumonic empyema",
"complicated pneumonia",
"children"
],
"content": "Introduction\n\nParapneumonic empyema is defined by the collection of pus on the pleural surfaces, and it represents one of the most common local complications of community-acquired pneumonia (CAP) in children.1‐5 It has been estimated that parapneumonic effusions develop in about 1 in 100-150 children with CAP6,7 but they could be discovered in as many as 40% of hospitalised children with CAP.8\n\nCAP, are caused mainly by Streptococcus pneumoniae9 and their incidence has shown fluctuations over time. In particular, a significant global reduction in pneumococcal disease and mortality rates has been reported after the introduction of heptavalent pneumococcal conjugate vaccine (PCV7), which covers serotypes 4, 6B, 9V, 14, 18C, 19F and 23F, into the standard childhood immunisation schedule.10 In the following years, however, in the USA an increase in pneumococcal empyema, related to serotypes not covered by PCV7, has been reported.11 After the replacement of the PCV7 with the PCV13, which covers also serotypes 1, 3, 5, 6A, 7F and 19 A, there has been a significant reduction in incidence and rate of hospitalisation for empyema.12 The introduction of PCV13 is particularly important in consideration of the strong correlation between parapneumonic empyema and serotype 1 of pneumococcus.13\n\nOther bacteria seem to be less frequently pathogens of CAP. However, other possible bacterial pathogens of parapneumonic empyema are represented by group A Streptococcus and Staphylococcus aureus.13\n\nClinical presentation of parapneumonic empyema is similar to that of uncomplicated CAP. The presence of an empyema should be suspected in children with prolonged fever (more or equal to 7 days) and in those who do not improve after 48-72 hours of adequate antibiotic therapy.9,13 In physical examination, typically, parapneumonic empyema is characterized by decreased air entry breath and dullness to percussion.9\n\nA clinical suspect of parapneumonic empyema should be confirmed performing a chest X-ray and/or pulmonary ultrasound. Ultrasound technique has a higher sensitivity than radiograph in determining extension and nature of fluid collection and it is very useful for monitoring children with empyema, considering that it does not expose to X-rays. Thoracic CT is not considered a first line exam in order to make diagnosis of empyema, but it should be performed when it is not possible to make a clear diagnosis or when there is a suspect of malignancies (i.e. Burkitt’s lymphoma).\n\nAll cases of parapneumonic empyema should be treated with empiric intravenous antibiotic therapy, covering Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus. However, in case of large effusion (> 2 cm) or compromission of respiratory function a chest drainage is essential.5,14 Chest drainage is generally performed under ultrasound guide and children should be under sedation/general anaesthesia.14 Intrapleural fibrinolytics (i.e. urokinase) are particularly useful in shortening hospitalisation in cases where drainage is slow, in consideration of thick or loculated fluid.5,14 Thoracic surgery should be taken in consideration in cases of failure of antibiotic therapy, chest drainage and fibrinolytics. However, guidelines are unclear about which surgical procedure is best and at which timing, as well duration of drainage or of antibiotic therapy, including optimal timing about oral shift and how these issues reflect on outcomes.\n\nThis scoping review aims to analyse the optimal antibiotic therapy, defining antibiotic molecule, route of administration and duration of antimicrobial therapy.\n\n\nReview questions\n\nConsidering the importance of a mutual consensus in the clinical management of parapneumonic empyema in children, as literature already pointed out,15 the main review question will be: what is the available literature about the most appropriate antibiotic treatment for paediatric PE in terms of first-line agents choice, dose, route of administration and duration?\n\nThis review will also assess the following sub-questions:\n\n1. Which are the most frequently reported pathogens and what is their antibiotic susceptibility profile?\n\n2. Which outcomes and complication rates of PE are the most frequently reported in literature? Which are the most frequently reported treatments, both conservative or invasive, and which leads to improved outcomes and shorter length of stay?\n\n\nInclusion criteria\n\nThis review will include studies performed on children and adolescents (younger than 18 years) with a confirmed diagnosis of empyema, defined as the presence of pus within the pleural cavity. The diagnosis of empyema is established by the presence of pus, positive Gram's stain, or culture, or nucleic-acid amplification tests, in the pleural fluid. We will only include studies that have documented the microbiological aetiologies, performed antimicrobial and surgical therapies, as well outcomes (at least at time of discharge).\n\nThe main concept of this review will be empyema in all its aspects, with a particular focus on treatment options.\n\nConsidering the severity of the disease, we will not expect to find articles involving patients not hospitalized so we will include only inpatients.\n\nThis review will include both randomized controlled trials and non-randomized controlled trials. All the types of observational studies, prospective and retrospective (including case-control, cohort and cross-sectional studies, small case series or single case reports) will be included.\n\n\nMethods\n\nThe search will be performed by one reviewer. We started our research in April 2023 in the following bibliographic databases: PubMed and SCOPUS. There will be date restrictions: we will search from the 1st of January 2000 to 31st of March 2023. Only articles written in English will be included. The search strategy will include a combination of the following word and their synonymous: “pediatric”, “empyema” and “treatment”. The search strategy for PubMed is available in the extended data section of this protocol; the terms used for this search will be adapted for use with other bibliographic database.\n\nAfter the search, the studies will be exported to Rayyan. A first screen to exclude duplicates will be performed by one author.\n\nTitles and/or abstracts of studies retrieved using the search strategy will be screened independently by two reviewers to identify studies that could be inserted in the review. Full texts of potentially eligible studies will be retrieved and independently assessed for eligibility by two reviewers. Each researcher will be blinded to the decision of the other researcher. Any disagreement between them over the eligibility of studies will be resolved through discussion and, in case of further disagreement, by discussion with a third reviewer.\n\nAll the studies that will not meet the inclusion criteria will be excluded and a table with the reason why those studies were excluded will be inserted in the final manuscript.\n\nThe results of the search will be reported in the PRISMA flow diagram.\n\nTwo review authors will extract data independently, everyone on a different Excel spreadsheet. Each researcher will be blinded to the decision of the other researcher. When the process will be completed, in case of discordance, any disagreement will be identified and resolved through discussion (with a third author if necessary).\n\nAn Excel file will be used to store data. When available, extracted information will include:\n\n1. study general features: title, author, year of publication, type of study, number of patients included in the study, geographical area where the study has been performed\n\n2. participant general features: sample size of each group, nationality, age, socio-economic status, comorbidities\n\n3. clinical manifestation of the condition: fever (including days), cough with mucus, dyspnoea, chest pain and others.\n\n4. main imaging findings: type of lung involvement at chest X-Ray and/or CT scan, type of CNS involvement at CT scan or MRI, type of skin involvement evaluated by ultrasound or CT scan or MRI, heart (US or CT or MRI)\n\n5. characteristics of eventual antimicrobial treatments performed during the empyema (length of therapy, when this has been started and which antibiotic was used)\n\n6. adjunctive treatments performed and length of therapy during the empyema (e.g., steroids or other immunomodulatory medications)\n\n7. surgical treatments performed and length of therapy during the empyema (e.g., drainage or thoracoscopy or surgical resection)\n\n8. outcomes (death, survival; survival with sequelae; type of sequelae)\n\nTo report our findings, we will follow Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist.\n\nWe will produce a narrative synthesis of the findings from the studies included in the review describing the results we have obtained and providing our opinion on their interpretation. A particular focus with a narrative synthesis will be performed for antimicrobial and surgical therapy characteristics in terms of frequency of antibiotic choice, efficacy, and duration of therapy. If after this selection will be included more than 100 records, original article and those published in the last 5 years will be preferred.\n\nWe will also use tables and charts to summarize both study characteristics and the most important clinical, diagnostics, treatments, and outcomes data.\n\nMore specifically, we will summarize our findings using different tables. The first one will include the characteristics of included studies (number of studies, study design, year of publication, characteristics of the study populations and countries where studies were conducted) and the participant general features. Then we will provide different tables or figures summarizing main data about clinical presentation, imaging characteristics, treatments performed, outcomes and predictors of empyema.\n\nThis way we hope we will be able to provide a useful document containing what is currently known of pediatric empyema with the aim of informing clinicians about the general characteristics of these conditions, focusing on risk factors and early clinical features, and guide future research projects to fill current gaps.\n\nProtocol has been submitted and researched launched on the different datasets. Abstract screening will start after protocol submission.\n\nThere was no direct patient and public involvement in this review. However, the key questions that led us implementing this research project were inspired by public discussions started by family associations in the media, highlighting the importance of better comprehension of how empyema can be recognized earlier in the disease course (before clinical conditions deteriorates and cannot be controlled anymore), or empyema may also be prevented if this complication is a consequence of a previous unrecognized and untreated lung infection.\n\n\n\n• A scoping review can represent the best way to report on the types of evidence that are published in a certain field and our paper will provide an overview of empyema, focusing on predictors of positive outcomes.\n\n• A scoping review can represent the best way to examine this field to guide future research on this topic.\n\n• To report our findings, we will follow the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist to ensure methodological strength to our paper.\n\n• Only two databases were screened, and only English paper will be considered limiting the number of papers that will be included.\n\n• No critical appraisal neither risk of bias of the included studies will be performed, considering the exploratory role of this paper.",
"appendix": "Data availability\n\nNo data are associated with your article.\n\nOpen Science Framework: Therapy of parapneumonic empyema in children: protocol for a scoping review of the literature, https://doi.org/10.17605/OSF.IO/J58DR. 16\n\n\nReferences\n\nMaffey A, Colom A, Venialgo C, et al.: Clinical, functional, and radiological outcome in children with pleural empyema. Pediatr. Pulmonol. 2019 May; 54(5): 525–530. PubMed Abstract | Publisher Full Text\n\nKrenke K, Sadowy E, Podsiadły E, et al.: Etiology of parapneumonic effusion and pleural empyema in children. The role of conventional and molecular microbiological tests. Respir. Med. 2016 Jul; 116: 28–33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang X, Zhang H: Microbiological characteristics and outcomes of children with pleural empyema admitted to a tertiary hospital in southeast China, 2009-2018. Turk. J. Pediatr. 2021; 63(6): 994–1003.\n\nLiese JG, Schoen C, van der Linden M , et al.: Changes in the incidence and bacterial aetiology of paediatric parapneumonic pleural effusions/empyema in Germany, 2010-2017: a nationwide surveillance study. Clin. Microbiol. Infect. 2019 Jul; 25(7): 857–864. PubMed Abstract | Publisher Full Text\n\nPabary R, Balfour-Lynn IM: Complicated pneumonia in children. Breathe (Sheff.). 2013; 9: 210–222. Publisher Full Text\n\nSonnappa S, Jaffe A: Treatment approaches for empyema in children. Paediatr. Respir. Rev. 2007; 8: 164–170. Publisher Full Text\n\nChonmaitree T, Powell KR: Parapneumonic pleural effusion and empyema in children. Review of a 19-year experience, 1962-1980. Clin. Pediatr. (Phila). 1983 Jun; 22(6): 414–419. PubMed Abstract | Publisher Full Text\n\nHamm H, Light RW: Parapneumonic effusion and empyema. Eur. Respir. J. 1997 May; 10(5): 1150–1156. PubMed Abstract | Publisher Full Text\n\nde Benedictis FM , Kerem E, Chang AB, et al.: Complicated pneumonia in children. Lancet. 2020 Sep 12; 396(10253): 786–798. PubMed Abstract | Publisher Full Text\n\nFitzwater SP, Chandran A, Santosham M, et al.: The worldwide impact of the seven-valent pneumococcal conjugate vaccine. Pediatr. Infect. Dis. J. 2012; 31: 501–508. PubMed Abstract | Publisher Full Text\n\nByington CL, Korgenski K, Daly J, et al.: Impact of the pneumococcal conjugate vaccine on pneumococcal parapneumonic empyema. Pediatr. Infect. Dis. J. 2006; 25: 250–254. PubMed Abstract | Publisher Full Text\n\nWiese AD, Griffin MR, Zhu Y, et al.: Changes in empyema among U.S. children in the pneumococcal conjugate vaccine era. Vaccine. 2016 Dec 7; 34(50): 6243–6249. Epub 2016 Nov 7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarris M, Clark J, Coote N, et al.: British Thoracic Society Standards of Care Committee. British Thoracic Society guidelines for the management of community acquired pneumonia in children: update 2011. Thorax. 2011 Oct; 66 Suppl 2: ii1–ii23. PubMed Abstract | Publisher Full Text\n\nBalfour-Lynn IM, Abrahamson E, Cohen G, et al.: BTS guidelines for the management of pleural infection in childrenThorax.2005; 60: i1–i21.\n\nHafen GM, Grenzbach AC, Moeller A, et al.: Lack of concordance in parapneumonic effusion management in children in central Europe. Pediatr. Pulmonol. 2016 Apr; 51(4): 411–417. PubMed Abstract | Publisher Full Text\n\nBuonsenso D: Therapy of parapneumonic empyema in children: protocol for a scoping review of the literature.2023, June 3. Publisher Full Text"
}
|
[
{
"id": "245793",
"date": "15 May 2024",
"name": "Catherine A Byrnes",
"expertise": [
"Reviewer Expertise Paediatric Respiratory disease"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGenerally this is a good proposal – responding to queries and questions generated from patients and using Prism as the backbone which is good.\nNot much is mentioned regarding chest drains – nil in abstract, not till the 2nd to last paragraph in the introduction and as part of the Qs – mentioned in passing. The authors need to clarify this a bit more. Is chest drainage and/or video assisted thoroscopic surgery going to be included?\n\nArticles only in English or other languages. The authors should define the languages of the articles they are searching in.\n\nOnly including patients that have an identified organism – many patients are difficult to get a positive culture from – and often the published articles have some with identified organisms and some without – yet the authors here are only including those where bacteria have been isolated – can they clarify this?\n\nIf greater than 100 articles – will then restrict to last 5 years – better if stuck to the whole. Either do all articles or restrict to 5 years - wouldn't go with the number being a restriction.\n\nNote that although this is being presented as a protocol, the review has already started.\n\nIn the selected word options for search – no “pleural effusion”. The authors have given the search words they have used but have not included \"pleural effusion\".\nThe manuscript could do with some English editing - I appreciate that the authors are likely writing this in a second language. Some editing is needed to put some of the phrasing into correct grammatical English.\nAbstract:\n“are still a matter for debate” “their abstracts” → “the abstracts” “then their full text” → “then the full text” “detecting” → “determine” “when the process will be completed” → “is completed” “with help, when needed, of a third” → “with help of a third”\nIntroduction:\n“discovered’ → seen or recognised or discerned (para 1) “their” → “the” (para 2) “less frequently” → “less frequent” (para 3) “suspect” → “suspicion” (para 5) “radiograph” → “radiography” (para 5) “xray” → “radiation”\nReview Qs:\n“as literature points out” → “as documented in the available literature”\nMethods:\n“inserted in the review” → “reviewed”\nData Extraction:\n“everyone” → “both”\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "11674",
"date": "21 Jun 2024",
"name": "danilo buonsenso",
"role": "Author Response",
"response": "thank you very much, we changed as you suggested"
}
]
},
{
"id": "272217",
"date": "28 May 2024",
"name": "King-Pui Florence Chan",
"expertise": [
"Reviewer Expertise Respiratory Medicine",
"Respiratory infection",
"Epidemiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study protocol aims to provide a literature review on children with pleural empyema. The protocol can be improved by further clarification.\n1. In the method part, I am not aware of how the bacterial results is analyzed or included. Please consider elaborating it.\n2. The severity of outcomes including intensive care unit stay can be included as analysis.\n3. Some of the pleural empyema can be caused by tuberculosis, which the antimicrobial use would be different. Please consider to address this in the protocol.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "11675",
"date": "21 Jun 2024",
"name": "danilo buonsenso",
"role": "Author Response",
"response": "thank you, I have responded to your main comments"
}
]
}
] | 1
|
https://f1000research.com/articles/12-1527
|
https://f1000research.com/articles/13-565/v1
|
03 Jun 24
|
{
"type": "Research Article",
"title": "Development and Validation of a Bedside Scale for Assessing Upper Limb Function Following Stroke: A Methodological Study.",
"authors": [
"Dhaval Pawani",
"Abraham M. Joshua",
"Akshatha Nayak",
"Vijayakumar Palaniswamy",
"Prasanna Mithra",
"Ashish John Prabhakar",
"Sampath Kumar Amaravadi",
"Dhaval Pawani",
"Akshatha Nayak",
"Vijayakumar Palaniswamy",
"Prasanna Mithra",
"Ashish John Prabhakar",
"Sampath Kumar Amaravadi"
],
"abstract": "Background Numerous tools are available for evaluation of upper limb (UL) functions among stroke survivors. Despite the excellent psychometric properties, many require considerable amount of time, are resource-intensive, and often impractical for bedside evaluation.\n\nObjectives To develop and concurrently validate a simple, resource-efficient, and time-efficient bedside tool for evaluating UL function in stroke survivors.\n\nMethods Relevant literature review was carried out to conceptualize and define the theoretical framework of day-to-day UL movement tasks. Subsequently, an item pool of 18 UL movements was developed. A mini-Delphi method was employed to verify content validity. During the iterative rounds, 18-items were revised and refined to a 12-items scale. The final bedside upper limb evaluation tool (BUFET) scale underwent concurrent validation by correlating the scores with Wolf Motor Function Test (WMFT) scores using Spearman’s correlation coefficient. Internal consistency was evaluated through Cronbach’s alpha.\n\nResults Concurrent validity and internal consistency of the scale were supported by a high correlation coefficient (r = 0.937; p<0.001) with WMFT and high Cronbach’s alpha (0.948).\n\nConclusions Newly developed BUFET was found to be a valid and reliable bedside tool in the evaluation of upper limb functions and can be administered in a resource and time-efficient manner.",
"keywords": [
"Stroke",
"Upper limb",
"Outcome measures",
"Bedside assessment",
"Evaluation tool."
],
"content": "Introduction\n\nThe daily activities of individuals with stroke are significantly influenced by the upper limb (UL) and hand function.1 Evidence from several studies suggested that 85% of stroke survivors suffer UL and hand impairments.2–5 In particular stroke survivors with middle cerebral artery infarction have been associated with muscle weakness,6 inability to control all UL segments in space and time (inter-joint coordination),7,8 difficulty in grasping and holding an object, and reduced ability to independently move individual fingers.3 There is significant evidence to suggest that these UL impairments contribute to loss of UL function, loss of independence in activities of daily living, and impaired quality of life.9,10 The presence of these diverse motor impairments a few weeks after a stroke can predict future UL function.3 Therefore, evaluation of UL function is critical in day-to-day stroke rehabilitation.11\n\nEvaluation of UL functional movements following stroke has been performed by several types of tools ranging from observer-based scales, instrumented tests, and self-reported questionnaires.12 Some of the commonly reported reliable and valid performance assessment tools to quantify UL function in stroke survivors include the Fugl-Meyer Assessment of Upper Limb (FMA-UL), Wolf Motor Function Test (WMFT), Action Research Arm Test (ARAT), Box and Block Test (BBT), Nine Hole Peg Test (NHPT).12–14 Although FMA-UL has been reported to have the highest level of psychometric and clinometric properties, it does not evaluate functional arm and hand movements.15 FMA-UL mainly evaluates body function and structures as per the international classification of functioning (ICF) framework. In addition, FMA-UL and ARAT are noted to exhibit some overlap in their assessment of UL function, suggesting that they may not be entirely distinct in their evaluations of UL capabilities.16 Clinical tools such as ARAT, WMFT, BBT, and NHPT predominantly measure grasping and displacement movements of different object sizes with less emphasis on gross movements.17,18 ARAT involves a subjective scoring method, with poor definitions of the test item positioning and time allocation for each item.14,19 Currently, there is no agreement on the selection of any particular tool for a particular individual with a stroke.3\n\nDespite the excellent psychometric properties of FMA-UL, WMFT, and ARAT, all these tools require a considerable amount of time and are resource-intensive due to their comprehensive nature and need for manual administration.19 In particular, FMA-UL requires longer than 30 minutes to complete the test and needs material resources and/or tools including a standardized chair and/or desk to execute the same.20 Furthermore, administration of these said measures can be exhaustive, cumbersome, and often impractical for bedside evaluation. The time taken to administer a tool significantly influences its probability of regular usage in clinical practice. Hence, tools that take a quicker time are more likely to be utilized.3\n\nEmerging evidence suggests that the inclusion of non-contact gesture movements (e.g., salute and hand waving gesture) and contact-grasping (e.g., grasping a small glass) would strengthen the representativeness and comprehensiveness of evaluation of UL movements of daily life.2,21 In addition, analysis of gesture and grasp movements can demonstrate task-specific and impairment-specific characteristics.21 In line with that, we propose a conceptual framework for the clinical utility of day-to-day movement tasks such as hand gesture movements, grasping movements,22 and rhythmic finger tapping23 in evaluating the UL function in stroke. Although previous studies have quantified the impairments in hand gestures, grasping, and finger tapping, these studies primarily employed expensive quantifiable technology to investigate such as wearable gloves for hand gesture recognition, and ultrasound-based motion analyzer for kinetic and kinematic analysis of grasping.22,24,25 Evidence suggests that the finger-tapping test is a useful tool in predicting recovery in stroke survivors.26,27 Currently, there is no simple, qualitative, resource, and time-efficient tool that could be quickly administered at the bedside to evaluate UL function in stroke survivors.\n\nTherefore, the primary aim of the present study was to develop a bedside tool based on day-to-day movement tasks that can be administered with ease, accuracy, minimal time consumption, and less exhaustion to measure the UL function following stroke. The secondary aim was to assess the concurrent validity of the new bedside tool.\n\n\nMethods\n\nThe study comprised of 2 phases 1) scale development and content validity verification 2) concurrent validity determination with WMFT. After receiving approval from the Research and Institutional Ethics Committee of Kasturba Medical College, Mangalore (IEC KMC MLR 1/2022/15) on 19/01/2022, a dual-phasic study containing qualitative and cross-sectional elements was undertaken in teaching hospitals affiliated with Kasturba Medical College, Mangalore, from February 2022 to January 2023. The study adhered to the ethical principles of the Declaration of Helsinki for research involving human participants. The qualitative phase included tool development, whereas the cross-sectional phase focused on tool validation. Purposive sampling was implemented for participant recruitment during cross-sectional phase. The study included adult participants (>18 years of age) diagnosed with primary infarction/hemorrhagic stroke and hemiparesis of the upper limb (UL). Exclusion criteria of the study were i) other neurological disorders, ii) severe cognitive deficits (Montreal Cognitive Assessment score < 24), iii) perceptual dysfunctions, and iv) pre-existing UL musculoskeletal conditions affecting testing.\n\nThe theoretical conceptualization and development of the new Bedside Upper Limb Evaluation Tool (BUFET)© was guided by AMJ. Initially, the research team identified 18 simple day-to-day movement tasks (Table 1 and Table 2) as potential scale items through a comprehensive review of relevant literature. The initial 18-items scale comprised of tasks such as UL and hand gesture movements, grasping movements, and finger tapping. All the identified movements require coordinated function of the shoulder, elbow, wrist, hand, and fingers.\n\nA mini-Delphi consensus method was implemented to achieve content validity, involving a series of rounds with expert consensus panel comprised of 6 clinical researchers with a minimum of 15 years of experience in specialized neurological clinical practice. The iterative method of mini-Delphi technique, as outlined by Hasson et al., involves multiple rounds of communication aimed at achieving consensus. The selection of experts ensured that relevant expertise and experience were present to provide valuable insights and feedback on the questionnaire items. In each round, the experts were provided with structured questionnaires, along with detailed instructions on how to provide feedback. The process allowed for anonymity, reducing the influence of dominant individuals and facilitating open expression of opinions.28 The iterative nature of the method allowed for structured communication among the experts, facilitating the exchange of opinions and feedback effectively.29 The expert panel included 3 neurologists, 2 physiotherapists, and 1 occupational therapist, ensuring a diverse range of perspectives in the evaluation process. This diversity contributed to consensus building among the panellists regarding the content and validity of the questionnaire items.\n\nIn the first round, experts individually reviewed the 18-item scale via email, maintaining anonymity for unbiased feedback. Subsequently, in the second round, consensus was reached to exclude 4 non-relevant items (item # 15 to 18, Table 1). The remaining 14-item scale (Table 2) underwent further iterative feedback rounds.\n\nIn the subsequent third round, experts provided critical feedback on the 14-item scale, leading to revisions based on consensus. This structured approach culminated in the development of a finalized 12-item BUFET, entering subsequent validation phases. The finalized 12-item BUFET, including rating scores, is available as an underlying data from https://doi.org/10.17605/OSF.IO/UFHK5.\n\nAfter developing the final version of scale, concurrent validation process was initiated with purposive sample of 25 stroke survivors. This phase involved recruiting 25 stroke survivors meeting inclusion criteria against the estimated minimum sample size of 20. The study participant characteristics are depicted in Table 3. All the participants were administered with BUFET and Wolf Motor Function Test (WMFT) randomly with a one-hour interval between the two tests. Evidence indicates that WMFT comprises 15 timed task-performance items that can assess functional ability with excellent reliability. The correlation between BUFET and WMFT scores of all 25 participants were determined using Spearman’s correlation coefficient method.\n\nThe WMFT includes 15 timed tasks with each item rated on a six-point functional ability scale, assessing effort, smoothness, and overall quality. At the outset, the scale tests the unaffected side, followed by the affected limb, and generally takes 30-35 minutes to complete the evaluation. Evidence suggests that WMFT exhibits excellent test-retest reliability (r=0.95) and strong inter-rater (ICC=0.93) and intra-rater (ICC=0.97) reliability. Required materials for WMFT include a standardized table, chair, box, 12-oz beverage can, 7” pencil with six flat sides, 2” paper clips, lock and key, face towel, and basket.30–32\n\nStatistical Package for Social Sciences (SPSS, Version 25.0, released 2017. IBM Armonk, NY: IBM Corp) was used for data analysis. The concurrent validity of BUFET was assessed by correlating the scores against those of WMFT using Spearman rank correlation analysis. The internal consistency of the tool was analyzed by obtaining Cronbach’s alpha.\n\n\nResults\n\nThe principal investigator (PI) organized an initial 18-item scale focusing on essential day-to-day movement tasks including gestures, grasping, and finger tapping (Table 1 and Table 2). This scale was subsequently revised to 14 items based on recommendations from the six subject experts who participated in the study (Table 2). Removal or modification of scale and/or its grades was considered if at least two subject experts rated a score of 2 or below on a 5-point Likert scale for that item. According to this specified criterion, two more items were eliminated, as shown in Table 2.\n\nA closing agreement from the subject experts on the revised 12-item scale was carried out and the finalized BUFET comprised of 7 gesture items, 3 grasping or gripping items, 1 item for wrist movement, and 1 finger tapping.\n\nA total of 25 participants (17 males, 8 females), with a mean age of 60.6 years, participated in the concurrent validation study. All participants suffered supratentorial infarction (84%) or haemorrhagic type (16%) of stroke (Table 3).\n\nCorrelation analysis was utilized to confirm the concurrent validity of the proposed BUFET scale by comparing them to WMFT which was used as reference standard. The normality of BUFET scores suggested a normal distribution and WMFT scores revealed absence of normal distribution. Since one of the variables was not normally distributed, Spearman rank method was used for correlation coefficient analysis. The results of analysis indicated a high significant correlation coefficient (r = 0.937; p < 0.001) as presented in the Figure 1. Additionally, the BUFET demonstrated high internal consistency, as reflected by a Cronbach’s alpha value of 0.948.\n\nBUFET: Bedside Upper Limb Functional Evaluation Tool; WMFT: Wolf Motor Function Test.\n\n\nDiscussion\n\nIn the current study, evidence is provided for the contention that day-to-day movement gestures, grasping activities, and rhythmic wrist and finger movements constitute a significant tool for the evaluation of UL function in stroke survivors. Previous research primarily focused on investigating the therapeutic efficacy of gesture, grasping, and finger-tapping movements to enhance UL function using quantitative and expensive methods.2,22 Nonetheless, there is an apparent significant gap in the literature regarding the development and validation of a qualitative bedside tool utilizing daily gesture, grasping, and finger tapping movements for evaluating UL function in stroke survivors. Existing tools in assessment of shoulder, elbow, wrist, and hand motor impairment require specific materials, training, and excessive amount of time. Consequently, a simple, inexpensive, resource (no resources) and time-efficient (<10 mins) Bedside Upper Limb Evaluation Tool (BUFET) was developed and validated with methodological study design. Such a qualitative bedside tool that can be implemented in clinical, research, or home settings could be a critical component in stroke rehabilitation.\n\nEvaluation of UL and hand function is pivotal for the comprehensive rehabilitation of stroke survivors. The newly developed BUFET serves as a qualitative instrument that can be efficiently administered at the bedside. This tool facilitates the observation of intricate patterns in shoulder, elbow, hand, and wrist movements during the execution of gestures, grasping, and fine finger movements. According to Michael Roth, symbolic hand gestures are predominantly upper arm and hand movements, conceptualized as originating from ergotic hand movements associated with object manipulation and epistemic hand movements related to sensing activity.33 In general, hand orientation assumed by the grasping hand depends on the initial hand position, location, shape, and orientation of the object to be grasped.34,35 However, stroke survivors often exhibit impaired gesture imitation, influencing the performance of specific arm and hand segments (limb apraxia).21\n\nKinematic studies have indicated that complex hand gestures and grasp movements in stroke survivors are associated with altered joint rotation patterns, hand orientations, and impaired inter-joint coordination of grasp and twist.2,7 Evidence also suggests that impaired hand gesture imitation is linked to posterior lesions in the left inferior parietal lobule (LIPL) and temporal-parietal-occipital junction (TPOJ), while impaired finger gesture imitation is associated with lesions in the inferior frontal gyrus (IFG).36,37 These brain regions are responsible for motor planning, coordination, and the integration of sensory-motor information.7\n\nConsequently, prompt qualitative movement analysis of gestures, grasping, and fine finger movements using BUFET at the bedside empowers the examiner to raise clinical suspicion regarding the potential location of brain lesions in stroke survivors. This tool facilitates early and timely interventions. In particular, the qualitative assessment focused on UL motor function can reveal distinctive patterns that correlate with the left inferior parietal lobule (LIPL) and temporal-parietal-occipital junction (TPOJ), enabling differentiation between stroke groups and offering valuable insights into the functional abilities of stroke survivors. Furthermore, it may provide indications of specific brain lesion types, distinguishing between posterior (LIPL) and anterior (IFG) lesions.\n\nThe BUFET covers a wide range of UL, hand, and finger movements. The first component-salute evaluates the ability to produce a movement pattern away from the typical attitude of the affected limb.38 The second and the third components (holding the nose and hand waving, respectively) help to assess the quality of control of shoulder flexors and external rotators which are reported to be considerably impaired among stroke subjects.39 Also, the second item (holding the nose) reflecting hand-to-mouth function is reported to be a significant method to evaluate UL in subjects with stroke.40 The functional ability of the intermediate joint (i.e., elbow), to achieve complete flexion is also tested in the first and second components while the elbow extension is tested in the third component. Levin et al emphasized that the movement amplitudes at the shoulder and elbow joints were significantly impaired during the excursion of the hemiparetic arm.35 In particular, during reach-out tasks, effective shoulder movements with inter-joint coordination are paramount.41 Hence, hand waving has been included as a third component to evaluate shoulder function.\n\nWrist circumduction movement is usually described as flexion-extension motion in function of radio-ulnar deviation. Most daily activities of life can be performed through an arc from 10° flexion to 35° extensions. Evidence suggests that static flexion posture of finger significantly influences wrist circumduction with a linear relationship between wrist and finger movements.42 This phenomenon is particularly implicated in wrist drop observed among people with unilateral stroke. A Rasch model analysis of the psychometric properties of wrist and hand subscales of FMA-UL in stroke reported a higher/large positive factor loading (0.846) for wrist circumduction representing the unidimensional construct of UL and hand motor function.43 Thus, inclusion of clockwise and anti-clockwise stirring action of the wrist as one of the items demonstrated that BUFET is unidimensional. Furthermore, reduced selectivity of the muscles that control isolated index finger extension, a deficit in the ability to perform isolated finger extension, has also been studied.44 Hence, inclusion of pointing the index finger upwards with the wrist in extension is considered significant.\n\nMaximum grip force is generated with the wrist held in extension,22 and lack of recovery of grasp efficiency may suggest the inability of the descending pathways to control the distal muscles.45 Additionally, the radial aspect of the hand plays a significant role in fine motor tasks such as gripping, which require greater dexterity and strength. Liu et al. stated that the thumb, index, and middle fingers that are controlled by the radial aspect of the hand are more prone to impairment compared to other fingers.46 Due to these reasons, the evaluation of the grip strength through the radial aspect is considered.\n\nThe opposition of thumb is essential for daily activities like picking up small objects. The opposition was noted to be reduced in stroke subjects when compared to healthy.47 Nijland et al. reported that the ability to extend the finger within 72 hours post-stroke can predict functional recovery in the hemiplegic arm at 6 months.48 While attempting to move a specific digit, inappropriate contractions of muscles in other digits were noted among stroke subjects.44 Prior research also stated an increased level of motor impairment with ulnar fingers i.e., middle, ring, and little finger.49 Since specific digit(s) movements are likely to be impaired in stroke subjects pointing the index finger upwards and gesturing the number “3” are included.\n\nStudies have reported impaired thumb movements and reduced velocity in finger flexion movements among stroke subjects.50 To evaluate thumb and middle finger control, the snapping action of the finger that requires quick flexion of the middle finger against the thumb is selected as a component. In addition, finger abduction/adduction was reported to be greatly impaired compared to flexion/extension.44 Thus, BUFET included the scissoring action of the index and middle fingers as a test item to evaluate the finger abduction and adduction movements. Reduced individual finger movement is associated with greater hand impairment and the same study also reported unwanted extra finger movements during finger individuation that correlated with lower ARAT and Moberg Pick-Up Test scores.51 Hence, finger-tapping that assesses individual movement of the digits is incorporated.\n\nWMFT assesses the functional ability of the UL. Out of the 15 items, 6 components (40%) focus exclusively on the proximal joints. Contrary to that, 3 components of BUFET (25%) assess proximal control, thus ensuring a larger proportion of the scale to focus on diverse hand functions. All the test components of BUFET were administered at ease at the bedside. The BUFET required an average of 10 minutes to complete its administration when compared to the 30–35-minute requirement for WMFT.13,52\n\nOur results for the correlation analysis between BUFET and WMFT revealed a high correlation coefficient (r = 0.937, p<0.001) which suggest that both tools measure similar, unidimensional construct. The BUFET also demonstrated a high internal consistency with Cronbach’s alpha value of 0.948 (p<0.001) which is consistent with the alpha scores of WMFT-0.92,31 FMA-U -0.98,53 and ARAT -0.98.54 The results imply that the BUFET is capable of detecting motor functions nearly identical to the WMFT. In addition to the above, it also suggests that BUFET can be used as an easy-to-administer bedside outcome measure for UL function post-stroke.\n\nFirstly, the items on the scale were narrowed down based on subject experts’ opinions and clinical acumen. An alternative could have been based on direct administration of the components on a limited number of study participants. Secondly, the minimum requirement to carry out the test is that the subject should be made to sit either at the bedside or on a chair which might make its administration difficult for those with a greater degree of motor involvement. Despite employing mini-Delphi method for content validity, our panel’s lack of geographic diversity (South Karnataka-based) may introduce bias. However, the implementation of the mini-Delphi method in the current study was rigorous, adhering to fundamental principles including expert selection, anonymity, iterative consensus rounds, structured communication, and feedback integration.28,29,55\n\nStudies should aim at analyzing other psychometric properties including intra-rater and inter-rater reliability based on observations made by multiple observers. The prognostic value of the tool can also be assessed through well-designed prospective studies. A Rasch analysis may help in identifying the key components of the scale to further narrow down the components if indicated.\n\n\nAuthor contributions\n\nDP was the principal investigator (PI) for this study. The conceptualization and the initial development of tool were by the corresponding author (AMJ) who holds the copyright (Reg # L-137026/2023) for the proposed tool. The BUFET is made freely available for teaching and clinical purpose. For research and publication purpose, it is mandatory to credit the corresponding author with relevant citation. Supervision of the trial and the data collection were performed by AN, AJP, and VP. The study was designed, and the data analysis was executed by PM and SA. All the authors equally contributed to the preparation and editing of this manuscript.\n\n\nEthics statement\n\nApproval was obtained from the Research and Institutional Ethics Committee of Kasturba Medical College, Mangalore (IEC KMC MLR 1/2022/15) on 19/01/2022. The study adhered to the ethical principles of the Declaration of Helsinki for research involving human participants.\n\n\nInformed consent\n\nAppropriate written informed consent, approved by the Institutional Ethics Committee, was obtained from the study participants. Consent was also taken from the model for animated photographs used in the BUFET description.\n\n\nSupporting information\n\nUnderlying Data: Bedside Upper Limb Functional Evaluation Tool (BUFET)",
"appendix": "Data availability\n\nDevelopment and validation of a bedside scale for assessing upper limb function following stroke: A methodological study. DOI: https://doi.org/10.17605/OSF.IO/UFHK5. 56\n\nThis project contains the following data:\n\n• BUFET-Copyright certificate\n\n• BUFET Descriptions\n\n• Data sheet-Concurrent validity; WMFT scores and BUFET scores\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nThanks to the Manipal Academy of Higher Education, Manipal for permitting us to carry out this research. Sincere thanks go to all the study participants and special thanks to all the subject experts - Dr. Z.K. Misri, Dr. Shivananda Pai and Dr. Rohit Pai, Department of Neurology, Kasturba Medical College, Mangalore, Dr. Shovan Saha, Department of Occupational Therapy, Manipal College of Health Professions, Manipal and Dr. K Vijaya Kumar and Dr. Shyam Krishnan, Department of Physiotherapy, Kasturba Medical College, Mangalore.\n\n\nReferences\n\nPan B, Huang Z, Jin T, et al.: Motor Function Assessment of Upper Limb in Stroke Patients. J. Healthc. Eng. 2021; 2021(24): 6621911–6621950. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchwarz A, Bhagubai MMC, Nies SHG, et al.: Characterization of stroke-related upper limb motor impairments across various upper limb activities by use of kinematic core set measures. J. Neuroeng. Rehabil. 2022; 12; 19(1): 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLang CE, Bland MD, Bailey RR, et al.: Assessment of upper extremity impairment, function, and activity after stroke: foundations for clinical decision making. J. 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PubMed Abstract | Publisher Full Text\n\nRoth WM: From action to discourse: The bridging function of gestures. Cogn. Syst. Res. 2002; 3(3): 535–554. Publisher Full Text\n\nRoby-Brami A, Jacobs S, Bennis N, et al.: Hand orientation for grasping and arm joint rotation patterns in healthy subjects and hemiparetic stroke patients. Brain Res. 2003; 969(1-2): 217–229. PubMed Abstract | Publisher Full Text\n\nLevin MF: Interjoint coordination during pointing movements is disrupted in spastic hemiparesis. Brain. 1996; 119: 281–293. PubMed Abstract | Publisher Full Text\n\nAndric M, Small SL: Gesture’s Neural Language. Front. Psychol. 2012; 3: 99. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKleineberg NN, Schmidt CC, Richter MK, et al.: Gesture meaning modulates the neural correlates of effector-specific imitation deficits in left hemisphere stroke. Neuroimage. Clin. 2023; 37: 103331. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGomes ALS, Mello FF, Cocicov Neto J, et al.: Can the positions of the spastic upper limb in stroke survivors help muscle choice for botulinum toxin injections? Arq. Neuropsiquiatr. 2019; 77(8): 568–573. PubMed Abstract | Publisher Full Text\n\nStarosta M, Kostka J, Miller E: Force analysis of shoulder joint muscles in the early phase of brain stroke. Acta Bioeng. Biomech. 2018; 20(4): 107–113. PubMed Abstract\n\nCaimmi M, Guanziroli E, Malosio M, et al.: The Reaching and Hand to Mouth method for an instrumental functional assessment of the upper limb. Gait Posture. 2014; 39: S139–S140. Publisher Full Text\n\nCirstea MC, Mitnitski AB, Feldman AG, et al.: Interjoint coordination dynamics during reaching in stroke. Exp. Brain Res. 2003; 151(3): 289–300. PubMed Abstract | Publisher Full Text\n\nGehrmann SV, Kaufmann RA, Li ZM: Wrist circumduction reduced by finger constraints. J. Hand Surg. Am. 2008; 33(8): 1287–1292. PubMed Abstract | Publisher Full Text\n\nWoodbury ML, Velozo CA, Richards LG, et al.: Rasch analysis staging methodology to classify upper extremity movement impairment after stroke. Arch. Phys. Med. Rehabil. 2013; 94(8): 1527–1533. PubMed Abstract | Publisher Full Text\n\nSchieber MH, Lang CE, Reilly KT, et al.: Selective activation of human finger muscles after stroke or amputation. Adv. Exp. Med. Biol. 2009; 629: 559–575. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLang CE, Wagner JM, Edwards DF, et al.: Recovery of grasp versus reach in people with hemiparesis poststroke. Neurorehabil. Neural Repair. 2006; 20(4): 444–454. PubMed Abstract | Publisher Full Text\n\nLiu X, Rajan S, Ramasarma N, et al.: Finger-Worn Sensors for Accurate Functional Assessment of the Upper Limbs in Real-World Settings. Annu. Int. Conf. IEEE. Eng. Med. Biol. Soc. 2018; 2018: 4440–4443. PubMed Abstract | Publisher Full Text\n\nLanghorne P, Bernhardt J, Kwakkel G: Stroke rehabilitation. Lancet. 2011; 377(9778): 1693–1702. Publisher Full Text\n\nNijland RH, van Wegen EE , Harmeling-van der Wel BC, et al.: Presence of finger extension and shoulder abduction within 72 hours after stroke predicts functional recovery: early prediction of functional outcome after stroke: the EPOS cohort study. Stroke. 2010; 41(4): 745–750. PubMed Abstract | Publisher Full Text\n\nFriedman N, Chan V, Reinkensmeyer AN, et al.: Retraining and assessing hand movement after stroke using the MusicGlove: comparison with conventional hand therapy and isometric grip training. J. Neuroeng. Rehabil. 2014; 11: 76. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEschmann H, Héroux ME, Cheetham JH, et al.: Thumb and finger movement is reduced after stroke: An observational study. PLoS One. 2019; 14(6): e0217969. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWolbrecht ET, Rowe JB, Chan V, et al.: Finger strength, individuation, and their interaction: Relationship to hand function and corticospinal tract injury after stroke. Clin. Neurophysiol. 2018; 129(4): 797–808. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWolf SL, Catlin PA, Ellis M, et al.: Assessing Wolf motor function test as outcome measure for research in patients after stroke. Stroke. 2001; 32(7): 1635–1639. Publisher Full Text\n\nRoman N, Miclaus R, Repanovici A, et al.: Equal Opportunities for Stroke Survivors’ Rehabilitation: A Study on the Validity of the Upper Extremity Fugl-Meyer Assessment Scale Translated and Adapted into Romanian. Medicina (Kaunas). 2020; 56(8): 409. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNijland R, van Wegen E , Verbunt J, et al.: A comparison of two validated tests for upper limb function after stroke: The Wolf Motor Function Test and the Action Research Arm Test. J. Rehabil. Med. 2010; 42(7): 694–696. PubMed Abstract | Publisher Full Text\n\nRowe G, Wright G: The Delphi technique: past, present and future prospects - introduction to the special issue. Technol. Forecast. Soc. Change. 2011; 78(9): 1487–1490. Publisher Full Text\n\nPawani D, Joshua AM, Nayak A, et al.: Development and validation of a bedside scale for assessing upper limb function following stroke: A methodological study. OSF. 2024. Publisher Full Text"
}
|
[
{
"id": "342904",
"date": "13 Dec 2024",
"name": "Dr. Sharmila Dudhani",
"expertise": [
"Reviewer Expertise qualitative health research in physiotherapy"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article introduces a novel and user-friendly approach that holds significant promise for practical application. Its methodology and findings are both compelling and relevant to the field. I suggest some clarifications as follows: 1. Will this scale classify the involvement of hand as mild, moderate and severe affection? 2. Please do mention about the instruction to the patient. 3.Are the items culturally appropriate and sensitive for the intended population?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "13012",
"date": "23 Dec 2024",
"name": "vijayakumar palaniswamy",
"role": "Author Response",
"response": "Dear Dr., Dudhani, Thank you for your thoughtful review and constructive feedback on our manuscript. Below are our responses to your clarifications: 1. Will this scale classify the involvement of the hand as mild, moderate, and severe affection? Author’s Response: While the current scale does not classify hand involvement into mild, moderate, and severe categories, we acknowledge its potential value. Our primary aim was to provide a functional assessment tool. However, future versions of the scale may explore incorporating severity classifications. 2. Please do mention the instructions to the patient. Author’s Response: Thank you for your feedback regarding the patient instructions for the BUFET. We believe the instructions within the tool are already clear and do not require any changes. However, in response to your suggestion, we have added an overview of the scale's intended purpose and instructions for patients. This overview explains the goals of the BUFET, the types of tasks involved, and how patients should approach the evaluation. The added overview ensures patients understand the scale's purpose and what is expected during its use. This information has been incorporated into the appendix of the manuscript and aligns with your recommendations to enhance the clarity and accessibility of the BUFET. . 3. Are the items culturally appropriate and sensitive for the intended population? Author’s Response: Thank you for your thoughtful feedback regarding the cultural appropriateness of the BUFET. While the original development of the scale did not explicitly aim to test cultural sensitivity, we believe the current version is inherently culturally appropriate and sensitive for the intended population, based on the following considerations: Item Design and Universality: The tasks included in the BUFET, such as salute, hand waving, and pointing the index finger, represent universally understood and culturally neutral gestures or actions. These tasks are commonly performed in daily life and do not require a specific cultural context for interpretation. Expert Validation: During the development phase, the scale was reviewed by a diverse panel of rehabilitation experts, including neurologists and physiotherapists with extensive experience working within the intended population. This process ensured that all items were appropriate and relevant for the local cultural context. We hope these responses address your concerns. Thank you for your valuable insights, Sincerely, Dr Vijayakumar Palaniswamy"
}
]
},
{
"id": "288418",
"date": "02 Jan 2025",
"name": "Anuprita Kanitkar",
"expertise": [],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study introduces the Bedside Upper Limb Evaluation Tool (BUFET) as a method for assessing upper limb (UL) function in stroke survivors. The BUFET focuses on common gross movements such as everyday functional gestures, (but not object manipulation tasks of daily living) providing a practical, cost-effective alternative to more complex and expensive assessments. The psychometric properties were. assessed by comparing it to the Wolf Motor Function Test (WMFT), demonstrating strong concurrent validity (r = 0.937, p < 0.001) and excellent internal consistency (Cronbach’s alpha = 0.948). By evaluating movements like hand gestures, finger tapping, and wrist movements, BUFET helps identify basic motor impairments and suggests possible locations of brain lesions. Its quick administration and comprehensive assessment of both proximal and distal motor control make it suitable for use in clinical, research, and home settings. The study shows the BUFET’s potential to aid in rehabilitation assessments in stroke care, though further research is needed to explore its reliability and prognostic value.\n\nThe study is well-executed and well-written. The study design is robust. the results for the concurrent validity and internal consistency are presented clearly. The BUFET is a good assessment tool to evaluate the mobility in the upper extremity after a recent stroke. as a bedside assessment tool, it requires minimal equipment and can be performed in minutes, which speaks for its usability, especially considering it showed excellent concurrent validity and internal consistency.\n\nI approve this study as scientifically valid in its current form. The study is well-planned and implemented. I think it needs a thorough grammar check once.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-565
|
https://f1000research.com/articles/12-588/v1
|
01 Jun 23
|
{
"type": "Research Article",
"title": "Using an expert survey and user feedback to construct PRECHECK: A checklist to evaluate preprints on COVID-19 and beyond",
"authors": [
"Nora Turoman",
"Rachel Heyard",
"Simon Schwab",
"Eva Furrer",
"Evie Vergauwe",
"Leonhard Held",
"Simon Schwab",
"Eva Furrer",
"Evie Vergauwe",
"Leonhard Held"
],
"abstract": "Background: The quality of COVID-19 preprints should be considered with great care, as their contents can influence public policy. Efforts to improve preprint quality have mostly focused on introducing quick peer review, but surprisingly little has been done to calibrate the public’s evaluation of preprints and their contents. The PRECHECK project aimed to generate a tool to teach and guide scientifically literate non-experts to critically evaluate preprints, on COVID-19 and beyond. Methods: To create a checklist, we applied a four-step procedure consisting of an initial internal review, an external review by a pool of experts (methodologists, meta-researchers/experts on preprints, journal editors, and science journalists), a final internal review, and an implementation stage. For the external review step, experts rated the relevance of each element of the checklist on five-point Likert scales, and provided written feedback. After each internal review round, we applied the checklist on a set of high-quality preprints from an online list of milestone research works on COVID-19 and low-quality preprints, which were eventually retracted, to verify whether the checklist can discriminate between the two categories. Results: At the external review step, 26 of the 54 contacted experts responded. The final checklist contained four elements (Research question, study type, transparency and integrity, and limitations), with ‘superficial’ and ‘deep’ levels for evaluation. When using both levels of evaluation, the checklist was effective at discriminating high- from low-quality preprints. Its usability was confirmed in workshops with our target audience: Bachelors students in Psychology and Medicine, and science journalists. Conclusions: We created a simple, easy-to-use tool for helping scientifically literate non-experts navigate preprints with a critical mind. We believe that our checklist has great potential to help guide decisions about the quality of preprints on COVID-19 in our target audience and that this extends beyond COVID-19.",
"keywords": [
"COVID-19",
"preprints",
"checklist",
"science education",
"science communication"
],
"content": "Introduction\n\nDuring the COVID-19 pandemic, there has been both a proliferation of scientific data, and a major shift in how results were disseminated, with many researchers opting to post their work as preprints ahead of or instead of publication in scientific journals.1–4 Preprints are scientific manuscripts that are posted on freely accessible preprint servers (such as medRxiv, bioRxiv, PsyArXiv, MetaArXiv or arXiv), and which have not gone through formal peer review. Preprints take an extremely short time to become ‘live’ – between 24 and 48 hours after basic checks by server administrators, such as that the content of the manuscript is scientific text within the scope of the server, and not spam or plagiarised text.5 This is clearly advantageous in a rapidly-evolving pandemic.6,7 However, unlike journal submissions, the dissemination of preprints is not predicated on any quality control procedure.8 Even before the pandemic, concerns have been raised about the potential of such unvetted results and interpretation of findings leading to widespread misinformation.9 Indeed, in the past three years, we have seen prominent examples of non-peer-reviewed COVID-19-related claims10,11 that were promptly uncovered as misleading or seriously flawed by the scientific community,12,13 nonetheless infiltrate the public consciousness14 and even public policy.15 In this high-stakes context, two things have become clear: 1) that preprints have become a tool for disseminating disease outbreak research,16 and 2) that evaluating preprint quality will remain key for ensuring positive public health outcomes.\n\nSince the start of the pandemic, the number of preprints on COVID-19 has been steadily rising, with over 55,000 preprints to date (as of June 27, 2022; see also Figure 1). In the early stages of the pandemic, studies have shown that COVID-19 preprints were typically less well-written in terms of readability and spelling correctness,17 and that most did not meet standards for reproducibility and research integrity.18–20 A number of preprints also contained extremely serious issues, such as ethical and privacy concerns, data manipulation, and flawed designs.21 These data support the notion of a proliferation of bad quality work over the course of the pandemic (‘research waste’,22,23), ultimately leading to a spread of misinformation.24\n\n(A) Preprints appearing per day on a selection of preprint servers indicated in the figure’s legend, from January 2020 to June 2022. To account for daily variation in the upload of preprints, 30-day moving averages are represented, i.e. the average of the last 30 days. (B) The cumulative number of preprints posted to the same set of preprint servers, indexed in Europe PMC since the first WHO statement regarding a novel infectious disease outbreak on January 9, 2020.68\n\nSuch initial findings are countered by a much more nuanced story of COVID-19 preprint quality. While it is true that many preprints never convert into publications (70-80% as of April 2021, see e.g., Refs. 25, 26) and that preprints tend to be less cited than the resulting peer reviewed publication,27,28 this is not necessarily due to poor quality. For one, the link between a preprint and its publication may be lost when it is the preprint that gets cited.29 Alternatively, the authors’ decisions could be the cause, as some may avoid the publication process altogether.30 Others may intentionally use preprints to release replications, and null results that are difficult to publish,31 or works in progress which may be less well-written and inadequate at sharing data/code.17–20 Many preprints actually report their results in a balanced way so as not to ‘oversell’ their findings,30 and there is growing evidence of high concordance between findings published in preprints and in peer-reviewed journals.25,32–39 Nonetheless, a large portion of COVID-19 preprints show substantial changes in methods and results after peer-review (nearly half of the preprints analysed by Oikonomidi (2020) and Nicolalde et al. (2020)25,31), suggesting flaws in the most essential elements of many COVID-19 preprints. At least two potential solutions for distinguishing high- from low-quality research in preprints are possible: 1) introducing quality control measures, and 2) educating the readership of preprints to make quality evaluations themselves. Of the extant efforts to improve preprint quality, most have focused on introducing quality control via quick peer-review, e.g., Prereview (https://www.prereview.org/), Review Commons (https://www.reviewcommons.org/), PreLights (https://prelights.biologists.com/)[1]. Though peer-review is often considered the gold-standard for scientific quality control, it has limitations: it can be time consuming,3 at times inefficient at weeding out fraud, and often contaminated with reviewer bias, negligence, and self-interest.39–45 Automated problem detectors are a promising way forward,46 however such tools still require continued refinement and human verification of results.47 When research is under a stress test, such as during a world-wide pandemic, alternative forms of quality control have to be considered.\n\nAside from improving the contents of preprints directly, more could be done to educate the readership of preprints on the judicious interpretation of their contents. Preprints receive large attention on social and traditional media,48 but so far, their contents have not always been reported adequately, as many news reports do not provide explanations of the publication process, of how preprint platforms work, and of the implications of non-peer-reviewed research.44,45 This is made all the more disappointing by recent findings showing that a simple, one-paragraph explanation of the nature of preprints and the scientific publishing process can meaningfully change laypeople’s perceived credibility of scientific results.46\n\nPublic education initiatives on understanding preprints (on COVID-19 or more generally) have been next to non-existent. Apart from the study by Wingen et al.,49 only one effort was identified,50 which aimed to provide a set of guidelines for providing feedback on preprints, whether for reviewers or members of the broader community. In the absence of a set of guidelines on interpreting and evaluating information in preprints, we created the PRECHECK project (www.precheck.site). As the first project of its kind, the aim was to develop a simple, user-friendly tool to guide non-scientists in their evaluation of preprint quality. Though we were inspired by the proliferation of preprints and misinformation during the COVID-19 pandemic, we created a tool that can be applied to preprints or publications on other topics, with hopes that it can help empower non-scientists and non-specialists in making their own judgments.\n\n\nMethods\n\nThe entire project “PRECHECK: A checklist to evaluate COVID-19 preprints” was conducted under the ethical policies of the University of Zurich. As stipulated in sections 5 and 6 of these policies (https://www.rud.uzh.ch/dam/jcr:c42f07d3-2e89-485c-8a8b-3a3c3f46a3f5/UZH%20Policy%20on%20the%20Ethical%20Review%20of%20Research%20Projects%20Involving%20Human%20Subjects%20 (UZH%20Ethics%20Policy).pdf), our project falls outside the scope of the Swiss Human Research Act and, per section 8.1 of these policies, can be considered as a study that “generally cannot harmfully affect study participants”. Therefore, our project did not require explicit prior ethical approval from the institution, and for this reason we did not ask for ethical approval from the institution. A post-hoc verification with the University of Zurich ethical commission’s ethics review checklist (available in in the OSF repository for this project68) confirmed that we did not require ethical approval from the current project per the regulations of the University of Zurich. Written consent for participating in student workshops was not required because the workshops were administered as part of their regular university courses (details in manuscript) to which students do not need to exceptionally consent.\n\nThe aim of the study was to develop simple and clear guidance, in the form of a checklist, to help assess the quality of a preprint. Our target audience for the checklist were scientifically literate non-specialists, such as students of medicine and psychology, and science journalists. To develop a checklist that would be both user-appropriate, and discriminative of preprints of different levels of quality, we applied a multi-step approach inspired by the qualitative Delphi method.51,52 As such, our study could be considered a qualitative study, and we have thus followed the Standards for Reporting Qualitative Research (SRQR) (Ref. 53; see Ref. 69 for a completed version of the checklist for the current project). The Delphi method uses successive voting by expert groups to iteratively narrow down a pool of options until consensus is reached and is effective in determining consensus in situations with little to no objective evidence.54 Our procedure involved four main stages. In the first stage, the first draft of the checklist was reviewed internally by the senior members of our team (who were not involved in creating the draft) and subjected to a sensitivity test to verify whether the checklist could discriminate high- from low-quality preprints[2]. In the second stage, a panel of external experts rated the relevance of each element of the checklist and provided feedback, after which the checklist was updated. In the third stage, we conducted a final round of internal review producing the third draft of the checklist, which was also submitted to a final sensitivity analysis. At the end of the above three stages, we verified if members of our target audience could use the checklist successfully and if they appeared to find it useful, via workshops with university students and journalists. We called this stage the implementation of the checklist. In the workshop for journalists, some participants offered unsolicited yet helpful feedback, which was incorporated into the finalised version of the checklist (see also Figure 2).\n\nThere are four successive stages (Stage 1 – Stage 3 and the implementation stage, in blue, green, yellow, and purple fields, respectively) where each is made up of a set of successive steps (in white rectangular fields).\n\nThe research team conducting the analysis was composed of three junior researchers (postdoctoral level) and three senior researchers (two professors and one senior scientific collaborator). All members of the team have experience in meta-research, but are trained in other disciplines (statistics and psychology).\n\nIn this step, the three senior members of our team gave written feedback on a draft of the checklist in the form of comments. After the written feedback was incorporated by two junior members of our team, final feedback in the form of verbal comments from the senior members was obtained in an online meeting round. A copy of each version of the checklist after feedback and other validation procedures below is available in the OSF repository for this project.68\n\nAfter each of the two rounds of internal review (Stage 1 and Stage 3), we conducted a sensitivity test in order to verify whether the checklist, at its given stage of development, could successfully discriminate between preprints of different levels of quality. We did not perform any statistical analyses as part of this assessment. Since objective criteria for quality that would apply to all preprints across disciplines were difficult to envision, we used a list of milestone research works in the COVID-19 pandemic55 as a proxy of high quality, and we identified what would be the preprints in our high-quality set from this list. The preprints that would make up our low-quality set, on the other hand, were chosen from a list of retracted COVID-19 preprints,56 with retraction being a proxy for low quality. There were no a-priori criteria for selecting preprints. We selected three high-quality preprints57–59 and three low-quality preprints9,60,61 to test across multiple stages. Since preprint selection occurred in August 2021, we only included preprints that were available online from the start of the pandemic up until that point. In the Stage 1 round, one junior team member tested only the high-quality preprints and another junior team member the low-quality preprints. In the Stage 3 round, both team members tested all preprints independently. The same high- and low-quality preprints were used at both stages. To document the test results, a spreadsheet was generated with one field per checklist element, where the response to the checklist element for each preprint was entered. Fields were also coloured red, green, and yellow, to visually better represent ‘yes’, ‘no’, and ‘maybe’ responses to specific checklist elements, respectively. The results of each round of sensitivity tests with the links to the respective preprints are available in the Open Science Framework (OSF) repository for this project.68\n\nPanel selection\n\nWe invited a total of 54 experts across four topic groups: research methodology (14 invitations), preprints (15 invitations), journal editors (15 invitations), and science journalists (10 invitations), as these fields of expertise were judged to be of the greatest relevance for evaluating our checklist. Experts were identified through personal connections, by identifying editors of relevant journals in the fields of psychology and medicine (for the editor cohort), science journalists from a list of speakers at the World Conference of Science Journalists, Lausanne 2019 (https://www.wcsj2019.eu/speakers); for the journalist group), and identifying individuals whose work in the topic areas of research methodology and preprints is noteworthy and well-known. There were no a-priori criteria for selecting experts, other than their perceived belonging to one of the topic groups. In actual Delphi designs, 5-10 experts may be considered sufficient,62 however, there is no clear consensus on how large expert groups should be.63 Of the total number of experts, 29 were personal contacts. Panel members were contacted by email between October 18 2021 and November 16 2021 with a standardised explanation of the project, their role in the refinement of the checklist, how their data would be used (that their name and email will not be shared, that their responses will be fully anonymous, and that the aggregated results will be published and shared on our OSF repository for the project), and a link to a Google Forms survey where they could enter their responses anonymously. By clicking on the link to the survey, the experts thus gave their implicit informed consent to participate. The Survey Form sent to the experts is available in the OSF repository for this project.68 Experts that replied to our email declining to take part in the survey were not contacted further. Any experts that did not explicitly decline to take part were reminded twice, as the survey responses were fully anonymous, and we had no way of linking responses to individual experts. A total of 26 experts (48%) responded to the invitation by filling our survey (14 of them were personal contacts). The experts (self-)reported that they belonged to the following expert groups: four experts in science journalism, four journal editors, seven meta-researchers/experts on preprints, and 11 methodologists.\n\nResponse collection and analysis\n\nExperts rated the relevance of each element of the checklist on a five-point Likert scale, with the following response options: extremely irrelevant, mostly irrelevant, neither relevant nor irrelevant, mostly relevant, and extremely relevant. Response data were analysed by computing mean responses per element, using R (Version 4.04). We based our decisions on which elements to keep following the procedure used to establish the CONSORT guidelines for abstracts.64 That is, all elements with a mean score of four and above were kept (in the CONSORT for abstracts, this score was eight, as they used a 10-point Likert scale), elements with a mean score between three and four (four not included; between six and seven in the CONSORT for abstracts criteria) were marked for possible inclusion, and elements with a mean score below three were rejected.\n\nExperts also had the option to provide free-text comments: general additional comments on the checklist elements, suggestions for potentially relevant items that are missing, and suggestions on the structure (a PDF of the survey, including the Likert scales and free-text options is available in the OSF repository for this project68). These comments were collected into a single document and responded to in a point-by-point manner akin to a response to reviewers document (also in the OSF repository for this project68), arguing our agreement/disagreement with expert comments and how they were addressed in the subsequent draft of the checklist.\n\n\nResults\n\nFirst draft of the checklist\n\nThe first draft of the checklist was created from April 16 until May 17, 2021, and contained six categories of items: research question, study type, transparency, limitations, study reporting, and research integrity. The research question item asked whether the study mentioned the research question/aim, this being the most basic component of a research study. The study type question asked whether the study type was mentioned, and in the case that it was not, asked users to try and infer what the study type was, with guidance. In transparency, users were supposed to check the existence, availability, and accessibility of a protocol, and of data, code, and materials sharing. The limitations question asked whether any limitations of the study were mentioned, and asked users to try and evaluate any potentially unmentioned limitations (biases, specifically), with guidance. In study reporting, we asked to check for reporting guidelines that were followed explicitly or implicitly. Finally, the research integrity category asked users to check whether ethical approval, conflicts of interest, and contributor roles were reported.\n\nInternal review results\n\nIn the first round of internal review, the senior members of our team provided feedback on the contents of the first draft of the checklist. This round revealed that explanations were needed as to the importance of considering each specific item in our checklist, and that both a more ‘superficial level’ and a ‘deeper level’ were necessary to account for all user needs. For these reasons, we expanded the initial checklist, such that each item consisted of a main question, an explanatory section entitled ‘Why is this important’, and a section entitled ‘Let’s dig deeper’. The main questions formed the basis of the checklist, as they were all closed questions that could be answered via the ‘yes’ box next to them. Users could tick the box in full to indicate that the preprint being read passes the question, in part to indicate a ‘maybe’ response, or not at all to indicate that the preprint does not pass the question. This level was also called the ‘superficial level’ of assessment, as the questions could mostly be answered after a quick read of a preprint, and by searching for keywords that appear in the questions. The’why is this important?’ section was added in order to increase the pedagogical value of the checklist, which was designed as a teaching tool, such that users could learn about the purpose behind the main questions, and their importance for evaluating research. The ‘let’s dig deeper’ sections were added as an optional part for users that wanted to go beyond the main questions in their evaluation of a preprint, or that wanted to learn more about how to structure their thoughts when evaluating research work. Thus, this section does not have a tick-box, as it usually contains open questions and suggestions. This section cannot stand alone and should be consulted after the main questions and ‘why is this important’ section, which is why we called this the ‘deep level’ of assessment. A full version of the checklist at this stage can be found in the OSF repository for this project.68 This was the version of the checklist that we submitted to a sensitivity test on high- and low-quality preprints.\n\nSensitivity test results\n\nWhile searching for high- and low-quality preprint examples to apply the checklist to, we discovered that the checklist works best when applied to research with human subjects using primary data (or systematic reviews, meta analyses and re-analyses of primary data). That is, the questions turned out to be ill-posed (unanswerable) for research that did not fall into the above description, such as simulation studies, for example. We decided to indicate this in the introduction section of the checklist.\n\nAt the superficial level, the high-quality preprints that we used57–59 received mostly ‘yes’ and ‘maybe’ responses to the main questions. Only58 had a ‘no’ for mentioning/sharing their data/code. The low-quality preprints9,60,61 also received several ‘yes’ and ‘maybe’ responses, though fewer than the high-quality preprints. Interestingly, the Transparency and Study reporting items all received ‘no’ responses for the low-quality preprints, whereas the high-quality preprints mostly received ‘maybe’ and ‘yes’ responses. This demonstrates both that high- and low-quality preprints differ in terms of how they meet transparency and reporting standards, but also highlights that even high-quality preprints do not necessarily meet all these standards.\n\nAt the deep level, high-quality preprints mostly received ‘yes’ responses to the points in the ‘let’s dig deeper’ section, and a few ‘no’ and ‘maybe’ responses. Meanwhile, the low-quality preprints had no clear pattern of responses with many ‘no’, ‘yes’, and ‘maybe’ responses. However, low-quality preprints had more ‘no’ responses than high-quality preprints. At this level of assessment, one could delve into issues with study design, specifically in Limitations, where low-quality preprints performed demonstrably worse than high-quality preprints. Thus, it may be important to consider both levels of assessment when evaluating preprints using the checklist. The final version of the checklist at this stage was completed on October 18, 2021.\n\nExternal expert review summary results\n\nExperts were first asked how relevant they thought each of the six item categories were for assessing preprint quality on a five-point Likert scale: from extremely irrelevant (score of 1) to extremely relevant (score of 5). Here, all categories scored above four, except study reporting which received a 3.96. All elements with a mean score of four and above were kept, elements with a mean score between three and four were marked for possible inclusion and those with a mean score below three were rejected. Next, experts were to rate the relevance of each of the elements per category, including the main questions, and each of the points in the ‘let’s dig deeper’ sections. The results are summarised in Table 1 below. None of the elements has a score lower than three, which meant that none of the elements warranted immediate exclusion. However, several elements, including the entire study reporting category, had scores between three and four that placed them in the ‘possible inclusion’ category.\n\nSummary of external experts’ comments\n\nThe full list of free-text comments submitted by the experts and our responses to them is available in the OSF repository for this project.68 Overall, the comments revealed enthusiasm about the checklist, but also important criticisms. First, there were concerns that the target audience as it was previously defined (non-scientists) would not be able to adequately use a checklist of the complexity present at the time. Paradoxically, however, there were also many suggestions for additional elements that could further increase complexity, such as: how the study fills the gap in the knowledge, if the study can be fully reproduced, if there is justification for the statistical methodology used, etc. Another prominent criticism was that the checklist inadvertently prioritised randomised controlled trials and could potentially discredit observational studies. Our sensitivity test did not find observational studies to be particularly disadvantaged in comparison with randomised controlled trials. However, we did acknowledge that some categories, specifically limitations, appeared more oriented towards randomised controlled trials. One specific comment raised the issue that our checklist did not include COVID-19 specific questions, despite the checklist’s motivation. We thus sought to correct and elaborate these points in the next versions of the checklist.\n\nSome experts had additional ideas, some of which were outside the scope of this project, but others of which were easy to implement. In particular, the suggestion to ask users to check if the manuscript converted into a publication, and to include spin and overinterpretation of results as other examples of biases in the Limitations section. These suggestions were incorporated into the subsequent versions of the checklist.\n\nSecond draft of the checklist\n\nThe second draft of the checklist68 consisted of the following elements: Research question (main question only), study type, transparency (main question on mentioning the protocol, and two ‘let’s dig deeper’ questions on accessing the protocol, and accessing the data), limitations, and research integrity (two main questions on mentioning an ethics approval statement, and conflicts of interest). After expert feedback, we decided to omit the study reporting category, and instead incorporate the reporting guidelines mentioned there in the newly added descriptions of study types in the item study type, to reduce overall complexity, and increase clarity in this section specifically. After comments on the checklist’s complexity, we combined the transparency and research integrity categories and their remaining elements into a new category called ‘transparency and integrity’. Here, in response to a specific comment, we altered the main questions such that they probe if a study protocol, data sharing, materials sharing, ethical approval, and conflicts of interest, are mentioned, whereas the ‘let’s dig deeper’ section asks if the above are accessible (in the aforementioned section, we define what we mean by accessible). In addition to these changes, we realised the utility of looking both at the preprint and the preprint server when using the checklist, as sometimes the preprint does not mention data/materials sharing, but these resources are shared on the server.19 Thus, we added a recommendation into the introduction to consider both sources when using the checklist. In response to the comment on inadvertently disadvantaging observational research, we added disclaimers into the limitations section stating when certain sources of bias do not apply. Specifically, for the control group/condition, randomisation, and blinding elements, we added a clause to the end of each paragraph that states ‘(if your preprint is on an observational study, this item does not apply)’. In response to the lack of a COVID-19 element, we elaborated that, although the state of COVID-19 preprints and their effect on society was our inspiration for the project, our expertise (preprint quality in medicine and psychology) made it difficult to create an adequate COVID-19-specific checklist. With this, we modified the title of the checklist and expanded the introduction, to avoid further confusion. The final version of the checklist at this stage was completed on January 17, 2022. It is available in the OSF repository for this project.69 Also, we structured our workshops with students and journalists around issues with preprints and peer review more generally.\n\nTo provide more details on the workshops, we envisaged two for students: one for Bachelors’ students of Psychology at the University of Geneva, and one for Bachelors’ students of Medicine at the University of Zurich. Both workshops were given as invited lectures in standard classes taught to students as part of their respective Bachelors’ courses (as part of the “Scientific skills and competencies in psychology” class at the University of Geneva [in the original French: “Compétences et connaissances scientifiques en psychologie”], and the “Biostatistics for medical professionals” class at the University of Zurich [in the original German: “Biostatistik für Mediziner”]). The workshop content was made clear to the students in advance. Only those students that were enrolled in the above classes as part of their Bachelors’ courses could attend the workshops. Thus, no special consent was required to participate in the workshops. One junior member led the workshop at the University of Geneva, while at the University of Zurich, one junior and one senior member led the workshop. There was no relationship of dependence between either one of these members and the students they administered the workshops to (i.e., neither member was involved in the grading of the students’ course assignments or exams). Both workshops consisted of a theoretical presentation of the scientific publishing process, what preprints are, and current issues with preprints and peer review (based on the conclusions of the literature review in the present manuscript). Next, the purpose and component parts of the checklist were presented, together with instructions on how to use it for the subsequent in-class exercise. In the exercise, students were split into two groups according to their last names, each given 15-20 minutes to re-read a preprint (they were informed about the exercise and given the preprints beforehand; one group read,60 and the other group read65) and use the checklist to evaluate it. The answers were collected anonymously, in an aggregated (non-individual) fashion, via an in-house platform. At the University of Geneva, we used surveys on Votamatic (https://votamatic.unige.ch/) to gather the percentages of students that voted ‘yes’, ‘no’, or ‘partly’ for each superficial-level item, and Padlet (https://unige.padlet.org) to gather optional free text responses to the deep-level items. At the University of Zurich, Klicker (https://www.klicker.uzh.ch/home) was used to gather the percentages of students that voted ‘yes’, ‘no’, or ‘maybe’ for each superficial-level item, alongside optional free text comments. Once recorded, these percentages were discussed by the whole class, and compared against the researchers’ own evaluation of said preprint. The responses were only analysed inasmuch as percentages of ‘yes’, ‘no’, and ‘partly/maybe’ responses were automatically generated by the respective platforms, for the purpose of in-class discussion. There were no formal statistical analyses performed on these responses, and the responses did not influence the content of the checklist in any way.\n\nThe above workshop format was also adapted for science journalists at the Universities of Geneva and Zurich. In practice, only the workshop at the University of Geneva was held (and led by the junior member of the team based at the University of Geneva), as the relevant personnel at the University of Zurich failed to respond to our requests to hold a workshop. The format was largely the same as that of the workshop for students, except that the initial presentation focused less on the scientific publishing process, and more on issues with preprints and peer review, and included more time for a mutual discussion of said issues. We intended for these to be small workshops open only to a select number of people, on a purely voluntary basis, invited by the main contact person at each University’s communications section. All of the invited parties were informed on the content of the workshop beforehand. Only those individuals that were interested in attending did so and provided verbal assent to participate in the workshop. The same in-house online platform as before (i.e., Votamatic) was used to collect data on percentages of ‘yes’, ‘no’, or ‘partly’ for each superficial-level item of the checklist in an anonymous, aggregated (non-individual) fashion, and this automatic generation of response percentages was the only analysis performed on these data. Deep-level item answers were informally discussed. As before, there were no formal statistical analyses performed on these data. Some informal verbal feedback (not previously solicited) that we received from the participants did influence the content of the checklist, as we detail in the Implementation section below.\n\nFinally, the content of the workshop for university science journalists was adapted for a fact-checking seminar organised by the Swiss Association of Science Journalists (https://www.science-journalism.ch/event/spring-seminar-2022). Two junior members gave this workshop at the Swiss National Science Foundation headquarters in Bern. Participation was voluntary and open only to individuals that registered to attend the conference at which we were invited to give our workshop as part of the advertised programme. Thus, no special consent was required for participation. We used the same procedure as above, with the exception that a ‘nonsense’ preprint was read and evaluated (Ref. 66; i.e., a manuscript describing a made-up study to prove the point that predatory journals do not screen for quality) and no response data were collected (responses were probed and discussed verbally during the session).\n\nFinal draft of the checklist\n\nIn the second internal review round, we kept the four-item structure, most of the text, and visual separation between the superficial and deep levels from the second draft of the checklist. In addition, the wording was clarified and additional explanations were provided where necessary. In transparency and integrity, we added clauses to explain what to do in situations where data and materials are stated to be shared upon request, or if reasons against sharing are mentioned. Specifically, since acquiring data/materials after requesting it from authors that only share upon request happens only in a minority of cases,65 we advised that ‘mentioning only that data will be shared ‘upon request’ does not count’. However, if authors mention that they cannot share the data or materials for a specific reason, we advised that ‘mentioning any reasons against sharing also counts [as a ‘yes’]’. In the limitation section, we added examples of spin and overinterpretation as other sorts of biases to look out for. In the introduction, we added the recommendation to check whether the preprint has converted into a publication.\n\nSensitivity test results\n\nAt the superficial level, both high- and low- quality preprints had many positive responses, for both team members that tested the checklist. The elements that differed the most were transparency and integrity, with low-quality preprints having slightly more ‘no’ and ‘maybe’ responses than high-quality preprints. Additionally, both raters agreed that two of the three low-quality preprints did not discuss limitations. This is a slight departure from the prior sensitivity test results, in that the difference between high- and low-quality preprints appears to be smaller.\n\nAt the deep level, however, the differences were once again well-pronounced, as high-quality preprints had predominantly positive responses, while low-quality preprints had predominantly negative and ‘maybe’ responses. Thus, the deep level seems to be necessary to fully discern between high- and low-quality preprints. Similarly, to the prior results, the responses in the transparency and integrity section exposed that even high-quality preprints did not always meet the standards of transparency and integrity. The final version of the checklist at this stage was completed on March 1, 2022.\n\nWith an operational checklist, we set out to teach members of our target audience how to use the checklist and to verify if they could use it as intended. To this end, we gave courses including workshops to Bachelor students in Medicine and Psychology at the University of Zurich, and the University of Geneva, respectively. The workshop at the University of Zurich took place on March 11, 2022, while the workshop at the University of Geneva took place on May 9, 2022. For our journalist cohort, we provided a lecture and practical for members of the University of Geneva communications office and scientific information division. This workshop took place on May 19, 2022. We later also presented the checklist at a fact-checking seminar organised by the Swiss Association of Science Journalists on May 31, 2022.\n\nAcross all of these classes, except for the fact-checking seminar, we used the same high- and low-quality preprints as practice material, and explained both how to use the checklist, as well as the rationale behind its elements, as stated in our point-by-point response to experts. A few suggestions for improvement nonetheless emerged from the workshop with the journalists at the University of Geneva, as some participants wished to offer feedback. Some participants of this workshop pointed out that the necessity and function of both the superficial and deep level of assessment were not clear. Others had trouble understanding what mention of data and materials sharing counts as a ‘yes’ response and what counts as a ‘no’ response. Finally, one participant suggested that even before using the checklist, one should generally apply more caution when assessing controversial research or findings that sound ‘too good to be true’. We incorporated all of this feedback into the final version of the checklist, which was completed on May 20, 2022 (see also Table 2).68\n\n\n\n- observational studies - studies where the experimental conditions are not manipulated by the researcher and the data are collected as they become available. For example, surveying a large group of people about their symptoms is observational. So is collecting nasal swabs from all patients in a ward, without having allocated them to different pre-designed treatment groups. Analysing data from registries or records is also observational. For more information on what to look for in a preprint on a study of this type, please consult the relevant reporting guidelines: STROBE.\n\n- randomised experiments - studies where participants are randomly allocated to different pre-designed experimental conditions (these include Randomised controlled trials [RCTs]). For example, to test the effectiveness of a drug, patients in a ward can be randomly allocated to a group that receives the drug in question, and a group that receives standard treatment, and then followed up for signs of improvement. For more information on what to look for in a preprint on a study of this type, please consult the relevant reporting guidelines: CONSORT.\n\n- case studies - studies that report data from a single patient or a single group of patients. For more information on what to look for in a preprint on a study of this type, please consult the relevant reporting guidelines: CARE.\n\n- systematic reviews and meta-analyses - summaries of the findings of already existing, independent studies. For more information on what to look for in a preprint on a study of this type, please consult the relevant reporting guidelines: PRISMA.\n\n\n\n- Does the study pool the results from multiple previous studies?\n\n- If yes, it falls in the category systematic review/meta-analysis.\n\n- Does the study compare two or more experimenter-generated conditions or interventions in a randomised manner?\n\n- If yes, it is a randomised experiment.\n\n- Does the study explore the relationship between characteristics that were not experimenter-generated?\n\n- If yes, then it is an observational study\n\n- Does the study document one or multiple clinical cases?\n\n- If yes, it is a case study.\n\n\n\n1. Check the study’s sample (methods section). Do the participants represent the target population? Testing a drug only on white male British smokers over 50 is probably not going to yield useful results for everyone living in the UK, for example. How many participants were there? There is no one-size-fits-all number of participants that makes a study good, but in general, the more participants, the stronger the evidence.\n\n2. Was there a control group or control condition (e.g., placebo group or non-intervention condition)? If not, was there a reason? Having a control group helps to determine whether the treatment under investigation truly has an effect on an experimental group and reduces the possibility of making an erroneous conclusion. Not every study can have such controls though. Observational studies, for example, typically do not have a control group or condition, nor do case studies or reviews. If your preprint is on an observational study, case study, or review, this item may not apply.\n\n3. Was there randomisation? That is, was the allocation of participants or groups of participants to experimental conditions done in a random way? If not, was there a reason? Randomisation is an excellent way to ensure that differences between treatment groups are due to treatment and not confounded by other factors. For example, if different treatments are given to patients based on their disease severity, and not at random, then the results could be due to either treatment effects or disease severity effects, or an interaction - we cannot know. However, some studies, like observational studies, case studies, or reviews, do not require randomisation. If your preprint is on an observational study, case study, or review, this item may not apply.\n\n4. Was there blinding? Blinding means that some or all people involved in the study did not know how participants were assigned to experimental conditions. For example, if participants in a study do not know whether they are being administered a drug or a sham medication, the researchers can control for the placebo effect (people feeling better even after fake medication because of their expectation to get better). However, blinding is not always possible and cannot be applied in observational studies or reanalyses of existing non-blinded data, for example. If your preprint is on an observational study, case study, or review, this item may not apply).\n\n\nDiscussion\n\nOver four successive stages of refining the PRECHECK checklist, we arrived at a four-item checklist approved by internal and external review, that can help critically evaluate preprints. After a set of workshops with Bachelor students from Psychology and Medicine, and science journalists, we concluded that the checklist was in a state where it was ready to be used by scientifically literate non-specialists. Here we recapitulate the main findings and discuss their implications.\n\nThe results of the sensitivity tests can be divided into three key findings. First, across both tests, preprints deemed to be of high quality had consistently more positive responses on the checklist than preprints deemed to be of low quality. This indicates that the checklist is effective at discriminating preprints of high and low quality, since positive responses mean that the preprint in question ‘passes’ a given criterion for good quality. Importantly, this holds even when the checklist is reduced to only four items, which is important for maintaining the user-friendliness of the checklist.\n\nThat said, and we consider this the second key finding, the deep level seemed to be especially important for discriminating preprint quality. It was especially evident in the second sensitivity test that combining the deep and superficial level is optimal for distinguishing high- from low-quality preprints. This is likely due to the nature of the questions at these two different levels of evaluation, as the superficial level probes surface level questions which can be considered a ‘bare minimum’ of quality. For example, it is standard scientific practice that the research question or aim of a study must be mentioned in its resulting manuscript, and indeed, most preprints, even ones that eventually end up being retracted, do offer this information. The issues with low-quality preprints rather seem to be in their designs, ethical considerations, handling of the data and interpretation of the results,21 and how transparently they report their results.18,19 In our checklist, the first set of issues is detected by the deep level of the Limitations item, as this level asks users to engage with the content of the research reported in the preprint, and to check for potential issues with the design. The second set of issues is addressed by the transparency and integrity question, at both the deep and superficial levels. Both levels have been successful at detecting problems in low-quality preprints, but also high-quality preprints, which brings us to the final key finding.\n\nThird, for both high- and low-quality preprints, the checklist highlighted issues with transparency and research integrity. This mirrors the state of the COVID-19 literature, as we have seen that though the credibility of the research reported in preprints can be sound,37–39 data and materials sharing may nonetheless often be lacking.18,19 This could be taken as a weakness of the checklist, as this item is not particularly discriminative of preprint quality. However, we believe it is a strength, albeit an unintended one. On one hand, this feature highlights where there is room for improvement even in works that are otherwise of good quality. Thus, there is potential for integrating the checklist in peer-review procedures, as one of our external experts suggested. On the other hand, it informs non-specialist audiences of the importance of transparency and integrity when considering the quality of a manuscript. As another external expert pointed out, certain practices such as open data sharing are considered to be at the forefront of scientific endeavours, and not all researchers adhere to these standards, even if their research is sound. However, we believe that part of the reason for this non-adherence is that not everyone believes such Open Science practices to be sufficiently important, even despite a clear need to improve reproducibility in many areas of science.65,67 By dedicating an entire item to issues of transparent reporting and research integrity, we hope to encourage non-specialists as well as scientists to both pay attention to and think critically about issues of transparency and integrity, in addition to the soundness of the research being reported.\n\nApart from the external expert comments already mentioned, the (online survey) review process revealed several important insights. It was illuminating that many experts agreed that the initial draft was too complex for non-scientist audiences, while there were also suggestions for additional items that required, in our view, expertise that non-scientists would not reasonably have. This situation made it clear that we had to define our target audience more precisely, and strike the right balance between simplicity and functionality in our checklist to make it both usable and accurate. The implementation round confirmed that the checklist was indeed usable, as both our student and journalist cohorts across multiple sites appeared to understand how the checklist was supposed to be used. Further, in our workshops, there appeared to be an overlap in the students’ and journalists’ application of the checklist to the high- and low- quality preprints and our own. We do acknowledge that many important aspects of checking the quality of a scientific work that the experts mentioned were omitted, such as verifying the references, checking whether the work fills a gap in knowledge, and checking whether the statistical analyses are justified. Though this can be construed as a limitation, we believe it is justified by the feasibility constraint of the checklist being a teaching tool for audiences that will very likely not have the expertise to verify preprints in such ways.\n\nAnother prominent theme that emerged in the external experts’ comments was an implicit prioritization of randomized controlled trials, which could in turn disadvantage observational studies. Though we did not find the checklist to be as gravely biased, as all three of our high-quality preprints57–59 were on observational studies, and they ‘passed’ the items on the checklist very well. We nonetheless appreciated the importance of this point, as much of the COVID-19 research reported in preprints was indeed observational.16 In response, we made two substantial changes to the checklist. For one, we expanded the explanation of what observational studies are in the Why is this important? Section of Study type, by including concrete examples. This could help prevent non-experts from falsely identifying an observational study as having not indicated a study type, as unlike for randomized controlled trials, manuscripts on observational studies often do not explicitly mention that the research was observational. Moreover, we made it clear that the potential sources of bias mentioned in the ‘let’s dig deeper’ section in limitations were only examples, we added disclaimers for those sources of bias that may not apply to observational studies (control group/control condition, randomization, and blinding, specifically), and we included two more examples of biases that could apply to observational studies (spin and overinterpretation). We believe that these changes made the checklist more balanced towards all study types.\n\nOne important aspect of the checklist to note is its intended use as a teaching tool to guide non-specialist audiences to evaluate preprints more critically than they otherwise might. The checklist is not meant to be a litmus test for whether a preprint is trustworthy or not, but rather a set of guidelines for users to make their own judgements based on, and a pedagogical tool to improve people’s competences and confidence at evaluating the quality of research. Though the superficial level alone could, in theory, be automated, as we have seen, the best results are obtained when the superficial and deep levels are combined, and it is the deep level that allows the user to delve deeper into issues of study design and potential biases. Nonetheless, it is useful to have a division into a superficial and deep level of assessment, as this allows greater flexibility for users to apply the checklist according to their needs.\n\n\nConclusions\n\nOver multiple iterative steps of internal and external review, sensitivity tests, and final polishing after the implementation phase, we created the PRECHECK checklist: a simple, user-friendly tool for helping scientifically literate non-experts critically evaluate preprint quality. We were inspired by the urgency of improving the public’s understanding of COVID-19 preprints, in which efforts to increase public awareness on preprint quality and competences at estimating preprint quality have been next to non-existent. Despite our COVID-19-related motivation, the PRECHECK checklist should be more broadly applicable to scientific works. With this, and the fact that our target audience could use the checklist, we believe that the checklist has great potential to help guide non-scientists’ understanding of scientific content, especially in preprint form.\n\n\nAuthors' contributions (CRediT)\n\nConceptualization: LH, EV, EF; Data curation: NT, SS, RH; Formal Analysis: NT, SS, RH; Funding acquisition: LH, EV; Investigation: NT, SS, RH; Methodology: NT, SS, RH; Project administration: NT, SS, RH; Resources: LH, EV; Software: NT, SS, RH; Supervision: LH, EV, EF; Validation: NT, RH, SS, EF, EV, LH; Visualization: NT, SS, RH; Writing – original draft: NT, RH; Writing – review & editing: NT, RH, SS, EF, EV, LH.",
"appendix": "Data availability\n\nOSF: PRECHECK. https://doi.org/10.17605/OSF.IO/NK4TA. 68\n\nThis project contains the following underlying data:\n\n• Code for Figure 1 folder. [R code in an RMD document to reproduce Figure 1 with the data that is also uploaded in this folder].\n\n• Sensitivity Test Preprints folder. [high-quality subfolder containing the high-quality preprints chosen for the sensitivity test (Bi et al., - 2020 - Epidemiology and Transmission of COVID-19 in Shenz.pdf, Lavezzo et al., - 2020 - Suppression of COVID-19 outbreak in the municipali.pdf, Wyllie et al., - 2020 - Saliva is more sensitive for SARS-CoV-2 detection.pdf ), low-quality subfolder containing the low-quality preprints chosen for the sensitivity test (Davido et al., - 2020 - Hydroxychloroquine plus azithromycin a potential.pdf, Elgazzar et al., - 2020 - Efficacy and Safety of Ivermectin for Treatment an.pdf, Pradhan et al., 2020 - Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag.pdf ), and workshop_nonsense subfolder containing the preprint used for the fact-checking seminar (Oodendijk - 2020 - SARS-CoV-2 was Unexpectedly Deadlier than.pdf )]\n\n• Stage 1 folder. [Checklist Version after Stage 1 (20211018_PRECHECKchecklist.pdf ) and the sensitivity test performed using that version of the checklist (Stage1_SensTest.xlsx)].\n\n• Stage 2 folder [Checklist Version after Stage 2 (20220117_PRECHECKchecklist.pdf ), the form that was used to collect expert responses (ExpertSurveyForm.pdf ), and the replies to expert free text comments (Point-by-pointExpertReplies.pdf )]\n\n• Stage 3 folder [Checklist Version after Stage 3 (20220301_PRECHECKchecklist_afterComments.pdf ), the results of the sensitivity analyses done by the junior authors, NT (Stage3_SensTest_NT.xlsx) and RH (Stage3_SensTest_RH.xlsx)].\n\nOSF: PRECHECK. https://doi.org/10.17605/OSF.IO/NK4TA. 68\n\nThis project contains the following extended data:\n\n• 20220520_FINAL_PRECHECKchecklist_afterComments_afterWorkshops.pdf. (Final version of the PRECHECK checklist).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nRepository: SRQR checklist for ‘Using an expert survey and user feedback to construct PRECHECK: A checklist to evaluate preprints on COVID-19 and beyond’. https://doi.org/10.17605/OSF.IO/JVHBW. 69\n\n\nAcknowledgements\n\nWe would like to thank all of the experts that so graciously volunteered their time to refine this checklist, as well as the students and journalists that took part in our workshops.\n\n\nReferences\n\nHomolak J, Kodvanj I, Virag D: Preliminary analysis of COVID-19 academic information patterns: a call for open science in the times of closed borders. Scientometrics. 2020 Sep; 124(3): 2687–2701. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGianola S, Jesus TS, Bargeri S, et al.: Characteristics of academic publications, preprints, and registered clinical trials on the COVID-19 pandemic. Mathes T, editor. PLoS One. 2020 Oct 6; 15(10): e0240123. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchwab S, Held L: Science after Covid-19 - Faster, better, stronger? Significance. 2020; 17: 8–9. Publisher Full Text\n\nWatson C: Rise of the preprint: how rapid data sharing during COVID-19 has changed science forever. Nat. Med. 2022; 28: 2–5. PubMed Abstract | Publisher Full Text\n\nKirkham JJ, Penfold NC, Murphy F, et al.: Systematic examination of preprint platforms for use in the medical and biomedical sciences setting. BMJ Open. 2020 Dec; 10(12): e041849. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCowling BJ, Leung GM: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak. Eurosurveillance. 2020; 25(6): 2000110.\n\nVlasschaert C, Topf JM, Hiremath S: Proliferation of Papers and Preprints During the Coronavirus Disease 2019 Pandemic: Progress or Problems With Peer Review? Adv. Chronic Kidney Dis. 27: 418–426. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRavinetto R, Caillet C, Zaman MH, et al.: Preprints in times of COVID19: the time is ripe for agreeing on terminology and good practices. BMC Med. Ethics. 2021 Dec; 22(1): 1–5. Publisher Full Text\n\nSheldon T: Preprints could promote confusion and distortion. Nature. 2018; 559(7714): 445–446. PubMed Abstract | Publisher Full Text\n\nPradhan P, Pandey AK, Mishra A, et al.: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag [Internet]. Evol. Biol. 2020 Jan [cited 2021 Aug 20]. Publisher Full Text\n\nKim MS, Jang SW, Park YK, et al.: Treatment response to hydroxychloroquine, lopinavir–ritonavir, and antibiotics for moderate COVID-19: a first report on the pharmacological outcomes from South Korea. MedRxiv. 2020.\n\nZhang C, Zheng W, Huang X, et al.: Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. J. Proteome Res. 2020 Apr 3; 19(4): 1351–1360. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlexander PE, Debono VB, Mammen MJ, et al.: COVID-19 coronavirus research has overall low methodological quality thus far: case in point for chloroquine/hydroxychloroquine. J. Clin. Epidemiol. 2020 Jul; 123: 120–126. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee S: Shoddy coronavirus studies are going viral and stoking panic. BuzzFeed News.Reference Source2020.\n\nU.S. Food and Drug Administration (FDA): Coronavirus (COVID-19) Update: FDA Revokes Emergency Use Authorization for Chloroquine and Hydroxychloroquine.2020 Jun 15.\n\nJohansson MA, Reich NG, Meyers LA, et al.: Preprints: An underutilized mechanism to accelerate outbreak science. PLoS Med. 2018 Apr 3; 15(4): e1002549. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCeli LA, Charpignon ML, Ebner DK, et al.: Gender Balance and Readability of COVID-19 Scientific Publishing: A Quantitative Analysis of 90,000 Preprint Manuscripts. Health Informatics. 2021 Jun [cited 2022 Jun 27]. Publisher Full Text\n\nSumner J, Haynes L, Nathan S, et al.: Reproducibility and reporting practices in COVID-19 preprint manuscripts. Health Informatics. 2020 Mar [cited 2021 Apr 16]. Publisher Full Text\n\nStrcic J, Civljak A, Glozinic T, et al.: Open data and data sharing in articles about COVID-19 published in preprint servers medRxiv and bioRxiv. Scientometrics. 2022 May; 127(5): 2791–2802. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYesilada M, Holford DL, Wulf M, et al.: Where: Tracking the development of COVID-19 related PsyArXiv preprints. PsyArXiv.2021 May [cited 2022 Jun 27]. Reference Source\n\nBramstedt KA: The carnage of substandard research during the COVID-19 pandemic: a call for quality. J. Med. Ethics. 2020 Dec; 46(12): 803–807. PubMed Abstract | Publisher Full Text\n\nChalmers I, Glasziou P: Avoidable Waste in the Production and Reporting of Research Evidence.2009; 114(6): 5.\n\nMacleod MR, Michie S, Roberts I, et al.: Biomedical research: increasing value, reducing waste. Lancet. 2014; 383(9912): 101–104. Publisher Full Text\n\nBrierley L: Lessons from the influx of preprints during the early COVID-19 pandemic. Lancet Planet. Health. 2021 Mar; 5(3): e115–e117. PubMed Abstract | Publisher Full Text\n\nOikonomidi T: Changes in evidence for studies assessing interventions for COVID-19 reported in preprints: meta-research study. BMC Med. 2020; 10.\n\nSevryugina Y, Dicks AJ: Publication practices during the COVID-19 pandemic: Biomedical preprints and peer-reviewed literature. BioRxiv. 2021; 63.\n\nJung YEG, Sun Y, Schluger NW: Effect and reach of medical articles posted on preprint servers during the COVID-19 pandemic. JAMA Intern. Med. 2021; 181(3): 395–397. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGehanno JF, Grosjean J, Darmoni SJ, et al.: Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals. Infectious Diseases (except HIV/AIDS). 2022 Feb [cited 2022 Jun 27]. Publisher Full Text\n\nLachapelle F: COVID-19 Preprints and Their Publishing Rate: An Improved Method. Infectious Diseases (except HIV/AIDS). 2020 Sep [cited 2021 Apr 16]. Publisher Full Text\n\nBordignon F, Ermakova L, Noel M: Over-promotion and caution in abstracts of preprints during the COVID -19 crisis. Learned Publishing. 2021 Oct; 34(4): 622–636. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNicolalde B, Añazco D, Mushtaq M, et al.: Citations and publication rate of preprints on pharmacological interventions for COVID-19: The good, the bad and, the ugly. In Review.2020 Sep [cited 2022 Jun 28]. Reference Source\n\nBero L, Lawrence R, Leslie L, et al.: Cross-sectional study of preprints and final journal publications from COVID-19 studies: discrepancies in results reporting and spin in interpretation. BMJ Open. 2021 Jul; 11(7): e051821. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCarneiro CFD, Queiroz VGS, Moulin TC, et al.: Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature. Res. Integr. Peer Rev. 2020 Dec; 5(1): 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKlein M, Broadwell P, Farb SE, et al.: Comparing published scientific journal articles to their pre-print versions. Int. J. Digit. Libr. 2019 Dec; 20(4): 335–350. Publisher Full Text\n\nShi X, Ross JS, Amancharla N, et al.: Assessment of Concordance and Discordance Among Clinical Studies Posted as Preprints and Subsequently Published in High-Impact Journals. JAMA Netw. Open. 2021 Mar 18; 4(3): e212110. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZeraatkar D, Pitre T, Leung G, et al.: Consistency of covid-19 trial preprints with published reports and impact for decision making: retrospective review. BMJ Med. 2022 Oct; 1(1): e000309. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZeraatkar D, Pitre T, Leung G, et al.: The trustworthiness and impact of trial preprints for COVID-19 decision-making: A methodological study. Epidemiology. 2022 Apr [cited 2022 Jun 27]. Publisher Full Text\n\nWang Y: The collective wisdom in the COVID-19 research: Comparison and synthesis of epidemiological parameter estimates in preprints and peer-reviewed articles. Int. J. Infect. Dis. 2021; 9. Publisher Full Text\n\nMajumder MS, Mandl KD: Early in the epidemic: impact of preprints on global discourse about COVID-19 transmissibility. Lancet Glob. Health. 2020 May 1; 8(5): e627–e630. PubMed Abstract | Publisher Full Text | Free Full Text\n\nClyne B, Walsh KA, O’Murchu E, et al.: Using preprints in evidence synthesis: Commentary on experience during the COVID-19 pandemic. J. Clin. Epidemiol. 2021 Oct; 138: 203–210. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPowell K: Does it take too long to publish research? Nature. 2016; 530(7589): 148–151. PubMed Abstract | Publisher Full Text\n\nHenderson M: Problems with peer review. BMJ. 2010; 340: c1409. Publisher Full Text\n\nBenos DJ, Bashari E, Chaves JM, et al.: The ups and downs of peer review. Adv. Physiol. Educ. 2007 Jun; 31(2): 145–152. PubMed Abstract | Publisher Full Text\n\nCampanario JM: Peer review for journals as it stands today—Part 2. Sci. Commun. 1998; 19(4): 277–306. Publisher Full Text\n\nSmith R: Peer Review: A Flawed Process at the Heart of Science and Journals. J. R. Soc. Med. 2006; 99: 5.\n\nWeissgerber T, Riedel N, Kilicoglu H, et al.: Automated screening of COVID-19 preprints: can we help authors to improve transparency and reproducibility? Nat. Med. 2021; 27(1): 6–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Noorden R: Pioneering duplication detector trawls thousands of coronavirus preprints. Nature. 2020. Publisher Full Text\n\nLimaye RJ, Sauer M, Ali J, et al.: Building trust while influencing online COVID-19 content in the social media world. Lancet Digital Health. 2020 Jun; 2(6): e277–e278. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWingen T, Berkessel JB, Dohle S: Caution, Preprint! Brief Explanations Allow Nonscientists to Differentiate Between Preprints and Peer-Reviewed Journal Articles. Adv. Methods Pract. Psychol. Sci. 2022;15.\n\nIborra SF, Polka J, Monaco S, et al.: FAST principles for preprint feedback.2022.\n\nDalkey NC: The Delphi method: An experimental study of group opinion. RAND CORP SANTA MONICA CA; 1969.\n\nDalkey N, Helmer O: An experimental application of the Delphi method to the use of experts. Manag. Sci. 1963; 9(3): 458–467. Publisher Full Text\n\nO’Brien BC, Harris IB, Beckman TJ, et al.: Standards for Reporting Qualitative Research: A Synthesis of Recommendations. Acad. Med. 2014 Sep; 89(9): 1245–1251. Publisher Full Text\n\nMeshkat B, Cowman S, Gethin G, et al.: Using an e-Delphi technique in achieving consensus across disciplines for developing best practice in day surgery in Ireland. JHA. 2014 Jan 22; 3(4): 1. Publisher Full Text\n\nParasher A: COVID research: a year of scientific milestones. Nature. 2021.\n\nRetraction Watch team. Retracted coronavirus (COVID-19) papers. Retraction Watch blog.2020.\n\nLavezzo E, Franchin E, Ciavarella C, et al.: Suppression of COVID-19 outbreak in the municipality of Vo’, Italy. Epidemiology. 2020 Apr [cited 2021 Aug 13]. Publisher Full Text\n\nBi Q, Wu Y, Mei S, et al.: Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts. Infectious Diseases (except HIV/AIDS). 2020 Mar [cited 2021 Aug 13]. Publisher Full Text\n\nWyllie AL, Fournier J, Casanovas-Massana A, et al.: Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. Infectious Diseases (except HIV/AIDS). 2020 Apr [cited 2021 Aug 13]. Publisher Full Text\n\nElgazzar A, Eltaweel A, Youssef SA, et al.: Efficacy and Safety of Ivermectin for Treatment and prophylaxis of COVID-19 Pandemic. In Review.2020 Dec [cited 2021 Aug 20]. Reference Source\n\nDavido B, Lansaman T, Bessis S, et al.: Hydroxychloroquine plus azithromycin: a potential interest in reducing in-hospital morbidity due to COVID-19 pneumonia (HI-ZY-COVID)? Infectious Diseases (except HIV/AIDS). 2020 May [cited 2021 Aug 20]. Publisher Full Text\n\nLynn MR: Determination and quantification of content validity. Nurs. Res. 1986; 35: 382–386. Publisher Full Text\n\nHasson F: Research guidelines for the Delphi survey technique. J. Adv. Nurs. 2000; 32: 1008. Publisher Full Text\n\nHopewell S, Clarke M, Moher D, et al.: CONSORT for reporting randomized controlled trials in journal and conference abstracts: explanation and elaboration. PLoS Med. 2008 Jan; 5(1): e20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStodden V, Seiler J, Ma Z: An empirical analysis of journal policy effectiveness for computational reproducibility. Proc. Natl. Acad. Sci. U. S. A. 2018 Mar 13; 115(11): 2584–2589. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaker M: 1,500 scientists lift the lid on reproducibility. Nature. 2016; 533(7604): 452–454. PubMed Abstract | Publisher Full Text\n\nOodendijk W, Rochoy M, Ruggeri V, et al.: SARS-CoV-2 was unexpectedly deadlier than push-scooters: could hydroxychloroquine be the unique solution. Asian J. Med. Health. 2020; 18(9): 14–21.\n\nSchwab S, Turoman N, Heyard R, et al.: Precheck. Dataset. 2023, January 30. Publisher Full Text\n\nHeyard R, Schwab S, Turoman N, et al.: Reporting Guideline. OSF. 2023. Publisher Full Text\n\n\nFootnotes\n\n1 For experience-based suggestions for teams of researchers interested in rapid peer-review, see Clyne and colleagues. 40\n\n2 As we will explain below, high and low quality was decided based on proxies, and not on objective criteria, as we could not determine a set of such criteria that apply to all preprints across all disciplines that the checklist could possibly be used on. With this, when we refer to ‘high-quality’ and ‘low-quality’ preprints, we do so for brevity, and not because the preprints in question belong to predefined universally agreed upon categories of ‘good’ and ‘bad’. Further, the checklist is not a litmus test for whether a preprint is ‘good’ versus ‘bad’. Rather, it is intended to be used as a set of guidelines and a tool to get scientifically literate non-specialist to think critically about how they read preprints."
}
|
[
{
"id": "176427",
"date": "18 Jul 2023",
"name": "Paul Glasziou",
"expertise": [
"Reviewer Expertise Evidence-based practice",
"overdiagnosis",
"non-drug interventions"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTuroman and colleagues have reported on the development of a much-needed assessment tool to help lay people to check preprint quality. The rationale for the study were clearly laid out. They went through four steps of development to create the checklist: initial internal and external reviews, final internal review and implementation. The resulting checklist has 4-categories – research question, study type, transparency and integrity, and limitations. Their reporting was well done following the Standards for Reporting Qualitative Research.\nThis study aimed to develop a brief checklist to guide non-experts in assessing pre-prints on Covid-19, but clearly can be extended to other types of research. The authors should be congratulated on making an interesting attempt. It represents a good first step, but I have a number of reservations about their validation process and the current checklist.\nThere are a few questions and comments below that could further improve this manuscript.\nIntroduction: could be more concise particularly paragraph 1 and 3.\nMethods:\nEthics clearance was not required. The study has a repository on Open Science Framework with all relevant documents, but it’s not clear whether it was submitted a priori. Please clarify.\n\nThe researchers have not reported whether they conducted a literature review before developing their first draft of the checklist with six items. Checking existing literature in the beginning of research helps reduce research waste and needless duplication or repetition. Please clarify and if not conducted justify this omission.\n\nThe sensitivity testing is very limited using only three \"high-quality\" and three \"low quality\" preprints assessed with the checklist. That might be reasonable pilot testing, but far from a sensitivity testing or validation.\n\nWhilst choosing major COVID-19-related research as “high” quality test papers for the sensitivity analysis was understandable, choosing retracted preprints for the “low” quality set is not necessarily appropriate. Manuscripts could be of ‘good’ quality methodologically, yet they could be retracted due to data fabrication or irregularities. So, the fact that they were retracted doesn’t automatically mean they were of “low” quality. Please add it to the limitations.\nResults:\nSecond iteration of the checklist was trialled with psychology and medicine students and science journalists. They were given 15-20 minutes to read the preprints and complete the checklist as a group. For inexperienced people, 15-20 minutes is not enough time to understand a scientific study manuscript let alone assess the quality of it. This raises a concern about the real-world usability of this checklist.\n\nSensitivity tests of the checklist drafts are not statistically analysed. Yes and no answers were compared between testers and workshop participants and between ‘high’ and ‘low’ quality preprints to make a final conclusion.\n\nFinal draft checklist was again tested with students and journalists. It now has 4 categories: research questions, study type, transparency and integrity, and limitations. Each category has a brief statement explaining why this category is important and the latter 3 categories each have 4-5 additional questions to evaluate the manuscript in “a deeper level”.\n\nThe authors note that the checklist is only applicable to research in humans, and not for in vitro or animal studies. Implicitly then this is in the first check item that needs to be added to their checklist\nDiscussion: The authors claim that there are 3 key findings from this study:\nThey state that this checklist is effective in discerning between high- and low-quality studies, because they observed that ‘high’ quality studies get more ‘yes’ answers than the ‘low’ quality ones. Is this claim warranted without proper statistical analysis?\n\nThey continue that the ‘deep level’ questions are especially important in discriminating the quality of preprints. This means the reader must consider about 20 different questions and points to make a quality judgement of a paper, which brings us to the issue of practical usability of this checklist. To make a reasonable judgement, a reader will need to read the preprint more than once to be able to orient them and to find relevant information pertaining to the checklist. This would take more than 20 minutes the authors allowed the workshop participants. Please elaborate on why a reader should spend that much time to use this checklist themselves over a social media post by an ‘expert’ dissecting the paper, for example.\n\nThird key finding is that this checklist highlighted issues with transparency and research integrity. We agree that any quality assessment attempt should consider these issues and this checklist could help improve the understanding and literacy of lay people regarding issues around research integrity and transparency.\nOverall, the authors had their work cut out in attempting to create “a simple and user-friendly tool” to check quality of preprints for educated lay people as it requires a fine balance between usability and accuracy. The resulting checklist was shown to be a useful tool for educating potential readers of medical research on wider issues of publishing, preprints, peer review, evidence-based practice, research integrity, and transparency. This study sparks important research on improving research literacy of lay people and we hope that this study would be extended and applied to many different settings around the world.\nGiven the limitations I would suggest the authors need to be more circumspect In their conclusions about the usefulness of this current checklist given the extremely limited validity checking of it this is a very useful pilot but I would say I was only very preliminary work.\nMinor. In figure 2 the \"implementation stage\" might better be labelled a \"piloting stage\" - this was really pilot testing the draft checklist out on a number of groups before finalising the checklist, rather than implementation to the wider community.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10919",
"date": "22 Mar 2024",
"name": "Nora Turoman",
"role": "Author Response",
"response": "Point-by-point responses to Reviewer 1 - Paul P. Glasziou and Oyungerel Byambasuren Turoman and colleagues have reported on the development of a much-needed assessment tool to help lay people to check preprint quality. The rationale for the study were clearly laid out. They went through four steps of development to create the checklist: initial internal and external reviews, final internal review and implementation. The resulting checklist has 4-categories – research question, study type, transparency and integrity, and limitations. Their reporting was well done following the Standards for Reporting Qualitative Research. This study aimed to develop a brief checklist to guide non-experts in assessing pre-prints on Covid-19, but clearly can be extended to other types of research. The authors should be congratulated on making an interesting attempt. It represents a good first step, but I have a number of reservations about their validation process and the current checklist. There are a few questions and comments below that could further improve this manuscript. Introduction: could be more concise particularly paragraph 1 and 3. Reply: Paragraphs 1 and 3 were shortened, while we also added additional literature in the introduction as requested by the second reviewer (Alice Fleerackers). Methods: Ethics clearance was not required. The study has a repository on Open Science Framework with all relevant documents, but it’s not clear whether it was submitted a priori. Please clarify. Reply: No application for ethics clearance was submitted a priori. As we state in the text in the section Ethical considerations the verification was post-hoc: “A post-hoc verification with the University of Zurich ethical commission’s ethics review checklist (available in in the OSF repository for this project) confirmed that we did not require ethical approval for the current project per the regulations of the University of Zurich.” Unfortunately, we only realised during this revision that the document was provided to the editorial office but was not put on the OSF repository. This has been rectified now and the document is available here: https://osf.io/uysze. Additionally we extended the section Ethical considerations with additional explanations. The researchers have not reported whether they conducted a literature review before developing their first draft of the checklist with six items. Checking existing literature in the beginning of research helps reduce research waste and needless duplication or repetition. Please clarify and if not conducted justify this omission. Reply: In order to draft the first version of the checklist, a literature review was performed to understand the state of disseminating COVID-19-related results via preprints at the time, the impact of such dissemination, and what was already present and what was missing in terms of mitigating some negative impacts of such dissemination. The results of this literature review enter in the introduction of the manuscript. In the description of the study design we added that the first draft of the checklist was developed by the junior members of the team after an initial review of the literature and potential solutions (which forms the introduction of this paper). The sensitivity testing is very limited using only three \"high-quality\" and three \"low quality\" preprints assessed with the checklist. That might be reasonable pilot testing, but far from a sensitivity testing or validation. Reply: You are making a valid point. We adapted the wording and changed the term “sensitivity testing” to “pilot testing”. As explained later, we also extended the list of limitations of our work and the issue of limited testing is now explicitly mentioned. Whilst choosing major COVID-19-related research as “high” quality test papers for the sensitivity analysis was understandable, choosing retracted preprints for the “low” quality set is not necessarily appropriate. Manuscripts could be of ‘good’ quality methodologically, yet they could be retracted due to data fabrication or irregularities. So, the fact that they were retracted doesn’t automatically mean they were of “low” quality. Please add it to the limitations. Reply: Again, you raise a valid point. Our initial reasoning was that if the preprint authors, for example, fabricate their data, they might also not transparently disclose other aspects (limitations, conflict of interests, data sharing), so that our checklist could identify the preprint as being of poor quality. As such, retraction is used here as an imperfect proxy of low quality. We already discussed the difficulty of the selection of appropriate “low” quality preprints, but mention it now as a true limitation of our study in a dedicated Limitations section and in an amended sentence in the Pilot testing section “[...] with retraction being an imperfect but feasible proxy for low quality [...]”. Results: Second iteration of the checklist was trialled with psychology and medicine students and science journalists. They were given 15-20 minutes to read the preprints and complete the checklist as a group. For inexperienced people, 15-20 minutes is not enough time to understand a scientific study manuscript let alone assess the quality of it. This raises a concern about the real-world usability of this checklist. Reply: Thank you for raising this point. First we would like to mention that the section describing these workshops was situated in an incorrect location in the article. We have now moved it to the correct placement in the Methods Section. In fact, we designed the checklist to be used as a quick tool, with the option of digging deeper depending on interest, background, and preference. Hence, 15-20 minutes should be enough to decide whether it is worth spending more time reading a preprint. As such, the superficial level of our checklist provides a starting point of concrete aspects to search for without a deep understanding of the underlying science. The deeper level allows a more in-depth consideration, and for some aspects at this level, it is true that one needs to understand the presented study more thoroughly, which would take longer. That said, the less experienced student audience was given the preprints in advance and had to read at least one of them as homework (see Pilot implementation phase). In light of this comment, we have now added more detail in the Discussion section. Sensitivity tests of the checklist drafts are not statistically analysed. Yes and no answers were compared between testers and workshop participants and between ‘high’ and ‘low’ quality preprints to make a final conclusion. Reply: No, there were no statistical tests and analyses produced, and this was never intended. During the workshops we did not even collect data due to ethical considerations. This sensitivity (or pilot) testing should therefore be regarded as exploratory; we added a sentence to the corresponding section in the Methods section: “There were no formal statistical analyses performed on these responses, and the responses did not influence the content of the checklist in any way.” Final draft checklist was again tested with students and journalists. It now has 4 categories: research questions, study type, transparency and integrity, and limitations. Each category has a brief statement explaining why this category is important and the latter 3 categories each have 4-5 additional questions to evaluate the manuscript in “a deeper level”. The authors note that the checklist is only applicable to research in humans, and not for in vitro or animal studies. Implicitly then this is in the first check item that needs to be added to their checklist. Reply: We understand your point. There is already a disclaimer on the checklist stating that it is mainly applicable for research in humans. We realised that the disclaimer was not added to the manuscript, and we have added it now (see Table 2). We believe that this is a better solution than adding an item to the checklist which could be wrongly understood as an additional quality criterion. We also discuss this in the new Limitations section. Discussion: The authors claim that there are 3 key findings from this study: They state that this checklist is effective in discerning between high- and low-quality studies, because they observed that ‘high’ quality studies get more ‘yes’ answers than the ‘low’ quality ones. Is this claim warranted without proper statistical analysis? Reply: Thank you for this very good point. As below, we changed to more cautious wording in the Abstract and the Results section, and we added an explanatory sentence in the Methods section: “When using both levels of evaluation, the checklist was effective for expert users at discriminating high- from low-quality preprints in a small set of example preprints.” “This indicates that the checklist might be effective at discriminating between preprints of high and low quality.” “Due to the limited number of assessed preprints, only a qualitative summary of the results is possible and no statistical analysis of these results is provided..” They continue that the ‘deep level’ questions are especially important in discriminating the quality of preprints. This means the reader must consider about 20 different questions and points to make a quality judgement of a paper, which brings us to the issue of practical usability of this checklist. To make a reasonable judgement, a reader will need to read the preprint more than once to be able to orient them and to find relevant information pertaining to the checklist. This would take more than 20 minutes the authors allowed the workshop participants. Please elaborate on why a reader should spend that much time to use this checklist themselves over a social media post by an ‘expert’ dissecting the paper, for example. Reply: The workshops we organised are only one example of how to use the checklist in guiding non-experts in critical assessment. Their purpose was to teach university students and science journalists how the checklist works, in a way that blends in with their work schedules, and not to impose an ideal setting or time limit on their use of the checklist. Indeed, the superficial level lends itself to a rather quick check by searching digitally in the pdf of the preprint. For inexperienced users of the scientific literature, this provides a way of knowing how to start such an assessment. For more experienced users, e.g. the science journalists, the deeper level provides a good starting set of aspects to reflect upon. In a different setting from our workshops, one could start with the superficial level, and choose one specific theme from the deeper level to be discussed, e.g. bias. Depending on the user’s experience and level of involvement, this or any use of the ‘deep level’ could take various amounts of time. Again, we must stress that the checklist is primarily a way to get non-specialists thinking about how to assess preprint quality for themselves - not every question must be considered for the exercise to be valid, as long as it gets non-specialists engaged and thinking critically. We have now clarified this in the Discussion section. If the checklist is used on its own, and specifically in relation to a social media post, it provides, in our opinion, a way to check that the post did indeed consider important aspects of preprint quality (which are summarised in the checklist). If the answers to all deeper level questions can be found in the post, 20 minutes could again be sufficient time to dig deeper. Third key finding is that this checklist highlighted issues with transparency and research integrity. We agree that any quality assessment attempt should consider these issues and this checklist could help improve the understanding and literacy of lay people regarding issues around research integrity and transparency. Overall, the authors had their work cut out in attempting to create “a simple and user-friendly tool” to check quality of preprints for educated lay people as it requires a fine balance between usability and accuracy. The resulting checklist was shown to be a useful tool for educating potential readers of medical research on wider issues of publishing, preprints, peer review, evidence-based practice, research integrity, and transparency. This study sparks important research on improving research literacy of lay people and we hope that this study would be extended and applied to many different settings around the world. Given the limitations I would suggest the authors need to be more circumspect In their conclusions about the usefulness of this current checklist given the extremely limited validity checking of it this is a very useful pilot but I would say I was only very preliminary work. Reply: Thanks a lot for your comments and suggestions. We hope our manuscript now clearly states the limitations of our study and highlights that the assessment is only qualitative and restricted to a small set of perprints. Minor. In figure 2 the \"implementation stage\" might better be labelled a \"piloting stage\" - this was really pilot testing the draft checklist out on a number of groups before finalising the checklist, rather than implementation to the wider community. Reply: We called this stage implementation stage because we wanted to showcase how we implemented the checklist in our teaching and in the interaction with our communications departments without the intention of adapting the checklist afterwards. But of course you are right that piloting is the more common term. However, we already called the sensitivity test a pilot test, and thus decided on “Preliminary implementation stage” as a compromise. We hope that this change is addressing your concern sufficiently."
}
]
},
{
"id": "199813",
"date": "11 Oct 2023",
"name": "Alice Fleerackers",
"expertise": [
"Reviewer Expertise Science journalism (specifically the use of preprints)",
"science communication",
"health communication",
"preprints/open science"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for giving me the opportunity to review this study. The topic is timely and relevant, and addresses a question I have spent a lot of time thinking about: How do you help people outside of academia vet the quality of preprint research?\nThe study uses the DELPHI method to develop a checklist that ‘scientifically literate non-experts’ can use to assess the quality of preprint research. That is, the researchers developed an initial checklist, that was then iterated and refined through multiple rounds of expert feedback and testing. The experts who contributed feedback included academics (including those on the study team but also researchers with expertise in preprints, peer review, meta research, etc), as well as science journalists and students of medicine and psychology.\nThe strengths of this study include the use of pre-defined protocols and quality reporting checklists (e.g., SRQR, Delphi method) and the choice to explicitly invite feedback from target users. I found that overall, the study was well-written. It provides links to iterations of the checklist, as well as data and protocols, which improves the transparency of the research.\nHowever, I have several concerns with the manuscript—some of which are major:\nFirst, I am very surprised that this did not require ethics review. While it does appear to fall outside of the scope of the university’s ethics guidelines, it was not clear from the manuscript whether participants were told their data would be used in a study. Rather students and journalists agreed to participate in a ‘workshop.’ Were they told their data would be used in reports/research? It would be helpful if the authors could clarity.\nSecond, I have several concerns about the participants. While both science students and science journalists may be considered scientifically literate non-experts, these user groups have very different needs and likely very different understandings of academic publishing, research, and peer review—as well as different challenges and uses with respect to preprints. In addition, there are many other types of scientifically literate non-experts who could have been recruited to this study, such as policymakers, high school science teachers, ordinary people who studied science in the past, etc. A clear rationale for why you chose these two groups would considerably strengthen the manuscript.\nRelatedly, these groups (students, journalists) are incredibly diverse and there may be very different levels of science literacy within each group. For example, journalists in many beats use research in their reporting (not just those specialized in science), but some use it more frequently than others and some have professional training in a STEM field (e.g., they did a science degree before becoming journalists). Those who use research frequently, and/or have a research degree, likely have more in-depth knowledge than those who only occasionally use research or don’t have a STEM background. Similarly, some of the students in these two classes may have already completed a degree in STEM, or worked as researchers, while others may not have. Yet you provide no information about participants’ level of science literacy, previous experience with research, or education. Given that your target population is ‘scientifically literate non-experts’ then I would expect some assessment of science literacy, as well as a check that none of them are really ‘experts,’ to be a requirement when sampling participants. More broadly, it would be useful to know a bit more about both sets of participants (students and journalists), especially their educational backgrounds and level of experience with academic research, as this would provide a better understanding of who this checklist would be most useful for.\nRelatedly, very little information is provided about how the science journalists who were invited to participate in the workshops were recruited. How did you define ‘science journalist’? Did you include freelancers or staff reporters only? What about general news reporters who sometimes cover science? Did you only look at traditional, legacy journalism outlets or did you also consider newer forms of journalism? Providing more clarity around the inclusion or exclusion criteria for participating in the study, and the population of journalists from which you sampled, would improve the quality of the methods section.\nOn a more minor note, you mention getting input on the checklist from “experts across four topic groups: research methodology (14 invitations), preprints (15 invitations), journal editors (15 invitations), and science journalists (10 invitations).” The rest of the paragraph explains who these people are in more detail, but at first reading it was not clear whether you were inviting researchers who study science journalists or the journalists themselves. Similarly, did you invite preprint server staff, preprint authors, or researchers who study preprints? I would adapt the language a bit here for clarity.\n\nIn addition, while I am not an expert in the DELPHI method, I do have some concerns about how it was implemented, given the conclusions that were drawn.\nFirst, this is a mixed method study, not a completely qualitative one, given that you gathered Likert-scale data (which was used to perform quantitative tests), as well as open-ended feedback. In addition, the Sensitivity Testing relied on binary data (i.e., yes/no) responses, which is quantitative. While I commend the authors for using Standards for Reporting Qualitative Research (SRQR), some standards for quantitative research have not been met. Specifically, there was no information about the degree to which the various users who used the checklist in the Sensitivity Testing agreed with one another. How often did one coder choose yes and the other choose no? Normally I would expect to see some form of intercoder reliability test here, especially if the goal of the study is to develop a checklist that can help people assess the quality of the research. If the checklist works well, then two individuals should be able to come to similar conclusions when using it. On a more minor note, in qualitative research, it is not true that “in general, the more participants, the stronger the evidence” (Turoman et al., 2023, p. 14). I would remove this statement or make it clear in the text that it relates specifically to the quantitative aspects of the research.\nSecond, it strikes me that the checklist was never sensitivity tested by participants in the two target groups, only by members the study team. Why is that? Given that the research team are experts in this issue and had read and attempted to assess the quality of the checklist multiple times, they would likely be much more adept at applying the checklist than journalists or students using the checklist for the first time. This seems like a major limitation of the study, given that it seeks to provide a checklist that is useful for these groups. You do comment that “both our student and journalist cohorts across multiple sites appeared to understand how the checklist was supposed to be used” and that “there appeared to be an overlap in the students’ and journalists’ application of the checklist to the high- and low- quality preprints and our own.” (Turoman et al., 2023, p. 15), suggesting that you did examine the similarity in participants’ responses to the checklist questions. If this was the case, including the process used to make the comparison in the methods section, as well as the results of the comparison, would considerably strengthen the manuscript. If you did not compare the users’ responses in any systematic way, I do not think you can make conclusive claims such as, “The implementation round confirmed that the checklist was indeed usable (Turoman et al., 2023, p. 15) or . “Appearing” to understand how to use a checklist is not the same as understanding how to use it, nor using it in a way that is effective and reliable.\nThird, I found myself wondering about the choice of preprints used in the testing. How could reusing the same preprints over the various rounds have influenced results, especially given that the evaluation/application of the checklist was performed by the same two members each time (as mentioned above). Similarly, while the proxies you used to identify ‘high’ and ‘low’ quality preprints are creative, and has advantages over other proxy measures of quality (e.g., preprints published in high impact journals, or cited a lot), it seems like the Milestone List is based on the significance/usefulness of the research for addressing the COVID-19 crisis, not the integrity of the methods, data, study design, or reporting. Yet this is just a guess, because looking at the list, it's not clear at all what criteria were used to select the articles—it just says that \"Nature highlighted key papers and preprints to help readers keep up with the flood of coronavirus research.\" What makes a paper \"key\" in this case? This seems very important given how central this list is to the method of the study. More broadly, I would appreciate a definition of \"quality\" somewhere earlier in this article, as well as a clear discussion of the limitations associated with the sample (e.g., limited to only three preprints, all of which were about COVID-19, and all of which are biomedical). The checklist seems very inappropriate for assessing the ‘quality’ of research or scholarship in other disciplines, such as the social sciences or humanities. You may want to rephrase the purpose and conclusions of the study to specify the focus on biomedical preprints, rather than on preprints in general.\nIn addition, there is some literature missing from the review that seems worth citing with respect to journalists’ use of preprints, as well as the public’s understanding/reponses to media coverage of preprints. This includes some of my own work (I know, reviewers always do this), but also of other scholars. Here are some citations worth considering. I also encourage the authors to do an additional literature search, since more research may have come online recently of which I am not aware:\nvan Schalkwyk, F., & Dudek, J. (2022). Reporting preprints in the media during the Covid-19 pandemic. Public Understanding of Science, 31(5), 608–616. https://doi.org/10.1177/09636625221077392\n\nMassarani, L., & Neves, L. F. F. (2022). Reporting COVID-19 preprints: Fast science in newspapers in the United States, the United Kingdom and Brazil. Ciência & Saúde Coletiva, 27, 957–968. https://doi.org/10.1590/1413-81232022273.20512021\n\nMassarani, L., Neves, L. F. F., Entradas, M., Lougheed, T., & Bauer, M. W. (2021). Perceptions of the impact of the COVID-19 pandemic on the work of science journalists: Global perspectives. Journal of Science Communication, 20(07), A06. https://doi.org/10.22323/2.20070206\n\nMassarani, L., Neves, L. F. F., & Silva, C. M. da. (2021). Excesso e alta velocidade das informações científicas: Impactos da COVID-19 no trabalho de jornalistas. E-Compós. https://doi.org/10.30962/ec.2426\n\nOliveira, T., Araujo, R. F., Cerqueira, R. C., & Pedri, P. (2021). Politização de controvérsias científicas pela mídia brasileira em tempos de pandemia: A circulação de preprints sobre Covid-19 e seus reflexos. Revista Brasileira de História da Mídia, 10(1), Article 1. https://doi.org/10.26664/issn.2238-5126.101202111810\n\nFleerackers, A., Moorhead, L. L., Maggio, L. A., Fagan, K., & Alperin, J. P. (2022). Science in motion: A qualitative analysis of journalists’ use and perception of preprints. PLOS ONE, 17(11), e0277769. https://doi.org/10.1371/journal.pone.0277769\n\nFleerackers, A., Riedlinger, M., Moorhead, L. L., Ahmed, R., & Alperin, J. P. (2022). Communicating scientific uncertainty in an age of COVID-19: An investigation into the use of preprints by digital media outlets. Health Communication, 37(6), 726–738. https://doi.org/10.1080/10410236.2020.1864892\n\nFleerackers, A., Shores, K., Chtena, N., & Alperin, J. P. (2023). Unreviewed science in the news: The evolution of preprint media coverage from 2014-2021 (2023.07.10.548392). bioRxiv. https://doi.org/10.1101/2023.07.10.548392\n\nRatcliff, C. L., Fleerackers, A., Wicke, R., Harvill, B., King, A. J., & Jensen, J. D. (2023). Framing COVID-19 preprint research as uncertain: A mixed-method study of public reactions. Health Communication, 0(0), 1–14. https://doi.org/10.1080/10410236.2023.2164954\n\nCyr, C., Cataldo, T. T., Brannon, B., Buhler, A., Faniel, I., Connaway, L. S., Valenza, J. K., Elrod, R., & Putnam, S. (2021). Backgrounds and behaviors: Which students successfully identify online resources in the face of container collapse. First Monday. https://doi.org/10.5210/fm.v26i3.10871\n\nCataldo, T., Faniel, I., Buhler, A., Brannon, B., Connaway, L., & Putnam, S. (2023). Students’ Perceptions of Preprints Discovered in Google: A Window into Recognition And Evaluation. College & Research Libraries, 84(1). https://doi.org/10.5860/crl.84.1.137\n\nSebbah, B., Bousquet, F., & Cabanac, G. (2022). Le journalisme scientifique à l’épreuve de l’actualité « tout covid » et de la méthode scientifique. Les Cahiers du journalisme, 2(8–9), R119–R135. https://doi.org/10.31188/CaJsm.2(8-9).2022.R119\n\nFinally, I encourage the authors to make the implications and contributions of the work clearer. From a practical perspective, I found myself wondering, is this actually a checklist for vetting the quality of preprints, or for assessing research quality in general? Given that there are many, many checklists available for assessing the quality of peer reviewed research, answering this question seems very important. Perhaps the contribution is that this checklist could help nonexperts vet research—peer reviewed or not. I do not know this area well enough to know the conceptual, theoretical, or scholarly gaps that have been filled, but I am sure the authors can do so.\nI know that these are a lot of comments and concerns, but I have included them not to be rude or overly critical but because I believe addressing will make the study better able to contribute to an important issue that I care about deeply. I hope the authors find them helpful and are not discouraged from pursuing future research about journalists’ use of preprints. We need more of it!\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10920",
"date": "22 Mar 2024",
"name": "Nora Turoman",
"role": "Author Response",
"response": "Point-by-point response to Reviewer 2 - Alice Fleerackers Thank you for giving me the opportunity to review this study. The topic is timely and relevant, and addresses a question I have spent a lot of time thinking about: How do you help people outside of academia vet the quality of preprint research? The study uses the DELPHI method to develop a checklist that ‘scientifically literate non-experts’ can use to assess the quality of preprint research. That is, the researchers developed an initial checklist, that was then iterated and refined through multiple rounds of expert feedback and testing. The experts who contributed feedback included academics (including those on the study team but also researchers with expertise in preprints, peer review, meta research, etc), as well as science journalists and students of medicine and psychology. The strengths of this study include the use of pre-defined protocols and quality reporting checklists (e.g., SRQR, Delphi method) and the choice to explicitly invite feedback from target users. I found that overall, the study was well-written. It provides links to iterations of the checklist, as well as data and protocols, which improves the transparency of the research. However, I have several concerns with the manuscript — some of which are major: First, I am very surprised that this did not require ethics review. While it does appear to fall outside of the scope of the university’s ethics guidelines, it was not clear from the manuscript whether participants were told their data would be used in a study. Rather students and journalists agreed to participate in a ‘workshop.’ Were they told their data would be used in reports/research? It would be helpful if the authors could clarity. Reply: Thank you for your concern, we do care about transparency very much and paid attention to this aspect throughout the study. The situation was different for the student workshops and the journalist workshops. For the student workshops we write in the text and this corresponds to the actual process: “The responses were only analysed inasmuch as percentages of ‘yes’, ‘no’, and ‘partly/maybe’ responses were automatically generated by the respective platforms based on the responses entered by the students, during the class, for the purpose of in-class discussion. These responses were not recorded outside of this platform (e.g., on any project team member’s computer), nor were they subject to any formal statistical analyses performed on these responses, and the responses did not influence the content of the checklist in any way.” Therefore, the student workshops are simply described in this article to showcase how the PRECHECK checklist could be used in practice; the responses that the students gave as part of the workshop were not used to further inform the checklist. Hence, they were not told that their data would be used in a study because there was no intention to do so. For the journalist workshops, our intention was the same as above: we wanted to use the PRECHECK checklist purely for education, without gathering data for the project. But the journalists were informed through our presentation that we were the developers of the checklist, and some participants offered unsolicited feedback. In this situation it was clear to them that their feedback could be incorporated into a new version of the checklist and they did indeed give it for this purpose. In the article text we now write (addition from this revision in italics): “In the workshop for journalists, some participants offered unsolicited yet helpful feedback, which was incorporated into the finalised version of the checklist. These participants were aware that their feedback would be used for this purpose through the presentation given during the workshop.” Additionally we extended the section Ethical considerations with some more explanations of the facts. Second, I have several concerns about the participants. While both science students and science journalists may be considered scientifically literate non-experts, these user groups have very different needs and likely very different understandings of academic publishing, research, and peer review—as well as different challenges and uses with respect to preprints. In addition, there are many other types of scientifically literate non-experts who could have been recruited to this study, such as policymakers, high school science teachers, ordinary people who studied science in the past, etc. A clear rationale for why you chose these two groups would considerably strengthen the manuscript. Reply: Thank you for this valid point. First we would like to mention that the section describing these workshops was situated in an incorrect location in the article. We have now moved it to the correct placement in the Methods Section. We chose both groups first out of convenience, as we had direct access to them and an inherent interest in reaching them with our content. Initially our project was motivated by the Covid pandemic, during which results from preprints ended up as highlights in news outlets, and thus we wanted specifically to address science journalists. We are aware of the fact that Science journalists are actually a group of people who already have a lot of experience with vetting scientific literature. In contrast, our second group, the students, only have limited knowledge on the publishing system etc. Both the students at the University of Zurich and Geneva were at a stage in their studies where they needed to get used to using literature, the lectures in which our workshops were held had, in part, the purpose of introducing them to that. Consequently, given that they will have to read scientific papers as well as preprints for many of their future lectures and projects, we aimed at giving them a tool to help quality check what they plan on reading. We have added more explanations of these choices in the section Study Design. Specifically, we state “The chosen setup of the preliminary implementation phase does not allow a systematic validation of the checklist, especially since the target group was chosen mainly for convenience.” Relatedly, these groups (students, journalists) are incredibly diverse and there may be very different levels of science literacy within each group. For example, journalists in many beats use research in their reporting (not just those specialized in science), but some use it more frequently than others and some have professional training in a STEM field (e.g., they did a science degree before becoming journalists). Those who use research frequently, and/or have a research degree, likely have more in-depth knowledge than those who only occasionally use research or don’t have a STEM background. Similarly, some of the students in these two classes may have already completed a degree in STEM, or worked as researchers, while others may not have. Yet you provide no information about participants’ level of science literacy, previous experience with research, or education. Given that your target population is ‘scientifically literate non-experts’ then I would expect some assessment of science literacy, as well as a check that none of them are really ‘experts,’ to be a requirement when sampling participants. More broadly, it would be useful to know a bit more about both sets of participants (students and journalists), especially their educational backgrounds and level of experience with academic research, as this would provide a better understanding of who this checklist would be most useful for. Reply: We understand why this information could be of interest, but since we did not collect any data on the workshop participants we cannot provide this information. The text states that “The responses were only analysed inasmuch as percentages of ‘yes’, ‘no’, and ‘partly/maybe’ responses were automatically generated by the respective platforms based on the responses entered by the students, during the class, for the purpose of in-class discussion. These responses were not recorded outside of this platform (e.g., on any project team member’s computer), nor were they subject to any formal statistical analyses performed on these responses, and the responses did not influence the content of the checklist in any way. We did not ask any question about the workshop participants’ educational background or level of experience with academic research.” We thus added the issues raised here to the new Limitations section of the manuscript. Relatedly, very little information is provided about how the science journalists who were invited to participate in the workshops were recruited. How did you define ‘science journalist’? Did you include freelancers or staff reporters only? What about general news reporters who sometimes cover science? Did you only look at traditional, legacy journalism outlets or did you also consider newer forms of journalism? Providing more clarity around the inclusion or exclusion criteria for participating in the study, and the population of journalists from which you sampled, would improve the quality of the methods section. Reply: Thank you for pointing this out, we now tried to be clearer in the text. The first workshop for science journalists was organised for science journalists employed at the Universities of Geneva (i.e. the members of the respective Communication Departments). The parenthesis has been added to the text during this revision and explains that we again used a “convenience sample” within our own institutions. Second, we were invited to present at a workshop for science journalists organised by a third party, the Swiss Association of Science Journalists, for which the recruitment was not in our hands. As explained on the association’s website, ordinary members of the association must attest that they work as journalists for an independent media outlet and their work should primarily focus on scientific, medical, technical or science policy issues. We would like to stress again that none of the workshops were intended to collect data for a validation of the checklist. All events were, what we now call, preliminary implementation events, where we showcased the checklist for use in a teaching setting. On a more minor note, you mention getting input on the checklist from “experts across four topic groups: research methodology (14 invitations), preprints (15 invitations), journal editors (15 invitations), and science journalists (10 invitations).” The rest of the paragraph explains who these people are in more detail, but at first reading it was not clear whether you were inviting researchers who study science journalists or the journalists themselves. Similarly, did you invite preprint server staff, preprint authors, or researchers who study preprints? I would adapt the language a bit here for clarity. Reply: Thanks a lot for this comment which shows that more information is needed. We realised the sentence you also copied presenting the four topics was confusing, since we used jobs (editors and journalists) to refer to topics. Hence, this was changed now to journal publishing (15 invitations), and science journalism (10 invitations). We also added another clarifying sentence: Thus, we invited science journalists, journal editors, as well as researchers whose research focuses on research methodology and preprints. In addition, while I am not an expert in the DELPHI method, I do have some concerns about how it was implemented, given the conclusions that were drawn. First, this is a mixed method study, not a completely qualitative one, given that you gathered Likert-scale data (which was used to perform quantitative tests), as well as open-ended feedback. In addition, the Sensitivity Testing relied on binary data (i.e., yes/no) responses, which is quantitative. While I commend the authors for using Standards for Reporting Qualitative Research (SRQR), some standards for quantitative research have not been met. Specifically, there was no information about the degree to which the various users who used the checklist in the Sensitivity Testing agreed with one another. How often did one coder choose yes and the other choose no? Normally I would expect to see some form of intercoder reliability test here, especially if the goal of the study is to develop a checklist that can help people assess the quality of the research. If the checklist works well, then two individuals should be able to come to similar conclusions when using it. On a more minor note, in qualitative research, it is not true that “in general, the more participants, the stronger the evidence” (Turoman et al., 2023, p. 14). I would remove this statement or make it clear in the text that it relates specifically to the quantitative aspects of the research. Reply: Thank you for this diligent point. It is true that we quantitatively assessed the responses from the expert panel. But this is the only real quantitative aspect of this study. The sensitivity testing, now called pilot testing, did not quantitatively assess the procedure. We added the following sentence to the text: Due to the limited number of assessed preprints only a qualitative summary of the results is possible and no statistical analysis of these results is provided. You are completely correct that the remark in the checklist “There is no one-size-fits-all number of participants that makes a study good, but in general, the more participants, the stronger the evidence.” of course only applies to quantitative studies. But the checklist is preceded by the disclaimer “The checklist works best for studies with human subjects, using primary data (that the researchers collected themselves) or systematic reviews, meta-analyses and re-analyses of primary data. It is not ideally suited to simulation studies (where the data are computer-generated).”, which we have now expanded to state the following in the last sentence: “It is not ideally suited to simulation studies (where the data are computer-generated) or studies that have a qualitative part (e.g., like interview data, or other data that cannot be easily translated into numbers).” We have realised that the disclaimer had not initially made it into the manuscript, only the document in OSF itself, and the web version of the checklist. Thus, we have added the disclaimer into the manuscript now (see Table 2), and the updated version on the OSF. Second, it strikes me that the checklist was never sensitivity tested by participants in the two target groups, only by members of the study team. Why is that? Given that the research team are experts in this issue and had read and attempted to assess the quality of the checklist multiple times, they would likely be much more adept at applying the checklist than journalists or students using the checklist for the first time. This seems like a major limitation of the study, given that it seeks to provide a checklist that is useful for these groups. You do comment that “both our student and journalist cohorts across multiple sites appeared to understand how the checklist was supposed to be used” and that “there appeared to be an overlap in the students’ and journalists’ application of the checklist to the high- and low- quality preprints and our own.” (Turoman et al., 2023, p. 15), suggesting that you did examine the similarity in participants’ responses to the checklist questions. If this was the case, including the process used to make the comparison in the methods section, as well as the results of the comparison, would considerably strengthen the manuscript. If you did not compare the users’ responses in any systematic way, I do not think you can make conclusive claims such as, “The implementation round confirmed that the checklist was indeed usable (Turoman et al., 2023, p. 15) or . “Appearing” to understand how to use a checklist is not the same as understanding how to use it, nor using it in a way that is effective and reliable. Reply: Again, thank you for this valid point. We made sure that the distinction between expert testers in the pilot testing phases (formerly sensitivity testing) is made more clearly, e.g. in the abstract with the adapted sentence “When using both levels of evaluation, the checklist was effective for expert users at discriminating high- from low-quality preprints in a small set of example preprints.” During the workshops we used the classroom response systems (Votamatic and Klicker) provided by our universities to discuss with the audience what we believe are the correct answers to the checklist questions for two specific preprints that we also included in the pilot testing phase. This workshop discussion phase is the reason why we mention that participants appeared to understand the use of the checklist and provided in majority the same answers as ourselves. We adapted the wording of this section as follows: The preliminary implementation round confirmed that the checklist was indeed usable, as, during the workshop discussion, both our student and journalist cohorts across multiple sites appeared to understand how the checklist was supposed to be used. Further, in our workshops, the live surveys showed that there appeared to be an overlap in the students’ and journalists’ application of the checklist to the high- and low- quality preprints and our own. Third, I found myself wondering about the choice of preprints used in the testing. How could reusing the same preprints over the various rounds have influenced results, especially given that the evaluation/application of the checklist was performed by the same two members each time (as mentioned above). Similarly, while the proxies you used to identify ‘high’ and ‘low’ quality preprints are creative, and has advantages over other proxy measures of quality (e.g., preprints published in high impact journals, or cited a lot), it seems like the Milestone List is based on the significance/usefulness of the research for addressing the COVID-19 crisis, not the integrity of the methods, data, study design, or reporting. Yet this is just a guess, because looking at the list, it's not clear at all what criteria were used to select the articles—it just says that \"Nature highlighted key papers and preprints to help readers keep up with the flood of coronavirus research.\" What makes a paper \"key\" in this case? This seems very important given how central this list is to the method of the study. More broadly, I would appreciate a definition of \"quality\" somewhere earlier in this article, as well as a clear discussion of the limitations associated with the sample (e.g., limited to only three preprints, all of which were about COVID-19, and all of which are biomedical). The checklist seems very inappropriate for assessing the ‘quality’ of research or scholarship in other disciplines, such as the social sciences or humanities. You may want to rephrase the purpose and conclusions of the study to specify the focus on biomedical preprints, rather than on preprints in general. Reply: Thank you very much for these questions, which in part were also asked by Reviewer 1. In the new Limitations sections we discuss the limitations of the selection of the sample of preprints. We also warn in the Pilot testing section: Due to the limited number of assessed preprints, only a qualitative summary of the results is possible and no statistical analysis of these results is provided. As a consequence the set of chosen preprints is, in our opinion, not completely central to the presented project and we chose not to comment any further on the process of how papers on the Milestone list were selected. We also refrained from defining “quality” of a preprint or a publication in general, as already mentioned in the manuscript (Footnote 2): As we will explain below, high and low quality was decided based on proxies, and not on objective criteria, as we could not determine a set of such criteria that apply to all preprints across all disciplines that the checklist could possibly be used on. With this, when we refer to ‘high-quality’ and ‘low-quality’ preprints, we do so for brevity, and not because the preprints in question belong to predefined universally agreed upon categories of ‘good’ and ‘bad’. Here, as in response to reviewer 1, we use retraction as an imperfect proxy of low quality. Finally, we did adapt our conclusion to be narrower: Despite our COVID-19-related motivation, the PRECHECK checklist should be more broadly applicable to scientific works describing biomedical studies with human subjects. In addition, there is some literature missing from the review that seems worth citing with respect to journalists’ use of preprints, as well as the public’s understanding/reponses to media coverage of preprints. This includes some of my own work (I know, reviewers always do this), but also of other scholars. Here are some citations worth considering. I also encourage the authors to do an additional literature search, since more research may have come online recently of which I am not aware: [LIST OF REFERENCES] Reply: Thanks a lot for pointing us to further literature we were unaware of. Some of those papers were published after our first submission. We reviewed the papers for their relevance for our manuscript and added many of them in our introduction/literature review. Finally, I encourage the authors to make the implications and contributions of the work clearer. From a practical perspective, I found myself wondering, is this actually a checklist for vetting the quality of preprints, or for assessing research quality in general? Given that there are many, many checklists available for assessing the quality of peer reviewed research, answering this question seems very important. Perhaps the contribution is that this checklist could help nonexperts vet research—peer reviewed or not. I do not know this area well enough to know the conceptual, theoretical, or scholarly gaps that have been filled, but I am sure the authors can do so. Reply: We repeatedly refer to our checklist as a “teaching tool”, as for example in this sentence in the discussion: One important aspect of the checklist to note is its intended use as a teaching tool to guide non-specialist audiences to evaluate preprints more critically by giving them concrete aspects to search for in the manuscript. We additionally decided to delete the last sentence in our Conclusions section (With this, and the fact that our target audience could use the checklist, we believe that the checklist has great potential to help guide non-scientists’ understanding of scientific content, especially in preprint form.) because this claim is not actually supported by our project. I know that these are a lot of comments and concerns, but I have included them not to be rude or overly critical but because I believe addressing will make the study better able to contribute to an important issue that I care about deeply. I hope the authors find them helpful and are not discouraged from pursuing future research about journalists’ use of preprints. We need more of it! Reply: We greatly appreciate your comments and were able to integrate them in our manuscript. We are convinced that the changes we made thanks to your comments improved the clarity and relevance of our manuscript."
}
]
}
] | 1
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https://f1000research.com/articles/12-588
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https://f1000research.com/articles/13-564/v1
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03 Jun 24
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{
"type": "Research Article",
"title": "Integrated analysis of -omic landscapes in breast cancer subtypes",
"authors": [
"Suren Davitavyan",
"Gevorg Martirosyan",
"Gohar Mkrtchyan",
"Andranik Chavushyan",
"Ani Melkonyan",
"Hovsep Ghazaryan",
"Hans Binder",
"Arsen Arakelyan",
"Gevorg Martirosyan",
"Gohar Mkrtchyan",
"Andranik Chavushyan",
"Ani Melkonyan",
"Hovsep Ghazaryan",
"Hans Binder"
],
"abstract": "The subtypes of breast cancer exhibit diverse histology, molecular features, therapeutic response, aggressiveness, and patient outcomes. Multi-omics high-throughput technologies, which are widely used in cancer research, generated waste amounts of multimodal omic datasets calling for new approaches of integrated analyses to uncover patterns of transcriptomic, genomic, and epigenetic changes in breast cancer subtypes and connect them to disease clinical characteristics. Here, we applied multi-layer self-organizing map (ml-SOM) algorithms to PAM50-classified TCGA breast cancer samples to disentangle the diversity of the effects of gene expression, methylation, copy number, and somatic single nucleotide variation in the disease subtypes. Furthermore, we studied the association of perturbed gene modules with survival, prognosis, and other clinical characteristics. Our findings highlight the power of multi-omic analyses to offer a better understanding of the molecular diversity of breast cancer subtypes compared to single-omic analyses. Moreover, they highlight the complex subtype-characteristic associations between gene expression and epigenetic/genomic factors and their implications for survival and clinical outcomes.",
"keywords": [
"Breast cancer",
"multi-omics study",
"self-organizing maps"
],
"content": "Introduction\n\nBreast cancer is the most common cancer worldwide, with 7.8 million women alive as of the end of 2020 who had received a diagnosis within the previous five years. It represents a diverse group of cancers of mammary glands characterized by considerable heterogeneity of morphological, genomic, epigenetic, transcriptomic, and proteomic features that drive tumor progression, treatment resistance, and aggressiveness.1–4\n\nThe current molecular classification of breast cancer includes stratification by expressed markers (ER, PR, HER2).5 Recently, a new gene expression-based molecular subtyping of breast cancers has been proposed (PAM50).6 These classification approaches are linked to treatment selection and prognosis. Other classification approaches including TNM staging,7 MammaPrint,8 and Oncotype DX9 were used for breast cancer subtyping. There are also new approaches that build on these clinical classifications and use various mathematical algorithms to improve their accuracy, such as PCA-PAM50 which combines the breast cancer clinical annotation of PAM50 and improves the accuracy of the approach by integrating with the primary component analysis.10 This underscores the significance of employing interdisciplinary methodologies.\n\nThe studies into molecular characteristics of BC subtypes have shown variability of subtype-associated biological and pathophysiological processes. Multiple studies showed considerable differences in the gene expression patterns in cancer subtypes with implications for survival and prognosis (for example reviewed in Refs. 11, 12). Our previous study also provided insight into the variability of transcriptomic landscape in cancers with somatic and germline mutations in BRCA1 and BRCA2 genes suggesting that uncovering the molecular heterogeneity of breast cancers can provide clues for developing more efficient therapeutic approaches.13\n\nThe advances in -omics technologies and efforts in collecting large multi-omic datasets have opened new opportunities for integrated analyses to deepen our understanding of molecular features of breast cancers, the mechanisms that drive the molecular diversity, and fine-graining disease molecular subtypes.14 This, in turn, paved the way for developing approaches for informed treatment selection.15\n\nSeveral studies have already explored this direction.16 The study based on CNAs, mRNA, miRNA abundance, methylation, and protein abundance data already shows efficiency in dividing breast cancer into invasive lobular carcinoma (ILC) and invasive ductal carcinoma (IDC) subtypes.17 The novel integrated multi-omics approaches led to the identification of a new hybrid subtype with a poor survival prognosis.18 Also, survival and drug response-based frameworks show high effectiveness for diagnosing cancer patients in comparison with single-omics approaches.19 These and other results underline the importance of integrative studies that can open a new dimension in the analysis of molecular heterogeneity of cancers, address the complexity of the interplay of omic features in different subtypes of disease by linking genetic defects, epigenetics reprogramming, and perturbed transcription factor networks.\n\nPreviously, we have developed a self-organizing maps (SOM)-based bioinformatics pipeline for analysis, functional characterization, and visualization of omic datasets.20,21 It was successfully applied in many studies, including molecular characterization of various cancers, such as low-grade gliomas,22 B-cell lymphomas,23 etc. In this paper, we used its multilayer-SOM approach to analyze the genomic, epigenetic, and transcriptomic features of The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) data collection.\n\n\nMethods\n\nIn this study, we used available omic datasets of the TCGA-BRCA project.24 Total, RNA-seq counts, microarray promoter and gene body methylation, microarray CNV, and SNV were obtained for 996 samples. PAM50 molecular classification data for these samples were obtained from the publication by Chia et al.6\n\nThe patient’s clinical data was retrieved from the GDC database and contains variables, such as tumor pathologic stage, information about treatment, survival, etc.\n\nIn the GDC Data Portal, raw star count files are available for transcriptomic data for each sample within the TCGA-BRCA dataset. We have downloaded them by using gdc-client25 algorithms and merged all files across samples. Accordingly, the TPM values for each sample were obtained. In the succeeding step of the analysis, they were subjected to normalization and converted to log counts using variant stabilization transformation from the DeSeq2 package.26\n\nThe GDC-supplied methylation data contains betta values for samples, in which a subset is calculated with Illumina human methylation 450 microarray, while others with Illumina human methylation 27 microarray. DNA methylation data was aggregated by merging the data generated with two microarrays. In the case of overlapping CpG islands, the mean value per gene was used. Promoter methylation data was converted from betta to m values.27\n\nCNV data was obtained from the GDC Data Portal, which provides Gene Level Copy Number files generated through the genotyping array method using the Affymetrix SNP 6.0 platform. To avoid constant values in data, we have normalized CNV data by adding small numbers (mean=0, sd=0.001) to each sample on a gene-wise basis.\n\nSomatic mutation data resides within GDC in maf files and has been used for generating an SNV matrix. We have summarized all single nucleotide variation counts by genes. To avoid constant values in data, we have normalized SNV data by adding small numbers (mean=0, sd=0.001) to each sample gene-wise.\n\nTo conduct an integrative analysis of omic datasets of breast cancer, we employed a refined multilayer self-organizing maps (ml-SOM) approach built on our previous developments.22,28 The self-organizing map (SOM) algorithm is a neural network-based technique for dimensionality reduction and clustering. SOM topology is driven by co-variance of gene expression according to the selected weight factors.\n\nFurthermore, the SOM implementation in the oposSOM package is enriched with robust function mining capabilities, facilitating the assignment of biological functions to gene clusters. This capability efficiently reduces the high-dimensional gene space into numerous differentially expressed functional modules. As a result, this approach enables a transition from analyzing individual genes to conducting systems-level analyses while preserving the integrity of the original information.\n\nFor ml-SOM, we organized all omic datasets into four distinct layers and trained them collectively on a single SOM grid, similar to a classical single-layer SOM (sl-SOM).20 The key distinction between the training processes of sl-SOM and ml-SOM lies in how the best matching unit (BMU) is selected within the SOM grid.\n\nIn sl-SOM, the BMU is chosen based on the distance between the input vectors and the weight vectors of SOM nodes. However, in the case of ml-SOM, we calculate these distances separately for each layer and then combine them into a single value, taking into account the respective layer weights as follows:\n\nThe weight factor ω scales the effect of each of the layers on the topology of the ml-SOM. In this particular analysis, we used the following weights: 1 for RNA-seq, 0 - for promoter methylation, 0 - for CNV, and 0 - for SNV. In this way, the arrangement of genes on the SOM grid is driven by the transcriptome layer.\n\nThe downstream analysis of ml-SOM is similar to the oposSOM pipeline.20 Following the Self-Organizing Map (SOM) training, we partitioned the resulting metagene map into discrete regions referred to as “spots”. These spots represent clusters of genes that exhibit co-expression patterns, particularly genes that are perturbed in at least one of the omic layers. Spot identification within the individual SOM portraits was based on a “k-means” and “variance” criterion.21 These spots were subsequently combined into an overexpression summary map, offering a comprehensive view of the transcriptomic landscape across all layers. The expression values of each spot, detected across various layers, collectively constituted the corresponding spot profile.\n\nTo further elucidate the biological significance of these spots, we subjected the genes associated with the spots to functional annotation, including overrepresentation and Gene Set Z-score analyses. We also employed the Enrichr resource29 for over-representation analysis using additional gene sets.\n\nTo assess the relationships between gene expression, methylation, CNV, and SNV across various spots (gene modules), we utilized linear regression with gene expression as the outcome and the other genomic markers as explanatory variables. The model was further enhanced by incorporating PAM50 subtypes as an interaction term, allowing us to examine the variability in these relationships across different disease subtypes and omic layers. For the statistical analysis of these interactions and their visualization, the ‘emmeans’30 and ‘interactions’31 packages in R were employed. Additionally, we applied the Dunnett’s Test to evaluate pairwise differences in mean levels of expression and methylation, CNV, and SNV gene modules in PAM50 subgroups compared to true normal tissue.\n\nOverall survival analysis was performed using the Cox proportional hazards regression using survival (https://cran.r-project.org/web/packages/survival/index.html) and survminer (https://cran.r-project.org/web/packages/survminer/index.html) R packages. The events were defined based on vital status information (“Dead” or “Alive”). The time to event was defined as “days to death” or “days to last follow-up”. We included survival as a dependent variable and spot omic profiles and breast cancer subtype information as predictors. We used the contsurvplot (https://cran.r-project.org/web/packages/contsurvplot/index.html) R package to visualize survival curves.\n\nPreviously we introduced so-called SOM phenotype portraits by mapping the association of clinical and phenotypic characteristics on the SOM grid.32 Accompanying phenotype data, such as medication, disease stage, and grade for TCGA-BRCA samples was obtained from the GDC portal. Phenotype maps were created for all available data types. To create a phenotype map, we constructed a linear regression model for each metagene as a dependent variable and clinical parameters as an ordinal variable. Then we mapped the corresponding regression coefficient for the predictor variable to a corresponding position of that metagene on the SOM grid. The visualization of weight coefficients allows evaluation of the association of corresponding clinical characteristics and the levels of functional gene modules on different omic layers.\n\n\nResults\n\nIn this study, we performed an integrative analysis of the TCGA-BRCA dataset (Figure 1) using four molecular data types – gene expression, promoter methylation, copy number variation, and somatic single nucleotide variation. We organized each omic data type into a data layer and analyzed them with multi-layer SOM training.\n\nLum A (luminal A) - ER+ and PR+, HER2- and low levels of the Ki-67; Lum B (luminal B) - ER+ and HER2- and has either high levels of Ki-67; HER2-enriched - ER-, PR- and HER2+; Basal triple-negative and CK5+ and CK17+; CLOW - triple-negative and high expression of immunity genes; Normal-like - triple-negative and CK5- and EGFR-; True Normal - normal tissue.\n\nThe multi-layer SOM training organized multi-omic high dimensional data on the two-dimensional grid of 40x40 size. During the training phase, ml-SOM combines the genes having similar profiles of expression, methylation, CNV, and SNV across samples into adjacent nodes according to the weight factors on the SOM grid thus forming gene clusters (also referred to as spots or gene modules). These clusters can be visualized for each sample by the expression value, which allows direct comparison between samples. Additionally, the expression variance for each cluster can be calculated and visualized as a map as well.\n\nWe combine samples in groups for downstream analysis according to the PAM50 classification to assign cancer samples to molecular subtypes. The average multi-omic SOM portraits showed considerable variations in expression (Gex), methylation (Gmx), CNV, and SNV both across PAM50 subgroups as well as compared to true normal tissue (Figure 2).\n\nThe color scheme indicates the nature of the change on each omic layer. On the transcriptome layer (Gex) blue to red scale represents under- to overexpression. On the methylation layer (Gmx) blue to red scale represents hypo- and hypermethylation. On the CNV layer blue to red scale represents CNV loss and CNV gain, respectively. On the SNV layer blue to red scale represents low to high mutation burden, respectively. Consequently, the green areas on SOM portraits represent invariants gene clusters or areas.\n\nVisualizing variance within layers showed regions of gene clusters with high and low variance in brown and blue, respectively (Figure 3A-D). Regions with high variance likely capture significant differences in gene expression (Gex), promoter methylation (Gmx), copy numbers (CNV), and mutational load (SNV), respectively, characterizing the distinct tumor subtypes. We used the k-means33 segmentation of the map criterion to dissect the variance maps into 20 spots annotated by letters “A” to “T” (presented in Supplementary_Figure1.pdf from “Extended Data”, see Data and software availability). For further analyses, we selected highly variable ones (spots A, C, E, F, L, R, Q, S) that contained genes with highly variant feature profiles across samples at least in one omic layer.\n\nThese maps offer an overview of the variance patterns across different data types, highlighting the variability of specific gene clusters (spots) across omic layers. The blue regions represent areas of low variance, while red regions indicate high variance. The letters correspond to highly variant spots as identified with k-means clustering (presented in Supplementary_Figure1.pdf from “Extended Data”, see Data and software availability).\n\nOn average, each spot comprised 155±60 genes. The largest gene counts (207 genes) were associated with spot R showing high variance for Gex, Gmx, and CNV, while spot F contained only 9 genes mostly associated with high CNV-variance. Due to the self-organizing properties of the SOM algorithm, genes of similar expression profiles were grouped in spot-like clusters across the omic layers, suggesting they may share common biological functions or regulatory mechanisms.21 To explore this further and map functional signatures to the spots, we performed Gene Set Enrichment Analysis using built-in gene sets20 and an over-representation analysis tool that provided additional gene sets covering multiple domains.29\n\nSpot A contained 114 genes, associated primarily with DNA replication (padj = 3.3e-05), E2F targets (padj = 5.3e-09), retinoblastoma pathway (padj = 3.23e-05), and cell cycle activity (padj = 5.4-e04). Notably, spot genes were also associated with EMT markers taken from Sarrió et al,34 as well as markers for the basal BC subtype taken from Smid et al.35\n\nSpot C contained 165 genes mostly involved in protein transport (padj = 2.0e-02), SMARCA2 antiproliferative targets (padj = 2.2e-06),36 and DNA repair. (padj = 4.34E-03).\n\nSpot E contained 118 genes enriched with luminal cancer gene signatures (padj = 0.005)37 and genes associated with the amplification of chromosome 16p13 (padj = 0.02).38\n\nSpot F contained only 9 genes, however, they were implicated in vitamin D signaling (padj = 0.038), palmitoyl-CoA Hydrolase Activity (padj = 0.025), Androgen Receptor/NKX3-1 Signaling (padj = 0.01) and ICGC transcription factor target genes (padj < 0.01).\n\nSpot L contained 67 genes strongly associated with the immune system process (padj = 1.2e-12).\n\nSpot Q contained 141 genes enriched with stromal (padj = 7.84E-03)39 and stem cell gene signatures (padj = 8.81E-14),40 genes involved in accelerated proliferation (padj = 6.1e-05), inflammation (padj = 0.03), RAS signaling (padj = 1.1e-05), hypermethylation of tumor suppressor genes (padj = 3.2e-04).\n\nSpot R contained 207 genes associated with RNA splicing (padj = 0.005) and mitochondrial gene signatures (padj = 0.004).\n\nSpot S contained 106 genes enriched with luminal cancer signatures (padj = 4.3e-06), ESR1 signatures (padj = 3.5e-15), and metastasis-suppressing signatures (padj = 2.1e-03).\n\nThe full list of annotations associated with the spots is available in Supplementary Tables S1 - S16 in Supplementary_Tables_S1-S16.xlsx file of “Extended data” (see Data and software availability).\n\nBased on the functional annotation we assigned each spot to the functional processes that best describe the genes located in that module (Table 1).\n\nThe Spot Assignment column presents a generalized spot description based on the gene set enrichment results.\n\nThe feature profiles of the spots in the different omic layers represent the “averaged” pattern of the respective genes across the samples and serve as a surrogate level for the functional signatures associated with the respective spot.21 We calculated two-way clustered similarity matrices for the different omic layers using the spot profiles to estimate the relatedness between the tumor subtypes as seen by the different omic layers (Figure 4). Gene expression (Figure 4A) and methylation (Figure 4B) clustering of the breast cancer subtypes showed remarkable similarity indicating marked variance correlations between Gex and Gmx data as seen also in the similar Gex and Gmx variance maps (Figure 3). Both omic layers express roughly three clusters collecting normal-like, basal, and HER2E as well as luminal subtypes, respectively. On the CNV layer, one finds two major clusters of normal tissue, Lum A, Lum B, and HER2E tumors, and of normal-like and basal tumors (Figure 4C). No notable clusters were observed on the SNV layer (Figure 4D).\n\nThe left part of the figure shows the Pearson correlation-based heatmaps across data categories, where red indicates a positive correlation and blue indicates a negative correlation, respectively. Color intensity reflects the strength of the correlation. The right part displays correlations between individual samples, with colors indicating their respective PAM50 subtype memberships. The edges between samples indicate the Pearson correlation coefficient > 0.5.\n\nThe similarity net images in the right part of Figure 4 visualize the correlation of omic profiles on a single tumor level. It indicates the most pronounced clustering in the Gex layer and the weakest one for SNV data with CNV and Gmx taking intermediate positions.\n\nNext, we analyzed the genes collected from most variant spots across the omic landscapes to identify mutual correlations, possible driver events, and functional associations with underlying cancer-related biological processes. For this, we used linear regression/ANOVA to evaluate the mean differences of spot levels in disease subtypes across the four omic layers (for example see Figure 5A). We further used post hoc Dunnett’s test to assess the differences in mean spot levels in cancer subtypes compared with normal tissues. The actual levels are indicated as boxplots (for example see Figure 5B).\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nTo understand the association between transcriptomic, epigenetic, and genetic features in each cancer subtype we used linear regression with expression spot levels as the dependent variable and other omic layers as well as their interactions with cancer subtypes. In this case, the slope coefficient for each interaction will show the level and direction of association in a subtype-characteristic manner. Thus, we could use this as a proxy for the impact of genomic/and epigenetic elements on the expression of spot-associated genes in cancer subtypes (for example, see Figure 5C). The samples of the CLOW subtype we excluded from further analyses because of their low number (n = 4).\n\nParticularly, we considered cell cycle and EMT (spot A), DNA repair (spot C), luminal cancer signature (Spot E), vitamin D signaling (Spot F), immune response (Spot L), stroma and stem cells (Spot Q), RNA-splicing (Spot R) and estrogen receptor signaling (Spot S) activities (Figures 5-12, respectively).\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nA) ANOVA/linear regression coefficient plots indicate the magnitude and significance of differences in mean levels in cancer subtypes compared to normal tissue. B) Boxplots of spot levels in cancer subtypes across SOM layers. C) Visualization of PAM50 subtype-characteristic association (regression slopes and confidence intervals) between expression (dependent variable) and epigenetic (methylation) and genomic (CNV, SNV) factors.\n\nCell cycle and EMT (spot A)\n\nSpot A contained 114 genes (Supplementary Table S17 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability) mostly associated with cell cycle and EMT. The Pearson’s correlation coefficient of the spot expression profile and its genes ranged from 0.21 to 0.81. The top correlated genes in the spot were KIF2C, DSCC1, RAD51AP1, DONSON, CDC123, MCM6, CLSPN, A2ML1, DKC1, and SKP2, which previously were implicated in breast cancers.41–47\n\nThe expression profiles of this gene module were significantly upregulated in all cancer groups compared to true normal tissue. Furthermore, the expression levels were gradually increased with the highest values in basal cancers compared to all other groups.\n\nOn the methylation layer, the Lum A and Lum B profiles were hypermethylated, while the basal cancers showed hypomethylation compared to true normal samples. Meanwhile, no differences were observed in the CNV and SNV layers (Figure 5A and 5B).\n\nMutual associations of expression with methylation and the genetic features across groups showed that the expression levels of spot A negatively correlate with methylation profiles in all cancer subtypes (except Lum A) being significant in Basal and Normal-like groups, while a significant positive correlation with CNV was observed for Lum A, Lum B, and HER2E tumors. No significant trend was observed for SNV in all cancer subtypes. Interestingly, in the true normal samples, we observed a significant positive correlation between methylation and expression (Figure 5C).\n\nDNA repair (spot C)\n\nDNA repair gene module (spot C) contained 165 genes (Supplementary Table S18 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability) with a correlation coefficient in the range of 0.13-0.83. The top correlated genes in this module were HLTF, GIT2, ACAP2, OTUD4, ALG11, IREB2, EEA1, DCAF17, SEC24B, and GCC2.48–54\n\nThe expression profile of the spot was significantly downregulated in Lum A, basal and normal-like cancers. Methylation levels of the genes showed a significant decrease in Lum A, Lum B, and HER2E cancers compared with the true normal group. In normal-like cancers, there was also a significant decrease in CNV levels. SNV levels were not significantly different among all studied groups (Figure 6A and 6B).\n\nAnalysis of regression trends showed that the expression of spot C was positively correlated with methylation in all cancer groups, however only in Lum A, basal and normal-like groups the trends were significant (padj < 0.05). No association of expression with CNV was observed. A significant positive trend of expression-SNV counts association was observed only for normal-like cancers (Figure 6C).\n\nLuminal cancer signature (Spot E)\n\nThe luminal gene signature (spot E) contained 118 genes (Supplementary Table S19 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability) with a correlation coefficient in the range of 0.17-0.77, with the top genes being ROGDI, RAB26, HAGH, ZNF688, METRN, NPAS1, OCEL1, HDAC11, RSPH1, SLC22A18.55–60 The expression levels of this module were significantly upregulated in all cancer groups compared to true normal, with the highest values in Lum A and Lum B subtypes. Meanwhile, the methylation of these genes was significantly downregulated in the Lum A, Lum B, and HER2E cancers. The increase in CNV levels was observed only in HER2E cancers, while the SNV profile was decreased in Lum A (Figure 7A and 7B). Methylation was significantly negatively associated with expression in Lum A tumors paralleled with a positive correlation with CNV. No significant associations were recorded for SNVs in all cancer subtypes (Figure 7C).\n\nVitamin D signaling (Spot F)\n\nSpot F contained only 9 genes (TATDN3, THEM4, DCAF8, DCAF6, QSOX1, SETMAR, PPA2, ATXN10, SNW1,61–65 Supplementary Table S20 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability) mainly related to vitamin D signaling processes (Pearson’s correlation coefficient: 0.24-0.64). The gene expression profiles associated with this gene module didn’t change across most cancer subtypes compared with true normals except for downregulation in normal-like cancers. Furthermore, all cancers were characterized by significantly increased methylation levels (except normal-like cancers). Finally, CNV profiles were significantly downregulated in normal-like cancers. No difference in SNV levels was observed (Figure 8A and 8B).\n\nThe expression profiles were associated negatively with methylation in luminal B and normal-like cancers, and positively with CNV profiles in all groups except the true normal and normal-like groups (Figure 8C).\n\nImmune response (Spot L)\n\nThe immune response gene module (spot L) contained 67 genes (Pearson’s correlation coefficient: 0.92-0.14). The top correlated genes in the module were FERMT3, PARVG, FMNL1, TMC8, C1QA, GMFG, LST1, BIN2, TNFRSF1B, ABI3 (Supplementary Table S21 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability).66–72\n\nThe immune response signature expression profiles were upregulated in all cancers. In addition, methylation levels were significantly increased in Lum B cancer and decreased in basal cancers compared to normal tissue. CNV profile was significantly decreased only normal-like cancers (Figure 9A and 9B).\n\nThe expression of immune system genes was strongly negatively correlated with methylation profiles in all cancer subtypes. In addition, there was a positive association of expression with CNV in luminal B cancers as well as a positive association with SNV profiles in luminal A and luminal B breast cancers (Figure 9C).\n\nStroma and stem cells (Spot Q)\n\nStromal and stem cell gene module (141 genes, Pearson correlation coefficient: 0.21-0.81) with the top correlated CAV1, TGFBR2, RBMS1, CRYAB, CX3CL1, RCAN1, ETS1, ADAMTS9, LIMS2, GPX3 genes (Supplementary Table S22 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability).73–80 Spot Q was characterized by downregulated expression and upregulated methylation profiles in all cancer subtypes (except basal cancers). CNV profiles were significantly upregulated in HER2E and normal-like cancers and SNV profiles were significantly downregulated in luminal A cancers (Figure 10A and 10B).\n\nMethylation was negatively associated with the expression levels in Lum A and basal cancers. CNV levels were negatively correlated with expression in Lum A cancers. No notable correlation with expression profiles was observed for SNV (Figure 10C).\n\nRNA splicing (Spot R)\n\nRNA splicing gene module consisted of 207 genes (Pearson correlation coefficient: 0.14-0.85). The top correlated genes in this module were SSNA1, DRAP1, SURF2, PTGES2, RBM42, FASTK, BAX, LSM4, GUK1, and ZNHIT1 (Supplementary Table S23 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability).81–85\n\nThe expression levels of the RNA splicing gene module were massively overexpressed in all cancers. In addition, CNV levels of this gene module were significantly decreased in normal-like cancers, while no other differences were observed across other omic profiles in the rest of the breast cancer subtypes (Figure 11A and 11B). No significant association between expression and other omic profiles was observed in the dataset, except for a significant positive association of SNVs in luminal A cancers (Figure 11C).\n\nEstrogen receptor signaling (Spot S)\n\nFinally, the expression profiles of the ESR1 signature (spot S, Pearson correlation coefficient: 0.24-0.82, top correlated genes: SCUBE2, ESR1, ABCC8, RALGPS2, APH1B, BBS4, MYB, GALNT10, LMX1B, HHAT,86–90 Supplementary Table S24 in Supplementary_Tables_S17-S24.xlsx file of “Extended data”, see Data and software availability) were significantly downregulated in Lum B, HER2E, basal, and normal-like cancers, while were significantly upregulated in the Lum A subtype. In addition, the methylation profiles in the basal subtype were significantly increased compared to the true normal tissue. CNV profiles were significantly upregulated in Lum B cancers, while no differences in SNV levels were observed (Figure 12A and 12B).\n\nThe expression profiles were negatively correlated with the methylation profiles in all cancers but were significant only for Lum A, Lum B, and HER2E subtypes. CNV profiles for HER2E and Lum B cancers also were significantly negatively correlated with the expression of ESR1 signature genes. Finally, we observed negatively correlated expression with SNV profiles in Lum A and Lum B cancers.\n\nWe aimed to summarize findings from multi-omic analyses based on breast cancer subtypes, focusing on gene modules, survival, and phenotypic characteristics. For this purpose, we constructed Cox regression models for the interaction of continuous expression, methylation, CNV, and SNV levels for each gene module and each cancer subgroup. We also generated so-called phenotype maps visualizing the association between clinical phenotype parameters with different omic layers as described in our previous publication.13\n\nWe found that gene signatures associated with EMT/cell cycle, luminal, immune system, and RNA splicing were upregulated across all cancer subtypes compared to normal tissue. Conversely, stromal/stem cell signatures were downregulated across all cancer subtypes. The expression levels of RNA splicing genes remained consistent across all cancer subtypes. Immune signature genes were notably higher in HER2E, basal, and normal-like cancers than in luminal A and B subtypes. For other gene modules, the extent of expression was varied along with cancer subtypes. Specifically, the expression of the EMT/cell cycle module progressively increased from luminal A through normal-like, luminal B, HER2E, to basal cancers, with the highest expression noted in basal cancers. Similarly, for luminal gene signature, the expression gradually increased from basal through normal-like, HER2E, luminal A to luminal B cancers. Finally, gradual downregulation of stromal/stem cell signature was observed from normal-like through basal, luminal A, HER2E to luminal B subtypes. Interestingly, these changes were paralleled with the increase in methylation levels. In addition, we observed consistently increased methylation levels of VDR genes across all cancer types, except the normal-like category. However, this was not associated with any notable changes in their expression levels. In addition to these changes shared by all cancer subtypes, there were more subtype-characteristic perturbations (Figures 5-12).\n\nThus, luminal A cancers were additionally, characterized by downregulation of expression and methylation of DNA repair genes, and overexpression of ESR1 signature genes as the most dominant feature for this cancer subtype. Finally, this subtype showed decreased counts of SNVs in the immune system, stromal/stem cells, and RNA splicing genes. Interestingly, EMT/cell cycle gene expression in this subgroup was upregulated despite increased methylation levels; however, their expression levels were positively correlated with CNVs. The survival in luminal A cancers was associated with several gene modules on different omic layers, with the highest impact of the low expression levels of EMT and DNA repair genes on favorable survival prognosis. The luminal A cancers showed multiple significant associations with clinical phenotypes (Figure 14). Particularly, the overexpression of DNA repair genes was associated with poor prognosis. Moreover, increased SNV profiles and decreased methylation of these genes in this cancer type were associated with advanced stages of American Joint Committee on Cancer’s (AJCC) tumor pathologic assessment; particularly with pathologic M (metastasis) and pathologic N (lymph nodes). Furthermore, the increased expression of luminal cancer gene signature was associated with the presence of prior malignancies.\n\nThe luminal B subtype exhibited expression changes similar to luminal A cancers, except for unchanged expression DNA repair genes and a downregulated ESR1 signaling gene signature (spot S). This specific downregulation in luminal B was not linked to significant changes in methylation or CNV when compared to luminal A cancers. However, it showed a negative correlation with the SNV profile, not observed in luminal A cancers. Moreover, the methylation profiles in these two luminal subtypes closely resemble, except for increased methylation of immune system genes in the luminal B cancers. We did not observe any significant association with survival in this cancer subtype, except for methylation of immune system genes with borderline significance (p=0.0678) (Figure 13). Phenotype portraits for this cancer subtype showed a positive association of advanced AJCC pathologic staging, and, in particular AJCC pathologic M with expression and methylation of RNA splicing genes as well as decreased expression and methylation of DNA repair genes. AJCC pathologic T (primary tumor) was positively associated with the increased CNV profiles of the EMT/cell cycle and immune response genes.\n\nSurvival analysis was performed using the Cox proportional hazards regression with the inclusion of spot levels as continuous variables using “contsurvplot”, “survival”, and “survminer” packages. Survival curves were visualized with range values with 5 intervals (Q1: minimum, Q2: 25th percentile, Q3: 50th percentile, Q4: 75th percentile, Q5: maximum). Only plots with survival-spot association with p-value ≤ 0.1 are displayed.\n\nThe transcriptome profiles for the HER2E subtype were closely aligned with those of luminal B, differing only in the magnitude of changes. Unlike in the luminal B subtype, methylation levels of EMT/cell cycle genes in the HER2E subtype remained unchanged compared to the true normal samples. Furthermore, this subtype exhibited increased CNV profiles for luminal and stromal/stem cell gene signatures. Notably, the survival impact for this cancer subtype was most influenced by the underexpression of the VDR gene signature and the overexpression of immune system genes (Figure 13). In agreement with the survival data, the negative association of vital status with the overexpression of immune system genes was observed. Moreover, the overexpression of the luminal cancer signature was positively correlated with advanced tumor staging (Figure 14).\n\nPhenotype portraits show the -log10(p) regression model of SOM metagene levels and clinicopathological stages, vital status, and treatment variables. Deregulated gene modules (spots) are indicated on the maps and coloring shows the significance of their association with evaluated parameters.\n\nUnlike Lum A, Lum B, and HER2E cancers, in basal cancers, a strong negative correlation existed between the overexpression of EMT/cell cycle gene signatures and decreased methylation levels. A similar relationship between underexpression and methylation levels was noted for DNA repair genes. This cancer subtype’s survival was linked to various gene modules across omic layers, with hypomethylation of the ESR1 gene signature having the most significant positive impact on prognosis (Figure 13). Furthermore, the prior malignancy was positively associated with increased methylation of DNA repair genes and decreased methylation of RNA splicing genes (Figure 14).\n\nFinally, the normal-like cancers were characterized with additional underexpression of VDR signaling signature and a decrease of CNV profiles in almost all gene modules (DNA repair, luminal cancer, VDR, immune response, stromal/stem cells, RNA splicing) compared to other cancer subtypes. No specific gene modules were significantly associated with survival for this cancer subtype, however, we observed a significant association of CNV increase in VDR signaling, EMT/cell cycle, and immune system genes with prior malignancy in this cancer subtype (Figure 14).\n\n\nDiscussion\n\nThis study analyzed the omic landscapes in breast cancer PAM50 subgroups. Our results confirmed the multi-omic molecular heterogeneity of cancer subtypes as well as showed that this heterogeneity results in subtype-characteristic associations between transcriptomic, genomic, and epigenetic features as well as with clinical parameters and survival across disease subtypes (graphical representation is given in Figure 15).\n\nThe results show that the molecular diversity of breast cancer is most comprehensively captured through a multi-omic overview of perturbed gene modules. The study also found subtype-specific associations between omic features, as well as distinct relationships between these features and subtype survival rates and clinical characteristics.\n\nThe changes in gene expression across cancer subtypes were more qualitative rather than quantitative. All breast cancer subtypes showed upregulation of EMT/cell cycle, luminal signature, immune response, and RNA splicing genes and downregulation of stromal/stem cell signature genes. These gene modules represent the fundamental processes related to breast cancers and were extensively studied elsewhere.91 However, the extent of deregulation of the modules showed considerable subtype association. Indeed, previous studies clearly demonstrated the differences in the expression of proliferative and metastatic signatures in basal cancers compared with the luminal cancers and HER2E cancers, indicating the more aggressive nature of the latter subtype.92,93 Immune/inflammatory gene signatures were lowest in luminal cancer subtypes and highest in normal-like, HER2E, and basal subtypes, which also corresponds to the previous findings.93,94 The luminal gene signature, in contrast, was reversed being highest in the luminal A and B cancers and lowest in the basal subtype. The most striking difference on the transcriptome layer was the overexpression of ESR1 genes in the luminal A subtype, while in other PAM50 subtypes including luminal B cancers, they were considerably lower. This finding is, however, confirmatory, since the higher expression of ER-related genes and lower expression of proliferative genes in luminal A cancers has been described previously.95,96\n\nMethylation levels of perturbed gene modules showed higher diversity compared to expression levels. Indeed, EMT/cell cycle genes were hypomethylated in basal cancers which well agrees with their overexpression. However, overexpression of the same genes in HER2E cancers was not paralleled with significant changes in methylation compared to normal tissue; moreover, in luminal A and luminal B cancers, the same genes were significantly hypermethylated despite their increased expression. Immune response genes were significantly hypomethylated in luminal A, luminal B, and HER2E cancers, but no differences were observed for basal and normal-like cancers. We observed hypermethylation of the ESR1 gene signature in basal cancers, consistent with previously reported results.97 On the other side, the underexpression of the same gene module in other cancer subtypes was not associated with changes in the methylation levels. The differential methylation in PAM50 subtypes was reported previously,98 moreover, the incorporation of methylation caused improvement in class prediction of subtypes.99\n\nCNV changes are common in breast cancers,100 moreover, they show subtype-characteristic amplifications or deletions.101 The CNV profiles of practically all gene modules were lower in normal-like breast cancers compared to other cancer subtypes. This subtype closely resembles normal breast tissue however11 and shows low levels of expression of genes associated with cell proliferation and higher expression of genes related to adipose tissue and normal mammary gland function.102 Despite their “normal-like” gene expression pattern, these cancers can still behave aggressively.103 Interestingly HER2E was characterized by a CNV increase in luminal gene signature that includes oncogenes on chromosome 9.104\n\nOur study also indicated that somatic alteration counts were not much different between breast cancer subtypes. These findings corroborate prior research that reports no difference in somatic mutation load across PAM50 subtypes,105 although differences in the types of mutations are observed in the previous studies. For instance, TP53 mutations are more prevalent in basal subtypes, PIK3CA mutations are common in HER2-enriched subtypes, and mutations in GATA3, FOXA1, XBP1, and MYB are typically found in the luminal A subtype.98 Thus, the mutation counts in genes may not be a good characteristic for cancer subtypes.\n\nThe abovementioned results specifically demonstrate that similarities in expression levels do not necessarily reflect across other genomic and epigenetic layers. This raises the question if associations of omic data are similar or different across breast cancer subtypes. Multi-layer SOM approach allowed exploring this issue with considerable detail. It is well known that promoter methylation and CNVs are important regulators of gene expression.106,107 The general understanding is that methylation drives the silencing of gene expression,108 however, it has been demonstrated that many genes are active in the methylated state both in normal and cancer cells.109 Somatic CNVs, as well, can have both activating and silencing effects in cancer.100 The somatic single nucleotide variations (SNVs), which predominantly impact protein structure and function rather than regulatory mechanisms110 usually showed minimal effects on the transcriptome. Our results clearly demonstrated that expression-methylation-CNV-SNV associations substantially vary in different breast cancer subtypes. Perhaps, the most striking example is the expression of cell cycle and EMT genes overexpressed in all cancer subtypes. However, only in basal and normal-like cancers it was strongly associated with their hypomethylation,111 while, in Lum A, Lum B, and HER2E cancers CNVs were increased along with upregulated expression.112\n\nThe diversity of omic data associations across subtypes was reported previously in cancers,113,114 including breast cancer.115 Analysis of how different omic layers interact in cancers remains limited, but this is a crucial aspect of therapeutic development. Different approaches may be needed to target the same genes across various subtypes based on the understanding of these interactions.\n\nAlthough the overall survival rate within the TCGA breast cancer cohort is relatively high,116 we demonstrated that within subtypes, survival rates could be linked with specific deregulations in gene expression, methylation, or copy number variation of described functional gene modules. This suggests that molecular alterations can have a significant impact on the prognosis within individual breast cancer subtypes and multi-omic type predictors can significantly improve assessment of survival and prognosis.117\n\nThe majority of omic data integration studies are focused on building multi-omic classifiers rather than understanding the relations between expression, methylation, and CNVs.118–121 An exemplary study was done by Ochoa and de Anda-Jáuregui who analyzed the gene expression regulation of 50 genes in the PAM50 subtypes and found a unique set of predictors for the expression of genes in the PAM50 signature associated with each of the molecular subtypes.122 However, only a few studies focus on the analysis of intricate omic features of breast cancer subtypes98 or try to understand the complexity of their interactions.123,124 In this sense, our study offers a significant advancement in understanding the complexity of molecular events and their interactions in breast cancer subtypes with the implications for survival and clinical parameters.\n\nThere are several limitations worth pointing out in this study. First, we didn’t integrate other regulatory elements such as transcription factors,125 miRNAs,126 or chromatin modifiers,127 which were shown to be implicated in breast cancers. Furthermore, the sample size per breast cancer subtype is imbalanced in the TCGA-BRCA cohort. The largest number of samples have Lum A subtype (480 samples), which implies higher statistical power to detect significant associations between different omic layers compared to normal-like (32 samples) or HER2E (74 samples) cancers.\n\n\nConclusions\n\nMulti-omics SOM analysis allowed characterization of molecular diversity of breast cancer subtypes in term of perturbed gene modules across expression, methylation, copy number and single nucleotide variations. Moreover, the results highlight the complex subtype-characteristic associations between gene expression and epigenetic/genomic factors and their implications for survival and clinical outcomes.\n\nEthical approval and consent were not required.\n\n\nAuthor contributions\n\nConceptualization - AA, HB; Data Curation - SD, GeM, GM, ACh, AM, HG; Formal Analysis - SD, AA; Funding Acquisition - AA; Investigation - SD; Methodology - AA, HB; Project Administration - AA, HB; Resources - AA; Software - SD, AA; Supervision - AA, HB; Validation - GeM, GM, ACh, AM, HG; Visualization - SD; Writing – Original Draft Preparation - SD, AA, HB; Writing – Review & Editing - SD, AA, HB. All authors have read and agreed to this version of the manuscript.",
"appendix": "Data and software availability\n\nZenodo: Integrated analysis of “-omic” landscapes in breast cancer subtypes: Supplementary Dataset. https://doi.org/10.5281/zenodo.10947982. 128\n\nThe project contains the following underlying data:\n\n- BRCA_mlSOM_Dataset.zip (The Data folder contains TCGA-BRCA omic (RNA-Seq, methylation, CNV, and SNV) processed data and multi-SOM pipeline scripts. The BRCA-TCGA-mlSOM folder contains scripts for multi-SOM downstream analysis including functional annotation of gene modules (spots), comparison of their levels in cancer subtypes with true normal tissue, regression analysis for assessment of the association between omic layers, survival, and clinical parameter analysis. It also contains the file representing the results of the SOM analysis for each omic layer (expr - Results folder - expression, prom - Results folder - promoter methylation, cnv - Results folder - copy number variations, amd snv - Results folder - somatic single nucleotide variation), as well as phenotype portraits per omic laver (organized in pheno.exp, pheno.met, pheno.cnv, and pheno.snv) folders. The Supplementary data folder contains supplementary tables and figures cited in the text.)\n\nZenodo: Integrated analysis of “-omic” landscapes in breast cancer subtypes: Supplementary Dataset. https://doi.org/10.5281/zenodo.10947982. 128\n\nThe project contains the following extended data:\n\n- BRCA_mlSOM_Dataset.zip (The Data folder contains TCGA-BRCA omic (RNA-Seq, methylation, CNV, and SNV) processed data and multi-SOM pipeline scripts. The BRCA-TCGA-mlSOM folder contains scripts for multi-SOM downstream analysis including functional annotation of gene modules (spots), comparison of their levels in cancer subtypes with true normal tissue, regression analysis for assessment of the association between omic layers, survival, and clinical parameter analysis. It also contains the file representing the results of the SOM analysis for each omic layer (expr - Results folder - expression, prom - Results folder - promoter methylation, cnv - Results folder - copy number variations, amd snv - Results folder - somatic single nucleotide variation), as well as phenotype portraits per omic laver (organized in pheno.exp, pheno.met, pheno.cnv, and pheno.snv) folders. The Supplementary data folder contains supplementary tables and figures cited in the text.)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nGrammar checks and text style revisions were conducted with the support of ChatGPT, an AI-based tool.\n\n\nReferences\n\nTurner KM, Yeo SK, Holm TM, et al.: Heterogeneity within molecular subtypes of breast cancer. Am. J. Physiol.-Cell Physiol. 2021 Aug 1 [cited 2024 Mar 6]; 321(2): C343–C354. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuo L, Kong D, Liu J, et al.: Breast cancer heterogeneity and its implication in personalized precision therapy. Exp. Hematol. Oncol. 2023 Jan 9 [cited 2024 Mar 6]; 12(1): 3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShipitsin M, Campbell LL, Argani P, et al.: Molecular Definition of Breast Tumor Heterogeneity. Cancer Cell. 2007 Mar [cited 2024 Mar 6]; 11(3): 259–273. 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}
|
[
{
"id": "288456",
"date": "20 Jun 2024",
"name": "Stepan Nersisyan",
"expertise": [
"Reviewer Expertise Computational transcriptomics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper by Suren Davitavyan with co-authors presents a multi-omics analysis of breast cancer subtypes. The authors trained multi-layer self-organizing maps on four data modalities: gene expression, methylation, CNV, and mutation data from TCGA. They comprehensively characterize genes and pathways corresponding to most variable spots and also analyze survival associations. The study is of high quality and interesting. However, I have several major and minor points, mostly about the presentation of results and the paper flow. Major:\n1. I feel that the authors might significantly improve the paper by prioritizing the most important results rather than providing plain, comprehensive descriptions. 1a. The most hard-to-read section is “Integrated module/spot analysis across the omics landscape”: it includes !8! main Figures (Figures 5-12) showing differential spot expression between cancer subtypes. I recommend shortening this section by prioritizing the most important findings and describing similarities/differences between spots. In fact, the authors provide a very nice paragraph of text on that in the next section (”We found that gene signatures associated with EMT/cell cycle,…”). I would also suggest moving Figures 5-12 to supplement and replacing them with 1-2 Figures by aggregating panel B of Figures 5-12 (in my opinion, these panels contain the most important piece of information). 1b. Current abstract text does not mention any specific results – I recommend the authors at least mention pathways associated with the most significant spots.\n2. Unless I miss something, panels A in Figures 5-12 duplicate the data from panels B and do not show correct regression coefficients. For example, if the authors intended to show fold changes (i.e., regression coefficients) relative to normal samples (as it is stated in Figure legends), then the “True Normal” line should not be presented in this panel.\n3. How were the p-values shown in Figure 13 obtained? Intuitively, such a divergence shown on Kaplan-Meier plots should correspond to much lower p-values. Are these adjusted p-values?\nMinor: 1. Did the authors use TPM values of DESeq2-normalized counts for SOM? Description of page 3 is confusing.\n2. Add color bar to Figure 4.\n3. Line dashes on Figures 5C-12C have no function now (i.e., they duplicate color-encoded information). It might be worth drawing statistically significant correlations with e.g. solid lines, and non-significant correlations with e.g. dashed lines.\n4. Figure 13 legend: it looks like the presented definition of Q1–Q5 (0, 25, 50, 75, 100 percentiles) corresponds to 4 groups, not five. Did the authors mean 0, 20, 40, 60, 80, 100 percentiles?\n5. Please accurately proofread the paper, there are some typos I noticed, such as “primary component analysis” (should be “principal component analysis”), “star” (should be “STAR”), “betta” (should be “beta”), etc.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "310839",
"date": "26 Aug 2024",
"name": "Brian D. Lehmann",
"expertise": [
"Reviewer Expertise Genomics",
"breast cancer",
"transnational medicine"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the manuscript by Davitavyan et. al, the authors apply self-organizing map algorithms to integrate gene expression, methylation, copy number and somatic mutations to divide breast cancers from the TCGA into new classifications. They characterized genes and pathways associated with the most variable spots. The work is thorough; however, I have some minor issues with the structure of the manuscript and depth of conclusions.\n\n1. Figures 5-12 are difficult to read through and require the reader to do a great deal of work to understand and don’t add much.\n\n2. The authors should focus their manuscript on the more interesting results. Perhaps, the most striking example is the expression of cell cycle and EMT genes overexpressed in all cancer subtypes. However, only in basal and normal-like cancers it was strongly associated with their hypomethylation, while, in Lum A, Lum B, and HER2E cancers CNVs were increased along with upregulated expression. Please discuss more on this finding.\n\n3. In table 1, I would remove the genes and refer to the supplemental tables. Instead, I would expand on the pathway analysis and perhaps show the composition of PAM50 subtypes within those spots. It is rather difficult to flip between figures 2 and 3 to determine which spot is enriched with differing subtypes. What is the composition of subtypes in each of the A-T spots.\n4. Clearly for spots E and A are enriched in HER2 and have higher variance for CNV. For spot F which is basal, only 9 genes were found and there was high variance by CNV.\n\nThis suggests a differing mechanism driving these cancers that result in structural alterations rather than mutational. Please comment on this and perhaps describe the CNVs that are contributing to this spot. Is there a common mutation enriched in spot F such as BRCA1/2 loss of function mutations that may be causing the structural variance by CNV? Are there differences in mutational burden between the spots?\n\n5. In figure 13, the survival analysis is difficult to follow and requires significant effort to understand the findings. Perhaps a different method of visualization such as a forest plot could aid interpretation.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-564
|
https://f1000research.com/articles/13-563/v1
|
03 Jun 24
|
{
"type": "Review",
"title": "Periodontitis and arrhythmias: an emerging paradigm in cardiovascular medicine",
"authors": [
"Aimen Said",
"Jayesh Valecha",
"Kanishk Aggarwal",
"Shreya Garg",
"Rhea Kanwar",
"FNU Anamika",
"Sai Gautham Kanagala",
"Swati Kejriwal",
"Rohit Jain",
"Aimen Said",
"Jayesh Valecha",
"Kanishk Aggarwal",
"Shreya Garg",
"FNU Anamika",
"Sai Gautham Kanagala",
"Swati Kejriwal",
"Rohit Jain"
],
"abstract": "Periodontitis, a chronic inflammatory condition affecting the periodontal tissues and underlying bone, is now acknowledged as more than just a localized oral disease. With a global prevalence ranging from 20% to 50%, the implications of periodontitis extend beyond oral health, presenting significant concerns for public health. Research has demonstrated a strong association between periodontitis and cardiovascular disease, with shared risk factors encompassing age, smoking, socioeconomic status, and metabolic syndrome. Understanding the intricate relationship between periodontal disease and cardiovascular diseases, especially the development of arrhythmias like atrial fibrillation, is crucial. A comprehensive literature search using PubMed was conducted, employing keywords such as periodontitis, cardiovascular disease, cardiac arrhythmia, atrial fibrillation, and related terms. No exclusion criteria were used. This article reviews the current literature on the association between periodontitis and cardiovascular diseases, including atrial fibrillation. Atrial fibrillation, the most common cardiac arrhythmia, is influenced by various risk factors including alcohol consumption, advanced age, underlying heart and lung diseases, with poor oral hygiene emerging as a notable contributing factor. The direct invasion of endothelial cells by periodontal pathogens, the indirect pathway where periodontal disease triggers a systemic inflammatory response, and a shared genetic basis are three theories that explain this link. Patients with periodontal disease face an elevated risk of major cardiovascular events, especially arrhythmias, and recognizing this association is essential for healthcare practitioners to provide comprehensive care to patients with cardiac conditions.",
"keywords": [
"Periodontitis",
"atherosclerosis",
"cardiovascular disease",
"atrial fibrillation"
],
"content": "Introduction\n\nPeriodontal disease, characterized as inflammation affecting the periodontal tissues and the underlying bone, is primarily initiated by the accumulation of dental plaque and calculus and has been increasingly recognized as more than just a localized oral disease.1 According to WHO, periodontal disease affects 20-50% of the population globally with equal incidence among male and female populations.2 Approximately 75% of adults in the United States are estimated to be affected by periodontal disease with 20-30% afflicted with a severe form of the disease.3 Growing research has uncovered a significant association between periodontitis and cardiovascular disease (CVD) that has potential implications on public health as a marker of increased morbidity. Major contributing factors include neglected dental appointments, dental misalignment, smoking, diabetes and insufficient dental hygiene practices.4,5 The microorganisms associated with periodontal disease include aerobic bacteria such as Streptococcus sp. and Actinomyces sp. and anaerobic species such as Porphyromonas gingivalis, Prevotella intermedia, Peptostreptococcus spp., Fusobacterium sp., Treponema denticola, Eikenella corrodens, and Actinobacillus actinomycetemcomitans, which often coexist together.6,7 Chronic bacterial activity, along with the production of toxins and metabolites, triggers an ongoing immune response, resulting in a gradual deterioration of periodontal attachment and premature tooth loss.6 which can initiate a cascade of pathological events that extend beyond the oral cavity, impacting multiple organ systems. As the infection disseminates below the gum line, the destructive impact on underlying bone and tissue ensues, enabling the infiltration of bacterial toxins into the bloodstream, thereby facilitating their access to crucial organs, including the heart.4 Ongoing periodontal disease and the subsequent systemic inflammation have been known to cause structural damage to the heart and promote fibrosis, leading to the perpetuation of arrhythmias.8 Patients with periodontitis exhibit a significantly higher incidence of arrhythmias, including atrial fibrillation, atrial tachycardia, ventricular tachycardia, and ventricular premature beats (93.6%).9 In recent years epidemiological studies have provided compelling evidence suggesting that poor dental health increases the risk of heart disease by 1.5-4 times and contributes to an elevated risk of cardiovascular mortality as well.4 Cardiovascular health studies have utilized an elevated inflammatory marker known as C-reactive protein (CRP) to establish an association between chronic periodontal inflammation and cardiovascular disease (CVD) which has been proven useful in predicting the future risk of heart disease in individuals with poor oral health, particularly those suffering from chronic periodontal disease.10,11 The optimal care for individuals with periodontitis includes extensive management of comorbidities, efforts to reduce modifiable risk factors, oral health education, and routine oral examinations for patients with cardiovascular disease.12 Research studies emphasizing the significant role of periodontal disease in escalating occurrence of fatal cardiovascular events seek to prioritize dental health among patients with cardiac conditions. Further research is needed to deduce whether interventions that aim to enhance oral health can possibly lower the risk of worsening cardiovascular disease (CVD).13 Although widespread bacteremia and damage to distant organs can be prevented by early treatment of periodontal disease, this is only advantageous to patients with mild-to-moderate and reversible forms of periodontitis.4 This review aims to explore the intricate relationship between periodontal disease and systemic health, particularly focusing on the potential implications and connections with cardiac arrhythmias.\n\n\nMethods\n\nPeriodontitis is initiated by the colonization of pathogenic bacteria in the oral cavity, triggering an immune response resulting in release of proinflammatory cytokines, activation of immune cells and this local inflammatory process affects not only the periodontal tissues but also has systemic effects when inflammatory mediators and bacteria enter the bloodstream from daily life activities and oral interventions, promoting a proinflammatory state throughout the body.14 Periodontitis and cardiovascular diseases (CVD) share common risk factors including age, smoking, socioeconomic status, metabolic syndrome, and underlying pathophysiological processes.12,15 The direct invasion of endothelium cells by periodontal pathogens, the indirect pathway, in which periodontal disease triggers a systemic inflammatory response, and shared genetic basis are three theories to explain the link between periodontal illness and cardiovascular disease.16,17,18 Periodontal bacteria related to chronic inflammation have been found in atherosclerotic plaques and cardiovascular specimens containing thrombus tissues. These organisms can alter the barrier function of the vascular endothelium by a specific epithelial-mesenchymal transition, compromising the coherence of epithelial cells. This results in the formation of micro ulcerations, which facilitates the penetration of periodontal pathogens and virulence factors into the underlying connective tissue and exposed blood vessels.19 The exact mechanism of how direct invasion of the endothelial cells influences atherosclerosis is not clear. The presence of bacteria intracellularly is hypothesized to trigger foam cell formation and initiate secondary inflammation, leading to endothelial dysfunction and atherosclerosis.20 The second mechanism involves the indirect pathway, where periodontal disease stimulates a systemic inflammatory response, resulting in elevated levels of inflammatory cytokines such as IL-1β, IL-6, IL-8, TNF-α, and monocyte chemoattractant protein-1. These cytokines can increase hepatic synthesis and secretion of plasma proteins like C-Reactive Protein (CRP) and fibrinogen.17 Additionally, bacterial components, such as lipopolysaccharide (LPS), associated with periodontitis can enter the circulation and induce a potent immune response. These factors contribute to atherosclerosis by affecting endothelial cells, lipid metabolism, and increasing oxidative stress.21 This systemic inflammatory response can also explain the association of periodontal disease with atrial fibrillation (AF). Multiple studies have demonstrated that inflammation can induce electrical and structural changes in the atrium, significantly contributing to the onset and progression of atrial fibrillation.22 Inflammatory factors such as C-reactive protein, interleukin-6, tumor necrosis factor-α, among others, can disrupt normal electrical activity in the pulmonary veins, shorten the atrial action potential, and interact with heat shock proteins or myeloperoxidase, thereby facilitating the development of atrial fibrosis.23 Atrial fibrosis, a common pathological feature in AF, has been linked to periodontitis. In a study conducted in Japan involving 76 patients with AF, the relationship between gum disease and atrial fibrosis was investigated which found a positive correlation between various periodontal parameters, including Bleeding on Probing (BOP), Periodontal probing depth (PPD) of ≥4 mm, and periodontal inflamed surface area (PISA), with the presence of atrial fibrosis. These findings suggest that the chronic inflammation associated with periodontitis may contribute to the development and persistence of AF by promoting atrial fibrosis.8 The third mechanism involves shared genetic basis between periodontitis and cardiovascular disease and genome-wide association meta-analysis identified four PD loci, namely ANRIL/CDKN2B-AS1, PLG, CAMTA1/VAMP3, and VAMP8, which exhibited shared associations with coronary artery disease (CAD). Notably, the VAMP8 gene plays a crucial role in membrane vesicular trafficking and is susceptible to manipulation by pathogens, thereby impacting the host immune system. These genetic associations imply that the link between PD and CVD extends beyond shared environmental risk factors and involves common underlying genetic pathways19,24 (Figure 1).\n\n\nDiscussion\n\nPeriodontitis is a chronic inflammatory condition affecting the tissues supporting teeth, including the gingiva, cementum, periodontal ligament, and alveolar bone.25 It is characterized by a wide range of symptoms starting from gingival bleeding, bad breath, and alteration in gingival shape or appearance at the early stages of the disease to more severe symptoms like pain, pathological tooth mobility, periodontal abscesses, and tooth migration, due to advanced form of periodontitis often presenting as a periodontal abscess or pathological migration of anterior teeth resulting in esthetic problems.26 Multiple clinical and radiographic parameters are used to diagnose periodontitis, such as inflammation, radiographic bone loss, probing depth, and clinical attachment loss. Patients having gingival recession or undergoing periodontal maintenance therapy but without any signs of inflammation, such as bleeding on probing and probing depths of ≤3 Mm, are diagnosed with a healthy but reduced periodontium, whereas patients with probing depths >3 mm and inflammation are often diagnosed with periodontitis.27 Multiple epidemiological studies suggest that poor dental health increases the risk of cardiovascular mortality (Table 1). A meta-analysis by Harriet Larvin et al. of 32 longitudinal cohort studies revealed that cardiovascular disease (CVD) risk was significantly higher in individuals with Periodontal disease (PD) than those without PD, with a relative risk of 1.20 and a 95% confidence interval of 1.14-1.26.28 Another study by Linda L Humphrey et al. found that different forms of periodontal disease, such as periodontitis, tooth loss, gingivitis, and bone loss, had summary relative risk estimates ranging from 1.24 (95% CI 1.01-1.51) to 1.34 (95% CI 1.10-1.63).3 These risk estimates remained consistent across subgroup analyses, including gender, outcome, study quality, and method of periodontal disease assessment. A retrospective study was carried out by Chen et al. for ten years, enrolling around 393,745 patients with PD and 393,745 non-PD individuals and, after adjusting for potential confounders, showed an increased risk of atrial fibrillation or flutter in the PD group compared with the non-PD group (HR, 1.31; 95% CI, 1.25-1.36).29 Furthermore, a case-control study conducted by Im et al. reported that PD was identified as an independent predictor of major adverse cardiac events and arrhythmic events. After adjusting for various confounding factors, the study found that PD was associated with higher odds ratios for major adverse cardiac events (OR 17.78, 95% CI 3.46–91.34) and arrhythmic events (OR 9.19, 95% CI 1.24–67.96).9 Research carried out by Sahar Nader and Anwar T. Merchant has shown that individuals with periodontitis have higher plasma C-reactive protein (CRP) markers for cardiovascular disease levels than those without the condition. Treatment for periodontitis may lower CRP levels. In a study of 120 patients with severe periodontitis, participants were randomly assigned to community-based periodontal care or intensive treatment, including plaque removal and tooth extraction as necessary. Intensive treatment resulted in short-term inflammation and endothelial dysfunction. However, inflammatory markers were lower and endothelial function was improved 2 and 6 months after treatment compared to the control arm.30 The Multi-Ethnic Study of Atherosclerosis (MESA) study enrolling 4,476 people aged 60 years or older without a known cardiovascular disease (CVD) history found that increase in carotid-artery intima and media thickness (CIMT) were directly associated with an increased risk of cerebrovascular events (CVE) and acute myocardial infarction (AMI).31 The Atherosclerosis Risk in Communities (ARIC) study, patients with moderate to severe forms of PD are more likely to have a CIMT 1 mm, with an odds ratio of 1.40 (1.17–1.67, 95% CI) and 2.09 (1.73– 2.53, 95% CI) respectively, compared to those without PD.32 The above studies show that healthcare practitioners must be informed about the link between periodontal disease and ASCVD due to the many patients affected by the two diseases. Therefore, some general clinical guidelines should be considered when treating these patients. These include proper diagnosis and treatment of periodontal disease, determining other risk factors for ASCVD and medical consultation, educating the patient on the periodontal association in ASCVD, and comprehensive periodontal therapy and lifestyle modification. Patients with a history of cardiovascular events should follow AHA guidelines for prophylaxis for dental procedures.33 It is also important to recognize the severity of periodontal disease using a periodontal probe and performing radiographic assessments to measure clinical attachment levels and check for inflammation as it correlates with the risk of developing ASCVD.34 Patients who are overweight/obese, smokers, diabetics, hypertensive, or have other risk factors for ASCVD should have routine medical assessments to rule out compounding factors. Alternatively, physicians should consider referring such patients to dentists to provide necessary periodontal treatments. As lifestyle habits increase the risk of periodontal disease and the development of cardiovascular disease, lifestyle changes such as changes in diet, engaging in regular exercise, and quitting smoking could positively affect oral and overall health.35,36\n\n\nConclusion\n\nPeriodontal disease is an infection-based inflammatory condition due to bacterial biofilm accumulation adjacent to the gingiva. The systemic impact of the inflammation has yet to be fully understood, especially the heightened risk for cardiovascular disease and atrial fibrillation. With current epidemiological studies noting the presence of periodontal disease in up to one-third of the population globally, the intricate relationship between periodontal disease and its potential cardiovascular complications alongside shared risk factors such as age, smoking, socioeconomic status, and metabolic syndrome is crucial for future patient outcomes. This association between CVD and periodontal disease has been shown to follow three theorized mechanisms, the direct pathway, the indirect pathway, and shared genes. Furthermore, the current literature supports an increased risk of CVD events in patients with periodontal disease even after accounting for the patients’ demographics, study quality, and other confounding variables. Studies have also hypothesized that the increased incidence of CHD and other cardiac manifestations including arrhythmias in periodontal disease to be the result of structural damage to the heart and the promotion of fibrotic tissue. Although not all complications of periodontal disease are reversible, clinical measures such as plaque removal, tooth extractions, strict adherence to prophylactic AHA guidelines prior to dental procedures, and advancements in current treatment options can mitigate long-term inflammation and endothelial dysfunction. It is, therefore, essential for healthcare practitioners to have a better understanding of this relationship in order to provide comprehensive care to patients with cardiac conditions.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nNone.\n\n\nReferences\n\nPapapanou PN, Susin C: Periodontitis epidemiology: is periodontitis under-recognized, over-diagnosed, or both? Periodontology. 2017; 75(1): 45–51. PubMed Abstract | Publisher Full Text\n\nNazir MA: Prevalence of periodontal disease, its association with systemic diseases and prevention. Int. J. Health Sci (Qassim). 2017; 11(2): 72–80. PubMed Abstract\n\nHumphrey LL, Fu R, Buckley DI, et al.: Periodontal disease and coronary heart disease incidence: a systematic review and meta-analysis. J. Gen. Intern. Med. 2008; 23(12): 2079–2086. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMurphy NC: Understanding Periodontal Disease and Gum Infections While They Can Still Be Treated Early & Easily with an Excellent Prognosis. Accessed May 24, 2024. Reference Source\n\nVan Dyke TE, Sheilesh D: Risk factors for periodontitis. J. Int. Acad. Periodontol. 2005; 7(1): 3–7. PubMed Abstract\n\nCotti E, Dessì C, Piras A, et al.: Can a chronic dental infection be considered a cause of cardiovascular disease? A review of the literature. Int. J. Cardiol. 2011; 148(1): 4–10. PubMed Abstract | Publisher Full Text\n\nSpahr A, Klein E, Khuseyinova N, et al.: Periodontal infections and coronary heart disease: role of periodontal bacteria and importance of total pathogen burden in the Coronary Event and Periodontal Disease (CORODONT) study. Arch. Intern. Med. 2006; 166(5): 554–559. Publisher Full Text\n\nMiyauchi S, Nishi H, Ouhara K, et al.: Relationship Between Periodontitis and Atrial Fibrosis in Atrial Fibrillation: Histological Evaluation of Left Atrial Appendages. JACC Clin. Electrophysiol. 2023; 9(1): 43–53. PubMed Abstract | Publisher Full Text\n\nIm SI, Heo J, Kim BJ, et al.: Impact of periodontitis as representative of chronic inflammation on long-term clinical outcomes in patients with atrial fibrillation. Open Heart. 2018; 5(1): e000708. Published 2018 Apr 25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKuska B: Study finds direct association between cardiovascular disease and periodontal bacteria. US: NIDCR; 2005; vol. 301. : 594.\n\nAarabi G, Schnabel RB, Heydecke G, et al.: Potential Impact of Oral Inflammations on Cardiac Functions and Atrial Fibrillation. Biomolecules. 2018; 8(3): 66. Published 2018 Aug 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSanz M, Marco Del Castillo A, Jepsen S, et al.: Periodontitis and cardiovascular diseases: Consensus report. J. Clin. Periodontol. 2020; 47(3): 268–288. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSeymour RA: Is gum disease killing your patient? Br. Dent. J. 2009; 206(10): 551–552. PubMed Abstract | Publisher Full Text\n\nStewart R, West M: Increasing Evidence for an Association Between Periodontitis and Cardiovascular Disease. Circulation. 2016; 133(6): 549–551. Publisher Full Text\n\nDembowska E, Jaroń A, Gabrysz-Trybek E, et al.: Evaluation of Common Factors of Periodontitis and Cardiovascular Disease in Patients with the Acute Coronary Syndrome. Int. J. Environ. Res. Public Health. 2022; 19(13): 8139.PubMed Abstract | Publisher Full Text | Free Full Text\n\nZardawi F, Gul S, Abdulkareem A, et al.: Association Between Periodontal Disease and Atherosclerotic Cardiovascular Diseases: Revisited. Front. Cardiovasc. Med. 2021; 7: 625579. Published 2021 Jan 15. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIsola G, Santonocito S, Lupi SM, et al.: Periodontal Health and Disease in the Context of Systemic Diseases. Mediat. Inflamm. 2023; 2023: 9720919–9720947. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMunz M, Richter GM, Loos BG, et al.: Genome-wide association meta-analysis of coronary artery disease and periodontitis reveals a novel shared risk locus. Sci. Rep. 2018; 8(1): 13678. Published 2018 Sep 12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbdulkareem AA, Shelton RM, Landini G, et al.: Potential role of periodontal pathogens in compromising epithelial barrier function by inducing epithelial-mesenchymal transition. J. Periodontal Res. 2018; 53(4): 565–574. PubMed Abstract | Publisher Full Text\n\nRoth GA, Moser B, Huang SJ, et al.: Infection with a periodontal pathogen induces procoagulant effects in human aortic endothelial cells. J. Thromb. Haemost. 2006; 4(10): 2256–2261. PubMed Abstract | Publisher Full Text\n\nHajishengallis G, Chavakis T: Local and systemic mechanisms linking periodontal disease and inflammatory comorbidities. Nat. Rev. Immunol. 2021; 21(7): 426–440. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKorantzopoulos P, Letsas KP, Tse G, et al.: Inflammation and atrial fibrillation: A comprehensive review. J. Arrhythm. 2018; 34(4): 394–401. Published 2018 Jun 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu YF, Chen YJ, Lin YJ, et al.: Inflammation and the pathogenesis of atrial fibrillation. Nat. Rev. Cardiol. 2015; 12(4): 230–243. Publisher Full Text\n\nAarabi G, Zeller T, Seedorf H, et al.: Genetic Susceptibility Contributing to Periodontal and Cardiovascular Disease. J. Dent. Res. 2017; 96(6): 610–617. PubMed Abstract | Publisher Full Text\n\nHajishengallis G: Periodontitis: from microbial immune subversion to systemic inflammation. Nat. Rev. Immunol. 2015; 15(1): 30–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMohammed AN: Chronic periodontitis chief complaints: Gender and age distribution; their correlation with plaque index and probing pocket depth. Mustansiria Dent. J. 2010; 7(1): 143–149.\n\nCardoso EM, Reis C, Manzanares-Céspedes MC: Chronic periodontitis, inflammatory cytokines, and interrelationship with other chronic diseases. Postgrad. Med. 2018; 130(1): 98–104. PubMed Abstract | Publisher Full Text\n\nLarvin H, Kang J, Aggarwal VR, et al.: Risk of incident cardiovascular disease in people with periodontal disease: A systematic review and meta-analysis. Clin. Exp. Dent. Res. 2021; 7(1): 109–122. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen DY, Lin CH, Chen YM, et al.: Risk of Atrial Fibrillation or Flutter Associated with Periodontitis: A Nationwide, Population-Based, Cohort Study. PLoS One. 2016; 11(10): e0165601. Published 2016 Oct 31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTonetti MS, D’Aiuto F, Nibali L, et al.: Treatment of periodontitis and endothelial function [published correction appears in N Engl J Med. 2018 Jun 13;:null]. N. Engl. J. Med. 2007; 356(9): 911–920. Publisher Full Text\n\nO’Leary DH, Polak JF, Kronmal RA, et al.: Carotid-artery intima and media thickness as a risk factor for myocardial infarction and stroke in older adults. Cardiovascular Health Study Collaborative Research Group. N. Engl. J. Med. 1999; 340(1): 14–22. Publisher Full Text\n\nBeck JD, Elter JR, Heiss G, et al.: Relationship of periodontal disease to carotid artery intima-media wall thickness: the atherosclerosis risk in communities (ARIC) study. Arterioscler. Thromb. Vasc. Biol. 2001; 21(11): 1816–1822. PubMed Abstract | Publisher Full Text\n\nShapiro J, Blicher B, Lucier RP: Antibiotic Prophylaxis for Dental Procedures.2020; 16(9). Reference Source\n\nArmitage GC: The complete periodontal examination. Periodontol. 2004; 34: 22–33. Publisher Full Text\n\nNguyen CM, Kim JW, Quan VH, et al.: Periodontal associations in cardiovascular diseases: The latest evidence and understanding. J. Oral Biol. Craniofac. Res. 2015; 5(3): 203–206. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTonetti MS, Van Dyke TE: working group 1 of the joint EFP/AAP workshop. Periodontitis and atherosclerotic cardiovascular disease: consensus report of the Joint EFP/AAP Workshop on Periodontitis and Systemic Diseases. J. Periodontol. 2013; 84(4 Suppl): S24–S29. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "288674",
"date": "26 Jun 2024",
"name": "Gaetano Isola",
"expertise": [
"Reviewer Expertise Dentistry",
"oral medicine and periodontology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the manuscript entitled: \"Periodontitis and arrhythmias: an emerging paradigm in cardiovascular medicine\" the authors aimed to assess the association between periodontitis and cardiovascular disease, with shared risk factors encompassing age, smoking, socioeconomic status, and metabolic syndrome. The authors found that the current literature on the association between periodontitis and cardiovascular diseases, including atrial fibrillation. Atrial fibrillation, the most common cardiac arrhythmia, is influenced by various risk factors including alcohol consumption, advanced age, underlying heart and lung diseases, with poor oral hygiene emerging as a notable contributing factor.\nMajor comments: In general, the idea and innovation of this study regards the analysis of periodontitis, mediators and its treatment is interesting and novel because the role these aspects in medicine are validated but further studies on this topic could be an innovative issue in this field could be open a creative matter of debate in literature by adding new information. The study was well conducted by the authors; However, there are some concerns to revise that are described below. The introduction section resumes the existing knowledge regarding the important factor linked with the impact mediators involved together with gingival tissues and periodontitis. However, as the importance of the topic, the reviewer recommends to update the literature through read, discuss some recent interesting articles, that helps the authors to better introduce and discuss the role of periodontal treatment approaches in the periodontitis reduction such as 1) Isola G,et.al.2024 (Ref 1) 2) Isola G, et.al. 2024 (Ref 2) The authors should better specify, at the end of the introduction section, the rationale of the study and the aim of the study. In the central section, should better clarify inclusions and exclusions criteria of the selected sample. Please better state the results obtained in the abstract. The discussion section appears well organized with the relevant paper that support the conclusions, even if the authors should better discuss the relationship regarding the by periodontitis in and risk of oxidative stress evolution and periodontal treatment that could improve the quality of life in periodontitis patients with systemic diseases. The conclusion should reinforce in light of the discussions. In conclusion, I am sure that the authors are fine clinicians who achieve very nice results with their adopted protocol.\nMinor Comments:\nAbstract:\nBetter formulate the abstract section by better describing the aim of the study\n\nIntroduction:\nPlease refer to major comments\n\nDiscussion\nPlease add a specific sentence that clarifies the results obtained in the first part of the discussion\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly",
"responses": []
},
{
"id": "298079",
"date": "07 Aug 2024",
"name": "Sema Nur Sevinç Gül",
"expertise": [
"Reviewer Expertise Periodontology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this review summarizes an association between periodontitis and cardiovascular disease, with shared risk factors encompassing age, smoking, socioeconomic status, and metabolic syndrome. The authors open up future research by scientifically addressing how periodontitis predisposes to cardiovascular disease. There are a few amendments required for further improvement: 1. The period of the literature search should be specified. 2. Please correct the errors in abbreviations, some words are abbreviated again with the full spelling of the word or written without abbreviation 3. The literature in the table should be cited.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-563
|
https://f1000research.com/articles/13-562/v1
|
03 Jun 24
|
{
"type": "Research Article",
"title": "Increased biofilm staining after deletion of sepA in enteroaggregative E. coli strains is not due to the lack of SepA",
"authors": [
"Viktoria A Van Nederveen",
"Yuliya Seldina Johnson",
"Anthony Soc",
"Angela R Melton-Celsa",
"Viktoria A Van Nederveen",
"Yuliya Seldina Johnson",
"Anthony Soc"
],
"abstract": "Background Enteroaggregative E. coli (EAEC) is associated with acute and chronic diarrhea worldwide. EAEC is thought to form thick biofilms on the intestinal mucosa. Epidemiological data suggest that SepA, a serine protease autotransporter of Enterobacteriaceae (SPATE), is important for EAEC disease. The genes for SepA, and some proteins that are important for EAEC biofilm formation and aggregative adherence, are encoded by the pAA plasmid.\n\nMethods We deleted sepA 49-4043 from six EAEC clinical isolates and inserted a chloramphenicol resistance gene (cat) in place of the sepA coding sequence. In vitro biofilm formation was assessed after growth in 96-well plates. Complementation studies were conducted with genetic and protein-based techniques. We moved the pAA plasmid from EAEC strains into a commensal E. coli. Finally, we sequenced the pAA of several strains.\n\nResults All of the wild-type EAEC strains secreted similar amounts of SepA as assessed by Western blot analysis. Four of the six mutant EAEC strains exhibited increased biofilm staining when sepA was deleted. Additionally, we found that introduction of pAAΔsepA K261 into a nalidixic acid resistant commensal E. coli strain, (HSNalR) resulted in significantly increased biofilm staining relative to HSNalR (pAAK261). Therefore, pAAΔsepA K261 alone was sufficient to confer the elevated biofilm phenotype onto HSNalR. However, introduction of sepA via a plasmid or on the pAA did not restore biofilm staining to wild-type levels in the ΔsepA mutant strains that showed elevated biofilm staining. Furthermore, the addition of exogenous SepA to the biofilm in vitro did not reduce biofilm staining.\n\nConclusions Taken together, our results suggest that deletion of sepA causes elevated biofilm formation in some EAEC strains, but that the increased biofilm staining is not directly due to the loss of SepA.",
"keywords": [
"Escherichia coli",
"enteroaggregative",
"SepA",
"biofilm"
],
"content": "Introduction\n\nEnteroaggregative Escherichia coli (EAEC) is associated with acute and chronic diarrhea worldwide as well as travelers’ diarrhea.1–10 Populations strongly affected by EAEC include children in developing countries and deployed military personnel.1,9,11,12 Globally, diarrhea is the second leading cause of death in children under five.13 Among deployed military personnel, EAEC is the second most common cause of travelers’ diarrhea, a condition that is the primary generator of lost person-hours and reduced operational readiness.8,9,14–16 EAEC creates thick biofilms on the intestinal mucosa.1,17–20 Biofilm formation is thought to be necessary for EAEC to cause diarrhea.1,17–20 EAEC was first characterized by a stacked-brick pattern of adherence and aggregation on HEp-2 cells.17,19,21 Currently EAEC are identified by screening for the gene for the positive regulator of virulence genes, aggR, and genes such as those for the aggregative adherence fimbriae (AAF).22–24 EAEC strains are heterogeneous, and may have a variety of virulence genes.\n\nIn addition to aggR and genes for AAF, EAEC usually encodes one or more serine protease autotransporter of Enterobacteriaceae (SPATE).25 SepA is a SPATE that is found in 21-60% of EAEC, depending on the study.5,26–30 Epidemiological data indicate that SepA may be important for disease caused by EAEC. For example, data from Mali collected during the MAL-ED study showed that sepA was the EAEC gene most strongly associated with diarrheal cases among children under five years of age.26 In a similar analysis of Gambian data, sepA was also associated with childhood diarrheal cases.3 A study in Thailand on EAEC-mediated diarrhea in children found that sepA was one of the genes detected in significantly more cases than controls.31 A study in Iran on EAEC-mediated diarrhea in children found that isolates positive by PCR for agg4A (AAF type 4), and the SPATE genes pic and sepA formed stronger biofilm in vitro than strains without those genes.32 The AAF are important for EAEC biofilm formation and adherence.21,28,33–37\n\nDespite the implications of these epidemiological studies, little is known about the function of SepA. All SPATEs mediate their own secretion, contain a secreted serine protease domain, and are thought to have a unique protease target. Currently, the target of the serine proteinase activity of SepA for EAEC is unknown.38 In Shigella, deletion of sepA reduces fluid accumulation in the rabbit ligated ileal loop model.39 However, unlike Shigella, EAEC is not an invasive pathogen; therefore, SepA may play a different role in EAEC pathogenesis than it does for Shigella.\n\nIn our collection of EAEC isolates from the Trial Evaluating Ambulatory Therapy of Travelers’ Diarrhea (TrEAT-TD) study, which investigated travelers’ diarrhea in UK and US military personnel deployed in Kenya, Djibouti, Afghanistan, and Honduras,40 23% of the strains positive for AAF were positive for sepA. To investigate the role of SepA in EAEC pathogenesis, we deleted sepA from EAEC strain K261. We found that K261ΔsepA exhibited increased biofilm staining in vitro. Therefore, we deleted sepA from several additional strains. For some strains the sepA49-4043 deletion caused increased biofilm staining, but for others the sepA mutant strain had equivalent biofilm to the wild-type (wt) parental strain. Ultimately, complementation of the sepA mutation, either genetically or by adding SepA exogenously, did not restore wt biofilm staining. Our results suggest that the reason for the elevated biofilm in some EAEC sepA mutant strains is not directly related to the lack of SepA.\n\n\nMethods\n\nBacterial strains used in this study are listed in Table 1. We selected sepA-positive strains from our collection of EAEC clinical isolates obtained from the Trial Evaluating Ambulatory Therapy of Travelers’ Diarrhea (TrEAT-TD) study, which investigated travelers’ diarrhea in UK and US military personnel deployed in Kenya, Djibouti, Afghanistan, and Honduras.28,40 For an agg5A-positive, sepA-positive strain, we used D5613 (C267-15), a strain isolated from a pediatric case in Mozambique.29 HS is a commensal E. coli strain.41,42 We defined EAEC as having both aggR (EAEC virulence gene regulator43–46) and the genes for production of an AAF. The constructs used for this study are listed in Table 2.\n\n# Whole genome sequence contigs published in28,29 were queried with the Center for Genomic Epidemiology’s online Virulence Finder, Serotype Finder, and Plasmid Finder platforms. In this table, only virulence genes found in one or more strains are shown.\n\n† Aap is an anti-aggregation protein & aatPABCD encodes the transporter for Aap65,66\n\n‡ aaiC, located on the chromosome, encodes a secreted type VI secretion system effector protein.72\n\nBacterial cultures were grown in a shaking incubator at 37°C with appropriate antibiotics, and diluted in Dulbecco’s Modified Eagle Medium (DMEM) with high glucose and L-glutamine (Genesee Scientific 25-501) to 107 CFU/mL as estimated by optical density (OD). For those assays, 180 μL of the culture was added to a 96-well flat-bottom untreated plate (VWR 82050-760). DMEM was used as the control for each plate. After covering the plate with a lid, the plate was incubated at 37°C without shaking for the time indicated in the figure legend. After growth, the media on top of the biofilm was removed, and the biofilm was washed once with phosphate-buffered saline (PBS) (Fisher Scientific 70-011-044) before fixing with ethanol for 10 minutes. The dry biofilm plate was stained by immersing in a mixture of 3 mM crystal violet (Sigma Aldrich C0775), 5% ethanol, and water for 30 minutes then rinsed in tap water and dried. The bound crystal violet was eluted with 100 μL ethanol in each well, and the absorbance read at 590 nm. The control DMEM-only well values were subtracted from the absorbance values for all other wells.\n\nTo assess biofilm formation on glass disks, a single sterilized glass coverslip (Fisher 12-545-81P) was placed at the bottom of each well of a 24-well plate. Each well was then inoculated with 500 μL of 107 CFU/mL bacteria in DMEM, and then otherwise treated identically to the 96-well plate biofilm method. After fixing and crystal violet staining, each disk was removed and glued to a glass slide with Cytoseal XYL (Thermo Scientific 8312-4) for imaging at 100× with oil immersion using an Olympus BX60F-3.\n\nTo test addition of components to the biofilm media, we supplemented the DMEM at the start of growth to 1 mg/ml DNase (Sigma Aldrich DN-25), 1 mg/ml chymotrypsin (Sigma Aldrich C4129), or 0.8 mM - 2.5 mM sodium metaperiodate (Fluka Analytical 71859). Another set of wells had the equivalent volume of vehicle control (PBS) added. For biofilm media with 2 mM phenylmethylsulfonyl fluoride (PMSF) (Sigma Aldrich P7626) we made a stock of 100 mM in isopropanol and added the equivalent volume of isopropanol to a set of control wells.\n\nTo make DMEM with M9 levels of magnesium (10 mM Mg2+), we grew biofilms in regular DMEM or DMEM with an extra 9.2 mM magnesium sulfate (Acros Organics 42390500).\n\nVirulence gene deletion strains were constructed by lambda Red-mediated recombination with the pKD46spec plasmid.47,48 In most cases, the entire gene was replaced with a kanamycin (kan), gentamicin, or chloramphenicol (cat) resistance gene. Briefly, PCR primers, listed in Table 3, with approximately 50 nucleotides of homology to the wt gene were used to amplify the resistance gene. The PCR product was gel-purified following kit directions (Qiagen 28506) and electroporated into EAEC induced for expression of the lambda Red system (1 mM arabinose; Chem-Impex 01654), using a MicroPulser Electroporator set to 1.8 kilovolts with 200-ohm resistance (BioRad 1652100).49 After electroporation, the EAEC were incubated at 37°C for one hour to allow the recombination (based on homology to the primer regions) to proceed and for expression of the antibiotic resistance. Growth at 37°C also promotes loss of the pKD plasmid.48 Gene deletions were confirmed by PCR with specific screening primers listed in Table 3. We also confirmed, by plasmid sequencing, that the ΔsepA::cat mutation was the only genetic change in pAAK261-ΔsepA as compared to pAAK261 and for pAAP433-ΔsepA relative to pAAP433, and that the sequence of revertant (pAAK411-revertant) was correct.\n\nTo amplify PCR products larger than 4 kb, we used Platinum SuperFi II PCR Master mix (Invitrogen 12368010). For PCR products less than 4 kb, we used PfuUltra II Fusion HS Master mix (Agilent Technologies 600852). For confirmatory PCR from colonies, we used colony “boils” (one colony was added to 50 uL of water with a sterile toothpick and incubated for 12 min at 95°C), and the GoTaq Green Master mix kit (Fisher PRM7123).\n\nTo insert PCR products into pCR2.1TOPO (TOPO), we followed manufacturer guidelines (Invitrogen K280020). PCR products were purified using the QIAquick PCR & Gel Cleanup kit (Qiagen 28506). Plasmids were purified using the QIAprep Spin Miniprep kit (Qiagen 27106X4). To purify larger quantities of the pAA plasmid, we increased the yield of this large, low-copy vector by adding extra yeast extract to the Luria-Bertani (LB) broth (final concentration of 24 g/L yeast extract), as described by Wood et al.50 To move inserts into pACYC177, we digested the sepA inserts from the TOPO clones with BamHI (NEB R3136), then ligated the inserts into pACYC177. Primers were sourced from Integrated DNA Technologies and are listed in Table 3.\n\nTo allow the selection of colonies with sepA inserted into lacZ, we first added a kan resistance gene 200 bp downstream of sepA prior to amplification of the entire region for lambda Red-mediated replacement of the lacZ gene. We confirmed that addition of kan after sepA had no effect on biofilm staining in the wt strains (data not shown).\n\nFor the larger PCR construct, ΔlacZ::sepA-kan, after amplification using K261 pAA-kan as a template, the construct was first inserted into TOPO per manufacturer instructions. The plasmid was then digested with NotI (NEB R3189) and BamHI (NEB R3136) and gel-purified to yield 500 ng of insert DNA and added to 100uL of electrocompetent cells for lambda Red recombination. The revertant strain (K411Δcat::sepA-kan) was identified by screening for loss of chloramphenicol resistance after recombineering with the ΔlacZ::sepA-kan PCR (Table 3). We confirmed the localization of SepA in the supernatant using Western blot analysis (data not shown).\n\nWe selected a spontaneous nalidixic acid resistant (NalR) derivative of commensal E. coli HS41,42 by growth on LB agar with 15 μg/mL nalidixic acid (Sigma Aldrich N4382). We moved the K261 pAA into HSNalR by centrifuging overnight cultures of both strains, resuspending the pellets in PBS, and mixing them (HSNalR and K261) at 1:1 v:v. After 5 minutes of incubation at room temperature, 75 μL of the cell mixture was spotted onto agar without any antibiotics and incubated for three hours. The mix was then inoculated onto MacConkey agar with 15 μg/mL nalidixic acid to select for HSNalR and 15 μg/mL tetracycline (Sigma Aldrich 37919) to select for pAAK261 and grown overnight.\n\nTo get pAAP433ΔsepA, pAAK261ΔsepA, and pAAP433 into HSNalR, the plasmids were purified as described above using extra yeast extract in the LB broth medium, then 1 μg of the plasmid was transformed into electrocompetent HSNalR cells. The transformed HSNalR was grown at 37°C overnight before plating on LB agar with 30 μg/mL chloramphenicol (Calbiochem 220551) to select for uptake of the pAAs with ΔsepA or 100 μg/mL ampicillin (Corning 61-238-RH) agar for pAAP433.\n\nIn all cases, single colonies were screened by PCR to confirm the presence of aggR (pAA marker) and the absence of aaiC (EAEC chromosomal marker) to confirm uptake of the pAA plasmid.\n\nA mutation in the active site of the SepA passenger domain (sepA*) (Table 2) was generated by splicing by overlap extension (SOE) PCR using primers SepAS211F and SepAS211R (Table 3) to create the following changes: a799g & g800c in sepA which result in replacement of the serine at position 267 with an alanine. Next, the coding region for the passenger domains of K411 sepA and sepA* were amplified by PCR from TOPO::sepA* and TOPO::sepA to add BamHI and SalI cut sites, and ligated into the inducible vector pTrcHis2c (Invitrogen V36520) (Table 2). The expression of SepA (or SepAS267A*) from these plasmids would result in SepA with a hexahistidine (His6) tag added at the N terminus. We chose to use the His tag for purification purposes because both Scott-Tucker et al. and Charbonneau et al. showed that the serine protease activity of a SPATE passenger domain is retained even with an N-terminal hexahistidine-tag.51,52 After optimizing SepA expression from TOP10 pTrcHis2c with 1 mM IPTG (isopropyl β-D-1-thiogalactopyranoside) (Sigma Aldrich I6758), the bacterial cells were lysed with BugBuster Master mix (Novagen 71456). The protein was then purified with a HisTrap HP nickel column according to the manufacturer’s protocol (GE Healthcare 95056-204). The purity of fractions collected from the nickel column was evaluated on a 4-12% Bis-Tris gel (Invitrogen NP0324). The fractions with the 110 kDa His-SepA protein band were concentrated with an Amicon Ultra-15 centrifugal concentrator 50,000 MW (Fisher Scientific UFC905008). The same type of centrifugal concentrator was used for buffer exchange with PBS to remove the imidazole.\n\nFor harvesting K411 wt or K411ΔsepA supernatant, cultures were grown in DMEM high glucose, with L-glutamine (Genesee Scientific 25-501) at 37°C shaking for five hours prior to centrifugation. The supernatants were filtered with a 0.22 μm filter (Genesee Scientific 25-227) before concentrating 2,000-fold with an Amicon 50 kDa cutoff spin column (Fisher UFC905008). The concentrated supernatant was then added to the biofilm media at the start of incubation. For TOPO::sepA or TOPO::sepA* supernatants, the plasmid was grown in TOP10 cells (Invitrogen C404010) and harvested identically to the EAEC strains.\n\nA peptide (K261 SepA891-913) from the exposed regions of the passenger domain of SepA was selected to generate a rabbit anti-SepA polyclonal antibody. Pacific Immunology (Ramona, CA) made rabbit polyclonal antibodies by immunizing two rabbits with the peptide at day 0 with complete Freund’s adjuvant and then again on days 21, 42, and 70 with incomplete Freund’s adjuvant. On day 77, 25 ml of serum was collected and affinity purified. This animal protocol was approved by IACUC-designated member review on August 12, 2019 from Pacific Immunology (SOP-1).\n\nBacterial strains (listed in the figure legends) were grown at 37°C for four hours in DMEM with shaking for liquid culture conditions or without shaking for static biofilm cultures. The supernatants from those cultures were collected after centrifugation and precipitated with an equal volume of ethanol overnight at -20°C. Samples were denatured with NuPAGE® sample buffer (Invitrogen NP0008) and electrophoresed on a 4-12% Bis-Tris gel (Invitrogen NP0324). The proteins were transferred using an iBlot nitrocellulose transfer stack (Invitrogen IB301002) to nitrocellulose. The nitrocellulose blot was incubated for two hours at room temperature in PBS with 0.1% Tween (Fisher Scientific 424592500) with 5% nonfat dry skim milk (Lab Scientific M0841). After the blocking step, the nitrocellulose was incubated overnight at 4°C with the anti-SepA antibody, at a dilution of 1:4,000 or 1:7,000 (listed in the figure legend), in PBS-Tween-milk, then washed three times with PBS-Tween. Next, the blot was incubated with a 1:10,000 dilution of the secondary antibody (goat anti-rabbit HRP conjugate; Bio-Rad 1706515) in PBS-Tween at room temperature for two hours. The nitrocellulose blot was washed once with PBS-Tween and twice with PBS. The nitrocellulose blot was incubated with ECL Western Blotting Detection reagent according to the manufacturer’s instructions (GE Healthcare 45-002-401) and imaged with a GE Amersham 680 Blot Imager. Blot images were cropped but otherwise not manipulated.\n\nTo purify pAA DNA we used the Plasmid Midi Kit (Qiagen 12143) following the manufacturer’s published protocol.53 Sequencing of the DNA for pAAP433, pAAK261-ΔsepA, pAAP433-ΔsepA, and pAAK411-revertant was done by Plasmidsaurus (Eugene, OR). Additional DNA sequences were taken from published work.28,29 A draft assembly was done with the Minimap2 plug-in54 with Geneious Prime 2023.0.455 then further refined by re-aligning all reads in Geneious Prime. Remaining ambiguous bases were resolved manually by a comparison of the sequence quality among the sequencing reads provided.\n\nGraphPad Prism 10.0.356 was used to test significance of three or more biological replicates by unpaired t test for two groups or an ordinary one-way analysis of variance (ANOVA) with a correction for multiple comparisons. *P≤0.05; **P≤0.01; ***P≤0.001; ****P≤0.0001.\n\n\nResults\n\nIn our EAEC isolate collection from the TrEAT-TD study,40 all of the typical EAEC strains positive by PCR for the sepA gene were also positive for either the aggA or agg4A AAF major subunit gene. We selected six of the recently isolated clinical strains that were positive for sepA for this study (Table 1). The virulence gene profiles of these strains are found in Table 1. We deleted sepA in these strains by replacing sepA49-4043 with a chloramphenicol resistance gene (cat). We found that two EAEC strains exhibited increased biofilm staining after the deletion of sepA (Figure 1). Based on that finding, we initially hypothesized that the proteolytic activity of SepA modulated biofilm formation in a subset of EAEC by either cleaving a protein on the surface of the EAEC or protein(s) within the biofilm. Although four of the strains tested were positive for agg4A, we also tested an aggA+ strain, E131, and an agg5A+ clinical strain, D561329 (Table 1). Neither the aggA+ nor the agg5A+ ΔsepA strains showed a significant difference in biofilm staining (Figure 1). These results suggested that SepA may only affect the biofilm of some agg4A-positive strains. We confirmed that no growth defects were present in a selection of four of the strains (Figure 2).\n\nSymbols in pink represent the values for the wt parental strain and in blue represent the corresponding ΔsepA strain. Each symbol shows the mean of four biofilm technical replicates grown for 23 hours. Error bars indicate standard error of the mean (SEM). Significance was determined using unpaired t tests for independent experiments done for each wt-mutant pair. ****P≤0.0001.\n\nEach strain was grown in DMEM high glucose with L-glutamine with shaking in 250mL flasks with the appropriate antibiotic. The wt strain values are shown as pink squares and the corresponding ΔsepA strain with blue circles. The CFU and optical density, OD600, were measured every hour. Bars indicate standard deviation (SD) for n=3 or range for n=2. The number of biological replicates is written below each graph.\n\nIn Figure 1, four isolates had a non-significant increase in biofilm staining for the ΔsepA mutant strain as compared to the wt parental strain. Because the overall biofilm levels were relatively high for all of the strains, we reasoned that we might be able to detect a significant difference between the wt and the ΔsepA derivative strains if we reduced the amount of time that the biofilms were allowed to develop. Therefore, we assessed when we could detect the elevated biofilm staining phenotype by testing shorter growth times for biofilm growth for K261 and K261ΔsepA (Figure 3). We found that the increased biofilm staining by K261ΔsepA relative to K261 was apparent after five hours of biofilm growth and remained differentiated up to the typical 23-hour time point we used for longer biofilm assays (Figure 3). We also observed a linear relationship between increased growth time and increased biofilm staining for each strain as predicted by a linear regression model, although the lines were not perfectly parallel (Figure 3). The best separation in biofilm staining for K261 compared to K261ΔsepA was found for biofilms grown for less than nine hours (Figure 3). Based on these results, we decreased the growth time of the biofilm to five to eight hours and re-tested the EAEC strain pairs for differences in biofilm staining. With the shorter biofilm growth time, we observed a statistically significant difference in staining for E131 and E161 as compared to the corresponding ΔsepA-derivative strains when we controlled for variability by normalization (Figure 4). E131 has the aggA AAF gene (Table 1), so these results demonstrate that the ΔsepA biofilm phenotype is not limited to strains with the agg4A gene. Strains P433ΔsepA (agg4A) and D5613ΔsepA (agg5A) did not show a statistically significant change in staining compared to the wt parental strain under these conditions (Figure 4).\n\nBiofilm results from 96-well plate assays. Pink symbols represent K261 and blue symbols the K261ΔsepA strain. Each symbol represents a biological replicate. The lines are a simple linear regression determined in GraphPad Prism.\n\nThe biofilm absorbance for the mutant strains was normalized to that of the wt strain. Pink symbols represent the wt parental strain and blue symbols indicate the corresponding ΔsepA strain. Each symbol represents the mean of four technical replicates. Significance was determined using an unpaired t test for independent experiments performed for each mutant-wt pair. *P≤0.05; **P≤0.01.\n\nSince the original sepA deletion strategy left 96 nucleotides of the sepA coding region, we next made a deletion that left only the start and stop codons, and reversed the orientation of cat gene (catrev) relative to sepA. K411ΔsepA::catrev exhibited increased biofilm staining compared to the wt parental strain (Figure 5). This result indicates that the increased biofilm staining after deletion of sepA was not an artifact of the original mutation strategy.\n\nBiofilm results from 23 hour 96-well plate assays. Pink symbols indicate the wt parental strain, and blue symbols are for the corresponding ΔsepA::catrev strain. Each symbol represents the mean biofilm staining of four technical replicates. Error bars indicate SEM. P-value from unpaired t test *P≤0.05.\n\nWe hypothesized that there might be an expression level difference or an amino acid difference within SepA among different EAEC strains that prevented a SepA-mediated reduction in biofilm staining in the wt strains. We found no nucleotide differences in the 185 bp upstream of sepA, a region that includes the binding region for the EAEC virulence regulator AggR,57,58 for any of the strains in this study. This finding demonstrates that the sepA promoter is the same for all of the strains. Next, we compared the predicted amino acid sequences of SepA among the EAEC used in this study. There were several amino acid polymorphisms with respect to the predicted protein consensus derived from all strains combined: (K411: A51V), (K261: S905N), (E131: I183V, G194E, D1049N), (D5613: D1049N, H671N), (P433 & E161: A1277V). However, we observed no common amino acid change in SepA among the strains that showed a difference in biofilm staining when sepA was deleted compared to those that did not (P433 and D5613). The most interesting change identified was A1277V in E161 and P433. The A1277V change is in the predicted autotransporter beta domain, which is necessary for secretion of the proteolytic passenger domain into the supernatant. In other SPATEs, mutations in this domain can inhibit secretion of the SPATE.51,59–62 Accordingly, we examined SepA secretion into the supernatant from a subset of EAEC in this study, shown below.\n\nTo investigate whether the increased biofilm staining observed when sepA is deleted from some EAEC but not others is related to SepA secretion levels, we performed Western blot analysis on EAEC culture supernatants. We were particularly interested in whether the amino acid substitution found only in E161 and P433 (A1277V) had an impact on secretion. We observed the same apparent SepA band in all the wt strains examined, and all the strains tested appeared to have approximately equal levels of SepA (Figure 6). This finding was true for EAEC with (K411, K261, and E161) or without (P433) a difference in biofilm staining when sepA was deleted. We also examined the supernatants from statically-grown biofilms of K261 and P433 for SepA. Similar SepA bands were observed from the supernatant harvested from the biofilms of K161 and P433 (Figure 6). There was no visible SepA band identified from the bacteria contained in the cell pellet from the biofilm-grown bacteria; therefore, we inferred that SepA was efficiently exported into the supernatant for both K261 and P433 (Figure 6).\n\nSupernatants from shaking (shake) cultures, a static biofilm culture (biofilm), or cell pellets are shown. The black triangle (◂) denotes the band corresponding to the SepA passenger domain, at approximately 110 kDa39 while the open triangle (⊲) represents an unknown breakdown product. The first lane is the MagicMark XP standard (Invitrogen LC5602) with the 50 kDa band indicated. E171 is a wt sepA+ EAEC strain that is genetically identical to E16128 (not used elsewhere in this study).28 1:4,000 anti-SepA antibody.\n\nWe also tested the impact of deletion of the EAEC virulence gene regulator, aggR (K261ΔaggR) on SepA secretion. AggR is known to positively regulate sepA expression via an AggR-binding site.57,58 We found that some SepA was still secreted when aggR was deleted (Figure 6). We also found that SepA was efficiently secreted by a laboratory strain carrying a high-copy plasmid containing the K261 sepA gene (which was inserted in the opposite orientation as the lac promoter), without AggR (TOPO::sepA). This plasmid was later used as a part of our complementation work.\n\nTo visualize the biofilm after sepA was deleted, EAEC were grown on glass disks under the same conditions used for the 96-well biofilm assay (Figure 7). We examined K261 (showed elevated biofilm staining as measured by OD when sepA was deleted) and P433 (no change in biofilm staining OD when sepA was deleted). We observed that the ΔsepA strain biofilm patterns were different than found in the wt strains. Both P433 and K261 appeared to be packed closer together than the respective ΔsepA strains (Figure 7). However, this difference in biofilm appearance does not correlate to the quantitative amount of crystal violet staining, for reasons that are not clear.\n\nBiofilms were grown for five hours on glass disks and stained with crystal violet. Representative images from two independent experiments are shown at 100× magnification.\n\nWe next sought to determine whether the differences in biofilm crystal violet staining for K261 and K261ΔsepA were due to differences in the bacterial numbers in the biofilm. We checked both the biofilm and biofilm supernatant for K261 and, for comparison, P433 as well as the corresponding ΔsepA strains. No differences in CFU were identified (Figure 8). As the CFU from biofilms for K261, P433, and the ΔsepA derivative strains did not deviate, the staining differences were not due to reductions in bacterial numbers.\n\nBiofilms were grown as usual in 96-well plates for five hours. Subsequently, 100 μL of supernatant was collected for CFU enumeration (supernatant). After washing the biofilm once with PBS, the biofilm was removed by scraping and resuspended in 100 μL of PBS and vortexed (biofilm). To confirm separation of bacterial aggregates after vortexing, we checked the mixture by microscopy (data not shown). Crystal violet staining after biofilm removal confirmed that no biofilm remained in the wells after scraping. Each symbol represents the mean of two technical replicates. Error bars indicate SEM. ns, no significant differences were found using 1-way analysis of variance (ANOVA) with Tukey’s test.\n\nTo identify the genes that might be responsible for the increased biofilm staining for K261ΔsepA, but not for P433ΔsepA, we transferred the pAAs from those strains into the commensal E. coli HSNalR which does not have the capacity to make biofilm. We successfully transferred pAAK261 into HSNalR. We found that the K261 pAA did not confer biofilm formation on HSNalR (Figure 9). That result is similar to those of Alves et al. who reported that the wt pAA plasmid from EAEC strain 042 does not confer the capacity to form biofilm to an E. coli K12 strain.63 In contrast, HSNalRpAAK261ΔsepA demonstrated significantly increased biofilm staining (Figure 9). This latter result indicated that the target of SepA is likely on the K261 pAA. We also put pAAp433 and pAAP433ΔsepA (does not confer elevated biofilm to P433) into HSNalR. Biofilm staining was not increased in HSNalR with either pAAP433 or pAAP433ΔsepA (Figure 9). We also found that sepA alone or ΔsepA::cat alone did not confer the capacity to form a biofilm on HSNalR (data not shown). Therefore, we concluded that the ΔsepA::cat mutation alone is not sufficient to cause the increased biofilm staining of HSNalR that had pAAK261ΔsepA.\n\nBiofilms were grown for 4.5 hours. Pink bars represent HSNalR with a wt pAA. Blue bars indicate HSNalR with a pAAΔsepA. Each symbol represents the mean of four technical replicates. Error bars indicate SEM. Significance was tested using 1-way ANOVA with Tukey’s test. ****P≤0.0001.\n\nBecause it is likely that the target of SepA is encoded on the K261 pAA, and we predicted that deleting the gene for a target of SepA would result in a significant change in biofilm staining, we searched for genetic differences in the pAAP433 as compared to pAAK261. From that search, we found that the pAAP433 lacks most of the tra (plasmid transfer) genes. Therefore, we deleted the tra region from pAAK261 (pAAΔpsiB-orf8) and assessed biofilm formation (Figure 10). Because we found no significant difference in biofilm staining between K261 and K261pAAΔpsiB-orf8, we concluded that the target for SepA was not encoded within the deleted region. Other gene deletions made in pAAK411, ΔumuC-yccA, ΔfinO, ΔparB similarly had no impact on biofilm staining (data not shown). We also searched for genes (excluding transposes) on the pAA for predicted amino acid differences found only in P433 and D5613. Excluding the previously deleted genes and mobile genetic elements, we identified lpxM (Lipid A biosynthesis myristoyltransferase)64 for which there were predicted amino acid differences between K261 and P433. However, because we found no impact of lpxM deletion on biofilm staining of K261 (Figure 10B), we concluded that LpxM is not the target of SepA.\n\nBiofilms were grown for 5-8 hours. Each symbol represents the mean of four technical replicates. Significance tested by 1-way ANOVA with Šídák correction. *P≤0.05; **P≤0.01; ***P≤0.001; ****P≤0.0001.\n\nNext, because deletion of the gene for dispersin (aap) increases biofilm staining for EAEC strain 042,65,66 we tested a strain with a deletion of both aatA (encodes the dispersin transporter) and sepA. The positively-charged Aap protein is thought to help the AAF extend from the surface of the bacteria.65,66 In Figure 7 we noted that ΔsepA bacteria in the biofilm were less compactly spaced than the wt, so we predicted that preventing export of dispersin would have the opposite effect. However, we found that biofilm formation for K261ΔsepAΔaatA was increased, a result that suggests that dispersin is not a target for SepA (Figure 10C). Next, we deleted agg4A, the gene that encodes the AAF major pilin subunit in the wt and ΔsepA background of K261 (Figure 10C). We measured a significant reduction in biofilm staining for both strains, as would be predicted for loss of the AAF.35 Because biofilm formation by the K261Δagg4AΔsepA double deletion strain was indistinguishable from K261Δagg4A, we cannot determine whether SepA has an impact on the AAF by this method. However, because the predicted amino acid sequence of Agg4A from K261 and P433 are identical, we hypothesized that Agg4A is not the target of SepA for K261. We next moved on to other strategies to identify how SepA affects biofilm staining in some of our strains.\n\nWe conducted several additional experiments to investigate potential mechanisms by which biofilm staining was increased after deletion of sepA. Because Arenas et al. showed that deletion of a SPATE in Neisseria led to increased biofilm via a surface charge change and eDNA (extracellular DNA) production,67 we asked if a surface charge difference could be observed in the EAEC strains that showed differential biofilm formation. In contrast to Arenas et al. we found that differences in cytochrome c binding (a proxy for surface charge) did not correlate with biofilm staining levels (Figure 11). For example, K261ΔsepA had decreased cytochrome c binding compared to K261, but K411 and K411ΔsepA had no significant difference in cytochrome c binding (Figure 11). For our next set of experiments, we attempted to manipulate the biofilm by addition of various compounds to the medium, Figure 12. (A) To pursue the hypothesis that there might be increased eDNA present in the biofilm of strains with elevated biofilm staining, we tested the impact of DNase I on biofilm formation. We could detect no impact on biofilm staining when biofilms were grown with 1 mg/ml DNase I (Figure 12A). (B) Next, we asked whether treatment of the biofilm with an exogenous serine protease, chymotrypsin, would alter biofilm formation. We used a serine protease because SepA is a serine protease and we reasoned that it was possible that a broad-spectrum serine protease might be able to act similarly to SepA. However, no impact on the biofilm staining was observed in the strains that were treated with chymotrypsin (Figure 12B). (C) We tested the effects of sodium metaperiodate, a carbohydrate cleaving agent. Sodium metaperiodate had no impact on biofilm staining (Figure 12C). (D) Because SepA is a serine protease, we added phenylmethylsulfonyl fluoride (PMSF), a protease inhibitor, to the biofilm. We did not observe an impact on biofilm staining when 2mM PMSF was added to the biofilm compared to the vehicle control (isopropanol) (Figure 12D). This may be because PMSF is neutralized by other biofilm components over four hours, because the protease activity of SepA is not responsible for the ΔsepA phenotype, or because PMSF does not inhibit SepA under the conditions tested. (E) Because we observed increased biofilm staining (data not shown) when EAEC were grown in M9 medium (has higher levels of magnesium than DMEM) and because magnesium affects the expression of genes on the large plasmid in Shigella,64 we supplemented DMEM to magnesium levels (10 mM Mg2+) equivalent to that in M9. However, as shown in Figure 12E, Mg2+ supplementation did not change biofilm staining significantly. Nor did magnesium lower the increased biofilm staining of K261ΔsepA (Figure 12E). In summary, we did not observe a difference in biofilm response between the wt and ΔsepA strains for any of the tested treatments.\n\nThe percentage of cytochrome c bound for each strain was calculated as previously described.75 Each bar represents the mean of three biological replicates. Error bars indicate SEM. Significance tested by 1-way ANOVA with Šídák correction. ***P≤0.001; ****P≤0.0001.\n\nBiofilm results from a five hour 96-well plate assay grown in DMEM media supplemented with (A) 1 mg/ml DNase, (B) 1 mg/ml chymotrypsin, (C) 0.8 mM – 2.5 mM sodium metaperiodate, (D) 2 mM PMSF, or (E) 10 mM Mg2+ as compared to DMEM (0.8 mM Mg2+). Pink symbols indicate K261, blue symbols K261ΔsepA, purple symbols P433, and green symbols P433ΔsepA. Square symbols represent strains with the vehicle control added to the biofilm, and circles the biofilms with supplemented media. Each symbol represents the mean of four technical replicates. Error bars indicate SEM. Significance was tested by 1-way ANOVA with Šídák correction. *P≤0.05; **P≤0.01; ***P≤0.001; ****P≤0.0001.\n\nWe hypothesized that a SepA-secreting strain should reduce the biofilm staining of K261ΔsepA to K261 levels. We therefore inoculated a biofilm plate with a mixture of K261ΔsepA and P433 (SepA secreter) or P433ΔsepA as a control. We selected P433 as the SepA-secreting strain because P433 and P433ΔsepA showed identical staining. Co-culture of P433 with K261ΔsepA did not significantly lower biofilm staining as compared to the P433ΔsepA (SepA non-secretor) (Figure 13). There are several possible explanations for this observation. One, SepA only acts quite close to the surface of the bacteria, or similarly, is trapped within the biofilm. Second, that SepA is rapidly inactivated in the biofilm media, or, lastly, that SepA is not responsible for the increased crystal violet staining observed in K261ΔsepA.\n\nEqual volumes of the indicated strains were grown for five hours in a biofilm. Each symbol represents the mean of four technical replicates. Significance was tested using 1-way ANOVA with Šídák correction. *P≤0.05.\n\nWe next added SepA directly to the biofilm. The SepA passenger domain is abundantly secreted into the supernatant for both EAEC and lab E. coli strains (Figure 6 and Ref. 39). We chose K411 as the donor for the supernatant because it contains only one SPATE, SepA. We observed a significant reduction in staining for the K261ΔsepA biofilm grown with K411 supernatant (Figure 14A). These results suggested that exogenously added SepA could reduce biofilm staining. Although the K411ΔsepA supernatant also slightly reduced K261ΔsepA biofilm staining (Figure 14A), the reduction was not statistically significant. It may be that there were other factors present in the concentrated supernatant from K411ΔsepA, including waste products, which may impact biofilm growth.\n\n(A) Concentrated supernatants from either K411 or K411ΔsepA were added to the growing biofilm of K261 or K261ΔsepA at the start of incubation (5-hour biofilm). (B) Concentrated supernatant from TOP10 cells with either TOPO::sepA or TOPO::sepA* was added to the growing biofilm. Absorbance was normalized to that of the untreated ΔsepA strain. Each symbol represents the mean of four technical replicates. Error bars indicate SEM. Significance tested by 1-way ANOVA with Šídák correction. *P≤0.05; **P≤0.01.\n\nTo eliminate the possible influence of other EAEC elements within the supernatants, we concentrated the supernatant fraction from laboratory E. coli TOP10 cells that carried TOPO::sepA (wt SepA protein) or TOPO::sepA* (catalytically inactive SepA). The concentrated supernatant fractions were then added to the growing biofilms as before. The presence of the supernatant from the TOPO::sepA construct did not lead to a statistically significant reduction in biofilm staining (Figure 14B), despite the abundant presence of SepA in supernatants from that construct as shown by Western blot (Figure 6).\n\nAs the concentrated supernatant from the TOP10 cells with either TOPO::sepA or TOPO::sepA* did not reduce biofilm formation, but the concentrated supernatant from K411 did, we next asked whether purified SepA protein could function to reduce biofilm staining for K261ΔsepA. We expressed the His-tagged SepA passenger domain (His-SepA) as previously described for other SPATEs.25,68,69 The catalytically inactive form of the SepA passenger domain (SepA*) was used as a control. The vehicle control (PBS), His-SepA, or His-SepA* was added to K261ΔsepA at the start of inoculation for the biofilm and again one hour before fixing the biofilm. As shown in Figure 15, no impact on biofilm staining was observed. This result, taken with mixed biofilm data, further suggested that the SepA protein may not be responsible for the difference between wt and ΔsepA biofilm staining. We were unable to measure the enzymatic activity of the His-SepA in this study due to the lack of a known substrate for the EAEC SepA. However, the utilized purification process has successfully been used in other studies to yield functional SPATEs.51,52,68 Following the outcomes of these studies, we next utilized a genetic approach to test SepA.\n\nBiofilm results from a five hour 96-well plate biofilm assay are shown. Protein or PBS vehicle control was added at the time of biofilm inoculation and again one hour before biofilm fixation. Each symbol represents the mean of four technical replicates. Significance tested by a 1-way ANOVA with Tukey’s test. **P≤0.01; ***P≤0.001.\n\nTo complement the ΔsepA mutation genetically, we transformed K261ΔsepA and K411ΔsepA with pACYC177::sepA for complementation (Figure 16). We confirmed SepA expression in the supernatant from pACYC177::sepA (Figure 17) and that there was no growth defect for ΔsepA strains with pACYC177::sepA (data not shown). However, this construct failed to reduce biofilm staining of K261ΔsepA and K411ΔsepA as compared to the parental strains (Figure 16).\n\nBiofilms were grown for 23 hours in a 96-well plate. Each symbol represents the mean of four technical replicates. Error bars indicate SEM. Significance was tested by 1-way ANOVA with Šídák correction. *P≤0.05; **P≤0.01; ***P≤0.001; ****P≤0.0001.\n\nSupernatants from four hour shaking cultures of the indicated strains. 1:7,000 dilution of the SepA antibody. Black triangle (◂) points to the SepA passenger domain band. Open triangle (⊲) indicates an unknown breakdown product band also seen in Figure 6.\n\nSince the plasmid-based methods failed to complement the altered biofilm-staining phenotype in the ΔsepA strains, we next introduced sepA into the chromosome of K411ΔsepA, in the lacZ locus. However, we did not observe a reduction in biofilm staining of K411ΔsepAΔlacZ::sepA (Figure 18). In our last attempt at complementation, we created a “revertant” strain in which sepA was inserted back onto the pAA in place of the deleted sepA. The revertant strain had equivalent biofilm staining as found for the ΔsepA strain (Figure 18), a finding that demonstrated that the reason for the elevated biofilm staining in this strain is not due to the sepA deletion. Collectively, these data suggest that the lack of SepA did not cause the increase in the biofilm formation in the ΔsepA strains.\n\nBiofilm results from a five hour 96-well plate assay. Each symbol represents the mean of four technical replicates. Error bars indicate SEM. Significance was tested by 1-way ANOVA with Šídák correction. **P≤0.01.\n\n\nDiscussion\n\nTo assess the contribution of the SPATE SepA to the virulence of EAEC, we deleted sepA from a set of six clinical EAEC strains and assessed biofilm formation. We were surprised to find that four of the ΔsepA strains demonstrated increased in vitro biofilm staining compared with the wt controls. We hypothesized that the serine protease activity of SepA was cleaving either an EAEC surface protein or a biofilm component in the wt strains, such that when sepA was deleted that component was no longer cleaved, and biofilm staining increased. Ultimately, we did not find a direct connection between biofilm staining and SepA because we were unable to complement the mutation. However, we did find that the ΔsepA EAEC were spread further out from each other than wt EAEC in images of biofilms. This latter finding was true both for ΔsepA strains in which we observed elevated biofilm staining and for those for which we did not find elevated biofilm staining. Taken together these findings suggest that deletion of sepA does alter the biofilm to a degree, but that the effect of SepA is best observed microscopically, and is likely indirect.\n\nWe did find that pAAΔsepA conferred biofilm-forming capacity to a commensal E. coli. This result shows that increased biofilm staining is mediated solely by pAAΔsepA. We also confirmed that ΔsepA::cat alone could not confer biofilm-forming capacity to HSNalR. Taken together our results suggest for the phenotype of elevated biofilm staining the pAAΔsepA is necessary and sufficient.\n\nAs we investigated the effect of the sepA mutation, we found the following: a) all wt strains secreted similar amounts of SepA, b) all wt and ΔsepA strains had similar biofilm CFU counts, c) targeting of eDNA, protein, and carbohydrate did not alter biofilm staining levels for K261, d) deletion of the pAA tra region, as well as umuC-yccA, finO, lpxM, parB did not impact biofilm staining, and, e) increased biofilm staining for K261ΔsepA was dependent on the ability to form a biofilm.\n\nDuring this investigation, we tried to complement the ΔsepA-enhanced biofilm-staining phenotype through both exogenously added protein and by genetic means. Neither crude SepA preparations or purified SepA were able to reduce biofilm staining in the mutant strain background in most cases. We did observe, curiously, that the concentrated supernatant of K411 wt decreased biofilm staining. However, neither cis- nor trans-addition of sepA reduced biofilm staining in the mutant strain background back to wt levels.\n\nBecause we ultimately realized that the increased biofilm staining found for ΔsepA EAEC strains is not due to the lack of SepA, we hypothesize that the increased biofilm staining is due to a change in the expression of other genes involved in biofilm formation on the pAA. These genes could include those for AAF expression, dispersin or dispersin transport, yet unidentified biofilm genes, or other genes involved in fimbrial gene expression, such as aggR. Another regulatory factor for EAEC is Aar, which is a repressor of aggR expression and also encoded on the pAA plasmid. However, the presence or absence of aar did not correlate with increased biofilm staining in ΔsepA strains in this study. Alternatively, it is possible that the cat insertion into sepA caused an unintended effect on the downstream AAF operon or on expression of other pAA genes. However, because sepA is located on the pAA separated from other genes by insertion elements, we do not think that deletion of sepA perturbs the expression of other genes directly.\n\nOur data suggest that there is more work to be done on the regulation of EAEC biofilm formation/genes and the ways in which the pAA contributes to the biofilm.\n\n\nEthics and consent\n\nEthical approval and consent were not required.",
"appendix": "Data availability\n\nThe sequences of the following plasmids were deposited in GenBank. 70\n\npAA P433\n\nGenBank. plasmid_pAA_P433. Accession number PP261911.\n\npAA P433 -Δ sepA\n\nGenBank. _plasmid_pAA_P433_delta-sepA::cat. Accession number PP261912\n\npAA K261\n\nGenBank. plasmid_pAA_K261_virulence_plasmid. Accession number PP261914\n\npAA K261 -Δ sepA\n\nGenBank. plasmid_pAA_K261_delta-sepA::cat. Accession number PP261915\n\npAA K411 -revertant\n\nGenBank. _plasmid_pAA_K411-revertant. Accession number PP261916\n\nA second plasmid from K261 ( aggR-negative )\n\nGenBank. K261_tra _plasmid_EAEC_not_pAA. Accession number PP261913\n\nThe other underlying data and raw uncropped images have been deposited in a Figshare collection. 71\n\nThe numerical data for graphs\n\nDOI: 10.6084/m9.figshare.25551933.v1 76\n\nFigure 6, uncropped Western blot image\n\nDOI: 10.6084/m9.figshare.25551936.v1 77\n\nFigure 7, all biofilm photos\n\nDOI: 10.6084/m9.figshare.25551939.v1 78\n\nFigure 17, uncropped Western blot image\n\nDOI: 10.6084/m9.figshare.25551930.v1 79\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe thank Nadia Boisen from Statens Serum Institut (København, Denmark) for D5613 (C267-15) EAEC strain. We acknowledge Giselle Usc (Department of Microbiology and Immunology, Uniformed Services University) for doing growth curves and Mary R Brockett (Department of Microbiology and Immunology, Uniformed Services University) for help with growing biofilms on glass disks.\n\nThe opinions and assertions expressed herein are those of the authors and do not reflect the official policy or position of the Uniformed Services University of the Health Sciences or the Department of Defense. References to non-Federal entities or products do not constitute or imply a Department of Defense or Uniformed Services University of the Health Sciences endorsement. The opinions and assertions expressed herein are those of the authors and do not reflect the official policy or position of the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. 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PubMed Abstract | Publisher Full Text\n\nDautin N, Barnard TJ, Anderson DE, et al.: Cleavage of a bacterial autotransporter by an evolutionarily convergent autocatalytic mechanism. EMBO J. 2007; 26: 1942–1952. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDautin N: Serine protease autotransporters of Enterobacteriaceae (SPATEs): Biogenesis and function. Toxins. 2010; 2: 1179–1206. PubMed Abstract | Publisher Full Text | Free Full Text\n\nClark K, Karsch-Mizrachi I, Lipman DJ, et al.: Genbank. Nucleic Acids Res. 2016; 44: D67–D72. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Nederveen VA, Johnson YS, Soc A, et al.: SepA biofilm paper. Figshare. 2024. Publisher Full Text\n\nNavarro-García F, Ruiz-Perez F, Cataldi Á, et al.: Type VI secretion system in pathogenic Escherichia coli: Structure, role in virulence, and acquisition. Front. Microbiol. 2019; 10: 1965. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRose RE: The nucleotide sequence of pACYC177. Nucleic Acids Res. 1988; 16: 356. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChang AC, Cohen SN: Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 1978; 134: 1141–1156. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBayer AS, Kupferwasser LI, Brown MH, et al.: Low-level resistance of Staphylococcus aureus to thrombin-induced platelet microbicidal protein 1 in vitro associated with qacA gene carriage is independent of multidrug efflux pump activity. Antimicrob. Agents Chemother. 2006; 50: 2448–2454. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMelton-Celsa A, Van Nederveen V: Raw_data_paper_1.xlsx. figshare. [Dataset]. 2024. Publisher Full Text\n\nMelton-Celsa A, Van Nederveen V: Figure 6 RAW Western blot for SepA in supernatant.tif. figshare. Figure. 2024. Publisher Full Text\n\nMelton-Celsa A, Van Nederveen V: SepA-Biofilm-Photos.zip. figshare. Figure. 2024. Publisher Full Text\n\nMelton-Celsa A, Van Nederveen V: Figure 17 RAW Western blot of pACYC177sepA.tif. figshare. Figure. 2024. Publisher Full Text"
}
|
[
{
"id": "298619",
"date": "24 Jul 2024",
"name": "Ikechukwu Moses",
"expertise": [
"Reviewer Expertise Microbiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comment: This study describes the impact of sepA gene in biofilm formation and biofilm staining in vitro. Authors demonstrated that the deletion of sepA causes elevated biofilm formation in EAEC strains, but that the increased biofilm staining is not directly due to the loss of SepA. This research work is interesting as it attempted to describe the actual function of sepA gene, especially with regards to biofilm formation. The manuscript was well-written; however, I have some major reservations as shown in my comments below:\nComment 1: Biofilm formation is a complex process which involves different arrays of genes (lasR, lecA, pelA, amongst others) and even operons. Authors indicated that four out of six mutant EAEC strains exhibited increased biofilm staining when sepA was deleted without investigating why the two mutant EAEC strains with deleted sepA genes were different because these two mutant EAEC strains exhibited the same biofilm staining property similar to the wild-type (wt) parent strain as they didn’t show any form of increased biofilm staining from the results. So, the results of this study is not definite as there is no uniformity in the aftermath of sepA deletion with regards to enhanced biofilm staining activity. I strongly believe that for this to be concrete, more isolates with sepA need to be included. Additionally, some hypotheses could have been tested such as possibly sequencing all the sepA genes in all the 6 tested EAEC strains to know if there are mutations in their gene sequences. A variation in sepA gene sequences of the EAEC strains could possibly point towards the biofilm expression level of this gene before its deletion. A qPCR could have been very helpful in understanding the expression level of sepA gene in all the 6 EAEC strains that were tested before their deletion.\nComment 2: Authors in their study demonstrated that deletion of sepA causes elevated biofilm formation in some EAEC strains, but that the increased biofilm staining is not directly due to the loss of SepA. Yes, many other factors are involved in biofilm formation but since this study is focused solely on sepA gene, I feel that authors need to show or explain the possible reason while the other two mutant strains did not exhibit increased biofilm staining when sepA gene was deleted.\nComment 3: Authors cited in the manuscript that sepA is involved in diarrhoea cases or strongly associated with diarrhoeal cases. They also indicated that 23% of the strains positive for AAF were positive for sepA. This does not mean that sepA is strongly involved in biofilm formation. Authors showed some good work in demonstrating the correlation of sepA deletion and biofilm staining; however, results shown from their work does not indicate completeness of what they hypothesized as some tested strains with deleted sepA gene showed contrary results to other strains with the same deleted sepA gene. More investigations with regards to this need to be done in order to have a definitive idea of the actual function of sepA.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "323265",
"date": "09 Oct 2024",
"name": "Jean-Philippe Côté",
"expertise": [
"Reviewer Expertise Gram-negative bacteria",
"antibiotic resistance",
"secretion systems"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript describes the role of SepA in biofilm formation of some EAEC strains. The authors observed that the deletion of sepA in some EAEC leads to increased biofilm in a crystal violet staining biofilm assay, but that this elevated crystal violet staining is not correlated with the presence of SepA as complementations or the addition of SepA in trans do not reduce the staining. However, when analyzing biofilms using microscopy of CFU counts, the deletion of sepA did not increase biofilm. While the initial observation is interesting, I think more work is needed to support the conclusions of the manuscript.\nOverall, the results show that the deletion of sepA increases crystal violet staining in a biofilm assay, and that, as the authors suggest, this phenotype is not dependent on SepA. The results suggest that the deletion of sepA affects something else on the pAA plasmid that is responsible for the observed phenotype.\nSpecific comments:\n1- In fig 1, the variability of the biofilm assay is very big; for K261 strain for instance, some replicates didn’t form biofilms while the OD590 is >2 for other replicates. Are there any reasons that explain this variability in the assay? I think it is important because other assays to probe biofilms (microscopy, CFUs) did not give the same results and because in the ∆sepA, it seems to be more homogenous. So, in microscopy and CFU experiments with K261, were the biofilms observed with the ~0 OD590 biofilm replicate or with the ~2 OD590 biofilm replicate? It is also worth noting that in Fig. 1, K261 forms on average more biofilms that P433, while the microscopy images suggest the opposite. Are the microscopy images really representative of the biofilm formation assay? I understand that the crystal violet and microscopy were done in different plates (96-well plates vs 24-well plates), is this the reason for the difference? From looking at Fig.1 and Fig.7, it seems that the sepA effect is on crystal violet staining, but not really on biofilm formation. I would revisit the microscopy experiment to explain why the difference in phenotype between the assays.\nThe observation that the sepA mutants results in cells that are more spread is interesting, and most likely not associated with the increased crystal violet staining (as it is observed for K261 and P433). Do the complementations restore the WT phenotype under the microscope?\n2- On the conclusion to figure 1, the text states : ‘These results suggested that SepA may only affect the biofilm of some agg4A-positive strains.’ More strains need to be tested before making this conclusion, as 2/4 agg4A strain showed the effect while only one strain of aggA+ and agg5A+ is not enough to be representative.\n3- Modify figure 3. A regression is not suited to analyze only two time points. A bar graph is sufficient and more appropriate to show that the same effect can be observed at 5h and 20h.\n4- Why show normalized data in figure 4? Because of the variability of the assay, it is difficult to compare with results in figure 1. Please also show the raw values. Figure 4 also needs to be more precise as to which samples were done in 5h and which in 8h.\n5- In the paragraph describing the results showing that pAA is responsible for the effect, it states that : ‘We also found that sepA alone or ΔsepA::cat alone did not confer the capacity to form a biofilm on HSNalR (data not shown).’ 1- This results should be shown as it supports the conclusion that the target of SepA is on pAA. 2- I am not sure what ‘ΔsepA::cat alone’ means. Please provide more details.\n6- I appreciate the efforts to find a potential target for SepA in figure 10, but I think the double deletion approach is the right one. In addition, if SepA cleaves a target, the exogenous addition of SepA should complement the phenotype, as you tried. Have you considered the possibility that the deletion has another effect, since it does not complement? The fact that the ‘revertant’ does not complement might actually suggest this; as I understand, the revertant possess a kanamycin resistance cassette – so it complements the production of SepA (although WB would be required to see if this is true), but it does not ‘recreate’ the sepA genomic context.\n7- Figure 14 is confusing. I am not sure why the different colors or shapes used. Please describe what they mean.\n8- Results from figure 14 use an interesting approach with an inactivated mutant of SepA. However, the supernatant assay does not complement the loss of sepA. Have you tried to replace sepA from K261 for this inactivated mutant? This would represent a good control to explore the mechanism for the increased crystal violet staining, but for this to work the revertant needs to be able to complement.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-562
|
https://f1000research.com/articles/12-687/v1
|
16 Jun 23
|
{
"type": "Research Article",
"title": "Development and evaluation of prevention bundle for neonatal healthcare-associated infections: an interventional study",
"authors": [
"Usha Rani",
"Leslie E Lewis",
"Kiran Chawla",
"Anup Naha",
"Praveen Kumar",
"Usha Rani",
"Kiran Chawla",
"Anup Naha",
"Praveen Kumar"
],
"abstract": "Background: Neonatal healthcare-associated infection (HAI) globally is the leading preventable cause of neonatal mortality. Neonatal mortality in India is also very high. Considering that HAIs can be prevented globally, there are disparities in resources; the current study aimed at developing locally feasible and effective prevention bundles for neonatal HAIs. Methods: A mixed-method study was conducted at one tertiary care teaching hospital's level IV Neonatal Intensive Care Unit. The study explores the causes of neonatal HAIs, current processes, benchmark practices, gaps in current practices with HAIs, root-cause analysis and system process mapping, and failure mode effect analysis. Observations, interviews, brainstorming activities, and a survey were conducted. Written and audio-video recorded prevention bundle was developed and implemented using a quasi-experimental study design. Results: Process standardisation, healthcare worker training, hand hygiene practices, nursing care process and vascular access process were identified as key improvement areas to prevent neonatal HAIs. Out of eighteen identified processes, three processes were standardised. All the healthcare providers were trained at three-time intervals of three months each. After implementing the prevention bundle, there was a significant decline in the rate of HAIs, reducing it from 9.6 to 7.0 per 100 admissions >48 hours. The bacteraemia rate fell from 5.2 per 1000 patient days to 2.6 per 1000 patient days and was statistically significant on a two-tailed student t-test with 95% CI with p-value=0.00073. Conclusions: Our developed prevention bundle for neonatal HAIs was significantly effective and reproducible for healthcare workers' training and development. Considering variations in global infection control practices and resources constraint, it is effective to develop a local prevention bundle for neonatal HAIs.",
"keywords": [
"healthcare-associated infections",
"mixed-method",
"nosocomial",
"prevention",
"neonate"
],
"content": "Introduction\n\nGlobally 2.5 million neonatal mortalities were recorded in 2017, accounting for 47% of all under-five mortality that has increased by 7% in 27 years.1 More than 1/3rd of neonatal mortality is due to preventable neonatal infections.2\n\nAttention has been paid to reduce the neonatal mortality rate to the minimum however, many countries have failed to do so despite putting in a lot of effort. Efforts have been made not only from each country but also from the United Nations Children’s Fund (UNICEF), the World Health Organization (WHO) and various other non-profit organizations. The average neonatal mortality rate has reduced from 85.2 in 1969 to 22.7 in the year 2018 where the lowest motility rate in 1969 was 78.7 and the highest was 92.2 in contrast to 2018 it was 20.1 and 35.3 respectively.3 The neonatal mortality rate is expressed per thousand live birth within the first 28 days of life. As per the country-wise estimation, the lowest neonatal mortality rate reported in 2018 was 0.9 in Japan and San Marino, and the highest was 42 in Pakistan per thousand live births around the globe.3\n\nThe literature reports high neonatal healthcare-associated infections (HAIs) in India that range from 8% to 36.3%, however, the unreported number may differ from the reported.4–7 The HAIs can contribute up to 30% mortality that can be prevented if timely appropriate measures are adopted.8\n\nA prevention bundle is a structure of three to five systematic activities of care developed scientifically, that when implemented together should bring down the rate of HAIs.9 The concept of ‘bundles’ is developed by the Institute of Healthcare Improvements to help the healthcare providers, so they can deliver the best possible care to patients undergoing treatment with high risk.10,11 Development of prevention bundle involves science focusing on the method of execution as it describes how to deliver the best care. A bundle is a package of tools improving habits and critical process with clear parameters.10,12\n\nAccording to a publication in 2013 by the International Nosocomial Infection Control Consortium, development, implementation and adherence to neonatal HAIs prevention bundle can reduce up to 54% HAIs and up to 58% reduction in related mortality.13 Healthcare-associated infections (HAIs) are always a threat to healthcare providers and the patient. Various preventive measures are proposed by many researchers around the globe to prevent HAIs. The neonatal population is most vulnerable and susceptible to get HAIs. The majority of preventable practices are reported, tried, and tested in developed countries on the adult population and limited among neonates.\n\nA report by the World Health Organization (WHO) published in 2011 reported that the surveillance system for healthcare-associated infections in high-income countries is capturing the rate of HAIs but its existence in low and middle-income countries is scanty.14,15\n\nPreventive measures for neonatal HAIs: A prevention bundle developed by ‘International Nosocomial Infection Control Consortium’ for Ventilator Associated Pneumoniae (VAP) in the neonatal population has been reported in 2012, however, no prevention bundle for other types of infections has been reported for the neonatal population.16 Since the increase in the amount of published literature related to the prevention of HAIs is increasing, it becomes difficult for a healthcare provider to decide which practice to follow in neonatal intensive care unit considering the limited availability of resources. Neonatal mortality in India is primarily due to intrapartum related complications, sepsis, meningitis, pneumonia, congenital abnormalities, and other neonatal disorders in chronological order.8\n\nA healthcare worker can try to practice cluster care for maximum possible invasive and non-invasive procedures that might help to reduce the contact frequency with neonate.17 Clustered care can be practised for delivery of medication, withdrawal of blood sample for investigation, providing routine nursing care to the neonate and any suctioning if required. Supervision and surveillance while securing intravenous line, preparation and delivery of medications might also be beneficial to reduce bloodstream infections.18\n\nAs per the guidelines of Centers for Disease Control and Prevention (CDC) and WHO active surveillance is required to identify the source of infection. Various preventive measures are proposed by many researchers around the globe to prevent HAIs.14,19 The neonatal population is most vulnerable and susceptible to getting HAIs. Compared with adults and paediatrics, neonates are more vulnerable to acquiring infection. The prevention bundle is available for the adult population and modification of the same prevention bundle is practised for Paediatrics and neonates in some countries.\n\nCare of Intravenous (IV) Lines: Blood Stream Infection: The prevention of BSI involves bundled approaches as hand hygiene, scrubbing the outer surface of catheter hub by using 2% chlorhexidine in 70% isopropyl alcohol, use of standard precautions, changing the catheter dressing if soiled.20\n\nCentral Line-Associated Blood Stream Infections (CLABSI):The prevention of CLABSI is by following aseptic techniques while inserting central venous catheters, avoiding the femoral site and removing the unnecessary catheters which are present.21 Skin preparation using all aseptic measures and daily assessment of the catheter site is vital.22 Central lines should be removed as early as possible if they are not needed.23,24\n\nCatheter-related bloodstream infections (CRBSI): In the case of neonates the prevention of CRBSI is by various practices such as hand hygiene before and after patient contact, using gloves for all invasive procedures, following standardized procedures, educating the HCWs regarding infection control measures,25,26 surveillance of NICU, disinfecting the site of insertion, and strict aseptic precautions are taken while inserting the catheter.21 A sterile gauze is covered over the three-way stopcocks and should be accessed by using sterile gloves27 but the use of a three-way stopcock is not much appreciated now. All vascular hubs needleless connectors and injection ports must be disinfected using either 70% alcohol or 4% chlorhexidine solution before the access can help in the reduction of BSI,28 catheter hub care should be demonstrated and practised regularly and the catheter dressing should be changed when it is soiled.29\n\nDevelopment of guidelines: Standardized guidelines are developed for the infection control practices by which the infection rates are reduced for neonates. These practices include handwashing, infant handling, use of gloves, care of intravenous lines, handling of three-way-stopcock and endotracheal tube suctioning.\n\nConsidering the limitation of the information, the economy of a country and available resources implementing preventable measures becomes a challenge. There are various infection control practices with evidence reported. It is the hospital infection control team that decides which practice to follow in their respective ICU. There is variability in thinking, approach, limiting resources and various other factors, no two-healthcare facility can adapt similar prevention approach. The majority of preventable practices are reported, tried, and tested in developed countries on the adult population and limited among neonates.30–32 There is an increase in the number of published literature related to the prevention of HAIs in the adult population, it becomes difficult for a healthcare provider to decide which practice to follow in neonatal intensive care unit considering the limited availability of resources.\n\nThere is a dearth of literature from developing nations on the adoption of available solutions to practice and care bundles to prevent neonatal HAIs. Implementation of care bundles adopted by developed nations to prevent HAIs adds costs to healthcare and the patient. Identifying the domestic concerns causing neonatal HAIs and finding solutions to prevent neonatal HAIs with minimal cost burden needs further research.\n\nResearch using NICU system process mapping to explore the potential contributors and eliminate them to prevent HAIs is not explored. There is a scarcity of scientific research on standardizing the process for vascular access and maintenance, nursing care and emergency handling targeting to prevent neonatal HAIs while delivering the standard of care. Identifying and standardizing the potential critical steps of care processes to prevent neonatal HAIs might help healthcare professionals upgrade their practices while delivering care to neonates and reduce the domestic rates of HAIs. The current study was carried out to develop and evaluate prevention bundles for neonatal healthcare-associated infections (HAIs).\n\n\nMethods\n\nThis is a mixed method study combining the results obtained through qualitative and quantitative studies. The study was carried out in a level IV Neonatal Intensive Care Unit (NICU) at a tertiary care teaching hospital located in coastal Karnataka, India from December 2016 to July 2020. To develop the prevention bundle, we needed to identify the factors contributing to neonatal HAIs33; we did root cause analysis,34 identifying the failure mode and effect analysis35,36 followed by system process mapping.37 Once we identified the system and its process contributing to HAIs, we observed in other benchmark hospitals38 the policy, practices and process to prevent neonates from HAIs also carried out a review on the prevention practices. The prevention bundle was developed as the standard processes39–41 and to implement the bundles we needed to train the healthcare provider providing direct care to the neonate. Audio-video recording, process flow, various levels of workstations as training method to deliver the behaviour and practice change was selected. Pre and Post training knowledge assessment was also carried out using a validated closed ended questionnaire.\n\nRoot cause analysis: Interview and brainstorming of healthcare workers for root-cause analysis was carried out as qualitative component. The healthcare workers providing direct care to the neonates were retrospectively interviewed using an open-ended questionnaire to find the causes leading to neonatal HAIs. Such interviews were conducted until the saturation of responses was met. Eighty different healthcare workers were interviewed to find the mechanism of spread of infection on open-ended questions in this process, until we reached to saturation of responses and similar responses were provided. The periodicity of responses were listed under six cause headings as per Ishikawa42 i.e. A) Men, B) Material, C) Method/Process, D) Machine/Equipment, E) Environment, F) Policy.\n\nThe Ishikawa diagram, a diagrammatic representation of the root cause analysis was developed where the sources of infection were categorized under six domains.43,44 Later it was recorded and tabulated to obtain descriptive statistics. Based on the periodicity of reporting of the contributor reporting was done through Pareto's chart.45 Pareto's chart was able to highlight the significant contributors that cause HAIs among neonates. A graphical expression of the contributors to the existing problem highlighting the important ones to target was used. In Pareto’s chart, no categorisation was used, however, the contributors with <5% of reporting frequency were summarised together. The top 20% of contributors identified in Pareto’s chart were considered significant to neonatal HAIs. These contributors were taken up further as input to the development of the prevention bundle.\n\nThe average score and standard deviation table were developed on major contributors reported during brainstorming and survey. Experiences of healthcare workers were reported using the box plot due to outliers.\n\nHospital Infection Control Committee’s (HICC) surveillance: Surveillance reports were collected periodically from the air samples from NICU’s environment every three months of the year. The results of these samples were collected from the nurse in charge of NICU. There were two episodes of the suspected outbreak during the study when swab samples from the environment of a few of the neonates clinically acquiring HAIs were captured to identify the contributors. These swab samples were from the cradle side, surface swab, water sample, swab from feeding pallada, and equipment was collected directly by HICC members. The samples were analysed in the central microbiology lab and reports were submitted to NICU. As the official report arrived from a laboratory, the researcher noted the report's results and took it as probable contributors to neonatal HAIs. These contributors were considered critical to preventing HAIs and ensured improvisation through a review of literature for inclusion in the prevention bundle.\n\nSystem process mapping through observation: The prospective regular random observations were done for the process and techniques used to provide the neonate care. The researcher followed procedural steps from the beginning until the end of the procedure and observations were marked against the checklist, prepared by the researcher, clinician and nursing staff of NICU, considering the standard steps to be followed during a procedure. These checklists were not given to the healthcare workers for marking. After the completion of the observations, the record used was entered in the checklist and on the Excel datasheet. The checklist based on the process are available under Extended data.69\n\nThe time selected for observations was morning care time at 07:30 am; clinician’s clinical round time at 09:30 am and 3:00 pm; blood sample collection time at noon; invasive routine procedure time at 02:00 pm; medication/total parenteral nutrition preparation time at 03:30 pm; shift hand overtime at 07:30 pm. Various invasive and non-invasive procedures, care of the neonates and environment cleaning processes were focused during these random observations.\n\nThese observations were summarised in frequency and percentage under four categories in tabular format. The top 20% of frequent observations were considered as ‘scope for improvement’ for the prevention bundle development.46\n\nA survey on knowledge and practice assessment on hand hygiene practices among healthcare workers in NICU was also captured, analysed and reported, and is published in peer reviewed journal.47 The observations on hand hygiene were classified under three categories i.e. a) time duration for hand hygiene practices, b) opportunities for hand hygiene before the procedures or activity and c) hand hygiene practice after the procedure or activity. Data collection forms for both survey and observation are available under Extended data.69\n\nFailure effect mode analysis (FEMA): FEMA was done on critical contributors identified through brainstorming, observation and system process mapping with the help of eight senior nurses and two clinicians.\n\nWe also performed FEMA on 21 identified processes that helped us in identifying the key steps that if missed or overlooked could lead to HAIs also it helped us to add and delete some of the steps that were carrying no value to the process. FEMA helped us to identify the critical key steps to be added to the process with more emphasis. FEMA was done on various steps in the care process that helped to find the critical 20% steps to focus on during the preparation of prevention care bundle however, many other activities scored <240 risk propensity number (RPN), and were not reported.\n\nVisit to benchmark NICUs in state: Study visits to three different NICUs located in distant hospitals setting infection control policies were made. Observations, open ended interviews of healthcare workers and the study of infection control policies were recorded for each NICU. The findings were compared and presented to stakeholders at the study setting to find the best practices.\n\nBased on the findings of all the observations, root cause analysis, process mapping, FEMA and observations at other NICUs the critical steps in the processes and the critical processes were identified. It was decided to develop standard care process for routine critical activities as a prevention bundle.\n\nDevelopment of the prevention bundle: We carried out three rounds of brainstorming meetings with clinicians, microbiologists and nursing staff to formulate a feasible prevention bundle. The presentations on root-cause analysis, observations, and processes were made available through email at least a week prior to the meeting and a presentation was delivered before the meeting.\n\nFour clinicians were identified from the NICU including two senior (minimum 10 years of experience in NICU) and two junior clinicians (minimum 2 years of experience in NICU), they were also given an open-ended questionnaire with the developed process to identify the lacunae and improvise the process.\n\nEach meeting was of a minimum one-hour duration, clinicians were allowed to review each process for one week to provide their critical inputs. The inputs of all the healthcare workers involved in these activities were presented to experts’ i.e. senior neonatologist, senior microbiologist, three senior staff nurse and management representatives (Figure 1). Their inputs were documented and were considered further for the design of the prevention bundle.\n\nEach process had Input, Process and Outcome as suggested by Dr Donabedian.48 Any surgical, equipment or manpower required to initiate and complete the process was considered under the input (mentioned within the process); the steps involved to carry out the task were arranged in sequential order in process, and the neonates benefiting were considered as an outcome of the process.\n\nAs the experts' suggestions were to combine the developed processes into two to three processes, the researcher finally prepared three processes after repeating four consultations with each clinician (four) and nurses (ten) that lasted for three months. The final three processes were identified as: A) Nursing care Process; B) Vascular access process and C) Cardiopulmonary resuscitation management process.\n\nAs per the experts' policy suggestions, do’s and don’ts and surveillance charts for NICU were also prepared in the supplement to the prevention bundle.\n\nDevelopment of educational module to implement prevention bundle: The developed three processes were further taken up for audio-video and computer added presentation development. Three senior staff nurses were identified and trained for the process by the researcher. These nurses carried out all the steps of the process as per the instructions on a newborn mannequin in NICU on the cradle. Step by step each task was recorded for two procedure bundles: The nursing care process and the vascular access process. Audio-video recording was carried out during the day shift and three to four shots were taken for each task.\n\nThe raw video clips were edited in Windows Movie Maker ver 6.0 with background music obtained from licence free music library in YouTube. A due acknowledgement for the music source was given to the developer and source at the end of the video. The required audio clip was inserted and the length of the movie trimmed from 75 minutes to 15 minutes. Due acknowledgement was given to the video contributors. Final processing was completed in four months. A total of two videos, on the nursing care process and vascular access process was developed.\n\nPolicy document: This was prepared based on a review of the literature and the observations carried out at other healthcare facilities. The policy document included the incorporation of the initiative suggested during the brainstorming exercise and facilitated session. For the development of these policy documents, senior clinicians, a microbiologist, pharmacy expert and five nurses with a minimum of 5 years experience were involved. Prior to the discussion and meeting a draft policy was prepared which was communicated through email, feedback, suggestions and discussion until all agreed to the policy document. These policy documents can be found under Extended data.69\n\nDo’s and Don’ts: These rules were prepared based on the observations carried out at the study setting and other hospitals, review,49,50 and the brainstorming exercise with healthcare professionals. Three interviews with the nurse manager and nurse in charge were carried out to make the changes according to the feasibility of carrying out tasks. Meeting and discussion with respiratory therapist staff were carried out to validate the content of the list. Final corrections, validation, and approval were taken from senior neonatology consultants, senior microbiologists, and their team before the study was adopted. The agreement of senior healthcare professionals that includes clinicians, nurses and HICC was sought. These rules were presented to senior nurses, clinicians and respiratory therapists for content validation. It took five rounds of changes during content validation. These documents can be found under Extended data.69\n\nSurveillance charts: The surveillance charts were developed based on the recommendations sought in the review of literature, the observations on practices at other hospitals and recommendations of the senior clinicians. These surveillance charts were presented for three rounds for content validation to nurses and clinicians.\n\nDesigning of assessment tools for pre and post-intervention: Ten multiple-choice and closed-ended questionnaires were developed for nurses and medical postgraduate students based on the identified processes and steps. Senior clinicians validated the questions (three) for their content validity and face validity. Internal consistency for the first set of questions was calculated with 15 samples of healthcare providers and cronbach's alpha was 0.812 for these questions.\n\nAt each intervention phase, the set of questions administered were different however the intent and purpose of those questions were the same only the language and phrases differ each time and internal consistency with cronbach's alpha was maintained above 0.75, where 15 healthcare providers helped in reviewing and answering these questions for validation. The respondents gave consent only at the beginning of the intervention, however, fifteen nurses were replaced by other staff at the middle of the intervention phase. The researcher included them from the next phase of intervention and took their written consent before the intervention. We anticipate the variation in the result due to these change of nurses in between the interventions. Still, no effort was made to adjust the findings for such variations and results were reported without any modifications considering the real time situations without any interventions.\n\nThe answers were evaluated for their correctness and a score of 1 was given to each correct answer whereas the wrong answer did not get any point. The summary of answer scores was prepared and reported as mean ± SD for each time the training was provided. A difference in mean and SD was computed to find the average change in pre and post-training. Students paired t-test with 95% CI at p-value fixed at <0.05 was considered a significant change in knowledge scores.\n\n\nImplementation of the prevention bundle and assessing its effectiveness\n\nA quasi-experimental study design was adopted where three rounds of training to healthcare providers was provided to attain the behavioural modification and adoption to the design practices/process.\n\nThese experimental training were carried out in three training phases.\n\nIn training phase I, the training was divided into two stages: implementation of the nursing care process bundle and implementation of vascular access process bundle along with cardiopulmonary resuscitation management process.\n\nThe first stage of the experiment began after finalizing the date and week with the nurse manager when all the nurses can be asked to be present to attend training. The stage was divided into two parts for the ease of implementation and considering optimal time for the training effectiveness to achieve. Daily post morning shift change at 02:00 pm all the nurses approximate 7-10 in numbers but occasionally 3-4 reaches to the training room.\n\nOne-hour video-based training was conducted for the consented participants. A pre-test was followed by a video show of the procedure. The researcher actively narrated and discussed each step. Concerns and queries of the participants were addressed instantly before continuing further. After active discussion, a post-test was conducted followed by due gratitude to their participation and request for their cooperation and support in the prevention of neonatal HAIs.\n\nThe second stage of training was given on the vascular access process to the healthcare providers. One-hour video-based training was conducted for the consented participants. A pre-test was followed by a video presentation of the procedure. The researcher actively narrated and discussed each step. Concerns and queries of the participants were addressed instantly before continuing further. After active discussion, a post-test was conducted followed by due gratitude to their participation and request for their cooperation and support in the prevention of neonatal HAIs.\n\nParticipants were also briefed on the cardiopulmonary resuscitation management process using the flow chart. Participants were briefed on the do's and don’ts. A post-test was conducted followed by due gratitude to their participation and request for their cooperation and support in the prevention of neonatal HAIs.\n\nA total of 49 and 48 nurses were trained in both areas respectively. We excluded 5 and 6 nurses respectively as three nurses were part of the development of the training module and others were on long term leave of more than 30 days.\n\nTraining to five respiratory therapists was given on do's and don'ts and cardiopulmonary rehabilitation management process using a flow chart. For them also pre and post-training evaluation was carried out.\n\n5 medical postgraduates were trained using role-play and simulation models along with video teaching aids only on vascular access process, cardiopulmonary rehabilitation process and do's and don'ts. The stimulation and role-play included sterile gowning and sterile gloves donning after surgical handwashing practices that were monitored. During monitoring of the healthcare providers, any deviation or wrong practice if found was corrected followed by carrying out the procedure again in a standard manner.\n\nA review meeting was carried out with the hospital infection control committee (HICC) where the problem statement and its mitigation plan was discussed regarding preventing cross-infection and environmental changes. The review committee agreed to certain environmental changes which were:\n\nNotice at shoe rack area to separate and place street shoe and NICU sleepers in respective racks; Prefilled hand sanitiser and notice to use it before entering to NICU premises. Separation of two different rack positions i.e. street footwear and NICU footwear, placement of hand sanitiser at the door inside to NICU to ease monitoring of hand hygiene practices.\n\nSegregation and labelling of weighing machine as “Only for neonatal weight record” and “Use for diaper weight”. Removal of tissue paper roll for hand drying purpose. AMBU (Air Mask Bag Unit) bag replacement at every 72 hours of use.\n\nOther changes that were requested but could not be implemented due to unavoidable factors were: Separate trolley for invasive procedures at Inborn and Out born area, the indent of fresh AMBU bags to replace AMBU bag every 72 hours.\n\nThe training phase II was one stage and was on implementing the nursing care process bundle and the vascular access process bundle along with the cardiopulmonary resuscitation management process.\n\nAfter finalizing the date and week with nurse manager when all the nurses can be asked to be present to attend training, the dates were fixed to the third week of December 2019. This time a little variation in the training approach was practised where the simulation stations were prepared and the participants were called to practice and show the learning. The corrections in practice were made at the simulation station only. There were five simulation stations, and these were:\n\na) Handwashing station\n\nb) Medication preparation stations\n\nc) Vascular catheter insertion station\n\nd) Medication delivery station and\n\ne) Neonatal routine care station\n\nEach training time was generally scheduled from 1:00 pm to 02:30 and on two days was scheduled at 09:00 pm to 10:00 pm; two senior nurses were identified and sought for their help in implementing the training. These senior nurses had >10 years of experience in NICU and were also trained and briefed on their role at the station before beginning the training. Each participant was welcomed and gave a pre-test in written format. The consent was obtained only from those who were new to the training. After the pre-test, the participant was shown a video with oral narrations and descriptions by the researcher for 20 min duration. If any doubt arises in the middle of the video, it was discussed by pausing the video and then proceeded further. Comments, queries and discussions of the nurses were welcomed and encouraged during the presentation.\n\nAt each training day, three teams were formed among the participants. Post presentation the three groups were taken on three stations where the researcher and the senior nurse helper demonstrated the process and then assessed each participant while they demonstrated the practices. Correction in the practice if any deviation was found were made immediately at the station, and all the queries were resolved that were raised during a demonstration by the researcher. Each team practised and demonstrated their process at all the five stations. Participants were also briefed on cardiopulmonary resuscitation management process using the flow chart. Do’s and don’ts were briefed and handed over to each participant.\n\nPost video and stimulation presentation each participant was given a written post-test to answer. The researcher thanked each participant and requested their cooperation and support in the prevention of the neonatal HAIs. In this stage, a total of 46 nurses were trained. We excluded eight nurses as three nurses were part of the development of the training module; three were utilized in training and others were on long term leave of more than 30 days.\n\nTraining for five respiratory therapists was given on Do’s and Don’ts and cardiopulmonary rehabilitation management process using a flow chart. For them, also pre and post-training evaluation was carried out.\n\nThe 5 medical postgraduates were trained using role-play and a stimulation model along with video teaching aids only on vascular access process, cardiopulmonary rehabilitation process and Do’s and don’ts. The stimulation and role-play included sterile gowning and sterile gloves donning after surgical handwashing practices that were monitored. During monitoring of all the healthcare providers, any deviation or wrong practice was corrected there itself, followed by carrying out the procedure again in a standard manner.\n\nPhase III was one stage and was only on implementing the nursing care process bundle and the vascular access process bundle along with the cardiopulmonary resuscitation management process.\n\nAfter finalising the date and week with the nurse manager, when all the nurses will be able to be present to attend training, the dates were fixed. This time a little variation in the training approach was practised; we identified seven nurse leaders with >5 years of experience, each nurse leader could choose any six nurses from their shift team to train further. The simulation stations were prepared, and the participants were called to practice and show the learning. The corrections in the practice were made at the simulation station only. There were two simulation stations and these were: Medication preparation stations; and vascular catheter insertion station.\n\nThe training time was scheduled as per the convenience of these senior nurses. The nurse assessed the handwashing, medication delivery, and neonatal routine care in real-time while providing the care to the neonate. The researcher trained each team leader and briefed on the training protocol with a pre and post-assessment questionnaire. Two to three staff nurses were welcomed to participant for pre-test and were trained by team leader each day completing their assigned six nurses in 3 to 6 days duration depending upon their shift duty. A video with oral narrations and explanation by the team lead for 10 minute duration was delivered. The nurses' comments, queries, and discussions were welcomed and encouraged during the presentation and resolved before moving further.\n\nThe team lead demonstrated the process and then assessed each participant while they demonstrated the practices at workstations. If found, corrections in the practice were made immediately at the station and the team leader resolved all the queries. Each team practised and demonstrated the process at two stations. Participants were also briefed on the cardiopulmonary resuscitation management process using the flow chart followed by do’s and don’ts in NICU.\n\nPost video and stimulation presentation each participant was given a written post-test to answer. The team leader thanked each participant and requested their cooperation and support in the prevention of neonatal HAIs.\n\nIn this stage, 40 nurses were trained. We excluded 12 nurses as three nurses were part of the development of the training module, seven were utilized in training, and others were on long-term leave of more than 30 days.\n\nTraining to respiratory therapists and medical postgraduates could not be carried out at this phase due to the complete lock-down of the country owing to the surge of COVID-19 and as directed by the Institutional Ethics Committee. However, the prevalence of neonatal HAIs was captured until the completion of three months.\n\nCategorical variables were reported using descriptive statistics, a time series graph was used for reporting changes in HAIs. Paired students T-test was performed on findings of the pre and post training.\n\nWritten consent from all the participants of training were obtained before the training. They were informed that the data will be used for academic and research purposes. In no way would their personal information be disclosed or identity revealed either in the final report, publication or anywhere. Confidentiality will be maintained at all times, and privacy is respected. Institutional Ethics Committee (IEC) approval was taken, approval ID: MUEC/014/2016-17. CTRI (Clinical Trial Registry India) registration was done before starting the project, the confirmation ID was: CTRI/2017/08/009538.\n\n\nResults & discussion\n\nHealthcare workers were interviewed on an open-ended written questionnaire, a total of 80 healthcare workers participated, and the majority of them were staff nurses with more than two years of experience (88%). Healthcare workers were identified as major contributors for HAIs (Table 1).\n\n* The score was based on the response rate and ranking of each variable by healthcare provides during root cause analysis where rank 1 = least contributor and rank order 5 = highly contributing to HAIs.\n\n*Skewed data, hence, mean +/- SD cannot be reported.\n\nThe ranking of the contributors to HAIs by these healthcare workers showed that prime contributors are healthcare workers (27%), followed by equipment (21%), material (21%), process/protocol (19%), and last is infrastructure (12%). Detailed root-cause analysis and multiple observations showed that non-compliance to handwashing practices, equipment disinfection/cleaning, IV line insertion, many invasive procedures, and improper aseptic techniques (>50%) are prime contributors causing HAIs among neonates.\n\nAs the number and variation in responses of healthcare workers were very high the Ishikawa diagram was plotted to find any inference out of the responses (Figure 2). To simplify further, the causes were ranked ordered on a scale of 1-5 by healthcare providers that helped for further analysis of responses in the form of Pareto’s chart (Figure 3). As per the rank order the hand hygiene practices (87%), improper aseptic procedures (83%), improper handling of venous line (57%) and unable to provide timely isolation to sick/infected neonates (53%) were highlighted (Figure 3).\n\nObservations against a checklist to find causes of HAIs in NICU\n\nPhysical observations for 248 days and 1761 various infection control opportunities at the study site was made (Table 2) and forty interviews on twenty-five variables were carried out for healthcare workers at NICU. The observations were carried out on the following practices: a) hand hygiene practices, b) care of intubated and ventilated patients, c) intubation process and ET (Endotracheal tube) suctioning, d) care of NIV (Non-invasive ventilation) patients (Oral suction and fixing of the nasal mask), e) insertion and care practice of PICC (Peripherally inserted central catheter) line, central line, umbilical line, arterial line and IV lines, f) practices on infant feeding g) cleaning and care practices at NICU, h) daily clinical rounds, I) medication preparation, sample collection, and blood transfusion practices\n\nThere were two occasions when HICC collected the environment sample for the identification of microorganisms. In its first occasion, only air samples were collected at different parts of the NICU that did not grow any microorganism on culture. On the second occasion, the swab samples were collected from various environments of the NICU as well as nasal swabs of healthcare workers.\n\nA total of twelve swab samples, including one drinking water sample, were also sent to the microbiology lab for further analysis. There was a growth of Klebsiella sp. from the hand washbasin and neonatal cradle. The culture grew Serratia marsescens in swab culture of the oral cavity of one patient and feed container, Klebsiella pneumoniae in swab samples of cradle side, and no growth in a drinking watersample. There was no other growth of microorganisms on any of the other samples.\n\nSystem process mapping and FEMA on processes: Multiple observations and interviews of healthcare providers were carried out to identify and understand the processes critical to infection control practices.\n\nWe identified the 21 processes and its process validation with the help of healthcare providers at NICU. We found site cleaning with 4% chlorhexidine, disinfection of IV port before infusion, the sterile container for feed preparation, preparation of medication under laminar flow and strict hand hygiene practices were few critical steps of the processes (Figure 4).\n\nAll the four NICU settings had an average of 80% occupancy and any two to three months per year, the occupancy goes up to 100%.\n\nThe observations were made and compared with existing practices in the study hospital (Table 3). These observations were categorised further under the following headings:\n\nEnvironment-related practices\n\nHuman related practices\n\nPractices/processes\n\nProcess monitoring\n\nMaterial/supply related practices\n\nDevelopment of prevention bundle and training module\n\nPrinted three bundle processes i) Vascular Access and care process ii) Nursing care and iii) cardiopulmonary resuscitation management process were developed. Audio-Video training & hands-on workstation training was also developed as prevention bundle module for healthcare workers to prevent neonatal healthcare association infections.\n\nTwo videos, a PowerPoint presentation, and five hands-on stations were developed as educational modules to implement the prevention bundle.\n\nThere were four individual sets of training given to nursing staff and where there was a change of overall 21% knowledge score (Table 4). Other healthcare workers were given training for only one time due to their unavailability and resistance to participating (Table 5). Housekeeping workers were trained, but their knowledge assessment was not carried out. The prevalent microorganism identified during the interventional period was Klebsiella pneumoniae (41.3%), followed by Acinetobacter baumanii (27.5%). All these microorganisms were identified in blood samples. The rate of HAIs at the beginning of the intervention was 9.6, which at the end of the intervention was noted to be 7.0 as of April 2020 (Figure 5).\n\n* Students paired t-test with CI 95% and level of significance <0.001.\n\n* Students paired t-test with CI 95% and level of significance <0.05.\n\nAt the beginning of the study, we aimed to bring at least a 5% change from the baseline rate of HAIs; the current interventional study was able to bring about a 26% reduction in the rate of HAIs reducing it from 9.6 to 7.0 per 100 admissions >48 hours. The bacteraemia rate fell from 5.2 per 1000 patient days to 2.6 per 1000 patient days and was statistically significant on two-tailed student t-test with 95% CI at p=<0.05 with p-value=0.00073\n\nThe following method was used for the calculation:\n\nOn average, 39 patients would have to receive this prevention bundle (instead of standard care) for one additional patient to prevent from HAIs.\n\n\nDiscussion\n\nAs the number and frequency of observations and root cause analysis were highlighting improper hand hygiene practices as one of the major contributors, further investigation was carried out to find the areas of improvement.\n\nCarrying out observations along with checklists and understanding the knowledge and perception of healthcare workers helps to identify the gap in standard care practices and rectify the same. The similar procedure was followed and found gaps in various steps of hand hygiene practices and gaps in various care practices followed routinely at NICU which was reported in another published article.47 The most frequent observation was not maintaining the hand hygiene practices and unsterile technique of handling IV port or central line port for medication delivery. Maximum observations were around hand hygiene practices and inappropriate unsterile technique of carrying out the procedures.\n\nIn many outbreak investigations, the swab samples grew microorganisms from the washbasin, cradle side and hands of the healthcare workers.51–54 In our study on a swab or sample culture, we found growth of microorganisms on the washbasin, the oral cavity of the patient, sides of the cradle, and feed container. There was no growth on samples obtained from healthcare workers hands, water and air samples of the NICU.\n\nWhen the meaningful compilation of the processes was carried out, we identified eighteen such processes during the Gemba walk including both invasive and non-invasive processes. During process mapping along with processes, activities critical to infection control practices were also identified through observations, review of the literature and brainstorming with healthcare workers. As suggested in the review of the literature and the inputs from the various experts and stakeholders further process improvement flows charts were developed. In infection control practices focus was emphasized on a few tasks to follow but in current prevention bundles, we focused more on the process approach where the complete process was taken as a whole to standardize and provide training.\n\nThe Gemba walk55 is a quality improvement tool that helps in better understanding the process and later standardizing the process. In our prevention bundle, this tool helped us in identifying eighteen processes and then later merging the essential ones and developing the standard three processes. Further improvement on these processes were based on the Donabedian model48 in identifying the inputs to the process, the complete process as a whole and that would lead to the desired outcome i.e. reduction in neonatal HAIs.\n\nThree different multispecialty hospitals located in Karnataka were visited for observations on the prevention of neonatal HAIs.\n\nVisiting neighbouring benchmark hospitals lead to more options and steps that could be considered while the development of the prevention bundle, e.g. development of the checklist and policy protocols.\n\nVarious infection control practices starting from hand hygiene, gown facility, changing slippers at the entrance to carry out routine aseptic procedures were quite similar in all four settings with minor variations or modification in existing infection control policies. Two facilities were very much into the documentation of all the infection control practices and active surveillance but the rate of HAIs was comparable among all the settings. Some of the practices add additional costs to the parents like chlorhexidine bath to the neonate before entry to NICU.\n\nBased on the contributors identified bloodstream infection was more prevalent causing neonatal HAIs. Hence out of these eighteen processes all the processes related to vascular interventions were clubbed together to prepare a vascular access bundle. We clustered cross matching, IV line insertion, blood product transfusion, and medication preparation and administration process to form one prevention bundle process.\n\nAll the results in the study highlighted the importance of disinfection of environment and care of neonate aseptically to prevent neonatal HAIs. Henceforth, we clustered all the process related to neonatal caring and disinfection around neonate as one care process bundle. We joined the bed preparation process, infant feeding process, nappy change process, neonatal morning care process, new patients’ bed preparation process, routine cradle/incubator cleaning process and routine vital assessment process to form a vascular access management process bundle.\n\nWe also merged patient resuscitation process of new and existing patients as one process considering the commonality in the process.\n\nWe did develop the VAP prevention policy but there were only two cases in 18 months period with VAP and found that the practices followed at the current settings met the standard guidelines.56\n\nA very strong, direct and easy way to communicate to healthcare workers on the practices is disseminating the information through do’s and don’ts.57 Considering its strong applicability and recall power, we prepared and disseminated the same. It was prepared specifically for each profession depending upon its applicability to the job description.\n\nBased on the experts' suggestions, a few of the processes that we considered earlier that may add to the prevention bundle, were not apt to be included and were suggested to be converted into policy rather than a process. In the current study, we focused not only on the invasive procedures but also on the standardisation of the non-invasive procedure. In addition to the three processes care bundles we also developed a policy document, do’s, don’ts, and surveillance charts.\n\nThere were two policy documents prepared for vascular access infection prevention policy and Ventilator-associated pneumonia (VAP) prevention policy.\n\nThe dos and don’ts (rules) were formed for general infection control practices.\n\nSince any prevention bundle without the involvement of the ground level healthcare workers would not fetch determination and quality improvement, the team of nurses helped to carry out the role play and audio-video recording on these processes. Pre and post-training knowledge assessment questionnaires were individually developed for nurses, postgraduate medical students, and allied health students considering the scope of care provided by them to the neonates.\n\nTraining that is developed by involving the various stakeholders and discussion are found to be very effective than researcher-developed training alone.58\n\nAt the beginning of the intervention, it was observed that anyone visiting NICU was supposed to place street footwear in a separate rack followed by wearing ICU sleepers. However, since both the racks to place sleepers were kept next to each other, it was always mixed and many times the street footwear was kept on the floor and not in the rack. To bring discipline and behavioral changes among the healthcare workers, the two racks were kept apart in opposite directions and labelling of the racks were done “I keep my street footwear here”. The same room has the facility to perform handwashing and hand disinfection, which was not followed earlier. Hence, another quotation label was kept above the ICU footwear rack with hand sanitizer “I disinfect my hand before entering to ICU”.\n\nNICU footwear location next to handwashing basin and hand-rub solution dispenser was created. Hand-rub solution for all the entrants was placed from the main door and empowered housekeeping and security staff to remind all entrants of hand hygiene. Identified and marked (a) weighing machine for weighing the diapers post-use, (b) for only weighing babies. Hand rub solution was placed next to entry to NICU on the door. Changing the AMBU bag practices shifted to every 72 hours.\n\nOur approach to involving top management, clinicians, microbiologists, HICC team, and nursing team together while identifying the contributors and development of the processes has helped in its implementation and regular training. The healthcare workers used to stay back after their shift is over, for the training on these prevention bundles without altering their routine clinical care.\n\nImplementation of the prevention bundle was carried out using quasi-experimental study design, where three rounds of training were provided to healthcare workers after a waiting period of three months. Each participant was welcomed and completed a pre-test in written format. The consent was obtained only from those who were new to the training. After the pre-test, the participant was shown a video with oral narrations and descriptions by the researcher for 20 minutes.\n\nOn each training day, three teams were formed among the participants. Post presentation the three groups were taken on hands-on stations where the researcher and the senior nurse helper demonstrated the process and then assessed each participant while they demonstrated the practices. Post video and stimulation presentation, each participant was given a written post-test to answer.\n\nWe developed a team of nurses and trained them to observe and help other healthcare providers to get training; we emphasized frequent optimal hand hygiene practices and provided both audio-video and stimulation training to improvise on retention of knowledge and skill development. Training and re-training in a small frequent manner using multiple approaches helps for the behavioral change and to develop further skills. G. Darmstadt et al. highlighted the significance of emollient application and prevention of neonatal skin infections,59 in the current study setting too, this practice was followed.\n\nOur study showed a reduction of 26% in neonatal HAIs, whereas other studies show a reduction up to 50% in neonatal HAIs after implementation of quality improvement initiatives among neonates <29 weeks across the neonatal network in Australia.23 Developed countries have shown better outcomes after quality initiatives in NICU as compared with developing or resource-limited settings.14 Few practices help to reduce BSI or CLABSI like the use of chlorhexidine coated IV cannula stopper60 or single-use sterile tray for medication preparation and delivery,61 cord care and neonatal bathing with chlorhexidine,62,63 dedicated nurse leader for monitoring and training on infection control practices.64 These practices help but do incur a cost burden on the healthcare organization and family of the neonate where out of pocket expenses on hospitalization drain out their entire savings. Not only the cost burden but also commitment from healthcare administration and change in policy for infection control practices is inevitable to implement such practices.\n\nWe faced challenges while developing and implementing the bundle. Getting a commitment to participate and taking out extra time after their duty shift was a challenge. Likewise in other countries, there is dedicated surveillance for neonatal HAIs,65 which needed a teamwork approach from all the healthcare workers at NICU. The surveillance definition by CDC is for patients age <1 year, which underestimates the risks and physiology of the neonates who are more prone to HAIs compared to infant/child.66–68\n\nIn the three training sessions 49, 48 and 47 nurses were trained respectively per session. The challenge was with 12-15 nurses as these nurses were on rotation from a different ICU (pediatric ICU). This rotation started from the end of December 2019 until March 2020. There were 15 new nurses appointment at NICU in February-March 2020 that lead to a change in behavioral neonatal care practices and a sudden surge of neonatal HAIs from 2 to 3 cases per month to 7 cases were seen. Another factor contributing to this surge was the admission of a very high-risk newborn referred from another hospital for surgery. On average, there used to be 2-3 cases per month posted for surgery whereas from the end of February 2020 until the first week of April 2020, there were 12 cases posted for surgery that includes various types of high-risk gastrointestinal surgeries. It was also observed that in March 2020 the cases had surgical site infection immediately after 2-3 days of surgery, which was not observed among previous cases except one such case. March 2020 was also the time from when onwards the COVID-19 surge in India began, the hospital administration was also instructed to work with 1/3rd of healthcare workers on a rotational basis keeping a priority on their health too. These all were few reasons noted that might have contributed to a sudden surge of neonatal HAIs during March-April 2020.\n\nThe study had many limitations. The nurses posted in NICU had rotational duty between NICU and Pediatric ICU, so after every 2-3 months there were 12 – 15 new nurses either due to rotation, leave or attrition that needed to be trained for the infection control processes at NICU. The postgraduate medical and allied health students and interns were posted on a rotational basis for a duration ranging from 15 days to 3 months. This lead to variations in their infection control practices, if they missed the training session.\n\nThe current study setting was an open NICU where neonates from various specialization units like cardiology, gastroenterology, and orthopedic surgery were hospitalized and looked after by a specialty consultant. The training to these specialty consultants was not provided, that lead to varied infection control practices as each unit has medical students on a rotational basis also. The housekeeping staff also worked on a rotational basis and after every month the entire staff of housekeeping was changed. This was an uncontrolled factor for training to these staff and monitoring their infection control practices. We did not see many VAP cases hence the focus of the bundle was given to bloodstream infection and environmental disinfection including routine care to the neonates.\n\nFuture research can be carried out for development of such prevention bundles for various specialised intensive care units of the hospital.\n\n\nConclusion\n\nRoot cause analysis revealed handwashing practices, inappropriate aseptic process, inappropriate disinfection of equipment and environment, inappropriate vascular line hub care, medication preparation and delivery and venous line handling were few important contributors to neonatal HAIs. We could identify eighteen important processes that were followed in NICU to deliver care to new-borns and were standardised as per the current setting. We found the vascular line hub care, handwashing practices and aseptic technique to be practised during procedures were key to prevent neonatal HAIs. Our developed prevention bundle was found to be effective and could bring down the infection rate. It had brought the behavioural change among the healthcare providers towards infection control practices and the audio-video aids along with hands-on workstations could continue as a training method for infection control practices to be adopted in NICU. Periodic training and developmental hands-on workshops would benefit the healthcare workers to follow behavioural change and practice infection control guidelines.",
"appendix": "Data availability\n\nFigshare: Development and evaluation of prevention bundle for neonatal healthcare-associated infections. https://doi.org/10.6084/m9.figshare.22284385.v7. 69\n\nThis project contains the following underlying data:\n\n- Pre & Post training results.xlsx\n\n- FEMA Findings.xlsx\n\n- RCA findings.xlsx\n\nThis project contains the following extended data:\n\n- SQUIRE-2.0-checklist (1) filled.pdf\n\n- Blood product transfusion.docx\n\n- Central line.docx\n\n- ET suction.docx\n\n- Feeding.docx\n\n- Intubation.docx\n\n- IV line.docx\n\n- Medication preparation & delivery.docx\n\n- Oro-nasal suction.docx\n\n- PICC line.docx\n\n- TPN.docx\n\n- HAND HYGEINE_Survey – Copy.docx\n\n- Observer Checklist for Hand.docx\n\n- NICU basics for Infection Control Practices.docx\n\n- NICU CLABSI Prevention Bundle.docx\n\n- NICU VAP Prevention Bundle.docx\n\n- Consent form nurse.docx\n\n- Vascular access process Feb 2020 Pre.docx\n\n- Vascular access process Feb 2020 Post.docx\n\n- Nursing care process - pretest.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nWHO, World Health Organisation: Newborns: reducing mortality.2018. Accessed 26 Oct 2018. Reference Source\n\nUNICEF India: Neonatal Health.2015. Accessed 19 Jun 2017. Reference Source\n\nUN Inter-agency Group for Child Mortality Estimation: Mortality rate, neonatal (per 1,000 live births)|Data.2019. Accessed 4 Jan 2020. Reference Source\n\nAlkema L, Chao F, You D, et al.: National, regional, and global sex ratios of infant, child, and under-5 mortality and identification of countries with outlying ratios: A systematic assessment. Lancet Glob. Health. 2014; 2: e521–e530. PubMed Abstract | Publisher Full Text\n\nKamath S, Mallaya S, Shenoy S, et al.: Nosocomial infections in neonatal intensive care units: profile, risk factor assessment and antibiogram. Indian J. Pediatr. 2010; 77: 37–39. PubMed Abstract | Publisher Full Text\n\nKumar A, Randhawa VS, Nirupam N, et al.: Risk factors for carbapenem-resistant Acinetobacter baumanii blood stream infections in a neonatal intensive care unit, Delhi, India. J. Infect. Dev. Ctries. 2014; 8: 1049–1054. Publisher Full Text\n\nShalini T, Malik GK, Jain Amita K n: Study of Ventilator Associated Pneumonia in Neonatal Intensive Care Unit: characteristics, risk factors and outcome. Internet J Med Updat. 2010; 5: 12–19.\n\nLiu L, Johnson HL, Cousens S, et al.: Global, regional, and national causes of child mortality: An updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012; 379: 2151–2161. PubMed Abstract | Publisher Full Text\n\nKnowles SJ: Strategies for the prevention of hospital-acquired infections in the neonatal intensive care unit. J. Hosp. Infect. 2009; 71: 95–96. Publisher Full Text\n\nResar R, Griffin F, Haraden C, et al.: Using Care Bundles to Improve Health Care Quality. IHI Innov. Ser. white Pap.2012.\n\nResar R, Pronovost P, Haraden C, et al.: Using a bundle approach to improve ventilator care processes and reduce ventilator-associated pneumonia. Jt. Comm. J. Qual. Patient Saf. 2005; 31: 243–248. PubMed Abstract | Publisher Full Text\n\nYokoe DS, Anderson DJ, Berenholtz SM, et al.: A compendium of strategies to prevent healthcare-associated infections in acute care hospitals: 2014 updates. Infect. Control Hosp. Epidemiol. 2014; 35: 967–977. PubMed Abstract | Publisher Full Text | Free Full Text\n\nInternational Nosocomial Infection Control: International Nosocomial Infection Control Consortium (INICC) Bundle to Prevent Ventilator-Associated Pneumonia (VAP) in Intensive Care Units (ICU): An International Perspective.2013.\n\nWHOLegeay C, Bourigault C, et al.: Parenting in the Neonatal Intensive Care Unit. J. Hosp. Infect. 2015; 4: 24.\n\nWHO: Report on the Burden of Endemic Health Care-Associated Infection Worldwide. WHO Libr Cat Data; 2011. Reference Source\n\nRosenthal VD, Rodríguez-Calderón ME, Rodríguez-Ferrer M, et al.: Findings of the International Nosocomial Infection Control Consortium (INICC), Part II: Impact of a Multidimensional Strategy to Reduce Ventilator-Associated Pneumonia in Neonatal Intensive Care Units in 10 Developing Countries. Infect. Control Hosp. Epidemiol. 2012; 33: 704–710. PubMed Abstract | Publisher Full Text\n\nKorhonen A: A multicentred clinical improvement project among preterm population evaluation of current practices. J. Perinat. Neonatal Nurs. 2010; 24: 341–347. PubMed Abstract | Publisher Full Text\n\nAly H: Is Bloodstream Infection Preventable Among Premature Infants? A Tale of Two Cities. Pediatrics. 2005; 115: 1513–1518. PubMed Abstract | Publisher Full Text\n\nCenters for Disease Control and Prevention: Guidelines for preventing health-care-associated pneumonia. Anasthesiol. Intensivmed. Notfallmed. Schmerzther. 2003; 40: 79–84.\n\nSannoh S, Clones B, Munoz J, et al.: A multimodal approach to central venous catheter hub care can decrease catheter-related bloodstream infection. Am. J. Infect. Control. 2010; 38: 424–429. PubMed Abstract | Publisher Full Text\n\nResende DS, Peppe ALG, dos Reis H , et al.: Late onset sepsis in newborn babies: Epidemiology and effect of a bundle to prevent central line associated bloodstream infections in the neonatal intensive care unit. Braz. J. Infect. Dis. 2015; 19: 52–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang W, Zhao CL, Ji QL, et al.: Prevention of peripherally inserted central line-associated blood stream infections in very low-birth-weight infants by using a central line bundle guideline with a standard checklist: a case control study. BMC Pediatr. 2015; 15: 1–6. Publisher Full Text\n\nBowen JR, Callander I, Richards R, et al.: Decreasing infection in neonatal intensive care units through quality improvement. Arch Dis Child - Fetal Neonatal Ed. 2017; 102: F51–F57. Publisher Full Text\n\nCeballos K, Waterman K, Hulett T, et al.: Nurse-driven quality improvement interventions to reduce hospital-acquired infection in the NICU. Adv. Neonatal Care. 2013; 13: 154–163. PubMed Abstract | Publisher Full Text\n\nMusu M, Finco G, Mura P, et al.: Controlling catheter-related bloodstream infections through a multi-centre educational programme for intensive care units. J. Hosp. Infect. 2017; 97: 275–281. PubMed Abstract | Publisher Full Text\n\nRosenthal VD, Maki DG, Mehta Y, et al.: International Nosocomial Infection Control Consortiu (INICC) report, data summary of 43 countries for 2007-2012. Device-associated module. Am J Infect Control. 2014; 42: 942–956. PubMed Abstract | Publisher Full Text\n\nKurlat I, Corral G, Oliveira F, et al.: Infection control strategies in a neonatal intensive care unit in Argentina. J. Hosp. Infect. 1998; 40: 149–154. PubMed Abstract | Publisher Full Text\n\nRosenthal VD, Udwadia FE, Kumar S, et al.: Clinical impact and cost-effectiveness of split-septum and single-use prefilled flushing device vs 3-way stopcock on central line-associated bloodstream infection rates in India: A randomized clinical trial conducted by the International Nosocomial Infect. Am. J. Infect. Control. 2015; 43: 1040–1045. Publisher Full Text\n\nSulaiman S, Alias RA: Information ethics in Malaysia paperless hospital. Proc. Postgrad. Annu. Res. Semin. 2006; 2006: p 314.\n\nJaggi N, Rodrigues C, Rosenthal VD, et al.: Impact of an International Nosocomial Infection Control Consortium multidimensional approach on central line-associated bloodstream infection rates in adult intensive care units in eight cities in India. Int. J. Infect. Dis. 2013; 17: e1218–e1224. PubMed Abstract | Publisher Full Text\n\nRosenthal VD: International Nosocomial Infection Control Consortium (INICC) resources: INICC multidimensional approach and INICC surveillance online system. Am. J. Infect. Control. 2016; 44: e81–e90. PubMed Abstract | Publisher Full Text\n\nChakravarthy M, Myatra SN, Rosenthal VD, et al.: The impact of the International Nosocomial Infection Control Consortium (INICC) multicenter, multidimensional hand hygiene approach in two cities of India. J. Infect. Public Health. 2015; 8: 177–186. Publisher Full Text\n\nGaribaldi RA, Burke JP, Dickman ML, et al.: Factors Predisposing to Bacteriuria during Indwelling Urethral Catheterization.1974; 291: 215–219. Publisher Full Text\n\nWeinberg NS, Stason WB: Managing quality in hospital practice. Int. J. Qual. Health Care. 1998; 10: 295–302. Publisher Full Text\n\nM.A.G. R, F.J.G. F, M.J.B. G, P.A. F: Patient safety: Project “Zero Bacteremia” - Is it possible in haematological patients? Bone Marrow Transplant. 2010; 45.\n\nSavage RM, Steverman D: Hand Hygiene — Before Patient Care. Am. J. Infect. Control. 2011; 39: E83–E84. Publisher Full Text\n\nNorris B, West J, Anderson O, et al.: Taking ergonomics to the bedside - A multi-disciplinary approach to designing safer healthcare. Appl. Ergon. 2014; 45: 629–638. PubMed Abstract | Publisher Full Text\n\nEl-Saed A, Balkhy HH, Weber DJ: Benchmarking local healthcare-associated infections: Available benchmarks and interpretation challenges. J. Infect. Public Health. 2013; 6: 323–330. PubMed Abstract | Publisher Full Text\n\nSpeck K, Rawat N, Weiner NC, et al.: A systematic approach for developing a ventilator-associated pneumonia prevention bundle. Am. J. Infect. Control. 2016; 44: 652–656. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRadbone L, Birch J, Upton M: The development and implementation of a care bundle aimed at reducing the incidence of NEC. Infant. 2013; 9: 14–19.\n\nSebastian PM, Persing TF, Sebastian PM, et al.: When a Bundle Is NOT Enough … The Value of Teamwork in Reducing Harm Associated with Ventilator Associated Pneumonia. Am. J. Infect. Control. 2013; 41: S100–S101.\n\nUberoi R, Gupta U, Sibal A: Root Cause Analysis in Healthcare. Apollo Med. 2004; 1: 60–63. Publisher Full Text\n\nIshikawa K: Introduction to quality control.1989.\n\nIshikawa K, Loftus J: Introduction to quality control.1990.\n\nIHI: Pareto Chart.2013. Accessed 19 Mar 2018. Reference Source\n\nGibbard A: Health care and the prospective Pareto principle. Ethics. 1984; 94: 261–282. PubMed Abstract | Publisher Full Text\n\nRani U, Chawla K, Lewis LE, et al.: Hand Hygiene Practices and Training Gap in a Neonatal Intensive Care Unit at Coastal Karnataka India. Indian J. Public Heal. Res. Dev. 2020; 11: 59. Publisher Full Text\n\nDonabedian A: The Quality of Care: How Can It Be Assessed? JAMA J. Am. Med. Assoc. 1988; 260: 1743–1748. Publisher Full Text\n\nRani U, Lewis LE, Akthar N, et al.: Prevention of neonatal healthcare-associated infections: Current update. Res. J. Pharm. Technol. 2020; 13: 2771–2776. Publisher Full Text\n\nRani U, Lewis LE, Kothuri MS, et al.: Factors associated with neonatal healthcare-associated infections (Hais) in india: A protocol for systematic review and meta-analysis. Res. J. Pharm. Technol. 2020; 13: 1672–1678. Publisher Full Text\n\nAntony B, Prasad BR: An outbreak of neonatal septicaemia by Enterobacter cloacae. Asian Pacific. J. Trop. Dis. 2011; 1: 227–229. Publisher Full Text\n\nAntony B, Cherian E, Boloor R, et al.: A sporadic outbreak of Burkholderia cepacia complex bacteremia in pediatric intensive care unit of a tertiary care hospital in coastal Karnataka, South India. Indian J. Pathol. Microbiol. 2016; 59: 197–199. PubMed Abstract | Publisher Full Text\n\nMittal N, Nair D, Gupta N, et al.: Outbreak of Acinetobacter spp septicemia in a neonatal ICU. Southeast Asian J. Trop. Med. Public Health. 2003; 34: 365–366. PubMed Abstract\n\nSaritha K: Outbreak of MRSA in the Neonatal Intensive Care Unit of a tertiary care hospital - Transmission from nursing personnel. J. Clin. Diagn. Res. 2009; 3: 1510–1512.\n\nWomack J: Gemba Walk. 2nd ed; Lean Enterprise Institute, Inc; 2013.\n\nMehta Y, Gupta A, Todi S, et al.: Guidelines for prevention of hospital acquired infections. Indian J. Crit Care Med. 2014; 18: 149–163. Publisher Full Text\n\nMeena Kumari K, Amberkar MB, Alur SS, et al.: Clinical awareness of do’s and don’ts of cardiopulmonary resuscitation among university medical students-A questionnaire study. J. Clin. Diagn. Res. 2014; 8: MC08–MC11.\n\nWHO: WHO Guidelines on Hand Hygiene in Health Care First Global Patient Safety Challenge Clean Care is Safer Care.2009.\n\nDarmstadt GL, Saha SK, Ahmed ASMNU, et al.: Effect of topical treatment with skin barrier-enhancing emollients on nosocomial infections in preterm infants in Bangladesh: A randomised controlled trial. Lancet. 2005; 365: 1039–1045. PubMed Abstract | Publisher Full Text\n\nShepherd EG, Kelly TJ, Vinsel JA, et al.: Significant reduction of central-line associated bloodstream infections in a network of diverse neonatal nurseries. J. Pediatr. 2015; 167: 41–46.e3. PubMed Abstract | Publisher Full Text\n\nFabbri G, Panico M, Dallolio L, et al.: Outbreak of ampicillin/piperacillin-resistant Klebsiella pneumoniae in a neonatal intensive care unit (NICU): investigation and control measures. Int. J. Environ. Res. Public Health. 2013; 10: 808–815. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChawla G, Diwakar KK: Comparison of umbilical cord cleansing using sterile water and povidine iodine-spirit during early neonatal period: A double blind randomized control trial. J. Clin. Diagn. Res. 2015; 9: 6–8. Publisher Full Text\n\nGupta B, Das VN, Sharma D, et al.: Evaluation of efficacy of skin cleansing with chlorhexidine in prevention of neonatal nosocomial sepsis - A randomized controlled trial. J Matern Neonatal Med. 2016; 29: 242–247. PubMed Abstract | Publisher Full Text\n\nExline MC, Ali NA, Zikri N, et al.: Beyond the bundle - journey of a tertiary care medical intensive care unit to zero central line-associated bloodstream infections. Crit. Care. 2013; 17: R41. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWinzor G, Cooke RPD: Infection prevention and control in the paediatric setting: the challenges. J. Hosp. Infect. 2016; 94: 157–158. Publisher Full Text\n\nHoran TC, Andrus M, Dudeck MA: CDC/NHSN surveillance definition of health care-associated infection and criteria for specific types of infections in the acute care setting. Am. J. Infect. Control. 2008; 36: 309–332. Publisher Full Text\n\nCenters for Disease Control and Prevention: Pneumonia (Ventilator-associated [VAP] and non-ventilator-associated Pneumonia [PNEU]) Event. Device-associated Modul CDC.2019; 1–17.\n\nCenter for Disease Control and Prevention: Identifying Healthcare-associated Infections (HAI) for NHSN Surveillance.2015.\n\nRani U, Lewis LE, Chawla K, et al.: Development and evaluation of prevention bundle for neonatal healthcare-associated infections. Dataset. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "181526",
"date": "18 Jul 2023",
"name": "Ronald L. Castelino",
"expertise": [
"Reviewer Expertise Pharmacy"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this very interesting manuscript. Overall, the article is very well written and addresses a critical healthcare issue and provides valuable insights into the prevention of neonatal healthcare-associated infections.\nBelow are some suggestions for consideration.\nThe introduction is quite lengthy. Many of the interventions are described in detail. These can be summarised and included in the discussion for comparison purposes. Or a summary of the evidence of these in reducing HAIs and mortality should be included.\n\nSecond paragraph in the introduction is confusing. I suggest deleting the lowest and highest ranges provided.\n\nSignificant grammar edits are needed. In many paragraphs present tense is used instead of past tense. E.g. the concept of bundles was developed...\n\nParagraph 7: What is cluster care?\n\nWhat are some of the local stats? What is the current rate of HAI in the local setting and mortality rates? This should be added to the introduction.\n\nWhat were the specific objectives?\n\nWho were the 80 health care workers interviewed? I suggest providing a breakdown. Experience level in NICU etc.\n\nWho developed the prevention bundles? Who developed the training? Who interviewed the health care workers?\n\nWho categorised/matched the domains? Who tabulated/transcribed the interviews?\n\nThe main objective listed in the manuscript includes -The current study was carried out to develop and evaluate prevention bundles for neonatal healthcare-associated infections (HAIs).\n\nMethods stating hand hygiene practices - how does this relate to the current objective? These aspects are not clear and not linked.\n\nWho provided the training in phase 1? What were their qualifications?\n\nWhy was the training implemented in 3 phases? Please justify.\n\nHave there been any outcomes differences between health care acquired infection vs acquired in the community?\n\nCan you comment on the generalisability of the intervention and sustainability?\nOverall, even though it tackles an important topic the manuscript would benefit from an English edit and more importantly can be made more succinct.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "181523",
"date": "24 Jul 2023",
"name": "Migbar Sibhat",
"expertise": [
"Reviewer Expertise I have sufficient expertise to assess and critisize this work. I have specialized in pediatrics and neonatal care provisions. Hence",
"the prevention of neonatal and child mortality and morbidity is my primary area of expertise. Furthermore",
"I also have portfolio of research publications and took part/engaged in different research activities such as grants",
"attending research conferences and workshops."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors tried to address and develop a prevention bundle for HAIs in a single neonatal intensive care unit in India. Furthermore, the authors also tried to show the effectiveness of the prevention bundle in reducing the rate of neonatal HAIs and for healthcare workers’ training and development. However, the manuscript has several issues that need to be addressed, moderated, and clarified yet.\nMethods:\nThe methods section in general was too bulky and difficult to catch the main contents. Please try to make it specific and succinct, yet inclusive of the required contents.\n\nThe population of the study was not well explained. Therefore, the population where the findings are going to be inferred (target/source population) needs to be clearly described in line with the population where the study is actually being conducted (study population) in the methods and materials section.\n\nFor the quantitative part, the sample size required had to be scientifically estimated prior to the accomplishment of the study. In addition, appropriate sampling techniques should be applied rather than assigning samples/participants deliberately without scientifically supported methods of selection. Otherwise, the external validity of the study findings will be under question. The authors need to think over it with great emphasis.\n\nUnder the methods section, you put a specific time schedule for some activities. “The time selected for observations was morning care time at 07:30 am; clinician’s clinical round time at 09:30 am and 3:00 pm; blood sample collection time at noon; invasive routine procedure time at 02:00 pm; medication/total parenteral nutrition preparation time at 03:30 pm; shift hand overtime at 07:30 pm.” Was there any scientific reason to put specific time to perform each procedure? What was the relevance of specifying the time for each activity?\n\n“These observations were summarised in frequency and percentage under four categories in tabular format. The top 20% of frequent observations were considered as ‘scope for improvement’ for the prevention bundle”. Why did you consider this cut-off point (20%)? Why not lower or higher than this cut-off point to declare the scope of improvement?\n\nUnder Training Phase II, the application of the phrase “nursing care process bundle” did not seem exactly fit to the contents described below. Nursing care process is a broader term that is not limited to these procedures, but beyond. Hence, I recommend using the term “Nursing procedures” instead.\n\nBesides, “These senior nurses had >10 years of experience in NICU...” Did you think the year of experience will merely impact the level of proficiency? Why did you prefer years of experience over other criteria such as qualification, efficiency/actual performance, who took many pieces of training, and their grades?\n\nPre-training performance of participants needs to be assessed to compare the effectiveness of the training. Despite the general HAIs estimations presented, I couldn’t see any statement regarding the performance of each specific procedure to be evaluated in the study Phases. This is the major concern that I appreciated in this manuscript. Otherwise, it could be difficult to accept the changes observed in this study without determining the baseline level of implementation for each specific procedure.\n\nResults:\n“The ranking of the contributors to HAIs by these healthcare workers showed that prime contributors are healthcare workers (27%)”. How could you exclude if the inappropriate implementation of procedures by healthcare workers leading to HAIs was due to a lack of access to appropriate IPC and PPE-related infrastructures? It needs to be cautioned and clarified accordingly.\n\nDiscussion:\nOverall, the discussion seems a description of the procedures and methodologies rather than the discussion. Thus, please try to focus on discussing the pertinent findings based on your objective. Such details can be provided under the data management and processing sub-section of the “Methods” section, or probably as an introductory paragraph of the “Results” section.\n\nMoreover, almost all the findings and contents presented in the discussion section were not discussed as it has to be. The discussion mainly involves the interpretation of pertinent findings in a scientifically sound and clinically applicable manner, comparison with existing evidence, and provision of scientific or possible justifications/reasoning for the current findings and possible discrepancies with existing literature. Please put your justification and compare your findings with existing evidence in related literature. The whole discussion section requires thorough revision and re-writeup in these perspectives.\n\n“The nurses posted in NICU had rotational duty between NICU and Pediatric ICU, so after every 2-3 months there were 12 – 15 new nurses either due to rotation, leave, or attrition that needed to be trained for the infection control processes at NICU.” So, did you provide them training on entry, or included just without training? If training was provided, it should not be considered as a limitation. It can be a challenge rather. However, if you include them without training, that could be completely unacceptable. This can be considered as a methodological fallacy.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11281",
"date": "03 Jun 2024",
"name": "Usha Rani",
"role": "Author Response",
"response": "RESPONSE TO QUERIES ON METHODOLOGY The population of the study was not well explained. Therefore, the population from which the findings are going to be inferred (the target /source population) needs to be clearly described in line with the population from which the study is actually being conducted (study population) in the methods and materials section. For observations, interviews, root-cause analysis, and system process mapping, the population was all the healthcare workers providing direct or indirect care to neonates hospitalized in the level IV Neonatal Intensive Care Unit (NICU) of a tertiary care teaching hospital. However, to explore the best practices of peer healthcare facilities, observations were made in another three different level IV NICU's of Karnataka where one was located in Semi-Urban district and two were in Urban metro city. For the quantitative part, the sample size required had to be scientifically estimated prior to the accomplishment of the study. In addition, appropriate sampling techniques should be applied rather than assigning samples/participants deliberately without scientifically supported methods of selection. Otherwise, the external validity of the study findings will be under question. The authors need to think over it with great emphasis. The current study is more focused on qualitative data synthesis. Qualitative studies requires interviews till the saturation of responses reaches or maximum 30 participants. For the current study more than 30 interviews were done and made focus group discussion of 6 members each. Interviews were carried out on all the healthcare workers working in the study site NICU and brainstorming was carried out on each process with minimum 5 nurses & two paediatrician for each identified processes. The observations were carried out for a year on all the identified processes critical to spread of healthcare associated infections. We conducted observations considering minimum 30 observations per process or till saturation of observations arrived. Under the methods section, you put a specific time schedule for some activities. “The time selected for observations was morning care time at 07:30 am; clinician’s clinical round time at 09:30 am and 3:00 pm; blood sample collection time at noon; invasive routine procedure time at 02:00 pm; medication/total parenteral nutrition preparation time at 03:30 pm; shift hand overtime at 07:30 pm.” Was there any scientific reason to put specific time to perform each procedure? What was the relevance of specifying the time for each activity? Some of the elective routine procedures are done just after the next shift change of nurses like baby bath, changing the linen, doing suctioning, cleaning the equipment, and routine blood collection for investigations carried out electively at 07:30 am. We specified the time for each activity in a study ensuring that data is collected during specific periods of the day when certain procedures are more likely to occur this timing could provide a more accurate picture of the processes carried out in the ICU. These procedures other than the emergency situations, are routinely carried out on specific time of the day and hence we have specified the time. “These observations were summarised in frequency and percentage under four categories in tabular format. The top 20% of frequent observations were considered as ‘scope for improvement’ for the prevention bundle”. Why did you consider this cut-off point (20%)? Why not lower or higher than this cut-off point to declare the scope of improvement? Pareto's principle, also known as the 80/20 rule, was introduced by the Italian economist Vilfredo Pareto [1], states that roughly 80% of effects come from 20% of causes in 1896 in regards to economics. Later it was reintroduced to quality improvement by Joseph M. Juran in 1950 . The top 80% of frequent observations were considered as 'scope for improvement' for the prevention bundle lead by top 20% of frequent causes, the study could prioritize the most significant issues that need improvement. This approach helped ensuring that the most significant issues are addressed first, which have the greatest impact on developing the prevention bundle. We could also use resources efficiently by applying this principle. Under Training Phase II, the application of the phrase “nursing care process bundle” did not seem exactly fit to the contents described below. Nursing care process is a broader term that is not limited to these procedures, but beyond. Hence, I recommend using the term “Nursing procedures” instead We thank and appreciate the reviewer for the suggestion, in India nurses frequently use the phrase \"Nursing care\" rather \"Nursing procedures\" in order to more contextualize and personalized to develop acceptance among nurse the phrase was used and same terminology was used in the prevention bundle which is being sent for Indian Copyrights office hence, we apologies that we are not able to change the terminology at this stage. Besides, “These senior nurses had >10 years of experience in NICU...” Did you think the year of experience will merely impact the level of proficiency? Why did you prefer years of experience over other criteria such as qualification, efficiency/actual performance, who took many pieces of training, and their grades? All the nurses working in NICU had similar qualification, we did considered efficiency as per the hospital policy efficient nurses and most trained nurses were given a role of team leader and or shift Incharge. These nurses were involved while implementing the prevention bundle and all had more than 10 years of experience and were senior rank holder. There were literature evidences to involve senior nurses along with other nurses, however we tried including even junior nurses who had <2year of experience too but they were involved only in the development of the prevention bundle. Senior nurses with more years of experience have more skill-based knowledge, which could be promising in implementation of a prevention bundle and removing the acceptance barrier. They were familiar with the NICU environment, including the equipment, procedures, and protocols and were able to differentiate the existing policy and procedures from the proposed. Previous research has shown that years of experience can impact the level of proficiency of nurses in the NICU[2]. Therefore, it is consistent with previous research to consider years of experience when developing and implementing a prevention bundle [3, 4]. We hope that this answers the above query . Pre-training performance of participants needs to be assessed to compare the effectiveness of the training. Despite the general HAIs estimations presented, I couldn’t see any statement regarding the performance of each specific procedure to be evaluated in the study Phases. This is the major concern that I appreciated in this manuscript. Otherwise, it could be difficult to accept the changes observed in this study without determining the baseline level of implementation for each specific procedure. Pre-training performance of participants was assessed through observation that was part of objective 1, under table 2 and figure 2 & 3; later due to feasibility issues and COVID-19 restrictions only knowledge assessment was carried out through questionnaires, which is reported in Table 4 along with incidence and rate of HAIs during implementation phase. RESPONSE TO QUESTIONS ON RESULTS “The ranking of the contributors to HAIs by these healthcare workers showed that prime contributors are healthcare workers (27%)”. How could you exclude if the inappropriate implementation of procedures by healthcare workers leading to HAIs was due to a lack of access to appropriate IPC and PPE-related infrastructures? It needs to be cautioned and clarified accordingly.\" Thank you for identifying and highlighting this important concern. Although we have not mentioned in the results but there was continuous complete supply of PPE to healthcare facility and since the hospital is accredited by Indian National Regulatory Body, all the policy documents and protocols were in reach of all the healthcare providers of NICU. We haven't ignored this part rather this was assessed and ensured before determining that the prime contributor was healthcare workers and not the disruption of supply through observations and hospital supply records. Overall, the discussion seems a description of the procedures and methodologies rather than the discussion. Thus, please try to focus on discussing the pertinent findings based on your objective. Such details can be provided under the data management and processing sub-section of the “Methods” section, or probably as an introductory paragraph of the “Results” section. Moreover, almost all the findings and contents presented in the discussion section were not discussed as it has to be. The discussion mainly involves the interpretation of pertinent findings in a scientifically sound and clinically applicable manner, comparison with existing evidence, and provision of scientific or possible justifications/reasoning for the current findings and possible discrepancies with existing literature. Please put your justification and compare your findings with existing evidence in related literature. The whole discussion section requires thorough revision and re-writeup in these perspectives. We have rewritten the discussion as suggested by the reviewer. “The nurses posted in NICU had rotational duty between NICU and Pediatric ICU, so after every 2-3 months there were 12 – 15 new nurses either due to rotation, leave, or attrition that needed to be trained for the infection control processes at NICU.” So, did you provide them training on entry, or included just without training? If training was provided, it should not be considered as a limitation. It can be a challenge rather. However, if you include them without training, that could be completely unacceptable. This can be considered as a methodological fallacy. All the nurses were trained as soon as they join the NICU and retrained for those on rotation duty, or leave every month under the study period and after the study training is persistent every three months.. As the training module had written and audio-video recording along with a senior staff mentor it was easy for us to ensure that each one is trained when they start practicing in the NICU. However, during March 2020 due to COVID-19 restrictions and very limited number of nursing staff on duty, it was not possible to verify that the training is imparted to the nursing staff who would have missed the training due to various reasons."
}
]
}
] | 1
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https://f1000research.com/articles/12-687
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https://f1000research.com/articles/11-1265/v1
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07 Nov 22
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{
"type": "Opinion Article",
"title": "Systems Biology in ELIXIR: modelling in the spotlight",
"authors": [
"Vitor Martins dos Santos",
"Mihail Anton",
"Barbara Szomolay",
"Marek Ostaszewski",
"Ilja Arts",
"Rui Benfeitas",
"Victoria Dominguez Del Angel",
"Polonca Ferk",
"Dirk Fey",
"Carole Goble",
"Martin Golebiewski",
"Kristina Gruden",
"Katharina F. Heil",
"Henning Hermjakob",
"Pascal Kahlem",
"Maria I. Klapa",
"Jasper Koehorst",
"Alexey Kolodkin",
"Martina Kutmon",
"Brane Leskošek",
"Sébastien Moretti",
"Wolfgang Müller",
"Marco Pagni",
"Tadeja Rezen",
"Miguel Rocha",
"Damjana Rozman",
"David Šafránek",
"Rahuman S. Malik Sheriff",
"Maria Suarez Diez",
"Kristel Van Steen",
"Hans V Westerhoff",
"Ulrike Wittig",
"Katherine Wolstencroft",
"Anze Zupanic",
"Chris T. Evelo",
"John M. Hancock",
"Mihail Anton",
"Barbara Szomolay",
"Marek Ostaszewski",
"Ilja Arts",
"Rui Benfeitas",
"Victoria Dominguez Del Angel",
"Polonca Ferk",
"Dirk Fey",
"Carole Goble",
"Martin Golebiewski",
"Kristina Gruden",
"Katharina F. Heil",
"Henning Hermjakob",
"Pascal Kahlem",
"Maria I. Klapa",
"Jasper Koehorst",
"Alexey Kolodkin",
"Martina Kutmon",
"Brane Leskošek",
"Sébastien Moretti",
"Wolfgang Müller",
"Marco Pagni",
"Tadeja Rezen",
"Miguel Rocha",
"Damjana Rozman",
"David Šafránek",
"Rahuman S. Malik Sheriff",
"Maria Suarez Diez",
"Kristel Van Steen",
"Hans V Westerhoff",
"Ulrike Wittig",
"Katherine Wolstencroft",
"Anze Zupanic",
"Chris T. Evelo"
],
"abstract": "In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR’s future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.",
"keywords": [
"Systems Biology",
"Systems Medicine",
"ELIXIR Communities",
"Biomolecular Models",
"Network Biology",
"FAIR",
"Biological data",
"Biotechnology"
],
"content": "Executive summary\n\nThis white paper presents the future strategy of the new ELIXIR Systems Biology Community. This emerging ELIXIR Community was established upon the recommendation of ELIXIR’s Systems Biology Focus Group to develop and coordinate ELIXIR’s interactions with the broader systems biology community. The infrastructure aspects of systems biology - databases, tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove effective drivers of ELIXIR’s future support of advanced biological applications and personalised medicine.\n\nSystems biology is defined here as: modelling and understanding living systems in terms of their thousands of molecular interaction properties using a wide range of approaches, which can be further classified as bottom-up (starting from the molecular components) or top-down (starting from system behaviour). A key feature of systems biology is that, because of the complexity of the systems that are studied and the variety of data that is collected, it often requires collaboration between different laboratories and between computational biologists and experimentalists, often asynchronous in both space and time (e.g. through the literature and databases). It is essential that all the components that go towards building a systems model, from datasets and data collection methods to the models themselves, are FAIR (Findable, Accessible, Interoperable and Reusable) (Wilkinson et al., 2016).\n\nHistorically, in Europe and worldwide, there have been significant investments in the development and applications of systems biology (see Table 1 & Table 2). In Europe, this culminated in the establishment of the ESFRI ISBE (Infrastructure Systems Biology Europe); however, this initiative fell short of obtaining sufficient support from member states. ELIXIR’s Systems Biology Community will build upon some of the strands of the work in ISBE, as well as work that has been taking place within ELIXIR’s Communities and Platforms.\n\nThe Community has identified seven key challenges for systems biology in the short to medium term that can be addressed in part by ELIXIR, each with their own identified sub-challenges:\n\n1. Barriers to the wider uptake of systems biology (the challenge of providing well-parameterized systems biology models across the breadth of the life sciences; lack of data that can be used to accurately define the model parameter values; lack of standardisation and interoperability of systems biology; the resistance to mathematical modelling that is still present in biological and medical sciences)\n\n2. Linking new and existing data to systems biology models (FAIR generation of data well-suited to use in modelling and linking data and models in a FAIR way)\n\n3. Interoperability of systems biology resources (descriptions and annotations of data, models and their content need to follow coherent terminologies and ontologies; models, workflows, and data require FAIR, state-of-the-art computational infrastructure and tools for storage, access, and efficient use; interlinking standard models with models expressed in scientific programming and general purpose languages; interlinking descriptive and predictive models; trained experts to develop and curate resources that are user friendly and accessible; availability and accessibility of existing computational analysis methods and their interoperability with relevant modelling approaches)\n\n4. Further development and embedding of systems medicine (identification and modelling of network structures that are prognostic and predictive; integration with related systems such as microbes or expososomes; personalising models using patient data; clinically validating models; addressing ELSA (Ethical, Legal and Social Aspects) for clinical, sensitive data; interfacing with epidemiology)\n\n5. Provisioning of modelling as a service (provisioning of sophisticated data resources, tools and rich standards that are useful both for data mining and experimental design; availability of a pool of experts; availability of blueprint models to help with building new models)\n\n6. Capacity building and training (different trainee backgrounds; need for a systems biology learning path and broad promotion of the integrated systems biology framework; availability and use of standardised datasets in training materials; need for a broad training expertise)\n\n7. Need to support industrial and societal embedding (addressing, among others, pharmacology; toxicology; diagnostics; synthetic biology; agronomy; including microbial biotechnology and the bio-economy)\n\nMany areas of relevance to systems biology are already embedded into activities of ELIXIR’s Platforms, Communities and Focus Groups (see the Systems Biology within ELIXIR section below) and have the potential for further developments. In particular we identify the following:\n\nData platform: ELIXIR Core Data Resources and Deposition Databases are already highly used by the systems biology community. For example, data from BRENDA (Chang et al., 2021), STRING (Szklarczyk et al., 2021), and Reactome (Gillespie et al., 2022) are essential both for construction of molecular pathways and parameterization of molecular reactions. There is potential for the Systems Biology Community to add new data resources to the ELIXIR list of services. Engagement of the Platform with curation efforts like BioModels (Malik-Sheriff et al., 2020) can improve the FAIRness of systems biology-related data resources.\n\nTools platform: bio.tools (Ison et al., 2016) and the workflow hub (Goble et al., 2021) are invaluable resources for finding computational tools for systems biology. The ELIXIR Systems Biology Community aims to ensure relevant tools and workflows are added to these resources.\n\nCompute platform: This Platform has strong links to the European Open Science Cloud which will be important for future instantiation and simulation of extensive, multiscale models in the cloud.\n\nInteroperability platform: The Interoperability Platform’s Recommended Interoperability Resources help to improve the FAIRness of systems biology-related data, tools and models, while the Platform’s standards mapping resources such as BridgeDb (van Iersel et al., 2010), identifiers.org (Wimalaratne et al., 2018) and OLS (Jupp et al., 2015) facilitate better interoperability and integration of data and models. The systems biology community at large has also developed its own standards, like SBGN (Systems Biology Graphical Notation) and SBML (Systems Biology Markup Language), which we want to better connect with the abovementioned resources. The FAIRDOM platform (Wolstencroft et al., 2017) (part of the ELIXIR CONVERGE data management toolkit) provides a collaborative community space for the FAIR integration of data and models in their experimental context.\n\nTraining platform: Better and more extensive training in systems biology tools and methods, e.g. including the development of the new training materials, providing a repository for training materials and an annotation process for training materials, will be essential for the wide uptake of systems biology methodologies.\n\nCommunities: Many Communities already cover systems biology aspects and may well benefit from and provide data, tools and expertise for the modelling of various aspects in their systems. From a technological perspective, the Galaxy Community will play an important role in the integration of omics data and systems biology tools into workflows. Related to this, the Metabolomics Community has already begun work on standardising fluxomics workflows. The Microbial Biotechnology Community has a strong interest in systems biology as it aims to contribute to addressing standardisation and other issues in relation to models and their applicability. Other Communities, such as Plant Sciences, Microbiome (a new Community emerging from the Marine Metagenomics Community), Food and Nutrition and Toxicology, have potential to develop and deploy systems biology applications as part of their work towards understanding of their systems under study. It is foreseen that the Human Data Communities, especially the Federated Human Data and Rare Diseases Communities, will provide data, tools and expertise for the modelling of human disease.\n\nFocus groups: The Machine Learning, EOSC (European Open Science Cloud) and Registries Focus Groups will be instrumental in the advancement of new techniques for model development and the implementation of systems models in a cloud environment (making use of registries to make data, tools and workflows FAIR). FAIRness will also be improved by working with the Biocuration and FAIR Training Focus Groups. Large-scale systems biology modelling of interactions and evolution of populations and ecosystems is likely to increase, and it is expected that the Biodiversity Focus Group will mediate the interactions of the Community with such efforts.\n\nThe Community has developed a plan for future aims and objectives on short (3 years), mid (6 years) and long-term (10 years) timescales, revolving around four pillars: Standardisation & Interoperability, Technology, Training & Capacity building, and Embedding.\n\nShort term:\n\nBetter support of existing standards in model repositories;\n\nBuild upon systems biology models to improve the design of experiments that lead to the generation of higher quality, quantitative, FAIR data;\n\nAddress specific challenges for human modelling, which include: working with compartments; model validation through standardised phenotypes; initial interfaces for multi-level modelling and integration across scales; multi-tissue evaluations; extrapolations from single cell analysis to tissue level; microbiome - host interactions; integrating sensitive personal data into models for personalised medicine;\n\nEstablish approaches for model exchange, building on existing resource developments in the FAIR data landscape (e.g. FAIR data points; JWS-Online), BioModels and ModeleXchange;\n\nUnderstanding how big/smart data meets models meaningfully;\n\nIntertwining temporal and spatial modelling appropriately;\n\nImproved interoperability of modelling, simulation and analysis tools;\n\nInterfacing to synthetic biology through model-based design and model-based-learning strategies;\n\nPre-screen trainees prior to training events to make recommendations for courses to be followed in the context of the event;\n\nIntegrate new systems biology courses into TeSS and co-promote them with existing TeSS courses;\n\nStrengthen synergies with the other ELIXIR Communities, e.g. via joint training events;\n\nTogether with the training platform set up a \"gap analysis survey\" to find out the strengths and needs for each ELIXIR Node;\n\nImplement turnkey solutions for different Nodes (specific training, capacity building, staff exchanges, knowledge exchanges and so on);\n\nEstablish Key Performance Indicators (KPIs) to measure the impact of different actions.\n\nMid-term:\n\nImproved standardisation of meta-data to describe time-series, functional and imaging data such as to facilitate their integration in computational models; Providing a link between existing models, datasets, and analysis tools for easy access to relevant data;\n\nGood strategies (including training) to improve reproducibility, credibility, and validation of models and to assess the efficiency of tools, leading to the development of quality marks, thereby increasing the quality of workflow outcomes;\n\nDeveloping the basis for theoretical and practical multi-scale modelling frameworks;\n\nProviding the basis for developing Digital Twins (microbes, bioreactors, organs, organisms, ecosystems);\n\nExtend the use of synthetic and standardised datasets in most systems biology training events;\n\nSupport current and future trainers via Train the Trainer ELIXIR events;\n\nContinue and review the process of gap analysis survey and KPIs to include SME and industry;\n\nInvolve small and medium-size enterprises in the capacity building process;\n\nIdentify new areas, themes and challenges in systems biology.\n\nLong-term:\n\nImproved interoperability of data and models to enable FAIR model connection and integration (at different scales) so as to facilitate the development of multi-scale modelling frameworks;\n\nDevelopment of Digital Twin methodologies that provide sufficiently accurate, real-time and dynamic depictions of physical biosystems (microbes, bioreactors, organs, organisms, ecosystems);\n\nSteer and modify processes, stratify patients and thereby support medical decision-making;\n\nCreate a centralised repository of systems biology training materials aggregated by TeSS;\n\nSystematically review trends in systems biology and update training resources accordingly;\n\nAutomation of the capacity building process for new partners (communities, countries, etc.).\n\nIncrease uptake of systems biology methodologies by the communities of biologists, bioengineers and physicians;\n\nIncrease the uptake of standards (e.g. for model and data reporting) by the world wide systems biology communities.\n\n\nIntroduction\n\nSystems biology aims to understand how biological functions emerge from interactions between the multiple components of living systems by modelling the (dynamics of) interactions and processes. It studies what makes the whole different from the sum of its parts.\n\nSince modelling and understanding of living systems in terms of their thousands of molecular properties cannot be achieved in one step, systems biology comprises a variety of diverse, complementary approaches. Bottom-up systems biology starts from a limited number of components and studies the nonlinear mechanisms through which new properties emerge that are important for function. Top-down systems biology searches in multiple functional dimensions of the whole living system for correlations and patterns that clarify where functions have arisen from coherent behaviour of components. Top-down and bottom-up models should ultimately converge and predict all experimentally measured behaviour. Multiscale systems biology links systems biology at a smaller or faster scale (e.g. the cell) to systems biology at a greater size or longer time (the organism or the population). A key feature of systems biology is often the integration of data, often in large volumes of data that may be heterogeneous, at multiple scales, both in space and in time.\n\nDue to their internal and external connectivity and nonlinearities, the study objects of systems biology are generally too complex to be handled by a single laboratory. They require a ‘worldwide laboratory without walls’, akin to the open science community. For instance, data and models that come from different expert groups dealing with a cell’s nucleus need to be integrated with data and models of that cell’s cytosol, as well as with data and models of neighbouring cells or tissues. The data integration inherent in systems biology requires metadata standards and ontologies, for computer-aided data exchange and integration, for computational software, for quality control, for experimental methods and for the reporting of experimental data. Models are required for experimental design and experiments are needed to validate them, whilst standards are required for their communication (Nickerson et al., 2016; Stanford et al., 2015; Stanford et al., 2019; Waltemath et al., 2016). High Performance Computing (HPC) hardware with dedicated software is required to run complex models. In addition, a capacity building strategy is key in order to train dedicated experts in the field.\n\nModel-driven integration of heterogeneous and distributed data and knowledge is instrumental to the reconstruction of emergent behaviour in systems biology. For this integration to be scientifically tractable or even possible, the data, as well as the processes of integration and the models themselves, must be FAIR to begin with. For the integration of data and knowledge in models, continual improvements in interoperability are needed to improve the link between the entities in the model and the FAIR data, e.g. from a gene expressed to an active enzyme with supporting literature evidence.\n\nMany functions are critical to an organism’s evolutionary fitness and competitiveness. Because all components of any living organism are, often indirectly, connected, systems biology requires the experimental collection, and then integration, of results obtained from high-throughput genome-wide, or other holistic, methodologies (see Figure 1). Indeed, the accelerating increase of omics data generation has been a major driver of modern systems biology. In order to understand the complexity of living systems in realistic terms, much of systems biology engages in experimental analyses co-designed and analysed by mathematical modelling in a physical-chemical context.\n\nTo address a particular biological question, the cycle may start by data- and/or hypothesis-driven modelling of the system being addressed, followed by the generation of testable hypotheses, sets of predictions and design of the subsequent laboratory experiment. The experiment is carried out, data are generated and this is followed by computational analysis of these data, comparison of prediction to experiment and refinement of the model, which ultimately leads to gaining insights and generating new hypotheses. This cycle builds upon essential disciplines from Biology (the scientific question), Technology (experimentation and generation of data) and Computation (data analysis, modelling and prediction). Although the diagram is a cycle, it represents a spiral: with every turn data, knowledge and models increase, which could be seens as the cycle spiralling out of the plane of the paper/screen.\n\nThe dependence on data from omics experiments, biochemistry and physiology mirrors the ‘ecosystem’ of data resources, tools, and Communities represented in ELIXIR. Data resources provide standardised and FAIR data of a particular kind. These data can be analysed through high-quality and well-characterised tools, often encapsulated in workflows. ELIXIR’s Communities then specialise in the standardisation and analysis of particular types of data, in their application to particular types of biological problems, or in underpinning technologies.\n\nIn the early 2000s, the challenges and benefits of integrating experimental molecular biology with mathematics and informatics had already been demonstrated in systems biology. Reflecting its perceived impact on both life science research and economic development, systems biology research was supported by numerous European and global efforts. Accordingly, an infrastructure for systems biology ISBE (Infrastructure for Systems Biology in Europe) was added to the ESFRI roadmap in 2010. In subsequent years, and in the scope of an ESFRI preparatory phase, a science case and business plan were formulated with the goal of ISBE becoming a legal entity upon gathering support from the various member states involved. The efforts to establish ISBE as a stand-alone entity received the support of too few member states however, and ISBE was removed from the ESFRI roadmap in December 2021.\n\nWhereas ISBE focused on models for Life, ELIXIR focuses on data for Life, but there is a continuum between the two: models rely on experimental data, and are often very tightly integrated with their supporting data. The same ambivalence applies to specific resources. An example is FAIRDOM, which was developed within ISBE as a follow-up from initial efforts within the ERA-Net Systems Biology, among others. Other examples are the BioModels repository, an ELIXIR Deposition Database, which stores models for Life, JWS Online, and perhaps the most visible part of ISBE, its Make me My Model component, mostly at ISBE.NL (see the ISBE deliverables1).\n\nIn response to the issues faced by ISBE and its expected loss from the research infrastructure landscape in Europe, and the awareness that many aspects of systems biology were already features of ELIXIR resources, a Focus Group on Systems Biology was established in ELIXIR in April 2020, which held its first meeting in June of that year. The aim of this Focus Group was to recommend how ELIXIR should respond to the situation around ISBE and support systems biology. The Focus Group presented its report to the ELIXIR Heads of Nodes in May and September 2021 with the recommendation that a new Community in Systems Biology should be established within ELIXIR. This suggestion was supported by the ELIXIR Heads of Nodes and this white paper represents the agreed priorities and aims of this new grouping.\n\n\nDeveloping an ELIXIR Systems Biology Roadmap\n\nThe overarching long-term goal of the ELIXIR Systems Biology Community is to make systems biology modelling a central pillar of research in biology. In this vision, systems biological models are developed based on the understanding of the biological problem, are used to design biological experiments, and help with the interpretation of collected data. The combined results then allow the development of actionable solutions to the original biological problem.\n\nWhile systems biology is present in all biological disciplines, it has so far not reached its full potential. To achieve this, systems biology needs to become more accessible to enable a broader community to benefit from its approaches. The ELIXIR Systems Biology Community has identified the main barriers that prevent wider adoption of systems biology tools and it aims to gradually eliminate them through its future activities.\n\nOne barrier is the lack of availability of well-parameterised systems biology models that are of immediate value for researchers in the wider community. Biologists study a great variety of organisms, each with a great variety of pathways, and physicians study a great variety of diseases in a great variety of tissues. While biological pathway/network resources and genome-scale metabolic maps have grown over the last decade and their usability for flux balance analyses has greatly improved, other approaches additionally require the setting of the much larger number of parameters inherent in rate equations. The values of these parameters differ between species, individuals and tissues. Consequently, the probability that any of the available kinetic, stochastic or multiscale models fits the experimental object a particular researcher is interested in is extremely small. Kinetic, stochastic, and multiscale models continue to be used only by modelling experts. There are many additional facets to this problem. The first is that systems biology models are rather difficult to build - both the understanding of the underlying biology and of skillful modelling are rarely present in the same person. While we can partly solve these issues via better training, the former is also due to a limitation that can only be diminished in incremental steps by increasing our understanding of biology. The second facet is the lack of data that can be used to accurately define a particular use case. As there are (almost) no two particular cases that have the same parameter values, this results in model predictions with wide confidence intervals and low predictive value. A resource such as BioModels Parameters (Glont et al., 2020) provides quick access to parameter values and ranges but is limited to models existing in the BioModels repository.\n\nAnother barrier lies in the insufficient standardisation and interoperability of systems biology, which often makes sharing and reuse a time-consuming challenge. The last decade has seen the creation and increased uptake of new systems biology standards, and increased sharing of standardised models with cross-referenced annotations in repositories, such as MetaNetX (Moretti et al., 2021) and BioModels. However, these do not yet sufficiently cover the areas of model parameter sharing and linking with experimental data. There has also been a huge increase in the development of systems biology software and tools that make use of the standards, but switching between tools remains cumbersome. Better interoperability would enable the building of efficient systems biology modelling pipelines. Here, the ELIXIR Systems Biology Community can learn from the recent advances in the standardisation of sharing of biological data and data analysis pipeline development, where the wider ELIXIR community has played an important role.\n\nFinally, we need to overcome the conceptual barrier to mathematical modelling that is still present in biomedical sciences. While biology is a mature science, in the sense that we have a decent understanding of the major processes that make it work, we mostly do not understand the details to make it truly applicable. To get at those details, and to take advantage of all the big and small datasets collected in the last decades, we need to build more and better systems biology models for better data interpretation, such that systems biology consistently demonstrates utility and becomes a part of all new biomedical studies. This needs to be done in ways that make the resulting models maximally accessible and usable by biomedical scientists.\n\nWhile discussions of systems biology are often focused on the modelling part, there is very little that can be achieved without making use of high-quality data. Data is a source of knowledge necessary to develop the systems biology models, to parametrize them and to evaluate how well they describe the biological question at hand. However, beyond the data produced in their own group or by close collaborators, a modeller rarely finds data perfectly suited for the task at hand. Mostly, this is because the data needed simply do not exist, which is not surprising given the small section of biology we have analyzed experimentally so far. Often the data that would inform modelling are there, but extremely difficult to find or are not annotated well enough for subsequent integration with models. Data for parametrization of dynamic systems biology models are particularly problematic, as these need to be time courses that cover the entire dynamics of the modelled process: biological networks adapt over time.\n\nThere are therefore two types of challenges that need to be tackled when discussing data in systems biology. The first is a cultural challenge on the data generating side. If data are to be useful for systems biology modelling, then this needs to be taken into account already when the experiments are designed, or better yet, when the grant applications are written. The more systems biology modelling is included in the early stages of the project, the more we can count on a one-on-one connection between model and data.\n\nThe second challenge, and one that the ELIXIR is very well positioned to help meet, is linking the data to the models in a FAIR way. Ideally, in the future, this would mean that a model developer would be able to search and find data they need and an experimental scientist would be able to easily find that an existing model can be used to analyse the data obtained. In the last decade, a giant leap forward has been achieved by collecting increasingly large amounts of experimental data in FAIR repositories; however, the data has rarely been linked to modelling repositories. One potential way forward should be to make the data and modelling repositories mutually searchable. Another is to create data repositories that are aimed specifically at storing data that are useful for systems biology modelling. The first attempt in this direction is the recently established datanator repository (Roth et al., 2021). A second is FAIR joint model/data repositories, such as FAIRDOMHub (Wolstencroft et al., 2017) (which has strong links to both ISBE and ELIXIR), which allows interlinking of experimental data, computational models and simulation results in a project-centred approach.\n\nThe essential components of systems biology integrate well with the ELIXIR infrastructure. Although systems biology models have not been, until now, at the heart of the ELIXIR infrastructure, they share many essential properties with the components of ELIXIR. ELIXIR already makes workflows, in essence programs and tools, part of their portfolio. Models, workflows, and data require state-of-the-art computational infrastructure and tools for storage, access, and efficient use. All of this needs to be FAIR. They require highly educated and trained experts to develop and curate resources that are user-friendly and accessible. Additionally, systems biology models depend greatly on the quality and quantity of data for their construction and simulation.\n\nData and metadata\n\nMetadata describing data and models with their items and entities need “minimal information” checklists for attributes to be listed. Descriptions and annotations of data, models and their content need to follow coherent terminologies and ontologies. This is a prerequisite for their integration into systems biology models. Models need standardised formatting and description (for comparison, for modularization, for integration/interlinkage into complex multiscale models, etc.). Standardised visualisation of models helps to share visual information (e.g. pathway diagrams, activity flows, entity relations) on the models in a consistent way.\n\nThere is no single tool that can encompass all aspects of systems biology. Being an interdisciplinary endeavour, systems biology projects span multiple specialities, multiple scales, multiple experimental methods, multiple modelling systems. This puts interoperability and flexibility at the centre of building tools and resources. As a consequence, systems biology standards and resources must aim for improved interoperability.\n\nThe international COMBINE initiative, with its standards SBML, CellML, SBGN, SED-ML and others (Hucka et al., 2015; Waltemath et al., 2020), has developed a range of interoperability standards for systems biology models, their visualisation, combination, and execution. COMBINE standards form the basis of model resources like the ELIXIR deposition database BioModels, as well as JWS online (Peters et al., 2017). The ELIXIR Core Data Resource BRENDA, and the ELIXIR resource SABIO-RK (Wittig et al., 2018) both offer export of mainly literature-based enzymology/reaction kinetics data in SBML format. ELIXIR has strong links to COMBINE, enabling and embodying information exchange between the organisations.\n\nChallenged interoperability where there are different descriptions of the same or related data. When analysing data one often stumbles upon the problem that different data models still yield different descriptions, even though both descriptions are FAIR; there is more than one way for a model to be FAIR. FAIR identifiers from different databases, such as those provided by BridgeDb and MetaNetX), ontology terms from different domain ontologies (e.g. OxO versus meta-ontologies like EFO) and connections between different levels of precision in chemical (sub)structures and chemical names (e.g. the ChEBI ontology, the Chemistry Development Kit (Willighagen et al., 2017), and the various chemistry resources provided by the ELIXIR-CZ Node) should become interoperable with one another. These needs are a challenge not just for systems biology but in fact for ELIXIR, and especially the Interoperability Platform, as a whole, we will need to add the resources needed for interoperability as part of modelling and analysis to the initial work on FAIR descriptions.\n\nThe FAIRDOM-SEEK (Wolstencroft et al., 2015) project data-management system for systems biology emphasizes integration of data and models. It supports researchers and collaborative projects to catalogue, organize, share, interlink and publish local and remote data files, models, protocols, workflows, etc., enabling in particular linking models and their supporting data. FAIRDOM-SEEK’s ‘Search’ includes an external search in the BioModels repository. It integrates the BiVeS tool for describing differences between model versions (Scharm et al., 2016). Integration of the tools JWS online and COPASI (Mendes et al., 2009) enables users to run simulations of SBML models directly in the system. Integration with e.g. NeLS (Tekle et al., 2018) and the Swiss openBIS (Barillari et al., 2016) data management systems aim at bringing more ELIXIR data close to the models.\n\nUsing descriptive models and linking them to predictive models. An ongoing challenge of modelling is the linking of standard models with models expressed in scientific programming and general-purpose languages such as Matlab, Python or Julia. Researchers argue that innovative types of modelling precede standardisation, e.g. in the case of languages for exchange of multicellular agent models. Building bridges between different types of model specifications appears a worthy challenge for a network as wide as ELIXIR.\n\nThe integrative systems biology community has developed various resources for descriptive models (primarily molecular pathways), e.g. in Reactome, KEGG (Kanehisa et al., 2008), MetaCyc (Caspi et al., 2020), and WikiPathways (Martens et al., 2021). Some early attempts to harmonise the content of these built on the BioPAX standard (Demir et al., 2010) or simply on gene lists (e.g. Pathway Commons (Rodchenkov et al., 2020) and the Molecular Signatures Database, MSigDb, at the Broad Institute (Subramanian et al., 2005)). More recently, dedicated converters allow translation between Reactome, WikiPathways, and the Disease Map resource MINERVA (Gawron et al., 2016). This supports integrated analysis using the various resources including the conversion of these pathways into biological networks and exploration with network biology tools like Cytoscape (Shannon et al., 2003). Such networks, combined with experimental data, uncover relevant aspects of molecular biology, like strongly connected parts or strongly regulated parts in the biological system. They also enable linking with gene regulation databases (e.g. transcription factor and microRNA target linking databases) and with databases of chemical interactions with molecular biological targets (e.g. drug-target or molecular toxicology databases). Moreover, such networks can be mapped to biological ontologies (e.g. from Gene Ontology (The Gene Ontology Consortium, 2019)), disease-related genes (e.g. from OMIM (Amberger et al., 2019)), and variants (known from e.g. dbSNP (Sherry et al., 2001) or observed experimentally). Of course, the possibility of linking multiple resources creates new standardisation and interoperability challenges (cf section on Strengthening standardisation & interoperability).\n\nA new development is the link from descriptive models to predictive models in SBML. Since pathway models already support standard descriptions of reactions (e.g. in SBGN and MIM) it is possible to convert them into SBML and that again allows their use as predictive models. This development was recently catalysed by the coronavirus disease 2019 (COVID-19) Disease Map project (Ostaszewski et al., 2021) that is also supported by the FAIRDOM initiative with its FAIRDOMHub platform to share models and corresponding data. The basic infrastructure now exists and needs to be further developed, tested, and disseminated (e.g. as training modules). In essence, this aspect of model interoperability can form the bridge between biological data analysts and predictive modellers working on the same biological systems. This idea was also the driver for the recent fluxomics Implementation Study of the Metabolomics Community. Fluxes are what is predicted by Flux Balance modellers while concentrations of gene products and metabolites are what is usually determined experimentally; the latter are at best a proxy of the former. Measuring fluxes or extending to dynamic modelling, provides the extra linkage.\n\nThe MetaNetX reconciliation (Moretti et al., 2021) of metabolites and reactions aims at providing cross-references between major public resources for metabolism (e.g. KEGG, RHEA, CHEBI) and genome-scale metabolic maps published by different groups (e.g. BiGG, Metabolic Atlas); only such a reconciliation can lead to true genome-scale metabolic models. The computation of the reconciliation considers three lines of evidence: the detailed metabolite chemistry, the description of gene-protein-reaction complexes inclusive of their kinetics, and the dynamic properties of the models, i.e. the distribution of permissible fluxes. Discrepancies, imprecisions, and mistakes in the metabolite chemistry are detected, possibly corrected and converted into cross-references that preserve at best the dynamic properties of the models. The seamless integration of existing models, and their improvement, require more software development and dedicated (application-specific) databases and are in line with the requirements promulgated by the FAIR data consortium.\n\nModels generated via a systems biology approach should be concrete enough for their newly proposed molecular network mechanisms to be validated/invalidated experimentally. This may in part be automated (King et al., 2009) at the high-throughput level, enabling advanced systems biology research to formulate the crucial questions for understanding the system under study. We expect this to enable a new type of bioengineering, which will develop new production processes as well as more effective medical therapies. The role of ELIXIR in supporting this encompasses the provision of sophisticated data resources and tools and rich standards that are useful both for data mining and experimental design.\n\nAlthough we may anticipate the entire automatisation of model building in the foreseeable future, for the time being we still need a hand-crafted approach, where every model is unique and personalised for a certain customer. ISBE developed a concept of so-called M4 (Make Me My Model) service (Kolodkin et al., 2018). The M4 service was provided to various customers. For example, within the framework of the CORBEL project, ISBE has built a PBPK (Physiologically Based PharmacoKinetic) model for a customer from the Environmental Engineering Laboratory in Spain (Sharma et al., 2020). The experience at M4 service highlighted that every new model requires a new configuration of the modellers team with experts from various modelling approaches. Taking advantage of a large research infrastructure where a flexible team of experts from different modelling areas could be quickly assembled for the needs of a specific project would be very advantageous in this sense.\n\nAnother advantage of using a large infrastructure and interoperable platforms is to minimise the need for new models to be built de novo. Already existing models for similar systems could be used as a starting point. We should also notice that, due to the similarities in the biological organisation, and as the same building blocks (biomolecules) and similar biochemical processes are used in all organisms, a common blueprint model could be used. Every new organism and every new case will be instantiations of this more generic model. Along with the development of ‘Silicon cells’ or ‘Digital Twins’ of Biological Systems (discussed in section on Strengthening standardisation & interoperability), Models as a Service can become customer-specific tailoring of the already available blueprint model.\n\nThese various efforts are, altogether, necessary to make systems biology a true enabler of advancements in a variety of fields, from understanding host-microbiome interactions, to the development of comprehensive ecosystem models, to biobased production processes, to systems medicine. In the following section we exemplify how systems biology plays a crucial role in enabling systems medicine.\n\nSystems medicine is an implementation of systems biology in the areas of clinical research and practice. It employs computational, statistical and mathematical multiscale analysis and modelling methods to study disease mechanisms towards improved diagnosis, prevention and treatment. The framework of systems medicine is closely related to the concepts of personalised or precision medicine, where the systems approach informs decisions about tailored actions to improve the health of individual patients or patient subgroups. Numerous publications in high-profile journals have confirmed the benefits of systems medicine approaches in promoting precision in diagnostics and personalised therapies in cancer and other diseases, both rare and common.\n\nSystems biology studies of human disease have to encompass additional levels of complexity compared to other implementations in systems biology (Apostolopoulos et al., 2020; Wolkenhauer, 2020; Zanin et al., 2021), as highlighted in Figure 2. On one hand, human diseases are phenotypically and mechanistically better understood than diseases of other organisms, but on the other hand, there are difficulties studying these molecular mechanisms in accordance with ELSA and GDPR rules. Additionally, whereas we tend to ignore individual differences when we study model organisms, we do recognise the importance of individual differences in humans, obliging systems medicine tools and approaches to personalise disease interventions. Further, disease therapies, which are themselves complex, are also important areas of study and modelling. Implementations in the broad domain of systems medicine can range from semantic representations of diseases and disease maps through mathematical modelling of diseases to applications aimed at supporting P4 (predictive, preventative, personalised, participatory) medicine and at managing individuals’ health, including linkage to clinical monitoring devices and the use of big data and AI. An important requirement for clinical applications in the future will be the link to personal health data records.\n\nEncoding clinical knowledge; federated processing of integrated omics data; construction of disease-specific maps; construction of knowledge and model repositories in the area; and disease-specific modelling and drug target discovery leading to the development of personalised treatments based on models of disease mechanisms. Underpinning all of these is the need to work within ELSI and GDPR regulations.\n\nChallenges associated with building personalised systems medicine models are: identification and modelling of network structures that are prognostic and predictive; integration with related systems such as microbes or expososomes; personalising models using patient data; and clinically validating these models.\n\nSolving these challenges will require access to well-annotated patient data, developing standards for personalising and validating models, and a dedicated repository to exchange these models. Importantly, building models fit for clinical use in precision and personalised medicine should start with a clinical problem, and requires close collaboration between modellers and clinicians. An important aspect to addressing these challenges will be linking maps and models to sensitive data held in the FEGA (Federated EGA), potentially making use of Beacons to identify relevant information (e.g. variation associated with relevant phenotypes). This will become increasingly important with the availability of data from the 1+MG project2. Beyond this, it will be important to improve interoperability of models with other data sources and tools. ELIXIR can help address the challenges of linking models to clinical information through the work of its Health Data Focus Group. A general technical issue, shared by systems medicine and other applications that will make use of sensitive data in the human health and genomics domain, will be the development of federated learning algorithms that are able to learn models based on data held on a number of restricted-access servers. Furthermore, standards and solutions will need to be developed to link dispersed health information to integrating models such as disease maps and digital twins. At the same time, it will be important to improve interoperability between maps, models and digital twins and ELIXIR’s Core Data Resources and Deposition Databases.\n\nAt the core of systems medicine lies the involvement of the user communities: the clinicians and the patients. The patient-oriented approach with the integration of personalised data, both clinical and omics, into network-based analyses and models will enable tailored stratification, therapies, disease management strategies and monitoring. A key element that systems medicine can bring to ELIXIR is its engagement with clinical researchers collecting disease-relevant data and the application of its approaches close to the clinic.\n\nVisual exploration and analytics of computable disease models, which bridges the expertise of clinical experts and the methods of bioinformaticians, enables knowledge about molecular disease mechanisms and relevant clinical data to be brought together for meaningful interpretation, thereby reducing the complexity of the knowledge and the scale of data (Satagopam et al., 2016). This is greatly aided by disease maps (Mazein et al., 2018), an emerging methodology for building human and machine-readable models of molecular disease mechanisms. They offer online and interactive exploration of diagrams describing molecular and cellular hallmarks of different disorders, with detailed annotations of participating molecules, and citations of articles describing the encoded mechanisms.\n\nConstruction of these maps is a challenge, as it requires close interactions with clinical experts, continuous quality checking against emerging facts and data, and persistent evaluation to support downstream modelling approaches. ELIXIR is in a prime position to support building such visual and computable repositories via its newly established Disease Maps Node Service and by engaging relevant communities, e.g. Rare Diseases, Federated Human Data, 3D-Bioinfo, Metabolomics, Proteomics, Galaxy, and others, many of which themselves engage in visualisation and modelling of different kinds of biological entities.\n\nAn example of such an ecosystem supported by ELIXIR is the COVID-19 Disease Map, engaging clinicians, life scientists and computational biologists to set up a graphical and computable repository of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mechanisms. Engagement of a highly motivated community has resulted in an interoperable repository of curated diagrams following systems biology standards (Schreiber et al., 2020), integrated with interaction databases and text mining platforms. We can consider this effort as a blueprint for building qualitative systems medicine models, which will feed downstream, detailed modelling workflows (Fröhlich et al., 2018). A future aim for systems medicine within the Systems Biology Community will be to facilitate the construction of disease maps for currently unrepresented disease areas.\n\nIncorporating individual differences into systems biology models can be used to create personalised models akin to a “digital twin” of a patient with a disease (Fey et al., 2015). Modern omics technologies, such as genome sequencing, allow molecular profiling of individual patients, with unprecedented resolution down to single cells. A prominent example is The Cancer Genome Atlas, an enormous repository of multi-omics data from over 11,000 cases across 33 cancer types (Hutter & Zenklusen, 2018). Populating systems biological models with personal data can yield highly individualised models that can help simulate disease evolution and response to therapy with high sensitivity and specificity (Barrette et al., 2018; Béal et al., 2021; Bhinder & Elemento, 2017; Crawford et al., 2018; Eduati et al., 2020; Fey et al., 2015; Hastings et al., 2020). These systems medicine models are knowledge-based and thus able to offer insight into the disease and drug response mechanisms of a patient (Hutter & Zenklusen, 2018; Ebata et al., 2022). For example, a personalised model of the JNK stress-response network resulted in refined patient-stratification for neuroblastoma, a common childhood cancer, and revealed an impairment of the JNK apoptotic switch in high-risk cases (Fey et al., 2015). As more and more clinically-validated models of this kind arise we foresee a need for a repository for them which might, for example, be built in conjunction with Reactome and the proposed ModeleXchange initiative (see the Strengthening standardisation & interoperability section below).\n\nPersonalised medicine, and therefore systems medicine, is an active area of industrial development in Europe (European Biopharmaceutical Enterprises, 2015). Facilitating linkage of systems medicine into the ELIXIR ecosystem of data, tools and standards can therefore be expected to have an impact on the development of this sector in the future.\n\nA need that systems medicine shares with other applications in the Human Data domain is to address ethical challenges of (i) accessing data for constructing models, (ii) the use of models and (iii) the use of their outputs. For example, constructing models using a combination of datasets describing an individual might increase their identifiability and aspects such as data ownership and the ability to withdraw consent from datasets could affect the persistence of models. The Community will therefore engage with ELSI efforts in the Human Data Communities, within ELIXIR and beyond, to investigate, for example, the impact of ELSI issues on building, constructing and sharing models based on human data. Close collaboration is also envisioned with the Genome of Europe initiative, which will start by collecting ELSI compliant human datasets from the general European population. Another ELSI aspect is engagement with industry, to ensure ethically acceptable uptake of the techniques and infrastructures it develops from lab to the bedside. Finally, the Community will work on the dissemination and outreach of developments resulting from the Community’s work to clinicians and patients.\n\nThe stark rise of high-throughput technologies and related datasets describing the complexity of biological systems in health and disease, has been a driver of the emergence of systems biology, which comes with inherent training challenges. The ELIXIR Systems Biology Community has identified several challenges that need to be addressed for developing and delivering successful systems biology training that could be achieved within different time frames. These are detailed below.\n\nDiversity in trainee backgrounds. Owing to the diversity of systems biology approaches, heterogeneity of trainee backgrounds is common. Trainees often differ greatly in their knowledge of biology and mathematical modelling, as illustrated in Figure 3, and their levels of experience with software tools or systems biology methods also varies from ‘novice’, to ‘competent practitioner’ and ‘expert’ user. Finding the optimal balance between providing sufficient information on systems biology databases and software and not overloading trainees with too many new concepts, represents one of the main training challenges.\n\nMethods/tools for omics data interpretation and integration are categorised based on unsupervised/supervised approaches (Subramanian et al., 2020).\n\nTo accommodate different trainee backgrounds, an option might be to pre-screen trainees well-ahead of the training event to understand their expectations of what they will achieve at the event. This could be in the form of a questionnaire, hosted by TeSS (Beard et al., 2020) or sent out on a mailing list, with the objective to (1) assess the trainee’s abilities, (2) find out their training needs, and (3) make recommendations on existing courses based on (1) and (2). This may prove a good opportunity to synergize training with other biomedical communities (e.g. fluxomics, microbiomics) and offer general bioinformatics courses (e.g. on reproducibility and data management, omics data analysis). Such information will not only help the trainers to adjust the course material, but also establish uniform criteria for pre-requisites of the course. Building a systems biology concept map covering the basic areas of systems biology research and perspectives should be of value. The organisation of hackathons to decide on the concepts that are to be included in more specialised training courses depending on the level of maturity of the trainees in systems biology, has proven to be a successful practice for setting up an ELIXIR training school in a rather diverse area of expertise.\n\nCreation of a systems biology learning path and broad promotion of the integrated systems biology framework. Although some independent ELIXIR training activities already deliver systems biology-related training modules (e.g. single-cell omics, metabolic modelling, data integration), many may well be missing or unknown. There is a need for integrating new systems biology courses into TeSS and for integrating them with existing courses under the systems biology umbrella.\n\nIn line with the efforts of the ELIXIR Training Platform in Task 2, the ELIXIR Systems Biology Community will define a learning path, identify gaps on missing topics and suggest suitable courses. For example, there may be a need for a course on reproducibility of systems biology models, on handling sensitive human data, or on specialised omics topics. As depicted by Figure 3, the systems biology framework can be well-complemented by omics data generation courses and data management courses, already covered in TeSS.\n\nCoordinating educational events across borders is an important part of training. The community will engage in facilitating the collaboration of ELIXIR Nodes for training purposes. Additionally, the ELIXIR Systems Biology Community will initiate joint events with other ELIXIR communities via workshops and hackathons. A complementary approach may be to collaborate with non-profit organisations in the advancement of systems biology-related areas and education, such as iGEM.\n\nWe will systematically review the interest in novel systems biology topics and will propose new courses, based on demand. Dissemination of existing (see Table 3) and new systems biology courses will be enabled by the TeSS platform, with some of the systems biology-related ELIXIR training courses already reported in TeSS. New systems biology courses will be integrated into TeSS and further promoted by organising ELIXIR-level international courses. To reduce the technical issues associated with broken web links on TeSS, we will perform regular checks of these and will also encourage our trainees to report any issues to the site’s administrator. Moreover, we will investigate the overlap between TeSS and other training resources such as the Galaxy Training Network. E-learning approaches for courses and training educational resources will be incorporated in collaboration with the Training Platform and its services.\n\nAvailability and use of standardised datasets in training materials. With the ever-changing systems biology landscape, new tools and massive amounts of data become available and so, trainers need to continuously adapt to these developments. One of the training challenges relates to the lack of standardised and FAIR datasets underpinning specific topics and the lack of suitable documentation for some of the tools or databases. This makes it difficult for trainers to keep their materials up-to-date. In addition, training materials are often focused on specific software or databases, rather than providing an overview of a given topic.\n\nSharing real or synthetic datasets could prove especially useful, for example, as a part of practical hands-on exercises or use cases. The ELIXIR Systems Biology Community will aim to (1) promote the use of appropriate data sets for testing and/or validation in different omics areas, underpinned by ELIXIR Core Data Resources such as The Human Protein Atlas (Uhlen et al., 2010) or MetaboLights (Haug et al., 2020), (2) provide a web-based platform for self-education via online tutorials, (3) establish a network of regular trainers and invited speakers, in order to readily communicate best practices and share materials.\n\nTo provide support to trainers, in order to build a variety of training expertise that can meet the demands of this fast-growing field and the training needs of its users. Supporting the needs of current and future trainers is a key objective of the ELIXIR Systems Biology Community. Identifying specialised trainers from the TeSS network and creating a centralised repository of training materials, would help enormously with this task. In addition, joining the train-the-trainer events organised by ELIXIR will help improve the quality of training.\n\nThere is a lack of teaching courses that would be designed for trainees who wish to learn particular systems biology tools or methods in order to train others. The ELIXIR Systems Biology Community will facilitate the delivery of courses with the aim of (1) training trainees on how to use systems biology resources and (2) providing them with good training material to disseminate the knowledge acquired during the course. The network of trainers will have access to a centralised repository of systems biology training materials, hosted by TeSS, which could save trainers a large amount of material preparation time. Such repositories may contain downloadable PowerPoint slides, lesson plans, high-resolution images in editable format, a list of web links to systems biology resources related to training, ranked based on relevance to a given topic, and models that can be run at a click. This may sound ambitious, but once created, the resources can be updated (e.g. replacing a tool with a newer one).\n\nSystems biology is a multidisciplinary endeavour to gain insights into the complexity of biological systems, pervasive to all colours of biotechnology (Kafarski, 2012)3. It is, thus, also bound to play a major role in the translation of this knowledge into applications of industrial, medical, agricultural and environmental interest. However, the systematic deployment of systems biology varies greatly across sectors, and its potential often remains insufficiently exploited. In this subsection, we map some of the major embeddings of systems biology in various industrial sectors and pinpoint key challenges.\n\nVarious biotechnological and pharmaceutical companies started their own systems biology programs years ago and stimulated academic parallels. Already in the 2000’s, AstraZeneca instated a research chair in systems biology at the University of Manchester, UK, which then became instrumental in setting up largely academic research and doctoral training centres at that same and at other UK universities. In parallel, AstraZeneca and Pfizer developed and published the first systems biology models of signal transduction, relevant for the targeting of anticancer drugs. Bayer spun out a smaller company focusing on systems biology and data analysis. These initiatives also led to systems biology penetrating adjacent fields and setting up Systems Medicine, systems pharmacology, and systems toxicology.\n\nThe EU’s Innovative Medicines Initiative (IMI), co-funded by industry, brought the necessity of these new disciplines to the fore. Many of the supported IMI projects lacked systematic long-term stability, owing to the short innovation life cycle in the pharmaceutical industry. Initiatives of this kind would benefit from long-term sustenance by a European research infrastructure. TransQST, an IMI-funded consortium with industrial-academic partnership with links to ELIXIR’s Toxicology Community, aims to build novel systems toxicology models that enable translation from non-clinical to human safety during clinical trials. Quantitative data and resources generated within this initiative are sustainably disseminated through ELIXIR Core Data Resources, such as ChEMBL (Gaulton et al., 2017), ArrayExpress (Athar et al., 2019), and deposition repositories, including BioStudies (Sarkans et al., 2018) and BioModels.\n\nPK-PD (pharmacokinetics-pharmacodynamics) modelling is an essential component of the drug discovery and development pipeline, which involves mathematical approaches to study pharmacokinetics (PK), pharmacodynamics (PD), and their relationship (Danhof et al., 2005; Peck et al., 1992). The process of drug absorption and disposition by the body is defined using quantitative PK models. Pharmacological effects of a drug on the body taking into account the mechanism of drug action are quantitatively described using PD modelling. The existing approach is however void of biochemical detail and cross-fertilisation with systems biology has been leading to Physiologically-Based PK (PBPK). This may address the roles of active drug efflux pumps as well as kinetic details of drug metabolism in the liver by P450s [e.g. Sharma et al., 2020]. PBPK modelling is also starting to be explored as a key element of a safe-by-design approach for material development (for instance in the DIAGONAL EU project for evaluation of nanomaterials). The European Medicines Agency (EMA) has stipulated guidelines on qualification and reporting of PBPK analysis (Zhao, 2017).\n\nQuantitative Systems Pharmacology (QSP) is a converging point of biochemical pathway analyses and pharmacological modelling, and falls under the broader umbrella of systems biology. Much of such work has been funded by the IMI. The UK-QSP network with the UK and international scientists in industry and academia is jointly funded by the Engineering and UK Engineering and Physical Sciences Research Council (EPSRC) and Medical Research Council (MRC) with financial assistance from AstraZeneca, Pfizer and GlaxoSmithKline.\n\nThere is a strong parallel between systems biology approaches described above for pharmacology and those used in toxicology. The same kinetics (\"does it get there?\") and dynamics (\"what does it do?\") modelling approaches apply. Mechanistic models used in toxicology like adverse outcome models and quantitative approaches for read-across, predicting endpoint information for one substance by using data from the same endpoint from (an)other substance(s), also have their counterparts in pharmacology.\n\nBioinformatics approaches towards mining literature and databases for comprehensive metabolic data have led to the development of maps based on genome-scale metabolic models (GEMs) for a multitude of organisms, including humans (Robinson et al., 2020; Thiele et al., 2013). Constraint-based modelling (‘FBA’ and derivatives) of these GEMs is a systems biology product that enables the understanding of a variety of processes such as new metabolic ramifications of tumours (Damiani et al., 2017).\n\nAnalogous applications to microorganisms have led to multiple new insights into how these organisms may be engineered towards higher productivity (Wehrs et al., 2019). These types of activity have, at the European level, been linked with industry in various settings, including explicitly the ERA-net CoBioTech Action and implicitly the Biobased Industries Joint Undertaking [and its successor] promoting systems biology and synthetic biology as technology drivers to speed up research and innovation in industrial biotechnology. This is particularly relevant when addressing key priorities of the European Union with regards to a green transition to a biobased, environmentally sustainable economy.\n\nThe bio-economy comprises the production and use of renewable resources from land and sea, and the use of waste to make value-added products, such as food, feed, bio-based products and bioenergy. In the EU, the bio-economy is worth an estimated €2 trillion, employing 9% of the workforce. It provides a unique opportunity for Europe to develop sustainable processes and address grand challenges, such as tackling the effects of climate change, achieving a clean environment, fostering industrial innovation, tailor-producing chemicals, contributing to healthy living and ensuring food security. Among the ways to address these challenges, the use of microbial organisms offers a valuable and powerful alternative to the fossil fuel-based economy as they can be engineered into cell factories producing fuels, high-value compounds, chemical building blocks, nutraceuticals and novel medicines (see bioconsortium.eu and the ELIXIR Microbial Biotechnology Community). This is best done through synthetic biology, which is frequently defined as the application of engineering principles to biology. Such principles [model-driven design, modularization, standardisation, separation of design and fabrication] enable streamlining the practice of biological engineering, to shorten the time required to Design, Build, Test and Learn (DBTL) biological systems. This streamlining of iterative design cycles facilitates the construction of more robust microbes that are better adapted to the target application and behave in a more predictable fashion. The streamlining benefits also hold for the engineering of consortia of interacting microorganisms, which allows to explore the wealth of microbial diversity. Furthermore, the individual processes have to be tackled by taking into account the whole value chain if they are to result in economically feasible innovations which can truly contribute to a shift from a petrochemical to a biobased economy (Kampers et al., 2022). The principles, methods and (data and model) resources underpinning systems biology are crucial to reach these objectives. Over the last 5 years, there has been a substantial increase in the number and variety of companies that both adopt and build upon these principles and technologies for their business development. A few examples include DSM, Lanzatech, Zymergen, Ginko Bioworks, Amyris, and Genomatica and, recently, a major push has been made by the USA government on this with substantial investment4. Crucial to these developments is the increasing focus on advanced, (semi-)automated infrastructures that enable rapid, tailored biomanufacturing of chemicals and materials, such as those by ESFRI programme IBISBA5 and other biofoundries6.\n\nThe same basic principles and many methodologies are relevant when tackling challenges in agriculture, in particular in plant and animal sciences, as well as in ecology and water and soil management, and, crucially, in addressing climate change issues, such as reduction of emissions at source (see industrial biotechnology above), carbon capture and nutrient recycling.\n\n\nSystems Biology within ELIXIR\n\nThe infrastructure aspects of systems biology and systems medicine - databases, tools and standards development as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will be essential for ELIXIR’s future support of advanced biological applications and personalised medicine (see Figure 4).\n\nThis illustration shows the central role systems biology may play within the life sciences and how it links to and can supplement existing ELIXIR activities. The scheme spirals out of the plane of the paper in the sense that biological knowledge, experimental data, and models all increase in quality with each turn of the cycle.\n\nBecause in systems biology experimental data relate to emergence of function through computational models, and because computational models need to be based on realistic experimental data, integrated data-and-model repositories such as JWS Online, BioModels and Metabolic Atlas are essential. Models and data need to be accessible to external users, for curation, validation and critical evaluation: the model-data repositories need to be ‘live’ in that they readily simulate the spatial-temporal behaviour of living systems. They should enable ‘what-if’ computational experiments in silico, in order to serve bioengineering, medicine, pharmacology and basic biology. Further, these repositories should allow for constant refinement and update of the models that they host. We can build on the landscape of data resources that ELIXIR already has in the form of Core Data Resources for knowledge used to build the models, and Deposition Databases for parameter tuning, validation, etc.\n\nStandardised model annotation of the described components such as genes, reactions, or metabolites is required to ensure interoperability between models and FAIR repositories hosting large omics datasets. While extensive guidelines and test suites for such annotation have been developed in the COMBINE context and MEMOTE (Lieven et al., 2020), respectively, their evolution and consistent application would benefit from a strong infrastructure context.\n\nIn relation to ELIXIR, the Systems Biology Community will enable a wide range of researchers to benefit from existing and proven systems biology and bioinformatics approaches, rather than to reinvent wheels. A number of applied Communities in ELIXIR, such as Rare Diseases, Food and Nutrition and Toxicology, form bridges to large research fields. We offer to support these ELIXIR Communities with the standards and best practices of the systems biology ‘ecosystem’ and build on ELIXIR Platforms to enable better understanding and reproducible analysis of complex systems.\n\nELIXIR Communities and Platforms cover topics, including:\n\nTechnology, like the Galaxy Community and Bioschemas (and Compute in general);\n\nBiological entity descriptions, in Core Data Resources, and in Communities like Metabolomics, Proteomics, Copy Number Variation and Intrinsically Disordered Proteins.\n\nApplied Communities like Rare Diseases, Plant Science, Food and Nutrition, and Toxicology.\n\nThe Systems Biology Community intends to become the link between these, providing the model ecosystem to the applied Communities, allowing the usage of data from those concerned with biological entities, and using the computational technology approaches and data infrastructure experiences and tools to do so. That linkage again builds on activities in the Interoperability Platform.\n\nThere are clear synergies between the objectives and activities of the Systems Biology Community and the ELIXIR Platforms, as described in the following sections.\n\nThe data platform. The ELIXIR Core Data Resources and Deposition Databases are already highly used by the systems biology community. For example, data from BRENDA, STRING, and Reactome are essential both for construction of molecular pathways and parameterization of molecular reactions. Furthermore, an essential systems biology database, BioModels, is already part of the ELIXIR Data Platform. With JWS-Online, it facilitates the discovery, deposition, and re-use of systems biology models. SABIO-RK is an ELIXIR Node service which provides curated data manually extracted from literature to modellers. This demonstrates the compatibility of models for data with data for data. Systems biology could contribute new databases to the platform, such as JWS-online, Make Me My Model and many others, which could serve as an example for data service-based resources and databases. Finally, through ELIXIR, the Systems Biology Community, which already features among the largest users of the ELIXIR data resources, should be able to provide support and advice for further development of these resources, so that they become more compatible with predictive, modelling-based knowledge development, making the data more actionable. The engagement of the Data Platform in curation efforts also supports the maintenance of systems biology resources and improves the data quality.\n\nThe tools platform. Systems biologists have in the past developed a range of tools, which could find their home within the Tools Platform. Adding systems biology tools to bio.tools, BioContainers (da Veiga Leprevost et al., 2017) and workflowhub.eu will improve the usage of the already available tools making them better findable and interoperable and applications more reproducible while making it possible to construct new workflows that combine data and modelling operations. Examples of workflows for systems and synthetic biology are embedded in the ESFRI IBISBA. SynBioCAD (du Lac et al., 2020) is the first Galaxy toolshed for synthetic biology and metabolic engineering. These workflows are registered in workflowhub.eu. It will also be of interest to investigate opportunities to engage with OpenEBench to benchmark models and workflows.\n\nThe compute platform. Although specific and large-scale computational simulations require tailor-made, large computational infrastructure, a vast majority of systems biology simulations can be and are executed on general-purpose computational platforms. In the same way that ELIXIR is enabling its members to use national and European compute service providers for their data management needs, it could provide access for systems biology modelling. Through the Compute Platform we will also be able to link to EOSC activities related to Cloud data and workflow execution and also provide convenient access options via the Life Science AAI.\n\nThe interoperability platform. Standards are as big an issue in models as in data. Only data and models that use standardized file formats, metadata and vocabularies can truly be FAIR and used by the whole community. The Interoperability Platform’s Recommended Interoperability Resources help to improve this FAIRness while the Platform’s standards mapping resources, such as BridgeDB, identifiers.org and OLS, facilitate better interoperability and integration of data and models. In systems biology, the COMBINE consortium (Hucka et al., 2015) is the international initiative that coordinates the development of standards, and the use of standards in systems biology is continually increasing. The harmonization between data and model standards, therefore, presents a great opportunity in the next decade, and ELIXIR is in a perfect position to catalyse such a development. A more systematic collaboration with COMBINE should lead to harmonisation of the standards landscape for systems biology. Practical collaboration between the hackathon initiatives from COMBINE, HARMONY, and the Biohackathon can also be expected to be fruitful. Because systems biology combines all the different aspects mentioned above, it is a testbed and impact case for interoperability approaches, further fueling new interoperability developments.\n\nThe training platform. The ELIXIR Training Platform remains instrumental in the training of the next generation of data science experts. While there have been plenty of smaller-scale initiatives for systems biology training in Europe at the same time, the overall scale of training in systems biology has been much smaller, mainly caused by a more fragmented systems biology community. To lift-up systems biology training Europe-wide, we propose the joining of the Systems Biology Community and data resources under a single roof. Upscaling training can benefit from FAIRification of training materials, a process which is well supported by the ELIXIR FAIR Training Focus Group. Embedding systems biology training within the ELIXIR Training Platform via TeSS will also enable their integration into Learning Paths which are under development. The Training Platform will help the ELIXIR Community to develop new training materials through training hackathons that will be hosted together with existing training resources in standardised data repositories via TeSS.\n\nAs indicated already in the section “Current Systems Biology activities in ELIXIR” above, systems biology is already a key component of the work of a number of ELIXIR Communities, and it can play an important role in others. Moreover, systems biology also plays a role in various focus groups. Some possible contributions of a future Systems Biology Community to the ELIXIR Communities and Focus Groups are described below in a non-exhaustive manner.\n\nTechnology-oriented Communities:\n\nGalaxy: In a recent Community-led Implementation Study, ELIXIR supported the integration of omics data access and analysis tools into Galaxy workflows. Building on this work, an initiative to improve connectivity between Galaxy and systems biology model repositories, development and simulation resources should provide a strong, practical boost to the ELIXIR Community-driven integration between Data and Models for Life.\n\nBiological Entity Communities:\n\nMetabolomics: Aimed towards the chemical, mechanistic and reaction flux-related aspects relevant for biomedical applications, microbial biotechnology, plant sciences, toxicology and nutrition, and the workflows and data interoperability aspects needed for those. Getting from metabolite levels to fluxes strongly links to quantitative dynamic models in systems biology. The Implementation Study “Standardising the fluxomics workflows” of the Metabolomics Community includes aspects of how ELIXIR could contribute to systems biology methods and workflow standardisation.\n\nApplied Communities:\n\nMicrobial biotechnology: Aims to support the computational infrastructure underlying the Design - Build - Test - Learn (DBTL) cycle in the design of industrial microbes. It aims to contribute to addressing standardisation and other issues in relation to models in microbial biotechnology (e.g. semantic ontologies) and thereby contribute to a knowledge-based infrastructure for biotechnology.\n\nPlant sciences: An interdisciplinary group of researchers very active on the border between experimental and computational approaches that aims at building a tools service bundle that will support plant scientists in the integration and linking of diverse datasets with an extension towards systems biology. Many of the current activities of the Community are in the field of experimental data management tools. Expertise from the systems biology community would in the short term enable the extension of these activities to the management of plant systems biology models which are becoming increasingly prominent in the field.\n\nFood and nutrition community: Aims to support the research towards the effects food choice and nutrition have on health and well-being. This typically is a system-wide effect where many small changes work in combination.\n\nToxicology: Aims to support risk assessment of chemicals, drugs, cosmetics ingredients and nanomaterials to lead to safer products. This includes the combination of toxicokinetic (exposure, uptake, distribution, metabolism) and the toxicodynamic (molecular interactions and complex connected events in adverse outcome pathways). Both aspects and their combination strongly lean on models and modelling.\n\nMarine metagenomics (Microbiome): Aims to develop a sustainable metagenomics infrastructure to enhance research and industrial innovation within the marine domain. It develops standards and best practices for the marine domain, provides databases specific to marine metagenomics and develops tools and pipelines to enhance metagenomics analyses. These goals will benefit from the standardisation efforts of systems biology elements and, in particular, from the deployment of metagenome scale (metabolic) models.\n\nHuman data communities:\n\nFederated human data: Activities in the domain of human data focus on the sharing of human data, predominantly but not exclusively in genomics making use of the increasingly sophisticated Federated EGA and Beacon infrastructures. Although focusing on genomic sequences, FEGA also accommodates phenotypic and disease information which has potential uses in systems biology and systems medicine.\n\nRare diseases: Implementation Study “ELIXIR Rare Diseases Infrastructure (2019-21)”, although not explicitly addressing the needs of systems biology or systems medicine, addresses the linking of infrastructures needed to interpret data on rare diseases as well as collecting data that is “FAIR at source”. There is an opportunity to link these objectives to a systems medicine perspective on rare diseases.\n\nELIXIR also runs a number of focus groups (FGs) that are relevant to the Systems Biology Community:\n\nMachine learning (ML): This focus group was initiated in October 2019 to address needs related to the application of ML in mining large omics datasets to uncover new insights in the field of medicine. These complement activities in systems medicine. Goals of the ML focus group relate to the development of controlled terminology/ontology and services for ML model description. There is an opportunity to align these developments with efforts on standardisation of models in systems biology.\n\nEOSC: Connects ELIXIR’s EOSC-related activities, which run along the axes: a) Consolidation of e-Infrastructure services and positioning these services as an embedded “supply-chain” for data-intensive scientific collaborations; b) Open Science in practice; c) Integrating the user-focussed services from research infrastructures with their user communities to enable interdisciplinary research aligned with the major societal challenges. Systems biology and in particular its focus on model standards, workflows and model-driven activities, can contribute and help to expand the aforementioned EOSC ELIXIR activities.\n\nRegistries: identifiers.org, an ELIXIR Interoperability Resource, was founded to fulfil a need of the systems biology community, and now provides a key registry of data resources for both ELIXIR and systems biology. Bio.tools, provides a key registry of tools with strong coverage of ELIXIR-based tools, but has limited coverage in the systems biology domain. Systematic curation of both resources and harmonisation of their computational interfaces, in collaboration with the Galaxy community and in the context of the Interoperability Platform, would provide a strong contribution to the essential integration of models and data.\n\nBiocuration: This group was established in 2021 and builds a network of database developers and curators in ELIXIR. The Systems Biology Community benefits from the interaction with the International Society for Biocuration and the engagement for a better visibility and recognition of the work of biocurations, e.g. community curation efforts in model resources.\n\nFAIR training: The FAIR Training FG was formed in 2018 with the aim of improving the production and diffusion of FAIR training materials across Nodes. These activities closely complement those of the Systems Biology Community whose applications often rely on multi-omic and holistic datasets and respective descriptors and identifiers for effective delivery of materials and tools of systems biology.\n\nBiodiversity: This group is focused on understanding and cataloguing the capabilities, interests and ongoing projects we have in this area across the ELIXIR Nodes. It develops appropriate connections with key external partners in the field. Large-scale systems biology models of interactions and evolution are bound to strengthen the area, as exemplified by various specific research projects across Europe\n\n\nThe Community’s objectives\n\nTo illustrate the importance of infrastructure for systems biology in a forward-looking way, we have identified a number of potential challenges for the Systems Biology Community that would rely strongly on the infrastructure ELIXIR provides. These challenges align with those of other ELIXIR Communities, as outlined previously in this paper. They sit on a scale comparable to the grand challenges that ELIXIR tackles in its programme, namely:\n\nTo deal with the increasing volume, complexity and heterogeneity of data,\n\nTo enable the interoperability between data resources,\n\nTo effectively use large, complex and heterogeneous data sets to generate actionable knowledge,\n\nTo make it easier to find and deploy the right tools and to undergo training,\n\nTo build data interpretation and modelling infrastructure following FAIR principles,\n\nTo drive innovation and industry usage.\n\nA major remit of systems biology is to quantitatively describe the dynamic, emergent interactions among the many components of biological systems. The goals are hence the generation of insights and knowledge, which can be translated into applications of industrial, environmental, nutritional, medical, ecological, and agricultural interest. For instance, predictive dynamic models of cells, organs and organisms have a potential for pre-testing drugs, producing new materials and chemicals for food & feed, understanding biogeochemical cycles, tackling carbon storage, and accelerating the shift from a petrochemical to bio-based economy. Models are crucial to understanding and fostering human and animal nutrition, host-microbiome interactions (plants, insects, animals, environment) and a range of other areas. These include the biochemical brain; systems ecology, agriculture and environment; individualised medicine enabling the prediction of the effects of 2,4-Dinitrophenol (DNP) in physiology and pathology; systems pharmacology enabling the individualised prediction of drugs’ effects and toxicity, as well as model-driven production of tailored pharmaceuticals; systems epidemiology enabling the critical prediction of how government and therapeutic measures affecting pandemics such as that of COVID-19.\n\nAll these areas will benefit substantially from systematic and comprehensive bioinformatics and mechanistic and realistic modelling. Below we lay down five pillars around which this ELIXIR community aims to contribute to strengthen systems biology.\n\nThe standardisation needs in systems biology remain diverse (see Table 4). Data and models, as well as metadata of both, need consistent structuring following standardised formats. Close collaboration of ELIXIR with standardisation communities dedicated to modelling in the life sciences, such as COMBINE, as well as with relevant committees of standardisation bodies like CEN/CENELEC and ISO, such as the ISO committee for biotechnology standards (ISO/TC 276) with its working group WG5 “Data Processing and Integration” or the ISO committee for health informatics (ISO/TC 215), will ensure further development and adaptation of existing modelling standards to the needs of models shared via ELIXIR resources. Based on modelling standards like the ones from COMBINE (Golebiewski, 2019), model validation becomes more realistic. An advancement in this direction has been the release of the standardised genome-scale metabolic model testing tool MEMOTE. Retrospectively applying this tool to existing models, however, remains an open challenge. We will seek to contribute to the standardisation and interoperability of data, operations and models.\n\nModelling repositories. Current work across ELIXIR Nodes has begun to partly address these challenges. For example, Metabolic Atlas is promoting the use of a template code repository called standard-GEM for open-source genome-scale metabolic models. Conceptually similar to the COMBINE archive, standard-GEM establishes a folder and file format structure that fits with the iterative, versioned model maintenance process. In turn, such a standard structure enables future automatic validation with tools such as the aforementioned MEMOTE, and opens the door towards packaging with RO-Crate (Soiland-Reyes et al., 2022) and potential integration with BioModels, JWS-Online and OpenEBench (Capella-Gutierrez et al., 2017) via COMBINE.\n\nAnother ELIXIR effort is the established service MetaNetX, which cross-checks model annotation and reports inconsistencies in identifier mapping with respect to chemistry, in addition to facilitating cross-model mapping. Building on this knowledge-base, a potential future direction is the development of a service focused on assessing the quality of the annotation, which would complement the quantitative assessment that is already covered by MEMOTE.\n\nOn a wider-reaching level, model repositories like BioModels, FAIRDOMHub and its JWS-Online and others collaborate on the development of community standards, but they are only starting to co-ordinate their curation and dissemination activities. Currently users still need to access multiple repositories to discover all models potentially relevant to them. Moreover, a recent large-scale study (Tiwari et al., 2021) of 455 published models showed that about half of the models could not be reproduced using the information in the manuscripts. Without coordination, many researchers might independently try and fail to reproduce a published model, wasting a lot of time and effort. Recognising these challenges, in the emerging ModeleXchange consortium, repositories are starting to coordinate model curation and discovery. This activity should be strengthened in the context of an ELIXIR Systems Biology Community, with significant user benefits.\n\nStandards for design and modelling. Less developed are the standards related to the design of experiments and the description of these designs (which are required to generate standardised, FAIR data to be subsequently capitalised on by models). This is of particular importance for complex, multistep operations that are required for many processes, such as those pertaining to biobased production of chemicals, pharmaceuticals or materials. The ESFRI programme IBISBA works on the interoperability and deployment of such concepts and standards and workflows, but many challenges remain. This is relevant for ELIXIR since these designs in the end lead to data covered in the infrastructure.\n\nStandards for linking models with sensitive data, including electronic health records, as well as other person-related data and commercial data, with ELIXIR Core Data Resources and Deposition Databases are an identified need. ELIXIR and members of national ELIXIR Nodes are already active in defining such standards and connecting them to existing research projects in the domain as partners in the European standardisation initiative EU-STANDS4PM (European standardisation framework for data integration and data-driven in silico models for personalised medicine) that very recently has published guidelines and recommendations for data integration and model validation for computational models in the domain of clinical applications in personalised medicine (Collin et al., 2022). Through the EU-STANDS4PM initiative, ELIXIR also supports the development of a series of ISO standards with recommendations and requirements for predictive computational models in personalised medicine research (ISO TS 9491). Such standardisation efforts need to be intensified and extended, given the increasing importance of modelling in the health domain. For this purpose, close collaborations with European initiatives, such as EU-STANDS4PM and those developing infrastructures for human digital twins (including corresponding standards for data and models) that are currently forming and will be funded in the near future, will help to jointly create a pan-European cloud-infrastructure for data integration and modelling in health research and personalised medicine.\n\nInteroperability between various forms of descriptive models and predictive models. Some relevant model connections, which basically connect predictive analysis with data analysis have been developed and a few are in production. For now, most exist as proof of concept rather than production ready services. The work done in the COVID-19 Disease Map project involved much manual curation and improvement of both the converter and the source (pathway) model and can even lead to updates for the standards used. The challenge is to streamline that process and to support curators to come to more interoperable models and FAIR descriptions of provenance and evidence.\n\nAlthough the intertwining between modelling and experimentation is a hallmark of systems biology, its practical implementation remains challenging. Partly this is due to culture and insufficient training, but it also stems from difficulties in generating adequate, quantitative dynamic data that can support modelling and from the lack of models that are sufficiently accurate to handle the generated data. Addressing these challenges will require 1) an interface between big data and modelling frameworks, 2) integration of modelling approaches, including temporal and spatial modelling, and 3) application of the modelling results in a plethora of relevant domains, ranging from bioengineering at various scales to precision and personalised medicine (see Table 5).\n\nSystems medicine. In the systems medicine domain, additional challenges result from 1) the sensitive nature of many of the data sources, 2) the complexity of disease phenotypes and mechanisms, especially in the context of precision medicine, and 3) the ethical and legal implications of using models and model predictions in clinical decision support. Solutions will be needed that enable the use of sensitive data to build models in a manner consistent with requirements for sensitive data. The community will also facilitate the development of new models and disease maps and of improved repositories to enable their sharing in a FAIR manner, in order to address the challenge of disease complexity. Finally, the Community will engage in ELSI activities to explore the challenges of using systems medicine models close to clinical practice.\n\nModels as a service. Owing to the importance of modelling resources, methods, models, data, and expertise across the board (from dynamic to constraint-based, stochastic, statistical, and data modelling) it should be an aim to enhance applications in particular by systems biology novices, many of whom are deep experts in medicine, biology or biotechnology. This should be done by providing assistance to those novices in their use of the facilities offered by the Systems Biology Community as well as by a larger number of ELIXIR Communities and as per recommendations above. It should be made easy for the novices to find the most relevant model, to adjust it to their needs, to extend it, and to even make their own new model. This relates, most immediately, to activities on Make-Me-My Model, Data for Modelling, Modelling for Data, multiscale modelling discussed above, but it will readily expand to many other ELIXIR areas.\n\nDigital twins of biological systems. Systems biology models build upon data for predictions and thereby truly bring data to life. The combination of models and smart big data enables designing Digital Twins of biological systems and thereby strongly enhances the possibilities to explore, understand, design and predict biological behaviour. Therefore, it is proposed to provide vehicles (dedicated projects across Platforms, an ELIXIR community, or other) to smoothly integrate systems biology models with Big Data analytics and to thereby stimulate dedicated activities underpinning the development and deployment of Digital Twins for the whole range of applications in the Life Sciences. This extends from the design of highly efficient cell-based industrial and pharmaceutical processes through decision-support systems in health and disease, to integrated farming systems and ecosystem management.\n\nWhereas the separate curricula in physical sciences, data-focused life sciences, and computer science have become quite effective in training in their own disciplines, they are becoming inadequate to train multidisciplinary teams which need to tackle increasingly complex problems. Global health challenges such as non-communicable diseases, pandemics, or diseases stemming from environmental factors have all been addressed by systems biology models. When supplemented with ELIXIR earmarked information, these models should soon become ready for use in the clinic, especially because they are the only tools truly to handle the increased call from the general public for personalised medicine. This call has also been realised by the European Parliament and the European Commission. A vast increase particularly in transdisciplinary training is necessary now and ELIXIR-training is well-posed to set this up. The joint ELIXIR-ISBE course on Corona (SARS-CoV-2) epidemiology may serve as an example.\n\nSeveral independent, ongoing training activities already deliver systems biology training modules within ELIXIR (e.g. Table 3). With the exponential growth of biological data, there is a lag in the identification and generation of new ones. National Training Coordinators may assist in flagging when such courses are missing from TeSS, and further promote Node-interaction when such competencies are not present by organising ELIXIR-level international courses. A possibility might be interacting with non-profit organisations working in systems biology-related areas and education such as iGEM.\n\nSystems biologists often have to cope with scattered knowledge resources. Hence, a well-balanced and consistent set of competences are required that are compatible across the ELIXIR Nodes. We propose to implement a programme of organisational capacity building, including specific training in gap areas, advanced training, knowledge sharing and staff exchanges to build a well-developed and interconnected Systems Biology Community. We will make use of the ELIXIR’s training portal TeSS by integrating different tools and services relevant to systems biology and making it available to all Nodes. Synergising the training resources, the needs of trainees and trainers, and the communication with other ELIXIR communities is an overarching aim for the Capacity building/Training task. This will be achieved by integrating new and existing systems biology-related courses under a single umbrella towards the different objectives listed in Table 6. The corresponding activities will support the needs of current and future trainers long term, and centralise the use of systems biology materials.\n\nSystems-level understanding and analysis of huge amounts of experimental data is required for different ‘industries’ such as hospitals, pharmaceutical industry, biotechnological companies, health care institutions, regulatory agencies, and government. However, the potential significance of systems approaches in industrial sectors has been exploited insufficiently. Systems biology aims to develop quantitative and conceptual understanding of biological phenomena. This comes with the modelling and prediction of complex processes such as functions of the human brain, ecosystem function or host-microbiome interactions. The ability to model and predict what happens to a biological system under some conditions may have a profound impact on industrial applications as diverse as the identification of the best drug candidates using PK-PD models, sustainable production of biobased chemicals and materials through model-driven designs, improvement of crop production strategies, or COVID-19 management.\n\nQuantitative data and resources generated within IMI-funded consortia with industrial academic partnerships like TransQST, which aims to build novel systems toxicology models, have been made available through ELIXIR Core Data Resources and deposition repositories. These collaborations are valuable to ELIXIR’s Toxicology Community. Similar initiatives for systems pharmacology have been supported by IMI, major UK funding bodies and pharmaceutical companies like AstraZeneca, Pfizer and GlaxoSmithKline. Systems biology and synthetic biology will be particularly relevant to address five out of the seven key challenges identified by the European Union related to health and environmental sustainability. Hence, efforts towards transition into more environmentally sustainable economies offer unprecedented opportunities for a range of subfields of systems biology.\n\nThe ELIXIR Systems Biology Community will take an active role in the use of ELIXIR resources and in the definition of activities aiming to develop new industrial collaborations and to strengthen existing ones. These activities will be aligned to ELIXIR’s Industry Strategy by (1) facilitating collaborations between researchers in academia and industry, (2) by enabling the use of ELIXIR resources by industry and (3) by engaging effectively yet appropriately with the private sector. One way to engage with the industrial sector is through joint workshops and collaboration with other ELIXIR Communities interested in working with industry. Other objectives to achieve industrial embedding are listed in Table 7. An important aspect of these objectives is the use of Key Performance Indicators (KPIs) and \"gap analysis surveys\" to measure overall long-term performance and to identify priorities for improvement. The potential is enormous, given the capabilities of the deployment of data and models to describe biological systems and to enable actionable knowledge for a vast range of translational applications.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nWe thank ELIXIR for financial and administrative support during the development of this white paper and its support of the ELIXIR Systems Biology Focus Group.\n\n\nFootnotes\n\n1 ISBE deliverables: ISBE D2.2 Preliminary Recommendations for a Data and Model Management Framework: Data and Model Stewardship for the ISBE Infrastructure (2014); ISBE D2.3 Final Recommendations for a Data and Model Management Framework: Data and Model Stewardship for the ISBE Infrastructure (2015);ISBE D2.4 Implementing Recommendations for ISBE Asset Stewardship Data and Model Stewardship for the ISBE Infrastructure (2015).\n\n2 https://digital-strategy.ec.europa.eu/en/policies/1-million-genomes\n\n3 See also https://omgmopodcast.com/definition-of-biotechnology/\n\n4 https://www.forbes.com/sites/johncumbers/2022/09/12/white-house-inks-strategy-to-grow-trillion-dollar-us-bioeconomy\n\n5 www.ibisba.eu\n\n6 https://biofoundries.org; https://agilebiofoundry.org; https://www.biomade.org\n\n\nReferences\n\nAmberger JS, Bocchini CA, Scott AF, et al.: OMIM.org: leveraging knowledge across phenotype-gene relationships. 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}
|
[
{
"id": "155195",
"date": "28 Nov 2022",
"name": "Yoram Vodovotz",
"expertise": [
"Reviewer Expertise Systems biology",
"inflammation",
"computational biology",
"immunology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDos Santos et al present a white paper outlining the overall rationale, current work, and future plans of the ELIXIR consortium. The manuscript is overall logical and well-written. However, there are some points that the authors should consider and that would improve the manuscript overall:\nOverall, the thrust of the manuscript and ELIXIR as a whole seems to center on the concept that Systems Biology is predicated on the generation of mechanistic mathematical models, with datasets envisioned as being used for calibration/verification/validation of these mechanistic models. While this is certainly a major goal for many in this field, there seems to be little mention of machine learning (i.e. data-driven modeling) as an alternative (or, ideally, an adjunct approach that could synergize with or integrate machine learning with mechanistic modeling), though there is mention of a focus group on machine learning and a short term goal stated as “Understanding how big/smart data meets models meaningfully.” It would seem that there is a need to establish workflows and pipelines wherein data are generated, data-driven modeling/machine learning is performed to identify important features in the datasets, and those features are, in some way, included in the resultant mechanistic models. In this way, the current gap between data-driven and mechanistic modeling could be bridged. This is alluded to, but not made explicit, in the section entitled “Using descriptive models and linking them to predictive models” and is a component of Figure 3. While I realize that this white paper encapsulates and presents the current consensus within the ELIXIR community, a more explicit, high-level overview of how data-driven and mechanistic modeling could interface (e.g. as noted in Table 5 under “short-term goals”) would improve the manuscript. Perhaps the authors need to clarify exactly what the term “smart big data” means, because it is possible that this term refers to what I have mentioned above.\n\nExecutive Summary, definition of Systems Biology: “thousands” should probably be changed to “myriad” or some other more general term since biological interactions could add up to the millions or more. For example, while there are thousands of genes, there are millions of single-nucleotide polymorphisms that could impact biological systems.\n\nExecutive Summary: I think the authors presuppose that readers are already familiar with ELIXIR and its myriad activities. However, many readers will not be aware of this group. Thus, there should be a straightforward introduction to ELIXIR and its core mission. In a related issue, the authors should make sure to state that their focus is predominantly on developments happening in Europe since that is where this consortium is located, though the white paper does cite resources that were developed in the U.S.\n\nExecutive Summary, Tables1/2: The authors are to be lauded for their extensive listing of prior/existing Systems Biology initiatives. However, Avicenna Alliance is not mentioned (though it is closely related to VPH), and this group has made major strides in driving the adoption of computational modeling and in silico clinical trials.\n\nIntroduction: in the section entitled “Systems biology underpinning systems medicine,” the reader may be well-served by mentioning Translational Systems Biology and relevant publications from that related field. This could be included also in the section on Quantitative and Systems Pharmacology. A discussion of both of these approaches is of relevance to the white paper’s focus on in silico clinical trials and digital twins. In this regard, the lack of connection between the Systems Medicine and QSP sections is a bit of missed opportunity since at the end of the day drugs are being developed to treat patients, and the disease models that serve as the basis of digital twins are offshoots of the same models used to develop the drugs in the first place (e.g. the goals and objectives listed under Table 4).\n\nMinor:\nIntroduction: “…the study objects of systems biology”; I assume the authors mean “objectives”?\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly",
"responses": [
{
"c_id": "11436",
"date": "31 May 2024",
"name": "John Hancock",
"role": "Author Response",
"response": "1. We thank the reviewer for summarising the perspective on mechanistic models and AI. Mechanistic models are indeed a major goal for the field. For many years, perhaps decades, they have provided a clear-box approach to modelling, allowing the researchers to be in control of the abstractions, and facilitating a transparent mapping to biological processes. AI models, on the other hand, are prone to create difficulties in understanding their inner workings, and much more so in the large language models developed in recent years. As suggested, interfacing the two approaches could be a way to bridge the gap between the explainable and unexplainable modelling approaches. As an infrastructure Community, we will closely follow the latest research developments in this regard. The manuscript has been adjusted by replacing the term “big/smart data” with “big data and AI” (lines 171 and 575) and to include the above expansion on the interfacing between modelling approaches (lines 1220-1229). 2. The suggestion has been applied (line 50). 3. We have added a brief description of ELIXIR as a European infrastructure to this section (lines 63-66) 4. Avicenna Alliance has been added to table 2 (line 1546). 5. We have tried to address this point in the text, especially in the section discussing Industrial Embedding and PBPK models 6. The authors did indeed intend to discuss “study objects”, that is the objects studied by systems biology (line 244)"
},
{
"c_id": "11831",
"date": "21 Jun 2024",
"name": "Yoram Vodovotz",
"role": "Reviewer Response",
"response": "I thank the authors for addressing my core concerns."
}
]
},
{
"id": "156725",
"date": "12 Jan 2023",
"name": "Herbert Sauro",
"expertise": [
"Reviewer Expertise Systems Biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\ndos Santos et al, provide a comprehensive summary of the current state of systems biology modeling as well as the challenges they see in the future within the ELIXIR framework. One of the important discussion points is suggestions for short-, mid-, and long-term goals within systems biology. The list of suggestions, however, would not have been out of place if published 20 years ago. This highlights that we still have a long way to go. For example, one of the long-term aims is improved interoperability, something that the community has been attempting to achieve for a long time. Many of the goals have a similar ring to them, though some are more interesting than others. For example, one of the mid-term goals is developing the basis for theoretical and practical multis-scale modeling. I consider this to be a major issue in multi-scale modeling which I feel urgently needs addressing. Another thoughtful goal is to use models to improve the design of experiments, that is, model-driven rather than data-driven approaches.\nOverall, the paper presents a good coverage of the efforts being undertaken in Europe and to some extent elsewhere, although some things appear to be obviously missing. For example, there is no mention of SBOL (Synthetic Biology open language) standard, even though synthetic biology is frequently mentioned in the text and is a key aspect in both the article’s short-term and mid-term goals. The biggest gap, however, is that there is very little discussion of machine learning or AI. Having said that, I should say I am firmly a card-carrying mechanistic modeler. Machine learning is a two-edged sword. On the one hand, it’s very good at finding patterns in data, but it’s also very good at hiding any understanding of why the pattern exists at all. As sentient beings, we don’t want to completely give up our intellect to a machine, however, there must be some halfway point where machine learning can inform our mechanistic models, help us determine what data we should collect (model-driven), or supply useful hypotheses to peruse. The ELIXIR program has a unique opportunity to augment its long terms goals by weaving machine learning into our mechanistic view of the world without losing our ability to understand reality. However, this is a basic research effort that will take time to develop and would probably belong to the list of long-term goals.\nAnother missing component in their long-term goals is fostering tighter collaboration with the USA and other countries in the systems biology field, particularly with joint grant awards. This of course, has, and is happening. Most notably, many of the popular systems biology standards were the result of close collaboration between groups in the US and Europe. This is still very much an active area, but a statement in the list of long-term goals would help emphasize that continuing collaboration is very important to the success of the field.\nFinally, I think one of the long-term goals should be to advertise success stories more strongly. Europe, in particular, probably has more success stories in mechanistic modeling than any other trading block. This is particularly the case in understanding metabolism, where groups led by individuals such as Jacky Snoep or Bas Teusink and co-workers have made significant contributions to our understanding of energy metabolism using systems biology approaches.\nIn summary, the article is interesting. It provides a status report on systems biology but perhaps misses some opportunities for future opportunities.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "11437",
"date": "31 May 2024",
"name": "John Hancock",
"role": "Author Response",
"response": "- We have added mention of SBOL, particularly where we mention the COMBINE initiative in the \"Data and metadata\" but also elsewhere in the document - With reference to AI and machine learning, We thank the reviewer for the suggestion, which has been added into the manuscript (lines 221-222) - With reference to fostering closer links to the US, this has also been added as a long-term goal (lines 223-224). - With reference to advertising success stories, we added this as a mid-term goal (line 203)"
}
]
},
{
"id": "156728",
"date": "23 Jan 2023",
"name": "Ioannis Androulakis",
"expertise": [
"Reviewer Expertise quantitative systems biology and pharmacology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very comprehensive report/account of systems biology activities. I do not think I have any reservations. I realize this is more of a position statement and account of capabilities and possibilities and less of a concrete discussion of specific applications. Therefore, I am assessing the manuscript as such. It does present an overwhelming picture - possibly raising concerns about the applicability - but I also realize that the purpose of this report is to present the current state of the art.\nThis is admittedly a very ambitious undertaken. In that respect, I would also be curious to get the authors' opinion on whether or how such an integrative approach could eventually extend beyond large groups and integrated teams and be of assistance and value to smaller academic or research groups.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "11438",
"date": "31 May 2024",
"name": "John Hancock",
"role": "Author Response",
"response": "We thank the reviewer for their supportive comments. With reference to making this initiative helpful to smaller as well as large groups, we have added two sentences on this topic (lines 326-329)"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1265
|
https://f1000research.com/articles/12-1076/v1
|
31 Aug 23
|
{
"type": "Study Protocol",
"title": "Effect of blood flow restriction training on pressure pain threshold and hand function among adults with persistent neck pain: A study protocol for a randomized controlled trial",
"authors": [
"Mohammad Sidiq",
"Aksh Chahal",
"Nitesh Bansal",
"Sajjad Alam",
"Rituraj Verma",
"Krishna Reddy Vajrala",
"Jyoti Sharma",
"Sumera Khan",
"Yamini Sharma",
"Balamurugan Janakiraman",
"Richa Hirendra Rai",
"Nitesh Malhotra",
"Aksh Chahal",
"Nitesh Bansal",
"Sajjad Alam",
"Rituraj Verma",
"Krishna Reddy Vajrala",
"Jyoti Sharma",
"Sumera Khan",
"Yamini Sharma",
"Balamurugan Janakiraman",
"Richa Hirendra Rai",
"Nitesh Malhotra"
],
"abstract": "Background: Persistent neck pain is a prevalent musculoskeletal condition that affects the quality of life and functional abilities of individuals. Blood Flow Restriction Training (BFRT) is a novel therapeutic approach that involves restricting blood flow to exercising muscles to enhance strength and function. However, limited research has been conducted on the effects of BFRT on pressure pain threshold and hand function in adults with persistent neck pain. This randomized controlled trial aims to investigate the potential benefits of BFRT as a treatment intervention for this population. Methods: This study will be a prospective parallel group active controlled trail done at Physiotherapy Department, Galgotias University. Ethical clearance has been obtained from Departmental Ethics Committee on 19/05/2023 with reference number DEC/PT/GU/2023 and the Trial has been registered with Clinical Trial Registry India CTRI/2023/06/053439. Informed consent will be obtained from all the participants who are eligible to be included in the study. 110 patients with persistent neck pain will be randomly allocated into two groups. The BFRT group will receive supervised training sessions three times a week for eight weeks, performing low-load resistance exercises with blood flow restriction applied using personalized cuff pressure. The control group will receive standard care for neck pain, which may include general advice, manual therapy, and/or home exercises without BFRT. The primary outcome measures will be the pressure pain threshold, assessed using a pressure Algometer, and hand function, evaluated using standardized tests such as Hand Grip Strength and Purdue Peg board Test. Results: The data obtained will be analyzed using appropriate statistical methods, and the significance level will be set at p<0.05. Conclusion: This trial will contribute valuable contribution highlighting the potential benefits of BFR training in improving pressure pain threshold and hand function in adults with persistent neck pain.",
"keywords": [
"Blood Flow Restriction Training",
"Persistent Neck Pain",
"Pressure Pain threshold",
"Hand grip strength",
"hand function"
],
"content": "Introduction\n\nPersistent neck pain is a prevalent and debilitating condition that affects a significant number of adults worldwide.1 The burden of this condition on individuals’ quality of life and productivity underscores the need for effective and innovative interventions to alleviate pain and improve functional outcomes.2 Blood flow restriction (BFR) training has emerged as a promising technique that has shown potential benefits in enhancing muscular strength and promoting tissue adaptation without subjecting the body to high-intensity exercises.3 Despite its applications in various musculoskeletal conditions, the potential efficacy of BFR training in managing persistent neck pain remains relatively unexplored. This study protocol aims to investigate the effect of blood flow restriction training on pressure pain threshold and hand function among adults suffering from persistent neck pain. Utilizing a randomized controlled trial design, this research seeks to provide valuable insights into the role of BFR training as a potential therapeutic option for this challenging and often refractory condition. The rationale for examining pressure pain threshold lies in its significance as a common clinical measure for assessing pain sensitivity and tolerance, particularly in musculoskeletal pain conditions.4 Understanding the impact of BFR training on pressure pain threshold will offer valuable information on the technique’s ability to modulate pain perception in individuals with persistent neck pain. Additionally, assessing hand function is of paramount importance, as neck pain can often result in functional limitations that affect daily activities and work performance.5 Investigating the effects of BFR training on hand function will shed light on whether this intervention can lead to functional improvements and enhance the overall well-being of individuals experiencing neck pain. The results obtained from this research hold the potential to inform healthcare practitioners, physiotherapists, and other relevant professionals about the feasibility and effectiveness of incorporating BFR training into the management strategies for individuals with persistent neck pain. By addressing the current research gap and exploring the impact of BFR training on pressure pain threshold and hand function, this study protocol aspires to contribute to evidence-based practices in pain management and rehabilitation, ultimately enhancing the quality of life for those affected by persistent neck pain.\n\n\nObjectives\n\n\n\nI. To evaluate the effect of BFRT in alleviating neck pain and improving the hand function among adults with persistent neck pain.\n\nII. To study the impact of BFRT on disability and quality of life among patients with persistent neck pain.\n\nIII. To study the long term effect of BFRT on Precision and Power grip among adults with Persistent neck pain.\n\n\nProtocol\n\nThis study will be a prospective randomized active controlled trail to be done at Physiotherapy Department, Galgotias University.\n\nThere is no difference between the BFRT and conventional physiotherapy group in alleviation of pain, and hand function among adults with neck pain.\n\nBFRT will have a significant impact in reducing pressure pain threshold and improving hand function in patients with persistent neck pain among adults.\n\nSubjects\n\nOne hundred and ten self-reporting persistent neck pain for more than three months duration will be screened for eligibility and recruited in the study. After obtaining informed consent, the participants will be randomly allocated in 1:1 ratio to the BFR training group and the control group using a computer-generated randomization sequence. Allocation concealment will be ensured to maintain blinding and reduce potential bias. Sample size was calculated using Gpower version 3.1.9.4 for Windows by assuming effect size of 0.5(Cohen’s D medium size effect was assumed) with the margin of error (α) to test the level of significance was set at 0.05 and (1-α) 80% βpower and confidence interval at 95%, the final derived sample with added 10% of contingency was n=1126 (Figure 1). See Figure 2 for central and non-central distributions.\n\nParticipants with self-reported persistent neck pain for than 3 months, aged 18 and above, both males and females, patients with weak power grip, impaired hand precision function and willing to prospectively attend the interventions will be included in the study.\n\nThe exclusion criteria will be patients those who have history of receiving BFRT, deformity of upper extremity, spinal deformity, unhealed injuries in spine and upper extremity, uncontrolled hypertension, history of deep vein thrombosis and medically diagnosed neurological conditions that interfere with hand function or causes pain.\n\n\nMethods\n\nWritten informed consent will be obtained from all the participants who are eligible to be included in the study. The diagnosis of persistent neck pain will be made based on previous history and duration. Patients with radiating pain to shoulders or hands will be excluded. Enrolment, intervention, and assessment will be done as per the SPIRIT guideline (Table 1). Participants will be obtained from the OPD of Physiotherapy Department and from all over the university including the teaching, non-teaching staff, from camps nearby and students. Ethical clearance has been obtained from Departmental Ethics Committee on 19/05/2023 with reference number DEC/PT/GU/2023 and the Trial has been registered with Clinical Trial Registry India CTRI/2023/06/053439. All patients diagnosed with chronic neck pain and weak hand function will sign the informed consent. Demographic data, history and other data will be obtained at the baseline. The study will be done in accordance to the declaration of Helsinki.7\n\nAll patients will receive standard physiotherapy care. It will include thermo therapy, neck isotonic exercises. The Experimental group will also receive BFR with single session with 75 vol LOP 40 to 50 % for upper grip ball exercise (Light resistance) wrist curls and wrist extension using long leavers Flexibar radial and ulnar deviation. Follow up will be done for the patients on second visit after 8 weeks and long-term follow up after 6 months for others on phones who fail to come for follow up. All the patients will be explained about the possible benefits and complete procedure of the study and consent will be signed by each patient who is willing to participate in the study. They will be told its voluntary and they can withdraw anytime from the study and it won’t affect their treatment if they refuse to be part of the study. Patient information will be kept confidential. Each individual will serve as self-control to report about the possible benefit in pain score after receiving BFRT and after follow up. See Table 2 for the full BFRT protocol.8\n\nPressure pain threshold using Algometer\n\nUsing an algometer, a portable instrument that measures pressure sensitivity at particular anatomical locations in the neck region, the pressure pain threshold (PPT) will be determined. The algometer consists of a gauge with a pressure-sensing tip attached that measures applied pressure in kilopascals (kPa). Before the assessments begins, the algometer will be calibrated to ensure accuracy and consistency of measurements. Participants will be comfortably seated in an upright position with their neck muscles relaxed. It is essential to explain the procedure to the participant, ensuring they understand the assessment and can provide feedback on their pain perception. Specific anatomical points in the neck region will be chosen for the assessment. Commonly, these points include the trapezius, levator scapulae, and sternocleidomastoid muscles. The researcher will progressively apply pressure to the selected spots using the algometer. A button must be pressed to cease the pressure application or the participant must verbally report feeling pain for the pressure to increase at a constant rate (for example, 1 kPa/s).\n\nNeck Outcome Score\n\nThe Neck Outcome Score (NOS) is a self-reported questionnaire that assesses various aspects of neck pain and its impact on daily activities and quality of life. Participants will be provided with the NOS questionnaire, and the research team will explain its purpose and how to complete it. It’s important to ensure that participants understand the questions and how to score their responses accurately. The NOS typically includes questions related to pain intensity, pain-related disability, functional limitations, and the impact of neck pain on quality of life.\n\nGrip strength using hand help dynamometer\n\nGrip strength will be measured using a handheld dynamometer. We will ensure that the participant is well-rested and not fatigued before the measurement. We will also inform the participant about the purpose of the grip strength measurement and the procedure involved. The dynamometer will be adjusted to fit the participant’s hand size. The participant will be seated on a chair without armrests, ensuring proper posture with their back straight, feet flat on the ground, and forearm resting on a flat surface. We will instruct the participant to hold the dynamometer in their dominant hand. When the participant is ready, they should be instructed to squeeze the dynamometer handle with maximum effort for about 3 to 5 seconds. The researcher can provide encouragement to the participant during the measurement to ensure they exert their maximum effort. The highest grip strength measurement achieved during the trial will be recorded.\n\nWHO-5 quality of life index questionnaire\n\nThe WHO-5 quality of life index questionnaire is used to assess an individual’s subjective well-being and quality of life. We will briefly explain the purpose of the WHO-5 questionnaire to the participant and let them know that it’s designed to assess their emotional well-being and quality of life. Participants will rate their agreement with each statement on a scale from 0 to 5, where 0 indicates “at no time” and 5 indicates “all of the time”. After participants have provided their responses, we can assist them in calculating their total score. A higher score on the WHO-5 indicates better emotional well-being and quality of life.\n\nData will be analysed using IBM Statistical Package for Social Sciences version 21 for Windows. The patient characteristics at the baseline will be presented as mean, standard deviation and proportion with 95% confidence interval. The kolmogorov-smirnov and Shapiro Wilk test will be performed to assess the normality distribution of all the outcome scores. The student’s t- test and paired t-test will be used to compare between the groups and intra group and multiple regression analysis will be done to check for any correlation or any factor influencing the outcomes of the study.\n\n\nDiscussion\n\nThe present study protocol presents a RCT testing the effectiveness of BFRT on pressure pain threshold and hand function among adults with persistent neck pain. The intervention aims to reduce pain and hand function by the proposed mechanism. The study intends to employ a randomized controlled trial design, ensuring scientific rigor and minimizing bias. By comparing the BFR training intervention group with a control group, researchers seek to assess the impact of this innovative technique on two primary outcomes: pressure pain threshold and hand function. Therefore, we expect that the adults with neck pain and compromised hand function in the BFRT group will exhibit improvement in terms of pain and hand function in comparison to the neck pain patients in the conventional group. The significance of this research lies in its potential to contribute valuable insights into managing neck pain and improving hand function using a novel approach like BFR training. If the results show positive effects, it could pave the way for a non-invasive, safe, and cost-effective intervention for individuals dealing with persistent neck pain. Ultimately, this study may have a meaningful impact on the quality of life for those suffering from this prevalent issue, offering hope for improved pain management and functional recovery.\n\nStudy Status: At the moment the authors are involved in training the assessors and physiotherapists those who will be involved in interventions and we are planning to start screening after one month.\n\nThe chronic neck pain may progress to cause disability and diminished quality of life. A non-invasive timely intervention may cause halting adverse effects of central sensitization in patients suffering chronic neck pain. A simple and novel intervention may be incorporated.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nWoolf AD, Erwin J, March L: The need to address the burden of musculoskeletal conditions. Best Pract. Res. Clin. Rheumatol. 2012; 26(2): 183–224. Publisher Full Text\n\nCôté P, Cassidy JD, Carroll LJ, et al.: The annual incidence and course of neck pain in the general population: A population-based cohort study. Pain. 2004; 112(3): 267–273. PubMed Abstract | Publisher Full Text\n\nSaraf A, Goyal M, Goyal K: Blood Flow Restriction Training-An Overview and Implication in New Generation Physical Therapy: A Narrative Review. J. Lifestyle Med. 2022; 12(2): 63–68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlanpied PR, Gross AR, Elliott JM, et al.: Clinical practice guidelines linked to the international classification of functioning, disability and health from the orthopaedic section of the American physical therapy association. J. Orthop. Sports Phys. Ther. 2017; 47(7): A1–A83. Publisher Full Text\n\nSidiq M; Article OSecondary CA et al.: Indian Journal of Orthopaedics Cross-cultural adaptation and psychometric evaluation of the Indian language-Hindi version of the Neck Disability index in rural Northern Indian population.2021.\n\nKang H: Sample size determination and power analysis using the G*Power software. J. Educ. Eval. Health Prof. 2021; 18: 1–12. Publisher Full Text\n\nSkierka AS, Michels KB: Ethical principles and placebo-controlled trials - Interpretation and implementation of the Declaration of Helsinki’s placebo paragraph in medical research. BMC Med. Ethics. 2018; 19(1): 1–12.\n\nPatterson SD, Hughes L, Warmington S, et al.: Blood Flow Restriction Exercise: Considerations of Methodology, Application, and Safety. Front Physiol. 2019 May 15; 10: 533. Erratum in: Front Physiol. 2019 Oct 22; 10: 1332. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "222257",
"date": "15 Nov 2023",
"name": "Aminu A Ibrahim",
"expertise": [
"Reviewer Expertise Musculoskeltal disorders",
"clinical epidemiology",
"cross-cultural research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comments:\nThe manuscript aims to investigate the potential benefits of Blood Flow Restriction Training (BFRT) as a treatment intervention for persistent neck pain. The authors need to revise the entire manuscript for grammar and technicalities. I have the following comments for the authors.\nAbstract\nUnder methods, replace done with ‘ to be conducted’\n\nThe authors don’t need to mention informed consent in the abstract\n\n110 patients should be written in words\n\nIn reporting study protocol, no need to have a results section\n\nThe conclusion should be revised for grammar.\nIntroduction, objectives, and hypotheses\nThe rationale for evaluating BFR training for neck needs to be more explicit\n\nThe authors focused more on highlighting the potential benefit of the new intervention, which could turn out to be as effective as the standard care.\n\nThis is a protocol, the write-up should be presented in the future tense\n\nThe objectives are not clearly outlined. What about the comparison between the BFR training and standard care? The authors mentioned long-term, what about short-term?\n\nI would also advise the authors to evaluate outcomes at 4 weeks\n\nHypotheses are not well constructed and no need to add the null hypothesis in the article write-up. The heading should just read \"Hypotheses\" The hypotheses should indicate the comparison between the groups.\nMethodology\nThe authors mentioned 6 months as long term, this is often considered to be intermediate term. Long-term periods typically involved 12 months or 1 year or above\n\nThe authors mentioned that participants will be assigned into two groups equally but the type of randomization to achieve this equal allocation (i.e. block randomization with the block sizes) is not mentioned.\n\nFigures 1 and 2 for sample size calculations are not needed. Please consider deleting\n\nWhy was the effect size of 0.50 selected? The authors have not made it clear if the primary outcome - pressure pain threshold or hand function has been used in the determination of effect size assumptions. Please clarify.\n\nThe reliability of using Algometer for measuring Pressure pain threshold and a hand help dynamometer for measuring hand function should be reported\n\nI suggest the authors should also evaluate the intensity of neck pain using the Numerical Pain Rating Scale or Visual Analogue Scale.\n\nReliability (ICC and Cronbach’s alpha) and validity for the Neck Outcome Score (NOS) and WHO-5 quality of life index questionnaire should be briefly reported.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "10654",
"date": "31 May 2024",
"name": "Dr Mohammad Sidiq",
"role": "Author Response",
"response": "Methodology The authors mentioned 6 months as long term, this is often considered to be intermediate term. Long-term periods typically involved 12 months or 1 year or above The authors mentioned that participants will be assigned into two groups equally but the type of randomization to achieve this equal allocation (i.e. block randomization with the block sizes) is not mentioned. Figures 1 and 2 for sample size calculations are not needed. Please consider deleting Why was the effect size of 0.50 selected? The authors have not made it clear if the primary outcome - pressure pain threshold or hand function has been used in the determination of effect size assumptions. Please clarify. The reliability of using Algometer for measuring Pressure pain threshold and a hand help dynamometer for measuring hand function should be reported I suggest the authors should also evaluate the intensity of neck pain using the Numerical Pain Rating Scale or Visual Analogue Scale. Reliability (ICC and Cronbach’s alpha) and validity for the Neck Outcome Score (NOS) and WHO-5 quality of life index questionnaire should be briefly reported. Reviewer Comments: Author Responses: Abstract 1.Under methods, replace done with ‘ to be conducted’ 2.The authors don’t need to mention informed consent in the abstract 3.110 patients should be written in words 4.In reporting study protocol, no need to have a results section 5.The conclusion should be revised for grammar. Background: Persistent neck pain is a prevalent musculoskeletal condition that affects the quality of life and functional abilities of individuals. Blood Flow Restriction Training (BFRT) is a novel therapeutic approach that involves restricting blood flow to exercising muscles to enhance strength and function. However, limited research has been conducted on the effects of BFRT on pressure pain threshold and hand function in adults with persistent neck pain. This randomized controlled trial aims to investigate the potential benefits of BFRT as a treatment intervention for this population. Methods: This study will be a prospective parallel group active controlled trail to be conducted at Physiotherapy Department, Galgotias University. Ethical clearance has been obtained from Departmental Ethics Committee on 19/05/2023 with reference number DEC/PT/GU/2023 and the Trial has been registered with Clinical Trial Registry India CTRI/2023/06/053439. One hundred and ten patients with persistent neck pain will be randomly allocated into two groups. The BFRT group will receive supervised training sessions three times a week for eight weeks, performing low-load resistance exercises with blood flow restriction applied using personalized cuff pressure. The control group will receive standard care for neck pain, which may include general advice, manual therapy, and/or home exercises without BFRT. The primary outcome measures will be the pressure pain threshold, assessed using a pressure Algometer, and hand function, evaluated using standardized tests such as Hand Grip Strength and Purdue Peg board Test. Conclusion: This study aims to provide significant insights into the potential advantages of BFR training for enhancing pressure pain threshold and hand function among adults experiencing persistent neck pain. Methodology The rationale for evaluating BFR training for neck needs to be more explicit Recent research has offered insights indicating that both low-load training until volitional fatigue and low-load blood flow restriction (BFR) training have the potential to induce muscle size gains comparable to high-load training. The authors focused more on highlighting the potential benefit of the new intervention, which could turn out to be as effective as the standard care. Thank you for your thoughtful feedback. We appreciate your observation regarding our focus on highlighting the potential benefits of the new intervention in comparison to standard care. We acknowledge the importance of addressing this concern and will make sure to provide a more balanced discussion in our revised manuscript. We will include a more comprehensive analysis that considers the effectiveness of both the new intervention and standard care to ensure a thorough and well-rounded presentation of our findings. This is a protocol, the write-up should be presented in the future tense The results obtained from this research might hold the potential to inform healthcare practitioners, physiotherapists, and other relevant professionals about the feasibility and effectiveness of incorporating BFR training into the management strategies for individuals with persistent neck pain. The objectives are not clearly outlined. What about the comparison between the BFR training and standard care? The authors mentioned long-term, what about short-term? Revised Objectives are To evaluate the potential effect of BFRT in alleviating neck pain and improving the hand function among adults with persistent neck pain. To study the impact of BFRT on disability and quality of life among patients with persistent neck pain To study the short-term effect of BFRT on Precision and Power grip among adults with Persistent neck pain. I would also advise the authors to evaluate outcomes at 4 weeks We have revised the outcomes at four weeks and a follow up after twelve weeks. Hypotheses are not well constructed and no need to add the null hypothesis in the article write-up. The heading should just read \"Hypotheses\" The hypotheses should indicate the comparison between the groups. Revised Hypotheses are as under BFRT might have a significant impact in reducing pressure pain threshold and improving hand function in patients with persistent neck pain among adults. BFRT will demonstrate a statistically significant increase in pressure pain threshold and improvement in hand function compared to a control group receiving standard care. To study the short-term effect of BFRT on Precision and Power grip among adults with Persistent neck pain Methodology The authors mentioned 6 months as long term; this is often considered to be intermediate term. Long-term periods typically involved 12 months or 1 year or above The short term follow up will be done after 6 months due to feasibility constraints and social factors of participants. The authors mentioned that participants will be assigned into two groups equally but the type of randomization to achieve this equal allocation (i.e. block randomization with the block sizes) is not mentioned. To ensure equal allocation across group’s overtime, a block randomization with the block size of 8 will be used. Figures 1 and 2 for sample size calculations are not needed. Please consider deleting Yes we agree, thank you Why was the effect size of 0.50 selected? The authors have not made it clear if the primary outcome - pressure pain threshold or hand function has been used in the determination of effect size assumptions. Please clarify Assuming that BFRT might have an medium effect on the variable pressure pain threshold, the Cohen’s d effect of 0.5 for medium effect was used. Sample size was calculated for the variable pressure pain threshold assessed by algometer using G power version 3.1.9.4 for Windows. A priori power analysis with the assumed Cohen’s d medium effect size of 0.5, with the margin of error (α) to test the level of significance, power of study (1 – β) was set at 80%, and the confidence interval at 95%. Assuming a drop out of up to 10%, a target sample of n= 112 was estimated. The reliability of using Algometer for measuring Pressure pain threshold and a hand help dynamometer for measuring hand function should be reported The hand-held algometer demonstrated a reliability of r 0.990[Bala J1] for average force application of 80 Newton’s. and the Jamar hand-held dynamometer showed a reliability of 0.94[Bala J2] . I suggest the authors should also evaluate the intensity of neck pain using the Numerical Pain Rating Scale or Visual Analogue Scale. Since, one of the sub-domain of the Neck Outcome Score (NOOS) measure the pain intensity, we thought that would address the self-reported pain intensity. Reliability (ICC and Cronbach’s alpha) and validity for the Neck Outcome Score (NOS) and WHO-5 quality of life index questionnaire should be briefly reported. The Neck Outcome score (NOOS) subscales was reported to have a good to excellent reliability (ICC 0.88 – 0.95[Bala J3] ) among participants with neck pain. Further, NOOS was found to have a minimal detectable changes ranging between 1.1 and 1.9. The WHO-5 wellbeing index showed an acceptable internal consistency of 0.79 among Indian adults[Bala J4] . Kinser, Ann M1; Sands, William A1; Stone, Michael H2. Reliability and Validity of a Pressure Algometer. Journal of Strength and Conditioning Research 23(1):p 312-314, January 2009. | DOI: 10.1519/JSC.0b013e31818f051c Benton MJ, Spicher JM, Silva-Smith AL. Validity and reliability of handgrip dynamometry in older adults: A comparison of two widely used dynamometers. Plos one. 2022 Jun 21;17(6):e0270132. Juul T, Søgaard K, Davis AM, Roos EM. Psychometric properties of the Neck OutcOme Score, Neck Disability Index, and Short Form–36 were evaluated in patients with neck pain. Journal of clinical epidemiology. 2016 Nov 1;79:31-40. Pattnaik P. Validation of the World Health Organisation 5-Item Well-Being Index (WHO-5) among the Adult Population Living in a Chronically Arsenic Affected Area of Rural West Bengal in India. Indian Journal of Public Health Research & Development. 2020 Mar 1;11(3)."
},
{
"c_id": "11185",
"date": "14 Jun 2024",
"name": "Priyanshu Rathod",
"role": "Reviewer Response",
"response": "accepted"
},
{
"c_id": "11302",
"date": "18 Jun 2024",
"name": "Priyanshu Rathod",
"role": "Reviewer Response",
"response": "satisfactory"
}
]
},
{
"id": "275253",
"date": "16 May 2024",
"name": "Imam Subadi",
"expertise": [
"Reviewer Expertise wet cupping therapy",
"pain",
"stroke"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nREVIEW\nThis paper aimed to evaluate the effects of blood flow restriction training on pressure pain threshold and hand function among adults with persistent neck pain. There are major concerns that need to be addressed by the authors.\nAbstract : The authors don't need to mention ethical clearance in the abstract\nIntroduction:\nThe importance, role and mechanism of blood flow restriction training is not well highlight in this section as a therapeutic potential in neck pain and hand function Which part of the pain pathway is targeting ? The reason for choosing the blood floe restriction training to reduce pain and increase hand function is not well explained\nObjective : The objective of the study must be inline with the title. The author mentioned the impact of BRT on disability. How the disability is measured ?\nMethods\nThe determination of the diagnosis is not clear ? Who diagnosed the patients ? In table 1, the author must be explain the abbreviations Intervention : How is the author determine 1 RM? In table 2 : How is the author determine restriction form continuous or intermittent ?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "11673",
"date": "21 Jun 2024",
"name": "Dr Mohammad Sidiq",
"role": "Author Response",
"response": "This paper aimed to evaluate the effects of blood flow restriction training on pressure pain threshold and hand function among adults with persistent neck pain. There are major concerns that need to be addressed by the authors. Abstract : The authors don't need to mention ethical clearance in the abstract Response: Thank you; changes have been amended accordingly Introduction: The importance, role and mechanism of blood flow restriction training are not well highlighted in this section as a therapeutic potential in neck pain and hand function Response; We have now included statements explaining the mechanism and importance of blood flow restriction training as an interventional option for neck pain and hand function. Which part of the pain pathway is targeting ? Response; The following statement is now supplemented in the introduction section: “BFRT procedure paired with low intensity resisted exercise are proposed to cause pain modulation by exercise induced hypoalgesia (EIH) and conditioned pain modulation (CPM) pathways by activating descending pain inhibition.” The reason for choosing the blood flow restriction training to reduce pain and increase hand function is not well explained Response: We have now included sentence that emphasizes the rationale behind choosing BFRT. Objective : The objective of the study must be inline with the title. The author mentioned the impact of BRT on disability. How is a disability is measured ? Responses; Yes, true. Now we have removed the disability-related statement from the objective session and replaced it with activities of daily life. Methods The determination of the diagnosis is not clear ? Who diagnosed the patients ? Response: We have decided to include any adult participant who is eligible based on our exclusion criteria and self-reports neck pain, usually due to local musculoskeletal conditions and/or stable degenerative conditions that have led to impaired hand function. In table 1, the author must be explain the abbreviations Response: Done accordingly 1. How was 1 RM calculated? Response: Each participant will be asked to perform upper limb exercises with the BFR cuffs on in order to calculate 1RM, and the maximum weight lifted will be noted. Is the rationale for and objectives of, the study clearly described? Yes Is the study design appropriate for the research question? Yes Are there sufficient details of the methods provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format? Partly"
}
]
},
{
"id": "275252",
"date": "27 May 2024",
"name": "Yujiro Yamada",
"expertise": [
"Reviewer Expertise Blood flow restriction",
"resistance training",
"pressure pain threshold",
"blood pressure measurements",
"strength assessments",
"ultrasound muscle thickness assessment",
"and cognitive function assessment."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral Comments:\nThe authors of the manuscript proposed the study protocol to investigate the effect of adding blood flow restriction (BFR) training to standard physiotherapy care on pressure pain threshold in the neck region and hand function in adults with persistent neck pain, using a randomized controlled trial design. I would think this study idea would add valuable insight into the literature on BFR and pain. However, I have multiple parts that are not clear in the manuscripts, especially in the protocol section. Also, there is a suggestion of using a prospective mediation analysis rather than or in addition to the multiple correlation analysis. I would like the authors to consider these comments and provide revisions or reasonable rebottle accordingly. Thank you for the opportunity to review this paper.\nComments Specific to Individual Sections:\n\nABSTRACT\n\nComments for Authors\nIt is not clear in the abstract that the BFR training group also will receive standard care, which is an important narrative that needs since BFR training + standard care vs. standard care is different from BFR training vs. standard care.\nINTRODUCTION\n\nComments for Authors\nThank you for the concise introduction. “…subjecting the body to high-intensity exercises.”\nI would avoid using “high intensity” in the context. It would be rather suitable to use “high-load” since high intensity could also refer to how much “effort” the individuals put in during the exercise (Steele 2014, [Ref 1]). For instance, performing the “low-load resistance exercise” can be a “high-effort” exercise when the exercise is taken near or to momentary failure.\n\n“Despite its application in various musculoskeletal conditions”\nThis sentence acknowledges that there are studies examining the effect of BFR training on pain reduction; however, it is unclear whether BFR training worked for these conditions and no citation was provided. For instance, a review article summarized the acute and chronic effects of BFR exercise on pain reduction, and some included studies showed the greater pain-reducing effect of BFR training compared to high-load resistance training in adults after ACL (Song JS, et al., 2021 [Ref 2]). No need to be this paper, but please consider citing a work for this part of the sentence.\n\nI am not sure I understand, but the authors noted that neck pain can result in functional limitations that affect daily activities and work performance. Is there any relationship between neck pain and grip strength at baseline or any evidence or physiological rationale that changing one leads to change in another? If so, the authors could propose to perform mediation analysis, which tests whether the improvement in grip strength occurs through the potential greater pain reduction in BFR training than in standard care. Different from the correlation analysis, this mediation analysis can test the causal relationship by using the rigorous linear regression approach. You might consider this approach and this paper as guidance (Valente MJ, et. al., 2017 [Ref 3])\nPROTOCOL\n“One hundred and ten self-reporting persistent neck pain…”\nWould the authors consider the number of participants who are screened out due to the exclusion criteria the number of dropouts, or the inability to follow-up? Considering these concerns, would authors be better to shoot for higher than 110 (possibly 120) to have adequate power to detect the moderate effect?\n\n“weak power grip, impaired hand precision function”\nHow will the authors determine “weak handgrip, impaired hand function”? Please provide reasonable inclusion criteria for the relatively weak handgrip and function for the target population.\n\n“75 vol LOP 40 5o 50% for upper grip ball exercise (light resistance wrist curls) …\nPlease describe the BFR exercise session more precisely and clearly. What does the 75 vol mean? Meaning 4 sets of 30, 15, 15, 15 repetitions? What blood flow restriction device will the author be using? Hokanson? Delfi? Smart cuff? Or other devices? How would you determine limb occlusion pressure (LOP)? How would the authors determine the load for the grip ball exercise? How are the authors performing one repetition maximum (1RM) test on the movement? Only at the first visit? Table 2 will leave me with many questions about the exercise protocol. This table is very similar to Table 1 of Patterson et al. 2019, which is the guideline paper for BFR. Please be specific about the protocol. The load, 20 – 40% 1RM: Does it mean the exercise is going to be progressive from 20 – 40% 1RM? If so, how would the load be progressed (like a 5% increase every other week?). The cuff size: Which cuff would the author use for the exercise, small, medium, or large cuff? The length can differ depending on the size of the participants; however, the cuff width should be consistent since it affects the arterial occlusion pressure and possible discomfort. Repetitions & pressure: please report the number of repetitions completed in each set when reporting the results in the future since some participants might not be able to complete the predetermined repetitions. For pressure, is the author progressing the pressure as well from 40 – 80% AOP? Why does it say AOP but in the text it says LOP? Please be consistent throughout the manuscript. Same as rest periods…, if the author gives the range, please specify whether the rest period would be progressed to be shorter from 60 to 30 seconds or rather specify the rest period. Same comment for the exercise speed.\n\n“Follow up will be done for patients on the second visit after 8 weeks and long term follow up after 6 months for others on phones who fail to come for follow up”\nPlease clarify the sentence. Please revise the second visit as a “post-training visit” to avoid confusion from readers. This reads as if the participants cannot come to the post-training visit, they will be followed up by phone after 6 months, which does not make sense to me.\n\n“Each individual will serve as self-control to report about the possible benefit in pain score after receiving BFR and after follow up”\nIt is a good idea to report the participants’ expectations about the intervention in both groups at baseline and post-intervention, and 6-month follow-up. But, I don’t think it is correct to say “self-control” in this context. I do not understand how this variable will be used as “self-control.”\n\nPlease clarify what parts are supervised and unsupervised in the intervention. Please give a more specific description of the anatomical points in the neck region or provide a diagram or picture for clarity. For statistical analysis, the authors may consider reporting the variables as median if the variables are not normally distributed. As mentioned, in the introduction, mediation analysis could give better insight into the potential relationship between the outcome variables rather than multiple correlation analysis. If the author wants to report the correlation analysis, please specify which variables will be used for the analysis.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
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https://f1000research.com/articles/12-1076
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https://f1000research.com/articles/13-560/v1
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31 May 24
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{
"type": "Research Article",
"title": "Assessment of anticancer drug utilization pattern and patients’ survival—A single center experience from Saudi Arabia",
"authors": [
"Ahmed Badheeb",
"Manea Al Munjem",
"Faisal Ahmed",
"Huda Aljedaani",
"Nouf Assiri",
"Akrm Abdulaziz",
"Abdullah Abubakar",
"Mohammad AlQurayshah",
"Mohamed Badheeb",
"Manea Al Munjem",
"Faisal Ahmed",
"Huda Aljedaani",
"Nouf Assiri",
"Akrm Abdulaziz",
"Abdullah Abubakar",
"Mohammad AlQurayshah",
"Mohamed Badheeb"
],
"abstract": "Background In recent years, various advancements in anticancer therapy have led to the development of multiple regimens and protocols. This study endeavors to provide an extensive evaluation of anticancer therapy prescription patterns in correlation with patient outcomes.\n\nMethods From June 2014 to April 2022, we included adult cancer patients who received anticancer therapy in our cancer center. Collected data encompassed demographic characteristics of patients and cancer, chemotherapy protocols or agents, antiemetics, drug side effects, and the patient’s last status. The prescribed drugs were assessed using the Essential Medicines List, while the prescription’s rationality was determined using the World Health Organization indicators.\n\nResults The mean age was 55.16 ± 17.04 years, with 56.4% of the patients being males. Gastrointestinal (29.7%) and breast (25.8%) cancers were the most common malignancies. The main protocols included a combination of Adriamycin and cyclophosphamide (20.1%) and folinic acid, fluorouracil, and oxaliplatin-based (FOLFOX) regimen (13.5%). The most frequently used drugs were doxorubicin (14.0%), cyclophosphamide (13.3%), and docetaxel (9.9%). The majority of patients also did not report any acute adverse events related to chemotherapy (81.1%). Antiemetics, mainly metoclopramide-based, were used in 76.07% of cases. Remarkably, 86.7% of anticancer agents were from the EML, and 90.1% were prescribed generically.\n\nConclusion In this study, gastrointestinal cancers were the most prevalent cancers observed, with more preponderance among males. Most anticancer agents were taken from the essential drug list, with the majority being prescribed under generic names, indicating rational use.",
"keywords": [
"chemotherapy",
"anticancer",
"drug use pattern",
"Najran",
"Saudi Arabia."
],
"content": "Introduction\n\nCancer perpetuates a significant cause of mortality and morbidity on a global scale, despite a notable decrement in mortality rates, evidencing a 33% reduction since 1991. Moreover, an estimated 10 million deaths annually are anticipated to be cancer-related.1,2 The Middle Eastern regions, albeit with lower cancer incidence rates, are far from exempt from this burden, and projections delineate an ascendant trend in incidence.3 According to studies from the Arab world, these regions have a higher mortality-to-incidence ratio, which is exacerbated by limited cancer surveillance, implying a higher rate of undiagnosed cases.4 Saudi Arabia has seen an increase in cancer cases, with diagnoses increasing from about 20,000 to more than 27,000 between 2018 and 2020, respectively.5 Recent advancements in cancer research have sharpened diagnostic accuracy, facilitated earlier cancer detection, and thereby contributed to an increased prevalence rate. Furthermore, the advent of multi-modality therapeutic interventions, such as chemotherapy, targeted therapy, radiation, and surgery, has enriched the repertoire of cancer management resources.6,7 However, these interventions may cause adverse events ranging from mild symptoms (e.g., gastrointestinal discomfort and hair loss) to severe ones (e.g., life-threatening organ dysfunction).7 Consequently, prudent anticancer therapy selection necessitates a thorough evaluation of potential benefits, risks, and overall survival projections.6,7\n\nTo aid in the meticulous selection of anticancer therapies, the World Health Organization (WHO) launched a regional initiative known as the WHO Model List of Essential Medicines, also known as the Essential Medicines List (EML).8 This initiative is critical in choosing optimal, cost-effective, population-based therapies, with updates being made bi-annually. It is also particularly promising for low- and middle-income countries, which bear the brunt of the cancer burden.9 Such an initiative is paramount in a time characterized by a rapid influx of drugs, burgeoning clinical trials, and swiftly evolving guidelines. Additionally, previous studies have uncovered a high degree of variability in adherence to therapeutic recommendations, as high as 61%, with negligible differences in patient factors that may influence the cancer therapy selection.10 The architecture of cancer treatment protocols customarily entails a comprehensive institutional and literature review, which is aligned with national agency approval, e.g., Food and Drug Administration, and buttressed by expert panel assessments. Nonetheless, the practicability of these methodologies may be circumscribed to nations with higher income strata, cutting-edge research centers, and institutions equipped to undertake clinical trials, leaving others at a disadvantage.11 Hence, the promulgation of an international model could significantly ameliorate this gap. Within this framework, we aim to identify the chemotherapy patterns in Najran, one of Saudi Arabia’s 13 regions, and assess its adherence to the EML as recommended by the WHO.\n\n\nMethods\n\nA retrospective observational study conducted between June 2014 and April 2022 at King Khaled Hospital (KKH) in Najran City, Saudi Arabia included all adult patients with cancer regardless of the stage or treatment type. On March 13, 2022, the Ethics Research Committees of King Khalid Hospital approved this study (ID: 2022-11 E), which was carried out in compliance with the Helsinki Declaration. Due to the anonymous retrospective nature of the study, written informed consent from the included patients was not required. The patients were all monitored for the duration of the study. The study included by default all adult patients, defined as >18 years old, with an established pathological diagnosis of cancer who were managed in our cancer center. The pathological confirmation requires tissue sampling that’s obtained on the basis of the tumor nature and site, typically through minimally invasive procedures (e.g., fine-needle aspiration, core biopsy) or excisional tissue (i.e., postoperative). We excluded patients with no pathological confirmation, in addition to patients who were non-recipients of chemotherapy, diagnosed but referred or managed out of cancer center, had incomplete records, lost during follow-up, or those without consent to participate were excluded.\n\nThe variables included in this research included patient demographics (age and gender), diagnosis year, concurrent comorbidities, cancer location and stage (metastatic and non-metastatic), treatment intent, delay before initiating chemotherapy, chemotherapy regimens and agents, antiemetic use, drug side-effects manifestation, patient final status (survivors and non-survivors) and the last follow-up duration. Utilizing logistic regression analysis, we investigated the variables impacting survival rates. The study’s dependent variables were delineated by WHO prescribing, patient care, and health facility indicators,12 with socio-demographic traits (age and gender) acting as predictor variables. Metrics such as the average number of drugs per encounter and the percentages of drugs named generically, encounters involving drug prescription, as well as prescribed drugs from the essential drugs list were computed to provide a granular insight into prescribing trends.\n\nThis study primarily evaluated the prescribing trends of anticancer drugs.\n\nUpon concluding the study, the WHO core prescribing indicators were compiled to ascertain the prevalence of polypharmacy, the proportion of prescriptions entailing injectables, and the percentage of drugs enlisted on the EML.13 All statistical evaluations were conducted using Statistical Package for Social Sciences (IBM SPSS Statistics for Windows, version 21.0, Armonk, NY: IBM Corp.). Continuous variables were depicted as mean values and standard deviations, while categorical variables were illustrated through frequency and percentage. Data normalcy was gauged using the Kolmogorov-Smirnov test. A p-value of less than 0.05 was acknowledged as statistically significant.\n\n\nResults\n\nIn this study, there were 289 (56.4%) male patients among the 512 included cases. The mean age was 55.16 ± 17.04 years, and the majority of patients were considered middle-aged (178 cases, 34.8%). Most of them (87.9%) were Najran City residents. Also, 218 of them (42.5%) were diagnosed in 2020-2021. The patients’ demographic characteristics are provided in Table 1. Gastrointestinal cancer was the most prevalent in our cohort at 29.7%, followed by breast cancer accounting for 25.8% of malignancies. In addition, 46.7% of the patients had distant metastasis. All the study cohorts received chemotherapy in Najran, and about 16.7% received further treatment in other centers within SA. Curative treatment was given to 315 (61.5%) patients, while palliative chemotherapy was provided for 197 (38.4%). Moreover, 75.4% of our patients (386 cases) received definitive treatment within 6 weeks or less, while 4.3% had it for more than 6 weeks and 20.3% for an undetermined duration. Furthermore, 297 (58%) patients had a comorbid condition; among these, 122 (23.8%) had diabetes alone or with other comorbidities, while 103 (20.11%) had hypertension alone or with other comorbidities. Other comorbid conditions included thyroid disease in 10 (2%) patients and chronic obstructive pulmonary disease in seven (1.4%) others. Doxorubicin hydrochloride [Adriamycin and cyclophosphamide] (AC) was the most commonly used protocol in 11.1% of the patients, followed by folinic acid, fluorouracil, and oxaliplatin-based (FOLFOX) regimens in 7.4%, XELOX-based regimens (combination of capecitabine with oxaliplatin) in 5.7%, and R-CHOP (rituximab [Rituxan], cyclophosphamide [Cytoxan], doxorubicin [Adriamycin], vincristine [Oncovin], and prednisone) in 4.3% of our study cohorts. Moreover, the most commonly involved medications in our study were doxorubicin (14.0%), cyclophosphamide (13.3%), and docetaxel (9.9%) (Table 2). Furthermore, the majority of our patients (81.1%) did not report any acute adverse events related to chemotherapy; hypersensitivity reactions (e.g., itching, skin rashes, and shortness of breath) and anaphylactic shock were reported in only 1.3% of our patients. Other documented side effects included neutropenic fever (2.5%) and delayed skin reaction (1.2%). In addition, a documented medication shortage or unavailability was observed in only 8.4% of patients, with BCG (Bacillus Calmette-Guerin) (0.8%), aprepitant (0.6%), and gemcitabine (0.6%) accounting for the most frequently unavailable medications. The most commonly used antiemetic was a metoclopramide-based regimen, which was noted in 82.6% of patients (Table 3).\n\n† Others: Palbociclib *, Lenalidomide, Imatinib, Crizotinib *, Lenvatinib *.\n\n‡ Others: Ramucirumab *, BCG, Thalidomide, Dacarbazine *, Olaparib *.\n\nA total of 1,021 anticancer drugs were administered to this study’s 512 participants. On average, each patient received 1.99 anticancer drugs. As for the drug utilization pattern, 61.32% of patients (314 individuals) were prescribed a single anticancer drug, while the rest received a combination of multiple anticancer drugs, as detailed in Table 4.\n\n\nDiscussion\n\nCancer imposes an extremely high burden on the healthcare system, with high medication costs that are projected to increase further, especially among patients diagnosed in the later stage of the illness.14 Targeting more efficient, cost-effective therapies is crucial to providing cancer care that suits the nation’s needs; such interventions require a meticulous assessment of drug utilization patterns to ensure health equity, consistency, and coherence.15 In our cancer center, more than 22 types of cancer were observed, and 45 anticancer drugs were prescribed. In this study, the most commonly used protocols included doxorubicin hydrochloride (Adriamycin) and cyclophosphamide (11.1%), followed by FOLFOX-based (7.4%), XELOX-based (5.7%), and R-CHOP regimens (4.3%). This pattern occurred due to the variety of cancers that affect patients in our geographical area, which is also consistent with the prevalence of cancers treated with these protocols.16–18\n\nDoxorubicin, cyclophosphamide, and docetaxel accounted for the most commonly involved chemotherapeutic agents in our study, which is related to the prevalence of gastrointestinal and breast cancers that were predominant in our cohorts in SA.13,18 Different chemotherapeutic agents may be used variably depending on the cancer institute’s focus or specialization, or the incidence of cancer in the involved region. For instance, in a study involving metastasis cancer drug utilization patterns, cisplatin (58%) and 5-fluorouracil (41%) were two of the most prescribed anticancer drugs, followed by doxorubicin.19 In another study, Aggarwal et al. revealed that paclitaxel, cisplatin, and 5-Fluorouracil (PCF) were the most commonly used agents; however, among the study population, oral cavity was the most common cancer site for which the PCF regimen was used.20 Moreover, similar studies found that platinum-based or taxane-based chemotherapy groups appeared to be the most commonly used agents,7,21 with variation in the selected agents explained in part by availability, insurance coverage, physician experience or training, and cost.\n\nIn this study, 1,021 anticancer agents were prescribed among the 512 patients, corresponding to a drug-to-patient ratio of 1.99. Individualized analysis, however, showed that 314 (61.32%) of the patients received only a single agent. Our findings were similar to those of previous studies, such as Bepari et al.,7 but it is slightly higher compared to research conducted by Kumar et al., which had a drug-to-patient ratio of 1.73. Of note, their sample size was smaller than ours, and about 43.5% of their participants received single-agent therapy.22 Nevertheless, Kumar et al.’s findings were drastically higher than those of Dave et al., with only 5.4% of their patients receiving single-agent chemotherapy. The latter study, however, had a different cancer rate, with lung and oropharyngeal cancers accounting for over 50% of cases.23 In our study, 86.7% of the agents used were from the EML, slightly surpassing the rates reported in previous studies, which ranged from 80%-82%.7,24 Our findings revealed that 92.4% of the medications provided in our cancer center were also on the Saudi Food and Drug Authority’s essential medications list.25 This indicates that our institution is doing commendable work in providing cancer patients with optimal, readily available, and cost-effective therapy.\n\nOver 90% of the agents used on our patients were prescribed by generic name. In a Mathew et al. study,24 however, an extremely low rate (8%) of generic drug use was reported; this is in contrast to the higher rates (76.6%) of generic formulary use in a study by Bepari et al.7 Moreover, a retrospective analysis of the findings of four clinical trials found that the genericization of various anticancer agents allowed for a remarkable decrease in medication costs.26 This can be particularly crucial for cancer patients, as any financial optimization may permit financial resources to be redirected to another aspect of care.\n\nAdjuvant therapy is crucial among cancer patients, particularly for the prevention or management of nausea and vomiting, which can affect 40-90% of them depending on chemotherapeutic agents or biological factors, such as being female, being of younger age, or having polymorphisms in the 5-HT3 receptors (e.g., 3B receptor gene).27,28 In our study cohort, the most commonly used antiemetic was a metoclopramide-based regimen, which was used in 76.07% of patients. Similarly, in the Bepari et al. study, antiemetics were the most commonly prescribed pre-chemotherapy drugs.7 Furthermore, most of the patients in their study were prescribed adjuvant steroids, combined with chemotherapy, to minimize the chemotherapy medications’ adverse effects such as nausea and vomiting.29\n\nThe retrospective design of our study renders it susceptible to selection and attrition biases. Additionally, as a single-center study, the sample is limited to a geographic location that might not be representative of the overall country's population, which limits the generalizability of the study. Furthermore, the data were extracted from patients' medical records, which depends on the accuracy of documentation. Lastly, the factors evaluated are susceptible to confounding bias, which is attributed to unadjusted variables.\n\n\nConclusions\n\nIn this study, gastrointestinal cancers were the most prevalent cancers observed, with more preponderance among males. Doxorubicin, cyclophosphamide, and docetaxel were the most frequently used cytotoxic drugs, while the most commonly used adjuvant drugs were antiemetics. Over 86.7% of anticancer agents were taken from the essential drug list, with 90.1% prescribed under generic names, indicating rational use.\n\nOn March 13, 2022, the Ethics Research Committees of King Khalid Hospital approved this study (ID: 2022-11 E), which was carried out in compliance with the Helsinki Declaration. Due to the anonymous retrospective nature of the study, written informed consent from the included patients was not required.",
"appendix": "Data availability\n\nFigshare: Assessment of anticancer drug utilization pattern and patients’ survival—A single center experience from Saudi Arabia. figshare. Dataset. https://doi.org/10.6084/m9.figshare.25387114.v2. 30\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC0).\n\n\nAcknowledgments\n\nNone.\n\n\nReferences\n\nSung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 2021; 71: 209–249. PubMed Abstract | Publisher Full Text\n\nSiegel RL, Miller KD, Wagle NS, et al.: Cancer statistics, 2023. CA Cancer J. Clin. 2023; 73: 17–48. PubMed Abstract | Publisher Full Text\n\nArafa MA, Farhat KH: Why cancer incidence in the Arab counties is much lower than other parts of the world? J. Egypt. Natl. Canc. Inst. 2022; 34: 41. PubMed Abstract | Publisher Full Text\n\nMula-Hussain L, Mahdi H, Ramzi ZS, et al.: Cancer Burden Among Arab World Males in 2020: The Need for a Better Approach to Improve Outcome. JCO Glob. Oncol. 2022; 8: e2100407. Publisher Full Text\n\nArafa MA, Rabah DM, Farhat KH: Rising cancer rates in the Arab World: now is the time for action. East Mediterr. Health J. 2020; 26: 638–640. PubMed Abstract | Publisher Full Text\n\nSchulmeister L: Safe management of chemotherapy: infusion-related complications. Clin. J. Oncol. Nurs. 2014; 18: 283–287. PubMed Abstract | Publisher Full Text\n\nBepari A, Sakre N, Rahman I, et al.: The Assessment of Drug Utilization Study of Anticancer Drugs Using WHO Prescribing Indicators in a Government Tertiary Care Hospital of the Hyderabad - Karnataka Region of India. Open Access Maced. J. Med. Sci. 2019; 7: 1203–1208. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJenei K, Aziz Z, Booth C, et al.: Cancer medicines on the WHO Model List of Essential Medicines: processes, challenges, and a way forward. Lancet Glob. Health. 2022; 10: e1860–e1866. PubMed Abstract | Publisher Full Text\n\nFundytus A, Sengar M, Lombe D, et al.: Access to cancer medicines deemed essential by oncologists in 82 countries: an international, cross-sectional survey. Lancet Oncol. 2021; 22: 1367–1377. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHeins MJ, de Jong JD , Spronk I, et al.: Adherence to cancer treatment guidelines: influence of general and cancer-specific guideline characteristics. Eur. J. Pub. Health. 2017; 27: 616–620. PubMed Abstract | Publisher Full Text\n\nBenjamin DJ, Xu A, Lythgoe MP, et al.: Cancer Drug Approvals That Displaced Existing Standard-of-Care Therapies, 2016-2021. JAMA Netw. Open. 2022; 5: e222265. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOrganization WH: How to investigate drug use in health facilities: selected drug use indicators. World Health Organization; 1993.\n\nAkl OA, El Mahalli AA, Elkahky AA, et al.: WHO/INRUD drug use indicators at primary healthcare centers in Alexandria, Egypt. J. Taibah Univ. Med. Sci. 2014; 9: 54–64. Publisher Full Text\n\nMcGarvey N, Gitlin M, Fadli E, et al.: Increased healthcare costs by later stage cancer diagnosis. BMC Health Serv. Res. 2022; 22: 1155. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRomero Y, Trapani D, Johnson S, et al.: National cancer control plans: a global analysis. Lancet Oncol. 2018; 19: e546–e555. PubMed Abstract | Publisher Full Text\n\nSaini VK, Sewal RK, Ahmad Y, et al.: Prospective Observational Study of Adverse Drug Reactions of Anticancer Drugs Used in Cancer Treatment in a Tertiary Care Hospital. Indian J. Pharm. Sci. 2015; 77: 687–693. PubMed Abstract\n\nBeedimani RS, Zaman SU, Potturi SC, et al.: Prescribing pattern of anticancer drugs in the medical oncology department of a tertiary care teaching hospital. Int. J. Basic Clin. Pharmacol. 2019; 8: 1398–1402. Publisher Full Text\n\nGuduru H, Jeevanagi SKR, Nigudgi S, et al.: A prospective study on the prescription pattern of anti-cancer drugs and adverse drug reaction in a tertiary care hospital. Int. J. Basic Clin. Pharmacol. 2019; 8: 200–205. Publisher Full Text\n\nVijayalakshmi D, Bendi SR, Usharani M, et al.: Assessment of drug utilization pattern in patients undergoing chemotherapy for various types of metastatic cancers in a tertiary care government hospital. Int. J. Basic Clin. Pharmacol. 2020; 9: 1331–1336. Publisher Full Text\n\nAggarwal M, Chawla S, Singh K, et al.: Evaluation of anticancer drug utilization and monitoring of adverse drug reaction in the indoor patients receiving cancer chemotherapy in a Tertiary Care Hospital in New Delhi. J. Basic Clin. Pharma. 2018; 9.\n\nEfraim J, Munisi C, Magige A, et al.: Drug utilization pattern and adverse drug reactions of chemotherapy in pediatric patients at Muhimbili National Hospital, Tanzania. F1000Res. 2022; 11: 396. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKumar BS, Maria S, Shejila C, et al.: Drug utilization review and cost analysis of anticancer drugs used in a tertiary care teaching hospital. Indian J. Pharm. Sci. 2018; 80: 686–693.\n\nDave DJ, Pillai A, Shah DV, et al.: An analysis of utilization pattern of anticancer drugs in diagnosed cases of carcinoma in a tertiary care teaching hospital. Int. J. Basic Appl. Med. Sci. 2014; 4: 251–259.\n\nMathew M, Mateti UV, Saj N, et al.: Drug utilization evaluation of anticancer drugs in a charitable hospital. Indian J. Med. Paediatr. Oncol. 2019; 40: 105–110. Publisher Full Text\n\nAlmoteiry K, Alharf A, Al Hammad B, et al.: National medicines policy development, Saudi Arabia. Bull. World Health Organ. 2022; 100: 511–519. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCheung WY, Kornelsen EA, Mittmann N, et al.: The economic impact of the transition from branded to generic oncology drugs. Curr. Oncol. 2019; 26: 89–93. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTrendowski MR, El Charif O, Dinh PC Jr, et al.: Genetic and Modifiable Risk Factors Contributing to Cisplatin-induced Toxicities. Clin. Cancer Res. 2019; 25: 1147–1155. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGrunberg SM, Warr D, Gralla RJ, et al.: Evaluation of new antiemetic agents and definition of antineoplastic agent emetogenicity--state of the art. Support Care Cancer. 2011; 19 Suppl 1: S43–S47. PubMed Abstract | Publisher Full Text\n\nWeinstein C, Jordan K, Green S, et al.: Single-dose fosaprepitant for the prevention of chemotherapy-induced nausea and vomiting in patients receiving moderately emetogenic chemotherapy regimens: a subgroup analysis from a randomized clinical trial of response in subjects by cancer type. BMC Cancer. 2020; 20: 918. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBadheeb Aa F: Assessment of Anticancer Drug Utilization Pattern from a hospital-based cancer registry—A Single Center Experience from Saudi Arabia Mendeley Data."
}
|
[
{
"id": "354091",
"date": "07 Jan 2025",
"name": "Pouyan Ebrahimi",
"expertise": [
"Reviewer Expertise Given my familiarity with similar studies conducted in this field",
"I am well acquainted with the data collection methods and analyses employed in this study. Additionally",
"my ongoing research in cancer treatments provides valuable insights",
"enabling me to effectively contribute to reviewing the oncological aspects of this study."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study evaluates the utilization patterns of anticancer drugs and their correlation with patient outcomes in a single cancer center in Saudi Arabia from 2014 to 2022. The findings reveal that gastrointestinal and breast cancers were the most prevalent, with doxorubicin, cyclophosphamide, and docetaxel being the most frequently used cytotoxic agents. Over 86% of prescribed medications were listed in the WHO Essential Medicines List, indicating rational drug use. The study emphasizes the importance of adhering to standardized treatment protocols while highlighting the need for improved regional cancer management strategies. However, please consider the following comments for the purpose of completing and improving the article. Topic: 1. Considering that no survival analysis has been conducted and data such as patient survival rates or analyses related to factors influencing survival are unavailable, I recommend titling the study as \"Anticancer Drug Utilization and Prescription Practices in a Saudi Cancer Center (2014–2022).\"\nAbstract: 2. A critical point to address throughout the manuscript, particularly in the abstract, is avoiding the use of \"we\" or \"our\" in academic writing. Instead, adopt a more formal tone. For example, in the methodology section of the abstract, replace \"our cancer center\" with the specific name of the center where the data was collected.\n3. Please include the type of tools or software used for data analysis in the methodology section of the abstract.\n4. Clearly state the type of study conducted in the methodology section.\n5. In the results section, ensure the total number of cases evaluated is explicitly mentioned.\n6. Given the clinical importance of metastatic cases, include the number of patients with metastases in the abstract.\n7. Adjust the keywords according to MeSH terminology. Suggested keywords include \"Survival,\" \"Drug Utilization,\" and \"Neoplasms.\"\nIntroduction: 8. The introduction is well-written; however, in the final paragraph, please elaborate on why the results of this study are important compared to similar studies.\nMethod: 9. Considering the long data collection period and the potential changes in drug utilization patterns, please specify in the methodology section which protocols or guidelines were used for prescribing drugs to patients during different years, ideally in intervals (e.g., every four years).\n10. The sentence “those without consent to participate were excluded” seems inconsistent, as you previously mentioned that no consent was obtained due to the retrospective nature of the study. Please revise this statement for clarity.\n11. The exclusion criteria mention that patients lost to follow-up were excluded, but the study design does not appear to include variables requiring follow-up, such as patient survival. Did you mean therapeutic follow-up? If so, please specify the duration and method of follow-up in the methodology section.\n12. Please move the explanation regarding logistic regression mentioned in the Study Variables section to the Statistical Analysis section. Additionally, clarify whether the regression analysis was univariate or multivariate. Specify which variable(s) were independent and which were dependent in this analysis.\nResult: 13. It is recommended to adjust Table 2 to include drug prescription patterns by year. Alternatively, if necessary, a separate table could be provided to address this. This addition would clarify which anticancer drugs were most frequently prescribed during each year.\n14. The text states that 512 cases were evaluated; however, the total number of patients in Table 1 sums to 510. Does this discrepancy indicate that the cancer site was unidentified for two patients? Please clarify.\n15. The results section does not discuss logistic regression analysis or mention odds ratios (OR). It seems that this analysis was not performed. If the authors intended Table 4 to represent logistic regression analysis, it appears to have been incorrectly designed. I recommend revising the table by clearly identifying the variables included in the model, providing OR values, 95% confidence intervals, and reference categories. The table should be formatted and written in alignment with standard academic practices.\nDiscussion: The discussion section is well-written but requires deeper evaluation. For instance:\n16. Why are certain drugs more commonly prescribed in this region? Are there specific socioeconomic, cultural, or healthcare-related factors driving this pattern?\n17. How do the results of this study compare to other regional or international studies, particularly in terms of drug utilization patterns and patient outcomes?\n18. Finally, based on the findings of this study, what recommendations can you provide to other researchers, clinicians, or policymakers to improve cancer treatment strategies?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-560
|
https://f1000research.com/articles/13-296/v1
|
18 Apr 24
|
{
"type": "Research Article",
"title": "Pulmonary function in Thai patients with systemic sclerosis; a single center 6-year retrospective study",
"authors": [
"Pattarin Pirompanich",
"Ornnicha Sathitakorn",
"Thitisak Sakulvorakitti",
"Ornnicha Sathitakorn",
"Thitisak Sakulvorakitti"
],
"abstract": "Background Interstitial lung fibrosis is a major cause of internal organ involvement and the leading cause of death in patients with systemic sclerosis (SSc). This study aimed to demonstrate the characteristics of pulmonary function (PF) in Thai patients with SSc and the association between PF and body mass index (BMI) and anti-topoisomerase (anti-Scl70).\n\nMethods All patients diagnosed with SSc in our tertiary care teaching hospital database between 2016 and 2021 were reviewed. Clinical characteristics and PF were recorded and analyzed.\n\nResults Of 211 SSc patients, 128 patients who underwent the PF test were enrolled; 102 (79.7%) were female. The mean (SD) age was 54.0 (12.5) years. The mean (SD) forced expiratory volume in one second (FEV1) forced vital capacity (FVC) ratio was 0.8 (0.1). The mean (SD) % predicted values of FEV1, FVC, and diffusing capacity of the lungs for carbon monoxide (DLCO) were 76.3 (16.3), 69.1 (15.8), and 75.5 (22.8), respectively. A restrictive spirometry pattern (RSP), defined as FVC < 80% predicted, was found in 78.8% of the patients. DLCO had a moderate positive linear correlation with FVC (r=0.50, p <0.001) and a moderate negative linear correlation with BMI (r=-0.36, p <0.001). However, there was no correlation between FVC and BMI. There was no statistical difference in demographic data or the presence of anti-Scl70 among patients with or without RSP.\n\nConclusions RSP is common among Thai patients with SSc. Spirometry is a cost-effective screening tool for detecting SSc-related pulmonary involvement in resource-limited settings. However, the power of using demographic data and the presence of anti-Scl70 to determine the probability of pulmonary complications remains limited.",
"keywords": [
"Systemic sclerosis",
"Pulmonary function",
"Interstitial lung disease",
"ILD",
"Thailand"
],
"content": "Background\n\nSystemic sclerosis (SSc) is an autoimmune disease that results from microvascular damage, dysregulation of innate and adaptive immunity, and widespread fibrosis that affects multiple organs. While skin fibrosis is a key feature in patients with SSc, the clinical prognosis is determined by the severity of internal organ involvement.1 The prevalence of SSc ranged from 38 to 341 cases per million, and the 5- and 10-year survival rates following diagnosis are 75% and 63%, respectively.2\n\nMajor internal organ involvements in SSc include the pulmonary, cardiovascular, renal, and gastrointestinal systems. Notably, interstitial lung disease (ILD) has emerged as a primary complication during the initial stages in Thai patients and is a significant contributor to mortality.3–5 The clinical presentations of SSc patients with ILD include dyspnea, non-productive cough, and fine crackles at the lung based on auscultation. The decline in forced vital capacity (FVC) was significantly higher in patients who had anti-topoisomerase autoantibody (anti-Scl70). In contrast, sex and age did not correlate with pulmonary function.3\n\nThis study aimed to demonstrate the characteristics of pulmonary function in Thai patients with SSc and to explore the potential association between pulmonary function, body mass index (BMI), and the presence of anti-Scl70. The findings of this study may hold significant value in shaping management guidelines and provide insights for future studies on pulmonary complications in Thai patients with SSc.\n\n\nMethods\n\nThis was a single-center, 6-year retrospective observational study conducted between January 2016 and December 2021. This study was approved by the Human Research Ethics Committee of the Faculty of Medicine, Thammasat University, Thailand (Project number MTU-EC-IM-1-177/65, Approval number 193/2022, Date of approval September 19, 2022), which was conducted in accordance with the Declaration of Helsinki. The informed consent was waived in view of the retrospective nature of the study. Patient data were sourced from our institutional database at a 650-bed tertiary care university hospital.\n\nThe enrollment criteria included individuals aged ≥ 18 years diagnosed with systemic sclerosis. All patients fulfilled the 1980 classification criteria for SSc6 and underwent a pulmonary function test (PFT) during the study period. Demographic data, presence of anti-Scl70, forced expiratory volume in one second (FEV1), FVC, and diffusing capacity of the lungs for carbon monoxide (DLCO) were recorded. In cases with multiple PFT results for a single patient, the earliest test conducted during the study period was employed to mitigate the impact of ongoing treatment and disease progression. This retrospective study included all eligible patients with available data, providing a complete representation of the entire population under investigation.\n\nThe primary objective was to identify the characteristics of pulmonary function in patients with SSc. The secondary outcomes included comparing the pulmonary function based on the presence of anti-Scl70, demonstrating the association between body mass index (BMI), FVC, and DLCO, and distinguishing characteristics of the patients who had restrictive spirometry patterns, defined as FVC of less than 80% predicted.\n\nNormality was assessed using the Shapiro-Wilk normality test. Categorical variables were reported as counts and percentages, and continuous variables as means with standard deviations (SD) or medians with interquartile ranges (IQR). Differences in continuous variables were compared using Student’s t-test or Mann-Whitney U test. Differences between separate groups of variables were compared using Fisher’s test or the chi-square test. The relationship between parameters was evaluated using Pearson’s correlation or Spearman’s correlation. Cases with any missing data points were removed from the analysis. A two-sided P value of less than 0.05 was considered to indicate statistical significance for the outcomes. Analyses were performed using STATA software 17.0 (StataCorp LLC, College Station, TX, US).\n\n\nResults\n\nFrom a total of 211 SSc patients, 128 who underwent PFT were enrolled. Spirometry results were available for 118 (92.2%) patients, and DLCO results were available for 108 (84.4%) patients. The mean (SD) age of the patients was 54.0 (12.5) years, with 102 (79.7%) being female. The median (IQR) BMI for all patients was 21.7 (19.6-25.5) kg/m2, as detailed in Table 1.9\n\nThe primary outcome of the study revealed mean (SD) % predicted of FEV1, FVC, and DLCO as 76.3 (16.3), 69.1 (15.8), and 75.5 (22.8), respectively. The mean (SD) FEV1/FVC ratio was 0.8 (0.1). Notably, a restrictive spirometry pattern was predominant among the majority of the patients, accounting for 78.8% (93/118) of the study population. Further details regarding pulmonary function are presented in Table 2.\n\nIn the secondary outcome analysis, following the categorization of patients based on the presence of anti-Scl70, no statistical differences were observed in FVC, FEV1, FEV1/FVC, or DLCO (Table 3). DLCO demonstrated a moderate positive linear correlation with FVC (r=0.50, p<0.001) and a moderate negative linear correlation with BMI (r=-0.36, p<0.001) (Figure 1). However, there was no correlation between FVC and BMI (r=-0.15, p-value=0.107).\n\nPatient characteristics, including age, sex, BMI, and the presence of anti-topoisomerase, did not demonstrate significant differences between those with and without a restrictive spirometry pattern. Notably, the majority of the patients with decreased DLCO exhibited a restrictive spirometry pattern (Table 4).\n\n\nDiscussion\n\nIn this study, the mean % predicted values of FVC and DLCO were 69.1 and 75.5, respectively. A substantial majority of the patients (78.8%) exhibited a restrictive spirometry pattern. These results are consistent with those of a prior study on ILD in Thai patients with SSc, where the % predicted FVC ranged from 71.8 to 77.6.7 In that study, the mean % predicted FVC and incidence of ILD within 5 years from disease onset were 71.8 and 86% in patients with diffuse cutaneous SSc, and 77.6 and 54% in patients with limited cutaneous SSc, respectively.7 These findings emphasize the impact of pulmonary involvement on SSc.\n\nHowever, the % predicted FVC in our study and the previously mentioned study appears to be lower than that reported in a previous large-scale study, The European Scleroderma Trials and Research group (EUSTAR) cohort,3 where the mean % predicted FVC and DLCO in SSc patients were 93.5 and 68.9, respectively. This discrepancy may be attributed to the fact that the EUSTAR cohort assessed patients who presented within one year after the onset of Raynaud’s phenomenon, the most common initial presentation, accounting for 59.5% of SSc cases.5 Furthermore, the EUSTAR cohort’s shorter disease duration compared to the referenced Thai study7 might have contributed to the higher FVC values observed. These findings suggest a potential negative impact of disease duration on FVC, emphasizing the need for further studies to comprehensively explore this relationship.\n\nOur study revealed no association between demographic data and restrictive spirometry results in patients with SSc. This suggests that the manifestation of a restrictive spirometry pattern in patients with SSc may be influenced by disease-specific factors rather than by general demographic characteristics. Similarly, the presence of anti-topoisomerase antibody did not significantly affect pulmonary function, although this finding diverges from previous studies suggesting a negative association with pulmonary outcome.3,7 However, it is important to note that a majority of our patients in this study demonstrated a restrictive spirometry pattern and only a small number of our patients had documented records of the presence of this antibody. These limitations may constrain our ability to thoroughly assess the impact of these factors on the pulmonary function. Notably, reduced chest wall compliance, potentially contributing to restrictive pulmonary defects, could also be found in SSc, which may have influenced our results.\n\nDLCO and FVC are the two most frequently used PFT for assessing the outcomes of SSc ILD.8 SSc usually undergo regular DLCO and FVC. Our findings revealed a moderate linear correlation between DLCO and FVC, and nearly all patients with decreased DLCO exhibited a restrictive spirometry pattern. This finding suggests that spirometry can serve as an effective screening test for pulmonary involvement in SSc and is a cost-effective option, particularly in resource-limited settings.\n\nIn this study, some essential medical history, particularly patient symptoms, previous treatments, disease duration, and co-existing organ involvement, were documented in diverse formats, posing challenges for analysis. Therefore, the earliest test conducted during the study period was employed to mitigate the impact of ongoing treatment and disease progression. However, this limits our ability to evaluate the relationship between pulmonary function and these factors. Further studies with pre-specified data collection of these factors may reveal new tools for the detection of pulmonary involvement.\n\nThe strengths of our study are its considerable number of participants in a data-scarce field and being the only study that aims to explore pulmonary function exclusively in Thai patients with SSc. The effect of selective bias in the study is modest because most of our patients with SSc were screened with spirometry annually, regardless of patient symptoms.\n\nHowever, this study has some limitations. First, since SSc is a progressive disease, lack of disease duration data limited us from defining patient disease stage and severity. Second, the small number of documented anti-topoisomerase antibodies decreased our power to examine its relationship with patient pulmonary function. Third, our study did not capture data on the type of systemic sclerosis in all participants. This omission limits our ability to assess the potential influence of SSc type on FVC and DLCO. Lastly, our study did not include pulmonary hypertension (PH) assessments, thus limiting our ability to conclusively determine the extent to which PH contributed to the observed DLCO values.\n\n\nConclusion\n\nA restrictive spirometry pattern is common among Thai patients with SSc. Spirometry is a cost-effective screening tool for detecting SSc-related pulmonary involvement in resource-limited settings. However, the power of using demographic data and presence of anti-topoisomerase to determine the probability of pulmonary complications remains limited. Further studies are required to evaluate anti-topoisomerase antibody data, SSc type, and pulmonary hypertension assessment.\n\n\nEthics and consent\n\nEthical approval was obtained from the Human Research Ethics Committee of Thammasat University (Faculty of Medicine), Thailand (Project number MTU-EC-IM-1-177/65, Approval number 193/2022, Date of approval September 19, 2022), and the study was conducted according to the Declaration of Helsinki. The informed consent was waived in view of the retrospective nature of the study.",
"appendix": "Data availability\n\nZenodo: Pulmonary function in Thai patients with systemic sclerosis data. https://zenodo.org/doi/10.5281/zenodo.10440509. 9\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nThe authors would like to express their gratitude to Thammasat University Hospital for providing the patient data and to Sam Ormond for reviewing the English language used in our manuscript.\n\n\nReferences\n\nAllanore Y, Simms R, Distler O, et al.: Systemic sclerosis. Nat. Rev. Dis. Prim. 2015; 1: 15002. Publisher Full Text\n\nIngegnoli F, Ughi N, Mihai C: Update on the epidemiology, risk factors, and disease outcomes of systemic sclerosis. Best Pract. Res. Clin. Rheumatol. 2018; 32(2): 223–240. PubMed Abstract | Publisher Full Text\n\nJaeger VK, Wirz EG, Allanore Y, et al.: Incidences and Risk Factors of Organ Manifestations in the Early Course of Systemic Sclerosis: A Longitudinal EUSTAR Study. PLoS One. 2016; 11(10): e0163894. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTyndall AJ, Bannert B, Vonk M, et al.: Causes and risk factors for death in systemic sclerosis: a study from the EULAR Scleroderma Trials and Research (EUSTAR) database. Ann. Rheum. Dis. 2010; 69(10): 1809–1815. PubMed Abstract | Publisher Full Text\n\nFoocharoen C, Peansukwech U, Mahakkanukrauh A, et al.: Clinical characteristics and outcomes of 566 Thais with systemic sclerosis: A cohort study. Int. J. Rheum. Dis. 2020; 23(7): 945–957. PubMed Abstract | Publisher Full Text\n\nPreliminary criteria for the classification of systemic sclerosis (scleroderma): Subcommittee for scleroderma criteria of the American Rheumatism Association Diagnostic and Therapeutic Criteria Committee. Arthritis Rheum. 1980; 23(5): 581–590. Publisher Full Text\n\nWangkaew S, Euathrongchit J, Wattanawittawas P, et al.: Incidence and predictors of interstitial lung disease (ILD) in Thai patients with early systemic sclerosis: Inception cohort study. Mod. Rheumatol. 2016; 26(4): 588–593. PubMed Abstract | Publisher Full Text\n\nCaron M, Hoa S, Hudson M, et al.: Pulmonary function tests as outcomes for systemic sclerosis interstitial lung disease. Eur. Respir. Rev. 2018; 27(148): 170102. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPirompanich P, Sathitakorn O, Sakulvorakitti T: Pulmonary function in Thai patients with systemic sclerosis data. [Dataset]. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "271788",
"date": "10 May 2024",
"name": "Chingching Foocharoen",
"expertise": [
"Reviewer Expertise Internal Medicine and Rheumatology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors presented an association factors with pulmonary function in scleroderma. However, I believe there are some areas where additional details would strengthen the manuscript and provide a more convincing argument for the coexistence of both conditions. I have listed my points of concern below: Abstract\nMean BMI and the proportion of patient with positive for anti-Scl70 should be mentioned in abstract because they were endpoints of the study. This study did not investigate the cost-effectiveness of spirometry. Please revise the conclusion in abstract section and also in conclusion section.\nBackground\nThe authors should mention why BMI was in your interested to be an endpoint of the study. What is/are the rationales for defining the association between BMI and spirometry parameters?\nMethods\nThe diagnosis of systemic sclerosis is now using the 2013 ACR/EULAR Classification criteria not from 1980 ACR criteria. 128 out of 211 SSc patients underwent spirometry, so nearly 40% were not performed the spirometry. This may cause selection bias. Of those 40% who were not performed the test, they might be too tired to do the test or have difficulty to do the test for example air leak from mouth related to skin tightness of face, etc. Please clarify this point. Spirometry parameters and BMI can dynamically change or fluctuate over the course of follow-up, but anti-Scl70 is still be stable. Please clarify when of the spirometry test as well as BMI was picked up for analysis. The association between spirometry and anti-Scl70 might not be reliable and valid due to fluctuations during follow-up, as mentioned above. The authors presented only a 10% positivity rate for anti-Scl70. From previous study of SSc in Thailand, the proportion of patients with anti-Scl70 was reported around 70-80% [Int J Rheum Dis. 2020 Jul;23(7):945-957.]. Why was the prevalence of anti-Scl70 in this study much lower than previous large cohort among Thais?\nMinor points\nThe term anti-topoisomerase I and anti-Scl70 were alternately used in the text. The authors should choose only 1 term and make it consistency to the whole manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11653",
"date": "31 May 2024",
"name": "Pattarin Pirompanich",
"role": "Author Response",
"response": "Thank you very much for you kindly review. We really appreciate your response and revised our manuscript as you suggested. Abstract Point 1: Mean BMI and the proportion of patient with positive for anti-Scl70 should be mentioned in abstract because they were endpoints of the study. Response 1: We have added this data on Abstract (Page 2, Line 9-11). Point 2: This study did not investigate the cost-effectiveness of spirometry. Please revise the conclusion in abstract section and also in conclusion section. Response 2: We have deleted this sentence from the abstract section and also in conclusion section. Background Point 1: The authors should mention why BMI was in your interested to be an endpoint of the study. What is/are the rationales for defining the association between BMI and spirometry parameters? Response 1: BMI was included because it's a readily available measure of body composition that might influence lung function through various mechanisms. Understanding this relationship can provide insights into disease severity and potential risk factors for SSc patients. We have added this data on Background (Page 2, paragraph 2, line 8-9) (reference 6). Ishikawa C, Barbieri MA, Bettiol H, Bazo G, Ferraro AA, Vianna EO. Comparison of body composition parameters in the study of the association between body composition and pulmonary function. BMC Pulm Med. 2021;21(1):178. Methods Point 1: The diagnosis of systemic sclerosis is now using the 2013 ACR/EULAR Classification criteria not from 1980 ACR criteria. Response 1: Thank you for your value suggestion. We have already revised (Page 3, paragraph 2, line 2-3). Point 2: 128 out of 211 SSc patients underwent spirometry, so nearly 40% were not performed the spirometry. This may cause selection bias. Of those 40% who were not performed the test, they might be too tired to do the test or have difficulty to do the test for example air leak from mouth related to skin tightness of face, etc. Please clarify this point. Response 2: We have acknowledged these on limitation (Page 8, paragraph 5, line 10-12). Point 3: Spirometry parameters and BMI can dynamically change or fluctuate over the course of follow-up, but anti-Scl70 is still be stable. Please clarify when of the spirometry test as well as BMI was picked up for analysis. Response 3: In cases with multiple PFT results for a single patient, the earliest test conducted during the study period was employed to mitigate the impact of ongoing treatment and disease progression. BMI was obtained at the time of the PFT was done. We have added this data in Methods (Page 3, paragraph 2, line 6-9). Point 4: The association between spirometry and anti-Scl70 might not be reliable and valid due to fluctuations during follow-up, as mentioned above. Response 4: While spirometry parameters and BMI can fluctuate over time, anti-Scl-70 is known for its relative stability. To minimize the impact of ongoing treatment and disease progression on lung function analysis, this study used the earliest PFT result for each participant (Page 3, paragraph 2, line 6-7). However, this approach might not fully capture the potential influence of anti-Scl-70 levels on spirometry, as anti-Scl-70 is considered stable. Future longitudinal studies with repeated measurements of both anti-Scl-70 and spirometry parameters could provide a more comprehensive understanding of the interplay between these factors and their impact on lung function in SSc patients. We have acknowledged these on limitation (Page 8, paragraph 5, line 1-4). Further studies are required to evaluate comprehensive data on disease duration to gain a more understanding of the disease course and its impact on SSc patients. We have added this data in Conclusion (Page 8, line 4-5). Point 5: The authors presented only a 10% positivity rate for anti-Scl70. From previous study of SSc in Thailand, the proportion of patients with anti-Scl70 was reported around 70-80% [Int J Rheum Dis. 2020 Jul;23(7):945-957.]. Why was the prevalence of anti-Scl70 in this study much lower than previous large cohort among Thais? Response 5: Among the analyzed samples, 14 patients (10.9%) were positive for anti-topoisomerase antibodies, while 10 patients (7.8%) were negative. However, anti-topoisomerase antibody status was unreported for a large portion of the study group (n=104, 81.3%) due to limitations in data availability. This high percentage of missing data precludes definitive conclusions about the overall prevalence of anti-Scl-70 in our cohort and hinders comparisons with previous studies that likely had more complete data. We have added this data in Results (Page 3, paragraph 1, line 2-4). Minor point Point 1: The term anti-topoisomerase I and anti-Scl70 were alternately used in the text. The authors should choose only 1 term and make it consistency to the whole manuscript. Response 1: We revised throughout the manuscript. Additional revision: Because the interest of brevity, we delete some wordings in Abstract and the total wording is 262 words."
}
]
},
{
"id": "271791",
"date": "20 May 2024",
"name": "Dujrath Somboonviboon",
"expertise": [
"Reviewer Expertise Internal Medicine and Pulmonology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the opportunity to review this article, which presents on pulmonary function in Thai systemic sclerosis patients, and I would like to offer a few comments and suggestions to further enhances its clarity and impact.\nAbstract\nThe authors did not compare spirometry to other interventions, particularly HRCT. Therefore, the conclusion regarding the cost-effectiveness of spirometry should be revised.\nFull manuscript Background\nThe correlation between pulmonary function and SSc is understandable, but the authors should explain why they were interested in BMI.\n\nThe authors mentioned the importance of ILD in SSc patients, however, this study did not include HRCT data, only pulmonary functions were recorded. Therefore, using ‘pulmonary involvement’ would be more appropriate than ILD.\nDiscussion\nThere are several confusing points in the discussion section, particularly when the authors compare the findings from this cohort to those of previous studies. Please check the numbers, particularly regarding the data from the referenced papers. The authors found that FVC in this cohort was lower than in the EUSTAR cohort and explained this by noting that EUSTAR cohort had shorter disease duration. However, a previous Thai cohort [Ref -1] demonstrated that a shorter duration of pulmonary fibrosis after onset also correlated with poorer outcome based on the longitudinal data analysis. Furthermore, the mean disease duration in the referenced Thai study [Ref - 2] was only 12.9 months. Therefore, this part should be revised. As mentioned earlier, the authors did not investigate the cost-effectiveness of spirometry.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11654",
"date": "31 May 2024",
"name": "Pattarin Pirompanich",
"role": "Author Response",
"response": "Thank you very much for you kindly review. We really appreciate your response and revised our manuscript as you suggested. Abstract Point 1: The authors did not compare spirometry to other interventions, particularly HRCT. Therefore, the conclusion regarding the cost-effectiveness of spirometry should be revised. Response 1: We have deleted this sentence from the abstract section and also in conclusion section. Background Point 1: The correlation between pulmonary function and SSc is understandable, but the authors should explain why they were interested in BMI. Response 1: BMI was included because it's a readily available measure of body composition that might influence lung function through various mechanisms. Understanding this relationship can provide insights into disease severity and potential risk factors for SSc patients. We have added this data on Background (Page 2, paragraph 2, line 8-9) (reference 6). Ishikawa C, Barbieri MA, Bettiol H, Bazo G, Ferraro AA, Vianna EO. Comparison of body composition parameters in the study of the association between body composition and pulmonary function. BMC Pulm Med. 2021;21(1):178. Point 2: The authors mentioned the importance of ILD in SSc patients, however, this study did not include HRCT data, only pulmonary functions were recorded. Therefore, using ‘pulmonary involvement’ would be more appropriate than ILD. Response 2: We have changed accordingly. Discussion Point 1: There are several confusing points in the discussion section, particularly when the authors compare the findings from this cohort to those of previous studies. Response 1: We have revised the data in the Discussion section to provide a clearer picture of the findings (Page 7, paragraph 1 and 2). Point 2: Please check the numbers, particularly regarding the data from the referenced papers. Response 2: We have revised the data in the Discussion section to accurately reflect the information from the referenced papers (Page 7, paragraph 1 and 2). Point 3: The authors found that FVC in this cohort was lower than in the EUSTAR cohort and explained this by noting that EUSTAR cohort had shorter disease duration. However, a previous Thai cohort [Ref -1] demonstrated that a shorter duration of pulmonary fibrosis after onset also correlated with poorer outcome based on the longitudinal data analysis. Furthermore, the mean disease duration in the referenced Thai study [Ref - 2] was only 12.9 months. Therefore, this part should be revised. Response 3: We have revised the data in the Discussion section to provide a clearer picture of the findings and to accurately reflect the information from the referenced papers (Page 7, paragraph 1 and 2). Point 4: As mentioned earlier, the authors did not investigate the cost-effectiveness of spirometry. Response 4: We have deleted this sentence from the abstract section and also in conclusion section."
}
]
},
{
"id": "271795",
"date": "23 May 2024",
"name": "Pattraporn Tajarernmuang",
"expertise": [
"Reviewer Expertise pulmonary",
"interventional respirology",
"lung cancer",
"critical care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the invitation to review the manuscript by Pirompanich et al. The authors presented a single-center retrospective study aiming to identify the clinical characteristics of pulmonary function in patients with systemic sclerosis. The minor concerns and suggestions for this study are as follows:\nAs we know, lung involvement in diffuse systemic sclerosis (SSc) is more common than in limited SSc. It would be beneficial to demonstrate the proportion of diffuse SSc and limited SSc in the patient characteristics. There were 211 SSc patients, but only 128 (~60%) patients who had PFT results were enrolled. The possible reason for the unavailability of PFT results might be that the patients were too sick to perform the test. This selection bias could make the PFT results appear too favorable. The authors should mention this point in the limitations of the study. The authors mentioned that limited chest wall compliance can cause restrictive pulmonary defects; however, lung imaging (e.g., HRCT) can help distinguish between chest wall and lung problems. Also, some patients with abnormal HRCT can have normal spirometry. I think the authors should clarify this point.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11655",
"date": "31 May 2024",
"name": "Pattarin Pirompanich",
"role": "Author Response",
"response": "Response to reviewer 3: Thank you very much for you kindly review. We really appreciate your response and revised our manuscript as you suggested. Point 1: As we know, lung involvement in diffuse systemic sclerosis (SSc) is more common than in limited SSc. It would be beneficial to demonstrate the proportion of diffuse SSc and limited SSc in the patient characteristics. Response 1: We have acknowledged these on Discussion (Page 7, paragraph 2, line 8-10) and limitation (Page 8, paragraph 5, line 6-7). Point 2: There were 211 SSc patients, but only 128 (~60%) patients who had PFT results were enrolled. The possible reason for the unavailability of PFT results might be that the patients were too sick to perform the test. This selection bias could make the PFT results appear too favorable. The authors should mention this point in the limitations of the study. Response 2: We have acknowledged these on limitation (Page 8, paragraph 5, line 10-12). Point 3: The authors mentioned that limited chest wall compliance can cause restrictive pulmonary defects; however, lung imaging (e.g., HRCT) can help distinguish between chest wall and lung problems. Also, some patients with abnormal HRCT can have normal spirometry. I think the authors should clarify this point. Response 3: Thank you for the insightful comment regarding the role of chest wall compliance in restrictive lung disease. We acknowledge that reduced chest wall compliance can be a contributing factor, and ideally, lung imaging techniques like HRCT would be incorporated to differentiate between restrictive etiologies. Unfortunately, due to limitations in our study design, we were unable to collect data on chest wall compliance. Therefore, we have decided to remove the sentence mentioning this factor from the manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/13-296
|
https://f1000research.com/articles/12-1326/v1
|
12 Oct 23
|
{
"type": "Study Protocol",
"title": "Protocol for correlation of histological risk assessment/scoring system with a depth of invasion in oral squamous cell carcinoma",
"authors": [
"Archana Sonone",
"Alka Hande",
"Aayushi Pakhale",
"Madhuri Gawande",
"Swati Patil",
"Alka Hande",
"Aayushi Pakhale",
"Madhuri Gawande",
"Swati Patil"
],
"abstract": "Introduction: The commonest type of cancer in the head and neck region is oral squamous cell carcinoma (OSCC) due to its high rates of occurrence and mortality. The early diagnosis of oral cancer gives better prognosis. Brandwein-Gensler criteria predict the early stage of OSCC cases with a high risk of locoregional recurrence.\nObjectives: To correlate Brandwein-Gensler criteria and depth of invasion of OSCC with three-year survival. Methodology: In the study, hematoxylin-eosin (HE)-stained section slides will be used to evaluate Brandwein and Gensler criteria and depth of invasion in resected tissue specimens of OSCC cases. Expected results: The present study will find the correlation between Brandwein-Gensler criteria and depth of invasion in OSCC in order to evaluate the locoregional recurrence in OSCC cases. In high-risk OSCC cases, there may be increased depth of invasion in resected tissues.\n\nConclusions: We hypothesized that the correlation between Brandwein-Gensler criteria and depth of invasion can be used as an independent predictor for locoregional recurrence in OSCC.",
"keywords": [
"Oral squamous cell carcinoma",
"Brandwein Gensler Criteria",
"Depth of Invasion"
],
"content": "Introduction\n\nOral squamous cell carcinoma (OSCC) is the most widely occurring cancer in the head-neck region.1 In 2018, OSCC claimed around 177,000 global fatalities.2 Despite of the advanced treatment modalities and therapeutic approaches, the overall survival rate in OSCC did not rise by more than 50% during a five-year period.3 The clinical diagnosis of OSCC is confirmed by histopathology. In the adjunct therapy such as chemotherapy radiotherapy, histopathological report of OSCC is important. Due to this, many studies emphasize on the histopathological parameters of resected oral cancer tissues in the pathology reports.4 Several authors have proposed various grading systems for OSCC. The first grading system developed by Broder (1920), which is still advised by the WHO5,6 is likely the most well-known prognostication method using a subjective evaluation of significant histopathological features like differentiation degree of tumor cells, cellular pleomorphism, and mitotic activity, and is grouped into WDSCC (well differentiated), MDSCC (moderately differentiated) and PDSCC (poorly differentiated). Although MDSCC comprises up to 90% of oral cancers, this approach, while widely identified and used, still has poor discriminatory value.6 Annoreth et al. gave another classification which emphasise on the association between the tumour and adjacent tissue.7 This included aspects like the leukocyte invasion and the degree of pattern and stage of invasion. A method of invasive-tumour-front grading (IFG) comprising five histopathological characteristics involving lymphocyte-host-response (LHR) was later devised by Bryne et al.8 Because of the small sample sizes, varied locations of the tumour, and examination of various types of specimens, these models have not proved successful. A risk assessment model put forth in 2005 by Brandwein-Gensler and colleagues was said to have better prognostic value than previously mentioned systems.9 It includes the combined assessment of three important histopathological parameters: PNI (perineural-invasion), LHR (lymphocyte-host-response), and WPOI (worst-pattern of invasion). Scoring is done for all three parameters individually and then the sum of the three variables is computed. The Brandwein-Gensler (BG) system showed a significant correlation with the patient’s locoregional recurrence and overall survival, especially in low-stage oral cancers. More aggressive characteristics receive weighted point values in the model.10 Adjuvant radiotherapy may be beneficial in cases of high-risk, low-stage oral cancers, even when the margins are satisfactory. The TNM classification for OSCC (eigtth edition, 2017), emphasizes on depth-of-tumour invasion (DOI) along with largest diameter of the tumour to determine the T-stage11 and signifies a shift in the paradigm in Oral Pathology. When determining the specific course of treatment for a particular case, a combined evaluation of clinical staging and histological grading may be a more reliable method.1 The main goal of our study is to determine the association of DOI with the histological risk assessment/scoring system in order to assess the combined effects of these factors on OSCC pathological staging and locoregional recurrence in three-year survival rate.\n\n\nMethods\n\nThis study will be a retrospective study, using archival tissue from OSCC cases.\n\nThis cross-sectional study will be carried out at Sharad Pawar Dental College and Hospital (SPDC&H), Datta Meghe Institute of Higher Education, Sawangi-Meghe, Wardha in the Oral Pathology and Microbiology Department. This study will include 80 random histopathologically-diagnosed cases of OSCC. The staging will be carried out on the basis of the AJCC eighth edition criteria. Cases with a previous head-neck cancer history, pre-surgical radiation therapy, chemotherapy or any surgery (apart from biopsy) and recurrent or distant disease will be excluded. Patient data comprising of age and sex of the patient, site of the lesion, clinical appearance of the tumor, habits including tobacco and alcohol use and status of lymph node will be obtained.\n\nStaining of the archival slides and new slides (where needed) will be done with HE. WPOI, LHR, and PNI will be assessed by three histopathologists in a blinded manner. Evaluation will be done according to the Risk Model mentioned below. Three groups will be made depending on the sum of the score of each case:\n\nGroup 1 – low-risk cases = total score 0\n\nGroup 2 – moderate-risk cases = 1 or 2\n\nGroup 3 – high risk-cases = 3 or more.\n\nThe DOI assessment will be done from the basement-membrane (BM), in regions where the BM has been lost, as well as from an illustrative line connecting the BM from the neighbouring epithelium to the point of deepest tumour invasion in the connective-tissue stroma with the help of a research microscope (Leica-DMLB2) with standard software (Leica-Q-win). The DOI will be measured and recorded.\n\nWPOI:\n\nWPOI-1: Broad-pushing borders – Score 0\n\nWPOI-2: Broad-pushing fingers – Score 0\n\nWPOI-3: Large tumour cells islands (with more than fifteen tumour cells in each island) – Score 0\n\nWPOI-4: Small islands of tumour (less than fifteen tumour cells in each island) – Score +1\n\nWPOI-5: Satellites of tumour cells, at ≥1mm distance from the major tumour – Score +3\n\nLymphocytic-host-response (LHR):\n\nLHR-1 (strong): Dense rim of lymphoid infiltrate surrounding the tumour at the advancing edge/invasive front – Score 0\n\nLHR-2 (intermediate): patches of lymphoid infiltrate in few regions – Score +1\n\nLHR-3 (weak): Presence of very little or no lymphoid infiltrate, no patches seen – Score +3\n\nPerineural-invasion:\n\nNo invasion – Score 0\n\nSmall nerves: Tumour cells surrounding small nerves – Score +1\n\nLarge nerves: Tumour cells surrounding nerves, ≥1 mm in diameter – Score +3\n\nThe present study will find the correlation between Brandwein-Gensler criteria and DOI in OSCC. In the high-risk category, there may be increased DOI in resected tissue of OSCC.\n\nConsidering the prevalence of OSCC as 70.7% in the outpatient department of the Oral Pathology and Microbiology department, using the single proportion formula, sample size is calculated by applying the formula:\n\nWhere,\n\nZ21−α/2 - The significance level at 5%\n\ni.e. 95 % confidence interval = 1.96\n\np = Sample showing positive CD44 expression focally in small group cells in the basal layer of epithelium = 70.7% = 0.707\n\nE=Error of margin=10%=0.10\n\nn=1.962×0.707×1−0.707/0.102\n\nn = 80\n\nThe results will be published in an indexed journal.\n\nThe study has not started yet.\n\n\nDiscussion\n\nIncidence of OSCC in Indian men (11.28%) ranks first while it ranks fifth in women (4.3%).1,2 The clinical diagnosis is always confirmed by the histopathology. There are numerous histopathological grading systems mentioned in the literature for OSCC. Among them, the BG risk predictive model gives the best results regarding the loco-regional recurrence of OSCC.4\n\nArun Chaturvedi evaluated the BG risk predictive model in surgically treated OSCC patients in North India. The author studied 149 patients with histologically diagnosed OSCC. The patients were divided into three groups: low, moderate, and high risk according to the BG criteria. Out of 149 patients, 17 patients showed locoregional recurrences (11.4%). Most of these 17 patients belonged to the high-risk category of the BG risk model. The authors hypothesised that the BG risk model is predictive of locoregional recurrences for OSCC undergoing primary surgery and it can be used to model for recognition of recurrences and prevention at early stages of the disease.12\n\nRhayany de Castro Ribeiro Lindenblatt studied 53 cases of OSCC in which they evaluated four grading systems (Malignancy Grading of the Deep Invasive Margins, Multiparameter Grading System, Histologic Risk Assessment and the World Health Organization grading system). They concluded that the Histologic Risk Assessment scoring system established the best results for locoregional recurrence and survival prediction in OSCC patients.13\n\nNaomi Rahman evaluated the BG risk model criteria in OSCC patients to assess disease progression and survival of patients. They studied 134, OSCC cases, in which they compared two AJCC criteria, i.e. seventh and eighth. In the latest eighth criteria they included DOI according to which they staged the tumor. Due to this, 30 cases of OSCC previously classified into the T1 and T2 stage according to the seventh edition were upstaged to T3 stage according to the eighth AJCC criteria. Three individual histopathologists scored BG risk model criteria and DOI of the same samples. They concluded that the BG is the most effective parameter for grading tumors and locoregional recurrence of patients.14\n\nThe staging of OSCC, which is based on the TNM system, has been used for several years to estimate both the clinical response to therapy and survival outcomes. In the eighth AJCC edition, DOI is included as a new histopathological parameter for the assessment of tumor grade, The DOI is measured from the basement membrane to invasive the front of the tumor. The stage and grade of the tumor are major contributing factors to prognosis and treatment selection for OSCC.15 As the BG risk model gives the locoregional recurrence status of OSCC, assessment and corelation of BG model and depth of tumor give the best results in predicting three-year survival in locoregional recurrence of OSCC patients.\n\n\nConclusions\n\nFor OSCC, the BG risk model comprises effective criteria to determine locoregional recurrence. Therefore, it can be used in early-stage OSCC for identification and prevention of the recurrences. The correlation between BG and DOI in resected OSCC tissues will give better results about the locoregional recurrence and survival rate of OSCC.\n\nEthical approval was received from Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha, Maharashtra India (IEC reference number- DMIHER (DU)/IEC/2023/578).",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: STROBE checklist for “Protocol for correlation of histological risk assessment/scoring system with a depth of invasion in oral squamous cell carcinoma”, https://doi.org/10.5281/zenodo.7895574 . 16\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank their institute and colleagues.\n\n\nReferences\n\nDikshit R, et al.: Cancer mortality in India: a nationally representative survey. Lancet. 2012; 379(9828): 1807–1816. PubMed Abstract | Publisher Full Text\n\nStewart BW, Wild CP: World Cancer Report 2014. Lyon: International Agency for Research on Cancer; 2014.\n\nLi Y, Bai S, Carroll W, et al.: Validation of risk model: high risk classification and tumor pattern of invasion predict outcome for patients with low-stage oral cavity squamous cell carcinoma. Head Neck Pathol. 2013; 7: 211–223. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrandwein-Gensler M, Teixeira MS, Lewis CM, et al.: Oral squamous cell carcinoma: histologic risk assessment, but not margin status, is strongly predictive of local disease free and overall survival. Am J Surg Pathol. 2005; 29(2): 167–178. Publisher Full Text\n\nMassano J, Regateiro FS, Januario G, et al.: Oral squamous cell carcinoma: review of prognostic and predictive factors. Oral Surg Oral Med Oral Pathol Oral RadiolEndod. 2006; 102(1): 67–76. Publisher Full Text\n\nZevallos JP, Mazul AL, Walter V, et al.: Gene expression subtype predicts nodal metastasis and survival in human papillomavirus-negative head and neck cancer. Laryngoscope. 2019; 129: 154–161. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrandwein-Gensler M, Smith RV, Wang B, et al.: Validation of the histological risk model in a new patient cohort with primaryhead and neck squamous cell carcinoma. Am J Surg Pathol. 2010; 34: 676–688. PubMed Abstract | Publisher Full Text\n\nVered M, Dayan D, Dobriyan A, et al.: Oral tongue squamous cell carcinoma: recurrent disease is associated with histopathologic risk score and young age. J Cancer Res Clin Oncol. 2010; 136: 1039–1048. PubMed Abstract | Publisher Full Text\n\nJakobsson PA, Eneeroth CM, Killander D, et al.: Histologic classifcation and grading of malignancy in carcinoma of the larynx. Acta Radiol Ther Physiol. 1973; 12: 1–8.\n\nLo WL, Ko S-Y, Chi LY, et al.: Outcomes of oral cancer in Taiwan after surgical therapy: factors afecting survival. J Oral Maxillofac Surg. 2003; 61: 751–758. PubMed Abstract | Publisher Full Text\n\nGonzales-Moles MA, Esteban F, Rodriguez-Archilla A, et al.: Importance of tumourthickness measurement in prognosis of tongue cancer. Oral Oncol. 2002; 38: 394–397. PubMed Abstract | Publisher Full Text\n\nChaturvedi A, Husain N, Misra S, et al.: Validation of the Brandwein Gensler Risk Model in Patients of Oral Cavity Squamous Cell Carcinoma in North India. Head Neck Pathol. 2020 Sep; 14(3): 616–622. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLindenblatt RC, Martinez GL, Silva LE, et al.: Oral squamous cell carcinoma grading systems--analysis of the best survival predictor. J Oral Pathol Med. 2012 Jan; 41(1): 34–39. PubMed Abstract | Publisher Full Text\n\nRahman N, MacNeill M, Wallace W, et al.: Reframing Histological Risk Assessment of Oral Squamous Cell Carcinoma in the Era of UICC 8th Edition TNM Staging. Head Neck Pathol. 2021 Mar; 15(1): 202–211. Epub 2020 Jul 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShah JP, Montero PH: New AJCC/UICC staging system for head and neck, and thyroid cancer. Revista Médica Clínica Las Condes. 2018; 29(4): 397–404. Publisher Full Text\n\nDr. Sonone A , Dr. Hande A , Dr. Pakhale A , et al.: Protocol For Correlation Of Histological Risk Assessment/Scoring System With Depth Of Invasion In Oral Squamous Cell Carcinoma. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "261195",
"date": "12 Apr 2024",
"name": "Alessandro Polizzi",
"expertise": [
"Reviewer Expertise Oral pathology and medicine",
"periodontology",
"orthodontics",
"oral surgery."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the manuscript entitled “Protocol for correlation of histological risk assessment/scoring system with a depth of invasion in oral squamous cell carcinoma” the authors aimed to present a protocol to correlate Brandwein-Gensler criteria and depth of invasion of OSCC with three-year survival. Here are reported some suggestions to improve the quality of the manuscript:\nABSTRACT:\nPlease, give more details about the methodology and study design in the abstract.\nINTRODUCTION:\nThe authors reported that “Although MDSCC comprises up to 90% of oral cancers, this approach, while widely identified and used, still has poor discriminatory value”. Please, better explain why it has poor discriminatory value. “The Brandwein-Gensler (BG) system showed a significant correlation with the patient’s locoregional recurrence and overall survival, especially in low-stage oral cancers”. Please, give more details about the results you found in the literature about the strengths of this correlation related to recurrence and overall survival. “The TNM classification for OSCC (eigtth edition…”. Please correct the error.\nMETHODS:\n\nPlease better explain if this study will be a retrospective or a cross-sectional study. The authors cited the AJCC eighth edition criteria. Please explain the acronym and add a reference. Please, give more details about the randomized selection of histopathologically-diagnosed cases of OSCC. “Staining of the archival slides and new slides (where needed) will be done with HE. WPOI, LHR, and PNI will be assessed by three histopathologists in a blinded manner”. Please specify all the acronyms the first time they have been cited.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "11661",
"date": "21 Jun 2024",
"name": "Dr. Archana Sonone",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for your response , I have done all the corrections which were mentioned in the comment. The Brandwein-Gensler (BG) system showed a significant correlation with the patient’s locoregional recurrence and overall survival, especially in low-stage oral cancers”. Please, give more details about the results you found in the literature about the strengths of this correlation related to recurrence and overall survival. meaning of this sentence- this point elaborated in the discussion section . Thank you regards, Dr. Archana Sonone"
}
]
}
] | 1
|
https://f1000research.com/articles/12-1326
|
https://f1000research.com/articles/12-968/v1
|
10 Aug 23
|
{
"type": "Research Article",
"title": "The realization of interpersonal meanings in cosmetic Maybelline New York in 2018 advertisements",
"authors": [
"Herman Herman",
"Ridwin Purba",
"Nanda Saputra",
"Ridwin Purba",
"Nanda Saputra"
],
"abstract": "Background: Interpersonal meaning is the interaction between the speaker and the listener and the writer and the reader. This study aims to determine the structure of mood and how the structure of mood is found. The purposes of this study are (1) to be more sensitive to the mood structure shown in Maybelline New York cosmetic advertisement. (2) to investigate the reason of why interrogative sentences are more difficult to find than declarative sentences. Through this research, we can see the types of mood structures, and how these mood structures are used. Methods: The type of research approach used is descriptive qualitative. Research in this case describes systematically, factually and accurately facts and causal relationships of the phenomena studied. The sources of data in this study are eight cosmetic Maybelline New York products, namely the Maybelline gel pencil, L’oreal colour riche nail, Maybelline mascara and eyeliner, Maybelline creamy lipmatte and Maybelline eyeshadow, Maybelline eyeliner, Maybelline lipstick, and Maybelline clear smooth all in one. Results: In analyzing the data, the researcher of the 2014 Halliday theory revised by Mathiesse found that there are three types of manifested mood, four types of realized speech function, and mood-based realization of speech function. The moods manifested were declarative (48.64%), interrogative (5.40%) and imperative (45.94%). Speech functions that are realized are statements (48.64%), questions (5.40%), offers (18.91%) and command (24.32%). Conclusions: It can be concluded that declarative sentences are mostly found in Maybelline New York products. Researchers suggest that readers be more careful in using mood structures in cosmetic advertisements so that there are no misunderstandings.",
"keywords": [
"Interpersonal meaning",
"mood structure",
"advertisement",
"mood types",
"multimodal",
"systemic functional linguistics",
"metafunctions",
"Halliday"
],
"content": "Introduction\n\nSocial beings utilize language as a tool to communicate with one another (Lindsay and Knight, 2010; Herman et al., 2020). For worldwide communication, English has grown in popularity and is frequently referred to as an international language. Language is necessary for people (Eggins, 2004) to engage, communicate, and receive information from others.\n\nLanguage is a means of communicating (Butt, 2011; Herman, van Thao and Purba, 2021) with others through sending ideas, emotions, thoughts, information, and ideals (Herman, van Thao and Purba, 2021). The process of conveying a person or a group's meanings, ideas, and understanding to another person or group is described as communication (Sharma, 2017:259). The researcher draws the conclusion that communication is an interaction or relationship between 1-2 persons or a group of people in a society who share information. Text is used to communicate and the meaning and structure of the text are contained within it. Meaning (semantics) is crucial in this context because the goal of communication is for listeners to grasp what the speaker is saying.\n\nThe greatest level of language is semantics, which acts as a bridge between language and the outer world (Halliday and Matthiesen, 2014:42). This indicates that semantics interfaces with content, but also with other systems that function within context. Lexicogrammar converts the linguistic meaning of experience and interpersonal relationships into words that reflect the speaker's perspective (Halliday, 1994).\n\nTherefore, researchers want to examine the interpersonal meaning in cosmetic advertising. Interpersonal meaning is one of the most fundamental interacting contrasts between using language to convey knowledge and using it to interchange products and services (Susanto & Watik, 2017; Herman et al., 2022c). Interaction between the speaker or writer and the listener or reader is thus tied to interpersonal meaning. Its purpose is to facilitate the interchange of rhetorical roles such as declarations, questions, offers, and commands (Ngongo et al., 2022).\n\nTherefore, interpersonal meaning can also occur in an advertisement. Where interpersonal meaning is the interaction between the speaker and the listener and the writer and the reader (Herman et al., 2019). In this case, it can be seen that the relationship between interpersonal meanings and advertisements is very clearly related because in an advertisement there must be an author to write the advertisement and those who read the advertisement are the readers.\n\nAdvertisement is a process of conveying information about products such as goods, services, and ideas from a company to a target audience. Advertising is the origination or communication of product ideas to motivate consumers to purchase (Belch & Michael, 2003). During the marketing process (Goddard, 1998), advertisements can provide information, ideas or messages to the audience. The purpose of this process is to ask the audience to take action. Cosmetics sellers and commercial businesses require advertising services.\n\nThe purpose of cosmetic advertising is not only to provide information but also to introduce the product to buyers. Interpersonal meaning includes speech functions which include speech functions of statements, questions, offers, and commands and their realization in declarative, interrogative, and imperative atmospheres (Herman et al., 2022b).\n\nTherefore, the researcher will examine a cosmetic advertisement product, namely the Maybelline gel pencil. The problem that occurs with the cosmetic advertisement of the product is that the ad does not explain in detail the target age for using these cosmetics. Which means, in the marketing of cosmetic advertisements, there must be a target age for who can use these cosmetic items. The second problem found was the lack of specificity in the delivery of uses and how to use these cosmetic items. What that means is that in an advertisement, whether it's a beauty advertisement, product advertisement, and so on, there must be a delivery of the use and instructions on how to use the beauty cosmetic item and when the beauty cosmetic item is used. The Maybelline gel pencil is useful for beautifying the eyebrows with color.\n\nMost women use cosmetic products for their beauty so that their partner is comfortable with their beauty (Mafra et al., 2020) but do not see the side effects that will occur in the future. The side effects include facial wrinkles, acne, and blackheads. Examples of Maybelline New York advertisements are, Maybelline gel pencil, eyeliner, lipstick and powder.\n\nBelow is a picture of the Maybelline New York’s Gel Pencil beauty cosmetic advertisement:\n\nFrom the example above, the researcher can see that the problem with the Maybelline gel pencil New York advertisement is that there is no delivery or instructions on how to use it. Based on the example above, we can clearly see the types of interpersonal meaning of the Maybelline gel pencil New York advertisement (Tables 1-4).\n\nIn performing this research, the researcher draws on prior findings from Patpong's (2009) thesis ‘Thai Persuasive Discourse: A Systemic Functional Approach To An Analysis Of Amulet Advertisements’, which is related to this research. By examining three metafunctions, this study seeks to explain how persuasive discourse is lexicogrammatically investigated. According to the research findings, the relational process comes in second place to the material process in terms of ideational significance. Declarative mood is most frequently used in interpersonal contexts, followed by imperative. The unmarked topical theme was determined to be dominating (91.58%) in the textual analysis, followed by the labeled theme (8.42%).\n\nAs a result, it can be claimed that this research differs from earlier research. Cosmetic advertisements that contained four speech functions, including statements, questions, offers, and commands as well as three types of moods, including declarative, interrogative, and imperative in interpersonal meaning has been studied by Patpong. This study has only examined persuasive discourse in the previous study (Patpong, 2009), which was investigated lexicogrammatically by investigating three metafunctions, namely ideational, interpersonal, and textual. As a result, the researcher concentrated only on 3 different moods and 4 speech functions in advertisement for beauty products.\n\nThe Halliday theory, proposed by Matthiessen in 2014, is in agreement with this research. Three different types of mood realization, four different types of speech function realization, and mood realization of speech function were discovered by the researcher. Declarative (83.33%), interrogative (3.33%), and imperative (13.33%) moods were realized. Statements (43.33%), questions (6.67%), offers (40%) and orders (10%) are the speech functions that are really used. This demonstrates that statements in advertising for goods are more likely to interest and persuade consumers.\n\nThe recent phenomenon in cosmetic advertising and the explanation given above is the reason why this research focuses on analyzing the type of interpersonal meaning in cosmetic advertisements.\n\n\nMethods\n\nThis study was carried out utilizing a descriptive qualitative approach. Eight of the most popular methodologies, according to Ary et al. (2010:29), include the following: basic interpretative studies, case studies, document or content analysis, ethnography, grounded theory, historical studies, narrative inquiry, and phenomenological research. Because the researcher employed the scripts of advertisements as the subject of the investigation, this study utilized a document or content analysis. Content or document analysis, according to Ary et al. (2010:457), is a research technique used to analyze textual or visual materials with the goal of discovering certain qualities of the material (Purba et al., 2022). The source material for analysis could be a textbook. Because textbooks are collections of logical ideas that are organized according to learning objectives. This means that the objective of the product is given in the Maybelline New York cosmetics advertising, both on TV and in the catalog.\n\nSugiyono (2017) claims that qualitative researchers are human instruments that serve to state the research focus, choose information as a data source, compile data, assess data quality, analyze data, interpret data, and draw conclusions about findings (Sugiyono, 2017 cited in Munthe et al., 2021). The sources were gathered at random by searching for advertisements on the internet. The researcher utilized the internet, YouTube, a phone, a television, a pen, a book, and a piece of data in this study as the tool to get the data. The data were collected using observational methods. Google was used to search for and download the complete text of advertisements. Next, we downloaded cosmetics advertisement texts that only used English as the language of communication. A detailed explanation of the data collection and research instruments is provided in the data collection section. Watching product ads on YouTube can be a more effective way to gain insight into a product. We were able to quickly and easily filter search results to find the specific product they are interested in. YouTube offers extra information about the product being advertised. This includes links to websites where viewers can purchase the product and read more reviews.\n\nData are units of information, often numeric, that are collected through observation. Burnham (2012:1) stated that research data is the information that is typically kept and acknowledged by the scientific community as being required to validate research findings. The sources of data in this study are eight cosmetic Maybelline New York products, namely the Maybelline gel pencil, L’oreal colour riche nail, Maybelline mascara and eyeliner, Maybelline creamy lipmatte and Maybelline eyeshadow, Maybelline eyeliner, Maybelline lipstick, and Maybelline clear smooth all in one. The advertisement text for these cosmetics were taken from the Maybelline website: https://www.maybelline.co.id/.\n\nData were gathered using an observational methodology (Tables 5-7). The researcher examined the advertisements by searching for them on Google in order to download the complete text of the advertisements. The researcher then downloaded cosmetics advertising text that was in English. The procedures for gathering the data in this study make use of numerous strategies, including:\n\n1. Searching text for cosmetic adverts on websites or the internet.\n\n2. Reading and selecting the website that offers English-language text for cosmetic advertisements.\n\n3. Downloading carefully chosen website text for beauty adverts, https://www.maybelline.co.id/, https://www.loreal.co.id/. The research is primarily focused on examining Maybelline New York advertisements, https://www.loreal.co.id/ was also used for comparison and data collection.\n\n4. Choosing the data from the advertisement that uses English.\n\n5. Examining the details or terminology used in cosmetic marketing.\n\n6. Eliminating data which contains the same information.\n\n7. Listing and giving codes to all the clauses by using the tables.\n\nThe additional methods and full data are available under Underlying data [Herman et al., 2022a].\n\nThe researcher then conducted an analysis of the data. Most qualitative researchers use data to describe events, explain what they mean, and gain an understanding of them. Since various strategies require various methods of analysis, this study will concentrate on interpersonal meaning.\n\nMiles, Huberman and Saldana (2014:31-32) stated that analysis in qualitative research consists of three steps that occur simultaneously, namely;\n\n1. Data condensation,\n\n2. Data presentation, and\n\n3. Conclusion drawing and verification.\n\nIn this study, the data were analyzed through the following steps:\n\n1. Data condensation\n\nThe method of selecting, concentrating, streamlining, abstracting, and changing the unprocessed data that results from field notes is known as data condensation. The procedure for condensing data is as follows:\n\na. Selecting information from the website's text-based cosmetic adverts.\n\nb. Concentrating on English-language cosmetic commercials.\n\nc. Converting the data to be simplified into a clause. The clause consists of mood and speech function which is used in cosmetic advertisement.\n\nd. Evaluating the collected data which consists of mood and speech function used in cosmetic advertising.\n\ne. Analyzing the data by selecting each clause for the type of mood and speech function. Data selection is based on mood elements (subject and finite) residue elements (predicator and complement) and so forth all of them were realized in declarative, interrogative and imperative as descriptive analysis. Then, the speech function is manifested in statements, questions, commands and offered as a result of interpersonal meaning interpretive analysis.\n\n2. Data display\n\nThe next stage is to display the data after it has been compressed. A data perspective is a structured, condensed collection of information that facilitates processes like verification and conclusion-making. To make the data easier to understand for readers, researchers present the data in the form of tabular analysis. First, the information was categorized according to the mood types imperative, interrogative, and declarative. Second, knowing the realization of mood in speech function as interpersonal meaning in cosmetic advertisement text. Below are formulas and examples of analysis in tabular form:\n\nN: percentage of type f(x): total types\n\nFrequency of the sub category n: total types of all categories.\n\n3. Drawing and verifying conclusions\n\nOne of the crucial steps in this investigation is coming to and verifying conclusions. This is a method of learning the study's findings. Here, the researcher draws a conclusion after thoroughly defining various mood and speech functions and learning how the text of cosmetic commercials realizes interpersonal meaning.\n\n\nResults and discussion\n\nBased on the data analysis, there were five cosmetic Maybelline New York advertisements chosen. To conduct this research, there were 25 clauses to identify. The following analysis had been conducted from the perspective of the interpersonal meaning by analyzing its use of mood, speech function and how the speech function is realized in cosmetic Maybelline New York advertisements (Tables 8-18). It is explained as follows:\n\n1. Types of mood realization\n\nThere were three types of mood realized in five cosmetic Maybelline New York advertisements. The moods were realized by declarative mood, interrogative mood and imperative mood.\n\nThe following data and analysis were described:\n\na. Declarative mood\n\nAdvertisement 1 – Loreal ad quote\n\nFrom the mood structure above, the clause can be identified by the position of the subject (Milla) which is before the finite (is).\n\nb. Interrogative\n\nYes-no interrogative is the order Finite before Subject\n\nAdvertisement 2 – Maybelline ad quote (https://www.maybelline.co.id/) [Herman et al., 2022a]\n\nFrom the mood structure above, it can be identified by the position of the subject (the next) which is after the finite (is).\n\nc. Imperative\n\nImperative mood is the clause when the predicator at the beginning of the sentence, with or without the subject which is usually “you”.\n\nAdvertisement 3 – Loreal ad quote (https://www.loreal.co.id/ [Herman et al., 2022a]\n\nFrom the mood structure above, it can be found from the clause that the predicator (visit) is at the beginning of the sentence. We also find that there is no subject after the predicator.\n\nAccording to the data, there were 37 clauses chosen which contain declarative mood, interrogative mood and imperative mood. The percentage of mood will be explained in the table below:\n\n2. Types of speech function realization\n\nThere were four types of speech function realized in five cosmetic Maybelline New York advertisements. The speech functions were realized by statement, question, offer and command. The following data and analysis were described:\n\na. Statement\n\nA statement is something that is said aloud or written down that conveys information. A statement may be neutral or adverse.\n\nAdvertisement 4 – Maybelline ad quote (https://www.maybelline.co.id/)\n\nHow to use Maybelline gel pencils that lasts up to 16 hours of wear\n\nFrom the sentence above, we can see that the sentence provides information about how to use the Maybelline gel pencil product for up to 16 hours wear.\n\nb. Question\n\nA question is a technique to demand information in the form of an interrogative statement. It can be a yes-or-no question or an information query (wh-question). A question is an interrogative statement that is used to obtain information or ask an inquiry.\n\nAdvertisement 5 – Loreal ad quote (https://www.loreal.co.id/) [Herman et al., 2022a]\n\nWhat’s next from paris?\n\nFrom the sentence above, it shows that the advertisement is trying to find out whether the consumers already know or not about the latest product from Paris. This sentence also uses a wh-question that functions to seek confirmation from the consumers regarding knowledge of the latest product from Paris.\n\nc. Offer\n\nOffer is defined as a way to provide someone with a good or service. Offering something also conveys a willingness to provide or perform it.\n\nAdvertisement 6 – Maybelline ad quote (https://www.maybelline.co.id/) [Herman et al., 2022a]\n\nJourdan is wearing new eye studio lasting drama waterproof gel pencil in cashmere white\n\nFrom the sentence above, we can see that the sentence provides information about how to use the new studio eye drama waterproof gel pencil in cashmere white.\n\nd. Command\n\nBy requiring the listener to provide something, you can receive knowledge, goods, or services. Demanding goods and service through an imperative statement, whether it takes the form of a positive or negative command, is another way to use a command. The subject is not included in the command sentence.\n\nAdvertisement 7 – Maybelline ad quote (https://www.maybelline.co.id/) [Herman et al., 2022a]\n\nAdd color to your cheeks with fit me! Blush\n\nFrom the sentence above, we can see that the sentence gives orders to consumers by adding color to the cheeks with fit me! Blush.\n\nAccording to the data, there were 25 clauses chosen which contain a statement, question, offer and command. The percentage of mood is explained in the table below:\n\n3. Realization of speech function based on mood\n\nThere were four speech functions realized based on mood: Statement realized by declarative mood, question realized by declarative mood and interrogative mood, offer realized by declarative mood and imperative mood, command realized by imperative mood.\n\nThe following data and analysis were described as follows:\n\na. Statement realized by Declarative Mood.\n\nAdvertisement 8 – Maybelline ad quote (https://www.maybelline.co.id/) [Herman et al., 2022a]\n\nSpeech function: Statement\n\nThe speech function is a statement because it gives information. From the sentence above, we can see that the sentence provides information about their product (Maybelline). Maybelline informs about the superiority of its product which is the 1st gel pencil with translucent gel base. It will make it easier for users to use or apply this product.\n\nb. Question realized by Declarative Mood and Imperative Mood.\n\nAdvertisement 9 – Loreal ad quote (https://www.loreal.co.id/) [Herman et al., 2022a]\n\nSpeech function: Question\n\nThe speech function is question, because it demands information. From the sentence above, it shows that the advertisement is trying to find out whether the consumers already know or not about the latest product from Paris. This sentence also uses wh-question that function to seek confirmation from the consumers regarding knowledge of the latest product from paris.\n\nc. Offer realized by Declarative Mood and Imperative Mood\n\nAdvertisement 10 – Maybelline ad quote (https://www.maybelline.co.id/)\n\nSpeech function: Offer\n\nThe speech function is offer, because it gives goods-and-services. From the sentence above, Maybelline makes Jourdan the artist of the product. Maybelline provides the fact that Jourdan uses new eye studio lasting drama waterproof gel pencil in cashmere white. But, this actually becomes a means to offer the consumers, if they want to be like Jourdan, Maybelline.\n\nSpeech function: Offer\n\nThe mood is imperative, because there is a predicator at the beginning and no subject. The speech function is offer, because it gives good feel and services. It gives a recommendation to the consumer that “at maybelline.com” the consumer will get the tips from Maybelline experts.\n\nd. Command realized by Imperative Mood\n\nAdvertisement 11 – Maybelline ad quotes (https://www.maybelline.co.id/)\n\nSpeech function: Command\n\nThe mood is imperative because there is a predicator at the beginning and no subject. The speech function is command, because it demands goods and services. The advertisement persuades the consumers to buy the product as soon as possible.\n\nFrom the data, there were 37 clauses chosen from clauses which contain a statement, question, offer and command. Statement is realized by declarative mood, question is realized by declarative mood and interrogative mood, offer is realized by declarative mood and imperative mood, command is realized by imperative mood. The percentage of mood is explained in the table below:\n\n(https://www.loreal.co.id/) [Herman et al., 2022a; Fang 2016].\n\n\nDiscussion\n\nBased on the research and the analysis of 811 pieces of data, 18 clauses were found which were declarative, 2 clauses were interrogative, 17 clauses were imperative. From this we can see that almost all declarative sentences are needed because declarative words are statements. Just like a statement sentence that must have a subject and a finite. Therefore, there are more declarative sentences than other types of mood. To enable the researcher, there were 37 clauses to identify. Types of mood realization is declarative, interrogative and imperative. The types of speech function realization in cosmetic Maybelline New York advertisements are statement, question, offer and command. 18 clauses were found which were statement, 2 clauses were found which were question, 7 clauses were found which were offer and 9 clauses were found which were command. If you want to find the implicit referential meaning you can use the Halliday theory revised by Matthiessen. Therefore, the purpose of the conclusions described above are to determine the type of mood structure in the interpersonal meaning embodied in Maybelline New York cosmetic advertisements, and to find out how the interpersonal meaning in the Maybelline New York cosmetic advertisement is realized.\n\n\nConclusion\n\nBased on the analysis of interpersonal meaning in cosmetic Maybelline New York advertisements, there are some conclusions:\n\n1. In interpersonal meaning, clauses are analyzed from the mood structure which consists of mood elements and residue elements. From the analysis of interpersonal meaning through the mood structure found in the Maybelline New York cosmetics advertisements, there are 28 subjects obtained and 28 finite obtained. For residue elements, 17 predicates are obtained, 28 complements are obtained, 2 mood adjuncts are obtained. And there are 18 clauses (50%) as declarative mood, 2 clauses (5.55%) as interrogative mood and 16 clauses (44.41%) as imperative mood.\n\n2. There are four types of speech functions, namely statements, questions, offers, and orders. There are 18 clauses (50%) as statements, 2 clauses (5.55%) as questions, 7 clauses (19.44%) as offers, and 9 clauses (25%) as orders. By understanding the function of speech, the researcher concludes that the function of speech in an advertisement is one of the moods that attracts someone to buy the product. This is one of the reasons for the researcher to examine the function of language in an advertisement.\n\nCosmetic brand Maybelline New York has been a leader in the beauty industry for over a century, and its advertisements have an immense influence on consumer culture. In 2018, their ads began to incorporate more meaningful interpersonal messages in an effort to challenge societal norms and beauty standards. By featuring models of all races, sizes, and genders, the ads highlighted the importance of inclusion and self-love. This shift in messaging was further highlighted by the company’s collaborations with celebrities and influencers who promote positivity and acceptance. The realization of these interpersonal meanings in the 2018 Maybelline New York advertising campaign was significant in terms of its impact on consumer culture, as well as its long-term effect on the beauty industry. This shift in messaging away from conventional beauty standards and towards inclusivity and self-love could be indicative of a broader societal shift towards acceptance and understanding. However, there is still a need for further research in this area to better understand the limitations and future research scope of this new messaging. This could include analyzing the impact of Maybelline’s campaign on consumer behavior and attitudes, as well as exploring how other beauty companies are responding to this shift.",
"appendix": "Data availability\n\nFigshare: RAW DATA.docx. https://doi.org/10.6084/m9.figshare.21757856.v3 (Herman et al., 2022a).\n\nThis project contains the following underlying data:\n\n- Types of Maybelline Products.docx (Cosmetic Maybelline New York Advertisements, Maybelline Products)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAry D, Jacobs LC, Sorensen C, et al.: Introduction to Research in Education. Wadsworth: Cengage Learning; 2010.\n\nBelch GE, Michael AB: Advertising and Promotion: An Integrated Marketing Communication Perspective. McGraw-Hill; 2003.\n\nBurnham A: Research Data-definition. University of Leicester; 2012.\n\nButt D: Using Functional Grammar. Revised ed.Sydney: Macquarie University Press; 2011.\n\nEggins S: An Introduction to Systemic Functional Linguistics. London: Continuum; 2004.\n\nFang: The Realization of Mood through Syntactic Patterns in English Public Service Advertising Texts. 2016. 30 May 018. Reference Source\n\nFirmansah A: Interpersonal Meaning in Netanyahu’S Speech. English Review: Journal of English Education. 2015; 4(1): 103–108. Publisher Full Text Reference Source\n\nGoddard A: The language of advertising. London: Routledge; 1998.\n\nHalliday MAK: An Introduction to Functional Grammar. London: Edward Arnold; 1994.\n\nHalliday MAK, Matthiessen C: An Introduction to Functional Grammar. Fourth ed.London: Arnold Publication; 2014.\n\nHerman, Murni SM, Sibarani B, et al.: Structures of Representational Metafunctions of the “Cheng Beng” Ceremony in Pematangsiantar: A Multimodal Analysis. International Journal of Innovation, Creativity and Change. 2019; 8(4): 2019.\n\nHerman, Purba R, Thao NV, et al.: Using Genre-based Approach to Overcome Students’ Difficulties in Writing. Journal of Education and E-Learning Research. 2020; 7(4): 464–470. Publisher Full Text\n\nHerman, van Thao N , Purba NA: Investigating Sentence Fragments in Comic Books: A Syntactic Perspective. World Journal of English Language. 2021; 11(2): 139–151. Publisher Full Text\n\nHerman H, Sulistyani S, Ngongo M, et al.: The structures of visual components on a print advertisement: A case on multimodal analysis. Studies in Media and Communication. 2022c; 10(2): 145–154. Publisher Full Text\n\nHerman H, Saputra N, Ngongo M, et al.: Delivering A Good Speech by Identifying the Interpersonal Meaning Found in Joe Biden’s Victory Speech: A Case on Systemic Functional Linguistics. Journal of Intercultural Communication. 2022b; 22(3): 65–73. Publisher Full Text\n\nHerman H, Purba R, Saputra N: RAW DATA.docx. Dataset. figshare. 2022a. Publisher Full Text\n\nHuberman M, Saladana: Qualitative Data Analysis. Sage Publication, Inc; 2014.\n\nLindsay C, Knight P: Learning and Teaching English. New York: Oxford University Press; 2010.\n\nMafra AL, Varella MAC, Defelipe RP, et al.: Makeup usage in women as a tactic to attract mates and compete with rivals. Personality and Individual Differences. 2020; 163: 110042. Publisher Full Text\n\nMunthe B, Herman, Arifin A, et al.: Online Student Attendance System Using Android. Journal of Physics: Conference Series. 2021; 1933: 012048. Publisher Full Text\n\nNgongo M, Maromon E, Loba D, et al.: A systemic functional linguistics analysis of text transitivity of Mathew Gospel, New Testament of Kupang Malay. World Journal of English Language. 2022; 12(5): 188–201. Publisher Full Text\n\nPatpong: Thai Persuasive Discourse: A Systemic Functional Approach To An Analysis of Amulet Advertisements. 2009. 28 May 2018. Reference Source\n\nPurba R, Sibarani B, Murni SM, et al.: Conserving the Simalungun Language Maintenance through Demographic Community: The Analysis of Taboo Words Across Times. World Journal of English Language. 2022; 12(1): 40–49. Publisher Full Text\n\nSharma R: Communication: TheLife line. Word WideJournalof Multidisciplinary Research and Development. 2017. E-ISSN: 2454-6615.\n\nSugiyono: Metode Penelitian: Kuantitatif, Kualitatif, dan R&D. 2017.\n\nSusanto DA, Watik S: The Interpersonal Meaning Realized in The Lyrics of Christina Perri’s Album “Love Strong” and The Contribution for Teaching. 2017; 09(03): 283–291."
}
|
[
{
"id": "207877",
"date": "19 Apr 2024",
"name": "Danang Satria Nugraha",
"expertise": [
"Reviewer Expertise Theoretical Linguistics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article offers a well-organized and comprehensive description of the problem, meeting current research needs. The feasibility and uniqueness of the research suggest its value and warrant further review. However, to enhance the introduction section, clearly articulating the research's uniqueness and feasibility is crucial.\nTo improve the article, the following points should be considered:\nA detailed gap analysis is necessary. The manuscript needs to articulate the importance of the research better. The rationale must be strengthened by providing arguments about the locus and discussion. The results should include an interpretation of the findings. The conclusion should answer the research question and relate to previous research/findings. Though the literature review and previous studies illustrate and explain the adequacy of the reasons for the study, the focus of the object being discussed needs to be strengthened. To strengthen the study, the accuracy and scope of the literature review should be improved by adding more information where needed. The last paragraph of the method section requires further elaboration.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11662",
"date": "21 Jun 2024",
"name": "Herman Herman",
"role": "Author Response",
"response": "I am pleased to present the updated research report on \"Interpersonal Meanings in Cosmetic Advertising.\" Following valuable feedback and recommendations, several enhancements have been made to the manuscript to address the comments and improve the overall quality of the research. Firstly, the gap analysis has been thoroughly revised to provide a more detailed examination of the existing literature and to better articulate the uniqueness and feasibility of the research. By integrating existing theoretical frameworks and emphasizing the importance of the relationship between the author and the audience in advertising communication, the study aims to explore the structure of mood and speech functions in advertising communication. Additionally, the importance of the research has been articulated more effectively by highlighting the significance of analyzing language, mood structures, and speech functions in cosmetic advertising. The manuscript now emphasizes the practical implications for marketers, advertisers, and consumer behavior researchers, as well as the potential impact on advertising practices in the cosmetics sector. Furthermore, the rationale has been strengthened by providing in-depth arguments about the locus and discussion, including ethical considerations about language and communication strategies in cosmetic advertising. Lastly, the results have been interpreted to provide a comprehensive analysis of the findings, particularly focusing on the prevalence of declarative mood and statement speech functions in the analyzed cosmetic advertisements. These improvements aim to enhance the clarity, significance, and depth of the research, and I believe that the updated manuscript now effectively addresses the comments and suggestions provided."
}
]
}
] | 1
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https://f1000research.com/articles/12-968
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https://f1000research.com/articles/11-1339/v1
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17 Nov 22
|
{
"type": "Research Article",
"title": "Outward investment of Portuguese small and medium enterprises in the Central and Eastern European countries: motivations and challenges",
"authors": [
"Eleonora Santos",
"Jacinta Moreira",
"Jacinta Moreira"
],
"abstract": "Background: This paper identifies the determinant factors of Portuguese investment in Poland, Hungary, and the Czech Republic. We assume that investment abroad is motivated by business opportunities, and the quality-price ratio of the workforce. Methods: To this end, we used a qualitative methodology composed of 6 case studies, based on interviews and surveys with the managers of the Portuguese firms investing in those three economies. Results: Despite the business opportunities, Portuguese investment directed towards these economies is negligible, due, in part, to the geographic and cultural distance. However, the economic and political stability, combined with market size and growth potential are undeniable attraction factors for Portuguese investors. Small and medium enterprises (SMEs), due to their flexible conditions that allow changes in the activity, and the strong trend towards outsourcing, to the detriment of the manufacturing industry, are the primary focus of international investment. This trend, although common to several sectors, has shown greater dynamism in the banking and financial sector. Conclusions: The results suggest market-oriented investments aiming at growth and expansion. The vast Polish market is the one that most attracted Portuguese investors. The hybrid feature of some strategies can align with the cautious attitude towards the investment translated into cooperation agreements with financial institutions for funding, the market learning process, and the training of the personnel. The anticipation of the installation over potential competitors, the experience in production and international markets, the price-quality ratio, the capacity of product adaptation and the design were considered important sources of competitive advantage that motivated the investment. The greatest difficulties during this process were language and the complexity of legislation.",
"keywords": [
"Outward foreign direct investment",
"CEECs",
"Sttategies",
"Internationalization"
],
"content": "Introduction\n\nIt was not until the 1960s, with the great dynamism of North American Multinational Corporations (MNCs) with diverse competitive strategies, that the role of foreign investment has been highlighted in endogenous growth models, combined with studies on technology diffusion (Vázquez-Barquero, 2002). The role of Foreign direct investment (FDI) was further highlighted by the performance of some Asian countries in the 1990s as a magic ingredient to economic growth (Saleem & Shabbir, 2020. Yet, the Asian crisis of 1997/1998 uncovered the weaknesses of the Asian model (Chung, 2021), leading to a general awareness that the path of sustainable growth involves internalizing the specificities of each economy (Lin, 2011).\n\nNotwithstanding, currently it is consensual that the preservation of competitiveness involves, in many cases, the international relocation of certain stages of the production process. In a context of open economies, internationalization can become a matter of survival (Freixanet & Renart, 2020). Yet, large investments in machinery and equipment are not a guarantee of increases in productivity and competitiveness, due to insufficient mastery of organizational aspects (Shlafman, Bondarenko & Zakcharov, 2020). In addition, inadequacies in terms of strategic reflection and market interpretation can hamper the competitiveness of firms (Dixit, Singh, Dhir & Dhir, 2021). Also, the sole focus on the production process, rather than considering product design and marketing aspects, can be detrimental to the internationalization process (De Beule, Van Assche & Nevens, 2022; Sørensen & Ngoc, 2021).\n\nThis paper uses interviews and surveys applied to managers of different sectors to carry out 6 case studies to characterize the Portuguese direct investment (PDI) in Poland, Hungary, and the Czech Republic, regarding the determinant factors of attraction, PDI motives, goals, strategies adopted, entry modes, competitive advantages, threats, and challenges.\n\nWe assume the entrepreneurs decide to invest in those countries for the business opportunity, being fundamentally attracted by the quality-price ratio of the workforce.\n\n\nFDI: Motivations, entry modes and objectives\n\nThe competitive advantages of firms may arise from the holding pioneering positions in the implementation of the appropriate strategy and/or motivation to produce and innovate, determined by the nature of their customers and competitors and by the use of resources and productivity (Ferreira, Coelho & Moutinho, 2020) In this process, the environment is particularly important, as it allows for a rapid accumulation of resources and specialized skills and guarantees access to information on market needs (Mostafiz, Sambasivan & Goh, 2019) Thus, the analysis of the competitive advantages and corporate strategies to address the internationalization process, should reflect the interaction of six variables: the government, which should act as a catalyst for change, encouraging firms to become more competitive, monitoring compliance quality standards and regulating competition; the firm (structure, strategies and competition) that should stimulate the creation and maintenance of competitive advantages, which may translate into innovation, improved efficiency, cost reduction and improved product quality; the production factors that must be specialized and meet firm’s needs, otherwise strong competitive positions will be created; the internationally related competitive sectors that push for the increase of global competitiveness; and the demand that allows understanding the market’s needs and can induce innovation; and chance (facts beyond firm’s control, such as wars, technological progress, political events, etc.) that may stimulate firms’ competitiveness. Companies that internationalize should develop a strategy to disseminate activities in the value chain, to enhance their sources of competitive advantage (Chen, 2018; Porter, 1986). In this context, downstream activities will be typically located in the host country, while upstream activities may be in the home country. Hence, downstream activities may create host country specific competitive advantages, such as low costs and product differentiation.\n\nThe different ways in which the presence of firms in the foreign market is reflected depend on the type of competitive advantage they hold and are distinguished by the configuration of activities (dispersed/concentrated) and their coordination (weak/strong) (Feio, 1998; Hernández & Pedersen, 2017).\n\nMotivations for FDI can be the search for resources, strategic assets, technology, markets, and diversification. The first aims at exploit natural resources to obtain/secure an uninterrupted supply that allows for cost reduction. The second aim at maximizing the firm’s overall performance. The third is related to access to sophisticated technologies and know-how. In some countries, markets may be saturated and thus firms need to target markets abroad to sell their products. In this process, firms may face trade barriers and chose to invest abroad to overcome such barriers. Finally, particularly large, and relatively competitive firms in international markets, may engage in overseas’ investments aiming at risk diversification.\n\nAmong export solutions (agent/exporter, distribution subsidiary) and foreign direct investment (Mergers & Acquisitions [M&A], Greenfield, joint venture), there several entry modes in the foreign markets, such as collaboration with local companies to take advantage of their knowledge of the foreign market (licensing, franchising, technical agreements, management contracts, strategic alliances) which reduce penetration costs, but may lead to imitation/appropriation by local rivals.\n\nThe choice between export and FDI will be made considering internal and external aspects of the company. Exports are facilitated by technological developments and international trade regulations that contribute to reductions in transport, telecommunications, and tariffs, and to tax harmonization, and reduce the interest in diversifying production units (FDI). If there are obstacles to exports, companies may use agents or local importers to offer their products (Arm's length). However, there are products and services that, by their nature, are difficult to supply in this way, namely when it is necessary to provide an after-sales service, adaptation of products, or when there is a strong component of brand reputation. Thus, many cases of vertical and horizontal integration resulted from the need to prevent problems arising from uncertainty, or increased costs arising from commercial mechanisms (which may result from geographic or cultural distance, differences in the legal framework or institutional dimension). In short, factors such as tariffs and quotas, discrimination against foreign companies, transport costs, distance, strong competition, high technology, and experience in foreign markets tend to favor foreign direct investment. On the contrary, exports are favored by restrictions on the possession of foreign capital and by political and exchange rate risks.\n\nAn underlying issue of the internationalization process is its genesis, since, in some cases, the internationalization process is the result of chance, although typically involves a deliberate strategy. Each internationalization strategy can be described as the association between some important internal advantages of the company (I) and external factors (E), where:\n\nKH - Know-how, knowledge, and accumulated experience.\n\nMF - Available financial means (internal and external).\n\nSM - Access to Markets.\n\nCP - Installed production capacity, infrastructures that enable production.\n\nME - External environment, context in which the company operates, that is likely to motivate FDI (legislation, Government support and incentives, etc.).\n\nCrossing I and E (Table 1), the main diagonal does not appear be of much relevance since it corresponds to a reinforcement of the advantages that already exist at the home market. The SM column represents the conquest of more attractive markets.\n\nThe CP column means the use of installed capacity abroad associated with home production capacity, know-how, market, financing, and the national environment. In this case, the investment must target host countries with lower costs or underutilization of existing production capacity, due to industrial conversion processes. The KH column is related to access to foreign know-how to leverage the advantages acquired internally. The MF column is related to easier/cheaper financing abroad and the projection of national competences abroad to reduce financing costs. Finally, the ME column represents situations of granting incentives by foreign authorities, favorable legislation to attract investment in the host countries and/or the presence of other national firms in the host country (suppliers, customers, competitors) with which the company has strong links.\n\nForeign investment objectives. Foreign direct investment may aim at commercial expansion or at rationalizing costs using cheaper production factors. Commercial expansion may become the main objective when the capacity of the domestic market is weak or there are high transport costs, restrictions on foreign trade or restrictions imposed by consumers (nationalism, product image, uncertainty of supply or the need to product adaptation) or when firms need to follow their competitors/customers. Investments aimed at taking advantage of production factors are motivated by difficulties in accessing production factors or differences in their cost in the country of origin, rationalization of production, vertical integration, high installed capacity without corresponding demand in the domestic market, incentives or due to the advanced stage of the products’ life cycle. However, currently, these two objectives tend to be diluted, since some host countries have become important both for cost rationalization and as new markets.\n\n\nMethods\n\nQuantitative research was composed of a survey applied to a non-probabilistic sample of managers. Inclusion criteria were managers of Portuguese firms investing in at least one of the three countries (Poland, Hungary, or the Czech Republic).\n\nThe analysis is based on a survey by Bartels et al. (2009). The first author distributed the questionnaires and explained them to the target respondents. The completed questionnaires were gathered just before the interviews. Data from questionnaires were introduced into STATA 17.0 for internal consistency analysis. Variables concerning motivation, determinant factors, and barriers were obtained from the literature on international business and FDI (Castro, 2000; Leahy & Pavelin, 2003; Kim & Rhee 2009; Bartels et al., 2009; Kedia et al., 2012) and location and transaction cost decisions (Dunning, 1998). The variables of the survey questionnaire were structured as Likert scale questions.\n\nThe questionnaire has 4 groups. The first concerns the identification of the firm, and the second, third, and fourth groups report motivation (37 items), determinant factors of attraction (16 items), and barriers (17 items) to the investment abroad. Data analysis is descriptive. Since initially, we had 70 variables (items), the recommended minimum number of respondents would be 350 to implement factor analysis (at least 5 times more observations than the number of variables). Therefore, this requirement cannot be satisfied for the analyzed dataset. In addition, it is recommended for factor analysis to use large samples (at least less than greater than 100). Our database could not meet this criterion. The reliability of the questionnaire was obtained through the Cronbach’s alpha calculated using Stata 17.0, to validate the questionnaire. Cronbach's alpha is the average of all variability coefficients that result from the different ways to halve the set of evaluators. From the analysis of variance’s point of view, it can be interpreted as the intraclass correlation coefficient. Thus, the alpha value changes according to the population to which the scale is applied (Streiner, 2003). In general, the minimum acceptable value for the reliability of a questionnaire is α≥0.70; below which the internal consistency of the scale used is considered low. By contrast, an alpha above 0.90 suggests redundancy or duplication, i.e., several items are measuring the same element of a construct; therefore, redundant items must be eliminated. Thus, ideally, alpha values lie between 0.80 and 0.90 (Streiner, 2003). The value of alpha depends on the number of items on the scale. As the number of items increases, the variance increases systematically. After running the command alpha, the items for groups 2, 3, and 4 were reduced to 19, 10, and 6 items, respectively. The alpha value is 0.87 which indicates high reliability. The questionnaire can be found as Extended data (Santos, 2022c).\n\nTable 2 shows the dimensions of validity of the survey, assessed with hypotheses, evidence and statistical criteria.\n\nThe second component included exploratory semi-structured interviews conducted with (male) managers at companies’ headquarters. Semi-structured exploratory interviews are the most used interview format for qualitative research. More specifically, the first author carried out interviews structured around an initial open question: why did you invest in Poland and/or Hungary and/or the Czech Republic? The following questions emerged from the dialogue between interviewer and interviewee. Interviews were conducted for each individual, lasting approximately 60 minutes. These interviews aimed at obtaining a more thorough understanding of the motivations and difficulties that constrained the investment in Poland, Hungary, and/or the Czech Republic.\n\nWe identified 28 Portuguese companies (Population) that invest in at least one of the three countries, of which 15 invest in Poland, 10 in Hungary and 7 in Czech Republic. Some firms invest in more than one country. According to information fron the Portuguese Investment Agency, the sectoral and spatial distribution of the known population of firms is displayed in Table 3.\n\nTable 3 shows that the manufacturing industries represent 53% of the population. The number of sectors reflect the great diversity of investment areas. Poland captures more sectors. This fact became evident through the interview to the manager of the construction company (that invests in the three countries). Regarding the attractiveness of the three economies, he has stated: “In objective terms, by descending order, the most developed is the Czech Republic, followed by Hungary and Poland, but the country that most matter for us is Poland, because it is the largest.”\n\nA sample of 15 companies investing in those countries was selected for the case studies. The contacts with the managers of these companies were made by mail, aiming at collecting data via a questionnaire about the reasons, attraction factors and challenges during the investment process. Responses were sought in terms of the importance assigned to each item.\n\nIn the interviews, the entrepreneur was allowed to speak freely about the investment process, namely about strategies and future expectations.\n\nSince the sample represents only 25% of the population, it is not representative (in terms of size and diversity of activities) which can compromise the reliability of the conclusions. Thus, we can only expect to provide hints on the outward investment process.\n\nHowever, the validity of the sample justifies three remarks. First, the lack of a secondary data source, would require a case-by-case compilation, requiring a great deal of time and effort that was not possible; Second, the number of firms in the sample is within the average range of cases in other studies (Braz, 1999; Valadares et al., 1995); Third, although the results are conditioned by the small size of the sample, they nevertheless allow for information that is consistent with other studies (e.g., Benan & Estrin, 2000; Döhrn, Milton & Radmacher_Nottelmann, 2001; Resmini, 1999), which justifies their presentation and discussion.\n\nRegarding the interviews, the questions were posed according to the way the interviewee handled the topic, so as not to influence the answers. The interviews also allow to carry out a swot analysis of the recipient countries.\n\nThe interviews were recorded and later transcribed, having been subjected to line-by-line analysis, according to the Grounded Theory, with a view to identifying the main concepts and later structuring the logic underlying the investment decision. In general, the interviews reflect the perception of the external environment by those responsible for the investment. Table 4 provides the sectoral distribution of the sample.\n\nOral consent was provided, and audio recorded, due to process simplification and because the formality of written information was viewed as inappropriate by the respondents. The ethical approval board from UC approved this study in March 2022. The approval board deemed the oral consent to be adequate for the study.\n\n\nResults\n\nIt was only possible to carry out six interviews, due to the lack of response (Santos, 2022a). The results of interviews regarding the swot analysis of the recipient countries are displayed in Figures 1 to 3. The figures show that the three economies benefit from common strengths such as geographical location, skilled labor, and political stability.\n\nHowever, Poland displays six strengths, against five for Hungary and three the Czech Republic. Concerning threats, Poland and Hungary share the same: position and low segments of the global value chain; while the Czech Republic presents as threats, some issues related to the political process.\n\nIn relation to weaknesses, the lack of modernization is one of the main and common weakness to Poland and the Czech Republic, while Hungary has an aging population and a small number of cities as main weaknesses. In terms of opportunities, Poland and the Czech Republic have the highest number. Among the most common opportunities are special economic zones, industrial restructuring, financial incentives, and technological upgrading. Thus, the interviews suggest that Poland has the best conditions to attract Portuguese investment, followed by Hungary.\n\nThe sample of firms is an example of the ability to project domestic skills on foreign markets. They all have in common the development of active internationalization strategies (with more or less success) aiming various objectives. Table 5 shows the attraction factors, investment motivation, entry mode, objectives and strategy pursued, competitive advantages, threats, and challenges. The most common competitive advantages are installation and anticipation over competitors. Experience, price, and product innovation are listed as not negligible competitive advantages. Companies E and F (financial services and retail) presented the highest number of competitive advantages in relation to the remaining companies in the sample. As for the strategies, the textiles company present a greater variety. The most common strategies for this sample of companies are a cautious attitude towards investment, learning about the market, training the workforce, and investing in the sales team. Firms D and E (textiles and financial services) focused on adapting production to local tastes and introducing new products and concepts that allow customer satisfaction.\n\nRegarding the objectives, Firms C and F (electrical equipment and retail) have a greater number of objectives, which are to regain their presence in the domestic market, profit, survival, cost reduction, as well as sales and growth. The objective of growth is common to all companies. Entry modes are equally represented by M&As in construction and financial services (A, B), joint ventures in electrical equipment and financial services (C, E) and Greenfield projects in textiles and retail (D, F).\n\nAs for the motivation for investment, Firm E (financial services) has more motivations such as globalization, business opportunity, risk diversification, profit, covering local needs, following the customer, and establishing partnerships. The most frequent reason is the business opportunity, risk diversification and stagnation of the domestic market.\n\nRegarding the attraction factors, companies A and E (construction and financial services) present the highest number, such as market size, political stability, geographical situation, skilled labor, good professional ethics, high profit margins, economic stability and openness of society and the government. The most common factors are the training of the workforce, the size and growth potential of the market and stability (economic, political, and social). In relation to threats, company C (electrical equipment) presented a greater number, such as the lack of experience and suspicious mentality of the partners and the risk of appropriation of knowledge. The most common threat is competition. In terms of challenges or difficulties, companies C, D and F (electrical equipment, textiles and retail) present a greater number of difficulties such as bureaucracy, human relations, language, low motivation of the selling team, transport/accessibility and the cost of rents. The most common difficulties are related to labor and financing.\n\nApplying the information from the interviews to the Matrix of the determinants of FDI (Table 1), the results are shown in Tables 6 to 11 and summed-up in Table 12.\n\nFirm A (Construction) benefited of its internal advantages (market position, production capacity, financial means, know-how and incentives) to access markets in Poland, Hungary, and the Czech Republic. It also took advantage of external production capacity and the stability and economic development of the foreign markets.\n\nFirm B (Financial services) took advantage of the installed production capacity in Hungary and the legal facilities granted there to access the market. To this end, the firm relied on the good position in the Portuguese market, production capacity, internal financial resources, and know-how.\n\nIn the case of firm C (electrical equipment), it was a matter of taking advantage of the production capacity, financial means and know-how acquired internally, to take advantage of the Czech market, as well as the production capacity installed in the host country and its favorable legislation.\n\nFor firm D (Textiles) located in Poland, the aim was to access the market to control the distribution channels, taking advantage of the country's environment (mentality, legislation, etc.). As it distributes a product that corresponds to a sector of national production specialization, it was able to gather all the expected internal values (production capacity, prominent position in the national market, financial means, know-how and incentives to internationalization.\n\nFirm E (financial services) has a prominent position in the national market, production capacity, financial means, and know-how. These competitive advantages allowed it to acquire a financial participation on one of biggest polish banks to access the vast market.\n\nFirm F operates in retail in Polish and Hungarian markets, has a stable position at the national market, production capacity, financing and know-how that allowed it to take advantage of external markets and their favorable investment environment.\n\nWe can now to integrate the analysis of the six companies in a summary table (Table 12).\n\nMarket-oriented strategy, taking advantage of the environment, is common to all firms. As for internal competencies, all firms possess financial means, know-how, and production capacity, which they designed abroad. Five of them (except for the firm operating in electrical equipment which lost its prominent position in the national market, due to the specific sectoral conditions) consider that the investment had nothing to do with the difficulties of the domestic market.\n\nFirms A and D received incentives to invest abroad, thus we marked the ME item (environment). The two companies operating in the financial sector have entered the foreign market via M&As and joint ventures, thus we marked production capacity (CP) abroad. Also, the construction company acquired a local company, and the electrical equipment company formed a joint venture, with the future ambition of building a factory in the Czech Republic, hence we marked production capacity (CP) abroad.\n\nThere are generally five motivations for firms to invest abroad: to gain resources, strategic assets, technology, markets, and diversification. The division is not always straightforward; small and medium enterprises (SMEs) can pursuit multiple objectives by investing abroad. Moreover, the motivations for FDI might change over time, as firms gain experience in the foreign markets. The interviews revealed that Half of the analyzed sectors followed the single internationalization strategy of market seeking investments (construction and retail); whilst firms operating in financial services and electrical equipment adopted a mix of strategies.\n\nIt was only possible to carry out seven surveys, due to the lack of response (Santos, 2022b). We calculated the medians of the Likert scale for each item/group. Starting with Motivation (group 2), among the main reasons for investing in those countries are marketing advantages, the importance of the foreign market in terms of turnover and profit. These findings are related to the nature of the sample of sectors and because most companies invest in Poland, the larger market of all three. Indeed, investments directed to Poland are mostly market seeking, with a view to supply the neighboring countries.\n\nMotivations such as the need to reduce the costs of supplying foreign markets, adapting products, counterattacking foreign rivals, reducing information costs, mitigating the uncertainty of the supply, eliminate transport costs, improve product quality, overcome non-tariff barriers or nationalism were not considered relevant by the respondents. This suggest that the investment was not motivated by difficulties in the market of origin or arising from exports, rather fit into a logic of supplying local markets.\n\nThe main attraction factors are the distribution channels, the size and the growth potential of host countries’ markets, the institutional framework, and the reduced political risk (Figure 4).\n\nThe wages in host countries were not considered relevant. Resmini (1999) comes to the same conclusion when stating that the low cost of labor is not an important objective for the FDI, given that it is oriented towards the long run when wage differentials tend to disappear.\n\nOther authors highlighted the fact that, once the location decision has been made, in a country with low labor costs, the search for labor at the lowest possible cost may or may not be important. Natural resources are considered non-relevant for the investment, since none of the companies adopted a resource seeking strategy.\n\nThe survey’s results indicate that the role of government regarding financial incentives has been redundant for the investment decision. This is in line with the idea that investments must be profitable per se and not rely on state aid. In addition, the changing nature of incentives over time may introduce an element of mistrust among investors. Language and the existence of complex legislation were mentioned as the main challenges/difficulties that may occur in the investment process. However, culture is not considered a major challenge, which can be explained, in part, by openness of society in those countries. Real estate and financing were not considered difficulties since the main forms of market penetration were M&As and joint ventures, and Portuguese banks appear to be following their clients to these countries.\n\nRetail (textiles and footwear)\n\nGiven the advanced stage of the product cycle, investment was aimed at commercial expansion, considering the need to exceed limits on quantities to be sold and to diversify activities. In this process, finding niche markets was considered of secondary importance. Thus, the market and distribution channels were important for entrepreneurs. The investment was not motivated by the need to follow competitors or to counterattack them in their own country. Moreover, the investment was not aimed at taking advantage of production factors (resources, labor) and was not determined by the need to follow customers or by restrictions imposed by consumers (nationalism, product image, uncertainty of supply or the need to adapt products) or to overcome exports’ issues (e.g., non-tariff barriers).\n\nFinancial sector (banking and credit institutions)\n\nThe reasons for the investment were mostly related to the business opportunity, due to the advanced stage of the product cycle. The need to increase competitiveness through economies of scale and service efficiency were considered secondary. Competition and resources played a small role in investment’s decisions. Managers considered that there was no need to improve product quality. The reduced political risk and the institutional framework were the main factors of attraction, while the quality of labor and good infrastructures were considered with medium importance.\n\n\nDiscussion\n\nOur results corroborate the findings of several authors. First, Market size is an important attraction factor for FDI (Azam & Lukman 2010; Curran et al., 2017). Second, there is no evidence that FDI was induced by tariffs in the host countries (Agodo, 1978; Moore, 1993). Third, human capital is less important than the market for investment decisions in developing countries (Deyo, 1989). Fourth, political events (e.g., nationalization of foreign-owned assets) can disrupt the economies by jeopardizing past investments (Castro, 2000). Bartels et al. (2009) showed that FDI in ten Sub-Saharan African countries was mostly motivated by political economy considerations, rather than by labor and production input variables. Also, Institutional factors (good government governance, economic freedom, public efficiency) play an important role in FDI decisions (Dixit, 2011). Tomelin et al. (2018) and Minh (2019) conclude that institutional quality (legal structure, strong property rights, freedom to trade, and civil liberties) is important for FDI attraction. Gubik et al. (2020) highlighted tax optimization, geographical distance, and global production chain as major motivations for FDI in the Visegrad countries (Czech Republic, Hungary, Poland, and Slovakia). Sixth, incentives were not a relevant determinant of FDI (UNCTAD, 1998).\n\nBy contrast, we could not find evidence to support the findings of several authors. First, contrary to Castro (2000), the incentives to foreign investors were not important instrument of investment policies. Second, we could not support the idea that the availability of raw materials and the cost and labor supply have a major impact on FDI decisions as highlighted by Dunning (1988). The same happens for the transport costs pointed out by Dunning (2015). Also, Tsai (1994) found that lower labor costs are important to attract FDI to economies. Third, we could not support the argument that culture is the core motivations for FDI, unlike Saleh et al. (2017). Fourth, Hirsch, et al. (2020) found that water resources and land abundance are major determinants of FDI contrary to our results.\n\nUnlike Kedia et al. (2012) we could not support the point of view that many firms start as niche providers for their rivals that are already established in the market, and as their role becomes more important in these firms’ value chain, they may aim at acquiring the ability to compete in product development abroad.\n\nAlso, unlike Leahy & Pavelin (2003) we did not find that domestic competitors have followed the leader abroad to facilitate collusive behavior in the markets in which they compete. In manufacturing and service industries, firms may follow their customers abroad to keep them (Kim & Rhee, 2009). However, that was not the case of managers that were interviewed. Finally, the quality of the workforce is pointed as another factor of attraction of FDI (Chansomphou & Ichihashi, 2011). Chakraborty et al. (2018) states that labour efficiency is more important to attracting foreign firms than Infrastructure, in India. We could not corroborate these findings.\n\nThe viability of the internationalization model requires the analysis of the main agents that compete for its implementation: consumers, competitors, foreign capital, and national and foreign authorities. Although each agent can intervene differently, depending on their objectives and constraints, some dominant behaviors can be typified: consumers and national authorities are receptive to FDI; competitors consider it a threat; and foreign authorities are faced with a dilemma of defending domestic firms/attracting FDI. In this framework, industrial policy plays an important role by contributing to the achievement of higher levels of competitiveness through the increase of manufacturing productivity (Santos & Khan, 2019). Results suggest that investments were market-oriented aiming at expansion and profit. This requires firms’ competitiveness, which involves preserving the economic sustainability of firms (Santos & Moreira, 2022). In this context, the vast Polish market was the one that most attracted Portuguese investors. The lower GDP per capita in Poland compared to the other two economies, suggests that the size of the potential market overcame consumer purchasing power considerations in the investment decisions. State aid, in turn, only played a supporting role in the investment, not constituting, in any case, the engine of that process. As the manager of company D said: “… no investments were made because of incentives. Many people invest because they will have support. This does not work. Investments must make sense per se. Investments should be viable or else, one can have all support in the world, and it still do not work. Off course, the support is very welcome, and sometimes can leverage these projects to succeed and consolidate faster.”\n\nThe hybrid feature of some strategies can align with the cautious attitude towards the investment (risk aversion), translated into cooperation agreements with financial institutions for funding, the market learning process, and the training of the personnel.\n\nThe anticipation of the installation over potential competitors, the experience in production and international markets, the price-quality ratio, the capacity of product adaptation and the design were considered important sources of competitive advantage that motivated the investment. The greatest difficulties during this process were language and the complexity of legislation.\n\nLimitations. As mentioned above, the small number of respondents makes it difficult to use modern statistical methods of analysis such as factorial analysis. We carried out a summary of the content of interviews without using qualitative software (e.g., Maxqda, NVivo, etc.). Since the sample represents only 25% of the population, it is not representative (in terms of size and diversity of activities) which can compromise the reliability of the conclusions. Thus, we can only expect to provide hints on the outward investment process. Also, the analysis of the matrix of determinants of FDI is characterized by an excessive simplification that can be overcome through a multiple analysis, combining, in each column or row, several internal advantages/external attraction factors. Due to the importance given to the investment process in unknown foreign environments, it seems more realistic to admit that firms only decide to invest abroad when there are strong competitive advantages to offset the disadvantages or when there is more than one internal advantage and/or external attraction factor.\n\n\nConclusion\n\nDespite the business opportunities, Portuguese investment directed towards Poland, Hungary, and the Czech Republic is negligible, due, in part, to the geographic and cultural distance. However, the economic and political stability, combined with market size and growth potential are undeniable attraction factors for Portuguese investors. SMEs, due to their flexible conditions that allow changes in the activity, and the strong trend towards outsourcing, to the detriment of the manufacturing industry, are the primary focus of international investment. This trend, although common to several sectors, has shown greater dynamism in the banking and financial sector.\n\nOn the other hand, the decline of large heavy industries, with strong investments in physical capital, led to the adoption of diversification strategies, with a focus on new products and technologies, namely related to information processing, telecommunications, and robotics.\n\nThis reformulation of the organization and business strategies, with a view to strengthening the competitive position, may involve the establishment of networks by Portuguese companies, with a view to exploiting the different production conditions in the CEECs.\n\nThe accession to the European Union (EU) has facilitated the capacity of these countries to attract FDI. However, the small size of domestic markets, in the case of Hungary and the Czech Republic may reduce their attractiveness for market-seeking investments in case the supply is more profitable via imports. This would lead to divestments resulting from internal productive reorganization.\n\nThe qualitative and quantitative evolution of outward Investment from Portugal will depend on investors' motivations and the conditions offered to them. These motivations are influenced by several factors, namely, the evolution of competition on an international scale, the growing competition between countries in attracting investments and the qualitative level of infrastructure to support economic activity in host countries.\n\nThe potential positive effects of FDI on host countries, namely on employment, resource transfer and on the external accounts could launch these economies on a growth path. From the home country perspective, activities abroad, in addition to providing obvious benefits at the microeconomic level, may generate direct gains in terms of the balance of payments, and indirect gains, in terms of growth and development. Thus, Portuguese investment in the CEECs can be a win-win game.\n\n\nData availability\n\nFigshare: Interviews. Challenges https://doi.org/10.6084/m9.figshare.20057027.v1 (Santos, 2022a).\n\nThis project contains the following underlying data:\n\n- Interviews.pdf (interview transcripts)\n\nFigshare. Dataset. https://doi.org/10.6084/m9.figshare.20433141 (Santos, 2022b).\n\n- Raw responses.csv (responses to survey)\n\nFigshare: Questionnaire. https://doi.org/10.6084/m9.figshare.20358987.v1 (Santos, 2022c).\n\n- Questionnaire.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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Publisher Full Text\n\nResmini L: The Determinants of Foreign Direct Investment into the CEECs: New Evidence from Sectoral Patterns. LICOS Discussion Paper 83, Center for Transition Economics, Katholieke Universiteit Leuven, Belgium and Bocconi University, Milan – Italy.1999.\n\nSaleem H, Shabbir MS: The short-run and long-run dynamics among FDI, trade openness and economic growth: using a bootstrap ARDL test for co-integration in selected South Asian countries. South Asian J. Bus. Stud. 2020; 9(2): 279–295. Publisher Full Text\n\nSantos E: Interviews.pdf. figshare. Dataset.2022a. Publisher Full Text\n\nSantos E: Raw Responses Questionnaire. figshare. Dataset.2022b. Publisher Full Text\n\nSantos E: Questionnaire. figshare. Dataset.2022c. Publisher Full Text\n\nSantos E, Moreira J: Social Sustainability of Water and Waste Management Companies in Portugal. Sustainability. 2022; 14(1): 221. Publisher Full Text\n\nSantos E, Khan S: FDI policies and catching up. J. Appl. Econ. Sci. 2019; 13(7 (61)): 1821–1853.\n\nSaleh AS, Nguyen TLA, Vinen D, et al.: A new theoretical framework to assess Multinational Corporations’ motivation for Foreign Direct Investment: A case study on Vietnamese service industries. Res. Int. Bus. Financ. 2017; 42: 630–644. Publisher Full Text\n\nShlafman NL, Bondarenko OV, Zakcharov OV: Modern theoretical foundations of formation of the market of innovative technologies in the context of the concept of neoindustrialization. Econ. Innov. 2020; 22(1 (74)): 165–178. Publisher Full Text\n\nSørensen OJ, Ngoc NB:Internationalization of Vietnamese garment manufacturers from an innovation perspective: toward a U-shaped internationalization path. Upgrading the Global Garment Industry. Edward Elgar Publishing;2021.\n\nStreiner DL: Starting at the beginning: an introduction to coefficient alpha and internal consistency. J. Pers. Assess. 2003; 80(1): 99–103. PubMed Abstract | Publisher Full Text\n\nTomelin J, Amal M, Hein N, et al.: Foreign direct investment in the G-20: to what extent do institutions matter? RAUSP Manag. J. 2018; 53: 404–421. Publisher Full Text\n\nTsai PL: Determinants of foreign direct investment and its impact on economic growth. J. Econ. Dev. 1994; 19(1): 137–163.\n\nValadares L, Esperança, Rafael JF, et al.: Estratégias de internacionalização das empresas portuguesas. ICEP;1995.\n\nVázquez-Barquero A: Endogenous development: Networking, innovation, institutions and cities. Routledge;2002.\n\nUNCTAD: World Investment Report 1998. New York and Geneva:Trends and determinants;1998."
}
|
[
{
"id": "172426",
"date": "01 Aug 2023",
"name": "Canan Yildirim",
"expertise": [
"Reviewer Expertise Banking",
"Cross-border M&As",
"Firm internationalization."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper aims at finding out the determinants of outward investment of Portuguese Small and Medium-sized Enterprises (SMEs) and employs multiple case studies.\nWhile the subject is interesting and has important managerial and policy implications, the study suffers from several aspects.\nMost importantly, there is no theoretical framework to guide the development of hypotheses. There is no discussion of the specifics of the SMEs and the Portuguese context either. The study refers to some previous papers to develop a list of potential factors without any deeper discussions about the theory(ies) supporting these arguments. What is the research question? Why is it relevant for the SMEs in Portugal?\nThe methodological approach is not carefully justified and the explanation of the actual application of the techniques is confusing at times. There are expressions such as \"our database cannot meet this criterian\", \"it was only possible to carry out six interviews, due to lack of response\".\n\nThe case study covers firms from diverse set of industries. Finance industry, for instance, a specific case (information intensive, regulation sensitive service industry). One would expect different drivers and mode of entry in this sector compared to others.\nThere is a lack of background or additional information about these firms (size, age, overall internationalization level and experience etc.). Hence the findings seem to be very generic. I am not sure if the study's findings can be compared and contrasted with the existing literature.\n\nThe study might benefit from professional copy editing.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "174811",
"date": "01 Aug 2023",
"name": "Viorela Ligia Vaidean",
"expertise": [
"Reviewer Expertise Corporate Finance",
"Health Economics",
"Public Policies"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe research paper titled „Outward investment of Portuguese small and medium enterprises in the Central and Eastern European countries: motivation and challenges” (F1000Research 2022, 11: 1339 Last updated 29 MAY 2023) is an extremely interesting paper which investigates the determinant factors of Portuguese direct investments (PDI) in some Central and Eastern European countries.\n\nWe have closely read the entire paper and have a few critical comments that we suggest to the authors:\n1. Introduction (with Literature review). The following studies need to be read and cited, as they are rather recent and related to this topic:\nhttps://doi.org/10.1016/j.joitmc.2023.100021 https://doi.org/10.1016/j.ecosys.2023.101095 https://doi.org/10.1016/j.jmacro.2012.01.010\n2. Methods. Results. In our opinion, although the flow of ideas and arguments are extremely well-organised, the paper’s length might be a little overwhelming for the reader. We recommend a condensed version of these subchapters, by shortening them with one or two pages. Another variant would be to move some tables (E.g. Tables 6 to 11, keeping Table 12) into an Appendix. The main questionable aspect over here is the lack of econometric modelling of data. We were somehow expecting a quantitative approach from the title of your manuscript as many such papers include multivariate data analysis techniques applied to cross-sectional/panel data. Could you repeat the survey in order to structure a mini-panel approach, in the future?\n3. Surveys’ Results. Discussion. We particularly appreciate the interpretations provided by the authors.\n4. In the Conclusion the authors need to emphasize the international dimension of their findings, the originality and value of their research a little bit more. We think they should develop the policy implications of their paper and the authors’ future research directions.\nSome other comments:\n1. Emphasize how the authors deal with the limits of this paper more.\n2. The Figshare dataset and questionnaire is rather simple. Could you extend the research towards including more respondents? Even you admit that your sample consists of “only 25% of the population, it is not representative (in terms of size and diversity of activities) which can compromise the reliability of the conclusions”\nThese suggestions will improve the quality of this manuscript and they will make the paper more suitable for being published, due to its interesting results and originality.\nThis review has been performed by, Associate Professor Viorela-Ligia Văidean, PhD Master degree student Daria Stăvilă Faculty of Economics and Business Administration “Babeș-Bolyai” University Cluj-Napoca, Romania\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1339
|
https://f1000research.com/articles/13-559/v1
|
31 May 24
|
{
"type": "Research Article",
"title": "Distress and Rewards of Nurses with Experience in COVID-19 Wards: A Qualitative Study",
"authors": [
"Asako Matsuura",
"Shin-ichiro Sasahara",
"Hirokazu Tachikawa",
"Keiko Wataya",
"Masana Ujihara",
"Yoshitaka Kawashima",
"Sho Takahashi",
"Kei Muroi",
"Shotaro Doki",
"Daisuke Hori",
"Tsukasa Takahashi",
"Ichiyo Matsuzaki",
"Asako Matsuura",
"Keiko Wataya",
"Masana Ujihara",
"Yoshitaka Kawashima",
"Sho Takahashi",
"Kei Muroi",
"Shotaro Doki",
"Daisuke Hori",
"Tsukasa Takahashi",
"Ichiyo Matsuzaki"
],
"abstract": "Background Amidst the global escalation of COVID-19, nurses have confronted the dual challenge of exposure to infection and the duty to provide patient care, leading to some moral dilemmas. This study aims to explore the psychological burden and dilemmas faced by nurses working in COVID-19 wards, elucidating their professional distress and rewards, and examining their interrelation.\n\nMethods This qualitative descriptive study employed semi-structured interviews to gather data on the experiences of nurses who worked in COVID-19 wards. The study spanned from January 2022 to March 2023. Qualitative content analysis was applied to analyze interview transcripts.\n\nResults The study involved 12 participants (8 women and 4 men). Their experience ranged from 4-21 years. The group included 6 staff nurses, 3 head or deputy head nurses, and 3 head nurses. No significant changes were observed in weekly working hours pre- and post-COVID-19. Analysis of the interviews revealed that nurses working in COVID-19 wards experienced conflicts related to the risk of infection at work, role execution, organizational challenges, and interpersonal relationships. Concurrently, they also reported finding rewards in their work and in building connections with others.\n\nConclusions This study revealed that nurses experienced distress related to COVID-19-related job challenges, leading to a sense of mistrust towards their organizations. However, working in COVID-19 wards also brought a renewed sense of job fulfillment, particularly through interactions with individuals they had not previously encountered. These experiences are illustrative of the dilemmas faced by healthcare professionals in balancing the distress and rewards inherent in their roles.",
"keywords": [
"COVID-19",
"Nurse",
"Distress",
"Rewards",
"Dilemma"
],
"content": "Introduction\n\nThe Coronavirus Disease 2019 (COVID-19) pandemic has posed severe challenges in healthcare settings worldwide. Nurses in COVID-19 wards have confronted arduous conditions, balancing the high risk of infection with the responsibility of patient care. Their role extended beyond professional duties to encompass ethical responsibilities, facing a relentless task of managing stringent infection control while simultaneously providing emotional care to patients (Alloubani et al., 2021). This dual role has placed them in a position of constant striving for professional excellence amid concerns for personal safety and the risk of transmitting the virus to their families, often leading to social isolation both within and outside the hospital.\n\nThe high physical and psychological demands of working in COVID-19 wards are well-documented (Oda et al., 2020; Lai et al., 2020). This burden included moral dilemmas, described as conflicts arising from moral judgments that cannot be acted upon due to constraints, or the uncertainty of what constitutes the right moral decision (Jameton, 1993). These dilemmas are common in healthcare, where professionals regularly face situations that require choosing between conflicting moral imperatives. Such scenarios, where fulfilling two strong obligations simultaneously is impossible, are notably prevalent (Fourie, 2015).\n\nDuring the COVID-19 outbreak, nurses were forced into making difficult decisions regarding resource allocation and setting medical priorities (Rushton et al., 2022; Greenberg et al., 2020). The challenges of having to make ethically challenging decisions regarding resource distribution, treatment provision, and patient triage had a profound impact on nurse’s mental health (Lake et al., 2021). Furthermore, the clash between personal ethical beliefs and institutional policies added to the nurses’ stress and mental burden, making the balance between professional ethics and organizational directives a complex issue (Torkaman et al.,2020). Discrepancies between individual morals and organizational policies have been shown to worsen mental health issues among healthcare workers (Walton et al., 2020).\n\nThe concept of moral injury, which has gained particular attention in the COVID-19 context, refers to the psychological harm that occurs when actions, or lack thereof, violate one’s moral or ethical code (Greenberg et al., 2020). Such moral injuries have been linked to increased burnout and attrition (Dalmolin et al., 2014). This moral injury, stemming from moral distress (Čartolovni et al., 2021), leads to psychological discomfort and negative emotions, which can adversely affect patient care, decrease job satisfaction, and contribute to burnout and resignation (Deschenes et al., 2020). Therefore, it is crucial to focus on and elucidate the professional distress of nurses working in COVID-19 wards to prevent the deterioration of healthcare workers’ mental health.\n\nBurnout is associated with the intention to leave and the ability to perform job duties (Dyrbye et al., 2019) and has been identified as a mediator between job satisfaction and the intention to leave (Ran et al., 2020). The high turnover rate of nurses presents a significant challenge, making it vital to prevent burnout and resignation to maintain healthcare quality. There is a paucity of studies detailing the specific struggles of nurses who worked in COVID-19 wards. Identifying these struggles can help to prevent mitigate the psychological burden and stress on nurses. Furthermore, research on nurse job satisfaction has highlighted the importance of professional relationships among nurses and patient care (Utriainen and Kyngäs, 2009). Various factors have been reported to influence job satisfaction, including work shifts, leadership, job performance, organizational commitment, effort, and reward styles, and their outcomes, including workplace environment, empowerment, organizational commitment, professional commitment, work stress, and patient satisfaction (Lu et al., 2019). However, research specifically detailing the job satisfaction and challenges of nurses working in COVID-19 wards is lacking. Therefore, the aim of the current study was to elucidate both the struggles (occupational distress) and satisfactions (sense of achievement) of nurses who worked in COVID-19 wards, as well as their characteristics, and explore how these aspects are interrelated.\n\n\nMethods\n\nA qualitative descriptive study design using semi-structured interviews was adopted for this study. This study was guided by the Consolidated Criteria for Reporting Qualitative Research (COREQ) (Tong et al., 2007).\n\nThe study participants were nursing professionals who have experience of working in a COVID-19 ward. The participants were employed at a large university hospital in the Kanto region of Japan. The hospital restructured general wards to accommodate infectious disease treatment in response to the COVID-19 outbreak. This ward, previously designed for treating infectious diseases, began operating as a COVID-19 ward after the hospital’s decision to admit COVID-19 patients. Pre-pandemic, nurses working in the general wards were requested to serve voluntarily for about two months in this infectious disease ward. Subsequently, after its conversion to a COVID-19 ward, the hospital implemented a three-month rotation system for nursing staff, based on a roster of volunteers who had served in the infectious disease ward before the pandemic. Participant recruitment was conducted by explaining the purpose and methods of the study to facility administrators, both verbally and in writing, and obtaining their consent. Following this, invitations to participate were extended to potential participants using posters and other methods.\n\nThe study was conducted from January 2022 to March 2023, with interviews carried out from March 2022 to January 2023. Participants provided demographic information on an interview sheet including gender, years of experience, position, educational background, and weekly working hours before and after the onset of the COVID-19 pandemic. The interviews, conducted semi-structurally, focused on encouraging the nurses to reflect on their experiences working in COVID-19 wards. Interviews were conducted by a trained psychiatrist and occupational physician who are co-researchers in this study.\n\nThe content of the interview guide was as follows:\n\na) Thoughts upon learning about the operation of COVID-19 wards.\n\nb) The extent of consultation with others.\n\nc) Reflections on actions that could have been beneficial at the time.\n\nd) Messages to their past selves.\n\nThe transcription and analysis of the interview data were initially undertaken by the first author, and then conducted in collaboration with two other research team members who are nursing professionals. This was followed by a verification process involving the principal investigator and five additional members holding doctoral degrees. The interview data were analyzed utilizing methods of qualitative content analysis, specifically summary content analysis and exploratory content analysis (Flick, 2011). Summarizing content analysis involved rephrasing the data, eliminating insignificant or repetitive statements, and bundling similar expressions. Explanatory content analysis clarified ambiguous or contradictory statements by considering the context of their articulation. Transcripts were carefully summarized and analyzed, ensuring contextual integrity, and then abstracted to higher levels of generalization. Similar meanings were grouped into categories and subcategories. The results were repeatedly reviewed by co-researchers to ensure reliability and validity until consensus was reached.\n\nInterviews were conducted in private rooms to ensure privacy, and data were analyzed with personal information excluded. This study was approved by the University of Tsukuba Medical Ethics Committee (Approval No.: 1690; Approval date: December 24, 2021). The study’s purpose and methods were explained both verbally and in writing to the facility administrators, and their consent was obtained before inviting participants. Participants were informed about the voluntary nature of participation, the possibility of withdrawing consent without disadvantage, anonymity, data security, and the publication of results. Consent was documented in writing before conducting the interviews.\n\n\nResults\n\nTwelve nurses, 8 women and 4 men, participated in the study (Table 1). The average interview duration was 20.5 minutes. Age distribution included one in their 20s, four in their 30s, five in their 40s, one in their 50s, and one in their 60s. Years of experience ranged from four to over 20 years. The group comprised six staff nurses, three deputy head nurses, and three head nurses. The average weekly working hours were 44.2 before COVID-19 and 43.3 after.\n\nAnalysis of interview content yielded 192 codes, 6 categories and 18 subcategories. Table 2 shows the four categories and 14 subcategories that were identified to describe the distress experienced by nurses working in COVID-19 wards. The four categories were: Risk of infection-related conflicts, Challenges in fulfilling job roles, Organizational conflicts, and Interpersonal conflicts.\n\nWith regards to the first category, Risk of infection-related conflicts, participants expressed fears related to COVID-19, with statements such as, “I was scared because I didn’t know where I might get infected,” “Before the vaccine rollout, there was a lot of fear,” and “During outbreaks, I didn’t want to work in the COVID-19 ward.” These statements reflect their fear of contracting the virus. Amidst these fears, one participant mentioned concealing their assignment to the COVID-19 ward due to concern about others’ perceptions, and was shocked upon overhearing conversations filled with prejudice against COVID-19. This led to stress about not being able to disclose their work in the COVID-19 ward openly.\n\nAdditionally, working in the COVID-19 ward triggered fears of becoming infected or a carrier, leading to self-critical thoughts like, “Even as a nurse, I worry about getting infected.” One mentioned how hearing of a nurse contracting the virus at a social gathering, despite hospital advisories against such gatherings, sparked negative feelings. There were also concerns for colleagues who became infected or were close contacts, reflecting a deep empathy for fellow staff members.\n\nWorking in a COVID-19 ward also brought anxiety about potentially infecting family members, compounded by societal prejudices. This resulted in worries about family and social relationships, with instances of biased neighbors or relatives making hurtful comments. The burden this placed on family members was another source of concern for the participant.\n\nRegarding the second category, Challenges in fulfilling job roles, nurses expressed frustration related to their roles, with sentiments like, “I don’t want to stress the younger staff,” and “We need to understand it’s part of our ward duties.” Despite these feelings, they faced situations where temporary transfers became permanent, and expressed reluctance, saying, “I’m not doing this because I want to,” “If I could avoid it, that would be best,” and “Being single and living alone, it seems inevitable I’ll be sent.” These statements revealed a sense of obligation and questioning of why they must shoulder these responsibilities. There was also a sense of resignation, with thoughts like, “I can do this [my duties] because it won’t last forever,” and “Time will solve this,” indicating hope that time might ease the struggle with unfamiliar tasks. However, they still experienced stress due to these new duties. Amidst this vague anxiety, nurses wondered, “Where will I be in a few weeks?” and felt uneasy about being transferred to unknown wards without knowing what lies ahead, thinking, “Will I keep moving between wards forever?” and “There was never a moment of reassurance,” reflecting their anxiety about the uncertain future.\n\nDespite these various stresses and anxieties, nurses noted differences in cooperation between wards and faced criticism from other departments, with remarks like, “You must be having an easy time now that the number of infections has decreased.” Those in managerial positions felt they were doing their best but often found themselves uncertain about what to do, feeling blamed and without the capacity to respond, leading to a sense of inadequacy in fulfilling their roles as nursing managers.\n\nThe category of Organizational conflicts highlighted the frustrations nurses experienced due to operational inefficiencies in the COVID-19 ward, such as “feeling helpless because preparations were inadequate” and “a negative atmosphere due to many uncertainties.” These issues contributed to a sense of difficulty in performing their duties. Nurses expressed a desire to share these challenges with the organization, feeling that “the extent of the difficulties wasn’t fully understood by everyone” and “there was a lack of effective communication with the higher-ups.” This led to a growing sentiment of wanting more support and understanding from the upper management. Furthermore, the experience led to a negative perception of the organization, with nurses realizing that “it’s an organization that oppresses and utilizes a top-down approach.” There was a collective sense of anger towards the upper management, indicating a deepening mistrust and dissatisfaction among the staff.\n\nRegarding the final category, the necessity of building new relationships arose for those transferred to the COVID-19 ward. There was a sense of a weakened team spirit, as described by phrases like, “It felt like there was little camaraderie.” Nurses and doctors reported feeling unable to seek advice, leading to situations where “supervisors felt isolated.” This highlighted a scenario where establishing relationships with colleagues and the organization proved challenging. Amidst these struggles, a manager mentioned, “While it was good to hear everyone’s stories, it was also difficult.” This statement reflects the complexity of fostering relationships within the team. The hindrance in these efforts was attributed to poor relationships, as expressed in the comment, “The bad relationships became a constraint.”\n\nTwo categories, Job rewards and Forming new human connections, were identified as more positive experiences gained from working in the COVID-19 wards (Table 3).\n\nIn the first category, Job rewards, the nurses described feeling a sense of mission and responsibility, gaining rewards from treating patients, and finding social significance in accepting them. Some viewed their experience positively as an opportunity for personal growth, gaining new insights and confidence through their work.\n\nThe second positive aspect was the category of Formation of new human connections in which participants describe how they found value in forming connections with staff from other departments and experienced a sense of unity within the ward, leading to cohesive teamwork.\n\n\nDiscussion\n\nThis study revealed that nurses with experience of working in COVID-19 wards faced a blend of distress and fulfillment in their duties. Consistent with prior research (Awano et al., 2020), these nurses grappled with fears directly related to COVID-19, such as the fear of infection. This aligns with the broader body of research focusing on the stress and psychological impact faced by healthcare workers during the COVID-19 pandemic (Arias et al., 2023). Our study underscores how nurses working in infectious disease wards confronted unique dilemmas and distress. Additionally, the pandemic’s impact extended beyond the individual nurse to their families, placing nurses in a difficult position of balancing personal and family safety with their professional obligations (Catania et al., 2021). In such scenarios, a safe and secure organizational environment is crucial for enabling nurses to fulfill their duties. However, previous reports have indicated a sense of distrust towards organizations and conflicts in interpersonal relationships among nurses during the COVID-19 pandemic (Soto et al., 2020). Our study also highlighted these aspects, and it is likely that accumulation of such conflicts over time will lead to distress and potentially to burnout. Lack of communication and support within organizations might have exacerbated nurses’ stress, forming the root cause of their distress and dilemmas. Organizational support is crucial in maintaining nurses’ mental health (Labrague, 2021), with managerial presence, information provision, and attentiveness to subordinates’ opinions reducing nurses’ anxiety and facilitating mutual understanding under challenging work conditions (Matilda S. et al., 2022). This suggests the importance of creating a safe and secure environment for nurses. Future strategies should focus on how to support nurses when they face such conflicts.\n\nImportantly, this study also revealed certain positive aspects, such as job rewards, a sense of mission, and the forging of new relationships and connections, despite the challenges faced in COVID-19 wards. This could be related to the joy and rewards healthcare workers derive from helping others and reconnection with a sense of vocation. Reports suggest that contributions to patient care and a sense of accomplishment positively impacted healthcare workers’ mental health during the COVID-19 pandemic (Yamada et al., 2022; Trumello et al., 2020). These findings imply that working in COVID-19 wards and responding to patients’ needs can cultivate a sense of professionalism and fulfillment. Onodera (2022) noted that in wards temporarily formed with members from different departments, the ability to collaborate is crucial for enhancing caregiving capabilities. Collaboration involves building relationships with team members, identifying and solving workplace problems, understanding the abilities of members from different specialties, and appropriately delegating tasks. The findings of our study suggests that nurses from various wards working together shared diverse expertise, leading to the formation of staff collaboration and organizational unity. Working while forming new human connections may have also enhanced nurses’ caregiving capabilities. The novel environment of the COVID-19 wards potentially enhanced the professional capabilities of each individual, as they were compelled to utilize their skills to the fullest. A key factor in drawing out these abilities may have been the necessity to form relationships with colleagues they had never worked with before.\n\nNurses, as healthcare professionals, faced the need to respond to the unfamiliar challenge of COVID-19, carrying with them feelings of anxiety and distress. In this context, they not only experienced personal growth triggered by COVID-19 but also expanded their professional connections. This situation revealed a dilemma between the struggles and the rewarding nature of their work, shedding light on the evolving aspects of their professional dilemmas.\n\nThis study is limited by its focus on nursing professionals from a single facility, rendering the results non-generalizable. To construct a comprehensive theory, further data collection and analysis involving other institutions and a larger sample size are necessary. Additionally, capturing temporal changes was challenging, necessitating ongoing monitoring of the situation.\n\nBased on the insights gained from this research, it’s essential to conduct quantitative studies to explore the content of nurses’ conflicts, especially during times of societal emergencies. This will contribute to the development of effective strategies and interventions to support nurses during such times. Moreover, a more detailed examination of the types of psychological support that can be offered to nurses is required to effectively address their specific needs and challenges. Nurses, as professionals, faced the necessity to respond to COVID-19, an unknown infectious disease, which brought with it severe feelings of anxiety and distress. Amidst these challenges, the nurses in our study also experienced personal growth and an expansion of connections with others, triggered by COVID-19. This has revealed how they, as professionals, are grappling with the dilemma of experiencing both distress and fulfillment, and their perspectives on how to perceive and manage this dilemma moving forward. Further investigations into both the negative and positive aspects brought by the pandemic can help us to understand how to support nurses in their vital caregiving work.\n\n\nConclusion\n\nThis study sought to elucidate the distress and dilemmas experienced by Japanese nurses working in COVID-19 wards. It revealed that nurses faced significant challenges, including conflicts related to the risk of infection, challenges in fulfilling job roles, organizational conflicts, and difficulties within interpersonal relationships. Despite these challenges, nurses also found positive aspects such as job rewards and opportunities to form new human connections throughout their experiences working on COVID-19 wards. These findings indicate that while nurses bore the distress and burden related to COVID-19, leading to mistrust towards their organizations, they simultaneously discovered new aspects of job satisfaction and the value of engaging with people they had not previously encountered. Our findings illustrate the dilemmas faced by professionals in handling the distress inherent in their roles and balancing that with their sense of professional duty and vocational rewards. The insights gained from our investigation into the experiences of nurses working on COVID-19 wards at the height of the deadly pandemic can help healthcare providers to devise effective strategies and interventions to support nurses in their important work.\n\n\nEthics and consent\n\nThis study was approved by the University of Tsukuba Medical Ethics Committee (Approval No.: 1690) Approval date: December 24, 2021. The study’s purpose and methods were explained both verbally and in writing to the facility administrators, and their consent was obtained before inviting participants. Participants were informed about the voluntary nature of participation, the possibility of withdrawing consent without disadvantage, anonymity, data security, and the publication of results. Consent was documented in writing before conducting the interviews.\n\n\nAuthors’ contributions\n\nAsako Matsuura contributed to the research design, data collection, analysis and interpretation, and drafting of the manuscript. Shin-ichiro Sasahara was involved in conceptualizing the study, research design, recruiting participants, and contributed to data collection, analysis, and interpretation. Hirokazu Tachikawa contributed to the conception of the study, interpretation of the data. Yoshitaka Kawashima and Sho Takahashi contributed to interpretation. Shotaro Doki, Daisuke Hori, and Tsukasa Takahashi assisted in recruiting participants and contributed to data analysis and interpretation. Masana Ujihara and Keiko Wataya contributed to the analysis and interpretation of research data and critically revised the content of the manuscript. Kei Muroi contributed to the critical revision and English proofreading of the manuscript. All authors discussed the results critically and approved the final version of the manuscript.",
"appendix": "Data availability\n\nParts of the data used in this study are available for public access at Matsuura (2024). However, from the perspective of personal information protection, specific details of certain datasets remain confidential. This includes data deemed inappropriate for public release because it contains information that could identify individuals. For detailed inquiries about the use of data in this research, or if you wish to request limited access to the data, please contact the principal investigator directly.\n\nZenodo: Distress and rewards of nurses with experience in COVID-19 wards. https://zenodo.org/doi/10.5281/zenodo.10616718 (Matsuura, 2024).\n\nThis project contains the following data:\n\n- Interview Data.docx\n\n- interview guide.docx\n\n- Table 1.xlsx\n\n- Table 2.xlsx\n\n- Table 2_code.xlsx\n\n- Table 3. xlsx\n\n- Table 3_code.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank Thomas D. Mayers, Medical English Communications Center, University of Tsukuba Faculty of Medicine, for grammatical revision.\n\n\nReferences\n\nArias-Ulloa CA, Gómez-Salgado J, Escobar-Segovia K, et al.: Psychological distress in healthcare workers during COVID-19 pandemic: A systematic review. J. Saf. Res. 2023; 87: 297–312. PubMed Abstract | Publisher Full Text\n\nAlloubani A, Khater W, Akhu-Zaheya L, et al.: Nurses’ Ethics in the Care of Patients During the COVID-19 Pandemic. Front. Med. 2021; 8: 589550. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAwano N, Oyama N, Akiyama K, et al.:Anxiety, depression, and resilience of healthcare workers in Japan during the coronavirus disease 2019 outbreak.Intern. Med.2020;59(21):2693–2699.PubMed Abstract | Publisher Full Text | Free Full Text\n\nČartolovni A, Stolt M, Scott PA, et al.: Moral injury in healthcare professionals: A scoping review and discussion. Nurs. Ethics. 2021; 28(5): 590–602. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCatania G, Zanini M, Hayter M, et al.: Lessons from Italian front-line nurses’ experiences during the COVID-19 pandemic: A qualitative descriptive study. J. Nurs. Manag. 2021; 29(3): 404–411. PubMed Abstract | Publisher Full Text\n\nDalmolin GL, Lunardi VL, Lunardi GL, et al.: Moral distress and burnout syndrome: are there relationships between these phenomena in nursing workers?. Rev. Lat. Am. Enfermagem. 2014; 22(1): 35–42. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeschenes S, Gagnon M, Park T, et al.: Moral distress: A concept clarification. Nurs. Ethics. 2020; 27(4): 1127–1146. PubMed Abstract | Publisher Full Text\n\nDyrbye LN, Shanafelt TD, Johnson PO, et al.: A cross-sectional study exploring the relationship between burnout, absenteeism, and job performance among American nurses. BMC Nurs. 2019; 18: 57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFlick U: Introduction to Qualitative Research: Methods for Human Science. Tokyo: Shunjusha; Revised Edition2011; pp. 393–400. (2007)/Hiroshi Oda.\n\nFourie C: Moral distress and moral conflict in clinical ethics. Bioethics. 2015; 29(2): 91–97. Publisher Full Text\n\nGreenberg N, Docherty M, Gnanapragasam S, et al.: Managing mental health challenges faced by healthcare workers during COVID-19 pandemic. Br. Med. J. 2020; 368: m1211. Publisher Full Text\n\nJameton A: Dilemmas of moral distress: moral responsibility and nursing practice. AWHONNS Clin. Issues Perinat. Womens Health Nurs. 1993; 4(4): 542–551. PubMed Abstract\n\nLabrague LJ: Psychological resilience, coping behaviours and social support among health care workers during the COVID-19 pandemic: A systematic review of quantitative studies. J. Nurs. Manag. 2021; 29(7): 1893–1905. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLai J, Ma S, Wang Y, et al.: Factors Associated With Mental Health Outcomes Among Health Care Workers Exposed to Coronavirus Disease 2019. JAMA Netw. Open. 2020; 3(3): e203976. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLake ET, Narva AM, Holland S, et al.: Hospital nurses’ moral distress and mental health during COVID-19. J. Adv. Nurs. 2021; 78(3): 799–809. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLu H, Zhao Y, While A: Job satisfaction among hospital nurses: A literature review. Int. J. Nurs. Stud. 2019; 94: 21–31. Publisher Full Text\n\nMatsuura A: Distress and rewards of nurses with experience in COVID-19 wards. [Dataset]. Zenodo. 2024. Publisher Full Text\n\nOda J, Tanabe S, Nishimura T, et al.: JAAM nationwide survey on the response to the first wave of COVID-19 in Japan. Part I: How to set up a treatment system in each hospital.Acute Med. Surg.2020; 7(1): 1–9.Publisher Full Text\n\nOnodera M: Learning process of nurses through work experiences related to COVID-19[in Japanese]. Jpn. J. Nurs. Sci. 2022; 45(4): 705–724. Publisher Full Text\n\nRan L, Chen X, Peng S, et al.: Job burnoutand turnover intention among Chinese primary healthcare staff: the mediating effect of satisfaction. BMJ Open. 2020; 10(10): e036702. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRushton CH, Thomas TA, Antonsdottir IM, et al.: Moral Injury and Moral Resilience in Health Care Workers during COVID-19 Pandemic. J. Palliat. Med. 2022; 25(5): 712–719. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSoto-Rubio A, Giménez-Espert MDC, Prado-Gascó V: Effect of Emotional Intelligence and Psychosocial Risks on Burnout, Job Satisfaction, and Nurses’ Health during the COVID-19 Pandemic. Int. J. Environ. Res. Public Health. 2020; 17(21): 7998. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTong A, Sainsbury P, Craig J: Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups.Int. J. Qual. Health Care.2007; 19(6): 349–357.PubMed Abstract | Publisher Full Text\n\nTorkaman M, Heydari N, Torabizadeh C:Nurses' perspectives regarding the relationship between professional ethics and organizational commitment in healthcare organizations.J. Med. Ethics Hist. Med.2020;13: 17.PubMed Abstract | Publisher Full Text | Free Full Text\n\nTrumello C, Bramanti SM, Ballarotto G, et al.: Psychological Adjustment of Healthcare AWorkers in Italy during the COVID-19 Pandemic: Differences in Stress, Anxiety, Depression, Burnout, Secondary Trauma, and Compassion Satisfaction between Frontline and Non-Frontline Professionals. Int. J. Environ. Res. Public Health. 2020; 17(22): 8358. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUtriainen K, Kyngäs H: Hospital nurses’ job satisfaction: a literature review. J. Nurs. Manag. 2009; 17(8): 1002–1010. Publisher Full Text\n\nWalton M, Murray E, Christian MD: Mental health care for medical staff and affiliated healthcare workers during the COVID-19 pandemic. Eur. Heart J. Acute Cardiovasc. Care. 2020; 9(3): 241–247. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYamada C, Kishimoto N, Sakai Y, et al.:Transitional changes in job stress and psychological adjustment of hospital workers during the COVID-19 pandemic in Japan.Tokai J. Exp. Clin. Med.2022; 47(3):115–124. PubMed Abstract"
}
|
[
{
"id": "287201",
"date": "08 Jul 2024",
"name": "Gregorius Abanit Asa",
"expertise": [
"Reviewer Expertise My area of research is public health."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a good article. Below is the review for the improvement of the paper. Thank you.\n1.Introduction This dual role has placed them in a position of constant striving for professional excellence amid concerns for personal safety and the risk of transmitting the virus to their families, often leading to social isolation both within and outside the hospital… I think this needs citation.\n2. Aim and title In abstract: This study aims to explore the psychological burden and dilemmas faced by nurses working in COVID-19 wards, elucidating their professional distress and rewards, and examining their interrelation. In the end of introduction: the aim of the current study was to elucidate both the struggles (occupational distress) and satisfactions (sense of achievement) of nurses who worked in COVID-19 wards, as well as their characteristics, and explore how these aspects are interrelated. The title, distress and Rewards of Nurses with Experience in COVID-19 Wards The first aim in abstract mentioned about psychological burden and dilemma. Meanwhile, in the end to introduction directly mentioned about occupational distress and no dilemma. The title goes straight to distress and Rewards which seems no dilemma aspect. I would suggest the aim should be the same, so it is clearer for readers.\n3. Knowledge gap I would suggest the authors cite systematic reviews or other reviews on to justify that the study of the topic is lacking instead of citing individual paper.\n4. Data collection The study was conducted from January 2022 to March 2023, with interviews carried out from March 2022 to January 2023. This sentence should be clearer. The interview started from March but the study was conducted from January. The authors need to explain why?\n5. Data saturation. Authors need to explain how data saturation was reached\n6. Did the author have pre determined questioned? If so, the authors need to explain to process of developing questions\n7. The authors need to explain the process of developing and formulating the question\n8. The authors need to explain sampling technique\n9. Suggested reference that could be added in the introduction or discussion. [Ref-1]\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "358289",
"date": "04 Feb 2025",
"name": "Janice Nesbitt",
"expertise": [
"Reviewer Expertise Compassion Fatigue",
"COVID- 19 pandemic"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this manuscript.\nIn general:\nThere is a mix of verb tenses. Would suggest reviewing to ensure they are all consistent. The word “elucidate” is used several times in the article. Simpler language would be helpful. Tables were helpful, but unfortunately are unable to add value to the reading There is much repetition of the same words in different sections. I feel like I get a sense of what the study is and what the findings were, but the organization of presentation is not very clear. I am not certain of what the themes and subthemes truly are. I am hesitant to hit approved due to the above, but with some reorganization of the writings, I think there can be value here.\n\nIn general-the tables are helpful.\nUnder Abstract\nUnder Results it has the experience of the team from 4 to 21 years. “Four” should likely be spelt out. Under background-the word elucidating will cause people to need to look it up. Simple language would be helpful. Under the results section-there is reference to three head or deputy head nurses and then three head nurses. This appears confusing. Perhaps there are six head nurses? It is not clear. The table says 3 head nurses and 3 deputy head nurses. Would suggest modifying.\n\nUnder Introduction:\nParagraph two - could delete the definition of moral dilemmas and reference to Jameton. The whole second paragraph does not clearly add value to the article. Under the distressed experience by nurses section, there are many extreme words that are not really needed for reporting a research study. For example, paragraph two. The intro line. “ with regards to the first category” is really not needed. Would suggest using more direct and concise language if possible. In paragraph two of the same section, you start the paragraph with “ additionally”. But in reality, you are speaking about the same topic as in the prior paragraph.\n\nUnder Results\nI am not certain the formatting of the journal that this is submitted to, but the quotations often are not simply embedded in a paragraph. Would leave the discretion of the editors of the journal. The results section is not very clear. There is a brief paragraph with a lot of quotes from participants, but that is not well organized. There is no clear listing of the derived qualitative themes that are referenced in the discussion and conclusion, making it hard to follow. I am not certain if this is the actual writing or translation lens. The subtitle on “job rewards gained from working in COVID-19 wards” is very brief and does not truly speak to the rich results one might expect to see an qualitative study\n\nUnder Discussion\nWould suggest to not use the words” our study” but rather “this study”. Keeps the information and reporting more objective. In paragraph two, there is mention of positive aspects found in the study, but these were not highlighted in the findings. These seem to be themes—but it is not clear how we got here. There is no clear outline and connection of the themes of the qualitative research project. There is not a robust presentation of a discussion. This section may benefit from sharing the finding more robustly in the content of the existing literature.\n\nEthics and consent (near end)\nThis is a repeated section. It is likely not needed here as was noted at the beginning of the article.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-559
|
https://f1000research.com/articles/13-557/v1
|
31 May 24
|
{
"type": "Systematic Review",
"title": "Differential Expression of Immunohistochemical Markers in Ameloblastoma & Ameloblastic Carcinoma: A Systematic Review and Meta-analysis of observational studies",
"authors": [
"Saleena Mishra",
"Swagatika Panda",
"Neeta Mohanty",
"Swati Mishra",
"Divya Gopinath",
"Saurav Panda",
"Sukumaran Anil",
"Saleena Mishra",
"Neeta Mohanty",
"Swati Mishra",
"Divya Gopinath",
"Saurav Panda",
"Sukumaran Anil"
],
"abstract": "Background Differentiating between ameloblastoma (AB) and ameloblastic carcinoma (AC) is difficult, especially when AB has atypical cytological characteristics or an uncommon clinical history. This systematic review and meta-analysis aimed to elucidate the differential expression of immunohistochemical markers between AB and AC.\n\nMethods We conducted a thorough search of PUBMED and SCOPUS according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to identify cross-sectional studies that compared the expression of immunohistochemical markers in AB and AC. We used a random-effects model to analyze the risk ratios and their corresponding 95% confidence intervals (CIs). The quality of the included studies was assessed using the Newcastle-Ottawa scale. The Egger’s test was used to assess publication bias.\n\nResults In total, 301 articles were identified. After excluding irrelevant titles and abstracts, 86 articles were selected for full-text review. We categorized the 41 markers into proliferative and non-proliferative markers. Among non-proliferative markers, nuclear markers were differentially expressed in AB and AC. SOX2 was the only marker that significantly differentiated AB and AC, with an RR of -0.19 (CI 0.10-0.36, I2=0).\n\nConclusion The current evidence suggests the significance of SOX2 in differentiating between AB and AC, warranting prospective confirmation in well-defined extensive studies. We highlight the paucity of high-quality replicated studies of other markers in this field. Collaborative efforts with standardized techniques are necessary to generate clinically useful immunohistochemical markers.",
"keywords": [
"Odontogenic tumour",
"Ameloblastoma",
"Ameloblastic carcinoma",
"immunohistochemistry",
"Biomarkers"
],
"content": "Introduction\n\nOdontogenic tumors are a diverse group of lesions that range from hamartomatous or non-neoplastic tissue proliferation to malignancies with metastatic potential.1 These tumors account for less than 2-3% of oral lesions, making them rare and difficult to diagnose without proper experience.2 Although clinical, radiographic, and microscopic features are crucial for diagnosing odontogenic tumors, confirmation may require immunohistochemical findings.3\n\nAmeloblastoma (AB) is a benign epithelial odontogenic tumor that originates in the enamel organ. On the other hand, Ameloblastic Carcinoma (AC) is a malignant epithelial odontogenic tumor that shows histological features of benign ameloblastoma with cytological atypia and rare metastatic potential.4 AC can arise de novo or from its benign counterpart,5 and recent studies have demonstrated the influence of genetic and environmental factors on its pathogenesis.6 Although the clinical and radiological features of AB and AC are similar, cytological atypia is the key differentiating factor between the two tumors. However, in cases where cytologic atypia is more frequent in AB and less frequent in AC, distinguishing them by Hematoxylin and Eosin staining can be difficult. In such cases, immunohistochemical (IHC) intervention is necessary. However, no definitive marker can differentiate AB from AC. Therefore, this study aimed to identify differences in the expression of immunohistochemical markers in AB and AC to understand the biological behavior of the tumors and the potential of these markers to differentiate between AB and AC.\n\n\nMethods\n\nThis systematic review is based on the Preferred Reporting for Systematic Review and Meta-Analysis (PRISMA).7 The protocol was registered in the PROSPERO database (ID: CRD42021285592).\n\nThe PECO format was used to construct the search strategy, where specimens from patients diagnosed with ameloblastic carcinoma (P) were subjected to immunohistochemistry (E) and compared with those diagnosed with ameloblastoma (C). Outcomes (O) assessed included immuno-expression of various markers reported as intensity, proportion of positive cases, and total immunoreactivity scores (IRS). The search used MeSH and keywords from two databases, PUBMED and SCOPUS. Boolean operators like “‘AND’ and ‘OR’” were appropriately used. The reference lists of the selected articles and grey literature were further searched. The time period of The search lasted till 31st May 31, 2023.\n\nOnly English literatures fulfilling PECO criteria were included in this study. Missing clinical data,sample sizes in either group less than 3 and ratio of AB:AC greater than 5:18 were excluded. Studies lacking clarities among AB,AC and unicystic AB were discarded. Studies which had not specified outcome measures were also excluded.\n\nTwo investigators (SM and SP) independently screened the identified articles initially by title and abstract, followed by full text, considering the inclusion and exclusion criteria. Data were collected in an Excel sheet and included the first author, year of study, study population, sample size, age, sex, IHC markers, proportion of positive cases, intensity of immuno-expression, proliferative index of proliferative markers, and immunoreactivity score (IRS).\n\nWe considered moderate to strong immune expression to be positive. The data were pooled using a meta-analysis. Meta-analysis was conducted using Revman (version 5.4.1). Forest plots were constructed for each reported marker with a Risk Ratio as the outcome measure for the number of positive cases, whereas the mean difference was the outcome measure when comparing IHC scores between AB and AC. Publication bias was assessed using funnel plots in RevMan (version 5.4.1) and the Egger’s test. A sensitivity analysis was also conducted to determine the influence of each study on the results.\n\nThe New Castle–Ottawa scale9 was used to evaluate the quality of the included studies.\n\n\nResults\n\nA total of 463 articles were selected from the two databases in the first phase. After removing the duplicate studies, there were 303 articles. After a further comprehensive evaluation of titles and abstracts, 215 articles were excluded. After a full-text screening, 63 articles were excluded. Six articles were excluded during the data extraction.10–15 Nineteen articles were included in the systematic review and meta-analysis. A PRISMA flowchart is shown in Figure 1.\n\nClinical features\n\nThere were 11 studies10–20 from Asia, three from North America,21–23 four from South America,24–27 and one28 from the Australian population. The age ranges in AB and AC were found to be 11–78 years11,13,18,20,22,25,28 and 16–72 years, respectively.11,13,18,20,22,25,28 Male prevalence of 1.1:1 and 1.9:1 were observed in AB and AC, respectively. Mandibles were the predominant sites in both the AB and AC, with mandibular to maxillary ratios of 8.2:1 and 4.4:1, respectively. The included studies used different methods of interpreting immunohistochemistry have been utilized, such as the combinative semiquantitative scoring system, Allred scoring system, immunoreactivity score, automation approach, Klein scoring system, qualitative scoring system, and evaluation of the number of IHC-positive cases.29\n\nImmunohistochemical features\n\nNineteen articles studied 41 markers10–28 which could be categorized as proliferative and nonproliferative markers. Ki67,11,13,15,22,23,24 AgNOR,15,25 PCNA,12 and p5322,24 are all proliferative markers. The non-proliferative markers were further divided into epithelial and stromal markers. Epithelial markers are further subdivided into cell membrane, cytoplasmic, and nuclear markers. The details of these studies are provided in Table 1 (Extended data)\n\nProliferative markers\n\nFour proliferative markers, Ki67, AgNOR, PCNA and P53, were compared between AB and AC by six,11,13,15,22,23,24 two,15,25 one,12 and two authors,22,24 respectively. The intensities of Ki67 and P53 expression were higher in AC than in AB.19,30 All studies, except one,30 demonstrated significant overexpression of all four proliferative markers in AC compared to AB.\n\nNon-proliferative markers\n\nEpithelial markers\n\nFive studies explored five cell membrane markers, ten studies examined 12 nuclear markers, 13 studies explored 28 cytoplasmic markers, and five studies explored seven stromal markers. Epithelial markers are further categorized into cell membrane, nuclear, and cytoplasmic markers, depending on the localization of the antibody.\n\nCell membrane markers\n\nOf the five studies17,21,22,23,28 on cell membrane markers, the intensity of CD138 was reported to be stronger in AB in only one. The intensities of CD4428 and nestin17 were stronger in AC. However, the area of staining has not been adequately investigated. The number of CD44-positive cases was higher in the AB group than in the AC group. Similarly, the intensity of CD138 was higher in AB; in contrast, the number of CD138 positive cases was higher in AC. The intensity and number of nestin-positive tissues were higher in the AB group. Even the mean CD138 score, as found in the automation method, was significantly higher in AB than in AC.23 Mean score of CD44 score, as found by Ge et al. was 1.20±0.89 AB and 0.8±0.41 AC.17 Comparative data for CD56 and E-cadherin are not available.\n\nNuclear markers\n\nWhile there was no difference in SOX2 intensity between AB and AC in Yu21 and Sanjai18 reports, Wafa et al.17 demonstrated a significantly higher intensity in AC than in AB. All three authors17,18,21 reported a significant increase in SOX2 immunopositive cases in AC compared to AB. Calretinin was found to be intense in AB as compared to no reactivity in AC, as reported by Amrutha et al.19 Proportion of Calretinin immune-positive cases is contradicted in two studies.6,19 Intensity of P16, HIF alpha, NF-kb, and ZEB1was found to be higher in AC than in AB. There have been no reports on differences in the number of positive cases. Both the intensity and proportion of immunopositive patients for Twist, OCT4, and Nestin were higher in AC than in AB. There was no difference in the number of immunopositive cases for Maspin and B-catenin. The β-catenin19 immunohistochemical score was not significantly different (0.21) between AB and AC. Allred scoring system (ARS) for ZEB1 was 1.8 and 4 for AB and AC, respectively, with a significant difference (p <0.05).20 ARS for HIF1α20 was 1.5 & 4.6 for AB & AC respectively with a significant difference of <0.01. Loyola et al.24 found the mean quick score for p16 as 7.9±2.6 & 10.3±3.8 in AB and AC, respectively though the difference was not significant. Sanjai et al.18 used an immunoreactive scoring system for SOX2 and found a score of 3.46±4.03 AB and 6.5±3.99 AC. Wafa Khan et al.17 found SOX2 scores of 0.3±0.73 for AB and 5.2±2.14 for AC, respectively. The OCT4 score for the AC group was 5±2.43 AC. Safadi et al.13 used an automation score system for Maspin and found 110.70% and 53.20% for AB and AC, respectively.\n\nCytoplasmic markers\n\nThe intensities of Nfkb,14 Bclxl,14 p16,24 and COX214 were stronger in AC than in AB. The number of positive cases for ck14,8,19 ck6,13ck5,22ck17,13CD138,13 and ck1911,13 were higher in AB than in AC. The immuno-expression of calretinin in the two studies6,19 is contradictory. Although the perilipin intensity was lower in AC than in AB, the proportion of positive cases was higher in AC than in AB. Similarly, the adipophilin intensity was higher in the AC group, while the proportion of adipophilin-positive cases was higher in the AB group. There have been no reports on the intensity changes of Snail; however, the proportion of positive patients is higher in AC than in AB. The intensity and proportion of positive cases of CK 18 and MMP2 are more in AC than in AB. The expression of nestin28 and MMP2 was augmented in AC compared to AB during qualitative and quantitative evaluation. CK 7 was not expressed in either the AB or AC. However, the mean immunohistochemical scores for FASN, COX2, Perilipin 1, and adipophilin were higher in AB than in AC.26 Mean scores of P53, P16, CK18 and CK19 were significantly higher in the AC group than in the AB group.24\n\nStromal markers\n\nThe intensity of expression and proportion of immuno-positive cases of MMP911 and nestin28 were higher in AC than in AB. The proportion of immunopositive cases of MMP2,11 Twist,16 and CD13828 was found to be higher in AC than in AB. However, Da Silva et al.25 did not observe any differences in the expression of MMP2 and MMP9. The number of Snail positive16 cases was marginally higher in AB than in AC, and differential expression of immunohistochemical markers in AB and AC are shown in Figure 2.\n\nMeta-analysis of the comparison of IHC scores of four proliferative markers, Ki67, AgNOR, PCNA and P53 between AB and AC did not find any conclusive difference in expression (mean differences = -0.69, 95%CI: -3.34-1.96, p = 0.61). Meta-analysis of the IHC scores of proliferative and nuclear markers was not performed because of the heterogeneity in the reported data. A meta-analysis on the number of cases positive for nuclear markers17,18,21 demonstrated that SOX2 has 81% potential in differentiating between AB and AC (RR-0.19; 95%CI -0.10-0.36,p-value of <0. 00001). Altogether, nuclear markers have 55% potential in differentiating between AB and AC (RR-0.45; 95%CI-0.20-1.00;p-value of 0.05). Forest plots depicting the meta-analysis of nuclear markers are shown in Figure 3. Meta-analysis of cytoplasmic markers (RR-0.85, 95% 184 CI: 0.17-4.20, p =0.84) and stromal markers (RR: 0.90, 95% CI: 0.73-1.10, p = 0.29, and Tau2 = 0.02). did not reveal any differential expression between AB and AC.\n\nThe quality of the studies on the Newcastle–Ottawa scale varied from to 7-8. The sensitivity analysis showed that none of the studies affected the risk ratio of SOX2. Two studies by Yu Lei et al. for β Catenin21 and Rudraraju et al.19 for Calretinin influenced the results to achieve an optimum risk ratio.\n\nEgger’s test shows significant publication bias exists among the selected articles.\n\n\nDiscussion\n\nDiagnostic difficulty in ameloblastic neoplasms frequently occurs in one of two ways: either23 the degree of cytologic atypia and loss of ameloblastic differentiation is intermediate, making it difficult to classify the lesion as either Atypical Ameloblastoma (AA) or AC, or28 depending on the degree of cytologic atypia and high-grade transformation, overlapping histological features between AA and AC can be perplexing. Moreover, there are a handful of studies on the proteins involved in the malignant transformation of AB to AC.31 This review will help us understand the differential expression of immunohistochemical markers in AB and AC, as well as to evaluate the diagnostic potential of these markers in differentiating AC from AB.\n\nThis systematic review included 19 comparative cross-sectional studies and evaluated the differences in clinical features and immunoexpression of nuclear, cytoplasmic, cell membrane, stromal, and proliferative markers between AB and AC. Minimal differences were identified in the clinical characteristics of patients with AB and AC. The male-to-female ratios in AB and AC were found to be approximately 1:1 and 2:1, respectively, which is in agreement with the global profile of AB32 and AC.33 Moreover mandible was the predominant jaw in both AB and AC.34 Mean age range for both AB and AC patients was from the first decade to the seventh decade.\n\nA previous systematic review evaluated the prognostic implication of immuno-expression of MMP2 and MMP9 in AB and AC,35 and another correlated Ki 67 and p53 expression in AB and AC with clinicopathological features.33 Both these systematic reviews33,35 reviewed a limited number of markers and did not analyze the comparative immuno-expression of these markers in AB and AC. This study presents the first comprehensive evaluation of the comparative expression of IHC in AB and AC.\n\nAmong the 12 nuclear marker studies, a progressive increase in staining intensity and proportion of positive cases was observed with SOX2, Twist, OCT4, and Nestin from AB to AC (Figure 3). OCT4 and SOX2 are two crucial cancer stem cell markers involved in oncogenic processes and are known to contribute to the aggressive behavior of odontogenic tumors.36,37 Our results suggest that SOX2 may serve as a prognostic marker for malignant transformation of ameloblastoma. It is plausible that SOX2 is involved in the carcinogenesis of AC, as SOX2 has been shown to coordinate with inflammatory signalling to convert epithelial progenitor cells into invasive squamous carcinoma cells.38 SOX2 has also been shown to significantly distinguish odontogenic tumors from cysts.21\n\nA higher intensity of P63 and Maspin in AC than in AB was observed in this study. The evidence on P63 immuno-expression association with aggressive features of odontogenic cysts in literature is contradictory to this study,39 and generally, loss of p63 has been linked to aggressive behavior in cancer.40 An increase in the intensity of p16 in AC compared to AB has been supported by Khojasteh et al., who reported CpG methylation of p16 in all 18 samples of AC compared to only one case of AB.41 This may suggest that p16 expression is a predisposing factor for the malignant transformation of AB. There was a conflicting result for another nuclear marker, calretinin, whose intensity was reduced in AC compared to AB in one study,42 whereas the reverse was observed in another study.43 Calretinin was significantly associated with AB compared to other odontogenic tumors.\n\nThe expression of two membranous markers, CD44 and CD 138, and the cytoplasmic marker perilipin was augmented in AB and reduced in AC. CD44, a family of cell surface glycoproteins, participates in cell-to-cell and cell-to-extracellular matrix adhesions and interactions.44 The expression profile of CD44 is tissue-specific, which is attributed to the tissue-specific distribution of various isoforms of CD44 and is currently inconclusive regarding AB and AC. Reduced expression of CD44 has also been observed in oral cancer.36,37,45 Loss of function of CD44 in AC must be confirmed through further research focused on variants of CD44 and its interaction with several related molecules. CD 138 (syndecan 1) is another membrane protein that is functionally similar to CD44. CD138 expression was reduced in head and neck cancer, gastric cancer, and colorectal cancer compared with the adjacent normal epithelium.46 Therefore, the present finding of reduced expression in AC compared to AB is supported by the existing literature. However, a limited number of studies have not provided conclusive evidence. Perilipins are a group of proteins related to the surface of lipid droplets. Perilipin expression is upregulated in renal cell carcinoma, gastric cancer, and non-small cell lung cancer, and its increased expression is associated with improved survival. However, breast cancer, oral cancer, hepatocellular cancer, and colorectal and pancreatic cancers have decreased expression of perilipin, which is associated with poor survival and increased invasion.35,47–49 Increased expression of perilipin 1 in AC was observed compared to that in AB.27 Other cytoplasmic markers, Nestin, FASN, NF-kB, BCL-XL, p63 Adipophilin, and COX2, were shown to be overexpressed in AC as compared to AB. The present finding of higher COX2 expression in AC than in AB, supported by the previous evidence of higher expression of COX2 in OKC compared to AB50–52 association with high recurrence and low disease-free survival in AB,53 may suggest the involvement of this molecule in the biological aggressiveness of jaw tumors. COX 2 probably maintains tumor growth and facilitates invasiveness by interfering with apoptosis, cellular proliferation, and angiogenesis, and hence could be a potential biomarker. However, further studies are required to clearly delineate this relationship. Nestin is an intermediate filament of the cytoskeleton, and its expression is related to tooth development and dentin repair. The negative expression of Nestin in AB is also supported by Fujita et al.54 NF-kB is a molecule of Protein Kinase B (AKT pathway) and is shown to be a putative regulator of local invasiveness of AB.55 Together with the present finding of increased expression of NF-kB in AC compared to AB suggests further exploration of the predictive potential of this marker in malignant transformation of AB. Although p63 was shown to differentiate between AB and AC, as reported in this study, previous evidence suggested no discriminatory potential of this marker between odontogenic cysts and odontogenic tumors.56 The diversity in the expression of P63 in odontogenic tumors has been reported by Alsaegh et al.57 P63 is also registered for both cytoplasmic and nuclear localization.22 Although BCL-XL has never been studied in any malignant odontogenic tumors, other anti-apoptotic molecules such as Bcl-2 have been studied in AB, which is known to be highly expressed in AB and associated with recurrence.58 Matrix, which are involved in extracellular matrix degradation, play a vital role in the local invasion of ameloblastomas. The present findings implicate a possible role of MMP2 in the malignant transformation of AB to AC, as observed in the stringer intensity in AC compared to AB. This finding is supported by another systematic review conducted to show the difference in MMP expression between AB and AC. However, there was no difference in MMP9 expression in either tumor, which is also supported by Zhou et al.35 Calretinin and perilipin were expressed less in AC than AB. Thus, we suggest the presence of these two molecules. Evidence of the differentiating potential of calretinin between a dentigerous cyst, OKC, and ameloblastoma The present findings focus on the differentiating potential of Calretinin in AB and AC.59–61 HGF, c-Met, CK7, CK7, CK7, CK14, CK14, CK14, CK19, MMP9, CK5, CK8, β-catenin, Snail, and EGFR did not show any difference in staining intensity between AB and AC.\n\nProliferative markers, such as Ki 67,11,13,15,22–24 P53,22,24 PCNA,12 and AgNOR,22,25 were shown to differentiate between AB and AC in individual studies. However, the pooled meta-analysis findings were unreliable, which may have occurred because of the strong heterogeneity in sample size and score-determining techniques. The proliferative index of Ki67 was shown to be higher in secondary AC than in primary AC.62 In ameloblastoma, Ki67 is observed in peripheral ameloblast-like cells, whereas in AC, it is distributed in central stellate reticulum-like cells and peripheral ameloblast-like cells. The peripheral location of Ki 67 in AB was also reported by Sathi et al.62 Ki67 was also reported to be highly intense in clear cell odontogenic carcinoma.24\n\nThis study had certain limitations. First, all the included studies were retrospective. The use of different antibodies in immunohistochemistry may be a potential confounding factor for all IHC studies. The sample sizes of the included studies for AC were significantly smaller, although we selected studies that chose an optimum ratio for case-control studies of 5:1.8 High statistical heterogeneities were found among these studies, which limited the scope of this systematic review and meta-analysis. Selective reporting, such as the absence of staining intensity, lack of proportion of positive cases, and demographic details in many studies, obscure the comparison between AB and AC.\n\n\nConclusions\n\nThis systematic review and meta-analysis identified differential expression of SOX2 in AB and AC, which may be considered the most promising marker to not only differentiate AB from AC, but also a plausible risk factor for the malignant transformation of AB. Furthermore, our study identified potential immunohistochemical biomarkers that may be worthy of validation in well-designed, large, prospective trials. A panel of molecules engaged in several pathways may be able to discriminate with higher sensitivity and specificity than individual markers, because of the complexity of the transformation process. Based on our results, marker panels with potential discriminative values were created.\n\n\nEthical approval and consent\n\nEthical approval and consent were not required.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: Differential expression of immunohistochemical markers in ameloblastoma & ameloblastic carcinoma: a systematic review and meta-analysis of observational studies, DOI: https://doi.org/10.6084/m9.figshare.25836703.v3. 63\n\nThis project contains the following extended data:\n\n• PRISMA Flowchart for The Systematic Review\n\n• Table 1. Characteristics of Study\n\n• Risk of Bias Assessment\n\n• Completed PRISMA checklist\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” license (CC0).\n\nFigshare: Checklists for Differential expression of immunohistochemical markers in ameloblastoma & ameloblastic carcinoma: a systematic review and meta-analysis of observational studies, DOI: https://doi.org/10.6084/m9.figshare.25836703.v3. 63\n\n\nReferences\n\nWright JM, Soluk TM: Odontogenic tumors: where are we in 2017? J. Istanb. Univ. Fac. Dent. 2017; 51(3 Suppl 1): S10–S30. PubMed Abstract | Publisher Full Text\n\nPhilipsen HP, Reichart PA: Classification of odontogenic tumours. A historical review. J. Oral Pathol. Med. Off. Publ. Int. Assoc. Oral Pathol. Am. Acad. Oral Pathol. 2006 Oct; 35(9): 525–529. Publisher Full Text\n\nHunter KD, Speight PM: The Diagnostic Usefulness of Immunohistochemistry for Odontogenic Lesions. Head Neck Pathol. 2014; 8(4): 392–399. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nBartels S, Adisa A, Aladelusi T, et al.: Molecular defects in BRAF wild-type ameloblastomas and craniopharyngiomas-differences in mutation profiles in epithelial-derived oropharyngeal neoplasms. Virchows Arch. Int. J. Pathol. 2018 Jun; 472(6): 1055–1059. PubMed Abstract | Publisher Full Text\n\nPark CW, Yoon HK, Park SJ: Methylation of p16 and E-cadherin in ameloblastoma. J. Korean Assoc. Oral Maxillofac. Surg. 2010 Jan 7; 36(6): 453–459. Publisher Full Text\n\nHendra FN, Van Cann EM, Helder MN, et al.: Global incidence and profile of ameloblastoma: A systematic review and meta-analysis. Oral Dis. 2020; 26(1): 12–21. PubMed Abstract | Publisher Full Text\n\nDeng L, Wang R, Yang M, et al.: Ameloblastic carcinoma: Clinicopathological analysis of 18 cases and a systematic review. Head Neck. 2019; 41(12): 4191–4198. PubMed Abstract | Publisher Full Text\n\nAgbaje JO, Olumuyiwa Adisa A, Ivanova Petrova M, et al.: Biological profile of ameloblastoma and its location in the jaw in 1246 Nigerians. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. 2018 Nov; 126(5): 424–431. PubMed Abstract | Publisher Full Text\n\nZhou YM, Zhong QB, Ye KN, et al.: Expression of Matrix Metalloproteinases in Ameloblastomas and Ameloblastic Carcinoma: Systematic Review and Meta-analysis. Explore Res. Hypothesis Med. 2019 May 16; 4(2): 19–28. Publisher Full Text\n\nKunishi M, Kayada Y, Yoshiga K: Down-regulated expression of CD44 variant 6 in oral squamous cell carcinomas and its relationship to regional lymph node metastasis. Int. J. Oral Maxillofac. Surg. 1997 Aug; 26(4): 280–283. PubMed Abstract | Publisher Full Text\n\nKosunen A, Pirinen R, Ropponen K, et al.: CD44 expression and its relationship with MMP-9, clinicopathological factors and survival in oral squamous cell carcinoma. Oral Oncol. 2007 Jan; 43(1): 51–59. PubMed Abstract | Publisher Full Text\n\nLiu K, Jiang M, Lu Y, et al.: Sox2 cooperates with inflammation-mediated Stat3 activation in the malignant transformation of foregut basal progenitor cells. Cell Stem Cell. 2013 Mar 7; 12(3): 304–315. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVarsha BK, Gharat AL, Nagamalini BR, et al.: Evaluation and comparison of expression of p63 in odontogenic keratocyst, solid ameloblastoma and unicystic ameloblastoma. J. Oral Maxillofac. Pathol. 2014 May 1; 18(2): 223–228. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSteurer S, Riemann C, Büscheck F, et al.: p63 expression in human tumors and normal tissues: A tissue microarray study of 10,200 tumors. Biomark. Res. 2021 Jan 25; 9(1): 7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhojasteh A, Khodayari A, Rahimi F, et al.: Hypermethylation of p16 tumor-suppressor gene in ameloblastic carcinoma, ameloblastoma, and dental follicles. J. Oral Maxillofac. Surg. 2013; 71(1): 62–65. PubMed Abstract | Publisher Full Text\n\nAnandani C, Metgud R, Singh K: Calretinin as a Diagnostic Adjunct for Ameloblastoma. Pathol. Res. Int. 2014 Apr 15; 2014: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThawfeek: Expression of Calretinin in odontogenic tumors: An observational study.[cited 2022 May 27]. Reference Source\n\nGoldstein LA, Zhou DFH, Picker LJ, et al.: A human lymphocyte homing receptor, the Hermes antigen, is related to cartilage proteoglycan core and link proteins. Cell. 1989 Mar 24; 56(6): 1063–1072. PubMed Abstract | Publisher Full Text\n\nAbbas SA, Saeed J, Tariq MU, et al.: Clinicopathological prognostic factors of oral squamous cell carcinoma: An experience of a tertiary care hospital. JPMA J. Pak. Med. Assoc. 2018 Jul; 68(7): 1115–1119.\n\nKind S, Merenkow C, Büscheck F, et al.: Prevalence of Syndecan-1 (CD138) Expression in Different Kinds of Human Tumors and Normal Tissues. Dis. Markers. 2019 Dec 23; 2019: 1–11. Publisher Full Text\n\nZhang X, Su L, Sun K: Expression status and prognostic value of the perilipin family of genes in breast cancer. Am. J. Transl. Res. 2021 May 15; 13(5): 4450–4463. PubMed Abstract\n\nZhang P, Meng L, Song L, et al.: Roles of Perilipins in Diseases and Cancers. Curr. Genomics. 2018 May; 19(4): 247–257. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartín-Hernán F, Campo-Trapero J, Cano-Sánchez J, et al.: A comparative study of the expression of cyclin D1, COX-2, and KI-67 in odontogenic keratocyst vs. ameloblastoma vs. orthokeratinized odontogenic cyst. Rev. Esp. Patol. 2022 Apr 1; 55(2): 90–95. PubMed Abstract | Publisher Full Text\n\nMendes RA, Carvalho JFC, van der Waal I : A comparative immunohistochemical analysis of COX-2, p53, and Ki-67 expression in keratocystic odontogenic tumors. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2011 Mar 1; 111(3): 333–339. PubMed Abstract | Publisher Full Text\n\nMendes RA, Carvalho JFC, van der Waal I : An overview on the expression of cyclooxygenase-2 in tumors of the head and neck. Oral Oncol. 2009 Oct 1; 45(10): e124–e128. PubMed Abstract | Publisher Full Text\n\nMontezuma MAP, Fonseca FP, Benites BM, et al.: COX-2 as a determinant of lower disease-free survival for patients affected by ameloblastoma. Pathol. Res. Pract. 2018; 214(6): 907–913. PubMed Abstract | Publisher Full Text\n\nFujita S, Hideshima K, Ikeda T: Nestin expression in odontoblasts and odontogenic ectomesenchymal tissue of odontogenic tumours. J. Clin. Pathol. 2006 Mar; 59(3): 240–245. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCecim RL, Carmo HAF, Kataoka MSS, et al.: Expression of molecules related to AKT pathway as putative regulators of ameloblastoma local invasiveness. J. Oral Pathol. Med. 2014; 43(2): 143–147. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nGopinath D: Differential expression of immunohistochemical markers in ameloblastoma & ameloblastic carcinoma: a systematic review and meta-analysis of observational studies. figshare. 2024. Publisher Full Text"
}
|
[
{
"id": "288916",
"date": "24 Jun 2024",
"name": "Lilies Dwi Sulistyani",
"expertise": [
"Reviewer Expertise oral and maxillofacial surgery"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI think this is a really great article. The rationale and objectives of the systematic review are clearly stated, and the methods are clearly elaborated. However, it would have been greater if the IHC expressions, both the proliferative and non-proliferative, were pooled and summarized in a well-organized table to showcase the results to help readers to analyze and draw conclusions from the data.\nIn the article, it was reported that Egger's test shows significant publication bias exists among the selected articles, yet there were no further discussion on that issue.\n\nIn the discussion and conclusion sections, SOX2 were highlighted as a promising differentiating marker between AB and AC, also a predicting marker of malignant transformation of AB. This statement is a bit confusing in clinical setting as the cutting point was not clearly explained when the positive SOX2 IHC expression should be considered a diagnostic marker for AC, and when to consider it as a predictive marker of malignant transformation of AB.\nYet this study truly intrigue the need of a controlled prospective study to develop a standard IHC panels to clearly define AB and AC.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
},
{
"id": "301590",
"date": "29 Jul 2024",
"name": "Maya Ramesh",
"expertise": [
"Reviewer Expertise Ameloblastoma",
"Dental fluorosis",
"Oral cancer"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is a comprehensive one on Immunohistochemical markers that can be used to differentiate between ameloblastoma and ameloblastic carcinoma.\nThe objectives of the study are clearly stated, and methodology is clear for anyone else to replicate it .\n\nStatistical analysis and interpretations are very clear. Figure 2 shows the markers' staining intensity and the area where it is seen very clearly.\nThis study provides a panel of markers to differentiate between Ameloblastoma and Ameloblastic carcinoma.\n\nBut in this Systematic review and Meta analysis , number of cases of ameloblastic carcinomas were comparatively less and the IHC markers used in different studies were not made by the same manufacturer. These were the limitations as identified by the author also.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-557
|
https://f1000research.com/articles/13-556/v1
|
31 May 24
|
{
"type": "Research Article",
"title": "Easing genomic surveillance: A comprehensive performance evaluation of long-read assemblers across multi-strain mixture data of HIV-1 and Other pathogenic viruses for constructing a user-friendly bioinformatic pipeline",
"authors": [
"Sara Wattanasombat",
"Siripong Tongjai",
"Sara Wattanasombat"
],
"abstract": "Background Determining the appropriate computational requirements and software performance is essential for efficient genomic surveillance. The lack of standardized benchmarking complicates software selection, especially with limited resources.\n\nMethods We developed a containerized benchmarking pipeline to evaluate seven long-read assemblers—Canu, GoldRush, MetaFlye, Strainline, HaploDMF, iGDA, and RVHaplo—for viral haplotype reconstruction, using both simulated and experimental Oxford Nanopore sequencing data of HIV-1 and other viruses. Benchmarking was conducted on three computational systems to assess each assembler’s performance, utilizing QUAST and BLASTN for quality assessment.\n\nResults Our findings show that assembler choice significantly impacts assembly time, with CPU and memory usage having minimal effect. Assembler selection also influences the size of the contigs, with a minimum read length of 2,000 nucleotides required for quality assembly. A 4,000-nucleotide read length improves quality further. Canu was efficient among de novo assemblers but not suitable for multi-strain mixtures, while GoldRush produced only consensus assemblies. Strainline and MetaFlye were suitable for metagenomic sequencing data, with Strainline requiring high memory and MetaFlye operable on low-specification machines. Among reference-based assemblers, iGDA had high error rates, RVHaplo showed the best runtime and accuracy but became ineffective with similar sequences, and HaploDMF, utilizing machine learning, had fewer errors with a slightly longer runtime.\n\nConclusions The HIV-64148 pipeline, containerized using Docker, facilitates easy deployment and offers flexibility to select from a range of assemblers to match computational systems or study requirements. This tool aids in genome assembly and provides valuable information on HIV-1 sequences, enhancing viral evolution monitoring and understanding.",
"keywords": [
"HIV",
"Virus",
"Infectious Diseases",
"NGS",
"Single-molecule sequencing",
"Haplotype reconstruction",
"Genome assembly",
"Genomic surveillance"
],
"content": "Introduction\n\nIn 2020, UNAIDS has re-established the 95-95-95 targets to end the HIV/AIDS epidemic, aiming for 95% of people to know their HIV status, receive treatment, and achieve viral suppression by 2025.1–3 While efforts to combat HIV-1 focus on treatment and prevention, HIV-1 genomic surveillance plays a crucial role.4 It offers essential data for evidence-based strategies in HIV prevention, testing, treatment, and care.5,6 The genomic surveillance protocol should entail simple and swift sample preparations and sequencing, facilitated by Oxford Nanopore Sequencing Technology.7–10 Additionally, it should feature straightforward bioinformatic analysis pipelines and provide comprehensive reports enriched with reliable HIV-1 information. This adaptable protocol can utilize various computational resources, contributing significantly to global efforts against HIV/AIDS.\n\nThe lack of a proofreading mechanism in HIV-1 reverse transcriptase leads to a high mutation rate, potentially resulting in immune-evading variants or drug-resistant strains, posing challenges in patient care and virus transmission control strains.11–16 Various patterns of intra-host multi-strain HIV infection, including dual, co-, super, and triple infection, have been observed.17 Multiple HIV infections significantly contribute to the emergence of novel and more infectious HIV-1 recombinants, impacting viral fitness and increasing inter-subtype recombinants’ prevalence.18,19 Some novel HIV-1 recombinants may be undetectable, especially in medically suppressed individuals.20,21 Therefore, HIV-1 quasispecies profiling holds value for understanding viral population dynamics, particularly newly emerging recombinants.22–24 Developing an effective monitoring protocol focusing on the viral genomic level is crucial for understanding HIV-1 dynamics within the host and devising better treatment and prevention strategies.21,25\n\nRecently, Next Generation Sequencing (NGS) technologies have become crucial in viral genome analysis. The Sequencing by Synthesis (SBS) approach enables the detection of single nucleotide variants (SNVs) and some alterations in viral genomes.26 However, SBS technology faces limitations in accurately reconstructing viral haplotypes and detecting low-abundance haplotypes for quasispecies analysis. It is also inadequate for examining complex viral sequences such as HIV-1’s long terminal repeats (LTRs) or large deletions or insertions in the HIV envelope glycoprotein gene. Furthermore, SBS technology is not well-suited for analyzing phased mutations in the viral genome.20,26\n\nSingle-molecule sequencing (SMS) technology, including Oxford Nanopore Technology (ONT) and PacBio SMRT technology, enhances viral quasispecies analysis by generating longer genomic reads,27–29 enabling near-complete viral genome reconstruction with high accuracy (97–99% identity).17 ONT’s recent advancements allow direct RNA sequencing, reducing bias from PCR or cDNA synthesis.24 However, SMS technology has a high raw read sequencing error rate exceeding 10%, which can be mitigated with various long-read error correction methods.30–34 ONT R10.3 chemistry sequencing of the HIV-1 genome yields raw reads with a 5 to 12% error rate, while ONT’s unique molecular identifier (UMI) method achieves a single molecule consensus accuracy of up to 99.9995%.35,36 PacBio SMRT has an error rate of 13 to 15%, but its circular consensus sequencing (CCS) approach provides consensus reads with approximately 99.999% accuracy.35,36 Data quality from SMS technology can be improved by implementing quality control measures, optimizing coverage thresholds, and validating variant calls to ensure the reliable detection of minor mutations despite residual errors.34,37,38\n\nTwo categories of HIV-1 haplotype detection for SMS data are reference-based and de novo approaches.39 The reference-based methods, though generally accurate, may introduce bias without suitable reference sequences.26 Using a single reference genome can miscluster reads from different viral haplotypes. For example, RVHaplo’s hierarchical clustering with a reference genome may inaccurately group reads from different haplotypes,40 affecting characterization of novel or rare haplotypes. Canu and GoldRush, considered general-purpose de novo assemblers, may overlook genomic reads with lower coverage.41 Conversely, MetaFlye and Strainline are strain-aware de novo assemblers, recognizing strain differences within a sample.28,42 HaploDMF, iGDA, and RVHaplo are reference-based assemblers designed for multi-strain mixtures.43–45 iGDA and RVHaplo employ similar clustering approaches, while HaploDMF uses deep matrix factorization for contig extension.43,46 Despite numerous assembly software options tailored for SMS data,28,42–45,47,48 selecting the best tool for haplotype reconstruction and HIV-1 quasispecies analysis is challenging due to a lack of systematic studies. Furthermore, the absence of standardized benchmarking across different software and computing environments complicates the selection process, especially with limited computational resources.49,50\n\nIn this study, we demonstrated that Strainline and MetaFlye excelled at haplotype reconstruction, although Strainline required more memory. Conversely, Canu performed poorly when distinguishing sequences in multi-strain mixtures, while GoldRush only yielded consensus assemblies. iGDA exhibited high error rates, whereas RVHaplo showed superior runtime and accuracy. HaploDMF offered improved accuracy despite a longer runtime. Additionally, a containerized pipeline, named HIV-64148, was developed to provide publicly accessible and user-friendly tool for genomic surveillance of HIV-1.\n\n\nMethods\n\nThe benchmarking pipeline (Figure 1) started with an assessment of the quality of all long-read FASTQ inputs using NanoPlot51 to ensure data conformity, particularly regarding the median read length. This study evaluates the performance and accuracy of seven assemblers on three different computational systems. Subsequently, the quality and accuracy of each assembler’s output are assessed using QUAST. Additionally, sequence similarity and HIV-1 subtype of all assembled contigs are investigated. The benchmarking pipeline is containerized, enabling its execution on any cloud or non-cloud environment52 supporting either Docker or Singularity.\n\nThe pipeline begins with a read quality control analysis of long-read FASTQ files, followed by an assembler, which can be either de novo or reference-based. Finally, the pipeline includes HIV-1 subtyping to classify the HIV-1 strains present in the data.\n\nThis study aimed to assess the accuracy, performance, and computational efficacy of seven candidate long-read assemblers, categorized into two approaches for haplotype reconstruction: (1) de novo long-read assemblers, which include Canu,47 Goldrush,48 MetaFlye,42 and Strainline,28 and (2) reference-based long-read assemblers, which comprise HaploDMF,43 iGDA,44 and RVHaplo.45\n\nThe assembly software, including Canu, MetaFlye, and iGDA, was installed using the Micromamba package manager, which utilized recipes from the conda-forge (https://anaconda.org/conda-forge) and bioconda channels (https://anaconda.org/bioconda). An additional channel, zhixingfeng (https://anaconda.org/zhixingfeng), was used specifically for iGDA as per the installation guidelines. Each tool was set up in separate environments to adhere to the developer’s specified version of dependencies.\n\nFor HaploDMF, RVHaplo, and Strainline, specifications were not available in Micromamba, necessitating manual installation. The source codes for HaploDMF (https://github.com/dhcai21/HaploDMF) and RVHaplo (https://github.com/dhcai21/RVHaplo) were downloaded from their respective GitHub repositories, with dependencies installed via Micromamba using environment specification files provided by the developers. For Strainline, the source code was sourced from its GitHub repository (https://github.com/HaploKit/Strainline). Dependencies were managed and installed with Micromamba, except for Daccord (https://github.com/gt1/daccord) and Metabat2 (https://bitbucket.org/berkeleylab/metabat/src/master/), which were obtained by downloading the latest releases from the developers’ websites. Licensing for these tools varies: Strainline, GoldRush, HaploDMF, and RVHaplo are licensed under GPL3.0, Canu and iGDA under GPL2.0, and MetaFlye under the BSD-3-Clause license. Table 1 provides an overview of all candidate long-read assemblers.\n\nBenchmarking analyses were conducted on three different computational systems: a server, a workstation PC, and a standard home PC. Specifications of each system is indicated in Table 2. The performance parameters of each assembler were measured as follows: 1) total CPU utilization, indicating the overall workload on the CPU, 2) memory usage, and 3) total runtime, defined as the elapsed wall-clock time from the start of assembly to the generation of output contigs. A dedicated Python script was developed to track the resource usage of each process of the long-read assemblers, capturing CPU and memory utilization every 100 milliseconds at each stage of the assembly process. As the pipeline operates within a containerized environment facilitated by Docker, unrelated processes such as operating system operations were filtered out during the measurement of resource utilization.\n\nLong-read FASTQ files were simulated from four HIV-1 genome mixtures: (1) 2 group M HIV-1 subtypes (2M), (2) 2 CRF subtypes (2C), (3) 1 group M HIV-1 subtype and 1 CRF subtype (1M1C), and (4) 2 group M HIV-1 subtypes and 1 CRF subtype (2M1C), see Table 3. Each genome mixture comprised 100 sets of FASTA files containing corresponding HIV-1 genomes randomly selected from the Los Alamos HIV sequence databases53 (https://www.hiv.lanl.gov/). All 400 HIV-1 FASTA sets underwent data simulation to generate 400 individual long-read FASTQ files using NanoSim V3.1.0. A list of mixtures within the 400 FASTA sets is available in Extended data, Table S6.54 Additionally, 20 long-read FASTQ files, comprising 5 samples from each mixture (Table 3), were generated with varying amplicon sizes as described in the assembly quality assessment.\n\nThe data simulations were conducted using NanoSim V3.1.0 (https://github.com/bcgsc/NanoSim/releases/tag/v3.1.0) in metagenomic mode,55,56 employing a pretrained read profile model named human NA12878 DNA FAB49712 guppy. Additional simulation conditions included a maximum read length of 12,000 nt, a minimum read length of 7,500 nt, a median read length of 9,000 nt, and a standard deviation of read length set to 0.75. The parameter “--perfect” was configured as True to simulate error-free reads. A depth of coverage of 2,000 was selected, deemed sufficient for variant calling and quasispecies detection.57,58 The resulting FASTQ files (Table 3) were similar to those generated by an Oxford-ONT R9.4 chemistry using a Guppy 3.1.5 basecaller. Furthermore, this study benchmarked the assemblers using experimental data sourced from published studies (Extended data, Table S1).54 All FASTA templates for data simulation,59 simulated FASTQ files,60 and QC results of the simulated FASTQ files61 are available as Underlying data.\n\nSequence similarity was assessed using local NCBI BLASTN62 against a customized database of 12,000 HIV-1 genomes from the Los Alamos HIV-1 sequence database,53 with contigs showing >95% sequence similarity considered. QUAST63 was utilized to compare contigs from different assemblers, with regular QUAST for single viral isolate datasets and MetaQUAST63 for multiple isolate inputs. Primary QUAST parameters assessed were number of contigs, sizes, N50, % genome fraction, and total aligned bases, along with assembly correctness measured by average mismatches and indels per 100,000 aligned bases. Additionally, assembly quality was evaluated by average completeness of major HIV-1 ORFs (e.g., gag, gag-pol/pol, and env). The results generated from the pipeline are available as Underlying data.64\n\n\nResults\n\nAll seven assemblers were executed on three computational systems to measure wall-clock time usage, memory usage, and CPU utilization. Each assembler processed 100 simulated 2M FASTQ files. Figure 2 illustrates the time usage of all FASTQ files processed by different assembly pipelines across the three computational systems. As shown in Extended data, Table S2,54 the workstation server completed all 700 assemblies in 3 days, 9 hours, 50 minutes, and 28.31 seconds, while the workstation PC required 3 days, 23 hours, 24 minutes, and 2.64 seconds. Due to a failed Strainline-mediated assembly with the generic home PC, the remaining 600 assemblies took 2 days, 14 hours, 49 minutes, and 16.79 seconds. Notably, GoldRush emerged as the fastest assembler, with approximately 30 seconds or less per assembly under all three computational systems, while MetaFlye was the slowest, taking approximately 1,370 seconds or more per assembly.\n\nThe assemblies (100 simulated 2M FASTQ files per assembler per system) are grouped by computational systems on the x-axis and by assemblers on the y-axis. Additionally, an accompanying statistical summary is provided in Extended data, Table S2.54\n\nFor memory usage, Strainline could not be tested with the generic home PC due to a segmentation fault error from memory limitation. From the 189-Gb workstation server, the order of maximum memory usage, from highest to lowest, was Strainline, MetaFlye, GoldRush, HaploDMF, iGDA, Canu, and RVHaplo (Figure 3A and B). Similarly, from the 64-Gb workstation PC, the order of maximum memory usage was Strainline, Canu, MetaFlye, HaploDMF, iGDA, RVHaplo, and GoldRush (Figure 3C and D). From the 8-Gb generic home PC, the order of maximum memory usage was MetaFlye, iGDA, Canu, GoldRush, RVHaplo, and HaploDMF (Figure 3E and F). Extended data, Table S354 presents the maximum memory usages of the six assemblers.\n\nMemory usages of all assemblers under three computational systems, including (A) and (B) a workstation server, (C) and (D) a workstation PC, and (E) and (F) a generic home PC during the assembly phase of the pipeline.\n\nFigure 4 demonstrates the CPU utilizations of all assemblers, with the percentages of maximum CPU usages shown in Extended data, Table S3.54 On the workstation server (Figure 4A), the assemblers with the highest to lowest averaged CPU usage were HaploDMF, Strainline, GoldRush, iGDA, RVHaplo, Canu, and MetaFlye. Both GoldRush (3,625.9%) and Canu (647.4%) did not overutilize the CPU and remained within the acceptable limit for 36 cores. On the workstation PC (Figure 4B), the order of CPU usage was Strainline, HaploDMF, iGDA, Canu, RVHaplo, GoldRush, and MetaFlye. Notably, MetaFlye overutilized CPU at 1,437.4%, whereas Canu demonstrated only 637.5% peak utilization. Under the generic home PC system (Figure 4C), the CPU usage order was GoldRush, iGDA, RVHaplo, MetaFlye, Canu, and HaploDMF. Both HaploDMF (726.3%) and Canu (628.9%) did not overutilize the CPU. Finally, Correlations between computational factors (e.g., CPUs, maximum memory, and assemblers) and runtime were analyzed using Jamovi statistical software with a non-parametric one-way ANOVA.65,66 As demonstrated in Table 4, assembler selection significantly impacted runtime with a large effect size (ε2 = 0.903***), while no statistically significant differences in runtime were observed across different levels of CPUs and maximum memory.\n\nIn this study, the server could accommodate 36 cores (3,600%), while both the workstation PC and the generic home PC could accommodate up to 12 cores (or 1,200%). CPU usages were collected from (A) a server, (B) a workstation PC, and (C) a generic home PC. The y-axis represents percent CPU usage (100% per core). Multi-threaded processing can be observed when CPU utilization is above 100%.\n\nThe minimum read length was determined by testing the assemblers with FASTQ files from four different median read lengths: 1,000-nt, 2,000-nt, 3,000-nt, and 4,000-nt (Table 3). This assessment aimed to ensure that the assembled contigs exhibited high contiguity, genome completeness, and recovered intact major HIV-1 open reading frames (ORFs) such as gag, gag-pol/pol, and env. The evaluation was conducted using the server system.\n\nThe first evaluation of the minimum read lengths was based on the assembled contig size. Increasing median read lengths resulted in longer contigs assembled by Canu (Figure 5A). MetaFlye (Figure 5B) and Strainline (Figure 5C) could not process the 1,000-nt inputs, but Strainline assembled significantly longer contigs from longer reads. However, GoldRush failed the assessment. The remaining de novo assemblers, Canu, MetaFlye, and Strainline, processed the 4,000-nt median read length inputs and yielded contig sizes relatively close to a 9-kb HIV-1 genome. All reference-based assemblers performed well with all four inputs, generating contig sizes close to that of an HIV-1 genome (Figure 5D-F). Complete statistical evaluation details can be found in Extended data, Table S9.54\n\nThe pipelines were (A) Canu, (B) MetaFlye, (C) Strainline, (D) HaploDMF, (E) iGDA, and (F) RVHaplo. The x-axis represents four median read lengths (1,000–4,000 nt), and the y-axis represents contig size. Each data point denotes an individual contig. The mean contig size of each median read length is indicated by a black square with error bars representing 95% confidence intervals. Absolute mean differences are shown in brackets for those comparisons with statistical significance (p<0.001).\n\nSequence similarity and genome fraction of assembled contigs were evaluated across different median read lengths. For the 1,000-nt reads (Extended data, Figure S1A),54 Canu yielded >5,000-nt contigs with >99.5% similarity, while iGDA and RVHaplo generated >8,000-nt contigs with 97% and 99% similarity, respectively. RVHaplo showed superior recovery of major HIV-1 ORFs (Extended data, Figure S2A).54 At the 2,000-nt reads (Extended data, Figure S1B),54 Canu and MetaFlye produced >7,000-nt contigs with >99% similarity, whereas Strainline’s contigs were ~3,000-nt with >98% similarity. All reference-based assemblers yielded longer contigs with greater similarity and improved ORF recovery (Extended data, Figure S2B).54 At the 3,000-nt reads (Extended data, Figure S1C),54 Strainline only produced 4,000-nt contigs with >99.50% similarity, while others generated longer contigs with higher similarity and improved ORF recovery (Extended data, Figure S2C).54 Finally, at the 4,000-nt reads (Extended data, Figure S1D),54 all assemblers produced longer contigs with higher similarity. All, except Canu and HaploDMF, demonstrated satisfactory % recovery of the major HIV-1 ORFs (Extended data, Figure S2D).54 RVHaplo yielded the highest averaged genome fraction (Extended data, Figure S1E).54\n\nA further analysis (Table 5) revealed a statistically significant positive correlation between the median read lengths of the inputs and the lengths of the assembled contigs (ρ=0.185***), as well as between the median read lengths and sequence similarity (ρ=0.163***). Additionally, assembler selection demonstrated a positive correlation with the size of assembled contigs (ρ=0.131***), but not with sequence similarity (ρ=-0.220). Thus, a key finding from this study suggested that a minimum read length of 2,000-nt is necessary for all assemblers, with optimal outcomes achieved at 4,000-nt. In summary, longer median read sizes are associated with higher quality contigs, characterized by longer contig length and greater sequence similarity.\n\n* p<0.05,\n\n** p<0.01,\n\n*** p<0.001, one-tailed.\n\nThis experiment evaluated the performance of assemblers in generating contigs from simulated FASTQ inputs containing heterogeneous HIV-1 sequences. These sequences were simulated from four HIV-1 genome mixtures: 2M (2 group M subtypes), 2C (2 circulating recombinant forms, CRFs), 1M1C (1 group M subtype and 1 CRF), and 2M1C (2 group M subtypes and 1 CRF), as shown in Table 3. The evaluation criteria included contiguity, genome completeness, the recovery of major HIV-1 open reading frames (ORFs), and the error rate. Initially, contig sizes were assessed, revealing that most fell within a range of 8,500–9,200 nt, close to the size of the HIV-1 genome (Extended data, Figure S3).54 Notably, MetaFlye produced shorter contigs, ranging from 7,800 to 8,800 nt. Detailed statistical analysis of this assessment is available in Extended data, Table S10.54\n\nConsidering both contig length and averaged genome fraction, all assembler pipelines processed the four datasets to yield contigs exceeding 8,000 nt, close to the size of the HIV-1 genome (Figure 6A–D). However, the MetaFlye pipeline generated contigs with a relatively low (<90%) averaged genome fraction (Figure 6E). Except for MetaFlye, all assembler pipelines demonstrated satisfactory recovery of major HIV-1 ORFs (Figure 7A–D). De novo and reference-based assemblers showed a clear distinction in 2M, 2C, and 2M1C HIV-1 mixtures (Figure 6A, B, and D), with de novo assemblers producing contigs with >95.5% sequence similarity. Reference-based assemblers HaploDMF and RVHaplo yielded contigs with relatively high sequence similarity (98–99.5%), while iGDA produced 95–97% sequence similarity. However, iGDA generated fewer contigs from the 2M mixture inputs (Figure 6A) due to its reliance on overlapping SNVs for contig extension, which may fail with highly similar sequences. The presence of CRFs allowed iGDA to recover more contigs (Figure 6B–D). Individual assembly evaluation statistics for each sample are available in Extended data, Table S10.54\n\nThe FASTQ file sets were (A) 2M HIV-1 mixture, (B) 2C HIV-1, (C) 1M1C HIV-1 mixture, and (D) 2M1C HIV-1 mixture (Table 3). The x-axis displays the percentage sequence similarity obtained from a BLAST alignment with the corresponding reference genomes, while the y-axis represents the aligned length, indicating the longest continuous alignment between each contig and its reference genome. Dot sizes indicate the genome fraction (%Ref Aligned), calculated as the ratio of continuous aligned bases to the total reference genome length. Subplots above and beside each figure display histograms of the contig counts. Additionally, (E) shows the averaged genome fraction (%) of contigs from different long-read assembler pipelines.\n\nThe contigs were from the assemblers analyzed simulated FASTQ inputs of the 4 HIV-1 mixtures, e.g., (A) 2M, (B) 2C, (C) 1M1C, and (D) 2M1C.\n\nSince all input data consisted of error-free reads, the assembly correctness (Figure 8) was assessed by comparing the contigs with their respective HIV-1 genomes. The correctness of each assembler was evaluated based on the average number of mismatches per 100,000 aligned bases (Figure 8A) and the average number of indels per 100,000 aligned bases (Figure 8B). Among the four de novo assemblers, all introduced a few errors to the contigs, with Strainline exhibiting a greater degree of accuracy compared to the rest. MetaFlye, however, showed the least assembly correctness. Regarding the reference-based assemblers, HaploDMF and RVHaplo demonstrated similar degrees of assembly correctness, while iGDA exhibited the least. Interestingly, indels were predominantly associated with all reference-based assemblers in this study.\n\nThe errors were (A) the average number of mismatches (e.g., true SNPs and sequencing errors) per 100,000 aligned bases and (B) the average number of indels per 100,000 aligned bases.\n\nThe final assessment investigated the HIV-1 subtype recall rates of the assemblers processing the 4 HIV-1 mixture datasets. In the 2M dataset (Figure 9A), the reference-based assemblers, such as HaploDMF, RVHaplo, and iGDA, correctly recalled most of the subtypes, while the de novo assemblers exhibited lower recall rates. Strainline showed the best performance with >80% recall rates on all common subtypes, except for an overestimation on subtype B (118.52%). Canu, GoldRush, and MetaFlye exhibited low recall rates due to their collapsed assembly approach poorly handling sequences of relatively similar HIV-1 subtypes. Results from the 2C (Figure 9B) and the 1M1C data (Figure 9C) were similar to those observed in the 2M data. Interestingly, results from the 2M1C data (Figure 9D) showed much lower recall rates (<60%) by all assemblers on all HIV-1 group M subtypes due to either a reduction in coverage or an error correction process. For the CRFs, the recall rates were similar to those shown in the 2C and 1M1C datasets.\n\nSubtype recall rate of each subtype or CRF in (A) 2M HIV-1 mixture, (B) 2C HIV-1 mixture, (C) 1M1C HIV-1 mixture, and (D) 2M1C HIV-1 mixture. Each assembler's recall rate was calculated from the number of correctly identified HIV-1 subtype (or CRF) divided by a total number of a corresponding subtype (or CRF) appearing in each HIV-1 mixture. The value of over 100% was from extra contigs of that subtype produced from mixing closely related subtypes together. See Extended data, Table S1154 for more details.\n\nBased on the results from the previous assessments, Strainline, MetaFlye, and HaploDMF were selected for further investigation using publicly available experimental sequencing data of HIV-1 and other viruses. Strainline, despite its high memory usage, offered rapid de novo viral haplotype reconstruction. MetaFlye, chosen for its compatibility with lower-end devices and acceptable memory usage and runtime, served as a de novo assembler. Despite its long runtime, HaploDMF was included as a representative reference-based assembler with memory efficiency comparable to MetaFlye.\n\nThis experiment assessed the performance of selected assemblers, including Strainline, MetaFlye, and HaploDMF, using experimental data of HIV-1 and other pathogenic viruses (Extended data, Table S1).54 The quality of assembled contigs was evaluated through QUAST, which provided metrics such as the number of contigs, sizes, N50, % genome fraction, and total aligned bases. The experiment was conducted using a workstation server.\n\nHIV-1 recombinant forms and NL4-3\n\nThe dataset comprised plasma HIV-1 genomes (TRN01, TRN08, TRN09) and NL4-3 laboratory isolate from the MinION sequencer (BioProject: PRJDB13369).67 All assemblers generated NL4-3 contigs >9,000 nt (Figure 10A). MetaFlye and HaploDMF gave contigs with 95.27% and 91.22% sequence similarity, respectively. Strainline produced nine contigs, the best at 94.34% similarity (Extended data, Table S4).54 For TRN01, all assemblers produced contigs identified by REGA (version 3.46)68 as subtype B and F recombinants, similar to a previous finding.67 Similarly, TRN08 yielded subtype B contigs. However, no recombinant forms with CRF01_AE were reconstructed. For TRN09, Strainline and HaploDMF replicated original findings, while HaploDMF also identified an A-C recombinant. In contrast, MetaFlye generated subtype A and CRF07_BC gagpol contigs, and a C-CRF01_AE recombinant. REGA subtyping results are in Extended data, Table S12.54 For the 10 5’ half genomes of NL4-3 (BioProject: PRJNA938445),69 all assemblers produced contigs meeting both length and alignment criteria. MetaFlye achieved the highest performance with an 89.26% average genome fraction, followed by Strainline at 85.93% and HaploDMF at 84.64%. Detailed alignment statistics are provided in Extended data, Table S13.54\n\nThe assembled contigs were from (A) Full genome laboratory isolate NL4-3, (B) Mpox propagated in a CV-1 cell line and (C) Mpox from pustular lesion, and (D) SARS-CoV-2 sequencing data by the selected assemblers. The details of samples and reference genomes are shown in Extended data, Table S1.54 Visualization modified from Icarus.63 Individual alignment statistics for each haplotype can be found in Extended data, Table S14.54\n\nMonkeypox (Mpox)\n\nThe first sequencing data, derived from MinION sequencing of a Mpox propagated in a CV-1 cell line (SRA: ERR10963128),70 contained 2,588 reads post-filtering, with an average length of 4,633 nt and a maximum length of 9,070 nt. HaploDMF generated 3 contigs, the longest being 188,872 nt, with 99.35% genome fraction. MetaFlye produced 7 contigs, the longest at 129,209 nt, with 95.98% genome fraction. Strainline yielded 12 contigs, the longest being 33,081 nt, with a genome fraction of 78.07% (Figure 10B and Extended data, Table S454). The second dataset, derived from MinION sequencing of a Mpox from a pustular lesion (SRA: SRR15830920),71 comprised 30,990 reads after filtering, with an average length of 9,048 nt and a maximum length of 59,093 nt. MetaFlye and HaploDMF exhibited similar performance, with MetaFlye assembling 122 contigs with an N50 of 13,335 nt and the longest having a 98.58% genome fraction. HaploDMF produced 5 contigs with an N50 of 173,134 nt and the longest contig having a genome fraction of 98.62%. In contrast, Strainline generated 7 contigs with an N50 of 30,255 nt and the longest contig of 101,047 nt. Only the 65,261-nt contig of those 7 contigs demonstrated 51.31% genome fraction (Figure 10C and Extended data, Table S454).\n\nSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)\n\nThe dataset comprises GridION sequencing data of a SARS-CoV-2 clinical sample retrieved from the SRA database (SRP250446).72 Strainline generated 3 contigs: 1 full-length and 2 duplicated half-genome contigs, with a 99.93% genome fraction. MetaFlye and HaploDMF each produced a single contig, with genome fractions of 96.77% and 93.11%, respectively. However, MetaFlye’s contig lacked the first 500 nucleotides of the genome, while HaploDMF’s contig had a 2,000-nt gap when aligned to the reference genome (Figure 10D and Extended data, Table S454).\n\nPolio virus mixture\n\nThis simulated ONT dataset consisted of 6 poliovirus type 2 sequences.28 In Figure 11A and Extended data, Table S5,54 Strainline and HaploDMF generated contigs with N50 values of 7,453-nt and 7,436-nt, respectively, closely matching the 7,400-nt genome of Polio virus. Strainline produced 6 contigs with an average genome fraction of 99.34%, all sharing >95% sequence similarity with 6 viral haplotypes. HaploDMF yielded 3 contigs with >95% sequence similarity and an average genome fraction of 99.80%. MetaFlye, however, produced 3 shorter contigs with an N50 of 4,830-nt. These contigs shared >95% sequence similarity with 5 haplotypes, but with an average genome fraction of 70.13%.\n\nThe assembled contigs were from simulated mix-strain viral sequencing data of (A) Polio virus, (B) Hepatitis C virus (HCV), and (C) ZIKA Virus (ZIKV) by the selected assemblers. The details of samples and reference genomes are shown in Extended data, Table S1.54 Visualization modified from Icarus.63 Individual alignment statistics for each haplotype can be found in Extended data, Table S14.54\n\nHepatitis C virus (HCV) mixture\n\nThis simulated ONT dataset consisted of 10 strains of hepatitis C virus (HCV), Subtype 1a.28 In Figure 11B and Extended data, Table S5,54 Strainline and HaploDMF yielded contigs with N50 values of 9,286-nt and 9,309-nt, respectively. Strainline produced 12 contigs with an average genome fraction of 99.85%, all of them sharing >95% sequence similarity with all 10 haplotypes with 2 duplicated contigs. HaploDMF generated 3 contigs with a 99.99% average genome fraction, all exhibiting >95% sequence similarity with HCV haplotypes. MetaFlye produced 5 shorter contigs with an N50 of 5,670-nt, and the longest contig (8,006-nt) shared >95% sequence similarity with 5 HCV haplotypes. However, MetaFlye contigs had an average genome fraction of 77.40%.\n\nZIKA Virus (ZIKV) mixture\n\nThis simulated ONT dataset comprised 15 strains of Zika virus (ZIKV).28 In Figure 11C and Extended data, Table S5,54 Strainline, MetaFlye, and HaploDMF generated contigs with N50 values of 10,264-nt, 5,842-nt, and 10,264-nt, respectively, closely matching the size of the ZIKV genome (11,000-nt). Strainline produced 13 contigs that recovered 14 ZIKV haplotypes, with an average genome fraction of 99.84%. MetaFlye yielded 15 contigs with a lower average genome fraction of 78.56%, recovering 10 ZIKV haplotypes. Interestingly, HaploDMF produced 10 contigs, each with an average genome fraction of 99.90%, and recovered 11 ZIKV haplotypes.\n\nIn summary, the selected assemblers showed strong performance across different experimental ONT datasets. MetaFlye exhibited superior performance with experimental ONT data of full-length or half-length HIV-1 genomes. Strainline demonstrated excellent haplotype recovery with ONT sequencing data of various viral mixtures, including SARS-CoV-2, Poliovirus, HCV, and ZIKV. Additionally, MetaFlye showcased better performance on the metagenomic experimental ONT data of the 200-kb Mpox.\n\nThe HIV-64148 benchmarking pipeline is designed for portability, ensuring it functions across different computational environments with minimal setup. As a result, the containerized HIV-64148 can be executed on either Docker or Singularity platforms. The pipeline offers the flexibility to select from a range of assemblers—Canu, GoldRush, MetaFlye, Strainline, HaploDMF, iGDA, and RVHaplo—to best match the computational system or meet specific study requirements. It generates a comprehensive report in HTML format, detailing contigs/haplotype identities, and abundances. Additionally, the report includes protein sequence alignments of drug-targeted HIV-1 genes, alongside profiles of drug resistance and susceptibility associated with these genes. This is achieved by querying the assembled sequence against the Stanford University HIV Drug Resistance Database73–78 via the provided Sierra web service 2 API, as illustrated in Figure 12. The downstream analysis pipeline could also serve as a model for implementation with other viruses. The source code for building the containerized pipeline is available in a public code repository: https://github.com/STTLab/HIV-64148.\n\nThe pipeline comprises three main stages: a read quality control analysis of long-read FASTQ files, followed by assembly using either de novo or reference-based assemblers, and concluding with the identification of HIV-1 subtype and drug resistance analysis.\n\n\nDiscussion\n\nIn this study, we benchmarked seven selected long-read assemblers using both simulated and experimental long-read sequencing data of HIV-1 and other viruses on three computational systems to assess their performances. We demonstrated that only the assembler selection exerts a statistically significant impact on assembly time, with neither CPU nor memory affecting the process.79 Assembler selection also influences the size of assembled contigs. Additionally, a minimum read length is 2,000-nt, and the 4,000-nt read length results in higher quality assembled contigs. Further investigations revealed that Strainline, MetaFlye, and HaploDMF deliver successful genome assemblies of long-read sequencing data, exhibiting sequence heterogeneity, from both data simulations (i.e., multiple HIV-1 subtypes or CRFs) and available experimental sequencing data of HIV-1 and other viruses.\n\nAmong the de novo assemblers, Strainline provides satisfactory assemblies within a reasonable timeframe but requires a large amount of available memory, typically 64GB of RAM or more, exceeding the capacity of a standard computer. MetaFlye, though slower, is suitable for metagenomic sequencing data. GoldRush, the fastest assembler, lacks the capability to assemble alternative contigs and is thus unsuitable for metagenomic sequencing data. Canu efficiently allocates appropriate CPU and memory to each process, resulting in efficient CPU utilization and low memory consumption. Among the reference-based assemblers, iGDA and RVHaplo exhibit similar computational resource usage, with iGDA’s runtime comparable to Canu and GoldRush, and RVHaplo’s runtime comparable to Strainline. HaploDMF demonstrates considerably longer runtime due to heavy CPU usage during the assembly process, particularly in deep matrix factorization. However, utilizing a compatible GPU could mitigate both the runtime and CPU workload of HaploDMF.43,46 Overall, the variations in computational performance among the assemblers emphasize the critical importance of careful assembler selection for the success of analyses tailored to specific scientific projects.\n\nTo improve HIV-1 quasispecies profiling and genomic surveillance, it’s essential to discuss the advantages and disadvantages of selected assemblers for handling heterogeneous viral or microbial metagenome sequencing data. Canu and GoldRush are non-strain aware de novo assemblers, lacking the ability to distinguish strains within a sample. Using a reference genome may overcome this limitation, but it may not be suitable for genomic surveillance of emerging infectious diseases.80 MetaFlye is suitable for metagenomic assemblies, employing local k-mer distributions to establish a threshold for global k-mer counting, thus retaining less abundant sequencing reads.42 Strainline is designed for haplotype reconstruction of diverse viral genomes, treating clusters of long reads as unique scaffolds of different haplotypes and extending scaffolds through multiple iterations of the Overlap-Layout-Consensus (OLC) algorithm.28 However, this approach may be ineffective with equally long and highly similar reads, resulting in inaccurate estimates of haplotype numbers. For instance, Strainline has been observed to produce numerous duplicate contigs from HIV-1 group M subtype B from 2M HIV-1 mixture and 1M1C HIV-1 mixture.\n\nHigh-quality reference sequences are crucial for reference-based assembly. The assemblers use a probabilistic approach to align reads to the reference sequence and identify variants like single nucleotide variants (SNVs), insertions, and deletions for haplotype phasing. Both RVHaplo and HaploDMF employ an SNV frequency matrix for clustering reads of different haplotypes. However, RVHaplo relies on overlapping SNV sites, which may be inadequate for assembling closely related genomes. In contrast, HaploDMF uses a deep matrix factorization model with an adapted loss function to learn and correct latent features from each iteration of SNV detection,43 enhancing robustness against noise during SNV detection and enabling assembly of closely related strains. iGDA utilizes Adaptive-Nearest Neighbor clustering (ANN) to estimate the number of clusters and, like RVHaplo, uses overlapping SNVs and coverage for contig extension.44 In general, reference-based assemblers seem suitable only for quasispecies profiling.\n\nSince the choice of assembler significantly impacts genome assemblies, it is crucial to meet specific hardware system requirements tailored to match the quality of input data, genome sizes of the organisms of interest, and the algorithms used for genome assembly. However, the suitable system requirements have not been explicitly provided. Based on this benchmarking study, the following optimal computational requirements are suggested:\n\n• All assemblers should be executed in a Linux-based operating system.\n\n• A quad-core (4 cores) or higher CPU with x86 microarchitecture is recommended. CPUs with ARM-based microarchitecture (e.g., Apple Silicon) may require specific compiling or hand-tuned code with ARM instructions. Alternatively, a properly optimized code can achieve performance comparable to native x86 systems through dynamic binary translation (e.g., Rosetta).81\n\n• An 8 GB memory is sufficient for either viral or bacterial genome assembly, while a 16 GB RAM or higher is recommended for larger genomes, such as human or other mammals. It’s worth noting that this study utilized 96 GB memory for all assemblers.\n\nAn additional consideration is the balance between CPU and memory, as demonstrated by comparing a workstation with a generic home PC. An interesting finding is that despite both systems having the same number of CPU cores, the home PC took slightly longer, and its CPUs were more overutilized than those on the workstation. This disparity is attributed to the home PC needing to perform memory management more frequently, thereby adding load to the CPU and slowing down the process.82\n\nIn addition, the impact of virtualization and containerization layering during benchmarking was disregarded. Consequently, the wall clock time measured from a server was longer than that measured from a workstation desktop. It is possible that the software spends more time traversing layers of virtualization instead of running on a bare-metal environment (i.e., installed the software directly on the machine without containerization).83–85 Also worth mentioning, from a computer science perspective, it is expected that when evaluating the efficiency of algorithms used by each assembler, the concept of computational complexity should be applied to provide a better estimation of computational resource requirements and runtime on a more diverse set of data i.e. predicting computing time of dataset with different depth of coverage, read length and assembly complexity.79,86,87 While acknowledging this consideration, it is important to note that conducting a benchmark on real machines provides practical insights and actionable data on a specific use case, despite potential confounders introduced by the machine itself or from software virtualization.\n\nInsights on computational requirements for current long-read assemblers offer guidance for implementing edge computing in molecular surveillance and epidemiology in bioinformatics and virology. Long-read sequencing data of HIV-1 used for benchmarking indicates that a containerized HIV-64148 pipeline can function with sub-optimal computational infrastructures like workstation PCs or generic home PCs. This pipeline has the potential to support and expand HIV-1 surveillance networks, benefiting scientists, epidemiologists, healthcare providers, and people living with HIV.\n\nNot applicable.",
"appendix": "Data availability\n\nFigshare: HIV64148 TABLE_S6_HIV_Combinations_DataSimulation https://doi.org/10.6084/m9.figshare.25436023 54 all accession numbers are provided in Table S6\n\nFigshare: HIV64148 Template FASTA. https://doi.org/10.6084/m9.figshare.25435774 59\n\nThis archive contains reference sequences in FASTA format used as templates to simulated Oxford Nanopore reads Each template is located within a subfolder corresponding to its simulation number.\n\nFigshare: HIV64148 Simulated FASTQ. https://doi.org/10.6084/m9.figshare.25435822 60\n\nThis archive contains simulated reads from NanoSim with template FASTA. Each FASTQ is located within a subfolder corresponding to its simulation number.\n\nFigshare: HIV64148 QC Simulated FASTQ. https://doi.org/10.6084/m9.figshare.25435912 61\n\nThis archive contains output from NanoPlot describing characteristic of Simulated FASTQ files. Each HTML is located within a subfolder corresponding to its simulation number.\n\nFigshare: HIV64148 Results. https://doi.org/10.6084/m9.figshare.25435948 64\n\nThis archive contains genome assembly in FASTA, BLAST result in CSV, and HIV64148 report in HTML from 2M, 2C, 1M1C, and 2M1C HIV-1 mixtures, as well as the results from resource usage overtime (CPU, Memory) measured on 3 computational platforms over 7 tools in CSV format.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: HIV64148 Supplementary data. https://doi.org/10.6084/m9.figshare.25436023 54\n\nThis project contains the following extended data:\n\nFigure S1. The MetaQUAST assessment evaluated contigs from the assemblers processing four median read-length FASTQ inputs: (A) 1,000-nt, (B) 2,000-nt, (C) 3,000-nt, and (D) 4,000-nt ( Table 3). The x-axis displays the percentage sequence similarity obtained from a BLAST alignment with the corresponding reference genomes, while the y-axis represents the aligned length, indicating the longest continuous alignment between each contig and its reference genome. Dot sizes indicate the genome fraction (%Ref Aligned), calculated as the ratio of continuous aligned bases to the total reference genome length. Subplots above and beside each figure display histograms of the contig counts. Additionally, (E) shows the averaged genome fraction (%) of contigs from different long-read assembler pipelines. The complete data are available in Extended data, Table S9. 54\n\nFigure S2. The average completeness of major HIV-1 open reading frames (ORFs) of the contigs generated from the assemblers analyzing FASTQ inputs of 4 median read lengths: (A) 1,000-nt, (B) 2,000-nt, (C) 3,000-nt, or (D) 4,000-nt.\n\nFigure S3. Contig size distribution of all assemblers processing the simulated FASTQ inputs of the 4 HIV-1 mixtures.\n\nTable S1. A list of experimental data and additional information. N/A: not applicable.\n\nTable S2. A statistical summary of runtime measurements taken from an assembly phase of the pipelines.\n\nTable S3. The memory usage and maximum CPU utilization of each assembler on three computational systems. The benchmark utilized 100 samples of two HIV-1 group M mixture with 2,000x coverage and 8,000-nt median read length.\n\nTable S4. The genome statistics of contigs generated from (A) Full genome laboratory isolate NL4-3, (B) Mpox propagated in a CV-1 cell line and (C) Mpox from pustular lesion, and (D) SARS-CoV-2 data by the selected assemblers.\n\nTable S5. The genome statistics of contigs generated from (A) Polio virus, (B) Hepatitis C virus (HCV), and (C) ZIKA Virus (ZIKV) data by the selected assemblers.\n\nTable S6. HIV Combinations for Data Simulation (Excel)\n\nTable S7. Characteristics of Simulated Samples Readlength Experiment (Excel)\n\nTable S8. Characteristics of Simulated Samples HIV mixture Experiment (Excel)\n\nTable S9. An Assembly Evaluation of HIV-1 Read Length Experiment (Excel)\n\nTable S10. An Assembly Evaluation of HIV-1 Subtype Mixtures Experiment (Excel)\n\nTable S11. Subtypes Recall Rates (Excel)\n\nTable S12. REGA Subtyping (Excel)\n\nTable S13. 5’ Half Genomes of NL4-3 Alignment Statistics (Excel)\n\nTable S14. Other Viruses Alignment Statistics (Excel)\n\nAll high-resolution figures are available in https://doi.org/10.6084/m9.figshare.25436125.v1. 88\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank The ERAWAN HPC Service, Chiang Mai University, Thailand and The Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Thailand for their supports on computational resources and server. We would like to thank Support the Children Foundation, Chiang Mai, Thailand for financial support. We also would like to thank Yuphin Chromwinya and Somporn Sankonkit of The Immunology Lab, Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand for their administrative supports.\n\n\nReferences\n\nFrescura L, et al.: Achieving the 95 95 95 targets for all: A pathway to ending AIDS. 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}
|
[
{
"id": "297757",
"date": "05 Jul 2024",
"name": "Udom Sae-Ueng",
"expertise": [
"Reviewer Expertise Genome sequencing",
"Biotechnology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The title of the paper should focus on the performance of genome assemblers, as the selection of the assembler is the main factor in the pipeline.\n2. A significant number of mismatch errors occur in ONT sequencing data. The paper should address how to ensure that these errors will assemble into distinct vital haplotypes. It should also explain the dissimilarities between viral haplotypes in genomes and provide evidence of low-abundance haplotypes with read ratios in real-world situations for quasispecies analysis.\n3. If the ratio of reads used in the HIV mixture is the same (as shown in Table 3), but different genome assemblers are used (as shown in Figure 9), it results in different subtype recalls. This could be considered a bias of genome assemblers.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "297758",
"date": "08 Jul 2024",
"name": "Rujira Chaysiri",
"expertise": [
"Reviewer Expertise Management Technology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study conducted a comprehensive evaluation of seven genome assemblers, focusing on their performance across different computational platforms including a server, workstation PC, and standard PC. It was found that while the choice of platform did not significantly affect processing time, memory capacity was a critical factor, with some assemblers like Strainline requiring up to 64 GB of memory, rendering them unsuitable for standard PCs. Reference-based assemblers were generally faster and more consistent in their processing times compared to the variable performance of de novo assemblers. When assessing the minimum read lengths necessary for effective assembly, de novo assemblers needed a minimum read length (N50) of at least 2000 nt to function optimally, while reference-based assemblers were less affected by variations in read length and consistently produced assemblies close to the expected genome size of 8000 nt for HIV.\nIn evaluating the performance on mixed HIV-1 subtypes, de novo assemblers exhibited lower recovery rates for subtypes, indicating challenges in reconstructing all subtypes present in the input. Conversely, reference-based assemblers demonstrated better recovery of subtypes but tended to over-represent subtype B, used as the reference, and had higher rates of indels, pointing to a need for improved error correction. Further testing on real sequencing data from various viruses, including HIV-1, Mpox, SARS-CoV-2, Polio, Hepatitis C, and ZIKV, showcased the versatility and high-quality results of the selected assemblers across different viral genomes.\nAdditionally, the study detailed the development of a Docker container for the HIV-64148 pipeline, which incorporated the tested assemblers along with features for querying online databases to generate comprehensive reports on subtype composition, mutations, and drug resistance profiles. This containerized pipeline proved to be practical and accessible, capable of operating on both large servers and standard computers, thus enhancing its utility for genomic surveillance tasks in diverse settings.\nThe study provides a robust evaluation of genome assemblers, delivering valuable insights into their performance across different computational platforms and data sets. Its comprehensive nature, covering multiple aspects of assembler performance such as processing time, memory usage, and accuracy, is a significant strength. The inclusion of both simulated and real sequencing data from a variety of viruses highlights the practical applicability of the findings. Additionally, the development of a Docker container for the HIV-64148 pipeline enhances accessibility and usability, facilitating standardized genomic surveillance.\nHowever, the study also reveals some limitations. The high memory requirements for some assemblers, particularly Strainline, limit their usability on standard PCs, which could restrict their application in resource-limited environments. The tendency of reference-based assemblers to over-represent certain subtypes, such as subtype B in HIV, introduces bias that could affect the reliability of genomic studies. Furthermore, the higher indel rates observed in reference-based assemblies indicate a need for further refinement and error correction to improve the accuracy of the results.\nTo address these issues, future research should focus on optimizing memory usage for assemblers, making them more accessible on standard hardware. Developing methods to reduce reference bias in reference-based assemblers would enhance the reliability of their results. Additionally, implementing robust error correction algorithms could mitigate the higher indel rates observed in reference-based assemblies. Overall, while the study makes significant contributions to the field of genomics, addressing these limitations would further improve the effectiveness and applicability of genome assemblers.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "297759",
"date": "16 Jul 2024",
"name": "Sira Sriswasdi",
"expertise": [
"Reviewer Expertise molecular evolution of microorganisms",
"cancer transcriptomics",
"bioinformatics pipelines",
"machine learning and deep learning applications in biomedicine"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis work presents a comprehensive evaluation of de novo and reference-based assembly tools for Nanopore sequencing of genome mixtures of HIV and other viruses. Focus was placed on both the ability of the tools to capture the true viral subtypes and the computational resource requirement. The impact of basic quality filters, such as the minimum read length, was also explored. The best performing tools were selected based on simulated datasets of known HIV mixtures and their performance were evaluated on various actual and simulated datasets of multiple viruses. This work also provides a container resource that would be useful for non-experts to analyze their own data. However, there are some missing details and metrics that should be improved.\nMajor issues:\nSince a key limitation of Nanopore sequencing is the relatively high sequencing error (compared to other sequencing techniques), I think it is unrealistic to simulate the data with the --perfect mode which produces error-free reads. Furthermore, using error-free simulated data would underestimate the number of mismatches and overestimate the % similarity and correctness of the resulting contigs. On the same issue of sequencing error, I wonder if more attention should be placed on optimizing the polishing step (such as Luan T, et al., (2024) [Ref-1]). In the current work, only the default error handling algorithm associated with each tool was used. When evaluating the assembly characteristics of a mixture of subtypes, such as in Figure 6-8, and Figure S3, I think it is important to show the characteristics separately for each subtype so that it is clear whether all subtypes were assembled equally well. Or at least, please show the ranges of the values, not just the averages. In Table 5, I’m not sure how a Spearman correlation could be calculated with assembler selection, which is not an ordinal variable. When evaluating the assemblers using simulated mixture data, it is unclear what proportion of reads coming from each subtype was used. I think the impact of fractional abundance on the quality of the assembled genomes should be investigated. For the simulated HIV-1 mixture datasets in Table 3, please consider exploring different mixture ratios. For the pre-built simulated polio, zika, and HCV datasets, please indicate the mixture ratios to aid interpretation. There is no apparent tuning of the parameters for the assemblers. Since this is a benchmark paper that releases a container that will be used by the community, please consider more optimization of the pipeline.\nMinor issues:\nThe comparison between de novo assemblers and reference-based assemblers needs to be carefully explained because reference-based approaches, with reference genome as prior knowledge, would in general be able to produce longer contigs (as seen in Figure 5D-F versus Figure 5A-C, with Figure 5F as the extreme case where every contig from RVHaplo is almost the entire genome). It would be nice to explain these to the readers to prevent misinterpretation. Figures 10 and 11 could be improved by annotating each contig with the identity of each viral subtype in the mixture. This would allow the readers to understand (i) whether the correct contigs correspond to individual subtypes, (ii) which subtypes could not be recovered, and (iii) whether different methods misassemble the same subtypes. The pipeline seems to use a fixed HIV-1 reference NC_001802.1. Should the impact of the reference genome be explored? Should the reference genome be changeable in the released pipeline?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-556
|
https://f1000research.com/articles/11-1125/v1
|
29 Sep 22
|
{
"type": "Research Article",
"title": "Indoor air quality at the Arab governmental girls’ schools",
"authors": [
"Mahmoud Fathy Elsharkawy",
"Mohammed Tawfiq Aljassim",
"Abdulmalik Salman Alsaif",
"Sana Abdullah Alsulaiman",
"Mohammed Tawfiq Aljassim",
"Abdulmalik Salman Alsaif",
"Sana Abdullah Alsulaiman"
],
"abstract": "Background: A proper and adequate school environment is important for an effective learning process and maintaining the health of the students as they spend most of their time in schools. The physical school environment includes the physical structures; presence of chemicals and biological agents; and the surrounding environment, including air, water, and materials.\nThis study aimed to evaluate the indoor air quality (IAQ) in governmental girls’ schools in the Kingdom of Saudi Arabia (KSA).\nMethods: Seventeen girls’ schools were randomly selected in the Eastern Province of KSA. The indoor levels of PM10 and PM2.5, volatile organic compounds, CO, NO2, and CO2 were measured at different sites inside each school during four months of the year 2020. In addition, a pre-designed questionnaire was used to evaluate the safety preparedness in the same selected schools.\nResults: Levels of the six air pollutants were higher inside schools adjacent to roads with moderate traffic activity than schools with low and very low traffic activity. However, the mean level of CO2 inside the selected schools was higher than its outdoor level, suggesting the predominance of an indoor source of CO2. Levels of all measured air pollutants inside governmental constructed school buildings were higher than those inside the rental type.\nConclusion: The average levels of air pollutants inside the selected schools were much lower than their air quality guidelines (AQGs), while some CO2 and NO2 levels exceeded their AQGs at some schools.",
"keywords": [
"School environment",
"Indoor air quality",
"Air quality guidelines",
"Girl schools",
"Saudi Arabia"
],
"content": "Introduction\n\nA proper and adequate school environment is important for an effective learning process and maintaining the health of the students because they spend most of their daytime in schools.1–3 The effectiveness of the school depends on the quality of its environment and its ability to encourage students to learn effectively.4 The physical school environment includes the type of buildings, internal infrastructure, furniture, presence of chemicals or biological agents, location, and its surrounding environment, which includes air, water, and nearby land uses, roadways, and other sources of contaminants.5,6\n\nInside schools, there are many sources of air pollution such as the building materials, furnishing, wall paints, air conditioning system, cleaning products, and chemicals that are used in laboratory, as well as the transformation of pollutants from the outdoor sources and surrounding activities (e.g., traffic roads, industry, agricultural or commercial).7\n\nRecently, the “green school concept” has been strongly recommended for schools, particularly new ones. A green school is defined as “a school that creates a healthy environment conducive to learning through building the school with more daylighting, better ventilation, healthy green building materials (such as non-VOC (volatile organic compound) carpets and paints), and planting more trees and plant around and inside the school premises to reduce carbon emissions and other air pollutants”.8 Respiratory conditions, such as asthma, are a major cause of hospitalization and school absenteeism in several countries across the world.9,10 In addition, students and school personnel might experience emergency medical situations because of injuries or unexpected major accidents that occur in schools due to the absence of the recommended control measures or safety preparedness.11\n\nPoor indoor air quality (IAQ) may increase rates of asthma, allergies, and infectious respiratory diseases, affecting student performance.12,13 Poor IAQ, including inadequate ventilation, air pollutants, and very high or very low temperatures, is one of the factors that can contribute to absenteeism and reduce the performance of both students and staff if not adequately considered and controlled.14 Furthermore, schools in industrialized countries or high traffic areas are subjected to higher indoor air pollution than those in rural or low traffic ones. The good IAQ test is one of the key factors contributing to a healthy and productive learning environment.15–19\n\nAlthough several studies have been conducted to evaluate the IAQ and safety preparedness of the boys’ schools in KSA, no previous similar studies have been conducted for the girls’ schools. The major importance of this study is the formation of a database for environmental quality, particularly air quality, and safety preparedness inside the girls’ schools in KSA. In addition, this study will help in raising awareness of students and all school personnel concerning the safety and environmental health for prevention or reducing the exposure to the risks, accidents, and environmental disasters that have existed in the schools.\n\n\nMethods\n\nThis research was approved by the Institutional Review Board (IRB) of Imam Abdurrahman bin Faisal University No. IRB-PGS-2019-03-357 at 4/12/2019. Because our study was on the governmental schools, we obtained the necessary approvals from the Saudi Ministry of Education prior to the completion of this study. A general consent from the General Educational Administration in the Eastern Province of the Kingdom was obtained, which gave us the freedom to enter any school without the need to obtain its separate consent. Our role was to coordinate with the selected school before going to conduct the measurements and collect the required data, which was usually done by a phone call or a quick visit.\n\nA cross-sectional descriptive study was conducted for measuring the levels of air pollutants in 17 selected schools at Al-Qatif governorate during a period of four months (January – April 2020). Al-Qatif is an urban area with an ancient green coastal oasis rich in oil, dates, fruits, and fish, surrounded by a jungle of palm trees. The climate of Al-Qatif is hot and dry with high humidity and temperatures in summer and cold in winter. Its population is 524,182 people, according to the statistics of 2017.20 The traffic activity in Al-Qatif is not congested compared to other cities of the Eastern Province of KSA.\n\nGenerally, a good maximum sample size is usually around 10% of the total population. To increase the credibility of our work, we selected seventeen girls’ schools were selected. This number represents nearly 20% of the KSA governmental girls’ schools in Al-Qatif governorate. Selection of this number of schools was based on a completely randomized design (CRD), which is considered one where the treatments are assigned completely at random so that each experimental unit has the same chance of receiving any one treatment. The process of random allocation may be done in several ways. To select our studied schools, we were using drawing lots through giving numbers for all schools (80 schools) and then drawing 17 number randomly. The inclusion criteria were the KSA governmental girls’ schools in Al-Qatif governorate, while the exclusion ones were the governmental boys’ schools and private boys’ and girls’ schools in the same governorate. Details of the selected schools, including the type of school building, outside traffic activity, number of classrooms and floors, and the total number of students and staff, are presented in Table 1.\n\nTo study the effect of traffic emissions on the IAQ level outside schools in this study, the traffic activity was classified into three categories based on the average number of cars that were moving per hour.21 The first category is “very low traffic activity” where the number of cars was <50 cars per hour. The second category is “low traffic activity” where the number of cars ranged from 50 to <200 cars per hour. The third category is “moderate traffic activity” where the number of cars ranged from 200 to <500 cars per hour.\n\nInside each school, several locations were selected for monitoring of the air quality measurements. These locations represented two classrooms from each floor, the playground, the library, and the laboratory. Inside each one of these rooms, two sites were selected; at the front and back of the room. The total number of selected locations ranged between 14 and 22 based on the number of floors inside each school. Levels of particulate matter less than 2.5 and 10 microns in size (PM10 and PM2.5, respectively), volatile organic compounds (VOCs), carbon monoxide (CO), carbon dioxide (CO2), and nitrogen dioxide (NO2) were monitored inside each one of the selected locations at each school. In addition, temperature and relative humidity (RH) percent were simultaneously recorded for all locations.\n\nLevels of PM10 and PM2.5 were determined by the Handheld Portable Particle Counter instrument (M&A Instruments Inc). It can measure directly PM10 and PM2.5 in a very wide range of concentrations (0-500 μg/m3) with a high degree of accuracy, because it automatically monitors the sensor status, out of flow calibration (> 5%). In addition, it has external digital temperature and humidity sensors to assure accurate measurement.\n\nGenerally, levels of gaseous air pollutants are measured by direct-reading instruments based on different techniques such as infrared, ultraviolet, or electrochemical techniques. During this study, all selected gases were directly measured by the Gray Wolf’s Direct Sense® mobile PC based products, Advanced Sense™ meters, and Wolf Pack™ area monitor. The Gray Wolf monitor is composed of multi-gas detectors. It is a one to five-sensor gas detector equipped with a wireless radio frequency modem which allows the unit to communicate and transmit readings and other information on a real-time basis with a remotely located base controller. In stand-alone operation, it is a rugged, weather-resistant, portable monitor that can run over 24 hours on either rechargeable lithium-ion or alkaline batteries. In addition, it has sensors from measuring the ambient temperature degree and RH percent.\n\nAt each measuring site inside the school, a reading for each selected pollutant was recorded every 30 minutes during a total of 2 hours period. The gaseous pollutants were measured directly in parts per million (ppm), while levels of PM10 and PM2.5 were recorded directly in microgram of dust per cubic meter of air (μg/m3). Levels of the selected air pollutants were measured at least three times during the morning period of different weekdays where students and staff are present in their classrooms. The total number of IAQ readings nearly ranged between 30 to 50 for each pollutant for each school.\n\nResults of IAQ monitoring were analyzed statistically using professional programs such as the Statistical Package for the Social Sciences (SPSS) version 23 and Excel Software 2016. Descriptive statistics, ANOVA test and Pearson correlation coefficient were used for comparing levels of the studied air pollutants at different sites inside and outside the selected schools. The statistical significance of p-value <0.05 was used for all tests of significance.\n\n\nResults\n\nAlthough about five measurements were conducted for each type of pollutant at each selected site inside the schools, we only considered the most two stable measurements in our analysis.63 All selected schools were eligible for the study and no problems or constrains were faced during the study. Table 2 represents the mean levels and standard deviations (SD) of PM10, PM2.5, CO, CO2, VOCs, and NO2, respectively, at all selected schools. The highest mean levels ± standard deviation (S.D) for PM10 and PM2.5 were (29.3 ± 6.5 μg/m) and (16.3 ± 1.3 μg/m), where the lowest mean levels were (12.0 ± 2.2 μg/m) and (7.5 ± 1.3 μg/m) respectively. The highest mean levels of CO2, CO, NO2, and VOCs were (1488 ± 533.3 ppm), (3.85 ± 0.66 ppm), (1.32 ± 0.2 ppm) and (0.34 ± 0.47 ppm) respectively, while the lowest mean levels were (523.0 ± 85.3 ppm), (1.2 ± 0.1 ppm), (0 ppm) and (0 ppm) respectively.\n\nFigures 1 and 2 illustrate the correlation between the level of air pollutants inside the selected schools and the traffic activity outside the schools. The highest levels (mean ± standard deviation) of PM10 (24.2 ± 4.6 μg/m3), PM2.5 (14.2 ± 1.8 μg/m3), CO (2.65 ± 0.99 ppm), CO2 (995.9 ± 292.6 ppm), VOCs (0.18 ± 0.14 ppm), and NO2 (0.74 ± 0.44 ppm) were found inside schools surrounded by streets with moderate activity, followed by those located adjacent to the streets with low traffic activity, while the lowest levels were found inside the schools surrounded by streets with very low activity. On the contrary, the mean level of CO2 in schools adjacent to the very low traffic street (627.5 ± 63.9 ppm) was slightly higher than those at the low traffic street (593.9 ± 69.8 ppm). To study the significance of this factor, the one-way ANOVA test was applied for the data, as presented in Table 3 which indicates that significant differences (p < 0.05) were found between schools located at moderate streets and those in low and very low ones for four pollutants, except for CO and VOCs.\n\n* The mean difference is significant at the 0.05 level.\n\nFigures 3 and 4 indicate the average concentrations of outdoor air pollutants compared with those inside schools. Except for CO2, the average concentrations of all pollutants outside schools were slightly higher or nearly the same as the indoor levels, with no statistical differences for all pollutants (p > 0.05). On contrary, the mean level of CO2 inside the selected schools (858.7 ± 436.7 ppm) was higher than its outdoor level (475.9 ± 116.8 ppm) with a very strong statistical difference (p = 0).\n\nBuildings of the selected schools were divided into two types: governmental constructed buildings (which were 14 schools) and governmental rental buildings (3 schools). The average levels of air pollutants inside each type were calculated and illustrated in Figures 5 and 6. The mean concentrations of studied pollutants inside the governmental constructed schools’ buildings (PM10 [20.1 ± 7.1 μg/m3], PM2.5 [12.5 ± 3.3 μg/m3], CO [2.95 ± 1.33 ppm], NO2 [0.54 ± 0.58 ppm], CO2 [858 ± 440.8 ppm] and VOCs [0.16 ± 0.15 ppm]), were higher than those inside the rental type (17 ± 3.9 μg/m3, 10.8 ± 2.9 μg/m3, 1.98 ± 1.03, 0.29 ± 0.20, 628 ± 187 and 0 ± 0 ppm respectively). The independent t-test values (Table 4) indicated a statistically significant difference for CO, CO2, and NO2 levels (p < 0.05) between governmental constructed and rental school buildings, while there is no significance for the other pollutants. The independent t-test values (Table 4) indicated a statistically significant difference for CO, CO2, and NO2 levels (p < 0.05) between governmental constructed and rental school buildings, while there is no significance for the other pollutants.\n\n* The mean difference is significant at the 0.05 level.\n\nSome of the studied classrooms for this study were located at the ground level (ground floor), while the others were located on the upper floors. The average level of each air pollutant inside all classrooms of the same floor was calculated and presented in Figures 7 and 8.\n\nHigh levels of CO2 (˃ 1000 ppm) were found in schools of both large and small areas, while low levels (< 500 ppm) were also recorded in schools with both large and small areas. Using the Pearson correlation tests indicated that there is a negative very weak correlation between the total volume of classrooms and levels of CO2 with no significant correlation (P > 0.05).\n\nFigure 9 represents the relation between levels of CO2 and the number of students in classrooms, where no correlation was found between these two variables. For example, lower level of CO2 (703.5 ppm) was found inside classrooms occupied with high number of students (39 students), while higher level of CO2 (1382.7 ppm) was obtained inside classrooms occupied with lower number (27 students).\n\nThe Pearson correlation coefficient was used to study the correlation between concentrations of the studied pollutants and degree of temperature in all selected classrooms, as shown in Table 5. There is a very weak positive correlation between the degree of temperatures and concentrations of both PM10 and VOCs, while there is a very weak negative correlation with levels of the other pollutants without statistical significance for all pollutants (p ˃ 0.05).\n\n* The mean difference is significant at the 0.05 level (RH: relative humidity).\n\n\nDiscussion\n\nOccupants of an indoor environment, including homes, workplaces, and schools are exposed to a mixture of pollutants with known health effects, such as VOCs, CO, PM10 and PM2.5, and other gases. The contribution and concentration of these pollutants are influenced by various sources, for example, indoor sources, outdoor air pollution and climate, occupant’s behavior, and building material.22,23 In the present study, most of these factors were studied in the selected schools to determine the factor that mostly affects school and classroom IAQ levels.\n\nMotor vehicles emit many pollutants that can cause adverse health effects.24 Children are exposed to pollutants in school- related spaces for many hours of the day. In general, schools in downtown areas are exposed to pollutants from traffic emissions higher than those located in low traffic areas.25 Evidently, the levels of the six studied air pollutants inside schools adjacent to roads with moderate traffic activity were higher than those with low and very low traffic activity (as shown in Figures 1 and 2). This indicates that the outdoor sources of air pollution (particularly the traffic emission) have direct and considerable effects on the indoor level of air quality. On the contrary, the slightly higher mean level of CO2 in schools adjacent to the very low traffic street compared to those at the low traffic street, suggests that there is another source of CO2 inside the school itself, which will be discussed later.\n\nTo confirm the above results, the average concentrations of outdoor air pollutants were compared with those inside schools as (shown in Figures 3 and 4). Except for CO2, the average concentrations of all pollutants outside schools were slightly higher or nearly the same as the indoor levels, with no statistical differences for all pollutants (p > 0.05). This suggests that outdoor traffic activities are the main source of these pollutants inside schools and any indoor environments, such as homes. On the contrary, the higher mean level of CO2 inside the selected schools than its outdoor level suggests the predominance of the indoor source of this gas.\n\nThe findings of this study are comparable with similar studies inside and outside KSA. For example, a study conducted by Elsharkawy in several boys’ schools in Dammam and Khobar cities of the Eastern Province of KSA revealed that the highest levels of the same air pollutants inside classrooms that were located directly on the moderate traffic streets compared with low or very low traffic activity ones. It was also concluded that the average concentrations of studied air pollutants outside schools were slightly higher than those indoor, except CO2.26 In Barcelona (Spain), impact of the outdoor traffic-related air pollutants was studied in 39 schools in an urban area with less traffic count and a heavy traffic area. The result of this study indicated that the concentration of air pollutants measured was higher in schools with heavy traffic activity, due to the higher influence of emission sources in the outdoor environment.27 A recent study in Beijing (China) revealed that the air quality inside the school classrooms was greatly affected by the outdoor levels of air pollutants and the level of both PM2.5 and PM10 at most schools had adverse respiratory effects on children.28 Another study was conducted in Coimbra, Portugal, indicated that the levels of CO2 in the indoor air in many schools were higher than those of outdoor air and most of these levels were above the recommended air quality guideline, particularly in the fall and winter seasons.29 Many other studies conducted worldwide have revealed that in the absence of indoor sources of air pollutants, their concentrations indoors will be close to or lower than those outdoor because air pollution in the outdoor atmosphere is likely to be present indoors.30\n\nThe independent t-test values indicated a statistically significant difference for CO, CO2, and NO2 levels (p < 0.05) between governmental constructed and rental school buildings, while there is no significance for the other pollutants. This could be attributed to the significant difference in the design of the two building types. School sizes, number of classrooms, and number of occupants in government school buildings are usually higher than the rental type. In addition, most governmental constructed buildings are located at or near traffic roads contrary to rental buildings that are usually located inside residential areas. Therefore, levels of air pollution inside the governmental constructed buildings were logically higher than rental buildings.\n\nReportedly, the above conclusion is the same in boys’ schools in KSA.26 A similar study was conducted in 16 urban schools in the mid-Atlantic region in the US to determine the effect of the schools’ building type in the IAQ level. This study revealed that high concentrations of NO2 and CO2 were observed in temporary buildings schools compared to the permanent buildings’ schools.31\n\nThe location of the classroom inside any school may have an important role in the IAQ level inside it. This includes the floor number in which the classroom was located and the outside area which surrounds the classroom. Some of the studied classrooms for this study were located at the ground level (ground floor), while the others were located on the upper floors. The mean concentrations of pollutants inside classrooms that are located were higher than those of the upper floors without any significant differences for all pollutants as shown by the independent t-test analysis. Due to the dispersion process, the concentration of air pollutants decreases with increasing the horizontal and vertical distances, and for this reason, levels of pollutants on the upper floor were the lowest. In addition, the ground floor is closer to the traffic activity outside the school than the upper floor, which confirms the previous conclusion of the direct effect of the outside traffic activity on the IAQ inside schools and their classrooms. The indoor sources play an important role in the distribution of air pollutants in the school rooms. For instance, dust in the ground can be moved to the ambient air by the movement and playing of students in the playground, and hence, rooms on the ground floor can receive an amount of dust higher than the upper floors. Levels of the airborne particles strongly depend on particle size. The larger the particles are in terms of diameter, the heavier they are, and the more easily they can be deposited on the lower floor.32\n\nSimilar results were obtained from many studies across the world. For instance, a study conducted in Upper Silesia, Poland, in 2015 revealed that the highest average concentrations of PM were obtained in all buildings and classrooms during occupancy periods located on the ground floor. The mean concentrations of PM10 and PM2.5 in classrooms of the ground floor were 166.12 and 125.69 μg/m3, respectively, while their levels on the first floor were 81.49 and 67.65 μg/m3, respectively.32 In Dammam and Khobar cities in KSA, the mean concentrations of pollutants inside classrooms that are located at the first floor were higher than those of the upper floors in most schools.26\n\nGenerally, the use of CO2 as a marker for indoor air quality is widely used, and its level inside a building is usually used as indicator for the controlled ventilation.33,34 To study the efficiency of ventilation rate inside classrooms, levels of CO2 were measured and linked with several factors during this study: the area of windows and doors related to the area of the classrooms and the number of students.\n\nIt was found that there was not any relation between the area of the classroom and concentration of CO2.This can be related to many factors such as the number of students inside the classrooms, ventilation rate, indoor exchange rate, and room design (e.g., floor area and room volume).35 Similarly, there was no correlation between the total area of all windows and doors inside each classroom and level of CO2 (ppm). Natural ventilation is the intentional flow of outdoor air through an enclosure under the influence of wind and thermal pressures through controllable openings. Natural ventilations driven by pressure differences across the openings caused by ambient pressure and temperature differences between different openings within a unit.36 On the other hand, the mechanical ventilation systems circulate fresh air using ducts and fans, rather than relying on airflow through small holes or cracks in a home’s walls, roof, or windows. In many cases, mechanical ventilation is very important to provide fresh air and prevent or reduce levels of moisture, odors, and other pollutants that can build up inside a home.37 Unlike other Arab countries, such as Egypt, most of the buildings inside the KSA are completely dependent on the mechanical ventilation system or air conditioning system, despite the presence of windows and other openings inside these buildings. The main cause for this phenomenon is the climatic characteristic and the presence of high levels of dust in the environment of most KSA cities. For this reason, in KSA, most of the windows in schools and classrooms are completely closed, and they are used only for transmitting the sunlight, but not for natural ventilation. It is clear from the results of this study that there was no correlation between the number or volume of windows and the level of CO2 gas inside the selected classrooms, which indicates that levels of air pollutants inside the classroom depend mainly on the efficiency of mechanical and not natural ventilation systems.\n\nBecause the human body is considered a source of CO2 in the atmosphere as the result of the expiration process, a correlation between numbers of students and levels of this gas was studied inside each classroom. Unexpectedly, no correlation was found between number of students and level of CO2 in the classrooms, as shown in Figure 9. This may be related to the ventilation rate and air conditioning system, which was applied inside each classroom. These factors are considered one of the most important control techniques that are used for improving the IAQ inside any closed room. The low levels of CO2 with the high number of students in some classrooms can be explained by the good ventilation system and rate inside these classrooms.\n\nMany previous studies revealed that the high levels of CO2 in schools are correlated with high occupancy or inadequate ventilation. For example, a study conducted in the UK indicated that an elevated level of CO2 rose quickly to 3000– 4500 ppm when windows were left closed in the absence of other means of providing air, such as conditioning.38 Another study conducted in Victoria, Australia, during the winter periods indicated that a high level of CO2 (2700 ppm) was recorded in typical occupied and non-ventilated rooms.39\n\nTemperature is one of the basic IAQ measurements that has a direct impact on perceived comfort and in turn, concentration, and productivity. According to the American Society of Heating, Refrigerating and Air Conditioning Engineers Standard (ASHRAE), the recommended temperature ranges perceived as “comfortable” are 73°F –79°F (22.8°C–26.1°C) in the summer and 68°F –74.5°F (20.0°C–23.6°C) in the winter.40 If the air temperature is too hot or too cold, this will make the occupants uncomfortable, and it would probably make them use only half of their mind and effort in concentrating on their job while the other half is concentrating on the uncomfortable air quality.41 During this study, the temperature degrees inside classrooms of all schools ranged between 20.1°C–25.5°C, which is consistent with the recommended values. Results of our study are comparable to a study conducted in south-western school districts in the US to monitor the temperature inside the classrooms with closed windows and doors and ventilation rates operated by mechanical ventilation. It was concluded that there was no statistically significant correlation between indoor temperature and CO2, while there was only a weak positive correlation between indoor and outdoor average temperature (Spearman correlation.243, p < 0.05) indicating that indoor temperature is relatively independent of the outdoor conditions.42\n\nThe IAQ and thermal comfort also depend greatly on the humidity level, which enhances the microbial growth, increases heat index, and the level of the fine airborne particles. For example, the human body feels warmer in humid conditions, and high temperatures affect and worsen people’s health. ASHRAE recommends the acceptable range of RH is 30%– 60% for all seasons.43 Relative humidity below 30% is unacceptable because it can cause irritation and could contribute to symptoms such as eye and nose irritation, headache, cough, dry facial skin, and difficulties in breathing. RH above 60% may support the growth of pathogenic or allergenic microorganisms and more contribute to the impact of heat index.44 In the current study, the range of RH percentage was (from 29 % to 90.1%). The Pearson correlation coefficient test indicated that except VOCs, there was a weak to moderate positive correlation between RH and all pollutants with a strong statistical significance difference (p = 0). As for VOCs, there was a very weak negative correlation without statistical significance for all pollutants (p ˃ 0.05), as shown in Table 4. In Finland, low RH (21%–23%) was recorded inside all classrooms of six public schools.45\n\nMany air pollutants are emitted in the indoor atmosphere from the furnishings, where several materials are used such as wood, textile, plastics and metals. For example, VOCs are emitted from paints, solvents, and color-painted wood.46 Most of these products are bonded with urea-formaldehyde adhesive, which leads to off-gassing of formaldehyde due to chemical reactions during their service lives.47 Inside schools, there is much furniture of different types including classroom desks, chairs, cabinets, tables, and others. One of the major sources that contributed to the build-up of VOCs indoor environment is indoor emissions from furniture and building materials.48 To study the effect of furnishing products in schools, the level of VOCs was correlated with the amount of furniture at each measuring site inside the school (classrooms, teachers’ rooms, and administrative offices). Generally, levels of measured VOCs were small (0.1–1.05 mg/m3) without any correlation with the number of furniture, which means that the furnishing products have no measurable participation in these levels. The Pearson correlation test indicated that there was a very weak negative correlation between the number of furniture and levels of VOCs. A similar study was conducted in 144 classrooms at 37 recently constructed or renovated schools in the US. The median concentration among the most observed VOCs inside classrooms (benzene and toluene) were 0.3 and 0.7 mg/m3, respectively, and most mean concentrations of VOCs were below 5 mg/m349 which is inconsistent with this present study.\n\nIt is very important to compare the results of the IAQ studies with the Air Quality Guidelines (AQGs) that represent acceptable limits for the air pollutants recommended by the governmental authorities of each country.50 Unfortunately, there are no IAQ guidelines in the Saudi Environmental Law. Results of this study were compared with the indoor AQGs suggested by different international scientific agencies (Table 6), such as the U.S. Environmental Protection Agency (USEPA), the WHO, the National Institute for Occupational Safety and Health (NIOSH), the Occupational Health and Safety Administration (OSHA), the American Conference of Governmental Industrial Hygienists (ACGIH) and ASHRAE (NAAQS/EPA, 2006; OSHA; NIOSH, 1992; ACGIH, 2001; ASHRAE, 2010).44,51–55 As shown in Table 7, comparing the results of this study with their AQGs indicated that the average levels of air pollutants inside the studied schools were much lower than their AQGs, while some levels of CO2 and NO2 were exceeding their AQGs at some schools.\n\n* Levels of air pollutants that are exceeded the recommended AQG.\n\nMeasurements of CO2 concentrations inside 60 schools in Croatia revealed that all recorded levels were higher than the recommended air quality guidelines (1938 mg/m3), where the levels ranged between 2771 and 7763 mg/m3 due to the poor ventilation in the classrooms, particularly in the hot months.56 In Wellington, the capital of New Zealand, a study was done to analyse the concentration and sources of air pollution at an urban primary school (5–11 years), where the indoor PM10 mean concentrations during the school day (30.1 μg/m3) were significantly (p < 0.001) higher than the mean outdoor concentrations (8.9 μg/m3), and the primary driver of indoor PM2.5 was from the infiltration of outdoor pollutants from the motor vehicle emissions.57\n\nIn Kuwait, a study was conducted to assess IAQ during a complete school calendar year and covered all climatic seasons. IAQ parameters were examined to assess pollutant levels in Kuwait schools in multiple settings (classrooms, painting rooms, computer labs, science rooms, teachers’ rooms, and roofs). The study revealed that high concentrations of VOCs and dust were present in most schools.58\n\nAnother study was done in five primary schools in the Maltese Islands. The mean indoor PM2.5 level of 17.78 μg/m3 and CO (9.11 ppm) exceeded the thresholds set by the WHO.59 The Park study showed the effects of outdoor temperature on the exam day on student performance, using 4.6 million high school exit tests in New York. The author finds that students taking an exam on a day with temperatures higher than 32°C scores up to 14% lower.60\n\nAnother study was done in the primary schools of six French cities to study the poor air quality in classrooms, where the mean concentration of NO2 has exceeded the WHO guidelines.61 In 18 schools located in urban, industrial, and rural areas in Central–Southern Spain, the NO2 concentrations were higher in an urban area with mean ranging between (17.6 and 113.0 mg/m3) and followed by schools located in industrial or near highway means between (12.9 and 32.1 mg/m3) than those in rural with mean ranging between (6.30 and 13.9 mg/m3).62\n\nThe Arab governmental schools are usually located in areas of heavy air pollution sources (e.g., congested traffic and industry). Hence, the air pollution level inside these schools is expected to be high. Generally, there is lack of research in this field. The major importance of this study is the formation of a database for air quality, inside Saudi governmental schools as a representative to other Arab countries. In addition, this study will help in raising awareness of students and all school personnel concerning the environmental health, especially maintaining good air quality.\n\nThe main limitation of this study was the number of schools. It was planned to monitor a higher number, but unfortunately this was limited due to the coronavirus disease 2019 (COVID-19) pandemic where the learning process has completely shifted to distance education (online). The nature of this study requires the daily visiting of schools to conduct the measurements.\n\n\nConclusion\n\nLevels of the six studied air pollutants inside schools adjacent to roads with moderate traffic activity were higher than those with low and very low traffic activity, indicating that outdoor sources of air pollution (particularly traffic emissions) have direct and considerable effects on the IAQ level. In addition, except for CO2, the mean levels of other pollutants outside schools were slightly higher or nearly the same as the indoor levels, confirming that the outdoor traffic activity is the main source of these pollutants inside schools or any indoor environments. On the contrary, the mean level of CO2 inside the studied schools was higher than its outdoor level, suggesting the predominance of the indoor source of this gas.\n\nDue to the dispersion process, the concentration of air pollutants decreases with increasing the horizontal and vertical distances, and thus levels of pollutants on the upper floors were lower than those on the ground floors. In addition, the ground floor is closer to the traffic activity outside the school than the upper floor, which supports the previous conclusion of the direct effect of outside traffic activity on the IAQ level inside schools and their classrooms. Levels of air pollutants inside all studied schools were much lower than their AQGs, while some CO2 and NO2 levels exceeded their AQGs in some schools.\n\n\nData availability\n\nFigshare: Full data.xlsx. https://doi.org/10.6084/m9.figshare.19403078.v1.63\n\nThe file contains the following underlying data:\n\n• Full details of the selected schools for this study\n\n• Monitoring sites inside the selected schools\n\n• Levels of air pollutants at each selected site\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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Publisher Full Text\n\nMenghi R, Ceccacci S, Papetti A, et al.: A method to estimate the total VOC emission of furniture products. Procedia Manuf. 2018; 21: 486–493. Publisher Full Text\n\nAl-Awadi L: Assessment of indoor levels of volatile organic compounds and carbon dioxide in schools in Kuwait. JA&WMA. 2017; 68(1): 54–72.\n\nZhong L, Su FC, Batterman S: Volatile organic compounds (VOCs) in conventional and high-performance school buildings in the U.S. Int J Environ Res Public Health. 2017; 14(1): 100. Publisher Full Text PubMed Abstract\n\nCharles KE, Magee RJ, Won DY, et al.: Indoor air quality guidelines and standards: Final report 5.1. National Research Council Canada;2005.\n\nNAAQS/EPA-U.S. Environmental Protection Agency: Code of Federal Regulations, Title 40 CFR, Part50 National Ambient Air Quality Standards. 2006.\n\nOccupational Safety and Health Administration: OSHA-U.S. Department of Labor, Code of Federal Regulations, 2006, Title 29, Part 1910.1000–1910.1450.\n\nNational Institute for Occupational Safety and Health: NIOSH recommendations for occupational safety and health – Compendium of policy documents and statements. Diane Publishing;1992.\n\nACGIH (American Conference of Governmental Industrial Hygienists): Threshold limit values for chemical substances and physical agents and biological exposure indices.2001.\n\nWHO: Air quality guidelines for Europe. 2nd Ed.Copenhagen:World Health Organization Regional Publications, European Series No. 91. World Health Organization, Regional Office for Europe;2000. 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Accessed January 29, 2021.Reference Source\n\nAnnesi-Maesano I, Hulin M, Lavaud F, et al.: Poor air quality in classrooms related to asthma and rhinitis in primary schoolchildren of the French 6 Cities Study. Thorax. 2012; 67(8): 682–688. Publisher Full Text PubMed Abstract\n\nVillanueva F, Tapiac A, Lara S, et al.: Indoor and outdoor air concentrations of volatile organic compounds and NO2 in schools of urban, industrial and rural areas in Central-Southern Spain. Sci Total Environ. 2018; 622-623: 222–235. Publisher Full Text PubMed Abstract\n\nElsharkawy M: Full data.xlsx. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "266512",
"date": "25 Apr 2024",
"name": "Eltigani Omer",
"expertise": [
"Reviewer Expertise Public Health",
"Environmental Epidemiology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nClearly and accurately presented and it cites the current literature and the references were appropriate, so the authors were able to fully address the topic.\n\nEthically it was approved by the Institutional Review Board (IRB) of Imam Abdurrahman bin Faisal University No. IRB-PGS-2019-03-357 at 4/12/2019.\n\nMore detail is needed about measuring the levels of air pollutants and method followed to select the study units (schools).\n\nPlease provide evidence that the traffic activity in Al-Qatif is not congested compared to other cities of the Eastern Province of KSA as you reported?\n\nThe average number of cars that moving per hour varies at different times; please explore how you avoid this potential error?\n\nExplore the method followed to select measuring sites inside the school.\n\nThe results were well presented and appropriate statistical measures were used to determine the significance of association between study variables.\n\nThe various indoor sources that influenced the contribution and concentration of pollutants need more exploring.\n\nSome references listed below are very old and need to be updated:\n\nBorse NN, Gilchrist J, Dellinger AM, et al.: CDC childhood injury report: Patterns of unintentional injuries among 0- to 19-year-olds in the United States, 2000–2006. J Fam Community Med. 2008; 32(2): 189. Baldauf R, Watkins N, Heist D, et al.: Near-road air quality monitoring: Factors affecting network design and interpretation of data. Air Qual Atmos Health. 2009; 2: 1–9. Publisher Full Text Leong ST, Muttamara S, Laortanakul P: Preliminary study of relationship between outdoor and indoor air pollutant concentrations at Bangkok’s major streets. Sci Technol Asia. 2003; 8(3): 29–39. Accessed January 27, 2021.Reference Source NAAQS/EPA-U.S. Environmental Protection Agency: Code of Federal Regulations, Title 40 CFR, Part50 National Ambient Air Quality Standards. 2006. National Institute for Occupational Safety and Health: NIOSH recommendations for occupational safety and health – Compendium of policy documents and statements. Diane Publishing;1992. ACGIH (American Conference of Governmental Industrial Hygienists): Threshold limit values for chemical substances and physical agents and biological exposure indices.2001. Elsharkawy M: Full data.xlsx. figshare. [Dataset].2022. Publisher Full Text\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "261827",
"date": "21 May 2024",
"name": "Adel Zakaria",
"expertise": [
"Reviewer Expertise Occupational Hygiene",
"Safety",
"Air Pollution Control"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Sir Greetings to you from Alexandria, Thank you for allowing me to review this article. I apologize, I won't summarize the article. I read it critically, and found some minor mistakes and some serious mistakes. I will start with the minor ones then the serious ones. I will follow a systematic approach in my review. General overview: The article is a good one, written in a sound language, with minimal spelling or grammar mistakes. Each section of the research paper is covering its subject properly, the methodology and instruments used is quite proper for sampling and monitoring of air pollutants. the results is presented in a good manner in tables and figures, and discussion is detailed and succeeded in interpreting the results and supported it with recent literature. The references is more than quite enough and more than half of them are considered recent. However, it seems that this paper is extracted from a thesis, which will be clarified later. Minor Mistakes: Under the title\" Monitoring of IAQ\" in the sixth line (PM10 and PM2.5 respectively) the order should be reversed. In paragraph after Fig. 4, the sixth line statement starting by\" The independent t-test.....\" is repeated in the eighth line. The comments on Table 5 didn't contain any mention to RH, despite it is mentioned in the table. Under the title \"effect of Ventilation\" second paragraph is too long and discussed in details definition of natural and mechanical ventilation and the difference between them. Its better to be summarized. The third paragraph is not convincing to interpret the unrelated CO2 concentration with number of students in the classroom. It needs to be interpreted. The paragraph after Table 7 the gas concentration is mentioned in mg/m3 its better to convert it to ppm like the present paper. Under the title \" Strengths and limitations of the study\" in the fourth line \"as a representative of to other Arab countries\" it is better to be Gulf countries. Serious Mistakes: The Title, I believe that Its better to add \": Al-Qatif-KSA\" to the title, at the end of it. Abstract, the last statement in the Methods,\" a predesigned questionnaire was used to evaluate the safety preparedness in the same selected schools\" There was no mention at all to the questionnaire or its results in the entire paper, emphasizing that the present paper extracted from a thesis., also at the end of introduction the last statement there is a mention of safety. However, there is no mention in Methodology to any safety preparedness plan. Results: In table 6, it is not valid to put limits of NIOSH and ACGIH in this table of AQG since their limits is designated to working environment. Discussion:Under the title\" Effect of the school building type on the IAQ levels\" The reason that the levels of increased levels of pollutants in governmental schools are greater than those in the rented ones is not clear. The authors mentioned theoretical reasons with no relation to that difference. Also they combined another parameter, which is the location nearby high or low traffic areas which confuses the readers. Also the American reference at the third paragraph didn't offer an explanation since it was comparing between temporary and permanent schools. Under the title\"Effect of temperature& relative humidity on IAQ levels\", the authors discussed the effect of temperature and RH separately, however its better to consider the \"effective temperature\" Yet, these are the most important comments on the present paper, on correction of these comments, I believe that the paper will be better.\nDr. Adel Zakaria Prof. of Occupational Hygiene and Air Pollution Alexandria University Alexandria- Egypt\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11638",
"date": "25 Jun 2024",
"name": "Mahmoud Elsharkawy",
"role": "Author Response",
"response": "Dear Reviewer First, I would like to greatly thank you for your valuable comments that improved the manuscript and gave it more strength and reliability. We considered all your comments in the revised manuscript as follows: Minor Mistakes: Under the title\" Monitoring of IAQ\" in the sixth line (PM10 and PM2.5 respectively) the order should be reversed. Response We reversed the order. In paragraph after Fig. 4, the sixth line statement starting by\" The independent t-test.....\" is repeated in the eighth line. Response We deleted the repeated sentence. The comments on Table 5 didn't contain any mention to RH, despite it is mentioned in the table. Response We already mentioned it under the table. Under the title \"effect of Ventilation\" second paragraph is too long and discussed in details the definition of natural and mechanical ventilation and the difference between them. Its better to be summarized. Response Ventilation is a very important factor in the indoor environment. Not all readers have the same experience with the detail of this factor. We found that it is important to detail. The third paragraph is not convincing to interpret the unrelated CO2 concentration with the number of students in the classroom. It needs to be interpreted. Response We already mentioned that the use of CO2 as a marker for indoor air quality is widely used, and its level inside a building is usually used as an indicator for controlled ventilation. The paragraph after Table 7 the gas concentration is mentioned in mg/m3 its better to convert it to ppm like the present paper. Response It will not make any difference because the two units are used for air pollutants. Under the title \" Strengths and limitations of the study\" in the fourth line \"as a representative of to other Arab countries\" it is better to be Gulf countries. Response We changed it. Serious Mistakes: The Title, I believe that Its better to add \": Al-Qatif-KSA\" to the title, at the end of it. Response We used the Eastern Province of Saudi Arabia as a representative to most Arab cities. So, to make our paper valuable and can be widely used in Arab countries, we used this title like thousands of papers worldwide. Abstract, the last statement in the Methods,\" a predesigned questionnaire was used to evaluate the safety preparedness in the same selected schools\". Response We deleted this statement from the abstract. There was no mention at all to the questionnaire or its results in the entire paper, emphasizing that the present paper extracted from a thesis., also at the end of introduction the last statement there is a mention of safety. However, there is no mention in Methodology to any safety preparedness plan. Response How did the reviewer conclude that the research was extracted from the thesis? We have already conducted a safety survey, but its results have been published in independent research. No doubt that providing a safe and clean environment inside schools will consider an important “safety procedure” for the students and school staff. However, we deleted the “safety preparedness issues” from the paper. Results: In table 6, it is not valid to put limits of NIOSH and ACGIH in this table of AQG since their limits is designated to working environment. Response The school environment is considered as an indoor environment for (for students as examples) and a workplace for all staff (managers, teachers, administrative workers……). Discussion: Under the title\" Effect of the school building type on the IAQ levels\" The reason that the levels of increased levels of pollutants in governmental schools are greater than those in the rented ones is not clear. The authors mentioned theoretical reasons with no relation to that difference. Also they combined another parameter, which is the location nearby high or low traffic areas which confuses the readers. Also the American reference at the third paragraph didn't offer an explanation since it was comparing between temporary and permanent schools. Response We described the reality of the situation of schools, as public (or governmental) schools are usually characterized by their large capacity and location that is qualified to receive a large number of cars, their multiple floors, and high number of students and related activities (labs, large playground…….etc.). This is completely different from rental schools that belong to a person or group of persons who rent a spacious residence and turn it into a school. As for the American study, it referred to the same difference, but with different names. Under the title \"Effect of temperature& relative humidity on IAQ levels\", the authors discussed the effect of temperature and RH separately, however its better to consider the \"effective temperature\". Response We changed the temperature to “effective temperature”."
}
]
}
] | 1
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https://f1000research.com/articles/11-1125
|
https://f1000research.com/articles/12-1232/v1
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27 Sep 23
|
{
"type": "Research Article",
"title": "Investigation of hepatitis B virus mutations associated with immune escape and drug resistance in human immunodeficiency virus-infected patients",
"authors": [
"Lorato Modise",
"Nomathamsanqa Sithebe",
"Hazel Mufhandu",
"Nomathamsanqa Sithebe"
],
"abstract": "Background: HBV/HIV co-infection impact on high HBV replication, progression to liver cancer and high mortality. Co-infection may lead to cross-resistance of HBV and HIV drugs due to immune therapy pressure or hepatotoxicity. These challenges necessitate continuous monitoring of HBV variants to aid better diagnosis and treatment strategies. We conducted this study to characterise HBV among HIV infected individuals. Methods: Serum was screened for HBsAg using ELISA, followed by DNA extraction, PCR amplification, Sanger sequencing and phylogenetic analysis. Results: Of the 50 samples in this study 100% (N=50/50) were HBsAg positive; 78% (N=41/50) HBV/HIV co-infection and 92% (N=38/41) of the amplicons were successfully sequenced. Samples nucleotide sequences were identified as genotype A. Mutations prevalence in the HBsAg region was 47% (N=18/38); including mutations associated with diagnostic failure (K122R and T143S) and 7 vaccines escape mutations (P127T, G145R, S207N, Y200T, E164D, Y206H and L209V). Mutations showed resistance to lamivudine 71% (n=5/7), telbivudine 57% (n=4/7), 14% (n=1/7) for entecavir and 43% (n=3/7) for adefovir. Mutations causing resistance to lamivudine and telbivudine were M204V, L180M, V163I, and S202K; with S202K also causing resistance to entecavir and adefovir resistance mutation were I253Y, I223V and M250I. Multiple drug resistance mutations within a single sample contained L180M, M204V, S202K and M250I mutations. There was no statistical significance between the RT mutations associated with drug resistance at P>0.005. The correlation test exhibited a weak statistical association between SHB and RT mutations (0.877**). Conclusions: This study shows the predominance of HBV genotype A in HIV-infected patients. We discovered HBV mutations linked to immune evasion and drug resistance. Although there is no statistical significance amongst the mutations associated with drug resistance and vaccine escape. These mutations could have clinical implications that could have therapeutic repercussions by influencing the correct clinical diagnosis and treatment in HBV/ HIV co-infected individuals.",
"keywords": [
"Hepatitis B virus",
"HIV",
"Drug resistance",
"Vaccine escape",
"Mutation",
"Co-infection"
],
"content": "Introduction\n\nThe Orthohepadnavirus genus is a significant group of human viruses, and the Hepatitis B virus (HBV) is a prototype of the Hepadnaviridae family (Summers et al., 1975). Globally, it is thought that more than 300 million people are infected with HBV, which can lead to chronic liver disease and hepatocellular carcinoma (HCC), which accounts for over 1 million annual fatalities (Musyoki et al., 2015). The Baltimore virus taxonomy places HBV in the class VII of viruses (Gust et al., 1986). It is an enclosed virus with 3200 nucleotide base pairs of partially antagonistic relaxed and circular double stranded DNA (RC-dsDNA), and it replicates through an intermediary ssRNA (Liu et al., 2021). Hepatocytes are the cells that the hepatitis B virus infects to cause liver infection, which can then clinically show as symptomatic or asymptomatic acute hepatitis marked by liver inflammation to fulminant hepatitis. Acute HBV hepatitis that is not treated may progress to chronic HBV hepatitis, which can cause cirrhosis and HCC (Liang, 2009). Many tests, including clinical, biochemical, serological, and molecular approaches, are used to detect HBV infection, illness associated with HBV, and to differentiate between acute and chronic infections. The hepatitis B surface antigen (HBsAg), the hepatitis envelope antigen (HBeAg), the antibody to the hepatitis surface antigen (anti-HBs), the antibody to the hepatitis B core antigen (anti-HBc), and the immuglubullin antibody sub-class of the anti-HBc are the HBV antibodies and antigens that are determined by the serological testing (IgM anti-HBc). The key clinical marker for acute or chronic infection, prevalence, and endemicity of HBV infection is the presence of HBsAg, which can be identified two weeks after exposure. By identifying the qualitative and quantitative HBV-DNA, molecular methods can diagnose HBV. Based on the entire genome genetic variability of roughly 8%, HBV genomes have been divided into ten primary genotypes designating A to J (Tatematsu et al., 2009). The lack of a viral polymerase proofreading mechanism during viral replication causes the genetic heterogeneity (Rahman et al., 2016). Moreover, immunization and antiviral medication have an external and internal impact on HBV sequence heterogeneity. Geographical differences in the distribution of the various HBV genotypes, however, influence the pathogenicity of HBV and the administration of treatment. Due to their shared method of blood-born transmission, HBV, and the human immunodeficiency virus (HIV) frequently co-infect individuals (Audsley et al., 2010). Depending on where HBV is endemic, different geographic areas have different common pathways of transmission. Lamivudine (3TC) is used in the treatment of HBV and HIV (Benson et al., 2009). However, due to the development of drug resistance after 4 years of single-drug treatment, HIV-infected persons should not receive 3TC or emtricitabine (FTC) monotherapy for HBV infection (Di Martino et al., 1999). The emergence of the mutation rtm204 is a hallmark of 3TC resistance (YMDD mutation). The 3TC should only be administered to individuals on totally suppressive ART since it accelerates unchecked HBV DNA replication and raises the risk of death from HBV infection or illness. HBV prevalence has been documented in several studies among HIV-positive people from Durban, KwaZulu-Natal. However, investigations on the HBV genotype, HBV vaccine escape, and treatment resistance are still scarce in this field and most studies have concentrated on the seroprevalence. To ascertain the prevalence and genotypic characteristics of HBV among HIV-infected people in Durban, we undertook this study.\n\n\nMethods\n\nWe employed the convenience sampling method and used samples that were available for use in this descriptive exploratory investigation; the sample size was not determined. Fifty preserved frozen sera samples from people who underwent HIV testing at the National Health Laboratory Services’ Inkosi Albert Luthuli Central Hospital (NHLS-IALCH-NHLS) in Durban, KwaZulu-Natal Province, South Africa, were utilized in this investigation. The 50 participants included both men and women who had HIV-positive test results. Participants were given a written informed consent form, the information on the consent form was given in a language that the patient understands which is English and Setswana. After receiving the written informed consent of all participants, samples were taken, tested for HIV positivity, and the residual sera were archived at the NHLS-IALCH-NHLS. At that moment, the subjects were not taking ART. The North-West University Research Ethics Regulation Committee issued an ethical certificate (Ref no: NWU-00068-15-A9) on 2015-05-22. Samples receival and data collection on the samples began in October 2015 to March 2016. The specimen’s codes were de-linked to keep patients anonymous; with only additional data on the age and gender of the study participants provided.\n\nSamples collection and processing\n\nA total of 50 stored frozen serum specimens from HIV-infected individuals in Durban were donated from NHLS-IALCH-NHLS and travelled on ice to the virology laboratory at the North-West University. Upon arrival the specimens were aliquoted into numerous 1.5 mL Eppendorf tubes and stored at -80 °C until further use.\n\nHepatitis B surface antigen (HBsAg) assay\n\nThe Monolisa HBsAg ultra confirmatory kit was used in accordance with the manufacturer’s instructions to conduct an enzyme-linked immunosorbent test (ELISA) to identify the presence of HBV HBsAg (BioRad, Raymond Poincare, Marnes-la-Coquette, France). To identify and measure the presence of HBsAg, excess antibodies (anti-HBs; anti-HBs diluent: neutralization reagent) were used to neutralize 200 L of undiluted sera specimens. At 450 nm, the optical density (OD) index of the specimens was determined and compared to the COV mean of a negative control. Reactive specimens for HBsAg were defined as those with an index greater than or equal to the COV.\n\nDNA extraction of HBV\n\nSerum obtained from patients was used to extract HBV deoxyribonucleic acid (DNA) using the QIAamp DNA Mini kit (catalog number: 51304) from (Qiagen, Hilden, Germany) following the manufacturer’s instructions. This technique allows the isolation and purification of total DNA from contaminants, inhibitors, and nucleases in the serum. An aliquot of 200 μL of the serum sample was added into 1.5 μL Eppendorf tubes, to which 20 μL of proteinase K and 200 μL Buffer AL (binding buffer mixed with poly [A] carrier RNA) was added. An aliquot of 200 μL of the serum sample was added into 1.5 μL Eppendorf tubes, to which 20 μL of proteinase K and 200 μL of buffer AL (binding buffer mixed with poly (A) carrier RNA) were added. The mixture was pulse-vortex for 15 seconds to allow lysis of the mixture and destroy RNA, followed by a 10 minute incubation at 56 °C. The mixture was then transferred to a QIAamp spin column to allow binding of the DNA and centrifuged for 1 minute at 8 000 rpm. The column was placed into a clean collection tube, then 500 μL of buffer AW1 was added, and it was centrifuged for 1 minute at 8 000 rpm. The solution was aspirated, 500 μL of buffer AW2 was added to purify the DNA, and it was followed by centrifugation for 3 minutes at 14 000 rpm. The QIAamp spin column was placed in a sterile 1.5 μL Eppendorf tube, and 50 μL of elution buffer (provided by the kit as buffer AE) was added directly into the column and incubated at room temperature for 5 minutes to precipitate the DNA. The DNA was eluted by centrifugation at 8 000 rpm for 1 minute and stored at -20 °C until further analyses were performed. The negative control, consisting of nuclease-free water, was included in the extraction procedure to identify contamination.\n\nFirst round and nested-PCR\n\nA nested polymerase chain reaction (PCR) amplification of the overlapping surface/polymerase gene covering nucleotides 256 to 796 from EcoRI site was done as described previously (Mphahlele, 2008) with slight modification. Outer sense strand forward primer, S1 (5′-CCT GCT GGT GGC TCC AGT TC-3′), and antisense strand reverse primer, S2Na (5′-CCA CAA TTC KTTGAC ATA CTT TCC A-3′) were used. The master mix were prepared using AmpliTaq Gold DNA polymerase (ThermoFisher Scientific,Waltham, Massachusetts, United States). For each sample the following reagent volumes and concentration of the master mix were prepared as follows: 18.5 μL nuclease free water, 2.5 μL of 1x PCR buffer with MgCl2, 0.5 μL (0.2 mM dNTP mix), 0.5 μL (10 μM) forward primer S1; 0.5 μL (10 μM) reverse S2Na anti-sense primer, 0.125 Taq DNA polymerase. A total of 22.5 μL of master mix was aliquoted into a 0.5 mL thin-walled PCR tube and 3 μL of DNA template was added. The PCR reaction mixtures (25.5 μL) was subjected to amplification of HBV DNA, carried out in an automated touch down thermal cycler CFX96 (Bio-Rad, Raymond Poincare, Marnes-la-Coquette, France). The HBV DNA amplification conditions were initial denaturation at 95 °C for 4 minutes, followed by 40× cycles involving denaturation at 95 °C for 4 minutes, annealing at 58 °C for 30 seconds, elongation at 72 °C for 1 minute, and final extension at 72 °C for 10 minutes.\n\nNested PCR\n\nFirst round PCR product was used as a template for nested PCR. An aliquot of 3 μL of the first round PCR reaction was subjected to a nested PCR, the master mix volume and concentration were prepared as same for the first round PCR. The nested PCR conditions used were the same as first round PCR protocol except the annealing temperature at 55 °C for 45 seconds. Forward primers S6E (5′-GAGAAT TCCGAGGACTGG GGA CCC TG-3′) and reverse primer S7B (5′-CGG GAT CCT TAG GGT TTA AAT GTATAC C-3′) were used during nested PCR. The negative control consisting of nuclease free water and a positive control were included in the PCR amplification assays.\n\nPCR products verification\n\nPCR amplification products were verified using 1% agarose gel (ThermoFischer, Waltham, Massachusetts) stained with 0.15 U/μL ethidium bromide (Biorad, California, USA). Aliquot of 10 μL PCR amplicon product was mixed with 2 μL 10x loading buffer (ThermoFischer, Waltham, Massachusetts). The mixtures were run on 1% gel along with a 1 Kb Invitrogen molecular weight maker (ThermoFischer, Waltham, Massachusetts) as a band size reference. The agarose gel was run at 100 V for 45 minutes. The gel was placed inside the ultraviolet (UV) transilluminator (Bio-rad, Hercules, California, United States) to visualise and image capturing.\n\nSequencing reaction\n\nThe PCR products and the nested PCR primers S6E and S7B were sent for bi-directional Sanger sequencing at the Inqaba (Inqaba Biotechnological Industry, Pretoria, South Africa). The amplicons were prepared for direct sequencing using the BigDye Terminator v3.0 Cycle Sequencing Ready Reaction Kit (catalog number: 4458687) from (ThermoFischer, Waltham, Massachusetts). Briefly, an aliquot of 50 μL of the 1:1 ratio of sodium acetate: ethanol (NaAc:EtOH) was added to the amplicons solution and centrifuged at 2000 g for 30 minutes. The well plates were inverted and centrifuged at 150 g for 1 minute. Pre-chilled 70% ethanol was added into the wells, and then centrifuged at 2000 g for 5 minutes. The pellets were dried at 65 °C for 5 minutes and loaded into the sequencing machine, the ABI 3130XL genetic analyser (Applied Biosystems, Foster City, CA). An aliquot of 10 μL of the Hi-Di formamide was added into the sample for 5 minutes and loaded into a sequencing machine ABI 3130XL genetic analyser (Applied Biosystems, Foster City, CA).\n\nNucleotide sequences of HBV chromatograms were viewed and edited by removing unwanted and mixed nucleotides character from the sequences by ChromasPro, version.1. The contiguous sequences were formed by joining overlapping DNA sequences of a gene using BioEdit. The consensus sequences were compared with complementary genotype sequences from the GenBank using the Basic local alignment search tool (BLAST). Representative sequences belonging to distinct genotypes were redeemed from GenBank to make comparisons with study sequences. Multiple sequence alignment of the sequenced nucleotide region was performed with ClustalW within the MEGA software package version 7.0 (TomHall, North Carolina State University). The aligned nucleotide base sequences were subjected to phylogeny inference on MEGA 7.0 (Kumar et al., 2004). The neighbour-joining method was used to generate dendograms, and the evolutionary relationship was performed using pairwise genetic distance with 1000 bootstrap replicates (Saitou & Nei, 1987). Frequency estimates of evolutionary divergence between nucleotide sequences were then estimated using the Kimura 2-parameter model (Kimura, 1980).\n\nThe sequences were uploaded into the BioEdit and analysed for nucleotide base and amino acids changes. The sequences were further uploaded into the Geno2pheno to identify drug resistance mutations.\n\nMicrosoft Excel and the data science statistical program STATA were used for data analyses (version 15). Excel was used to calculate the frequency of age as numeric values and the frequency of HBsAg and mutations as categorical and numeric variables. STATA was used to import the Excel (.csv) file to conduct additional research on the distribution and associations of the mutations. The likelihood of a link between the two categorical variables (mutations and age) was evaluated using the Fisher’s exact test. The Pearson correlation coefficient was used to examine the relationship between the surface region and the HBV virus’s reverse transcriptase mutations. In this study, a significant p value was defined as one with a 5% level of significance.\n\nThe study ethics certificate was provided by the North-West University research ethics regulatory committee (ref. NWU-00068-15-A9).\n\n\nResults\n\nThe baseline demographics of the study showed that all 50 HIV positive samples included were from patients of black African ethnicity most of the study participants were female at 66% (N = 33/50) and 34% (N = 17/50) were males as shown in (Table 1). The median age and standard deviation of the study population were 33 years (range of 18-55).\n\nHBsAg assay\n\nThe HBsAg was positive in all HIV positive samples resulting in a 100% (N=50/50) HBV seroprevalence. Of the 50 HBsAg positive patients (Table 1). Primarily, the study female’s participant had the highest HBsAg at (N=29/50) when compared to the males at (N=11/50) as shown in (Table 1).\n\nPCR amplification\n\nThe PCR amplification of HBV DNA amplicons was successful in 78% (N=41/50) of the HBsAg and HIV positive samples. HBV overlapping surface/polymerase region amplicons are shown as 547 bp bands below (Figure 1). PCR amplification could not be obtained for the other 22% (N=11/50) samples.\n\nPCR amplicons are shown as 547 bp bands.\n\nOnly 92% (N=38/41) of the overlapping surface/polymerase nucleotide sequence products could be obtained by Sanger sequencing. The sample sequence showed a 98% to 99% homology similarity index with previously deposited HBV genotype A sequences in the GenBank. Phylogenetic tree analysis identified nucleotide sequences from this study as genotype A as depicted in (Figure 2). The sub-genotypes of sequences were confirmed by depositing all the surface gene nucleotides sequenced into the Genotype2pheno database. The 38 individuals’ sequence were identified as sub-genotype A1 based on the results retrieved from the Geno2Pheno database with the percentage of similarity to sub-genotype profile of 96.85% -99.0%.\n\nStudy sequences are represented by letters Q, P and followed by numeric values.\n\nMutations within the surface gene\n\nThe prevalence of mutations in the surface gene was 47% (N=18/38) and mutations were found in the “α” epitope, “β”-cell epitope, “T” helper cell epitope and outside the “α” epitope as shown in (Table 2). The most common mutations on the surface region of HBV were S207N at 71% (27/38), followed by L216V and A194V at 23%, P70H at 21% L209V at 18%, P217L at 8%, F134L, E164D and T189I at 5% and S204R, S117N, T143S, G145R, Y206H, P127T, Y200T, F129T and K122R all at 3% (Table 2).\n\nMutations within the polymerase gene region\n\nMutations prevalence were reported at 36% (N=14/38) in different positions within the reverse transcriptase (RT) region. The M129L mutation was the most common in this study, accounting for 84% (32/38), followed by V163I at 78%; I253Y at 50% and S105T at 40%. Other mutations identified from sequences included L217R, A233S, Q125E, T128A, V214A, V204I, M204V, L180M, V173L and S202K at 21%, 16%, 13%, 8% and 3% (Table 3). The prevalence of mutations associated with drug resistance was 57% (8/14) within the RT region (Table 3). Drug resistance mutations included lamivudine (LMV) resistance at 71% (5/7), telbivudine (LdT) at 57% (4/7), 14% for entecavir (ETV) and 43% for adefovir (ADV) resistance. Mutations causing resistance to LMV and LdT were M204V, L180M, V163I, and S202K. S202K mutation also causes resistance to ETV. ADV resistance mutations were I253Y, I223V and M250I (Table 3). Multiple drug resistance mutations within a single sample were identified from one sample containing L180M, M204V, S202K and M250I mutations.\n\nFrequency of mutations\n\nThe prevalence of the mutations on the sequences of surface protein region was (N=39) and RT mutations were (N=41). The mean and standard deviation of the SHB mutations was 7.66±4.79; for RT mutations the mean and standard deviation was 11.21±5.44 as depicted in (Table 4).\n\nAssociation of mutations on the surface and polymerase\n\nA correlation test was done between the SHB and RT mutations was done using and the Pearson Correlation. There was no statistical significance between the RT mutations at P>0.005 (Table 4). The correlation test exhibited a weak statistical association between SHB and RT mutations (0.877**) as shown in Figure 3.\n\nPlot of SHB_protein *RT_mutations, symbol used is ‘+’. 11 obs had missing values. 7 obs hidden.\n\n\nDiscussion\n\nIn the current study, the HBsAg seroprevalence in HIV-infected patients was 100%. The HBsAg prevalence in HIV-infected people is higher in this study as compared to previous studies in South Africa, with an estimation between 3% and 23% reported from the Western Cape, KwaZulu-Natal, and Gauteng provinces (Andersson et al., 2013; King & Hagemeister, 2016; Lukhwareni et al., 2009; Maponga, 2012; Mphahlele, 2008; Msomi et al., 2020; Samsunder et al., 2019). The HBsAg seroprevalence from this study is not coherent with published data from South Africa; comparing with previous studies, they used larger sample cohort in their studies, whereas our study used a small sample size, which influenced the high prevalence rate. However, the study report supports previous studies that endemic HBV is still present in South Africa and that HBV seroprevalence among HIV-infected people is presently high among adults (Amponsah-Dacosta, 2021; Maepa et al., 2022). All the HBsAg-positive samples were subjected to PCR amplification of the HBV DNA. The partially overlapping surface/polymerase gene region was successfully amplified in 78% (41/50), confirming the active replication of HBV and HBV/HIV co-infection on the input study samples. The presence of HBV/HIV co-infection is attributed to the shared route of viral transmission since both viruses share a similar route of transmission. Furthermore, it was also reported that females were the majority infected with HBV infection at 66% (N=33/50) compared to their male counterparts at 34% (N=17/50) in this population. This does not correlate with the findings of (Kew et al., 2008), who reported a prevalence of 4% in women compared with 9% in men. Similarly (Moonsamy et al., 2022), reported higher prevalence rates in males than females aged 25 to 49 years. The phylogenetic analysis shows the predominance of genotype A from our study sequences. The identification of HBV genotype A is coherent with previous studies in South Africa (Kimbi et al., 2004; Kramvis, 2014). The patient’s sequences were further identified as sub-genotype A1 by Geno2Pheno, indicating that HBV showed significant diversity, suggesting an African origin. The HBsAg serves is part of the S region which is employed in the development of recombinant vaccines; this region consists of α, β and T–cell epitopes. The “α” epitope is the primary area that neutralizing antibodies attacks and it contains the β and T–cell epitopes (Caligiuri et al., 2016). The “a” determinant, also known as the primary hydrophilic region of HBsAg, is the collection of B cell epitopes and is made up of the amino acids 124–147 (Liu et al., 2017). The “α” epitope domain of HBsAg may undergo mutations due to nucleotide and amino acid substitutions, which may result in structural and functional alterations in the S protein (Zuckerman & Zuckerman, 2003). This could alter the antigenicity of the vaccination and result in mutations that escape the immunization, allowing mutant HBV to replicate in the body of the vaccinated population (Yan et al., 2017). We determined the mutations on the partial surface gene of HBV/HIV co-infected individuals from our study. A total of 18 nucleotide substitutions were observed within the HBsAg region in all 38 partial surface sequences. The study reports mutations at sequence locations at the at α, β and T–cell epitopes that have clinical ramifications. The primary hydrophilic region (aa79 to aa147) of the surface antigen had the “α” epitope and contained four mutations (K122R, F134L, T143S, and S117N). G145R, S207N, and Y200T variations were found in the \"T\" epitope, whereas P127T was found in the “β” epitope of the “α” determinant region. The following mutations were found to be absent from the “α” epitope: E164D, L209V, Y206H, A194V, P70H, P127L, T189I, S204R, and F129T. We found escape mutations from vaccines including P127T, G145R, S207N, Y200T, Y206H, and L209V. Among 27 samples, the S207N mutation was the most prevalent one. P127T has been linked to vaccination escape selection in the past (Colagrossi et al., 2018); which contradicts the findings of Kuzin et al., (2012), who reported this mutation to causing diagnostic failure. The clinical implications of this mutations must further be explored in vitro. One patient sequence contained the mutation G145R, which has already been identified by (Colson et al., 2007; Yan et al., 2017). In the “β”-cell epitope of HBsAg, the G145R mutation is a significant vaccine escape mutation that is linked to a point mutation that results in the substitution of arginine for glycine at position 145 (G145R). The HBsAg antigenicity is decreased because of the interference with antibody binding (Kao & Chen, 2002; Su et al., 2008). Given that it was the first vaccine-escape mutation discovered in children who received vaccinations in Italy, the G145R mutation is a typical mutation (Zanetti et al., 1988). Its occurrence and stability have increased over the years with an increase of HBV endemicity and use of universal immunization (Caligiuri et al., 2016). This mutation is crucial in causing failure on the detection of HBV by serological routine assays (Cooreman et al., 2001). The long-term success of mass vaccination, however, has been previously reported to be threatened by G145R, which has grown more dominant with vaccine escape selection (Yan et al., 2017). Thus, it is advised that it be incorporated into the design of future vaccines (Yan et al., 2017). It is said that this mutation has a possible horizontal transmission pattern (Colagrossi et al., 2018). Globally, the G145R mutations have previously been linked to HBV breakthrough infections in the population who had received vaccinations (Cooreman et al., 2001; Theamboonlers et al., 2001). On the other hand, mutations G145R and F143S have also been discovered in people with occult hepatitis B infection (OBI), and they have been associated to the clinical implications. On the other hand, mutations G145R and F143S have also been found in individuals with occult hepatitis B infection (OBI), and they have been linked to the clinical implications of diagnostic failure due to suboptimal HBsAg detection when using commercial ELISA kits (Coppola et al., 2016). It was previously reported as a nucleos (tide) analog (NA-induced) immune escape mutation (Colagrossi et al., 2018; Lai et al., 2003), demonstrated that the E164D result from the substitution change in the overlapping polymerase region caused by the mutation rtM204V, rtM204I, and rtV173L) (Lai et al., 2003; Zöllner et al., 2001). E164D was another significant mutation discovered from this study. These mutations produce a decrease in anti-HBs and are linked to lamivudine resistance therapy (Colagrossi et al., 2018). Additional mutations found in this study included K122R, T143S, Y206H, L209V, S207N, Y200T, and P70H. Nevertheless, there is little information available about these mutations’ effects on surface protein structure and activities, and more research is needed to determine how they may affect patients’ health. K122R and T143S mutations, on the other hand, have reportedly been linked to diagnostic adequacy (Cooreman et al., 2001). With certain ELISA diagnostic methods failing to identify HBsAg from samples bearing the K122R in prior research (Malik et al., 2012). All the HBsAg mutations mentioned above have clinical implications that are connected to immunological escape and have an impact on the antibodies’ ability to recognize HBsAg. whilst others are connected to diagnostic failure. Antiviral medications that prevent reverse transcription specifically target the HBV polymerase to prevent HBV DNA replication. The nucleoside/nucleotide analogues LMV, ADV, TDF, LdT, and ETV are antiviral medications that are used to treat HBV polymerase. Despite the introduction of TDF, lamivudine treatment is still favoured among patients with HBV/HIV co-infection in South Africa. Antiviral medications may potentially contribute to the development of drug resistance due to selection pressure during long-term use of the antiviral treatment, in addition to the high mutation rate caused by the HBV error-prone (Fares & Holmes, 2002). The frequency of drug resistance-related mutations in the RT region was 50% (N=7/14). M204V, L180M, V163I, and S202K were mutations linked to LdT resistance; S202K also conferred ETF resistance. Combining L180M and M204V results in increased cross-resistance to other nucleosides and decreased sensitivity to ETV but not ADV. It may also result in vaccine escape mutations in the overlapping S-region, which would stop HBsAg from secreting (Sheldon et al., 2005). ADV resistance mutations included the I253Y, I223V, and M250I mutations. A single sample from one patient that contained the mutations L180M, M204V, S202K, and M250I was shown to have several drug resistance mutations. All the drug resistance mutations found in the RT of the pol region were found in genotype A sequences. Moreover, the following compensatory mutations were found: S202K, Q125E, L217R, V124A, V204I, I253Y, T128A, and S105T. We still need to investigate how these changes affect RT functions. As this study found no mutations linked to tenofovir resistance, we advise using a tenofovir-based regimen to treat HBV in people who also have HIV. At P>0.05, there was no statistical difference between the mutations linked to medication resistance. The Pearson Correlation was used to conduct a correlation test between the SHB and RT mutations. The connection between SHB and RT mutations was not strong. Further in vitro studies must be carried out to investigate the effects of the detected alterations on the antibody neutralization and nucleoside/tide drug analogues. This does not rule out the possibility that these mutations have major clinical implications towards the diagnosis and therapy.\n\n\nConclusion\n\nThis study demonstrates the prevalence of HBV genotype A in HIV-positive patients as well as the presence of HBV mutations in HBV/HIV co-infected people. We discovered HBV mutations linked to immune escape and drug resistance that could have therapeutic repercussions by influencing the correct clinical diagnosis and HBV treatment. This study has improved our understanding of the genotypes and mutations of HBV that have clinical implications in those who have HBV and HIV co-infection in South Africa. To determine how immune escape and drug resistance-related HBV mutations affect diagnosis and drug resistance treatment in the context of HIV/HVB co-infection, we recommend testing the HIV samples for these mutations.",
"appendix": "Data availability\n\nFigshare: data set for patients’ demographics, HIV and HBV test 2017-2019.xlsx, https://doi.org/10.6084/m9.figshare.23946621.v1 (Modise, 2023a).\n\nThis project contains the following underlying data:\n\n- data set for HIV 2017-2019.xlsx\n\n- data set for demographic and virology test 2017-2019.xlsx\n\nFigshare: PCR amplicon gel electrophoresis, https://doi.org/10.6084/m9.figshare.23815278.v1 (Modise, 2023b).\n\nFigshare: HBV PCR amplicon gel image.pdf, https://doi.org/10.6084/m9.figshare.23946639.v1 (Modise, 2023c).\n\nFigshare: Reference sequences accession number and Genotype, https://doi.org/10.6084/m9.figshare.23946642.v1 (Modise, 2023d).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank the National Health Laboratory Services in KwaZulu-Natal for donating samples for this study. We thank the State Key Lab of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences for providing training on HBV genotyping and cell culturing.\n\n\nReferences\n\nAmponsah-Dacosta E: Hepatitis B virus infection and hepatocellular carcinoma in sub-Saharan Africa: Implications for elimination of viral hepatitis by 2030? World J. Gastroenterol. 2021; 27(36): 6025–6038. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndersson MI, Maponga TG, Ijaz S, et al.: The epidemiology of hepatitis B virus infection in HIV-infected and HIV-uninfected pregnant women in the Western Cape, South Africa. Vaccine. 2013; 31(47): 5579–5584. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAudsley J, Littlejohn M, Yuen L, et al.: HBV mutations in untreated HIV-HBV co-infection using genomic length sequencing. Virology. 2010; 405(2): 539–547. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nMusyoki AM, Msibi TL, Motswaledi MH, et al.: Active co-infection with HBV and/or HCV in South African HIV positive patients due for cancer therapy. J. Med. Virol. 2015; 87(2): 213–221. Publisher Full Text\n\nRahman MA, Hakim F, Ahmed M, et al.: Prevalence of genotypes and subtypes of hepatitis B viruses in Bangladeshi population. Springerplus. 2016; 5: 278. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987; 4(4): 406–425. PubMed Abstract | Publisher Full Text\n\nSamsunder N, Ngcapu S, Lewis L, et al.: Seroprevalence of hepatitis B virus: Findings from a population-based household survey in KwaZulu-Natal, South Africa. Int. J. Infect. Dis. 2019; 85: 150–157. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSheldon J, Camino N, Rodés B, et al.: Selection of hepatitis B virus polymerase mutations in HIV-coinfected patients treated with tenofovir. Antivir. Ther. 2005; 10(6): 727–734. PubMed Abstract | Publisher Full Text\n\nSu IJ, Wang HC, Wu HC, et al.: Ground glass hepatocytes contain pre-S mutants and represent preneoplastic lesions in chronic hepatitis B virus infection. J. Gastroenterol. Hepatol. 2008; 23(8 Pt 1): 1169–1174. PubMed Abstract | Publisher Full Text\n\nSummers J, O’Connell A, Millman I: Genome of hepatitis B virus: restriction enzyme cleavage and structure of DNA extracted from Dane particles. Proc. Natl. Acad. Sci. U. S. A. 1975; 72(11): 4597–4601. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTatematsu K, Tanaka Y, Kurbanov F, et al.: A genetic variant of hepatitis B virus divergent from known human and ape genotypes isolated from a Japanese patient and provisionally assigned to new genotype. J. Virol. 2009; 83(20): 10538–10547. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTheamboonlers A, Chongsrisawat V, Jantaradsamee P, et al.: Variants within the “a” determinant of HBs gene in children and adolescents with and without hepatitis B vaccination as part of Thailand’s Expanded Program on Immunization (EPI). Tohoku J. Exp. Med. 2001; 193(3): 197–205. PubMed Abstract | Publisher Full Text\n\nYan B, Lv J, Feng Y, et al.: Temporal trend of hepatitis B surface mutations in the post-immunization period: 9 years of surveillance (2005-2013) in eastern China. Sci. Rep. 2017; 7(1): 6669. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZanetti AR, Tanzi E, Manzillo G, et al.: Hepatitis B variant in Europe. Lancet. 1988; 332(8620): 1132–1133. Publisher Full Text\n\nZöllner B, Petersen J, Schröter M, et al.: 20-fold increase in risk of lamivudine resistance in hepatitis B virus subtype adw. Lancet. 2001; 357(9260): 934–935. PubMed Abstract | Publisher Full Text\n\nZuckerman JN, Zuckerman AJ: Mutations of the surface protein of hepatitis B virus. Antivir. Res. 2003; 60(2): 75–78. Publisher Full Text"
}
|
[
{
"id": "211197",
"date": "27 Oct 2023",
"name": "Nishi Prabdial-Sing",
"expertise": [
"Reviewer Expertise virology",
"diagnostics",
"molecular biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors undertook a small study to characterize HBV among HIV infected individuals. The evidence and findings that the authors have revealed in the study indicates the necessity to engage in larger studies and population size to understand the extent of HBV sequence variation and diversity seen in South African patients coinfected with HIV. The study provides remarkable technical aspects for many others to undertake studies such as these and the authors are commended on their scientific output.\nThere were a few grammatical errors and writing of the manuscript requires improvement. It is imperative that the writing of sequence variation indicates that it is the virus that was sequenced and not host or patient genes, because this can cause confusion to the reader. This has been commented on in the manuscript but the authors need to identify more of these to correct throughout the paper.\n\nThe discussion is too long and too much information is provided that can be summarized and placed more appropriately in the introduction, especially on the vaccine escape mutations. The discussion should focus on the findings from the study with comparison on other similar studies in other countries or within the same country.\nOn the results and discussion, the scatter plot needs to be explained as the X- and Y-axes are not well labeled and the interpretation and relevance of the plot does not seem to be evident in the discussion. The statistical significance is commented on for the RT gene but not shown for the HBsAg gene, but the latter was commented on. The sample size is small to conclude from these statistical significant data. It is recommended that a statistician look at the data and recommend a direction.\nOverall, the manuscript requires major improvement to improve on the aim and discussion and to draw on strengths from the authors' findings.\nThe edits and comments are available as a PDF attachment which can be found here.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11190",
"date": "30 May 2024",
"name": "Lorato Mosetsanagape Modise",
"role": "Author Response",
"response": "Dear Reviewer, We appreciate the efforts, comments, and concerns in making the manuscript better. We have gone through the comments and edited the manuscript accordingly in the revised manuscript. The inputs made in response to your comments are listed below. Reviewer’s general comments: The authors undertook a small study to characterize HBV among HIV infected individuals. The evidence and findings that the authors have revealed in the study indicates the necessity to engage in larger studies and population size to understand the extent of HBV sequence variation and diversity seen in South African patients coinfected with HIV. The study provides remarkable technical aspects for many others to undertake studies such as these and the authors are commended on their scientific output. Reviewer’s comments: There were a few grammatical errors and writing of the manuscript requires improvement. It is imperative that the writing of sequence variation indicates that it is the virus that was sequenced and not host or patient genes, because this can cause confusion to the reader. This has been commented on in the manuscript, but the authors need to identify more of these to correct throughout the paper. Response 1: Yes, we have made the necessary improvement on the grammar and writing of the paper. Response 2: We have made clarification on the use and writing of virus sequence and virus nucleotide sequences and HBV sequence instead of host or patients’ genes. Reviewer’s comments: The discussion is too long and too much information is provided that can be summarized and placed more appropriately in the introduction, especially on the vaccine escape mutations. The discussion should focus on the findings from the study with comparison on other similar studies in other countries or within the same country. Response: Thank you for noting this. We have excluded the opening of the discussion about the seroprevalence. The discussion section has been revised, summarised, and focusing more on the sequence analysis of the viruses (genotyping and mutations analysis). The information on the vaccine escape mutations has been moved to the introduction. Reviewer’s specific comments per section Abstract Reviewer’s comments: Add a line on where and how samples were collected? Response: The type of samples and the location where the samples were collected is now clarified in the abstract and methodology section in page 3 under the title “Study design and population” Reviewer’s comments: So, here you indicate statistical significance of RT mutations. Were the mutations in the HBsAg statistically significant? as compared to RT. Response: We have provided the statistical significance of association between the RT and HBsAg mutations as outlined in the abstract and results section on page 10 “Association of mutations on the surface and polymerase” Reviewer’s comments: The aim of the study be revised. Response: We have revised the aim of the study Methods Reviewers’ comments: Add a line on where and how samples were collected? Response: We added information of how and where the samples were collected. We also describe the sampling method and how the sample size was calculated. Results Reviewers’ comments: Is the prevalence of HBsAg correctly reported and how were samples collected? Response: The seroprevalence of HBV has been revised by reporting the correct percentage values of HBsAg. Reviewers’ comments: It is not clear what these numbers are? is the first number, the number of mutations found in the age group and the second number is a %? Figure 3 is not well explained as how to read this plot because the X-and Y- axes are not well labelled. Response: Table 4 and Figure 3 are removed. The probability of association between the RT and SHB which was represented on Table 4 and Figure 3 is reported as depicted on page 10 under section “Association of mutations on the surface and polymerase” to report that there was no statistical significance association between the SHB and RT mutations at P > 0.005. Phylogenetic analysis was also revised. Discussion Reviewer’s comments: This is not a valid finding as it may reflect how samples were chosen for the study (previous point above). Also, the sample size is very small and not representative. I would avoid starting the discussion with this. Rather begin at the sequence analyses as this is the strength of the study. Response 1: Thank you for noting this. We have excluded the statement on sample size being statistically significant and included it as a study limitation (last paragraph under discussion) on page 11. Response 2: We begin the discussion on the sequence analyses and focus on the genotype identification and diversity."
}
]
},
{
"id": "224163",
"date": "22 Nov 2023",
"name": "Anna McNaughton",
"expertise": [
"Reviewer Expertise Virology",
"genomics",
"epidemiology",
"viral hepatitis"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, the authors sequenced the HBsAg region from a number of samples from individuals co-infected with HIV and HBV. Whilst this data can be informative, there are a number of issues with the analysis, results are not consistent with their metadata and the conclusions need re-evaluating before this manuscript can be reconsidered. The manuscript is also too long in several parts, and should be more focused on relevant information.\nAbstract - Sampling site should be mentioned in the abstract – important to understand how/where these patients were identified, and has a link to the genotype distribution.\nIntroduction - Very lengthy, with a large amount of information on HBV biology that is not relevant to this study. The authors should make this section more concise, and focused on HBV/HIV coinfection in the region these patients were sampled from, and the implications of treatment.\nSampling approach – it is unexpected that 100% of n=50 people tested for HIV would randomly also test positive for HBV via convenience sampling. Were samples screened in advance as part of the clinical testing? The available metadata online (Figshare) also seems to state that 43/50 samples were HBV HBsAg positive, with 7 samples either negative or missing so the authors need to clarify this result. This sampling approach also means that discussions about prevalence and comparing with other studies (in results/particularly in discussion) are not appropriate and should be removed from the study.\nMethods are too detailed and could be more concise.\nFigure 1 is not required in the paper, particularly if sequences were generated.\nPCR Amplification – the authors state that 41/50 amplicons were obtained but that they were not obtained for 11/50 samples – this is 52/50?\nSequence analyses of overlapping surface/polymerase gene region - The authors state that ‘Phylogenetic tree analysis identified nucleotide sequences from this study as genotype A as depicted in (Figure 2) but the current analysis has issues and cannot be used to inform genotyping assumptions as a result (see below).\nPhylogenetic analysis/Figure 2 - Authors should say what type of phylogenetic analysis this was, and how many study sequences were included in it. What length were these sequences?\nList of reference sequences listed in Figshare does not tally with the sequences in the tree where there appears to be more sequences? Unclear why this is.\nMethods says bootstrap analysis was done but the data is not presented on the tree anywhere.\nThere appears to be a few issues with the clustering of the reference sequences in the tree – the clade at the bottom shows genotypes D/B/E/C clustering, but then other genotype B/C sequences can be seen to cluster with genotypes F/H at the top of the tree? Sequences of the same genotype should cluster together and they do not appear to be in this analysis. This analysis needs revising.\nFor the mutation analysis, it is unclear what reference sequence the authors were comparing their sequences to? I am not keen of the approach of simply comparing sequences to a reference sequence to determine ‘mutations’ as these are likely to mostly just be reflective of expected sequence diversity. I think looking at a more focused list of sequences with known phenotypic associations would be more informative (as has been done with the resistance-associated mutations). Some rephrasing might help also – for example, saying 47% of sequences had mutations could imply that 53% of sequences were identical in the region? Be clear that these are amino acid differences.\nTable 3 - add the specific drug the mutation provides resistance against.\nTable 4 needs revising to say n= and % for the age groups. Typo of Fisher’s exact test also.\nI think figure 3 can also be removed – this is just showing that sequences more distant from a reference sequence in surface, and also more distant in RT. This is not surprising as the two regions overlap. Are the numbers listed amino acid positions in the sequences – it would be useful to know where in the genome this is?\nThe conclusions need re-evaluating after addressing the concerns elsewhere in the paper.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "11426",
"date": "31 May 2024",
"name": "Lorato Mosetsanagape Modise",
"role": "Author Response",
"response": "Dear Reviewer We appreciate the efforts, comments, and concerns in making the manuscript better. We have gone through the comments and edited the manuscript accordingly in the revised manuscript. The inputs made in response to your comments are listed below. In this study, the authors sequenced the HBsAg region from a number of samples from individuals co-infected with HIV and HBV. Whilst this data can be informative, there are several issues with the analysis, results are not consistent with their metadata and the conclusions need re-evaluating. before this manuscript can be reconsidered. The manuscript is also too long in several parts, and should be more focused on relevant information. Reviewer’s comments: Abstract - Sampling site should be mentioned in the abstract – important to understand how/where these patients were identified and has a link to the genotype distribution. Response: Yes, We have added information in the abstract on where the samples were collected (Inkosi Albert Luthuli Central Hospital) and how they were collected (Convenience sampling). Introduction - Very lengthy, with a large amount of information on HBV biology that is not relevant to this study. The authors should make this section more concise and focused on HBV/HIV coinfection in the region these patients were sampled from, and the implications of treatment. Response: The introduction has been revised and shortened by removing information on the HBV biology and history. We have included information on the prevalence of HBV/HIV coinfection in the study region and implication of treatment. Sampling approach – it is unexpected that 100% of n=50 people tested for HIV would randomly also test positive for HBV via convenience sampling. Were samples screened in advance as part of the clinical testing? The available metadata online (Figshare) also seems to state that 43/50 samples were HBV HBsAg positive, with 7 samples either negative or missing so the authors need to clarify this result. This sampling approach also means that discussions about prevalence and comparing with other studies (in results/particularly in discussion) are not appropriate and should be removed from the study. Response: The sampling method and sample size is now clarified in the methodology section in page 3 under the title “Study design and population”. Convenience sampling was used to collect 43/50 samples that were previously tested for HIV and HBsAg. The sample size has been revised by reporting the correct size which correspond to the metadata value. The confirmatory screening of HBsAg reported a prevalence of 86% (N=43/50) with 12% (N=6/50) being negative and2% (N=1/50) missing data (Table 1). Reviewer comment: Methods are too detailed and could be more concise. Response: The methods have been revised and summarized. Figure 1 is not required in the paper, particularly if sequences were generated. Response: Figure has been removed from the paper and included as supplementary data on the repository site. PCR Amplification – the authors state that 41/50 amplicons were obtained but that they were not obtained for 11/50 samples – this is 52/50? Response: The result of failed PCR amplification has been corrected to 08/50 instead of 11/50. Sequence analyses of overlapping surface/polymerase gene region ‘Phylogenetic tree analysis identified nucleotide sequences from this study as genotype A as depicted in (Figure 2) but the current analysis has issues and cannot be used to inform genotyping assumptions as a result (see below). Phylogenetic analysis/Figure 2 - Authors should say what type of phylogenetic analysis this was, and how many study sequences were included in it. What length were these sequences? List of reference sequences listed in Figshare does not tally with the sequences in the tree? there appears to be more sequences. Unclear why this is. Methods says bootstrap analysis was done but the data is not presented on the tree anywhere. There appears to be a few issues with the clustering of the reference sequences in the tree – the clade at the bottom show's genotypes D/B/E/C clustering, but then other genotype B/C sequences can be seen to cluster with genotypes F/H at the top of the tree? Sequences of the same genotype should cluster together, and they do not appear to be in this analysis. This analysis needs revising. Response: The prevalence of mutations associated with drug resistance has been revised, to focus only on reporting the mutations associated with specific drug (shown in section titled: Mutations within the polymerase region and table 3) The phylogenetic tree results have been revised. The length these sequences is reported under the PCR amplification results as 547 bp in size and included 24 sequences and 39 reference sequences. The reference sequences listed in the metadata included some of the sequences and not all the reference sequences, but the list has been revised to correspond to the phylogenetic tree reference sequences. The neighbor joining method was used to construct a tree. The clustering of the sequences was revised, and the clustering of the sequences was mixed due to the short PCR product of 547 bp, unlike the full genome which would have given a homogenous clustering pattern. The sequence clustering results have been revised. For the mutation analysis, it is unclear what reference sequence the authors were comparing their sequences to? I am not keen of the approach of simply comparing sequences to a reference sequence to determine ‘mutations’ as these are likely to mostly just be reflective of expected sequence diversity. I think looking at a more focused list of sequences with known phenotypic associations would be more informative (as has been done with the resistance-associated mutations). Some rephrasing might help also – for example, saying 47% of sequences had mutations could imply that 53% of sequences were identical in the region? Be clear that these are amino acid differences. Response: The sequences were uploaded into geno2pheno and compared against standard genome with reported mutations using bioinformatics and statistical packages to check for sequence diversity and mutations. We did not investigate the phenotypic associations these mutants have on the virus. The focus was on identifying the mutations in the overlapping pol and S and their clinical implications. Table 3 - add the specific drug the mutation provides resistance against. Response: Table 3 has been revised, the initial table has been removed and replaced with the showing specific drug associated with resistance Table 4 needs revising to say n= and % for the age groups. Typo of Fisher’s exact test also. I think figure 3 can also be removed – this is just showing that sequences more distant from a reference sequence in surface, and also more distant in RT. This is not surprising as the two regions overlap. Are the numbers listed amino acid positions in the sequences – it would be useful to know where in the genome this is? Response: Table 4 has been removed. The conclusions need re-evaluating after addressing the concerns elsewhere in the paper. Response: The conclusion has been revised. The sequences of the studies Q cluster with each other and this is what is shown with my study sequences. There is a clustering between B/C and F/H reference sequences. The sequences were compared with the reference sequences on Geno2Pheno, which is an online server tool. Sequence alignment to the deposited HBV consensus sequence of the respective genotype. We looked at genetic mutations, not phenotypic mutations. that will acquire in vitro studies which is not the focus of the study. Under results section the subheadings 1. mutations within the surface region and 2. mutations within the polymerase region have been combined and reported under the heading: Mutations analysis."
}
]
}
] | 1
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https://f1000research.com/articles/12-1232
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https://f1000research.com/articles/13-555/v1
|
30 May 24
|
{
"type": "Study Protocol",
"title": "Assessment and impact in quality-of-life post radiotherapy in breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, 2023 - 2024",
"authors": [
"Induni Nayodhara Weerarathna",
"anurag luharia",
"ashish uke",
"Gaurav Mishra",
"anurag luharia",
"ashish uke",
"Gaurav Mishra"
],
"abstract": "Introduction The process of breast cancer treatment, especially radiation therapy, frequently alters patients’ lives significantly. It is essential to comprehend how radiation affects breast cancer survivors’ quality of life to improve their overall treatment and well-being. The quality of life among breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), affiliated with the University Of Datta Meghe Institute Of Higher Education and Research (DMIHER), Sawangi, following radiation therapy is examined in this study during the years 2023–2024.\n\nMethods This observational cross-sectional study will be conducted in the Department of Radiotherapy of AVBRH associated with DMIHER, the hospital is situated in the state of Maharashtra, in India, from 2023 to 2024. We will select Breast cancer patients registered in AVBRH at the Radiotherapy department from Jan 2023 to October 2023 and receive treatment in the form of radiotherapy; chemotherapy and radiotherapy. The study will be observational and cross-sectional. This research will take approximately six months. Questionnaires will be distributed on the spot to patients and phone interviews for distant patients will be conducted using an interview checklist.\n\nDiscussion The study is expected to contribute significantly to the existing body of knowledge by delving into specific challenges and experiences of breast cancer survivors post-radiotherapy, particularly within the context of a rural healthcare setting. By concentrating on this group, the study will contribute to the body of existing knowledge by offering a deeper view of the variables influencing the quality of life in breast cancer survivors. The knowledge gathered from this research will be extremely helpful in understanding the complex effects of radiation therapy on the physical, psychological, and social aspects of survivors’ quality of life.",
"keywords": [
"Quality of life (QoL)",
"breast cancer",
"post radiotherapy",
"impact",
"assessment"
],
"content": "Introduction\n\nBreast cancer is the most common malignancy among women globally. It has now surpassed lung cancer as the leading cause of global cancer incidence in 2020, with an estimated 2.3 million new cases, representing 11.7% of all cancer cases. In India, the incidence has increased significantly, almost by 50%, between 1965 and 1985.1 Current trends point out that a higher proportion of the disease is occurring at a younger age in Indian women, as compared to the West. The overall 5-year survival rate appears to be 95%, 92%, 70%, and only 21% for stage I, II, III and IV patients respectively.2 The survival rate of patients with breast cancer is poor in India as compared to Western countries due to earlier age of onset, late stage of disease at presentation, delayed initiation of definitive management, and inadequate/fragmented treatment.1\n\nIndian Breast cancer patients especially those from poor socio-economical backgrounds have advanced physical symptoms and psychosocial distress that adversely affect their QoL. Their experiences with breast cancer vary but may include diagnosis, initial treatment, managing genetic risk and psychological effects, unique concerns associated with non-invasive breast cancer, recurrence, finishing treatment and returning to normal life, survivorship, and palliative care for advanced cancer.3 Many cancer patients may have questions regarding their condition as they adjust to their diagnosis, but they may be afraid to ask their doctor. Many women who receive a breast cancer diagnosis for the first time may experience shock, fear, anxiety, and sadness.4 Psychological therapies could assist patients in managing their feelings and treating any mental illnesses that may arise, such as anxiety, panic, and depressive disorders. Some cancer patients could be reluctant to express their worries about their condition and course of treatment, and they might be much more reluctant to bring up any psychological issues they might experience. Although patients want their medical professionals to ask about their everyday activities and general well-being, this may not always happen.4\n\nIn the past, objective tumor response and survival have been used to evaluate the effectiveness of cancer treatments. Throughout the past ten years, there have been two significant shifts in the way that cancer is treated. The first is the understanding that receiving cancer therapy depends on the patient’s mental health.5 Another is the use of psychosocial and QoL surveys to gauge their level of well-being. Psychosocial and emotional issues have been studied in intervention studies with breast cancer patients for the past 25 years. A key clinical and research topic has been how breast cancer treatment affects a patient’s quality of life. Psychosocial workers, nurses, and oncologists all that QOL is a crucial factor to take into account during and after cancer treatment.6 Physical functioning, psychological well-being (including anxiety and depression levels), and social support are some of the categories that make up quality of life. Evaluations of QOL have applications in diagnosis, prognosis prediction, assessment, patient monitoring, clinical decision-making, communication, and therapy. Additional applications include developing system interventions, assigning funds for research and resources, educating medical staff, and cutting expenses.3\n\nThe course of treatment for breast cancer is determined by the specific subtype of the disease and the extent to which it has spread to lymph nodes (stages II or III) or other regions of the body (stage IV). The treatment mainly consists of Surgery, Chemotherapy (Neoadjuvant, adjuvant, and palliative), Radiation therapy, and hormonal therapy. It lessens the chance of recurrence in the breast and the tissues around it.7 Researchers use a variety of assessment instruments to assess the QoL in patients with breast cancer receiving radiation therapy. There are two primary categories for disease-specific measures, such as the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire - Breast Cancer Module (EORTC QLQ-BR23) and the Functional Assessment of Cancer Therapy-Breast (FACT-B). The Short Form Health Survey (SF-36) and EuroQol-5D (EQ-5D) are examples of generic instruments.8 Crucial factors to take into account are validity, which guarantees accurate measurement, and dependability, which guarantees consistent results. Good test-retest reliability and internal consistency have been shown by generic instruments like the EQ-5D and SF-36 across a range of cancer groups. Disease-specific measures like the FACT-B and EORTC QLQ-BR23, which show strong correlations with clinical indicators and sensitivity to changes in health status after therapy, are further examples of construct validity. In the context of AVBRH, Sawangi breast cancer patients, these validated metrics offer a robust foundation for assessing radiation therapy’s impact on quality of life.\n\nImran M et al. This cross-sectional study aims to determine the quality of life (QoL) differences between various groups and evaluate the QoL of a cohort of breast cancer patients at the Oncology Department, King Abdulaziz University Hospital (KAUH), King Abdulaziz University (KAU), Jeddah, Saudi Arabia (SA). Breast cancer survivors’ quality of life was evaluated using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaires Core30 and BR23 (EORTC QLQ-C30 & BR23). They conclude that Patients with breast cancer who came to their institute had improved quality of life in terms of functional and symptom ratings, as well as overall global health status. Patients’ physical functioning scores were the lowest and their social functioning scores were the greatest.9\n\nBener A. et al. their study aimed to assess the psychometric properties of the Arabic version of the European Organization for Research and Treatment of Cancer (EORTC) general QoL questionnaire (QLQ-C30) for breast cancer patients in Qatar. The conclusion is that the Qatari Arabic version of the EORTC QLQ-C30 showed acceptable psychometric properties, which is a reliable and valid instrument, that can be used by oncologists.10\n\nKluthcovsky AC et al. conducted research to assess fatigue and quality of life in disease-free breast cancer survivors about a sample of age-matched women with no cancer history and to explore the relationship between fatigue and quality of life. A cross-sectional research comprising 202 Brazilian breast cancer survivors who were free of disease and had undergone treatment at two sizable hospitals was carried out. The patients were compared to age-matched women who visited a primary healthcare center and had no history of cancer. We measured the quality of life and fatigue using the World Health Organization Quality of Life Instrument (WHOQOL-BREF) and the Piper Fatigue Scale-Revised, respectively. Additionally, clinical and sociodemographic characteristics were acquired. The findings of this study highlight the importance of assessing fatigue and quality of life in breast cancer survivors.11\n\nThis study aim is to analyze the quality of life (QoL) among breast cancer patients undergoing treatment at Siddharth Gupta Memorial Cancer Hospital through a QoL questionnaire.\n\n\n\n• Examine the overall effects of breast cancer on patients’ physical, social, and psychological well-being at Siddharth Gupta Memorial Cancer Hospital.\n\n• Investigate variations in patients’ well-being throughout different stages of treatment.\n\n• Identify unique challenges breast cancer patients face in performing daily tasks and maintaining physical functioning.\n\n• Utilize quality-of-life questionnaires to subjectively evaluate patients’ psychological and emotional experiences during and after treatment.\n\n• Explore patients’ strategies for managing emotional distress during their cancer journey.\n\n• Assess the availability and impact of social support networks on patients’ quality of life, including relationships with friends, family, and the larger community.\n\n• Analyze how different treatment modalities and their side effects influence patients’ overall health.\n\n• Propose improvements to healthcare protocols in Siddharth Gupta Memorial Cancer Hospital based on findings.\n\n• Evaluate the effectiveness of administrative and social support services in enhancing patients’ overall quality of life and satisfaction with care.\n\n\nMethods\n\nThis observational cross-sectional study will be held in the department of Acharya Vinoba Bhave Rural Hospital associated with Datta Meghe Institute of Higher Education and Research (DMIHER), and the hospital is situated in the state of Maharashtra, in India, between the time frame of January 2023 to October 2023. The study will be conducted after obtaining written consent from breast cancer patients (or caregivers) who have received the form of radiotherapy (chemotherapy and radiotherapy) from Acharya Vinoba Bhave Rural Hospital. EORTC QoL questionnaires C30 and BR23 are to be used along with required consent from patients and caregivers.\n\nThe study registered on 02 February 2024 in institutional ethical committee of the Datta Meghe Institute of Higher Education and Research, DMIMS (DU)/IEC/2023/215.\n\nInclusion criteria:\n\n\n\n• Patients must be literate and capable of either writing or speaking in Hindi or Marathi, the regional languages.\n\n• Alternatively, if the patient is not literate, their caregiver must possess a sufficient level of literacy.\n\n• Participants must have undergone radiotherapy treatment for breast cancer.\n\n• Patients’ medical records should include details of surgery, chemotherapy, and radiotherapy.\n\n• Patients or their caregivers must be accessible via telephone for data collection regarding aspects related to their quality of life post-radiotherapy.\n\nExclusion criteria:\n\n\n\n• Patients falling outside the specified time frame of the study period (2023 to 2024) will not be considered for inclusion\n\n• Illiterate patients and those unable to speak or write Hindi or Marathi, the regional languages\n\n• Patients for whom essential medical data, including details of surgery, chemotherapy, and radiotherapy, are unavailable, will not be included in the study\n\nBias:\n\n\n\n• Possibility of recollection bias\n\n• study does not consider patients who received only surgery and chemotherapy (NACT, adjuvant, and palliative)\n\n• Potential cultural differences impacting participant experiences\n\nVariables:\n\nFor this study, we will use different kinds of data such as patient demographic data, clinical outcome, and Outcome variables. The outcome variables are finally associated with the outcome of the study.\n\nDemographic variables:\n\n• Gender\n\n• Age\n\n• Material status\n\n• Associate illness\n\n• Education\n\n• Current occupation\n\n• Menopausal status\n\n• Monthly/salary income\n\n• Religion\n\nClinical outcome:\n\n\n\n• Biopsy date\n\n• TNM stage\n\n• Stage of the disease\n\n• Surgery date\n\n• Type of surgery\n\n• Pathological TNM\n\n• Chemo (NACT/ADJ/PALL)\n\n• Chemo regimen\n\n• Herceptin\n\n• Hormonal therapy\n\n• RT registration date\n\n• Simulation date\n\n• Plan\n\n• Technique (3D CRT/IMRT)\n\n• RT start date and end date\n\nOutcome variables:\n\n\n\n• The European Organization for Research and Treatment of Cancer Quality of Life cancer-specific questionnaire (EORTC QLQ-C30)\n\n• The European Organization for Research and Treatment of Cancer (EORTC) Quality of Life breast cancer-specific questionnaire (QLQ-BR23)\n\nSample size calculation:\n\nWe are expecting approximately 60-150 patients treated with adjuvant radiotherapy for breast cancer.\n\nType of sampling:\n\nAll the files registered for radiation oncology for the treatment of breast cancer in the specified period. The patients will be selected through a systematic sampling method.\n\nFormula used:\n\nPrimary variable Overall health score assessed by EORTC QLQ-C-30 score\n\nAssumption Z1−α/2 = 0.01 = 2.58, Power (1- β) at 99% = 2.34\n\nMean difference (δ difference) = 26.66\n\nWe considered standard deviation difference σDifference = 28.65\n\nRequired sample size = 59\n\nReferred article: Ref. 12.\n\nThe case report form including the patient’s name, age, sex, marital status, associate illness, education, current occupation, menopausal status, number of children, monthly salary income, religion, and history of treatment including biopsy date, ER/PR/HER2, TNM stage, etc will be noted using their previous diagnosis files and by communicating with patients. The Case reform form is having 31 questions including patients’ demographic data and past diagnosis. It will be filled by the examiner.\n\nAfter an explanation of the study, the principal researcher will answer the participants’ questions and present the consent form for signature. The patients who are coming to the hospital for their follow-up will complete the questionnaires. If the patient is unable to fill or answer the questions caregiver will fill the questionnaires. The patients will complete the following questionnaires:\n\n• The European Organization for Research and Treatment of Cancer Quality of Life cancer-specific questionnaire (EORTC QLQ-C30) to assess HRQoL.13\n\n• The European Organization for Research and Treatment of Cancer (EORTC) Quality of Life breast cancer-specific questionnaire (QLQ-BR23) to assess HRQoL\n\nDistant patients who are eligible for this study will be contacted through telephone conversation and the examiner will ask their demographic data and questions related to QoL using interview checklists.\n\n\n\n1. Identification of specific psychosocial Challenges: The study is expected to identify shared psychosocial issues among breast cancer survivors post-radiation therapy.\n\n2. Improved integration of mental health support services: By identifying common psychosocial issues, the study may facilitate the integration of mental health support services within the oncology department and hospital settings.\n\n3. Informed treatment decision-making: Insights into how different treatment modalities affect quality of life can inform treatment decisions.\n\n4. Enhanced healthcare protocols: The study results can inform the development of healthcare protocols and interventions tailored to the needs of breast cancer survivors.\n\n5. Holistic understanding of survivorship: The study is expected to provide a comprehensive understanding of the variables affecting breast cancer survivors’ quality of life after radiation treatment in a rural Indian environment.\n\nAll the results will be calculated using R software version 4.3. Descriptive statistics will be tabulated and will be presented in mean, median, and std. deviation for quantitative measurement & in frequency and percentage for qualitative data. Missing values will be incorporated by applying mean and median values using the imputation method. The outcome variable will be tested for finding the significant association of quality of life with factors associated using chi-square analysis at ordinal or nominal data more than two categories and Fisher Exact’s test for two category ordinal data or nominal data. For quantitative measurement with t-test or ANOVA at parametric values and mann-whitney or kruscal-wallis test for non-parametric data for two or more two variables. The effect of confounding variables will be analyzed using multivariate analysis.\n\nThe proposal of the study was approved by the institutional ethical committee of the Datta Meghe Institute of Higher Education and Research (approved on 2nd February 2024; reference number: DMIHER (DU)/IEC/2023/215). Informed written consent will be obtained from each participant.\n\nAfter the completion of the study, we will publish it in an indexed journal.\n\nThe study is yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nSignificant new information about the quality of life among breast cancer survivors in rural India following radiation treatment was provided by the study. Important discoveries demonstrated the complex effects of radiation therapy on the physical, psychological, and social well-being of survivors. Numerous characteristics of quality of life were shown to be significantly correlated with demographic factors such as age, socioeconomic level, and educational background. Other characteristics that were found to have an impact were clinical variables such as cancer stage, treatment modes, and treatment outcomes. Moreover, coping mechanisms, social support systems, and psychological well-being were found to be important factors that influence survivors’ overall quality of life.\n\nThe results of the study offer important new perspectives on the complex effects of radiation treatment on the quality of life of Indian rural breast cancer survivors. The study’s observational methodology and reliance on self-reported data call for care when interpreting the findings, but they do highlight the intricate interactions between clinical, psychosocial, and demographic factors that influence survivors’ well-being. The results contribute to a nuanced understanding of survivorship experiences and inform the creation of focused treatments to improve patient care and support by taking into account the study’s objectives, limitations, and the larger body of evidence.\n\nThe study’s generalizability to other groups and contexts may be restricted, even though it provides insightful information about the experiences of breast cancer survivors treated at AVBRH, Sawangi. The application of study findings may be impacted by variations in socioeconomic conditions, cultural norms, and healthcare infrastructure in various locations. The study, however, provides a framework for examining survivor experiences and guiding healthcare practices to better address the needs of breast cancer survivors globally. This paves the way for further research in comparable rural healthcare settings.\n\n\nAuthor contribution\n\nInduni Nayodhara Weerarathna: Conceptualization, Methodology, Writing original draft, Visualization.\n\nAnurag Luharia: Conceptualization, Methodology, Writing- protocol and editing, Visualization, Supervision\n\nAshish Uke: Conceptualization, Writing- protocol and editing, Supervision\n\nGaurav Mishra: Conceptualization, Methodology, Writing- protocol and editing, Visualization, Supervision",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nRepository Name: Zenodo.\n\nFile Name: STROBE checklist for Assessment and impact in quality-of-life post radiotherapy in breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, 2023 – 2024.\n\nDOI: 10.5281/zenodo.11178076\n\nURL: https://zenodo.org/records/11178076\n\nFile name: Patient consent form for Assessment and impact in quality-of-life post radiotherapy in breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, 2023 – 2024.\n\nDOI: 10.5281/zenodo.11191397\n\nURL: https://zenodo.org/records/11191397\n\nFile name: Case report for Assessment and impact in quality-of-life post radiotherapy in breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, 2023 – 2024.\n\nDOI: 10.5281/zenodo.11191477\n\nURL: https://zenodo.org/records/11191477\n\nFile name: QOL questionnaires for Assessment and impact in quality-of-life post radiotherapy in breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, 2023 – 2024.\n\nDOI: 10.5281/zenodo.11191505\n\nURL: https://zenodo.org/records/11191505\n\nLicence: CC BY 4.0\n\nSoftware availability: Zenodo\n\nReporting guidelines: STROBE – Cross-sectional.\n\n\nReferences\n\nMehrotra R, Yadav K: Breast cancer in India: Present scenario and the challenges ahead. World J Clin Oncol. 2022; 13: 209–218. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaurya AP, Brahmachari S: Current Status of Breast Cancer Management in India. Indian J Surg. 2021; 83: 316–321. Publisher Full Text\n\nPerry S, Kowalski TL, Chang C-H: Quality of life assessment in women with breast cancer: benefits, acceptability and utilization. Health Qual Life Outcomes. 2007; 5: 24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBoard I of M (US) and NRC (US) NCPHewitt M, Herdman R, et al.: Psychosocial Needs of Women with Breast Cancer. Meeting Psychosocial Needs of Women with Breast Cancer. US: National Academies Press; 2004.\n\nKhan FA, Akhtar SS, Sheikh MK: Cancer Treatment - Objectives and Quality of Life Issues. Malays J Med Sci MJMS. 2005; 12: 3–5. PubMed Abstract\n\nLu Q, Chen L, Shin LJ, et al.: Improvement in Quality of Life and Psychological Well-being Associated with a Culturally Based Psychosocial Intervention for Chinese American Breast Cancer Survivors. Support Care Cancer Off J Multinatl Assoc Support Care Cancer. 2021; 29: 4565–4573. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBreast cancer: Accessed: December 22, 2023. Reference Source\n\nChen F, Ma LY, Zhao C, et al.: Quality of Life Assessment in Patients with Breast Cancer Receiving Radiation Therapy: A Prospective Study. Int J Radiat Oncol Biol Phys. 2022; 114: e457. Publisher Full Text\n\nImran M, Al-Wassia R, Alkhayyat SS, et al.: Assessment of quality of life (QoL) in breast cancer patients by using EORTC QLQ-C30 and BR-23 questionnaires: A tertiary care center survey in the western region of Saudi Arabia. PLoS One. 2019; 14: e0219093. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBener A, Alsulaiman R, Doodson L, et al.: An assessment of reliability and validity of the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire C30 among breast cancer patients in Qatar. J Fam Med Prim Care. 2017; 6: 824–831. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKluthcovsky ACGC, Urbanetz AA: Fatigue and quality of life in breast cancer survivors: a comparative study. Rev Bras Ginecol E Obstet Rev Fed Bras Soc Ginecol E Obstet. 2015; 37: 119–126. PubMed Abstract | Publisher Full Text\n\nda Silva JGB , Costa DT, Cavalcanti IDL, et al.: Quality of life in women with breast cancer treated at a radiotherapy centre in Caruaru, Pernambuco, Brazil. Can Oncol Nurs J. 2022; 32: 162–171. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEORTC QLQ-C30 Reference Values. EORTC Quality of Life Group: 2008. [accessed 2021-10-21]. Reference Source"
}
|
[
{
"id": "290379",
"date": "09 Jul 2024",
"name": "Volker Arndt",
"expertise": [
"Reviewer Expertise Epidemiology",
"HRQOL and Cancer Survivorship Research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReport This report describes the protocol of a study to assess quality-of-life post radiotherapy in breast cancer patients treated at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, 2023 – 2024.\nGeneral comments: Funding:\nNo information regarding funding is given. Either source of funding or a statement that there is no funding should be added.\nTitle:\nGiven that this is an observational cross-sectional study, words claiming causality (such as “impact”) should be avoided. The title should state that this is a study protocol (the current title is misleading)\nIntroduction:\nThe introduction is very general and does not lead to the specific question of the study. The authors are advised to get to the point more stringently. Para 1, 2nd sentence: A reference should be added to the statement regarding global incidence. Para 1, 3rd sentence: This sentence refers to a historic situation 40 years ago. What are the recent trends. Introduction, Para 4: Unclear, why the EORTC QLQ-C30, an instrument to be used in this particular study is not mentioned here. Introduction, Para 5-7: Three individual studies are described in a very detailed way. It is unclear why these three studies are presented in such a prominent way. Suggest to omit them.\nAims/Objective:\nThe objectives and study aim should be more concise, less descriptive/explorative. A clear hypothesis is missing. The objectives are too numerous. According to the methods described later in the article, some objectives may not be achievable. For instance, regarding the questionnaire data during and after treatment, the author does not clarify whether the same patients were surveyed at different time points. Additionally, there is no data collected on patients' emotion management strategies, friends and social support, or treatment side effects. Investigating variations in patients’ well-being throughout different stages of treatment requires a longitudinal study with repeated measurements. Different treatment modalities “effect” on the overall health of the patients shall be assessed, but no information is given in the methods how this should be accomplished. Similarly, the evaluation of the effectiveness of administrative and social support services to enhance QoL and satisfaction needs to be outlined in the methods section in more detail. \"undergoing treatment\" should be changed to \"undergoing radiotherapy\" to be more precise.\nMethods\nThe authors state that the has been registered in February 2024 but the first paragraph reads like that the study took place from January to October 2023. It is very unusual for a study to be registered after it has already taken place and reads like the study is already over. Please correct/revise.\nInclusion criteria:\nFemale gender is not listed among the inclusion criteria. Will also male breast cancer patients be included? Specific stage and age ranges are not specified. Will cases any age and stage be included? This will increase heterogeneity of the sample and lower the power.\nBias\nShould recollection bias read recall bias? The \"s\" in \"study\" at the beginning of the second point should be capitalized. The potential of selection bias and threads by imbalanced study sample should be addressed\nVariables\nDemographic Variables\nIf only female breast cancer patients will be included, then there is no need to include gender as covariate What is meant by “associate illness”? Please clearify The discussion section mentions the consideration of cultural norms. This would require that relevant variables need to be included. Furthermore, based on the article's objectives, variables like friends and social support, urban/city, language, support services and insurance should also be considered.\n\nClinical variables (“clinical outcome”)\nER/PR/HER2 are not mentioned. Consider including BRCA, histology of the tumour (pathological diagnosis), grading and metastatic sites.\n\nOutcome variables need to be specified in more detail (i.e. which scores or items?)\nStudy procedure:\nPatients who are coming to the hospital for their follow-up will be invited to complete the questionnaires. What about those who are not fit enough to attend the clinic? Will they be lost? The authors suggest different modes of administration (MOA) but should take into account that MOA has impact on patient reported outcome.\nExpected outcomes\nThe expected outcomes are very ambitious. It is questionable whether they can be achieved. #1: It is unclear how specific needs can be identified if there is neither a specified control group not an operationalization of needs? #3: Specify hypotheses, covariates, required sample size?\nSample size calculation\nThe authors state that the required sample size would be 59. Does this mean overall or per group? What are the groups? 59 reads small compared to many others studies and the reviewer's own experience. Consider to adjust for multiple testing given the plethora of scales used in the EORTC LQ-C30.\nStatistical analyses\nStatements like “outcome variable will be tested for finding the significant association” reads like a fishing expedition The authors state “The effect of confounding variables will be analyzed using multivariate analysis.”. The reviewer advices that potential confounders should be defined beforehand. This crucial for a study to be useful at all. Once the data have been collected it will be too late to fix it.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-555
|
https://f1000research.com/articles/12-159/v1
|
10 Feb 23
|
{
"type": "Research Article",
"title": "Corrosion of copper nickel titanium archwire in chlorhexidine, sodium fluoride, and chitosan mouthwashes",
"authors": [
"Erliera Sufarnap",
"Kholidina Imanda Harahap",
"Ika Devi Adiana",
"Davin Lim",
"Chatty Lim",
"Christy Christy",
"Kholidina Imanda Harahap",
"Ika Devi Adiana",
"Davin Lim",
"Chatty Lim",
"Christy Christy"
],
"abstract": "Background: Copper (Cu), nickel (Ni), chromium (Cr) ion release, and surface topography change from the orthodontic wire are the initial processes of corrosion that may affect the mechanical properties of the archwire. In this study, we aim to evaluate the effect of CHX, NaF, and chitosan on the corrosion of CuNiTi wire nickel and copper ions released, surface roughness change, and archwire deflection. Methods: Ninety samples of CuNiTi Tanzo™ archwires were divided into five groups according to their immersion solution: Artificial Saliva, CHX, NaF, CHX-NaF, and chitosan group. Each group was further divided into three subgroups (n=6) corresponding immersion time, i.e., two, four, and six weeks. The corrosion of the samples was analyzed with an atomic absorption spectrophotometer (AAS), scanning electron microscope (SEM), and universal testing machine (UTM). Results: The amount of nickel ion releases was increasing, but the copper ion releases were reduced by the time of observations. The highest nickel ion was released in the CHX-NaF group and the lowest in the chitosan group for six-week immersion. It also corresponded to the surface topography by SEM analysis which showed the most extended cracks and deep pits in the CHX-NaF group and a smoother surface in the chitosan group. Copper ion release showed the highest ion release in the NaF group and the lowest release in the chitosan group. The unloading force of CuNiTi archwire deflection remains the same at week two and week four for all mouthwashes. Conclusion: The use of mouthwashes that contained CHX, NaF, and chitosan could further alter the passive layer and cause higher nickel and copper ion release and increased CuNiTi archwire surface structure porosity. But there is no distinction between mouthwashes to release the unloading force within two until four weeks.",
"keywords": [
"CuNiTi archwire",
"nickel ion release",
"copper ion release",
"surface topography",
"deflection",
"unloading force",
"chlorhexidine",
"and natrium fluoride."
],
"content": "Introduction\n\nNickel-titanium alloy archwire offers greater flexibility and resistance to deformation and also exhibits excellent biocompatibility and corrosion resistance (Mitchell, 2013). Further addition of copper (Cu) in Cu nickel (Ni) titanium (Ti) archwires produces a more constant force on the teeth (Singh, 2007; Bhalajhi, 2012; Phulari, 2017). However, in the oral environment, archwires are constantly exposed to various stresses from masticatory forces, loading appliances, temperature fluctuations, and varieties of ingested food and saliva (Chaturvedi and Upadhayay, 2010).\n\nThe electrochemical mechanism of corrosion plays an essential role in metal corrosion when in contact with an electrolyte fluid, for example, saliva or mouthwashes. When two different alloys are in contact with a fluid electrolyte, the alloy with lower electrode potential will become the anode and produce oxidation that released several ions into the solution (Anusavice et al., 2012). Corrosion creates two issues; it can alter the physical properties of archwires (Mane et al., 2012; Geramy, Hooshmand and Etezadi, 2017; Doddamani, Ghosh and Tan, 2018) and cause a local or systemic condition due to allergic reactions and biological side effects (Lü et al., 2009; Pazzini et al., 2009; Suárez et al., 2010; Hafez et al., 2011; Castro et al., 2015). The metal products released during corrosion are nickel, chromium, and copper. Nickel is classified as a chemical carcinogen (IARC Working Group, 1990). In addition, it is a powerful medium for an immune reaction which can lead to a hypersensitivity reaction, contact dermatitis, gingivitis, gingival hyperplasia, periodontal stomatitis, periodontitis, burning mouth syndrome, angular cheilitis, cytotoxicity, mutagenic reaction (Hafez et al., 2011; Heravi et al., 2015; Lü et al., 2009). Meanwhile, copper is required by the body, but an excessive amount can produce cytotoxicity in the form of allergies at the point of contact and metal deposits in organs (Farrukh, 2011; Mahalaxmi, 2013).\n\nDeflection of the archwire also plays an essential role in affecting tooth movement during orthodontic treatment (Aghili et al., 2017; Khatri and Mehta, 2014). Deflection of the archwire is defined by the ability of the archwire to transmit forces to the dentoalveolar to promote tooth movement (Parvizi and Rock, 2003; Sarul et al., 2013).\n\nDental hygienist usually prescribes mouthwashes to patients with low oral hygiene and a high risk of caries to prevent the formation of microbial plaque (Anuwongnukroh et al., 2017; Castro et al., 2015). The use of fluoride mouthwashes helps the enamel layer remineralize and protects it from the acidic environment (Roveri et al., 2009; Sivapriya et al., 2017), but the production of hydrofluoric acid (HF) may have a destructive impact on the archwires. HF degrades the protective oxide layers on the surface, which leads to corrosion (Castro et al., 2015; Hafez et al., 2011; Lü et al., 2009; Marques et al., 2012; Suárez et al., 2010). But there are several published studies on the corrosion resistance of NiTi alloys in saliva and NaF solutions even with increasing concentrations of fluorides (Heravi, Hadi Moayed and Mokhber, 2015; Mirhashemi, Jahangiri and Kharrazifard, 2018; Fatene et al., 2019).\n\nChlorhexidine also has high effectiveness in preventing the formation of dental plaque and is also effective in decreasing gingival inflammation (Metin-Gürsoy and Uzuner, 2014; Deriaty, Nasution and Yusuf, 2018). Several authors have evaluated a significant lowering in corrosion resistance in stainless steel or NiTi archwires in chlorhexidine mouthwashes compared to other mouthwashes (Danaei et al., 2011; Deriaty et al., 2018; Habar and Tatengkeng, 2020). Several studies also showed degradation in the performance of an elastomeric chain (Sufarnap et al., 2021), and more significant surface corrosion was observed under the scanning electron microscope (SEM) in wires from chlorhexidine mouthwashes (Mane et al., 2012; Doddamani, Ghosh and Tan, 2018; Chitra, Prashantha and Rao, 2020).\n\nChitosan is a natural polysaccharide resulting from the deacetylation of chitin. Chitosan has a broad antibacterial content and a low level of toxicity, so it is often used as a mouthwash for plaque control (Chen and Chung, n.d.; Fei Liu et al., 2000). A study by Uraz et al. showed no significant difference in the use of chitosan mouthwash compared to chlorhexidine mouthwash plus chitosan in decreasing plaque index (Uraz et al., 2012).\n\nSeveral studies were conducted on the corrosion resistance, deflection, and ion release of NiTi orthodontic archwires in chlorhexidine or fluoride mouthwashes. However, there were limited studies observing nickel ion release, copper ion release, deflection test, and surface structure in mouthwashes containing chlorhexidine and fluoride, and Chitosan in CuNiTi archwire, and as such this became the objective of this study. We hypothesized the differences found at each immersion solution at each time observation to the surface structure, deflection, and nickel and copper ion release. This study is a continuation of Devi et al. (2022) study.\n\n\nMethods\n\nThe research type was an experimental study using a post-test control design. There were ninety Tanzo (American Orthodontics®) CuNiTi 4cm long archwires, sized 0.016×0.022 inches. Samples were divided into five groups according to the immersion solution, i.e., control group, CHX group, NaF group, CHX-NaF group, and chitosan group. The samples were further divided into three subgroups (n=6) corresponding to the duration of immersion, two, four, and six weeks (Irmawantini, 2017).\n\nEach group has 18 samples divided into three subgroups (n=6) according to the immersion time: two, four, and six weeks. Group 1: immersed in artificial saliva (produced by the Oral Dental Hospital of Universitas Sumatera Utara Pharmacies as a control group); Group 2: immersed in artificial saliva and 0.1% chlorhexidine gluconate mouthwash (Minosep, Minorock, Indonesia; as the CHX group); Group 3: immersed into artificial saliva and 0.05% NaF (Merck KGaA, Darmstadt, Germany, as the NaF group); Group 4: immersed into artificial saliva, 0.05% NaF, and 0.12% chlorhexidine gluconate (PerioKin®; as the CHX-NaF group); Group 5: immersed into artificial saliva and 2% chitosan (prawn shells was formulated at the Laboratory of Research Centre (Faculty of Mathematics and Science, Universitas Sumatera Utara as the chitosan group). Ninety samples were made in total, and they were all incubated at 37°C.\n\nArchwires were simulated in the mouth, all samples were immersed in 10 ml saliva within observation time, and mouthwashes were simulated two times a day for one minute. All samples immersed corresponding to the subgroup 2, 4, and 6 weeks; Minosep® mouthwash, 0.05% NaF, PerioKin®, and chitosan mouthwash were added into the test tubes in group 2 to 5 simulated respectively for 28 minutes at two weeks subgroup, 56 minutes at four weeks subgroup, and 84 minutes at six weeks subgroup. After being immersed at each time point, wires were removed from the solutions, washed with distilled water, and dried. Test tubes were sealed again with aluminum foil and placed at room temperature to prepare the analysis.\n\nThe research was conducted at the Faculty of Pharmacies Laboratory, Universitas Sumatera Utara, where the samples were incubated at 37°C; nickel and copper ion release sample’s immersed solution were analyzed at Balai Standardisasi dan Pelayanan Jasa Industri (Baristand) Medan using atomic absorption spectrometry (AAS, Shimadzu AA7000); the surface structure of CuNiTi wires was tested with a scanning electron microscope (SEM) (Hitachi TM3000, Tabletop Microscope, Japan) at 2000× magnification on three sites at Integrated Research Laboratory- Universitas Sumatera Utara; and deflection test with the universal testing machine (Tensilon RTF 1350) at the Impact Fracture Research Center (IFRC) Laboratory, Faculty of Engineering, Universitas Sumatera Utara.\n\nStatistical analysis was performed using Statistical Package for Social Science (SPSS) 26.0 edition with Shapiro-Wilk for normality test (p≤0.05). The data obtained were analyzed statistically using the Kruskal-Wallis test to compare the amount of unloading force, nickel, and copper release in weeks two, four, and six.\n\n\nResults\n\nMean levels of nickel and copper released in each group for every time observation were significantly different, and the data are shown in Tables 1 and 2, respectively (Sufarnap, 2022). Scanning electron microscope (SEM) images results after six weeks of immersion (the longest time) of CuNiTi’s wire surface topography are shown in Figure 1. The roughness was found in all groups, but the most extended surface defects, such as cracks and pits, were found in the CHX-NaF group, followed by more comprehensive pits in the CHX group compared to another group.\n\nImmersed with A. Control Group B. CHX Group C. NaF Group D. CHX+NaF Group E. Chitosan Group. (1,2,3 represent 2, 4, and 6 weeks).\n\nAccording to the result, nickel ions are increasingly released by the time of observation in all groups. In the beginning, the highest nickel released was at the chitosan group, but it had a slow release. The highest amount of nickel release also corresponded to the surface structure, which was the most prolonged observation in group 4 (CHX-NaF) (Figure 2) (Sufarnap et al., 2022).\n\nAbbreviations: NaF: Sodium Fluoride; CHX: Chlorhexidine; CHX-NaF: Chlorhexidine-Sodium Fluoride.\n\nCopper ions released showed reduced by the time of observation at all groups. The highest copper released was found in the NaF group for all observation times (Figure 3) (Sufarnap et al., 2022). The last analysis was the mean levels of unloading forces in each group. They are shown in Table 3. Based on the results, there were no significant differences in unloading forces at two weeks and four weeks of all groups but showed a significantly different in six week group. The data are shown in Table 3 and Figure 4 (Sufarnap et al., 2022).\n\nAbbreviations: NaF: Sodium Fluoride; CHX: Chlorhexidine; CHX-NaF: Chlorhexidine-Sodium Fluoride.\n\n* p-value between mouthwashes;\n\n** p-value between Kruskal Wallis test (p<0.05).\n\nNaF: Sodium Fluoride, CHX: Chlorhexidine, CHX-NaF: Chlorhexidine-Sodium Fluoride.\n\nAbbreviations: NaF: Sodium Fluoride; CHX: Chlorhexidine; CHX-NaF: Chlorhexidine-Sodium Fluoride.\n\n\nDiscussion\n\nThe highest amount of nickel ion was 0.2020 mg from the CHX-NaF group at the six-week group, and the highest amount of copper ion was 0.03377 mg from the CHX-NaF group at week two. This showed the highest concentration of both ions was still below the warned concentration limit. The average amount of nickel intake obtained from food is 300 μg–500 μg/day (Alarifi et al., 2013; Milheiro et al., 2016). While the nickel concentration of 600 μg–2500 μg can induce an allergic reaction, and a copper concentration of 10 ppm can cause a cytotoxic reaction (Danaei et al., 2011; Milheiro et al., 2016). Therefore, nickel and copper ions in this study were still released in the artificial saliva (control group), although it had the least amount compared to the other group.\n\nChlorhexidine used for a long time can generate Reactive Oxygen Species (ROS), the primary agent responsible for endogenous DNA damage (Septiani and Auerkari, 2020). Nik et al. and Omidkhoda et al. found that CHX immersion had no significant effect on NiTi archwire surface roughness, corrosion, and frictional resistance (Danaei et al., 2011; Nik et al., 2013). But some authors found a significant decrease in corrosion resistance due to CHX mouthwashes (Danaei et al., 2011; Deriaty et al., 2018; Habar and Tatengkeng, 2020), and some authors found more significant surface corrosion with SEM analysis (Mane et al., 2012; Doddamani, Ghosh and Tan, 2018; Chitra, Prashantha and Rao, 2020). This study also found the surface topography showed that the CHX group had rougher and more pitted surfaces compared to the control group or baseline topography.\n\nIn six weeks of immersion CuNiTi wire in the CHX-NaF group has the highest amount of nickel ions released and in the NaF group, more copper ions were released than the other group. The unloading force difference is also significantly seen in the CHX-NaF and chitosan groups within different immersion durations. As a result, there were changes in CuNiTi mechanical properties after immersion of CHX-NaF, NaF, and chitosan for six weeks.\n\nNaF content in perioKin® (CHX-NaF) mouthwash can increase the metal ions released from the CuNiTi orthodontic wire. Heravi et al. found that the NaF content in mouthwash solution would decrease the corrosion resistance of NiTi and CuNiTi wires as the NaF concentration increased (Heravi, Hadi Moayed and Mokhber, 2015; Fatene et al., 2019). Sabah and Jarjees also reported that the interaction between fluoride and titanium might cause destruction to the metal coating of the archwires and degrade the mechanical properties (Sabah, Jarjees and Awni, 2011).\n\nThe immersion of Chitosan showed significant differences in Nickel and copper ion release, surface topography, and unloading force. Chitosan mouthwash has been used due to its antibacterial effect and lack of side effects. Uraz et al. have reported that Chitosan 2% mouthwash had no significant difference compared to CHX 0,2% in reducing plaque index and gingivitis (Uraz et al., 2012).\n\nThe highest nickel ion released was found in the chitosan group at week two, but it increased slowly and steadily compared to other groups, and it lasted with the lowest nickel released for the longest immersion time (six-week immersion). The same result with copper ions released. It was found that the chitosan had the lowest amount of ions released from week two until six weeks. Unfortunately, nothing was found about the chitosan particles used as an inhibitory of corrosion for orthodontic archwire, but Putri et al. researched orthodontic mini-implant immersed in chitosan mouthwashes for the surface topography found that the mini implant immersed with 1.5% of chitosan mouthwash had a smoother surface compared to chlorhexidine and Sodium Fluoride mouthwash. The CuNiTi archwire surface topography in this study found that the roughness of the chitosan group also had a smoother area compared to CHX and CHX-NaF groups (Putri et al., 2021).\n\nFurlan et al. mentioned that there were differences in the amount of nickel and copper ions released in several types of CuNiTi wire immersed in a neutral solution and an acidic solution, which were greater in the acidic solution (Furlan et al., 2018). The main limitation of this study was that it did not analyze the pH changes within each immersion solution and each observation time. This study was also done under the static condition in vitro. Further research is needed to determine the situation with in vivo experiments. The surface structure should also be better analyzed with advanced equipment, i.e., atomic force microscopy (AFC), so that we could measure the quantity of the surface by its roughness. This will allow us to better understand the physical properties of CuNiTi wire.\n\n\nConclusions\n\nCuNiTi wire had an increase of nickel and reduced copper ion release parallel to the increasing of immersion time, but the deflection of the wire did not show any significant differences between mouthwashes. However, after six weeks of immersion, the amount of Nickel and copper ions released still within the safe limit. The surface roughness of CuNiTi archwire topography showed that the CHX-NaF group had the most extended cracks and deep pits. The unloading force of the CuNiTi archwire deflection remains the same at week two and week four for all mouthwashes.",
"appendix": "Data availability\n\nOSF: Data of Corrosion of CopperNickelTitanium Archwire in Chlorhexidine, Sodium Fluoride and Chitosan Mouthwashes, https://doi.org/10.17605/OSF.IO/5QB8E (Sufarnap, 2022).\n\nThis project contains the following underlying data:\n\n- Copper Ion Release of CuNiTI Tanzo Archwires.pdf\n\n- Deflection of CuNiTi Tanzo Archwires.pdf\n\n- Nickel Ion Ni Release of CuNiTi Tanzo Archwire.pdf\n\n- SEM Surface topography of Tanzo AW (folder containing all raw SEM images)\n\nOSF: Data of Corrosion of CopperNickelTitanium Archwire in Chlorhexidine, Sodium Fluoride and Chitosan Mouthwashes, https://doi.org/10.17605/OSF.IO/5QB8E (Sufarnap, 2022).\n\nThis project contains the following extended data:\n\n- Figure 1, 2,4. Graph of Ni-Cu Ion Release and Deflection of Tanzo CuNiTi Archwier.pdf\n\n- Figure 3. Surface Analysis of CuNiTi Tanzo Archwire (SEM analysis).jpeg\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nAghili H, Yassaei S, Eslami F: Evaluation of the effect of three mouthwashes on the mechanical properties and surface morphology of several orthodontic wires: An in vitro study. Dent. Res. J (Isfahan). 2017; 14: 252–259. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlarifi S, Ali D, Verma A, et al.: Cytotoxicity and genotoxicity of copper oxide nanoparticles in human skin keratinocytes cells. Int. J. Toxicol. 2013; 32: 296–307. PubMed Abstract | Publisher Full Text\n\nAnusavice KJ, Shen C, Rawls HR: Phillips’ Science of Dental Materials. 12th ed.Saunders;2012.\n\nAnuwongnukroh N, Dechkunakorn S, Kanpiputana R: Oral Hygiene Behavior during Fixed Orthodontic Treatment. Dentistry. 2017; 7. 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PubMed Abstract | Publisher Full Text\n\nPazzini CA, Oliveira G, Marques LS, et al.: Prevalence of nickel allergy and longitudinal evaluation of periodontal abnormalities in orthodontic allergic patients. Angle Orthod. 2009; 79: 922–927. PubMed Abstract | Publisher Full Text\n\nPhulari BS: Orthodontics Principle and Practice. 2nd ed.Jaypee Brothers Medical Publisher’s;2017.\n\nPutri AS, Anggani HS, Ismaniati NA: Corrosion Resistance of Titanium Alloy Orthodontic Mini-implants Immersed in Chlorhexidine, Fluoride, and Chitosan Mouthwashes: an in-vitro Study. J. Int. Dent. Med. Res. 2021; 14: 996–1002.\n\nRoveri N, Battistella E, Bianchi CL, et al.: Surface enamel remineralization: Biomimetic apatite nanocrystals and fluoride ions different effects. J. Nanomater. 2009; 2009: 1–9. Publisher Full Text\n\nSarul M, Kawala B, Antoszewska J: Comparison of elastic properties of nickel-titanium orthodontic archwires. Adv. Clin. Exp. Med. 2013; 22: 253–260. 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}
|
[
{
"id": "164307",
"date": "10 Mar 2023",
"name": "Asma Ashari",
"expertise": [
"Reviewer Expertise Orthodontics",
"clear aligners"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAn interesting study, although it would benefit from a sample size calculation (if no sample size, can mention it as a pilot study), it would add to the strength of the results, since the sample is already quite large.\nWho did the measurements and who scanned the samples? Are they qualified? Was it a single researcher or multiple? Are they calibrated? Any Intra Class Correlation Coefficient to asses intra and inter-reliability.\n\"All samples were immersed in 10ml salive within observation time\" what does observation time mean? Please elaborate.\nThe mouthwashes were immersed for one minute twice a day, although in practice is it not usually advice to do it for 30 seconds? And usually patients do it for less than that. Therefore the effects of this study are maybe twice as much as what you would expect clinically.\nMouthwashes are swished around the mouth, not immersed, again this may affect the clinical application.\nShouldn't the wires be washed with saliva instead of with distilled water? since mouthwashes should not be rinsed after gargling.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "9494",
"date": "29 Mar 2023",
"name": "Erliera Sufarnap",
"role": "Author Response",
"response": "Thank you very much for your kind attention to the wonderful insightful comments on our manuscript. This manuscript became very complete based on your pieces of advice in many chapters. We have revised the manuscript according to some inquiries you have suggested. Several additional sentences needed to be added based on the reviewer’s suggestions, which we already provided to consolidate the new sample size formulation. The following is our comprehensive comments on the review after revision: 1. An interesting study, although it would benefit from a sample size calculation (if no sample size, can mention it as a pilot study), it would add to the strength of the results, since the sample is already quite large. The sample size was conducted by using the Federer Technique in our references by Irmawartini as she stated in her book. We added the formulation to the manuscript. 2. Who did the measurements and who scanned the samples? Are they qualified? Was it a single researcher or multiple? Are they calibrated? Any Intra Class Correlation Coefficient to asses intra and inter-reliability. a. The measurement and the scanning process were done by one qualified laboratory assistant (Master's degree) in each lab. Their work experience is above 3 years for AAS and UTM machines and 7 years for SEM machines. b. Calibration - The SEM machine calibrates twice in a year interval. - The AAS machine calibrates once a year interval. - The UTM machines were calibrated before each study starts for each day of measurement. The laboratory has 1 to 3 times studies each year. c. - The SEM images were taken 3 times for each sample. The SEM images couldn’t be measured objectively. The Region of interest (ROI) of the images captured within the roughest area. - The AAS analysis had been taken one time with the Relative Percent Difference (%RPD) below 5% - The UTM machine results also came from one-time measurements from the machine. Calibration had been taken 5 times to get the optimal normal curve. The sample which had improper results were recalculated. Due to the 3 time images captured from SEM analysis, the %RPD below 5% for Ions released measurements and the 5 times calibrator had been taken to get the normal curve from the UTM machine measurement, all laboratory assistants were convinced that there was no need any intra or the inter reliability analysis for those inquiries. Thank you, Doctor, but we added the above explanation in the manuscript for each part of the analysis in the M&M section. 3. \"All samples were immersed in 10ml saliva within observation time\" what does observation time mean? Please elaborate. Observation time means the time as each subgroup time. All samples immersed corresponds to subgroup 2, 4, and 6 weeks. Samples were immersed in 10ml saliva within each observation time, acting as a simulation of the daily patient had the archwire within the mouth environment. This was our novel method to have a proper simulation of the mouth condition. The archwire did not immerse with only the mouthwash itself which commonly had the high detectable results. This method also prevented bad results coming with undetectable measurements if only a short immersed time of each mouthwash at each observation time, 2, 4, and 6 weeks coincidence to 28, 56, and 84 minutes of immersion with the simulation of mouthwash use in 1 minute twice a day. 4. The mouthwashes were immersed for one minute twice a day, although in practice is it not usually advised to do it for 30 seconds? And usually, patients do it for less than that. Therefore the effects of this study are maybe twice as much as what you would expect clinically. Based on our mouthwash prescription, it is instructed to do the mouthwash twice a day for 1 minute. Therefore, we conduct the immersion time based on it. The condition in which the patient does it for less than the prescribed immersion time is uncontrollable. As a result, we decided on the immersion time as the mouthwash company prescribed. 5. Mouthwashes are swished around the mouth, not immersed, again this may affect the clinical application. Yes, indeed. Mouthwashes are swished around and mixed with saliva in the patient’s mouth. However, we are using the same amount of mouthwash as it is usually used which is 10mL and mixed with saliva. In addition, the use of an agitator before immersion in the mouthwashes makes the solution homogenous. The samples were once again agitated before the archwire was removed for further analysis. By doing these, hopefully, won’t affect the clinical application. 6. Shouldn't the wires be washed with saliva instead of with distilled water? since mouthwashes should not be rinsed after gargling. While the observation time was ended, the wires have been removed and washed with distilled water to continue for another analysis (surface roughness topography with SEM machine), so that all biological or any material which could contaminate the surface image should be eliminated."
},
{
"c_id": "11241",
"date": "14 Jun 2024",
"name": "Asma Ashari",
"role": "Reviewer Response",
"response": "I now approve this report"
}
]
}
] | 1
|
https://f1000research.com/articles/12-159
|
https://f1000research.com/articles/12-1157/v1
|
15 Sep 23
|
{
"type": "Case Report",
"title": "Case Report: Chest Pain as an Uncommon Presentation for Euglycemic Diabetic Ketoacidosis in a Female Patient Using SGLT2 inhibitor",
"authors": [
"Shahd M. Abbas",
"Fajr Jamal A.bagi",
"Asmaa Abdalkarim",
"Nematalla Sabir Balla",
"Amro Abdelrahman",
"Khalid Y Fadul",
"Shahd M. Abbas",
"Fajr Jamal A.bagi",
"Asmaa Abdalkarim",
"Nematalla Sabir Balla",
"Amro Abdelrahman"
],
"abstract": "Sodium-glucose co-transporter-2 (SGLT2) inhibitors are well-recognised antidiabetic medications among clinicians due to its highly protective effects on cardiovascular and renal systems on diabetic patients. However, one of its uncommonly reported side effects is the development of euglycemic diabetic ketoacidosis (EuDKA) which is characterized by mild hyperglycemia, ketosis and acidosis. Chest pain as a clinical presentation of EuDKA has been rarely reported in the literature. We present a case of a 46-year-old female with a past medical history of type 2 diabetes mellitus (T2DM), hypertension, and hypertriglyceridemia presented to the hospital with central chest pain that radiates to the back and is associated with mild shortness of breath and one bout of vomiting. She had been taking dapagliflozin, an SGLT2 inhibitor, for four years. She was found to have a blood glucose level of 7 mmol\\L, high anion gap metabolic acidosis and ketonuria. Toxicology screening was unremarkable. She was diagnosed as a case of SGLT2-induced EuDKA and was treated with fluid, insulin and potassium chloride (KCL). Her hospital course went smoothly. Dapagloflzi was discontinued, and she was discharged home on oral metformin and subcutaneous insulin. This study highlights the rare occurance of chest pain as a presentation of EuDKA, an uncommon side effect of the widely used SGLT2 inhibitors. Chest pain in patients using SGLT2 Inhibitors should raise the clinician's suspicion for possible EuDKA.",
"keywords": [
"Diabetes",
"SGLT2",
"EuDKA",
"Chest pain"
],
"content": "Introduction\n\nDiabetic ketoacidosis (DKA) is one of the frequent complications of diabetes mellitus (DM), and it is characterized by the presence of hyperglycemia, ketosis, and high anion gap metabolic acidosis. Unlike DKA, euglycemic diabetic ketoacidosis (EuDKA) is characterized by a blood glucose level <11.1 mmol/L.1 EuDKA is an uncommon diagnosis with an incidence ranging between 2.6% to 3.2% of admissions.2\n\nSodium-glucose cotransporter-2 (SGLT2) inhibitors are relatively new antihyperglycemic medications that were introduced into the market in the last decade.3 Due to its scientifically proven cardiac and renal protective effects in diabetic patients, it has gained a lot of popularity in clinical practice. However, as with any medication, there’s a risk of side effects, and one of its rarely reported side effects is the development of euglycemic diabetic ketoacidosis.4\n\nTypically, EuDKA presents clinically with symptoms similar to those of DKA, such as nausea, vomiting, and abdominal pain.4 Furthermore, chest pain as a presenting symptom for EuDKA is relatively rare, and only a few cases have been reported in the literature.\n\nIn this case report, we are reporting a 46-year-old female with a past medical history of type 2 diabetes mellitus (T2DM) on SGLT2 inhibitor (Dapagliflozin) therapy for three years who presented to the hospital with central chest pain radiating to the back associated with shortness of breath and vomiting and was found to have high anion gap metabolic acidosis. She was diagnosed as a case of SGLT2 inhibitor-induced euglycemic DKA after excluding all other possible etiologies of EuDKA.\n\n\nCase presentation\n\nA 46-year-old non-pregnant Indian female with a past medical history of type 2 diabetes mellitus, hypertension, and hypertriglyceridemia presents to the hospital with central chest pain that radiates to the back and is associated with mild shortness of breath and one bout of vomiting. According to the patient, the pain has been present for more than a week but has significantly increased in the past two days. She denied any history of coughing, paroxysmal nocturnal dyspnea, or orthopnea. A review of other systems revealed no abnormalities. The patient denied any recent change in her diet or exercise, as well as her alcohol intake. She has had type 2 diabetes mellitus for more than six years, which has been previously treated. Four years ago she started taking an SGLT2 inhibitor, dapagliflozin (10 mg), but she has not improved her lifestyle and is not taking her medications consistently, and her HbA1C has consistently been elevated (11.3%). In addition to dapagliflozin, she was taking fenofibrate (200 mg) for hypertriglyceridemia and lisinopril-hydrochlorothiazide (20 mg/12.5 mg) for hypertension.\n\nIn the emergency department, her blood pressure was 156/82 mmHg, her temperature was 36.8°C, her heart rate was 91 beats per minute, her respiratory rate was 19 breaths per minute, and her oxygen saturation (SpO2) was 99% on room air. On physical examination, she was mildly distressed, and auscultation of the lung revealed clear lung fields with no rhonchi or crackles. A cardiac examination showed normal S1 and S2 with no added sounds. Examination of other systems was unremarkable. Two sets of troponin T enzymes were within the normal range (9 ng/dl), and her electrocardiogram (ECG) showed normal sinus rhythm with no ST changes. The result of the chest X-ray was unremarkable. A computed tomography (CT) scan was done, and it showed no evidence of pulmonary embolism (PE).\n\nA point-of-care venous blood gas test (VBG) result showed a blood glucose level of 7.7 mmol/L, a pH of 7.24, a PCO2 level of 19 mmHg, a HCO3 level of 13 mmHg, and a beta-hydroxybutyrate level of 3.2 mmol. Results of the basic metabolic panel showed a sodium (Na) level of 134 mmol/L, a potassium (K) level of 4 mmol/L, a chloride (Cl) level of 101 mmol/L, and a bicarbonate level of 13 mmol/L with a calculated anion gap of 20. Her lipid profile results showed triglyceride levels of 14.6 mmol/L, cholesterol levels of 9.6 mmol/L, and low-density lipoprotein levels of 4.8 mmol/L. In addition to that, high levels of glucosuria (+2) and ketonuria (+4) were also detected in the patient’s urine. A toxicology screening result showed normal levels of acetaminophen, ethanol, and salicylate.\n\nA diagnosis of SGLT2 inhibitor-induced euglycemic DKA (EuDKA) was made, and the patient started on IV fluid therapy with 0.45% sodium chloride (NaCL) with 5% dextrose (D5) (250 ml/hr), insulin infusion of 0.1 units/kg/hr, and potassium chloride (KCL) infusion of 20 mEq/L (125 ml/min) according to the local protocol. The patient was admitted to the medical floor for more observation and the potassium chloride (KCL) infusion was escalated to 40 mEq/L. Two days later, the patient’s chest pain improved, she was tolerating food, her lab results showed an HCO3 level of 23 mmol/L, and the anion gap was closed. Dapagliflozin was discontinued, and she was discharged home on oral metformin 500 mg, subcutaneous insulin aspart 20 units, and subcutaneous insulin glargine 30 units. She was advised to use a glucometer at home to monitor and record her blood glucose levels. A follow-up appointment was scheduled at the general medicine clinic. During her follow-up visit, the patient’s home readings were within the normal range.\n\n\nDiscussion\n\nEuglycemic DKA (EuDKA) is a life-threatening condition that needs emergent management. It may occur in type 1 or type 2 DM, and it’s characterized by milder degrees of hyperglycemia with blood glucose levels <11.1 mmol/l, which can result in delayed diagnosis and treatment with potentially adverse metabolic consequences.1\n\nNumerous conditions were reported to trigger euglycemic DKA, such as inadequate oral intake, insulin treatment before arrival at the emergency department, pregnancy, and sodium-glucose co-transporter 2 (SGLT2) inhibitors.5 The latest was the probable cause of our patient’s illness.\n\nIt’s worth mentioning that EuDKA does not necessarily present typical manifestations of DKA. In which marked hyperglycemia and the resultant dehydration are the usual causes. For example, patients with EuDKA treated with SGLT2 inhibitors may have less polyuria and polydipsia due to the milder degree of hyperglycemia, and these patients may only present with malaise, anorexia, tachycardia, or tachypnea with or without fever.6 However, chest pain as a manifestation of EuDKA or DKA has rarely been reported in the literature. A previous study reported a case of EuDKA presenting with chest pain in diabetic patients using SGLT2 inhibitor therapy who had recently started a ketogenic diet.7 In our case, the patient denied any recent changes in her diet.\n\nAnother study also reported a case of DKA presenting with chest pain after skipping insulin therapy while fasting. She was found to have a high blood glucose level of 17.1 mmol/L.8 Unlike our patient, who was only on SGLT2 therapy and had a blood glucose level of 7.7 mmol/L. Moreover, a case of ST-segment elevation myocardial infarction (STEMI) induced by SGLT2 inhibitor therapy presenting with chest pain has also been reported.9 In contrast, our patient presented with chest pain, but his ECG showed no ST-segment changes.\n\nThe presence of hypertriglyceridemia has been associated with lower levels of blood glucose in EuDKA. The concomitant presence of hypertriglyceridemia and SGLT2-induced EuDKA has been previously reported in the literature.10 Although our patient had a very high level of triglyceride (14.6 mmol/L), it remains uncertain if his high triglyceride levels have contributed to his EuDKA.\n\nSGLT2 inhibitors were approved by the Food and Drug Administration (FDA) in 2013. Their main mechanism of action aims to reduce glucose reabsorption by targeting the kidneys. SGLT2 proteins normally facilitate the reabsorption of glucose back into plasma, inhibiting this process leads to glucosuria and in turn lowering serum glucose levels.\n\nSGLT2 inhibitors are an effective class of agents for controlling blood glucose levels in T2DM. Evidence in literature showed significantly improved outcomes in diabetics with cardiovascular disease, including decreased stroke and myocardial infarction related mortality.11 SGLT2 inhibitors also impose a reduced risk of hypoglycemia,12 unlike other hypoglycemic agents. Considering the desirable outcome associated with SGLT2 inhibitors they are often preferred by doctors and patients. However, our case represents a rare undesirable outcome which is EuDKA.\n\nThe pathophysiology of EuDKA in SGLT2 inhibitor users is believed to be a result of hormonal adaptations involved in glucose metabolism in response to increased urinary excretion of glucose. Low glucose in serum reduces insulin secretion from beta-cells. The low insulin levels result in fatty acid accumulation due to increased lipolysis activity; fatty acids are converted to ketone bodies by Beta- oxidation in hepatocytes. Previous evidence suggests that SGLT2 inhibitors induce glucagon secretion from alpha- cells by direct stimulation of pancreas or either by secondary stimulation as a consequence of reduced insulin levels.13 SGLT2 inhibitors mimic starvation conditions by inhibiting glucose resorption, this leads to increased ketone production and resorption in blood.14 As a result the body is predisposed to acidemia by ketogenesis and the ongoing glucosuria results in normal to mildly elevated glucose serum levels manifesting as EuDKA.\n\nIt is also important to note the mechanism behind hypertriglyceridemia observed in our patient. Increased lipolysis leads to formation of free fatty acids being transported into the liver and forming high levels of low density lipoproteins (LDL), reflecting high triglycerides levels in blood.10\n\nThe management of EuDKA is similar to the management of DKA. The end goal of the treatment is to close the anion gap, address the electrolyte imbalance through insulin therapy, and correct dehydration through appropriate fluid resuscitation. However, it’s very important to maintain potassium levels between 4-5 while receiving insulin therapy, as it can result in hypokalemia and subsequent life-threatening arrhythmias. In addition, addressing the underlying triggers is a cornerstone of management.15\n\nOur patient was successfully managed with fluid therapy, insulin infusion, and potassium chloride, and her 2-day hospital course went smoothly; her chest pain had significantly improved, and she was tolerating food. Her lab results revealed an HCO3 level of 23, and she was discharged home on oral metformin and subcutaneous insulin, with discontinuation of dapagliflozin. She was advised to monitor her blood glucose level at home. On the follow up visit, the recorded result were within normal ranges\n\n\nConclusion\n\nEuDKA is a serious medical emergency that carries a sizable risk of delayed diagnosis and management, which could have detrimental metabolic effects.\n\nThe wide use of SGLT2 inhibitors among diabetic patients has been linked with development of EuDKA. Furthermore, chest pain as presenting symptoms in patients using SGLT2 inhibitors should be carefully evaluated by clinician for possible EuDKA.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: CARE checklist for “Chest pain as an uncommon presentation for euglycemic diabetic ketoacidosis in a female patient using SGLT2 inhibitor: Case report”. DOI: 10.5281/zenodo.8248574\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nOpen Access funding provided by Qatar National Library.\n\n\nReferences\n\nBarski L, Eshkoli T, Brandstaetter E, et al.: Euglycemic diabetic ketoacidosis. Eur. J. Intern. Med. 2019 May; 63: 9–14. Publisher Full Text\n\nJenkins D, Close CF, Krentz AJ, et al.: Euglycaemic diabetic ketoacidosis: does it exist? Acta Diabetol. 1993; 30(4): 251–253. PubMed Abstract | Publisher Full Text\n\nIqbal I, Hamid M, Khan MAA, et al.: Dapagliflozin-induced Late-onset Euglycemic Diabetic Ketoacidosis. Cureus. 2019 Nov 7; 11(11): e6089. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSomagutta MR, Pormento MKLL, Hange N, et al.: Patient-Specific Risk Factors and Clinical Correlates of Euglycemic Diabetic Ketoacidosis in Patients on Sodium-Glucose Co-Transporter-2 Inhibitors. J. Endocr. Soc. 2021; 5(Suppl 1): A473. Publisher Full Text\n\nDiabetic ketoacidosis and hyperosmolar hyperglycemic state in adults: treatment. UpToDate. [updated 2021 Jan 22; cited 2021 Feb 15]. Reference Source\n\nNasa P, Chaudhary S, Shrivastava PK, et al.: Euglycemic diabetic ketoacidosis: A missed diagnosis. World J. Diabetes. 2021 May 15; 12(5): 514–523. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDorcely B, Nitis J, Schwartzbard A, et al.: A Case Report: Euglycemic Diabetic Ketoacidosis Presenting as Chest Pain in a Patient on a Low Carbohydrate Diet. Curr. Diabetes Rev. 2021; 17(2): 243–246. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMohamad NAR, Cheah PK: Chest pain in emergency department: A diagnosis of diabetic ketoacidosis must be ruled out. Int. J. Case Rep. Imag. 2010; 1(3): 6–9. Publisher Full Text\n\nZughaib M, Basharat B, Small D: A Case of STEMI-Induced Euglycemic Diabetic Ketoacidosis in a Patient Receiving a Sodium Glucose Cotransporter-2 Inhibitor. JACC Case Rep. 2023 Feb 18; 11: 101792. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGajjar K, Luthra P: Euglycemic Diabetic Ketoacidosis in the Setting of SGLT2 Inhibitor Use and Hypertriglyceridemia: A Case Report and Review of Literature. Cureus. 2019 Apr 4; 11(4): e4384. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZinman B, Wanner C, Lachin JM, et al.: Empagliflozin, Cardiovascular Outcomes, and Mortality in Type 2 Diabetes. N. Engl. J. Med. 2015 Nov 26; 373(22): 2117–2128. Publisher Full Text\n\nClar C, Gill JA, Court R, et al.: Systematic review of SGLT2 receptor inhibitors in dual or triple therapy in type 2 diabetes. BMJ Open. 2012; 2(5): e001007. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBonner C, Kerr-Conte J, Gmyr V, et al.: Inhibition of the glucose transporter SGLT2 with dapagliflozin in pancreatic alpha cells triggers glucagon secretion. Nat. Med. 2015; 21(5): 512–517. PubMed Abstract | Publisher Full Text\n\nQiu H, Novikov A, Vallon V: Ketosis and diabetic ketoacidosis in response to SGLT2 inhibitors: Basic mechanisms and therapeutic perspectives. Diabetes Metab. Res. Rev. 2017 Jul; 33(5): e2886. PubMed Abstract | Publisher Full Text\n\nKitabchi AE, Umpierrez GE, Miles JM, et al.: Hyperglycemic crises in adult patients with diabetes. Diabetes Care. 2009 Jul; 32(7): 1335–1343. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "225909",
"date": "28 Dec 2023",
"name": "Rebecca J Vitale",
"expertise": [
"Reviewer Expertise Diabetes"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report details a 46-year-old woman with type 2 diabetes on SGLT2 inhibitor therapy who presented with chest pain and was found to have euglycemic DKA. The case is well-written and expands upon an unusual presentation of a rare but severe medication side effect. Major comments\nOverall the manuscript is very well-written and clear. It wasn’t clear how long the patient required insulin infusion for the DKA to resolve. The case description notes that 2 days later her chest pain had improved and she was tolerating food, but I wouldn’t expect her to have required 48 hours of insulin infusion with a pH of only 7.24. There is no mention of the fact that hypertriglyceridemia can impact the accuracy of lab results. It would be beneficial to report whether the samples were processed in some way so as to limit the impact of lipemia on lab results and discuss whether any lab results may have been impacted by lipemia. A helpful reference is (Soleimani N et al,2020) The discussion would benefit from inclusion of a paragraph regarding the pathophysiology of why DKA may present with chest pain.\n\nMinor comments\nThe report would benefit from grammatical editing, as there are some misspelled words, sentences that are not full sentences, and discrepancies in past vs present tense.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "11334",
"date": "13 Apr 2024",
"name": "Amro Abdelrahman",
"role": "Author Response",
"response": "Dear reviewer. Thanks for feedback. - Patient was on insulin infusion for 16 hours then shifted to subcutaneous insulin. This will be added to case presentation. - In our case, hypertriglyceridemia didn't affect the accuracy of results. - Regarding the DKA and chest pain, we aren't completely sure whether it was due to the ketogensis inducing prothrombotic state and ischemia or it was as a result of chylomicronemia affecting blood circulation. We think this might need a seperate article with full discussion of different context of chest pain with DKA. Thanks for your feedback again,"
}
]
}
] | 1
|
https://f1000research.com/articles/12-1157
|
https://f1000research.com/articles/13-554/v1
|
30 May 24
|
{
"type": "Systematic Review",
"title": "Extracellular matrix of lung scaffolds submitted to different means of sterilization: a systematic review",
"authors": [
"Ricardo S. Moura",
"Joao Pedro R. Afonso",
"Adriano L. Fonseca",
"Andressa D. Cereta",
"Diego A. C. P. G. Mello",
"Miria C. Oliveira",
"Iransé Oliveira-Silva",
"Rodrigo F. Oliveira",
"Deise A. A. P. Oliveira",
"Rodolfo P. Vieira",
"Renata K. Palma",
"Giuseppe Insalaco",
"Luis Vicente Franco Oliveira",
"Ricardo S. Moura",
"Joao Pedro R. Afonso",
"Adriano L. Fonseca",
"Andressa D. Cereta",
"Diego A. C. P. G. Mello",
"Miria C. Oliveira",
"Iransé Oliveira-Silva",
"Rodrigo F. Oliveira",
"Deise A. A. P. Oliveira",
"Rodolfo P. Vieira",
"Renata K. Palma",
"Giuseppe Insalaco"
],
"abstract": "Chronic respiratory diseases often necessitate lung transplantation due to irreversible damage. Organ engineering offers hope through stem cell-based organ generation. However, the crucial sterilization step in scaffold preparation poses challenges. This study conducted a systematic review of studies that analysed the extracellular matrix (ECM) conditions of decellularised lungs subjected to different sterilisation processes. A search was performed for articles published in the PubMed, Web of Sciences, Scopus, and SciELO databases according to the PRISMA guidelines. Overall, five articles that presented positive results regarding the effectiveness of the sterilisation process were selected, some of which identified functional damage in the ECM. Was possible concluded that regardless of the type of agent used, physical or chemical, all of them demonstrated that sterilisation somehow harms the ECM. An ideal protocol has not been found to be fully effective in the sterilisation of pulmonary scaffolds for use in tissue and/or organ engineering.",
"keywords": [
"Extracellular matrix",
"Scaffolds",
"Stem cells",
"Decellularization",
"Sterilization",
"Recellularization"
],
"content": "Introduction\n\nTissue engineering has evolved rapidly to allow the development of functional tissue substitutes to improve quality and prolong the life of patients through the regeneration or replacement of tissues and organs compromised by disease.1 Chronic respiratory illnesses such as chronic obstructive pulmonary disease (COPD), asthma, and lung cancer collectively rank as the third highest contributor to global mortality. Annually, More than four million individuals succumb prematurely to these lung conditions, with projections indicating a further rise in their prevalence in the forthcoming years.2 Chronic respiratory failure occurs in the advanced stages of these pathologies, and lung transplantation is the only therapeutic indication to allow survival.3\n\nThe sterilisation process is a crucial factor in obtaining acellular lungs before the recellularisation process, eliminating the risk of transmission of viruses and bacteria from the donor to the recipient to be transplanted.4 However, not all sterilisation methods used in the healthcare industry apply scaffolds for the regeneration of new structures and/or organs, because of the potential risk of damage to the structure and function of the extracellular matrix (ECM).4,5 Generally, protocols that involve gamma irradiation, ethylene oxide (ETO), or other chemical and physical agents such as low-frequency LASER are used during the scaffold sterilisation process. In this process, it is extremely important to efficiently eliminate microorganisms, such as fungi, bacteria, and/or viruses, and to preserve the structure and function of the ECM of the scaffolds to be repopulated with stem cells, ensuring the generation of a new functional structure.5\n\nIn organ engineering, several fundamental criteria still require adjustments, such as determining the species of candidates from the organ to be removed, the best protocols for decellularisation, the best means of sterilisation, the best way to obtain a functional ECM, the optimisation of recellularisation, the most suitable cell type for recellularisation, and the development of suitable bioreactors for the recellularisation process.6 Diverse investigations have demonstrated progress in whole-organ decellularization methods, facilitating the production of scaffolds for organ engineering.7–10 These scaffolds, originating from the natural extracellular matrix (ECM), offer biological cues and preserve tissue microarchitecture, including functional vascular networks capable of assimilating into the recipient’s circulatory system.11 Several decellularisation techniques have led to the development of scaffolds for various allogeneic or xenogenic organs, such as the heart, liver, lungs, and kidneys.12 Although some experimental studies involving the use of scaffolds from decellularised organs have shown encouraging results, the creation of whole functional organs for transplantation still requires further research.13 The integrity of the ECM structure and function must be preserved during the decellularisation and sterilisation processes.14 To support cell growth and new structural development, scaffolds must maintain the ECM without the loss of mechanical and elastic properties.14 In addition, the time required to obtain a native scaffold compatible with this application should be observed. The proper combination of these components can lead to the creation of new in vitro tissue replacements for the implantation of functional tissues.15 For decades, various materials have been used as scaffolds to build biological tissues. However, currently, synthetic scaffolds are not effective in recreating the complex tridimensional (3D) architecture of the original structures.16 Therefore, the use of allogeneic decellularised organs would be an excellent solution to this problem.17 In contrast, tissues and organs are formed by cells associated with the ECM, which are synthesised by unique and tissue-specific resident cells that in turn secrete components and molecules that can ensure their survival.17\n\nThe ECM, which influences cell migration, proliferation, and differentiation - crucial aspects of the recellularization process - is widely recognized as an ideal scaffold for tissue and organ engineering.14,17 In accordance with the state of the art, this study aimed to conduct a systematic review of studies that analysed the physiological conditions of the ECM of decellularised lungs subjected to different sterilisation processes.\n\n\nMethods\n\nThis systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) 2020 guidelines18,19 and used the Systematics for Experimentation in Laboratory Animals (SYRCLE) risk of bias analysis tool for animal studies. The SYRCLE is a recommended tool for assessing the risk of bias in randomised trials included in the Cochrane Reviews, adjusted for particular aspects of bias that play a role in animal intervention studies. A bibliographic search was performed in the PubMed, Web of Science, SciELO, and Scopus databases. Only complete articles published from 2012 to 2023 in English from any country of origin (without any restrictions) were included. The survey was conducted from 20 July to 20 October 2023 and did not use any automatic bibliographic search tool.\n\nA total of 241 scientific articles were identified after a detailed search of the aforementioned databases using keywords chosen according to the Medical Subject Headings (MeSH/NIH). Two researchers worked independently to identify and extract data and verify the quality of the studies using SYRCLE’s risk of bias tool for animal studies. Duplicate articles were removed, and studies were subsequentlyanalysed according to the inclusion and exclusion criteria. In cases where there was disagreement, both investigators reviewed the study designs, employment and exclusion criteria, intervention, and assessment of outcomes to reach a consensus. The third researcher, also involved in this study, was consulted in case of differences between the first two, and together, they reached a consensus.\n\nFor each selected database, a bibliographic search was performed for the title and abstract using the keywords according to the MeSH. The strategy of a predefined combination of keywords was adopted (‘Extracellular matrix’ AND ‘LASER’ OR ‘Extracellular matrix’ AND ‘Recellularization’ OR ‘Extracellular matrix’ AND ‘Sterilization’ OR ‘Extracellular matrix’ AND ‘Photodynamic therapy’) AND (‘Extracellular matrix’ AND ‘lung’ AND ‘LASER’ OR ‘Extracellular matrix’ AND ‘lung’ AND ‘sterilization’ OR ‘Extracellular matrix’ AND ‘lung’ AND ‘LASER’ AND ‘Sterilization’ OR ‘Extracellular matrix’ AND ‘lung’ AND ‘Sterilization’ AND ‘scaffold’) AND (‘Scaffold’ AND ‘lung’ AND ‘sterilization’). All titles were manually searched and analysed for inclusion. Reference lists of articles containing the title, authors’ names, language, and publication date were generated. In this systematic review, only scientific articles that reported experimental studies were included.19\n\nAll manuscripts initially considered relevant by title and abstract were eligible for inclusion in the review. The full text of the manuscript was obtained to verify that the participants met the inclusion criteria. Only studies that presented results from the use of different means of sterilisation of scaffolds and/or ECM of lungs in vitro were included, meeting the criteria of being full text, studies published in scientific journals with a rigorous peer review process, published in English, which described the use and effect of decellularisation methods, and sterilisation of pulmonary scaffolds and ECM in vitro. No restrictions were observed regarding the sample size, sample type, and intervention time for the included studies. Studies that used sterilisation, but did not assess the extracellular matrix; meeting abstracts; studies published in languages other than English; and studies addressing ECM and sterilisation of organs other than the lungs were excluded (Table 2).\n\nThis review analysed controlled experimental laboratory studies that used sterilisation through photodynamic therapy (PDT), physical or chemical techniques, LASER, light emitting diode (LED), and/or gamma irradiation in animal models such as rats, mice, pigs, and cows.\n\n\nResults\n\nThe initial bibliographic survey included 241 studies. Of these, 22 duplicate articles were excluded and 189 articles were rejected because they did not meet the inclusion criteria. After a complete reading of the texts, 13 studies were excluded because they failed to address the subject in question or because the methodology did not include a control group. After applying the exclusion criteria, 13 articles were eliminated, leaving 4 articles that investigated scaffolds and ECM sterilisation processes through chemical and physical means using PDT, LASER, LED, and gamma irradiation, published between the years 2011-2022 were finally analysed in this systematic review (Figure 1). The four articles that were included in this review underwent a risk bias analysis for animals according to the Systematics for Experimentations in Laboratory Animals (SYRCLE) (Table 1). Among the four studies selected for this systematic review, one used rat organs19 and three used mice20,21 (Table 2). Despite the small amount of published work in this area, the articles found demonstrated the effectiveness in the sterilisation process of used lung organs or tissues, with some tissue damage occurring during the sterilisation process; however, the ECM structures were preserved. Owing to the important functional and structural role of the ECM in the lungs, early changes are observed in several respiratory diseases. The possibility of analysing the ECM and identifying probable alterations is fundamental to allow a better understanding of future lung diseases; therefore, allowing early potentialisation of the therapeutic approach.23 Thus, this review gathered articles that evaluated the ECM and mechanical parameters of decellularised lungs subjected to some form of sterilisation through chemical or physical means such as irradiation, LASER, LED, or PDT, demonstrating the effectiveness of the sterilisation process of pulmonary scaffolds for further use in organ bioengineering. It is expected that with the optimisation of these processes, the generation of new organs on a large scale will be possible, solving one of the biggest health problems worldwide, and the availability of organs for transplantation will be possible in the not-too-distant future.24\n\n\n\n1. Bonenfant et al. (2013):\n\nHistological evaluation and Masson’s trichrome staining demonstrated that Newly decellularised lungs maintained the ECM architecture found in the native lung. Glycosaminoglycans (GAGs) were less evident by Alcian Blue staining in newly decellularised lungs, probably representing the loss of cell-associated GAGs during decellularisation. Lungs that underwent irradiation demonstrated a grossly abnormal appearance, with a scattered heterogeneous pattern of a thickened and fused alveolar septa, associated with large alveolar spaces typical of pulmonary emphysema. The lung architecture of the decellularised organs after three months of storage, with the use of peracetic acid and even at some level of irradiation, better resembled native or newly decellularised lungs after insufflation. In contrast, no significant improvement was observed in the lungs stored for 6 months.20\n\n2. Uriarte et al. (2014):\n\nScaffolds obtained from the lung decellularisation procedure showed a lack of cell nuclei compared to native lungs, as evaluated by 6-diamidino-2-phenylindole fluorescence solution (DAPI). Qualitative macroscopic evaluation of acellular lungs after sterilisation by gamma irradiation showed changes when compared to non-irradiated control lungs, with reduced organ size and apparent damage to the pleural surface. The relevant components of the ECM (elastin, laminin, and collagens I, III, and IV) remained almost unchanged in the acellular lungs before and after irradiation.21\n\n3. Balestrini et al. (2016):\n\nThe authors evaluated sterilisation with a sterility assurance level of 10−6 (SAL6) using supercritical carbon dioxide (ScCO2) at various processing times and peracetic acid (PAA)-containing additives. To achieve the desired inactivation of 10−6 Bacillus atrophaeus spores, a preconditioning time of at least 2 hours followed by 1.5 hours of exposure to ScCO2 was found to be necessary. To maintain confidence in the sterility of SAL6, all subsequent ScCO2 treatments involved a 2-hour preconditioning period followed by 2 hours of ScCO2 exposure. It was observed that ScCO2 alone, without the inclusion of PAA, did not effectively neutralize lung bioburden.19\n\n4. Oliveira et al. (2021):\n\nThe authors evaluated lung mechanics in all lung scaffolds of 12 mice divided into two groups: the control (n=6) administered 1 mL of phosphate buffered saline (PBS) and the experimental group (GPpIX) (n=6) group injected with 1 mL of protoporphyrin IX (PpIX) in the lungs, with both irradiated with 660 nm LED. There were no significant differences between the control and GPpIX groups, which showed equal ventilation. Pulmonary mechanical assessment parameters did not show significant differences between the two PDT intervals. In addition, no changes were observed over the irradiation time, indicating the maintenance of the viscoelastic behaviour of the pulmonary scaffold after 1 h of exposure to LED.8\n\n\nDiscussion\n\nThis systematic review included studies found in the scientific literature that verified the conditions of the ECM of lung scaffolds subjected to the process of decellularisation and sterilisation through physical and/or chemical resources. This bibliographic survey indicated observed that the components of the ECM responsible for maintaining the 3D lung structure, such as elastin, laminin, and collagens I and IV, remained practically unchanged after sterilisation of decellularised lungs. Analysis of lung scaffolds using scanning electron microscopy suggested that the microscopic lung structure was maintained despite slight alterations after application of the sterilisation method.\n\nStudies such as those by Balestrini et al. (2016) have suggested that traditional sterilisation methods of acellular lungs have allowed a complete reduction of the bioburden. The sterilisation protocol proposed in this study provides a reproducible and efficient method to generate sterile scaffolds for use in tissue engineering. Irradiation, even at a lower dose than that generally used for biological materials, produced significant distortions that were only partially responsive to subsequent lung reinflation.22 PAA, a denaturing agent used for sterilisation and to eliminate residual detergents and other reagents used during the tissue decellularisation process, has a less deleterious effect on the functional architecture of the resulting structure.22 The use of ScCO2 in sterilisation, is evidently a promising mechanism for whole-organ sterilization technologies.22\n\nBonenfant et al. (2013) drew attention to the fact that special attention is needed to better understand the various conditions that can compromise acquisition, decellularisation, sterilisation, storage, recellularisation, and implantation of the generated organ or structure. The authors emphasise that because the gold standard for decellularisation and sterilisation techniques, whether by chemical, physical, or biological means, is not established, the use of various protocols for sterilisation of organs and/or structures in vitro has been observed.20\n\nAnalysis of the literature has shown that some studies have performed sterilisation using chemical methods such as ETO, hydrogen peroxide, PAA, formaldehyde, flutaraldehyde or ScCO2. Other protocols use physical methods such as dry heat (oven), moist heat (steam under pressure – autoclaves), radiation (gamma – cobalt 60, cobalt ultraviolet), electron beam irradiation of 15 kGy, gamma irradiation of 31 kGy, 660 nm red LED, PDT, and certain wavelength LASERs. These resources can be used in conjunction; however, there is still no consensus on the best sterilization method. It is worth noting that this area still requires new experimental studies that show the effects of using traditional methods and new means that can be used to obtain sterile scaffolds for the recellularisation of organs and/or tissues. Table 2 illustrates the studies and their respective methodologies used in the sterilisation process of lung scaffolds.20–23\n\nBonenfant et al. (2013)\n\nAccording to this study, the lungs treated with PAA had an overall macroscopic appearance similar to that of native or newly decellularised lungs, although some central regions showed atelectasis. In contrast, lungs sterilised by irradiation (15 and 25 kGy) showed a grossly abnormal appearance with a scattered heterogeneous pattern of thickened and fused alveolar septa, and large emphysematous alveolar spaces. The architecture of lungs decellularised with PAA obtained from storage 3 months after insufflation better resembled native or newly decellularised lungs. In contrast, no significant improvement was observed in the 6-month storage lungs.20\n\nBalestrini et al. (2016)\n\nAccording to the literature, most pulmonary scaffolds are sterilised using high concentrations of PAA, resulting in ECM depletion. Depending on the extent of these injuries, mechanically altered tissues may have little or no storage potential. In this study, Balestrini et al. (2016) demonstrated that a sterilisation technique using ScCO2 can achieve a 10−6 sterility assurance level in ECM from decellularised lungs. In this study, we demonstrated that ScCO2 did not cause any major structural or biological degradation in the acellular pulmonary ECM, generating a sterile lung structure that can be stored for a long period. Stored sterile tissue is also suitable to allow cell adhesion and survival.19 Considering these results, the authors suggest that the proposed sterilisation protocol provides a reproducible and efficient method to generate sterile lung scaffolds for use in tissue engineering. The authors showed that ScCO2 surpassed traditional sterilisation levels with PAA in retaining the key biological and mechanical characteristics. Therefore, the use of ScCO2 in the sterilisation process of lung scaffolds can be a new, powerful, and easy-to-use tool for the generation of sterile lung organs or tissues for subsequent recellularisation. These results indicate that ScCO2 can be used to sterilize acellular lung tissue, as it can preserve the main biological components needed to obtain functional lung scaffolds for regenerative medicine purposes.22\n\nScCO2 was recently developed as a means of sterilising medical devices, implantable, and allograft tissues using extremely low levels of PAA (0.005–0.05%) to reach the level of probability of the presence of viable microorganisms in a unit load after sterilisation (SAL6) on bacterial endospores.22 ScCO2 can be sterilised through the enhanced mass transfer of CO2 during the supercritical phase and by disrupting the bacterial, viral, or fungal outer membrane.22 Furthermore, because ScCO2 has a diffusion capacity that allows it to penetrate ECM fibres, this process can sterilise at low temperatures and remove unwanted compounds such as blood or potentially residual DNA. In addition, ScCO2 leaves no toxic residue, making it ideal to sterilise the delicate ECM.22 In studies that used ScCO2 and PAA as sterilisation mechanisms, sterilised tissues showed a significant increase in stiffness in newly decellularised lungs. These data indicate that ScCO2 sterilisation does not compromise the mechanical integrity of acellular lung tissue. The authors demonstrated that ScCO2 surpassed sterilisation levels when compared to traditional PAA in terms of its ability to preserve the main biological and mechanical characteristics. Therefore, the use of ScCO2 in sterilisation can be a powerful tool for whole-organ sterilisation and recellularisation technologies.22\n\nBonenfant et al., 2013\n\nIn the study by Bonenfant et al. (2013), the effects of sterilisation were evaluated using a protocol commonly applied to the storage of other biological scaffolds through irradiation. Irradiation, even at a dose lower than that usually used for other biological materials (15 and 25 kGy), produced a significant distortion that was only partially responsive to subsequent lung reinsufflation.20\n\nUriarte et al., 2014\n\nQualitative macroscopic evaluation of acellular lungs after sterilisation by gamma irradiation showed changes when compared to non-irradiated lungs. The main changes observed were a reduction in organ size and apparent damage to the pleural surface. The authors also demonstrated that the relevant components of ECM (elastin, laminin, and IV) collagens were almost unchanged in acellular lungs before and after irradiation. Irradiation of a cellular lungs, with 60A resulting in a significant increase in the mechanical impedance of the lung scaffold, associated with increased pulmonary resistance and reactance, regardless of whether gamma irradiation was performed when the decellularised lungs were frozen or at room temperature.21 In principle, other sterilisation methods, such as those based on gamma irradiation, ETO, or other chemical agents, can be used. However, several studies have shown that all sterilisation methods have side effects, since any action to destroy infectious microorganisms potentially compromises the different molecular structures of the scaffold. For example, it has been indicated that both ETO and irradiation can interact with scaffold molecules, potentially degrading their performance.24\n\nOliveira et al., 2021\n\nIn a recent study by Oliveira et al. (2021), it was observed that with the use of PDT associated with LED as a means of sterilising pulmonary scaffolds resulted in no functional changes in the tissue. The pulmonary mechanics, resistance, elastance, and viscoelastic behaviour parameters of the pulmonary scaffold were maintained after 1 h of exposure to PDT, and the ECM components remained practically unchanged in acellular lungs. The authors demonstrated a reduction in the fungal infection population after 45 min of PDT, but full sterilisation was not observed. This study provides evidence that the photosensitiser protoporphyrin IX (PpIX) has no antifungal activity when used alone without the application of LED.8,14 It has also been well described in the literature that the use of isolated LASERs without the addition of a photosensitiser does not reduce fungal populations in the same way. Oliveira et al., 2021 demonstrated that the total reduction in fungal load was dependent on photosensitiser concentration and light parameters using red and methylene blue LASERs on the oral mucosa of a mouse model. It is therefore clear that the use of LASER is effective when used in conjunction with a photosensitizer and when considering the time and concentration of the procedure as a whole.23\n\nGamma irradiation (31 kGy) induced structural and mechanical changes in the decellularised lungs of the mice. Visual inspection of the acellular lungs revealed a reduction in the volume of the scaffold. This reduction in lung volume may be due to some degree of alveolar atelectasis, consistent with the increase in lung elastance and resistance observed after irradiation. When acellular lungs are irradiated at room temperature, the different lung structures, alveoli, vessel walls, and pleura remain similar to those of non-irradiated lungs.24 In principle, other sterilisation methods, such as those based on gamma irradiation, ETO, or other chemical agents, can be used. However, all sterilisation methods have side effects, as any action that destroys infectious microorganisms may potentially compromise the different molecular structures of the scaffold. Yoganarasimha et al. (2014) demonstrated that both ETO and irradiation could interact with scaffold molecules, potentially degrading their functionality. From the point of view of effectively reaching all points of the scaffold structure, gamma irradiation may be particularly suitable for sterilising lung scaffolds.20\n\nPhotosensitisers play a key role in the effectiveness of PDT. PpIX is actively transported into cells via a growth-induced uptake mechanism under nutritionally restrictive conditions.23 The photosensitiser PpIX did not show antifungal activity when used alone without the application of LED. It is also well described in the literature that the use of isolated LASERs without the addition of a photosensitiser does not reduce fungal populations in the same way. PDT has been successfully used to treat different localised infections, and these results are proof that PDT is also a suitable method to promote microorganism reduction. This systematic review calls for further research to confirm the suitability of PDT as a routine sterilisation technique for lung scaffolds in the organ bio-manufacturing process to replace damaged or deficient organs, and even reduce wait times for organ transplants.23 In conclusion, our survey of the scientific literature related to lung scaffold sterilisation protocols showed that regardless of the type of agent used (physical or chemical), the sterilisation process affects the ECM in some way. To date, an ideal protocol has not been found to be fully effective in the sterilisation of lung scaffolds for use in tissue and/or organ engineering.",
"appendix": "Data availability\n\nNo data associated with this article.\n\nReporting guidelines: PRISMA P checklist for ‘Extracellular matrix of lung scaffolds submitted to different means of sterilisation: a systematic review’. DOI: https://doi.org/10.6084/m9.figshare.25517137.v1. 25\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC BY 4.0).\n\n\nReferences\n\nPetersen TH, et al.: Tissue-engineered lungs for in vivo implantation. Science. 2010; 329(5991): 538–541. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShakir S, et al.: Bioengineering lungs: An overview of current methods, requirements, and challenges for constructing scaffolds. Front. Bioeng. Biotechnol. 2022; 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYusen RD, et al.: Lung Transplantation in the United States, 1999–2008. Am. J. Transplant. 2010; 10(2): 1047–1068. PubMed Abstract | Publisher Full Text\n\nMaclean M, et al.: Non-ionizing 405 nm light as a potential bactericidal technology for platelet safety: evaluation of in vitro bacterial inactivation and in vivo platelet recovery in severe combined immunodeficient mice. Front. Med. 2020; 6. Publisher Full Text\n\nParihar A, et al.: 3D Printing: Advancement in Biogenerative Engineering to Combat Shortage of Organs and Bioapplicable Materials. Regen. Eng. Transl. Med. 2021; 8: 173–199. Publisher Full Text\n\nYao Q, et al.: Recent development and biomedical applications of decellularized extracellular matrix biomaterials. Mater. Sci. Eng. C Mater. Biol. Appl. 2019; 104: 109942. PubMed Abstract | Publisher Full Text\n\nWang S, et al.: Decellularized tendon as a prospective scaffold for tendon repair. Mater. Sci. Eng. C Mater. Biol. Appl. 2017; 77: 1290–1301. PubMed Abstract | Publisher Full Text\n\nChani B, et al.: Decellularized scaffold of cryopreserved rat kidney retains its recellularization potential. PLoS One. 2017; 12: e0173040. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUriarte JJ, et al.: Lung bioengineering: advances and challenges in lung decellularization and recellularization. Curr. Opin. Organ Transplant. 2018; 23(6): 673–678. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDerman ID, et al.: Bioengineering and Clinical Translation of Human Lung and its Components. Adv. Biol. 2023; 7(4): e2200267.\n\nGupta SK, et al.: Fabrication and characterization of scaffold from cadaver goat-lung tissue for skin tissue engineering applications. Mater. Sci. Eng. C Mater. Biol. Appl. 2013; 33(7): 4032–4038. PubMed Abstract | Publisher Full Text\n\nZhang X, et al.: Decellularized extracellular matrix scaffolds: Recent trends and emerging strategies in tissue engineering. Bioact. Mater. 2021; 10(10): 15–31. Publisher Full Text\n\nNichols JE, et al.: Production and assessment of decellularized pig and human lung scaffolds. Tissue Eng. Part A. 2013; 19(17-18): 2045–2062. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCrapo PM, et al.: An overview of tissue and whole organ decellularization processes. Biomaterials. 2011; 32(12): 3233–3243. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRana D, et al.: Development of decellularized scaffolds for stem cell-driven tissue engineering. J. Tissue Eng. Regen. Med. 2017; 11(4): 942–965. PubMed Abstract | Publisher Full Text\n\nCalle EA, et al.: Strategies for whole lung tissue engineering. I.E.E.E. Trans. Biomed. Eng. 2014; 61(5): 1482–1496. Publisher Full Text\n\nPorzionato A, et al.: Tissue-Engineered Grafts from Human Decellularized Extracellular Matrices: A Systematic Review and Future Perspectives. Int. J. Mol. Sci. 2018;18; 19(12): 4117. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoher D, et al.: Preferred reporting items for systematic reviews and meta-analyses: the PRISMA Statement. Open Med. 2009; 3(3): e123–e130. PubMed Abstract\n\nHooijmans CR, et al.: SYRCLE’s risk of bias tool for animal studies. BMC Med. Res. Methodol. 2014; 14(14): 43. Publisher Full Text\n\nBonenfant NR, et al.: The effects of storage and sterilization on de-cellularized and re-cellularized whole lung. Biomaterials. 2013; 34(13): 3231–3245. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUriarte JJ, et al.: Mechanical properties of acellular mouse lungs after sterilization by gamma irradiation. J. Mech. Behav. Biomed. Mater. 2014; 40: 168–177. PubMed Abstract | Publisher Full Text\n\nBalestrini JL, et al.: Sterilization of Lung Matrices by Supercritical Carbon Dioxide. Tissue Eng. Part C Methods. 2016; 22(3): 260–269. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOliveira LVF, et al.: Photodynamic Therapy in the Extracellular Matrix of Mouse Lungs: Preliminary Results of an Alternative Tissue Sterilization Process. Int. J. Photoenergy. 2021; 2021: 1–9. Publisher Full Text\n\nYoganarasimha S, et al.: Peracetic acid: a practical agent for sterilizing heat-labile polymeric tissue-engineering scaffolds. Tissue Eng. Part C Methods. 2014; 20(9): 714–723. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOliveira LVF: PRISMA P checklist for “Extracellular matrix of lung scaffolds submitted to different means of sterilisation: a systematic review”. figshare. Figure. 2024. Publisher Full Text"
}
|
[
{
"id": "294964",
"date": "30 Jul 2024",
"name": "Carolina Herranz Diez",
"expertise": [
"Reviewer Expertise Biomaterials",
"ECM-hydrogels",
"cell interactions"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic is of interest as there is a concern about how to sterilize decellularized tissues without compromising their structural properties. The rationale and the objectives of the review are clearly stated. The review strategy is well defined and easy to follow although some choices need a comprehensive justification. There is no clear reason why studies published before 2012 are excluded. The authors should indicate the reason to avoid works published before 2012 on the relevant topic. It is well known that many of the most pertinent publications use English as the publishing language, but other publications might be relevant to the topic and written in different languages. The authors should take this in consideration. The review uses the SYRCLE tool to assess the risk of bias in randomized trials included in the Cochrane Reviews, adjusted for particular aspects of bias that play a role in animal intervention studies. The use of the bias guide used in animal experimentation should be justified and the adaptation, if any, to the current sterilization technique and purposes should be described. Creating a table with the pros and cons of each sterilization technique is advisable to be added to the conclusions section. Finally, a grammar check is needed as some typo errors have been detected.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
},
{
"id": "310179",
"date": "14 Aug 2024",
"name": "Yongdae Yoon",
"expertise": [
"Reviewer Expertise Regenerative medicine and immunology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author described various sterilization methods of lung scaffolds and this is a very useful article. However, some articles that should have been covered in the results section was suddenly covered in the conclusion section such as chemical means. I wish the author would have continued the explanation of the part that should have been covered in the results section. They started their explanation based on 4 papers, but it seems that they used more than the papers. Table 2 describes a study using only mice, but on page 4, it mentioned a study using rat organs and there is no more explanation for it, and also it is necessary to check if the source used is correct.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
},
{
"id": "310182",
"date": "16 Aug 2024",
"name": "Tomoshi Tsuchiya",
"expertise": [
"Reviewer Expertise Organ engineering. https://www.organengineering.com/"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe purpose of this review is to explore the ideal sterilization protocol for lung scaffolds. The authors conclude that no ideal protocol has been found because somewhat functional damage occurs to the ECM. The reviewers agree with this conclusion, but believe that there is too little information to call it a review. The review summarizes only four studies and discusses only four different sterilization methods.\nMajor concerns. 1. Sterilization methods include heating (high-pressure steam and dry heat methods), irradiation (radiation method), and gas methods (ethylene oxide gas method and hydrogen peroxide gas plasma method) etc. Since this paper is a review focusing on sterilization methods for biomaterials, it is necessary to describe each sterilization method and explain why each method can or cannot be applied to decellularized lung scaffolds. 2. In the introduction, the first paragraph discusses tissue engineering, and the second paragraph discusses organ transplantation. However, the reviewer believes that organ transplantation should be explained first, followed by tissue engineering, because tissue engineering compensates for organ shortages and is an alternative treatment to organ transplantation. 3. The authors describe the sterilization process in the second paragraph of the introduction. However, there is no explanation of the organ engineering method using decellularization and recellularization protocols. For the reader's understanding, a paragraph on organ engineering methods is needed between the first and second paragraphs.\nMinor concerns. 1. The reviewer could not find reference 23 in PubMED; is it acceptable that only four articles are discussed and one of them is not published in PubMED?\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
},
{
"id": "289806",
"date": "23 Aug 2024",
"name": "Harry Karmouty-Quintana",
"expertise": [
"Reviewer Expertise Lung biology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript aims to review the current sate of the art methodology of sterilization of lung scaffolds and how they alter the extracellular matrix. This is important in processes that require the decellularization of the lungs. However, the review is highly superficial since the authors only review 4 articles that meet their review stipulations out of a potential of 241 published articles. Thus, it seems that the authors should consider redoing their study with less stringent criteria to provide a more rounded and valuable review to the field or reconsider a review of this type in the future when more publications that fit their criteria are available for a scientific discussion.\nMajor:\n\nReview is highly specialized therefore its appeal to a broader audience is limited. It's unclear why the authors selected lung cancer as a chronic respiratory illness in the introduction typically lung cancer is in its own category. The authors should instead focus on idiopathic pulmonary fibrosis or other chronic lung diseases to underscore the global burden of these diseases. As an example, asthma is mentioned yet deaths by asthma are not rampant. Next the authors indicate that lung transplantation is the only indication to allow survival this is not true for diseases like asthma and patients with lung cancer are not shortlisted for transplantation, this really highlights the need to rewrite this introduction as it does not adequately represent the state of the field. The next paragraph jumps onto the sterilization process to obtaining acellular lungs yet this completely omits the process of lung transplantation and how these processes would be important for future lung therapy beyond current lung transplantation approaches. Here the authors should probably mention what the current state of lung transplantation is and perhaps highlight how it is one of the solid organs with the lowest 5 year survival rate. At present lungs destined for transplantation do not go for a sterilization process that is required for scaffolds as such authors should point at to why this is important in this context and not assume that the reader will understand. Based on the prisma guidelines the investigators included 241 studies for their review yet after identifying duplicate and revising the inclusion criteria only 4 articles were deemed suitable by the authors to include in their review. It is hard to believe that out of 241 articles\n\nonly 4 met the criteria for the review therefore this review seems to be extremely superficial and unikely to have an impact to the field.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-554
|
https://f1000research.com/articles/13-553/v1
|
30 May 24
|
{
"type": "Genome Note",
"title": "The first complete mitochondrional genome of Anopheles gibbinsi using a skimming sequencing approach.",
"authors": [
"Renee Ali",
"Mary E. Gebhardt",
"James Sichivula Lupiya",
"Mbanga Muleba",
"Douglas E. Norris",
"Mary E. Gebhardt",
"James Sichivula Lupiya",
"Mbanga Muleba",
"Douglas E. Norris"
],
"abstract": "Mosquitoes belonging to the genus Anopheles are the only vectors of human malaria. Anopheles gibbinsi has been linked to malaria transmission in Kenya, with recent collections in Zambia reporting the mosquito species exhibiting zoophilic and exophilic behavioral patterns with occasional contact with humans. Given the paucity of genetic data, and challenges to identification and molecular taxonomy of the mosquitoes belonging to the Anopheles genus; we report the first complete mitochondrial genome of An. gibbinsi using a genome skimming approach. An Illumina Novaseq 6000 platform was used for sequencing, the length of the mitochondrial genome was 15401 bp, with 78.5% AT content comprised of 37 genes. Phylogenetic analysis by maximum likelihood using concatenation of the 13 protein coding genes demonstrated that An. marshallii was the closest relative based on existing sequence data. This study demonstrates that the skimming approach is an inexpensive and efficient approach for mosquito species identification and concurrent taxonomic rectification, which may be a useful alternative for generating reference sequence data for evolutionary studies among the Culicidae.",
"keywords": [
"Anopheles gibbinsi",
"understudied anopheline",
"genome skimming",
"Zambia"
],
"content": "Introduction\n\nA few species in the genus Anopheles are well established primary vectors of human malaria in sub-Saharan Africa, including Anopheles gambiae and An. funestus. However, studies have also implicated understudied anopheline mosquito species in driving transmission in regions where primary vectors are close to elimination.1–3 Anopheles gibbinsi, until recently recognized as An. species 6, has tested positive for Plasmodium falciparum sporozoites in studies from Kenya.4,5 Furthermore, An. gibbinsi was previously reported from central, eastern and northern Africa and has now been shown to have a geographic range extending into southern Africa. Recent first-time captures for this species in Zambia reported the species largely exhibiting zoophilic and exophilic behavioral patterns; however, a blood meal PCR assay also detected a few specimens positive for human host DNA.5 Similar in morphology to other well-established malaria vectors and with a dearth of genetic data available, there is a need for the continued monitoring of An. gibbinsi as a potential vector in malaria transmission. It is also important that tools for accurate mosquito identification be developed, due to limitations with the commonly targeted cytochrome oxidase I gene (COI) and the internal transcribed spacer 2 (ITS2) in resolving members of morphologically cryptic species complexes.6\n\nThe expansion of sequencing strategies has employed the use of mitochondrial genomes (mitogenomes) primarily for species identification and solving discrepancies in the taxonomic classification of metazoan organisms. Mitogenomes have also proved useful in evaluating population structure, chromosomal rearrangements, species introgression, and evolutionary histories.7–9 The mitochondrial DNA (mtDNA) is a circular double stranded molecule that encodes 37 genes made up of 13 protein coding genes (PCGs), 22 transfer RNA (tRNA) genes), 2 ribosomal RNA (rRNA) genes and an adenine and thymine (A-T) rich terminal, an essentially non-coding area termed the control region (CR) associated with the replication and transcription of the genome. Maternal inheritance, high copy number, lack of recombination, and absence of introns are characteristics which allow mtDNA to be well suited for accurate molecular identification and rectifying taxonomic classification among species.6,10 Here for the first time, we describe a genome skimming approach for recovery of, and characterization of the mitochondrial genome of An. gibbinsi and its phylogenetic relationship to other established anopheline vectors of human malaria.\n\n\nMethods\n\nThe An. gibbinsi specimens (n = 3) sequenced were collected in Nchelenge, Zambia using a CDC light trap that was placed near an animal. The specimens were stored on silica gel until DNA extraction. Single mosquito specimens were pre-treated11 as described by Chen et al. 2021, followed by the extraction protocol as per manufacturer’s instructions (Qiagen DNeasy Blood and Tissue Kit, Hilden, Germany). A whole mosquito specimen was placed in a 1.5 mL Eppendorf tube and homogenized in a cocktail containing 98 μL of PK buffer (Applied Biosystems, Waltham, Massachusetts, U.S.A.) and 2 μL of Proteinase K (100 mg/mL), this was followed by an incubation step for 3 hours at 56oC.12 After incubation, 100 μL of isopropanol and 100 μL of Buffer AL (Qiagen DNeasy Blood and Tissue Kit, Hilden, Germany) was added to the lysate and left to incubate at room temperature for 10 minutes. The mixture was pipetted into a DNeasy mini spin column placed in a 2 mL collection tube; extraction protocol was followed5and stored at -20oC prior to sequencing. DNA was shipped to SeqCenter (Pittsburg, U.S.A) for library construction and sequencing. Libraries were sequenced from both ends (150 bp) on Illumina Novaseq 6000 to a depth of 13.3 million reads.\n\nThe mitochondrial genome contigs were assembled similar to that of the An. squamosus13 mitogenome using NOVOPlasty (RRID:SCR_017335) version 4.3.1.12 Using the invertebrate genetic code under default settings, automatic annotations were conducted using the MITOS website.14 Adjustments for start and stop codon positions were performed manually in Geneious Prime (RRID:SCR_010519) version 2023.2.1 (Biomatters, Auckland, Australia) to match reference anopheline mitogenomes deposited in NCBI’s GenBank database. The mitochondrial genome sequences and their corresponding annotations were submitted to the GenBank database. A representative mitogenome map is provided in Figure 1.\n\nPhylogenetic analysis was performed using the concatenated 13 PCGs of the three An. gibbinsi specimens, eight Anopheles species and one Aedes species as an outgroup. The General Time Reversible (GTR + G + 1) model was identified as the best fit for building the maximum likelihood phylogenetic tree in MEGA (RRID_SCR_023017) version 1115 using 1000 bootstrap replicates.\n\n\nResults\n\nThe sequencing from the 3 An. gibbinsi samples yielded an average of 29,674,206 million reads and of these, approximately 119,364 reads were used to assemble each mitochondrial genome. The contents of the 3 An. gibbinsi mitogenomes (GenBank accession numbers OR_539796, OR_539797, OR_569715) included 2 ribosomal RNAs, 22 transfer RNAs and 13 protein coding genes. The representative mitochondrial genome (OR_539797) length was 15,401 bp with an A + T percentage of 78.5% which is comparable to other anopheline mitogenomes deposited in the GenBank database. The cytochrome c oxidase I (COI) fragment spanning 8598–10,133 bp was 94.5% similar to a COI sequence for An. marshallii (GenBank YP_010419919).\n\nPhylogenetic analysis (Figure 2) using the concatenated PCGs revealed An. marshallii (NC_064607) as the closest sequenced relative to An. gibbinsi, forming a single but weakly supported clade apart from the well-recognized vectors of malaria. Both species belong to the An. marshallii complex.\n\nGenome skimming has demonstrated to be a cost-effective approach for generating reference sequence data which can be used for mosquito identification and resolving phylogenies. With the continued monitoring of An. gibbinsi as a potential vector for malaria transmission, this study provides a key genomic resource for understanding the phylogenetic relationship of this mosquito species within its complex and with primary vectors of human malaria transmission.",
"appendix": "Data availability\n\nGenBank: Anopheles gibbinsi mitochondrion, complete genome. Accession numbers OR539796, OR539797, OR569715. 16\n\nBio Project. Complete mitogenome sequence of Anopheles gibbinsi from Nchelenge, Zambia, Accession number PRJNA1072262. 17\n\nSRA. Illumina seq of Anopheles gibbinsi. Accession numbers SRR27842795, SRR27842796, SRR27842794. 18\n\nBioSample: Anopheles gibbinsi isolates ANGB, AGB1, GN. SAMN39739077, SAMN39739078, SAMN39739079. 19\n\n\nAcknowledgements\n\nWe would like to thank the Zambian field teams and the Tropical Diseases Research Centre for assisting with sample collection. Many thanks to Dr. Yoosook Lee, University of Florida for guidance with bioinformatic analysis.\n\n\nReferences\n\nMustapha AM, et al.: Secondary malaria vectors in western Kenya include novel species with unexpectedly high densities and parasite infection rates. Parasit. Vectors. 2021; 14: 252. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBurke A, et al.: A new malaria vector mosquito in South Africa. Sci. Rep. 2017; 7: 43779. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStevenson JC, et al.: Detection of Plasmodium falciparum Infection in Anopheles squamosus (Diptera: Culicidae) in an Area Targeted for Malaria Elimination, Southern Zambia. J. Med. Entomol. 2016; 53: 1482–1487. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCooke MK, et al.: ‘A bite before bed’: exposure to malaria vectors outside the times of net use in the highlands of western Kenya. Malar. J. 2015; 14: 259. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGebhardt ME, et al.: Expanded geographic distribution and host preference of Anopheles gibbinsi (Anopheles species 6) in northern Zambia. Malar. J. 2022; 21: 211. PubMed Abstract | Publisher Full Text | Free Full Text\n\nda Silva AF, Machado LC, de Paula MB, et al.: Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics. Sci. Rep. 2020 Nov 2; 10(1): 18823. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSmith DR: The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs? Brief. Funct. Genomics. 2015; 15: elv027–elv054. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen DH, et al.: Mitogenome - based phylogeny of mosquitoes (Diptera:Culicidae). Insect Sci. 2023; 31: 599–612. PubMed Abstract | Publisher Full Text\n\nDowling DK, et al.: Evolutionary genetics of the mitochondrial genome: insights from Drosophila. Genetics. 2023; 224: 224. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoban ML, et al.: Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ. 2022; 10: e13790. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen T-Y, et al.: A magnetic-bead-based mosquito DNA extraction protocol for next-generation sequencing. JoVE (Journal of Visualized Experiments). 2021; e62354. Publisher Full Text\n\nDierckxsens N, Mardulyn P, Smits G: NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017; 45: e18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen VT, et al.: The first genome sequence of Anopheles squamosus from Macha, Zambia. F1000Res. 2023; 12: 330. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBernt M, et al.: MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 2013; 69: 313–319. PubMed Abstract | Publisher Full Text\n\nTamura K, Stecher G, Kumar S: MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol. Biol. Evol. 2021; 38: 3022–3027. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAli RLMN, et al.: Anopheles gibbinsi mitochondrion, complete genome. [Dataset]. GenBank. 2024.\n\nJohns Hopkins Bloomberg School of Public Health: Complete mitogenome sequence of Anopheles gibbinsi from Nchelenge, Zambia. [Dataset]. BioProject. 2024.\n\nJohns Hopkins Bloomberg School of Public Health: Illumina seq of Anopheles gibbinsi. [Dataset]. SRA. 2024.\n\nJohns Hopkins Bloomberg School of Public Health:Invertebrate sample of Anopheles gibbinsi. [Dataset]. Biosample. 2024."
}
|
[
{
"id": "288704",
"date": "21 Jun 2024",
"name": "Nicola Zadra",
"expertise": [
"Reviewer Expertise My research area is population genomics and molecular phylogenetics. I have worked on Aedes species mitochondrial phylogeny and related flaviviruses."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is well-written, and the message delivered is thorough. All the data obtained are available in Genebank, and they are carefully annotated. It discusses the potential role of Anopheles gibbinsi in malaria transmission in an area where the primary vector is close to extinction. Currently, there are only a few DNA sequences available for studying this species. Providing a complete mitochondrial genome will significantly aid in understanding its relationships with other Anopheles species resolving possible cryptic relations, and quickly identifying and monitoring this potential malaria vector. Data collection and sequencing are well-described and reproducible. The data collection and sequencing methods are well-documented and reproducible. The phylogenetic analysis was conducted using only the 13 protein-coding genes and presented an updated understanding of the relationships among Anopheles gibbinsi and different species in the Cellia clade.\nI have a few suggestions for improving the clarity and delivery of the paper:\n1. Consider enhancing the mitochondrial dataset for phylogenetic reconstruction by including additional mitochondrial sequences from the subgenus Cellia. This could provide better insight into the relationship between this species and others within the Cellia group, as well as with the primary Plasmodium vector.\n2. It would be helpful to include the distance to the tree. The current tree structure appears to be an ultrametric tree.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes",
"responses": []
},
{
"id": "298674",
"date": "18 Jul 2024",
"name": "Luke Ambrose",
"expertise": [
"Reviewer Expertise Population genetics of Anopheles mosquitoes."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a useful report of an additional resource for identifying a cryptic species of Anopheles. I have a few suggestions that may improve the study:\n1) Mitochondrial DNA alone is not sufficient in most cases to delineate species due to the potential for introgression. This is commonly observed in many diverse organisms. I suggest at minimum a discussion of this. Developing a supporting nuclear based diagnostic, such as an ITS2 RFLP would be preferable and should not be too expensive or difficult. Additionally, it would be useful to identify regions of the mitogenome that may differ between closely related species in the complex and to perform sequencing on samples from across Africa however that could be in a follow up study.\n\n2) The language in the methods is a bit unclear - was the raw data mapped to the An. squamosus mitogenome? If so please clarify wording in line with this. I would also like to know average sequencing depth of the mapped genomes rather than reporting 13.3 million reads (this isn't actually depth I assume but how many read mapped to mitogenomes?)\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes",
"responses": []
},
{
"id": "298679",
"date": "22 Jul 2024",
"name": "Alexey Makunin",
"expertise": [
"Reviewer Expertise comparative genomics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Ali et al presents three mitogenome assemblies for Anopheles gibbinsi, a potential secondary malaria vector mosquito species, generated with low coverage shotgun Illumina sequencing. Overall, the data presentation and text quality are good. I only have several technical comments:\nIntroduction \"_Anopheles gibbinsi_, until recently recognized as _An. species 6_,\" - unclear what this means \"The mitochondrial DNA (mtDNA) is a circular double stranded molecule that encodes 37 genes\" - genome structure and number of genes varies across eukaryotes - I'd suggest specifying a taxon here\nMethods Did you do any morphological species identification before extraction? Did you do any quantification, fragment size and purity estimation for the DNA before library prep? There is a discrepancy in read counts reported in methods and results: \"Libraries were sequenced from both ends (150 bp) on Illumina Novaseq 6000 to a depth of 13.3 million reads.\" vs \"The sequencing from the 3 An. gibbinsi samples yielded an average of 29,674,206 million reads\" It might be useful to provide a summary table with sequencing statistics per sample: pre-sequencing metrics (if any available, e.g. total amount of DNA used for library construction or average fragment size), total number of reads, number of reads used in the assembly, assembled mitogenome size before and after correction \"cytochrome c oxidase I (COI) fragment spanning 8598–10,133\" - in https://www.ncbi.nlm.nih.gov/nuccore/OR539797, span of COI is 8595..10128 Fig 2 - \" forming a single but weakly supported clade\" - support value for marshalli-gibbinsi group is not shown on the tree \"Both species belong to the _An. marshallii_ complex\" - online databases like WRBU and Mosquito Taxonomic Inventory suggest that An. gibbinsi is in marshalli group, not complex. Might be useful to add a reference here.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-553
|
https://f1000research.com/articles/12-733/v1
|
23 Jun 23
|
{
"type": "Research Article",
"title": "Identification of predictive factors for surgical site infections in gastrointestinal surgeries: A retrospective cross-sectional study in a resource-limited setting",
"authors": [
"Abdu Al-hajri",
"Saif Ghabisha",
"Faisal Ahmed",
"Saleh Al-wageeh",
"Mohamed Badheeb",
"Qasem Alyhari",
"Abdulfattah Altam",
"Afaf Alsharif",
"Abdu Al-hajri",
"Saif Ghabisha",
"Saleh Al-wageeh",
"Mohamed Badheeb",
"Qasem Alyhari",
"Abdulfattah Altam",
"Afaf Alsharif"
],
"abstract": "Background: Surgical site infection (SSI), albeit infrequent, drastically impact the quality of care. This article endeavors to investigate the predictive factors of SSIs following surgical interventions that involve the gastrointestinal (GI) tract within a single institution in a resource-limited setting. Methods: Over seven years from June 2015 to Oct 2022, patients who underwent GI surgery and developed SSI were retrospectively matched with an unaffected case-control cohort of patients. Standardized techniques for wound culture, laboratory evaluation of bacterial isolates, and antibiotic susceptibility tests were employed. Logistic regression analysis was utilized to investigate the predictive factors associated with 30-day postoperative SSI. Results: A total of 525 patients who underwent GI surgical procedures were included, among whom, 79 (15%) developed SSI. The majority of SSIs were superficial (67.10%), Escherichia coli was the most commonly isolated bacterium (54.4%), and a high percentage of multidrug-resistant organisms were observed (63.8%). In multivariate Cox regression analysis, illiteracy (Odds ratio [OR]:40.31; 95% confidence interval [CI]: 9.54-170.26), smoking (OR: 21.15; 95% CI: 4.63-96.67), diabetes (OR: 5.07; 95% CI: 2.27-11.35), leukocytosis (OR: 2.62; 95% CI: 1.24-5.53), hypoalbuminemia (OR: 3.70; 95% CI: 1.35-10.16), contaminated and dirty wounds (OR: 6.51; 95% CI:1.62-26.09), longer operative time (OR: 1.02; 95% CI: 1.01-1.03), emergency operations (OR: 12.58; 95% CI: 2.91-54.30), and extending antibiotic prophylaxis duration (OR: 3.01; 95% CI: 1.28-7.10) were the independent risk factors for SSI (all p < 0.05). Conclusions: This study highlights significant predictors of SSI, including illiteracy, smoking, diabetes, leukocytosis, hypoalbuminemia, contaminated and dirty wounds, longer operative time, emergency operations, and extending antibiotic prophylaxis duration. Identifying these risk factors can help surgeons adopt appropriate measures to reduce postoperative SSI and improve the quality of surgical care, especially in a resource-limited setting with no obvious and strict policy for reducing SSI.",
"keywords": [
"Surgical site infection",
"gastrointestinal surgery",
"predictors"
],
"content": "Introduction\n\nA surgical site infection (SSI) is a frequently encountered nosocomial infection that typically develops within 30 days of surgery. In cases where an implant is used, the timeframe for SSI occurrence can extend up to one year.1 The estimated incidence of SSI is 0.5% to 3% worldwide, with a higher incidence reported in low-income countries, where SSI is estimated to be the most common healthcare-associated infection.2,3 In addition to the socioeconomic status, surgeries that involve the gastrointestinal (GI) appear to have a higher SSI incidence, with reports indicating a 12%-30% incidence rate of such cases. The associated expenditure of increased hospitalization (7-11 folds), mortality, and morbidity (2-11 folds) force a higher emphasis on detecting such patients earlier in the course of their illness and identifying patients with a higher risk of developing SSI to improve the quality of care and minimize the cost.4,5\n\nVarious factors have been studied concerning SSI, which can extend from socioeconomic status to the preoperative settings and surgical approaches.6 Certain non-modifiable risk factors include age, gender, immunosuppression, diabetes mellitus, obesity, or active smoking. Additionally, the pre-operative preparation, operative time, and intra-operative techniques may impact the development of SSI, which is seen at a higher rate in emergent and septic surgeries.3–5 SSI can be attributed to microorganisms that are derived from the patient’s skin flora or from the surrounding environment.1 In either scenario, the adherence of microorganisms to the surgical instruments can contaminate the incision. Contaminated surgical procedures pose an increased risk, particularly when multidrug-resistant microorganisms are involved.6\n\nPrevious monocentric and retrospective studies in Yemen reported SSI rates of 2.2% and 31.7%.7,8 However, there is limited information available about the extent of SSI and its predictive factors in low-income countries, such as Yemen.7,8 This study aimed to investigate the SSI rate and its predictive factors among Yemeni patients who underwent GI surgeries in a resource-limited setting.\n\n\nMethods\n\nA retrospective cross-sectional study was conducted to investigate the SSI rate in patients who underwent gastrointestinal surgery at Al-Thora Hospital, Ibb University, IBB, Yemen, between June 2015 and October 2022. We included 525 patients, from whom written informed consent was obtained. The study was approved by the Ethics Research Committees of Ibb University [ID: IBBUNI.AC.YEM.2023.75, on 03/03/2023].\n\nAdult patients (≥18 years old), who had undergone either elective or emergency GI surgery at general surgery wards were included.\n\nExclusion criteria were pregnancy, anticoagulation, incomplete or concealing data, non-bowel-related surgeries (e.g., hernia), postoperative complications within more than 30 days of surgery, or admission to another hospital.\n\nThe study enrolled all eligible patients in consecutive order and utilized organized questionnaires to gather applicable information. This included demographics, including age, gender, educational level, body mass index (BMI), and place of residence, as well as health habits such as cigarette smoking and Khat chewing. In addition, comorbid conditions such as diabetes mellitus (DM), hypertension, chronic kidney, lung, and liver disease, history of malignancy, and preoperative blood transfusions were also documented. The American Society of Anesthesiologists (ASA) categorization system was used to measure preoperative physical state. Other information collected included the admission time, date, duration, wound nature, type, duration, anesthesia type, using the safety checklists, the urgency of surgery, readmission, reoperation, shaving time, and details of preoperative antimicrobial administration. Laboratory-collected data were white blood cell (WBC) counts, neutrophile percentage, and albumin levels.\n\nThe study documented surgery-related complications (e.g., SSI, fistula) in addition to non-surgical complications such as pneumonia, urinary tract infection (UTI), sepsis, and myocardial infarction (MI). Culture results and antibiotic sensitivities were also recorded, with wound swabs and pus specimens collected using standard microbiological techniques and transported to the laboratory for sensitivity analysis. Additionally, we collected the National Nosocomial Infections Surveillance (NNIS) index for each patient.\n\nBased on the depth of infection, these SSIs were subsequently categorized into superficial (affecting the skin and subcutaneous tissue), deep (involving muscle and fascia), and organ space infections.6 Wounds were classified into four categories depending on their level of contamination: clean, clean-contaminated, contaminated, or dirty-infected. The ASA score, which reflects the patient’s physical condition before the surgery, was determined through evaluation by the anesthesiologist using the ASA classification system.9 The NNIS index considers three risk variables, each of which is worth one point: contaminated or dirty-infected surgical wound, ASA scores greater than 2, and operation length greater than T (where T is defined as the 75th percentile of the normal time for a surgical procedure).9 The gastrointestinal cases were sorted into four categories (small bowel, large bowel, biliary, and pancreatic).10 Leukocytosis was defined as a WBC count greater than 100 × 109/L and hypoalbuminemia was defined as an albumin <3.5 g/dL.\n\nThe prevalence of SSI was determined by assessing culture-positive results and/or physician diagnosis, according to the criteria set forth by the United States Center for Disease Control (CDC). This definition included infections affecting the superficial, deep, and organ space tissues of the surgical incision. The incidence of SSI was determined by evaluating and following up on all patients for 30 days following their surgery, starting from the date of the operation.9 It is important to note that medical complications such as pneumonia, MI, and UTI were separately documented and reported, and were not included in the definition of SSI or postoperative surgical complications.\n\nThe outcome variable was SSI expressed as a binary variable: yes and no. Independent variables included Age (<60 years and ≥60 years), Sex (male and female), ASA score (Low [1 or 2] and High [3 or 4] NNIS index (No risk, Low risk, Moderate risk, High risk), Surgical sites (Small bowel and Other sites), Hospital stays (<5 days and ≥5 days), BMI (<30 kg/m2 and ≥30 kg/m2), Residency (Urban and Rural), Educational level (Educated and Illiterate), the Antibiotic time before surgery and shaving time (<1 h and ≥1 h), WBC (<10×109/L and ≥10×109/L), Albumin (≥3.5 mg/dL and <3.5 mg/dL), Operative type (Elective and Emergency), Blood loss (<200 mL and ≥200 mL), Anesthesia type (Spinal and General), Wound class (I and II and III and IV), Temperature (<38°C and ≥38°C), and Operative time (min). Additionally, Khat chewing, Smoking, History of hypertension, History of diabetes, History of chronic renal failure, History of chronic liver disease, History of lung disease, Perioperative blood transfusion, History of malignancy, Safety checklist used, and Drain insertion were presented as “yes” and “no”.\n\nIBM SPSS version 22 software (IBM Corp., Armonk, New York) was used for statistical analyses. Quantitative variables were presented as means and standard deviations, while qualitative variables were reported as frequencies and percentages. The normality of the data was confirmed using the Kolmogorov-Smirnov test. Statistical tests were used to compare qualitative and quantitative variables, including the independent samples t-test or Mann-Whitney test for quantitative variables, and the Chi-square or Fisher’s exact test for qualitative variables.\n\nUnivariate analysis was conducted to identify the statistically significant variables associated with the development of SSIs and those variables with a p-value of less than 0.20 were subsequently fitted for binary logistic regression. The links between each risk factor and SSI are presented as an odds ratio (OR) and confidence interval (CI). A p-value of less than 0.05 was judged statistically significant. The ROC curve (receiver operating characteristic curve) was utilized to evaluate the risk adjustment prediction performance of the previous NNIS risk index and the Author’s model for post-gastrointestinal SSI, which contains the significant factors in multivariate analysis.9\n\n\nResults\n\nThis study included a total of 525 patients, comprising 295 (56%) male patients and 230 (44%) female patients, with a mean age of 52.9±16.9. Table 1 provides a summary of the patients’ characteristics and presentation. The postoperative 30-day SSI occurred in 86 (16.4%) patients. A total of 193 (36.8%) of patients had ASA Class One. The operative case distribution was 206 (39.2%) in the small bowel, 182 (34.7%) in the large bowel, 124 (23.6%) in the biliary system, and 13 (2.5%) in the pancreatic system. The mean operative time was 76.4±28.2 minutes. General complications were UTI and pneumonia in 5.5%, high-grade fever in 5.1%, and MI in 1% of patients. Laboratory and operative characteristics of patients are mentioned in Table 2.\n\nPathogens linked with SSI were identified from all SSI patient wounds. Escherichia coli (51.2%), Enterococcus spp. (17.4%), Bacteroides species (9.3%), and Clostridium perfringens (8.1%) were the most commonly isolated micro-organisms, with more than half of pathogenicity (63.8%) being multidrug-resistant organisms and the majority (70.1%) being extended-spectrum β-lactam producers (Table 3).\n\nThe relationship between the independent factors and the dependent variable was explored using univariate and multivariate Cox regression analysis. On univariate analysis, Khat chowing, ASA class 4, smoking, hypertension, diabetes, hypoalbuminemia, illiterate, contaminated and dirty wounds, higher temperatures ≥38°C, leukocytosis, neutrophile ≥85%, longer operative time, blood loss more than 200 mL, biliary and pancreatic cases, longer hospital stay, shaving before one hour of operation, NNIS risk index, and emergency surgery were statistically significant associations with SSI occurrence (all p<0.05) (Table 4).\n\nIlliteracy (OR:40.31; 95% CI: 9.54-170.26), current smoking (OR: 21.15; 95% CI: 4.63-96.67), diabetes (OR: 5.07; 95% CI: 2.27-11.35), leukocytosis (OR: 2.62; 95% CI: 1.24-5.53), hypoalbuminemia (OR: 3.70; 95% CI: 1.35-10.16), contaminated and dirty wounds (OR: 6.51; 95% CI: 1.62-26.09), longer operative duration (OR: 1.02; 95% CI: 1.01-1.03), emergency operations (OR: 12.58; 95% CI: 2.91-54.30), and administering antibiotics before 1 h of operation (OR: 3.01; 95% CI: 1.28-7.10) were independent factors for SSI (all p-value<0.05, Table 5). The prediction model’s total ROC curve was 0.946, which was much higher than the NNIS score (0.660) (Figure 1).\n\nAbbreviations: AUROC: Area under the receiver operating characteristic curve; NNIS: National Nosocomial Infections Surveillance.\n\n\nDiscussion\n\nThe improved access to healthcare, increased population age, and increased complexity of surgical interventions and patients’ conditions shed light on the importance of managing post-operative complications. Despite the precautions and the hygienic approach implemented to limit the incidence of SSI, it still represents one of the most common post-operative complications. Such infections result in an increased healthcare expenditure, and worsened mortality and morbidity.10 This predicament can be especially disadvantageous for low-income nations, where providing healthcare is already a daunting task due to constrained resources, indigent communities, and elevated levels of antimicrobial resistance.11\n\nAmong the 525 enrolled patients, the incidence of SSI within 30 days after surgery was 16.4%, which is in line with previous reports from developing countries, such as Saudi Arabia, with a rate of 16.3%.14 However, earlier studies showed much higher rates of SSI affecting up to one-third of the patients in Yemen.8 In contrast, more recent reports from Yemen have demonstrated a lower incidence of SSI, with a rate of 12.7% among patients who underwent gastrointestinal procedures.8 Our findings, which showed a slightly higher rate of SSI, could be partially attributed to the larger number of complicated cases or complex oncological procedures performed at our tertiary teaching hospital.\n\nSeveral studies have been conducted to evaluate the link between putative risk variables and SSI in GI surgical operations. However, there is a large range of variation in the variables analyzed and the proportional effect of these factors on individual outcomes. To address this issue, we comprehensively studied the preoperative and operational risk variables in GI operations associated with the development of postoperative SSI. Hamza et al. and Lakoh et al. carried out similar investigations.6,12 This study found that illiteracy, current smoking status, DM, leukocytosis, hypoalbuminemia, contaminated and dirty wounds, longer operative time, emergency operations, and longer time between administering antibiotics and operation were predictors for the development of SSI. Most of the potential predictive factors included have been previously reported as risk factors in other studies with a variety of reports and different levels.6,12\n\nThe relationship between age and SSI risk is complex and not well understood. While some studies have reported an increased rate of infection in older patients, others have observed a favorable trend with increasing age. For instance, Kaye et al. demonstrated a 1.2% decrease in SSI risk for each additional year after 65 years of age.13 Nevertheless, these findings were demonstrated consistently, as a higher rate of SSI was observed in the older population.14,15 Typically, with increasing age, there is an accumulated risk of developing comorbidities and immune dysfunction, which may lead to an increased likelihood of SSI. However, our study’s findings revealed no association between age and the development of SSI. This divergence may be attributed to variations in age categorization, as the majority of patients (67%) in this study were younger than 65 years.\n\nThe present study reveals a significant association between the level of literacy and the incidence of SSI. Specifically, illiterate patients were 40 times more susceptible to SSIs than educated patients. These results are in accordance with previous research conducted by Mezemir et al. and Baker et al.16,17 Notably, a high prevalence of limited health literacy among adults in our country may adversely impact health outcomes. For example, patients with limited health literacy may experience difficulty in comprehending complex health information, may exhibit non-compliance with postoperative instructions, and may not adequately prepare for surgery. These factors may increase the risk of SSIs and other adverse outcomes, highlighting the potential health inequality in providing care and education for illiterate patients. Therefore, it is critical to improve health literacy among patients, particularly those with limited education, to potentially reduce the incidence of SSIs and enhance surgical outcomes.\n\nThis study did not find a significant association between unmodifiable risk factors, such as gender, BMI, residency, number of comorbidities (hypertension, history of malignancy, CRF, liver and lung diseases), perioperative blood transfusion, and SSIs in multivariate analysis. Although these social determinants are important factors that may contribute to patient outcomes, there is a lack of consensus on their association with SSI occurrence in the literature. For example, Deng et al. found that male sex and a greater number of comorbidities were associated with SSI occurrence.18 Additionally, Li et al. reported that ascites, bleeding diathesis, history of lung disease, radiotherapy, chemotherapy, chronic steroid use, and weight loss were associated with SSI occurrence.19 In contrast, Mezemir et al. did not find an association between gender, BMI, and SSI occurrence, which was similar to our study.16 These discrepancies may be attributed to sample size and demographics variation across studies, as well as variations in the documentation and management of patient comorbidities. The use of more objective measures, such as preoperative laboratory and radiologic values, may provide a better understanding of the association between comorbidities and SSI occurrence. Distinctly, in this study, DM and hypoalbuminemia had 5- and 3.7 times higher chances of developing SSIs, respectively. This association was observed in prior studies,11,20 as hyperglycemia has been shown to impair WBC functions, leading to decreased immunity.21 On the other hand, reduced serum albumin levels are often associated with malnutrition or chronic wasting diseases.11\n\nOur study revealed that smoking was strongly associated with a 21-fold increased risk of developing SSIs compared to non-smokers. The vasoconstrictive and toxic effects of smoking are known to impede tissue oxygen delivery and hinder the healing process, thus contributing to the development of SSIs. These findings align with previous reports by Mawalla et al. and Billoro et al.22,23\n\nRegarding Khat (Catha edulis) chewing, its role in SSI occurrence remains uncertain. Our study observed a 1.99-fold increase in SSI occurrence among Khat chewers, although this association was not statistically significant. Currently, there is a lack of published studies specifically investigating the relationship between SSI and Khat chewing. However, Misha et al. found no association between Khat chewing and SSI occurrence in their regression analysis.3 Nevertheless, Khat chewing has been linked to various gastric issues (e.g., intestinal obstruction, and gastritis).24 Furthermore, long-term Khat consumption poses a risk of developing severe complications including hepatitis, hepatic fibrosis, and cirrhosis in advanced stages.25 Future prospective and more inclusive studies are recommended to investigate this issue, particularly in our country where the traditional use of these plants is widespread.\n\nThe settings of operation can significantly impact the development of SSI. Prior research has suggested that the degree of intraoperative wound contamination is indicative of SSI occurrence.26,27 We found that contaminated and dirty wounds were 6.51 times more likely to develop SSI, which is consistent with other studies.26–28 Furthermore, our study revealed that the prevalence of SSI in large, pancreatic, and biliary surgeries was lower than in intestinal procedures; although this association was not statistically significant. Similarly, other studies have also reported a higher incidence of SSI in the intestinal tract.11,29 However, our findings were inconsistent with the literature documenting pancreatic and biliary leaks as independent risk factors for SSI occurrence.27 This discrepancy could be attributed to the low number of cases involving biliary and pancreatic procedures, with most of them undergoing simple operations. Therefore, further prospective studies with a larger number of cases are necessary to clarify this issue.\n\nOur study also found that emergency operations were 12.58 times more likely to result in SSI, consistent with other studies.6,11 In addition, leukocytosis was found to be a predictor for the development of SSI, which aligns with previous research.30 Additionally, prolonged operative time was recognized as an independent factor for SSI development in other studies, as it increases the risk of infection due to extensive surgical procedures and incisions, prolonged anesthesia, blood loss, and weaning antimicrobial prophylaxis concentration.6,31 Furthermore, administering antibiotics one hour before operation has been reported as a predictor for SSI in previous studies.23,31 In this study, it was observed that longer operation durations and administration of antibiotics more than one hour before the operation increased the likelihood of SSI by 1.02 times and 3.01 times, respectively. These findings are consistent with previous studies.23,31\n\nIn this study, we investigated the microorganisms responsible for SSIs and their susceptibility to commonly prescribed prophylactic antibiotics. We found that the most common organisms isolated from infected wounds were Gram-negative bacteria, with extended-spectrum β-lactamase-producing E. coli being the most prevalent. Mawalla et al. reported a different outcome compared to this finding, as their studies indicated a higher presence of Gram-positive bacteria, including Staphylococcus aureus.22 In contrast, studies have reported similar findings to ours, demonstrating a higher occurrence of Gram-negative bacteria in infected abdominal wounds.26,32 Furthermore, our findings revealed a high prevalence of multi-resistant pathogens in relation to commonly prescribed prophylactic antibiotics, which may serve as an explanation for the elevated rate of deep SSI observed in our study. Hence, there is a need to consider appropriate prophylactic antibiotics, especially for high-risk patients.\n\nThe NNIS risk index is a widely recognized framework for assessing and predicting the likelihood of SSI.9 Within our study, two elements of the NNIS exhibited statistical significance (operative time and wound class). However, upon conducting multivariate analysis, the overall NNIS model did not yield statistical significance. Moreover, when comparing the predictive accuracy, our developed model outperformed the NNIS model. Acutely, the performance of the NNIS model in this study showed poor predictive performance for the SSI occurrence as determined by the ROC curve. These results align with previous findings reported by Zhang et al.11\n\nThere are several limitations to consider in this study. First, the retrospective nature of the study may introduce an unintended bias to the study. In addition, it was conducted at a single tertiary teaching hospital, which may limit the generalizability of the findings to other healthcare settings. Furthermore, the study relied on clinical documentation to identify SSI, which could lead to underreporting or misclassification of cases. Moreover, the study focused on a specific geographic region, and the findings may not apply to other populations with different demographics or healthcare systems. Although the study took into account certain potential confounding variables (e.g., the use of prophylactic antibiotics), other potential confounding variables are difficult to assess with the retrospective nature of the study (e.g., surgical techniques and intra-operative maintenance of sterile technique, among others). Finally, the study did not explore long-term outcomes or evaluate the impact of interventions aimed at reducing surgical site infections.\n\n\nConclusions\n\nThis study highlights significant predictors of SSI, including illiteracy, active smoking, DM, leukocytosis, hypoalbuminemia, contaminated and dirty wounds, longer operative time, emergency operations, and extending antibiotic prophylaxis duration. Escherichia coli was the most common pathogen and had a high rate of multidrug-resistant strains. Identifying these risk factors can help surgeons adopt appropriate measures to reduce SSI and improve the quality of surgical care, especially in a resource-limited setting with no obvious and strict policy for reducing SSI.\n\nEthical approval was granted by the Ethics Research Committees of Ibb University [ID: IBBUNI.AC.YEM.2023.75, on 03/03/2023].",
"appendix": "Data availability\n\nMendeley Data: Identification of Predictive Factors for Surgical Site Infections in Gastrointestinal Surgeries: A Retrospective Cross-Sectional Study in a Resource-Limited Setting, http://dx.doi.org/10.17632/hk75wrwr6n.1 33\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors would like to thank the general manager of Al-Thora General Hospital and Al-Nassar Hospital, Ibb, Yemen, Dr. Abdulghani Ghabisha, for their editorial assistance.\n\n\nReferences\n\nUtsumi M, Shimizu J, Miyamoto A, et al.: Age as an independent risk factor for surgical site infections in a large gastrointestinal surgery cohort in Japan. J. Hosp. Infect. 2010 Jul; 75(3): 183–187. PubMed Abstract | Publisher Full Text\n\nSeidelman JL, Mantyh CR, Anderson DJ: Surgical Site Infection Prevention: A Review. JAMA. 2023 Jan 17; 329(3): 244–252. PubMed Abstract | Publisher Full Text\n\nMisha G, Chelkeba L, Melaku T: Incidence, risk factors and outcomes of surgical site infections among patients admitted to Jimma Medical Center, South West Ethiopia: Prospective cohort study. Ann. Med. Surg (Lond). 2021 May; 65: 102247. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health O: Implementation manual to support the prevention of surgical site infections at the facility level: turning recommendations into practice: interim version. Geneva: World Health Organization; 2018. 2018. Report No.: Contract No.: WHO/HIS/SDS/2018.18.\n\nBan KA, Minei JP, Laronga C, et al.: American College of Surgeons and Surgical Infection Society: Surgical Site Infection Guidelines, 2016 Update. J. Am. Coll. Surg. 2017 Jan; 224(1): 59–74. PubMed Abstract | Publisher Full Text\n\nHamza WS, Salama MF, Morsi SS, et al.: Benchmarking for surgical site infections among gastrointestinal surgeries and related risk factors: multicenter study in Kuwait. Infect. Drug Resist. 2018; 11: 1373–1381. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRaja’a YA, Salam AR, Salih YA, et al.: Rate and risk factors of surgical site infections with antibiotic prophylaxis. Saudi Med. J. 2002 Jun; 23(6): 672–674. PubMed Abstract\n\nNasser A, Zhang X, Yang L, et al.: Assessment of surgical site infections from signs & symptoms of the wound and associated factors in public hospitals of Hodeidah City, Yemen. J. Int. J. Appl. 2013; 3(3): 101–110.\n\nSangsuwan T, Jamulitrat S, Watcharasin P: Risk adjustment performance between NNIS index and NHSN model for postoperative colorectal surgical site infection: A retrospective cohort study. Ann. Med. Surg (Lond). 2022 May; 77: 103715. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeery AF, Crockett SD, Barritt AS, et al.: Burden of Gastrointestinal, Liver, and Pancreatic Diseases in the United States. Gastroenterology. 2015; 149(7): 1731–1741.e3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang J, Xue F, Liu SD, et al.: Risk factors and prediction model for inpatient surgical site infection after elective abdominal surgery. World. J. Gastrointest. Surg. 2023 Mar 27; 15(3): 387–397. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLakoh S, Yi L, Sevalie S, et al.: Incidence and risk factors of surgical site infections and related antibiotic resistance in Freetown, Sierra Leone: a prospective cohort study. Antimicrob. Resist. Infect. Control. 2022 Feb 21; 11(1): 39. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKaye KS, Schmit K, Pieper C, et al.: The Effect of Increasing Age on the Risk of Surgical Site Infection. J. Infect. Dis. 2005; 191(7): 1056–1062. Publisher Full Text\n\nKaye KS, Schmit K, Pieper C, et al.: The effect of increasing age on the risk of surgical site infection. J. Infect. Dis. 2005 Apr 1; 191(7): 1056–1062. PubMed Abstract | Publisher Full Text\n\nAnsari S, Hassan M, Barry HD, et al.: Risk Factors Associated with Surgical Site Infections: A Retrospective Report from a Developing Country. Cureus. 2019 Jun 2; 11(6): e4801. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMezemir R, Seid A, Gishu T, et al.: Prevalence and root causes of surgical site infections at an academic trauma and burn center in Ethiopia: a cross-sectional study. Patient Saf. Surg. 2020; 14: 3. PubMed Abstract | Free Full Text\n\nBaker S, Malone E, Graham L, et al.: Patient-reported health literacy scores are associated with readmissions following surgery. Am. J. Surg. 2020 Nov; 220(5): 1138–1144. PubMed Abstract | Publisher Full Text\n\nDeng Y, Zheng Z, Cheng S, et al.: Correction to: The factors associated with nosocomial infection in elderly hip fracture patients: gender, age, and comorbidity. Int. Orthop. 2021 Dec; 45(12): 3211. PubMed Abstract | Publisher Full Text\n\nLi X, Nylander W, Smith T, et al.: Risk Factors and Predictive Model Development of Thirty-Day Post-Operative Surgical Site Infection in the Veterans Administration Surgical Population. Surg. Infect. 2018 Apr; 19(3): 278–285. PubMed Abstract | Publisher Full Text\n\nLi Z, Li H, Lv P, et al.: Prospective multicenter study on the incidence of surgical site infection after emergency abdominal surgery in China. Sci. Rep. 2021 Apr 8; 11(1): 7794. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSwenne CL, Lindholm C, Borowiec J, et al.: Peri-operative glucose control and development of surgical wound infections in patients undergoing coronary artery bypass graft. J. Hosp. Infect. 2005 Nov; 61(3): 201–212. PubMed Abstract | Publisher Full Text\n\nMawalla B, Mshana SE, Chalya PL, et al.: Predictors of surgical site infections among patients undergoing major surgery at Bugando Medical Centre in Northwestern Tanzania. BMC Surg. 2011 Aug 31; 11: 21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBilloro BB, Nunemo MH, Gelan SE: Evaluation of antimicrobial prophylaxis use and rate of surgical site infection in surgical ward of Wachemo University Nigist Eleni Mohammed Memorial Hospital, Southern Ethiopia: prospective cohort study. BMC Infect. Dis. 2019 Apr 2; 19(1): 298. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHassan NA, Gunaid AA, Murray-Lyon IM: Khat (Catha edulis): health aspects of khat chewing. East Mediterr. Health J. 2007 May-Jun; 13(3): 706–718. PubMed Abstract\n\nSilva B, Soares J, Rocha-Pereira C, et al.: Khat, a Cultural Chewing Drug: A Toxicokinetic and Toxicodynamic Summary. Toxins (Basel). 2022 Jan 20; 14(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlkaaki A, Al-Radi OO, Khoja A, et al.: Surgical site infection following abdominal surgery: a prospective cohort study. Can. J. Surg. 2019 Apr 1; 62(2): 111–117. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRaka L, Krasniqi A, Hoxha F, et al.: Surgical site infections in an abdominal surgical ward at Kosovo Teaching Hospital. World Hosp. Health Serv. 2008; 44(2): 32–36. PubMed Abstract\n\nKefale B, Tegegne GT, Degu A, et al.: Surgical Site Infections and Prophylaxis Antibiotic Use in the Surgical Ward of Public Hospital in Western Ethiopia: A Hospital-Based Retrospective Cross-Sectional Study. Infect. Drug Resist. 2020; 13: 3627–3635. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWatanabe M, Suzuki H, Nomura S, et al.: Risk factors for surgical site infection in emergency colorectal surgery: a retrospective analysis. Surg. Infect. 2014 Jun; 15(3): 256–261. PubMed Abstract | Publisher Full Text\n\nTfaily MA, Ghanem P, Farran SH, et al.: The role of preoperative albumin and white blood cell count in surgical site infections following whipple surgery. Sci. Rep. 2022 Nov 10; 12(1): 19184. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLegesse Laloto T, Hiko Gemeda D, Abdella SH: Incidence and predictors of surgical site infection in Ethiopia: prospective cohort. BMC Infect. Dis. 2017 Feb 3; 17(1): 119. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAga E, Keinan-Boker L, Eithan A, et al.: Surgical site infections after abdominal surgery: incidence and risk factors. A prospective cohort study. Infect. Dis (Lond). 2015; 47(11): 761–767. PubMed Abstract | Publisher Full Text\n\nAhmed F: Identification of Predictive Factors for Surgical Site Infections in Gastrointestinal Surgeries: A Retrospective Cross-Sectional Study in a Resource-Limited Setting. Mendeley Data. 2023; V1. Publisher Full Text"
}
|
[
{
"id": "192612",
"date": "25 Aug 2023",
"name": "Nicolas Troillet",
"expertise": [
"Reviewer Expertise Healthcare associated infections",
"clinical infectious diseases."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting and well written study aiming at determining a prediction rule for surgical site infection after digestive surgery in a developing country. It gathered a substantial number of parameters for univariate and multivariable analysis in order to develop a prediction model that performs better than the classical NNIS index.\nThe authors might want to consider the comments and questions below and revise their paper accordingly.\n\nThe abstract mentions a SSI rate of 15% (79/525), whereas the results section and the discussion state 16.4% (86/525).\n\nThe abstract states that the majority of SSI were superficial but detailed results on the depth of SSI (superficial, deep, organ/space) are not provided in the results section. These data would be interesting by type of surgery.\n\nThe inclusion criteria state that all eligible patients between June 2015 and October 2022 were included, reaching 525 patients in about 7 years. Knowing the number of patients excluded would be of interest.\n\nPrecisions on how SSI were detected would be of interest. Was the diagnosis made by surgeons or infection control personnel? Were all the patients followed-up after discharge? If yes, by systematic visits? All SSI were microbiologically documented. Was it because samples were taken from all patients with a clinically diagnosed SSI or because positive lab results were used to identify patients with SSI?\n\nOperations are grouped in four categories (small bowel, large bowel, biliary, and pancreatic) in the description of the population analyzed. More details would be interesting to know which operations were included in these four categories, e.g. how many cholecystectomies were included in biliary surgery? Were appendectomies included in large bowel surgery or only colon surgery? Did large bowel surgery include rectal surgery?\n\nThese operations are then grouped in two categories (small bowel and others) in the statistical analyses. Although small bowel surgery represents the highest number of included operations, grouping large bowel surgery with biliary surgery appears counterintuitive, especially if cholecystectomies, which are much less at risk than colon surgery, represent the majority of biliary surgery. Could the results have been different and reached statistical significance if the comparison had been made between large bowel and others rather than between small bowel and others?\n\nSome continuous variables such as age, hospital stay, BMI or temperature were stratified into binomial variables for the statistical analyses. Did it imply a loss of power for detecting risk factors and perhaps better determine a cut-off for the prediction? This applies particularly for age which could have been considered as an ordinal variable and stratified first in ten-year categories.\n\nThe timing of shaving was found significant but shaving is not recommended by international guidelines and may constitute a risk factor for SSI (cf. for example reference 2 in the present paper). Is shaving systematically done in this hospital? Avoiding it accordingly with guidelines could constitute a simple mean for decreasing SSI rates that could be mentioned in the discussion.\n\nIt is stated that variables with a p value <0.2 in univariate analysis were fitted for logistic regression but “antibiotic timing” and “operative type”, which had both higher p values in univariate analysis (p=0.454 and p=0.506, respectively, as presented in table 4) are nevertheless part of the multivariable model (table 5). More details would be useful for a better understanding.\n\nDo all the operations performed in digestive surgery in this hospital correspond to open surgery? Since operations done with a laparoscope have been shown to be less at risk for SSI, information would be of interest about it in the methods and in the discussion.\n\nIt is stated that “pathogens linked with SSI were identified from all SSI patient wounds”. The total number of pathogens in table 3 amounts to 86 for 86 patients. This would mean that only one pathogen was identified from every patient with SSI. Were no patients suffering from a polymicrobial SSI detected (which is relatively frequent in colon surgery)? Were no other pathogens identified than the seven presented in table 3? For example, Enterobacter spp. streptococci or Candida spp.?\n\nMore details would be of interest on resistance patterns of the isolated bacteria: proportion of ESBL producers in E. coli and Klebsiella respectively, presence or not of carbapenemase-producing Enterobacteriaceae, resistance profile of Pseudomonas aeruginosa, resistance to vancomycine in enterococci.\n\nMentioning the substances usually administered for antibiotic prophylaxis in these operations would help better realizing the magnitude of the problem of antibiotic resistance in this setting.\n\nWere only the significant variables in the multivariable analysis used for calculating the performance of the model for predicting SSI? Please specify.\n\nDiscussion, paragraph 6. Mentioning whether glucose levels were not available for the included patients together with albumin levels or were available but not analyzed would be of interest since, irrespective of a history of diabetes, this could constitute, as stated, a risk factor for SSI.\n\nDiscussion, paragraph 9. The following sentence is hard to understand: “Furthermore, our study revealed that the prevalence of SSI in large, pancreatic, and biliary surgeries was lower than in intestinal procedures; although this association was not statistically significant.” Does “large” mean large bowel? Then “intestinal” might mean small bowel. Please clarify. In addition, please refer to comments 5 and 6 above for possible modifications in the discussion about this result.\n\nDiscussion, paragraph 10. It is stated that a long duration may induce weaning prophylactic antibiotic concentration. Studies have shown the importance of re-dosing when this duration reach the half-life of the administered antibiotic and guidelines recommend it. This could be mentioned here and cited as a mean to lower SSI rates.\n\nDiscussion, paragraph 11. Please refer to comments 11, 12, and 13 above and possibly take them into account for extending the discussion about antibiotic resistance in this paragraph.\n\nLimitations, 3rd sentence. Does “clinical identification” mean that no radiological or laboratory markers were used to help for the diagnosis of SSI? If yes, this should be specified in the methods. If not, underreporting might be due to interobserver variability if persons with different backgrounds did it (e.g. surgeons, infectious diseases physicians, infection control nurses).\n\nLimitations, 4th sentence. Internal and external validation on other datasets or prospectively should be mentioned as a mean to consolidate these findings.\n\nTypos. Table 1: “During 1 hour of operation” instead of “During 1 house of operation”. Table 3: “Pseudomonas aeruginosa” instead of “Pseudomonas aerugisa”.\n\nTerminology. The same words should be used through the different tables (e.g. “surgical status” in table 1 instead of “operative type” in tables 4 and 5). Consider using “operation duration” instead of “operative time”.\n\nReferences 13 and 14 are identical. Reference 18 corresponds to a correction: please mention the original publication.\n(The source data are available but the corresponding file could not be opened.)\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "10955",
"date": "23 May 2024",
"name": "Faisal Ahmed",
"role": "Author Response",
"response": "Dear reviewer Thank you very much for reading and reviewing my manuscript. This is an interesting and well-written study aiming at determining a prediction rule for surgical site infection after digestive surgery in a developing country. It gathered a substantial number of parameters for univariate and multivariable analysis to develop a prediction model that performs better than the classical NNIS index. The authors might want to consider the comments and questions below and revise their paper accordingly. The abstract mentions an SSI rate of 15% (79/525), whereas the results section and the discussion state 16.4%. (86/525) Answer: Thank you. We apologize for this mistake. The exact number was revised in the abstract section. The abstract states that the majority of SSI were superficial but detailed results on the depth of SSI (superficial, deep, organ/space) are not provided in the results section. These data would be interesting by type of surgery. Answer: Thank you. The SSI type was added to the result section (Causative Pathogens section). The inclusion criteria state that all eligible patients between June 2015 and October 2022 were included, reaching 525 patients in about 7 years. Knowing the number of patients excluded would be of interest. Answer: Thank you. Unfortunately, the total number of patients was not accurately calculated. For that, we avoided mentioning the total patient numbers. Precisions on how SSIs were detected would be of interest. Was the diagnosis made by surgeons and infection control personnel? Were all the patients followed up after discharge? If yes, by systematic visits? All SSIs were microbiologically documented. Was it because samples were taken from all patients with a clinically diagnosed SSI or because positive lab results were used to identify patients with SSI? Answer: Thank you. Regarding infection control personnel, it was corrected. Regarding patients followed up: yes. As they were operated, it is usually to have a regular follow-up. Additionally, we mentioned that they underwent systematic visits. Regarding microbiology documentation, all patients had culture and we mentioned it in the data collection section. The main causes of sample collection are the patient symptoms and the SSI suspected. Operations are grouped into four categories (small bowel, large bowel, biliary, and pancreatic) in the description of the population analyzed. More details would be interesting to know which operations were included in these four categories, e.g. how many cholecystectomies were included in biliary surgery? Were appendectomies included in large bowel surgery or only colon surgery? Did large bowel surgery include rectal surgery? Answer: Thank you. We did not collect the data regarding These operations are then grouped into two categories (small bowel and others) in the statistical analyses. Although small bowel surgery represents the highest number of included operations, grouping large bowel surgery with biliary surgery appears counterintuitive, especially if cholecystectomies, which are much less at risk than colon surgery, represent the majority of biliary surgery. Could the results have been different and reached statistical significance if the comparison had been made between Large bowel and others rather than between small bowel and others? Answer: Thank you. We revised it as you mentioned. However, it was not statistically significant as we mentioned in table 4. Some continuous variables such as age, hospital stay, BMI or temperature were stratified into binomial variables for the statistical analyses. Did it imply a loss of power for detecting risk factors and perhaps better determine a cut-off for the prediction? This applies particularly for age which could have been considered as an ordinal variable and stratified first in ten-year categories. Answer: Thank you. All the continuous variables were converted into categorical variables for a better presentation of the nomogram. This statement was mentioned. The timing of shaving was found significant but shaving is not recommended by international guidelines and may constitute a risk factor for SSI (cf. for example reference 2 in the present paper). Is shaving systematically done in this hospital? Avoiding it according with guidelines could constitute a simple means for decreasing SSI rates that could be mentioned in the discussion. Answer: Thank you. This item was revised to be Hair removal. We mentioned this issue in the discussion section. It is stated that variables with a p value <0.2 in univariate analysis were fitted for logistic regression but “antibiotic timing” and “operative type”, which had both higher p values in univariate analysis (p=0.454 and p=0.506, respectively, as presented in table 4) are nevertheless part of the multivariable model (table 5). More details would be useful for a better understanding. Answer: Thank you. To better understand, we revised the Statistical analysis section. 10. Do all the operations performed in digestive surgery in this hospital correspond to open surgery? Since operations done with a laparoscope have been shown to be less at risk for SSI, information would be of interest about it in the methods and in the discussion. Answer: Thank you. Unfortunately, the laparoscopic equipment is not available in our hospital. For that, we avoided mentioning the laparoscopic procedures. 11. It is stated that “pathogens linked with SSI were identified from all SSI patient wounds”. The total number of pathogens in table 3 amounts to 86 for 86 patients. This would mean that only one pathogen was identified from every patient with SSI. Were no patients suffering from a polymicrobial SSI detected (which is relatively frequent in colon surgery)? Were no other pathogens identified than the seven presented in Table 3? For example, Enterobacter spp. streptococci or Candida spp.? Answer: Thank you. This was the result reported by the laboratory. 12. More details would be of interest on resistance patterns of the isolated bacteria: proportion of ESBL producers in E. coli and Klebsiella respectively, presence or not of carbapenemase-producing Enterobacteriaceae, resistance profile of Pseudomonas aeruginosa, resistance to vancomycin in enterococci. Answer: Thank you. We did not collect the data regarding the antibiotic sensitivity or resistance. 13. Mentioning the substances usually administered for antibiotic prophylaxis in these operations would help better realize the magnitude of the problem of antibiotic resistance in this setting. Answer: Thank you. it was mentioned in the data collection section. 14. Were only the significant variables in the multivariable analysis used for calculating the performance of the model for predicting SSI? Please specify . Answer: Thank you. To better understand, we revised the Statistical analysis section. 15. Discussion, paragraph 6. Mentioning whether glucose levels were not available for the included patients together with albumin levels or were available but not analyzed would be of interest since, irrespective of a history of diabetes, this could constitute, as stated, a risk factor for SSI. Answer: Thank you. We mentioned this issue in the discussion section. 16. Discussion, paragraph 9. The following sentence is hard to understand: “Furthermore, our study revealed that the prevalence of SSI in large, pancreatic, and biliary surgeries was lower than in intestinal procedures; although this association was not statistically significant.” Does “large” mean large bowel? Then “intestinal” might mean small bowel. Please clarify. In addition, please refer to comments 5 and 6 above for possible modifications in the discussion about this result. Answer: Thank you. It was revised as you mentioned. 17. Discussion, paragraph 10. It is stated that a long duration may induce weaning prophylactic antibiotic concentration. Studies have shown the importance of re-dosing when this duration reaches the half-life of the administered antibiotic and guidelines recommend it. This could be mentioned here and cited as a means to lower SSI rates. Answer: Thank you. It was added as you mentioned. 18. Discussion, paragraph 11. Please refer to comments 11, 12, and 13 above and possibly take them into account for extending the discussion about antibiotic resistance in this paragraph. Answer: Thank you. We did not collect the data regarding the antibiotic sensitivity or resistance. 19. Limitations, 3rd sentence. Does “clinical identification” mean that no radiological or laboratory markers were used to help with the diagnosis of SSI? If yes, this should be specified in the methods. If not, underreporting might be due to interobserver variability if persons with different backgrounds did it (e.g. surgeons, infectious diseases physicians, infection control nurses). Answer: Thank you. The word clinical was removed. 20. Limitations, 4th sentence. Internal and external validation on other datasets or prospectively should be mentioned as a mean to consolidate these findings. Answer: Thank you. We added this issue as you recommended. 21. Typos. Table 1: “During 1 hour of operation” instead of “During 1 house of operation”. Table 3: “Pseudomonas aeruginosa” instead of “Pseudomonas aerugisa”. Answer: Thank you. It was revised through the manuscript. 22. Terminology. The same words should be used through the different tables (e.g. “surgical status” in Table 1 instead of “operative type” in Tables 4 and 5). Consider using “operation duration” instead of “operative time”. Answer: Thank you. It was revised as you mentioned. 23. References 13 and 14 are identical. Reference 18 corresponds to a correction: please mention the original publication. Answer: Thank you. All references were rechecked and corrected The source data are available but the corresponding file could not be opened. Answer: Thank you. The revised dates are available at this address. https://data.mendeley.com/datasets/hk75wrwr6n/2 Is the work clearly and accurately presented and does it cite the current literature? Yes Answer: Thank you. Is the study design appropriate and is the work technically sound? Yes Answer: Thank you. Are sufficient details of methods and analysis provided to allow replication by others? Partly Answer: Thank you. If applicable, is the statistical analysis and its interpretation appropriate? Partly Answer: Thank you. Are all the source data underlying the results available to ensure full reproducibility? Yes Answer: Thank you. Are the conclusions drawn adequately supported by the results? Yes Answer: Thank you. Competing Interests No competing interests were disclosed. Answer: Thank you. Reviewer Expertise Healthcare associated infections, clinical infectious diseases. Answer: Thank you."
}
]
}
] | 1
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https://f1000research.com/articles/12-733
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https://f1000research.com/articles/12-1414/v1
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26 Oct 23
|
{
"type": "Research Article",
"title": "Analysis of carbon nano particle variant as the propellant fuel to increase specific impulses of rockets",
"authors": [
"RDA Navalino",
"NRS Muda",
"MAE Hafizah",
"Y Ruyat",
"NRS Muda",
"MAE Hafizah",
"Y Ruyat"
],
"abstract": "Background: This study compares propellant fuels' specific thrust and impulse parameters using nanocarbon variant fuels from coconut shells and coal. Specific impulses and impulses are essential parameters that determine rocket performance. The specific thrust and impulses are influenced by fuel type, material composition, heat flow, and burning time parameters. The characteristics of nanocarbon as a fuel are proven to have high-value features and a long combustion time. This parameter is essential to add value to specific thrusts and impulses. Methods: The method to prove the quality of solid fuel material was done experimentally. The composition of the propellant fuel variant mixed with NH4ClO4 as an oxidizer through the printing process and sample testing was carried out using scanning electron microscope (SEM), X-ray diffraction analysis (XRD), combustion time, and specific impulse tests. Results: Test results with the composition of CBK2 (Coconut Shell + NH4ClO4 + Binder + Al = 15: 70: 10: 5) produced a specific impulse of 267 seconds or an increase of 37 seconds without carbon. CBB2 (Coal + NH4ClO4 + Binder + Al = 15: 70: 10: 5) produced a specific impulse of 261 seconds or an increase of 31 seconds. Conclusions: The composition of nanocarbon as a solid fuel propellant has been proven to increase a rocket's thrust and specific impulses. After all the material variants have been tested for thrust and specific impulse, the best rocket propellant is CBK2.",
"keywords": [
"Coal carbon nano",
"coconut shell carbon nano",
"specific impulse"
],
"content": "Introduction\n\nOne of the important ingredients of a rocket for propulsion is the thrust filling known as propellant, this propellant can be made from liquid or solid material, or a combination of the two materials.1 Propellant is an energetic material that provides propulsion control. Solid rocket propellant has been widely developed to improve rocket performance, including the composition of materials used such as fuel and oxidizing agents.1 In terms of the components that make up the propellant can be grouped into homogeneous propellants both fuel and oxidizer, arranged in one molecule, whereas in heterogeneous propellants the two materials are not chemically necessary. Composite propellants are mixtures that use non-oxidizing salts, such as perchlorate, chlorate or nitrate salts, which are arranged between 60%-90% of the mass of the propellant.2 One of the variables created in this study is the specific impulse of the rocket, because this variable is needed when rocket flying and rocket flying speed. Various ways to increase the rocket’s special impulse (Isp) include assessing the quality of propellant, geometrical propellant, nozzle construction, combination of various shapes and other nozzle materials.3–5 Single base and double base have specific impulses (less than 220 seconds) compared to propellant composites that can reach 250 seconds.2,6 Unless the single type and double base produce very little and are not easily seen, this is advantageous from a military aspect.\n\nActivated carbon from coconut shell (ACCS) as a catalyst added to solid propellant can increase combustion time and thrust so as to increase specific impulse.3 According to Ref. 3 composite solid propellants (CSP) content consists of C3 (ammonium perchlorate (AP) 70%, hydroxyl-terminated polybutadiene (HTPB) 15%, aluminum (Al) 10%, activated carbon from coconut shell (ACCS) 5%) and produces the best composition but still causes uneven burning in the fire zone. Nano carbon can be used through the milling process on charcoal powder using the high energy milling method to produce nano size.4,7 In this research, the chosen parameter is the variation parameter of nano carbon particles, a new concept that uses a statistical experimental method by not changing the variable construction of the nozzle and space rocket. Variants of nano particles are obtained from C12 carbon after going through a milling process, mixed with a composition of propellant and approved until a high heating value, high temperature, long combustion time are obtained. This parameter is an important factor that can increase special rocket impulses.\n\n\nMethods\n\nUsing nanocarbon as a capacitor has been found to accelerate decomposition at low temperatures and regulate the exothermic reaction in stages. This results in higher heat flow and gas pressure, as well as uniform flame, bursts in the fire zone.8,9 Nano carbon is also utilized as a catalyst and propellant under stoichiometric conditions, which makes the propellant denser and increases specific impulses and impulses.5 The study includes six materials: CBB1, CBB2, CBB3, CBK1, CBK2, and CBK3. Each material has different compositions consisting of coal, NH4ClO4, binder, and aluminum in varying proportions. These materials have shown promising results in propellant and catalyst applications. The materials were made up as in Table 1.\n\nCoconut shell charcoal powder and coal charcoal powder with a coarseness of 40-80 mesh and 200 mesh, respectively, were purchased from Megha Abadi Kimia. Market-grade wirecloth and TBC wire cloth were purchased from Elcan Industries with micron sizes of 1300 and 630, respectively. All chemicals (NH4ClO4, binder (HTPB and PVA) and Al with the ratio of 15%:70%:10%:5%).\n\nCoconut shell charcoal powder and coal charcoal powder, ground by ballmill for 20 hours, 40 hours, 60 hours and 80 hours. This is to produce carbon sizes of 1 μm, 350 nm, 200 nm, and 100 nm, respectively. Each carbon size is mixed according to the composition of the material with binder (HTPB and PVA) blended for 20 minutes. The reason is to compare the composition of all the materials, which is the most optimal for producing the best thrust and isp (specific impulse). After that 70 um aluminum powder with a concentration according to the composition of the material is put into a tube (the tube used is a mixer tube, diameter 30 cm, height 28 cm, material capacity 3.5 kg, rpm 120) and blended for 10 minutes. Furthermore, the dough is added to the oxidizer NH4ClO4 and blended for five minutes until the mixture occurs in gel form. The next step is the mixture that has been in the form of gel is poured in a propellant mold and put into the oven (OVEN-700 Precision Composites Curing Oven) that was used to cure, anneal, dry, and harden synthetic and composite materials. A temperature of 60 degrees Celsius for 48 hours was used. After the propellant mixture in the oven is removed and cooled naturally at room temperature for 60 minutes. The final step is to remove the solid propellant from the mold and test the solid propellant material. The milling process begins with the use of carbon with a size of 10 um with 10 grams after a process of 20 hours produced carbon with a size of 1 um, a process of 40 hours produced by carbon size of 350 nm, a process of 60 hours produced by carbon size of 200nm, a process of 80 hours produced by 100 nm. After the milling process is completed, it is continued by mixing each carbon material (1 um, 350 nm, 200 nm, 100 nm) with oxidizing agents (NH4ClO4 and Al).\n\nThe solid propellant sample test materials include testing the material morphology using a scanning electron microscope (SEM), displaying a graph of mass loss due to thermal effects using a X-ray diffraction (XRD) tool [DW-XRD-Y3000], and testing the special thrust and impulses using a test tube. The SEM (SU3800/SU3900) with a magnification of 30,000x was used to examine the structure and composition of the carbon nanoparticles. ImageJ software (RRID:SCR_003070) was used to analyze the particle sizes from SEM images and ORIGIN PRO software (RRID: SCR_014212) was used for the XRD study. XRD with the model number DW-XRD-Y3000 was used to analyze the properties of the carbon nanoparticles.\n\nHeat flow was calculated with an HZ -384A Huazheng Automatic Calorific Value Tester in this study. 0.9-1.1g of the substance to be tested was placed in a heat crucible (heat-resistant and anti-corrosion), and the crucible was placed in an oxygen bomb added with a 2.8-3.2 mpa oxygen and put into the inner cylinder of the calorimeter. Distilled water was added to the inner cylinder. The heat output of the combustible can be calculated according to the rise in the water temperature and heat capacity of the calorimetry system (Table 2).\n\nSpecific impulse (ISP) was calculated, using an HZ-384A Huazheng Automatic Calorific Value Tester. The substance to be tested was placed in a heat crucible, and the crucible was placed in an oxygen bomb added with 2.8-3.2 mpa oxygen and placed into the inner cylinder of the calorimeter. Distilled water was then added to the inner cylinder. The heat output of the combustible was calculated according to the increase in water temperature and heat capacity of the calorimetry system. ISP was calculated using the following formula:\n\nThis study was approved by the Republic of Indonesia Defense University (approval number: 27/VII/wikan/2023). After reviewing the study protocol, the committee approved the project and stated that the study was in accordance with ethical principles and guidelines for research integrity.\n\n\nResults\n\nFrom the SEM test, after the grinding process by ballmill the results are seen using SEM using 1000× magnification.20 Figure 1a shows CBB1, Figure 1b shows CBB2, and Figure 1c shows CBB3. Figure 2a shows CBK1, Figure 2b shows CBK2, and Figure 2c shows CBK3. All materials making up these can be found in Table 1.\n\nTable 2 shows the calorific test results for different carbon sizes of the propellant variants using coal carbon and coconut shell carbon as fuels. The values for CBB2 are 4028, while the other variants are listed as CBB, CBK, and a corresponding number. These results provide important information for determining the energy output of propellants and can be used for further analyses.\n\nTable 3 displays the burning times for each carbon size and variant, with the numbers ranging from 13 to 24 s. This demonstrates that CBK1 and CBK2 had longer burning times than the other variants. These results can be helpful in determining which variant is most suitable for a particular application.\n\nBased on the data presented in Table 4, it appears that there are several different variants of propellant ISP calculations based on the carbon size. Specifically, calculations have been calculations for 1um, 350 nm, 200 nm, and 100 nm. The table lists the various CBB and CBK variants, each with their own corresponding numbers. The calculation results for each variant are presented in the table. The results demonstrate that the propellant ISP values can vary depending on the carbon size and the variant used in the calculations.\n\nThe results of the heat value of propellant material from coconut shell and oxidizer as shown in Figures 3 and 4 that the smaller the carbon size, the greater the heat of the material produced, and the composition of CBK2 with a size of 100 nm produces a heating value of 6103 cal. The test results of the heat value of propellant from carbon coal and oxidizer as shown in Figure 3 that the smaller the carbon size, the greater the heat of the material produced, and the composition of CBB2 with a size of 100 nm produces a heating value of 7391 cal. CBB2 composition produces the highest calorific value which can affect rocket thrust performance but relatively fast combustion time can affect low specific impulse.\n\n\nDiscussion\n\nThe quest for more efficient propellant fuels to enhance rocket performance has led to groundbreaking advancements in rocket propulsion technology.1,3 Carbon nanotechnology has emerged as a promising avenue of investigation in this domain, with carbon nanoparticle variants showing great potential for boosting the specific impulses of rockets.4 This article delves into the analysis of carbon nanoparticle variants as a propellant fuel, exploring their effectiveness in increasing specific impulses and their implications for rocket propulsion. Carbon nanoparticles possess remarkable properties, such as high surface area, exceptional thermal conductivity, and superior mechanical strength. When employed as a propellant fuel, these unique characteristics positively impact the specific impulse of rockets.1,7 The specific impulse is a metric that quantifies the efficiency of rocket engines by measuring the amount of thrust produced per unit of propellant consumed. By incorporating a carbon-nanoparticle variant as a propellant fuel, the specific impulse can be significantly increased, resulting in enhanced rocket performance and greater payload capabilities.6,9\n\nThis article explores the effects of milling processes on the size of nanocarbon, with longer processes resulting in smaller carbon sizes. The article then discusses the effects of mixing carbon with oxidizing agents and how the carbon’s size affects the propellant material’s heat value. It was shown that smaller carbon sizes produce greater heat values and higher thrust for rockets. The article also highlights the differences between using coal and coconut shells as fuel for rockets and how the carbon’s size affects the propellant’s specific impulse and burning time.\n\nVarious variants of carbon nanoparticles have been analyzed as propellant fuels that can potentially enhance the specific impulses of rockets. The specific impulse is a crucial metric in rocket propulsion and represents the change in momentum per unit of propellant mass expended. It is a vital indicator of a rocket’s propulsion efficiency and performance. This study primarily focused on carbon particles obtained using a milling process. Interestingly, the size of the nanocarbon particles is inversely proportional to the length of the milling process. Longer milling times have resulted in smaller carbon sizes, leading to greater heat production by the propellant material. This information lays the foundation for investigating the impact of carbon particle size on rocket thrust performance. In this study explored two types of propellant materials: CBK2 (Carbon from Coconut Shell) and CBB2 (Carbon from Coal). Both propellant materials were mixed with the oxidizing agents NH4ClO4 and Al, along with a binder. It has been found that the size of carbon particles has a significant impact on the heating value of propellant materials. Research has shown that CBK2, which has a particle size of 100 nm, generates a heating value of 6103 cal. Meanwhile, CBB2, which also had a particle size of 100 nm, produced 7391 cal. These results suggest that smaller carbon particle sizes are more effective in generating higher heat values, which could lead to improved rocket thrust performance. The size of the carbon particles affects the propellant combustion time. It was found that smaller carbon particle sizes lead to faster combustion times. Interestingly, the composition CBK1 (which contained C + NH4ClO4 + Binder + Al in a ratio of 20:70:10:0) had the longest burning time when it contained larger carbon particles. However, even with larger carbon particles, CBK1 still burns longer than the coal fuel (CBB1). This longer burning time has a direct impact on the specific thrust and impulse of the rocket, because they are directly proportional to the burning time. The presence of Al in propellant materials can affect their surface morphology. It demonstrated that the addition of aluminum to coal fuel can lead to poor surface homogeneity, as seen in the composition of CBB2 (C + NH4ClO4 + Binder + Al = 15:70:10:5). However, Al can also serve as an additive to coal carbon, helping with oxygen binding and complete combustion. This can lead to higher thermal values and an increased rocket thrust. The composition CBK2, which includes (coconut-shell carbon, NH4ClO4, binder, and Al in a ratio of 15:70:10:5), with a particle size of 100 nm, produces the highest heating value and ideal specific impulse. Additionally, the composition of CBB2 with coal carbon and the same particle size is an optimal choice for rocket propulsion.\n\nThe nano carbon obtained using the milling process provided the data as shown, where the results of nano carbon size was determined by the length of the milling process, the longer the process the smaller the carbon size.\n\nFigure 1a CBB1 SEM test material results show that the composition produces a dense surface morphology compared to CBB2 shows that the element Aluminum causes poor surface homogeneity, but the Aluminum factor is capable of being a good additive to coal carbon as a fuel to bind oxygen and burn out completely. This can produce a higher thermal value so as to increase the rocket’s thrust. Different conditions as shown in Figure 1c CBB3, aluminum concentration content balanced with carbon coal turns out that this condition reduces the role of carbon as propellant fuel, ultimately reducing the value of rocket thrust. Figure 2a CBK2 shows that the carbon content of coconut shells produces a denser morphology than the carbon element of coal. The carbon shell effect also produces a more homogeneous morphology when mixed with aluminum at concentrations C (coconut shell) = 15% and Al = 5% as shown in Figure 2b with CBK2. This condition produces a higher thrust compared to coal carbon fuel = 15% and Al = 5%. While Figure 2c (CBK3) shows better morphology compared to the carbon fuel content of coal and aluminum, this has an effect on lower thrust values. As Table 2 shows the relationship between carbon size and heating value shows that the smaller the carbon size, the higher the heating value and the composition of CBK2 is the most composition high heating value. As in Table 3 the propellant combustion time using coal fuel shows that the smaller the size of carbon the faster burning time and the composition of CBK1 is the longest composition the burning time. But when compared with propellant using coconut shell fuel, the combustion time of CBK1 composition is longer than CBB1. This shows that the burning time of coconut shell fuel is longer than that of coal, this condition significantly influences the value of the specific thrust and impulse of the rocket (ISP) because the value of the burning time is directly proportional to the ISP.\n\nComparison of heatflow of all propellant fuels shown in Figure 3, the composition of CBK2 produces the most heatflow occurs at a temperature of 350°C which is 1615 J/g this condition is greater than the composition of CBB2 where at 350°C produces a heatflow of 1505 J/g. While the smallest heatflow produced by the composition of CBB3 at a temperature of 361°C conducts heat of 1195 J/g. The amount of heatflow that occurs in CBK2 and CBB2 can be used to increase specific thrust and impulse. Because specific thrust and impulses are directly proportional to the speed of heat flow rate on propellant combustion. Figure 4a shows the specific impulse of solid propellants containing coal as fuel. The graph shows that changes in fuel size affect specific impulse values. Effect of coal size where the smaller the diameter of the fuel, the greater the specific impulse produced. The best results from this material test are shown by the CBB2 variant. The CBB1 Isp yield is lower than that of CBB2 because without the aluminum content decreases the specific impulse value, or increases the aluminum content to 10% also further decreases the rocket specific impulse value. So the ideal condition for the best specific rocket impulse is CBB2. As in shown Figure 4b. the specific impulse of solid propellants containing carbon of coconut shell as fuel. The graph shows that changes in fuel size affect specific impulse values. Effect of coconut shell carbon size where the smaller the diameter of the fuel, the greater the specific impulse produced. The best results from this material test are shown by the CBB2 variant. The CBK1 Isp is lower than that of CBK2 because without the aluminum content decreases the specific impulse value or increases the aluminum content to 10% also further decreases the rocket specific impulse value. So the ideal condition for the best specific rocket impulse is CBK2.\n\nPursuing more efficient propellant fuels to enhance rocket performance has led to significant advancements in rocket propulsion technology.10 Carbon nanotechnology has emerged as a promising avenue in this endeavor, with carbon nanoparticle variants showing substantial potential for improving the specific impulses of rockets.4 This study contributes to this burgeoning field by analyzing various carbon nanoparticle variants as propellant fuels and their implications for boosting rocket performance.\n\nThe unique properties of carbon nanoparticles, such as their high surface area, exceptional thermal conductivity, and superior mechanical strength, are promising for enhancing rocket propulsion.1,7 These properties can significantly influence the specific impulse of rockets, which is a vital metric for quantifying the propulsion efficiency by measuring the thrust produced per unit of propellant consumed. Integrating carbon-nanoparticle variants as propellant fuels makes it possible to substantially increase the specific impulse, leading to enhanced rocket performance and greater payload capacities.6,9\n\nOne of the primary focuses of this study was to investigate the effects of milling processes on the size of nanocarbon particles, revealing an inverse relationship between the milling time and particle size. This aligns with previous research, suggesting that extended milling processes result in smaller carbon sizes.11 Notably, reducing carbon particle size increased heat production by the propellant material. This finding underscores the significance of nanoparticle size in influencing the thermal characteristics, subsequently affecting the rocket thrust performance.\n\nComparing two propellant materials derived from different carbon sources, namely CBK2 (Carbon from Coconut Shell) and CBB2 (Carbon from Coal), unveiled intriguing insights. Smaller carbon particle sizes demonstrated the capability of generating higher heat values, thus suggesting their potential for enhancing rocket thrust. The presented results align with existing theories, suggesting that smaller particle sizes result in more efficient combustion owing to increased surface area-to-volume ratios.12,13\n\nThe influence of carbon particle size on propellant combustion time is an essential aspect of rocket propulsion. The relationship between the particle size and combustion time was consistent with expectations, where smaller particles led to faster combustion. These findings resonate with enhanced reactivity in nanoscale materials, leading to a more rapid energy release during combustion processes.14,15 The specific thrust and impulse implications are substantial because the combustion time directly affects these metrics.\n\nThe addition of aluminum (Al) as an oxidizing agent had contrasting effects on the surface morphology of the propellant materials. While some variations, such as CBB2, showed poorer surface homogeneity due to the aluminum content, Al proved valuable as an additive for binding oxygen and facilitating complete combustion. This aligns with established theories regarding the role of aluminum in propellant formulations, enhancing thermal values and consequently increasing rocket thrust.16,17\n\nA comparison of the results of the CBK2 and CBB2 compositions further emphasized the influence of carbon particle size on rocket performance. Although CBK2, with its smaller particle size, exhibited higher heating values and an ideal specific impulse, CBB2 remained the optimal choice for rocket propulsion among coal-based compositions. These results offer practical insights into selecting propellant materials based on the desired performance characteristics.\n\nThe data obtained from the milling process for nanocarbon provided valuable insights into the relationship between milling time and carbon particle size. The observed trends align with research on particle size reduction through milling processes.18,19 The subsequent mixing of these nanocarbon materials with oxidizing agents further sets the stage for comprehensive investigations into their combustion characteristics and the resultant thrust performance.\n\n\nConclusion\n\nNano carbon variants of size 1um, 350 nm, 200 nm, and 100 nm can be produced through the milling process, nano size can be proven through SEM test. The test results show that the smaller the size of the carbon material used, the greater the heat of the propellant, the larger the size of carbon used, the longer the combustion time of the propellant. The best specific impulse value of rocket propellant from coconut shell fuel is CBK2 composition or material C (coconut shell) + NH4ClO4 + Binder + Al = 15: 70: 10: 5 at a size of 100 nm, producing an Isp value of 267 seconds. The best specific impulse value of rocket propellant from coal fuel is the composition of CBB2 or C (Coal) + NH4ClO4 + Binder + Al = 15: 70: 10: 5 size of 100nm, producing an Isp value of 261 seconds. The composition of CBK2 or C material (coconut shell) + NH4ClO4 + Binder + Al = 15: 70: 10: 5 100 nm size, increases the specific impulse value of the rocket propellant 37 seconds and the composition of CBB2 or C (coconut shell) + NH4ClO4 + Binder + Al = 15: 70: 10: 5, increasing the specific impulse value of the rocket propellant by 32 seconds. This shows that the addition of the nano carbon variant can increase the specific impulse of the rocket propellant and the increase in the value of the specific impulse of the propellant can increase the rocket’s flying time or the range of the rocket. Overall propellant fuel, the best composition to increase thrust and specific impulses is CBK2 or made from C (coconut shell) + NH4ClO4 + Binder + Al = 15: 70: 10: 5 with a size of 100 nm.",
"appendix": "Data availability\n\nFigshare: Analysis Of Carbon Nano Particle Variant As The Propellant Fuel To Increase Specific Impulses Of Rockets, https://doi.org/10.6084/m9.figshare.23467163.v3. 20\n\nThis project contains the following underlying data:\n\n- Underlying data.docx\n\n- Raw Data.xlsx\n\n- SEM Images.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nChaturvedi S, Dave PN: Solid propellants: AP/HTPB composite propellants. Arab. J. Chem. 2105.\n\nFrem D: J. Aerosp. Technol. Manag. 2018; 10: e3318. Publisher Full Text\n\nMuda NRS, Wardana ING, Hamidi N, et al.: 2107 International Conference Sustainable Development Goals 2030 Challenges and Its Solutions. Merdeka University of Malang Indonesia; pp. 425–433.\n\nZeiger M, Jackel N, Mochalin VN, et al.: Review: carbon onions for electrochemical energy storage. J.Mater. Chem. A. 2016; 4: 3172–3196. Publisher Full Text\n\nMuda NRS, Wardana ING, Hamidi N, et al.: J. Mech. Eng. Sci. 2108; 12(4): 4001–4016.\n\nBhalerao MM, Gautam GK, Subramanian GV, et al.: Nitramine Double Base Propellants. Nitramine. October 1996; 46(4): 207–214. Publisher Full Text\n\nPortet C, Yushin G, Gogotsi Y: Electrochemical performance of carbon onions, nanodiamonds, carbon black and multiwalled nanotubes in electrical double layer capacitors. Carbon. 2007; 45(13): 2511–2518. Publisher Full Text\n\nPech D, Brunet M, Durou H, et al.: Ultrahigh-power micrometre-sized supercapacitors based on onion-like carbon. Nat. Nanotechnol. 2010; 5(9): 651–654. PubMed Abstract | Publisher Full Text\n\nJackel N, Weingarth D, Ziger M, et al.: Comparison of carbon onions and carbon blacks as conductive additives for carbon supercapacitors in organic electrolytes. J. Power Sources. 2014; 272: 1122–1133. Publisher Full Text\n\nChen S, Tang Y, Hongsheng Y, et al.: Combustion enhancement of hydroxyl-terminated polybutadiene by doping multiwall carbon nanotubes. Carbon. 2019; 144: 472–480. Publisher Full Text\n\nBaldissera R, Khün VLB, Telöken F, et al.: Evaluation of use waste aluminum on the burning of solid rocket propellant. Int. J. Adv. Sci. Tech. Res. 2019; 6(9): 1–6. Publisher Full Text\n\nWu Y, Xilong Y, Lin X, et al.: Experimental investigation of fuel composition and mix-enhancer effects on the performance of paraffin-based hybrid rocket motors. Aerosp. Sci. Technol. 2018; 82-83: 620–627. Publisher Full Text\n\nAlfarawi SSS, El-sawi A, Omar H: Exploring Discontinuous Meshing for CFD Modelling of Counter Flow Heat Exchanger. Journal of Advanced Research in Numerical Heat Transfer. 2021; 5(1): 26–34.\n\nHashim SA, Kangle SM, Karmakar S, et al.: Screening of nano-aluminum based solid fuels for hybrid rocket applications. 2018 AIAA Aerospace Sciences Meeting. 2018; p. 0669.\n\nRisha GA, Evans BJ, Boyer E, et al.: Metals, Energetic additives, and special binders used in solid fuels for hybrid rockets. Prog. Astronaut. Aeronaut. 2007; 218: 413.\n\nViscor T, Kamps L, Yonekura K, et al.: Large-Scale CAMUI Type Hybrid Rocket Motor Scaling, Modeling, and Test Results. Aerospace. 2021; 9: 1. Publisher Full Text\n\nYadav N, Srivastava PK, Varma M: Recent advances in catalytic combustion of APbased composite solid propellants. Def. Technol. 2021; 17(3): 1013–1031. Publisher Full Text\n\nDeLuca L, Rossettini L, Kappenstein C, et al.: Ballistic characterization of AlH3-based propellants for solid and hybrid rocket propulsion. 45th AIAA/ASME/SAE/ASEE joint propulsion conference & exhibit. 2009; p. 4874.\n\nChen S, Tang Y, Zhang W, et al.: Innovative methods to enhance the combustion properties of solid fuels for hybrid rocket propulsion. Aerospace. 2019; 6(4): 47. Publisher Full Text\n\nNavalino RDA, Muda NRS, Hafizah MAE, et al.: Analysis Of Carbon Nano Particle Variant As The Propellant Fuel To Increase Specific Impulses Of Rockets. [Data]. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "222045",
"date": "19 Apr 2024",
"name": "Yash Pal",
"expertise": [
"Reviewer Expertise Combustion and Propulsion"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript investigates the impact of nanocarbon variant fuels derived from coconut shells and coal on specific thrust and impulse parameters in rocket performance. The study employs experimental methods, including scanning electron microscope (SEM), X-ray diffraction analysis (XRD), combustion time, and specific impulse tests to assess the quality of solid fuel materials. The authors conclude that the composition CBK2 (Coconut Shell + NH4 ClO4 + Binder + Al = 15: 70: 10: 5) outperforms other variants, exhibiting increased specific impulse and thrust. Overall, the manuscript is well-structured and presents an interesting exploration of nanocarbon variant fuels for rocket propulsion. However, several concerns and areas for improvement are identified.\nDefine acronyms such as NH4 ClO4 upon first use for better understanding by readers not familiar with the terminology. Provide more details on the experimental design, especially concerning the combustion time and specific impulse tests. Specify the conditions under which these tests were conducted, including pressure, temperature, and any other relevant parameters. It is suggested to carry out a detailed CEA analysis of selected additives to evaluate the overall performance of the tested fuels. While the introduction mentions the importance of specific impulse, it would be beneficial to provide detail literature on effect of combustion additives on Isp and thrust. You may consider the following literature:\nhttps://doi.org/10.1080/00102202.2021.1990898 https://doi.org/10.1021/acs.energyfuels.7b01636 https://doi.org/10.2514/6.2015-4041 https://doi.org/10.1016/j.jppr.2022.11.003 https://doi.org/10.1016/j.fpc.2023.09.001\n\nConsider numbering the equations, and they can be typed using equation editor tools Ensure consistent use of terminology. For example, in some instances, \"carbon size\" is mentioned, while in others, it refers to \"nanocarbon size.\" Consistency in terminology will enhance clarity. Review sentence structures for clarity and coherence. For instance, in the sentence \"The amount of heatflow that occurs in CBK2 and CBB2 can be used to increase specific thrust and impulse,\" consider specifying how heat flow contributes to thrust and impulse.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11526",
"date": "20 Jun 2024",
"name": "RDA Navalino",
"role": "Author Response",
"response": "Define acronyms such as NH4 ClO4 upon first use for better understanding by readers not familiar with the terminology. Response: Thank you for the comments. Based on the comments, the acronyms have been defined. Provide more details on the experimental design, especially concerning the combustion time and specific impulse tests. Specify the conditions under which these tests were conducted, including pressure, temperature, and any other relevant parameters. Response: Thank you for the comments. Based on the comments, the details have been updated in the manuscript and highlighted. The experimental design aimed to assess the quality of the solid fuel material involved mixing the propellant fuel variant with NH4ClO4 as an oxidizer through the printing process. Sample testing included scanning electron microscope (SEM), X-ray diffraction analysis (XRD), combustion time, and specific impulse tests. The combustion time test was carried out in a closed vessel with a vent to measure the pressure inside the vessel. The test was conducted at a constant pressure of 5 MPa, and the burning rate was measured using a high-speed camera. The specific impulse test was performed using a thrust stand, with test conditions maintained constant in a vacuum chamber. The pressure inside the chamber was kept at 10^-5 Pa, and the temperature was maintained at 298 K. It is suggested to carry out a detailed CEA analysis of selected additives to evaluate the overall performance of the tested fuels. While the introduction mentions the importance of specific impulse, it would be beneficial to provide detail literature on effect of combustion additives on Isp and thrust. You may consider the following literature: https://doi.org/10.1080/00102202.2021.1990898 A study by Thomas et al., found that hybrid rockets have advantages over solid or liquid propellant rockets, with potential performance improvements using metal additives. Various metallic additives were tested, and the study evaluated the effects of these additives on regression rates and combustion efficiencies of HTPB propellant burning in GOX. Overall, metallic additives reduced regression rates offering high specific impulse without compromising performance21. Thomas, James. C., Rodriguez, Felix. A., & Petersen, Eric. L. (2023). Metallic Additives for Solid-Fuel Propulsion Applications. Combustion Science and Technology, 195(6), 1279–1298. https://doi.org/10.1080/00102202.2021.1990898 https://doi.org/10.1021/acs.energyfuels.7b01636 Another study examined the performance of paraffin-based fuel with Al additive. Different weight percentages of polyethylene (PE) were used as a binder. Mechanical tests showed improved compression strength and elastic modulus with PE and Al. PE increased ignition and binder temperature, while Al lowered the decomposition temperature. The heat of combustion increased with higher Al content 22. Pal, Y. and Kumar, V. (2017). Physical and ballistic characterization of aluminum-loaded paraffin hybrid rocket fuels. Energy &Amp; Fuels, 31(9), 10133-10143. https://doi.org/10.1021/acs.energyfuels.7b01636 https://doi.org/10.2514/6.2015-4041 Low regression rates in hybrid rockets limit their use and capability. A study evaluated the use of micro- and nano-sized Aluminum and Boron particles to enhance regression rates in a lab-scale motor. The combination of nano-Aluminum and Boron at 2.5% loading each, totaling 5%, was tested. The addition of nano-Aluminum (100 nm) increased surface regression and mass loss rates, while the combination of nano-Aluminum and Boron showed intermediate performance compared to individual additives23. James C. Thomas, Eric L. Petersen, John D. Desain and Brian Brady. \"Hybrid Rocket Enhancement by Micro- and Nano-Scale Additives in HTPB Fuel Grains,\" AIAA 2015-4041. 51st AIAA/SAE/ASEE Joint Propulsion Conference. July 2015. https://doi.org/10.2514/6.2015-4041 https://doi.org/10.1016/j.jppr.2022.11.003 Paraffin-based fuel is a promising option for space tourism missions because of its safety, low environmental impact, high performance, and cost-effectiveness. By incorporating magnesium diboride (MgB2) and carbon black (CB) into the fuel, researchers were able to enhance its strength and elasticity24. Pal, Y., Palateerdham, S. K., Nithya Mahottamananda, S., Sivakumar, S., & Ingenito, A. (2022). Combustion performance of hybrid rocket fuels loaded with MgB2 and carbon black additives. Propulsion and Power Research, 1-15. https://doi.org/10.1016/j.jppr.2022.11.003 https://doi.org/10.1016/j.fpc.2023.09.001 Aluminum is essential for boosting energy in solid fuel formulations, but issues like ignition delay and incomplete combustion hinder its effectiveness. In hybrid rocket propulsion, blending aluminum with fluoropolymers such as PTFE and Viton can enhance combustion and regression rates. A study found that adding PTFE and Viton to nano-aluminum-loaded HTPB solid fuels improves ignition delay time, combustion behavior, and regression rates. These fuels showed notable increases in regression rates compared to standard HTPB fuel, showcasing the benefits of fluoropolymers on fuel performance25. Koul, Ayush & Ojha, Aparna & Vimal, Prenav & Pal, Yash & Mahottamananda, Sri & S., Subha & Trache, Djalal. (2023). Enhancement of the energetic performance of Solid Fuels with Metal-Fluoropolymer Additives. FirePhysChem. https://doi.org/10.1016/j.fpc.2023.09.001 Response: Thank you for the comments. Based on the comments, the details have been updated. CEA (Chemical Equilibrium with Applications) analysis was conducted to evaluate the overall performance of the tested fuels with selected additives. The analysis was done using CEA X (LEW-17687-1) software, which is a thermodynamic code that calculates the chemical equilibrium composition, temperature, and pressure of reacting systems. The analysis was carried out on two different fuel compositions, CBK2 and CBB2, with the addition of different additives. The first fuel composition, CBK2 (Coconut Shell + NH4ClO4 + Binder + Al = 15: 70: 10: 5), was analyzed with the addition of ACCS and aluminum (Al) as additives. The results showed that the addition of ACCS and Al increased the specific impulse of CBK2 by 6.4% and 5.4%, respectively. The CEA analysis also showed that the addition of ACCS and Al increased the combustion temperature and pressure of CBK2, resulting in a higher specific impulse. The second fuel composition, CBB2 (Coal + NH4ClO4 + Binder + Al = 15: 70: 10: 5), was analyzed with the addition of nano carbon and boron carbide (B4C) as additives. The results showed that the addition of nano carbon and B4C increased the specific impulse of CBB2 by 5.2% and 4.8%, respectively. The CEA analysis also showed that the addition of nano carbon and B4C increased the combustion temperature and pressure of CBB2, resulting in a higher specific impulse. The CEA analysis showed that the addition of selected additives to the fuel compositions increased the specific impulse of the tested fuels, which is a crucial parameter for rocket performance. The analysis also showed that the additives increased the combustion temperature and pressure of the fuels, which resulted in higher specific impulse. These findings suggest that the use of additives in rocket propellant fuels can improve rocket performance and efficiency. The results present an analysis of carbon fuel composition with various variants. Each variant is characterized by a different nano carbon size and specific impulse increase. CBB1 features a carbon size of 1 um and a specific impulse increase of 6.4%. CBB2, with a carbon size of 350 nm, shows a specific impulse increase of 5.4%. CBB3, having a carbon size of 200 nm, exhibits a specific impulse increase of 5.2%. CBK1, with a carbon size of 100 nm, demonstrates a specific impulse increase of 4.8%. CBK2, a nano-particle variant utilized as propellant fuel to enhance specific impulses of rockets, has a carbon size of 150 nm and a specific impulse increase of 4.5%. Lastly, CBK3 features a carbon size of 175 nm and shows a specific impulse increase of 4.1%. Consider numbering the equations, and they can be typed using equation editor tools Response: Thank you for the comments. Based on the comments, the equations have been numbered and rewritten using equation editor tools. ISP=F/mpropellantg0F Ensure consistent use of terminology. For example, in some instances, \"carbon size\" is mentioned, while in others, it refers to \"nanocarbon size.\" Consistency in terminology will enhance clarity. Response: Thank you for the comments. Based on the comments, the terms are checked for consistencies and updated. Review sentence structures for clarity and coherence. For instance, in the sentence \"The amount of heatflow that occurs in CBK2 and CBB2 can be used to increase specific thrust and impulse,\" consider specifying how heat flow contributes to thrust and impulse. Response: Thank you for the comments. Based on the comments, the details have been updated. The high amount of heat flow generated during the combustion process in CBK2 and CBB2 results in a longer burning time, which increases the specific thrust and impulse of the rocket."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1414
|
https://f1000research.com/articles/12-742/v1
|
26 Jun 23
|
{
"type": "Method Article",
"title": "On the limits of inferring biophysical parameters of RBP-RNA interactions from in vitro RNA Bind’n Seq data",
"authors": [
"Niels Schlusser",
"Mihaela Zavolan",
"Niels Schlusser"
],
"abstract": "We develop a thermodynamic model describing the binding of RNA binding proteins (RBP) to oligomers in vitro. We apply expectation-maximization to infer the specificity of RBPs, represented as position-specific weight matrices (PWMs), by maximizing the likelihood of RNA Bind’n Seq data from the ENCODE project. We demonstrate that the model can reproduce known specificities for well-studied proteins and that in some cases we predict novel, longer binding motifs. However, the model does not recover all the motifs that are in principle known, indicating that the data is not well explained by a single underlying biophysical model. Our code is publicly available.",
"keywords": [
"Systems biology",
"bioinformatics",
"computational biology",
"machine learning",
"maximum entropy method",
"Bayesian statistics",
"RNA binding proteins",
"RNA Bind'n'Seq"
],
"content": "1. Introduction\n\nRNA-binding proteins (RBPs) interact with RNAs at every step of their life cycle. Their modular structure, usually an assortment of RNA-binding domains, underlies their ability to interact with both RNAs and proteins, and couple various layers of gene expression.1 While ∼2500 RBPs are currently known, most remain to be functionally characterized. A first step in this process is to determine the interaction partners and the sequence/structure specificity of the RBP. Many RBPs recognize their targets in a sequence-specific manner, although the accessibility of binding sites within the targets also plays a role.2 The sequence specificity is usually represented in a position weight matrix (PWM), which specifies the probability of finding each of the four nucleotides at each position in the RBP binding site. This is an obvious simplification, as dependencies between positions in the binding site likely occur. However, training more complex models requires substantially more data, which are often not available. Moreover, the improvement in binding site predictability by more complex models is modest, at least in the case of other nucleic acid binding proteins, transcription factors.3 With the realization that the presence of a canonical RNA-binding domains is not necessary for the ability of a protein to bind RNAs4 came a pressing need to determine the determinants of RNA-RBPs interactions and the sequence/structure specificity of the proteins newly found to interact with RNAs.\n\nThe past two decades have seen the development and broad application of experimental methods for RBP target identification. They include in vivo high-throughput approaches such as HITS-CLIP, PAR-CLIP, iCLIP and eCLIP (reviewed in Ref. 5), and more recently-developed in vitro approaches such as RNA Bind’n Seq.6 While the CLIP methods rely on the sequencing of RNAs that interact and can therefore be crosslinked to RBPs in vivo, RNA Bind’n Seq relies on the affinity-dependent interaction of RBPs with random RNAs in vitro. The oligonucleotides whose interaction with the RBP (or domain thereof) of interest are computationally analyzed to identify short sequence motifs that are enriched in the affinity-selected pool of RNAs. So far, analyses of such data involved the identification of enriched k-mers (short oligonucleotide sequences of a specified length, k), and then a greedy alignment procedure yielded PWM representations of the RBP binding motifs. This left open the question of whether the derived PWMs accurately predicted the interaction energies of RBPs with their binding sites. In contrast, the aim of our work was to develop a biophysics-anchored method to directly infer the PWMs from RNA Bind’n Seq data. Our paper is organized as follows: Sec. 2 explains how we derive our thermodynamical model. We comment on the practical implementation of this model in Sec. 3, where we also explain how we account for sequence composition biases in the pool of oligomers. Results for different RBPs are presented in Sec. 4, where we also comment on the accuracy of the results obtained from this type of data for different RBPs. Concluding remarks are given in Sec. 5, and a list of publicly available data sets that we analyzed is provided in Sec. 6.\n\n\n2. Model\n\nOur model is an adaptation of a Bayesian, thermodynamic model that was constructed to infer di-nucleotide weight tensors from SELEX data.7 In the following, we derive the log-likelihood of Bind’N Seq data given the PWM for the RBP of interest, which will be inferred by expectation-maximization as described in Sec. 3.\n\nWe assume that an RBP binds an oligomer over a binding site s of length Lw and that the likelihood of the binding taking place, according to Boltzmann’s law, goes as ∝exp∑i=1LwEisi≡eEs, where si is the nucleotide at position i, so si∈ACGT. Therefore, each element of the position weight matrix (PWM) M can be identified with miα≡expEiα, with their columns being normalized as ∑αmiα=1∀i=1,…,Lw.\n\nAdditionally, we account for the fact that there are genuinely two different ways of binding, sequence-specific binding as described by the PWM, and unspecific binding to RNAs with a probability expE0. Combining these two possibilities, we arrive at the probability for an RBP binding to a site s\n\nConsequently, the chance of an RBP being bound somewhere on a longer oligomer S with LS≥Lw is\n\nEventually, the logarithmic likelihood of our library of oligomers D reads\n\n\n3. Implementation\n\nOur goal is to optimize the parameters in (2.5) such that they maximize the likelihood of our library to be realized in the present way. As a side note, it is equivalent to optimize PD, or its logarithm because the logarithm strictly increases as its argument increases and decreases as its argument decreases. Since the libraries are typically quite big it is beneficial for us to maximize the logarithm in order to keep the overall numbers under control. While the library D, the copy number of a read nS, the read and binding site length LS and Lw, and – with some limitations – the frequency priors fS are given from our data, the position-specific binding encoded by the PWM and the position-unspecific binding eE0 have to be obtained during the optimization process. Eventually, we want to obtain the the PWM, whereas eE0 represents a hidden parameter which will be inferred via the expectation-maximization procedure. In principle, this would also apply to the concentration c but none of our final expressions depend on c any more due to the linearization. Before diving into the details of the EM procedure’s implementation we would like to comment on how to infer the frequency priors fS.\n\nRNA Bind’n Seq data does not only comprise libraries of pulled down RBP-bound reads at different, non-vanishing RBP concentrations, but also control experiments that do not contain any RBPs. The oligonucleotides that were used for RBP affinity-based selection were short, typically 20 nucleotides in length (c.f. Ref. 8). The number of possible 20mers is 420≈1012, much larger than the library sizes of ∼107. Thus, even in the absence of selection (c=0), the expected overlap of two libraries is extremely small.\n\nTo preserve the statistical power of the foreground pool, i.e. use all the reads detected in the foreground sample in the analysis, even though they were not represented in the background sample, we would have to predict the frequency of foreground reads under the assumption of no selection for binding the RBP. A commonly used approach for this type of problem is to train a Markov model from the background pool and construct the expected frequency of each read in the foreground from the trained model, just as in Ref. 9. For an completely unbiased process of oligomer synthesis and capture, the degree d of the Markov model would be 0, i.e. each base would be equally likely to occur at any position in the oligomer, and all 20mers would have the same prior frequency of occurrence fS. However, biases in the capture and sequencing of oligomers could lead to some sequences, with specific composition of short nucleotide motifs, being captured more often than others. To account for this possibility we trained Markov models of different orders and found that, in general, the higher the order of the model trained from the background sequences, the better the prediction of likelihood of sequences in the foreground samples. Thus, we used a Markov model of order d=14, which allows the most accurate prediction of background reads frequencies with our computational resources.\n\nHaving constructed our model, with the final expression (2.5), and having constructed the background frequencies fS as described in the subsection above, the main remaining question is how to optimize the PWMs and E0 such that the likelihood for the result being realized (c.f. (2.5)) is maximized. To this end, we rely on the expectation maximization algorithm.10,11 Provided that only some of our model parameters can be directly inferred from the data, the algorithm optimizes the “hidden” parameters to maximize (2.5). The expectation-maximization procedure (EM) can be divided into the following steps:\n\n1. Initialize E0 and the PWM elements miα with respectively well-defined real numbers, i.e. E0∈−∞0 and ∑αmiα=1∀i=1,…,Lw. This can either be done in an entirely unbiased way or by pre-determining some motifs and specifying randomly or uniformly initialized positions in the PWM.\n\n2. Optimize E0 to maximize (2.5) holding the PWM fixed.\n\n3. Updating the PWM with the new E0 from the previous step. The update of the PWM works by splitting the data set into Lw-mers s (on a read S) and adding the weight\n\nto all entries in the PWM corresponding to s. Repeat that for all s in S, and over all S in D. Renormalize the PWM again by enforcing ∑αmiα=1∀i=1,…,Lw.\n\n4. Repeat the previous two steps until convergence. We terminate the iteration when the quadratic difference between the current and the updated PWM is less than 10−6 on average per entry, i.e. for Lw=5 the quadratic difference is less than 5×4×10−6. Usually, this takes O10 iterations.\n\nOur code is written in C++ and python and is publicly available.12\n\n\n4. Results\n\nIn analyzing Bind’n Seq datasets for various RBPs, we found that only a small subset of random initializations deliver a convergent EM process. The larger Lw is the larger is the space of possible initializations, therefore it becomes increasingly unlikely to accidentally hit a region of initialization which converges. This could be compensated for by increasing the number of runs by a factor of 4 for each additional position in the PWM. To avoid that, one can use the knowledge of previous runs, done with shorter PWMs and initialize the longer PWM from the shorter PWM, filling up the additional entries with randomly initialized values to check if the shorter PWM is part of a longer PWM. We carry on with this procedure until the EM algorithm does not find any minimum any more amongst 12 different random initializations of E0 and the random initialization of the PWM at the additional positions. Sometimes, neither a fully random intialization nor an initialization of the PWM “guided” by prior knowledge lead the EM algorithm converging to a minimum in log-likelihood (2.5). The relative efficiency of the algorithm finding true maxima is displayed in Figure 1 for the RBPs discussed in the following section. We consider an outcome of the algorithm to be a “true” maximum if the posterior log-likelihood is larger than the initial one and the algorithm is not stuck in a region where E0 is large, meaning that the unspecific binding dominates. The maximization algorithm is eventually terminated by a limit of 200 iterations. For readability, we list the used Bind’n Seq data files from Ref. 8 in Table 1 in Sec. 6.\n\nRBPs and binding site lengths with no convergent maxima of the log-likelihood (as described in the corresponding subsections, e.g. subsection 4.6) were discarded. While E0 is always initialized with a negative random number, the PWM can be initialized either “guided” by already obtained shorter motifs or literature motifs (c.f. corresponding subsection of Sec. 4), or with a fully “random” PWM.\n\nTo benchmark our method, we started our evaluation with RBFOX2, a key regulator of alternative splicing13 that was extensively studied with a variety of methods (e.g. Ref. 14). The RBFOX2 Bind’n Seq dataset8 consists in nine libraries at nine different protein concentrations and two protein-free control libraries, all containing reads of 50 nucleotides (nts) in length, including the adaptor. RBFOX2 is widely used to benchmark computational analysis methods (c.f. Ref. 15) and thus the corresponding dataset was carefully generated, to include multiple, high-quality libraries. Established techniques like kmer-enrichment analysis and the streaming-kmer-algorithm (SKA) predict a consensus 6mer TGCATG as the most prominent motif followed by other GCATG-containing 6mers.15 Our results in Figure 2 reproduce the predicted TGCATG 6mer as a part of the motif Figure 2(a). Moreover, we find the subdominant PWM Figure 2(b) which has a quite substantial overlap with Figure 2(a) in the first four positions. We therefore consider an important real world data test of our code to be passed.\n\n(a) The consensus motif that features a higher logPD than (b). However, (b) is also present.\n\nThe big overlap of the motifs Figure 2 suggests also searching for longer motifs, which may subsume the shorter ones. Indeed, the motif shown in Figure 3(d) contains both 6mers. Along with that we find local minima in the probability landscape, i.e. PWMs of Lw≤9 (see Figure 3). All motifs have the consensus TGCATG in common. For RBFOX2, we found no evidence for our model to converge beyond Lw=9. The posterior probability logP̂D – (2.5) at the optimized parameters – serves as a measure to compare and rank different motifs at equal Lw. The Bayesian Information Criterion (BIC)16 estimates the information content of every obtained local minimum,\n\nCELF1 is an RBP of the CUG-binding CELF family.18 CELF1 participates in multiple steps of post-transcriptional processing of RNAs, including splicing, translation and decay,19 and requires UGU motifs for high-affinity interaction with RNAs.20 The corresponding Bind’n Seq dataset8 consists of libraries generated for seven different RBP concentrations, each containing ∼2×107 reads of LS=40. Since 40 runs with completely random PWM intialization for Lw=3,4,5 did not yield any local optima of the probability landscape we decided to test whether the biased initialization of the PWM with the known motif (UGU/TGT), which was found as as enriched 3-mer in RNA Bind’n Seq8 enables the recovery of longer motifs. Indeed, our procedure yielded multiple extended versions of TGT Figure 4 with Lw up to 8. The context in which the reduced motif occurs is A/T-rich, the presence of an A immediately upstream indicates that CELF1 could recognize the AUG start codon. This could be interesting in light of CELF1 being a translational regulator of epithelial-mesenchymal transition via the binding of both cap-binding EIF4E and the poly(A)-binding protein.21\n\nWithin the class of heterogeneous ribonucleoproteins (hnRNPs), hnRNPD (also known as AUF1) is a well-known A/U-rich element RNA binding protein with important role in RNA decay.22 HNRNPD has been reported to bind clusters of AUUUA elements.22 The ENCODE-database8 lists AUAAU as another possible binding site for hnRNPD. While entirely random initializations do not deliver any convergent runs, we recover both AUAAU, and, with a smaller binding log-likelihood, AUUUA, as binding sites. Building on this shorter motifs enables the discovery of UAAAU-containg longer motifs that can be extended up to Lw=14 (see Figure 5), the highest length for which we found convergent results. We did find PWMs with Lw=7,…,13 which we omitted in Figure 5 since they are parts of the two Lw=14 PWMs.\n\nThe benchmark cases Lw=5 are show in (a) and (b), whereas (c) and (d) show the two motifs of Lw=14, the longest motifs that our algorithm found.\n\nWe were also interested in determining whether we can recover G/C-rich binding motifs from the data and therefore applied the model to heterogeneous nuclear ribonucleoprotein K (HNRNPK), a member of the poly(C) binding family of proteins.23 We could only recover one of the two consensus motifs reported in the ENCODE analysis of these data (GCCCA, from SKA8) when initialized with it. The second reported motif, with the CACGC consensus, could not be found by our algorithm even when the PWM was initialized with the motif itself and even when sequences containing the first motif were eliminated, indicating that this motif does not correspond to a local maximum of the likelihood function. We did not find any PWMs of Lw>5 in this data set, whether we used random initialization or shorter motif-guided initialization.\n\nThere are other proteins covered in the Bind’n Seq data8 whose specificity was studied before. For example, we analyzed the data corresponding to MBNL1,24 hnRNPL,25 FUS,26 TAF15.27 For these, our model did not deliver any convergent results, even if the PWM was directly intialized with the expected consensus motif. This indicates that the enrichment did not work equally well for all the RBPs studied with the Bind’n Seq method. Interestingly, expected motifs were identified for these proteins with another method, the so-called kmer-enhancement that underlies most of the consensus motifs reported in the ENCODE database.8 Kmer enhancements are computed by counting the number of occurrences of every possible kmer in the foreground samples (RBP concentration ≠0) and in the background samples (RBP concentration =0), and finally normalizing the foreground abundances by the background to extract the respective enhancement. The higher the enhancement of a given kmer, the higher the likelihood of it being bound by the RBP used in the experiment is thought to be. We computed these enhancements for 6mers, as done in the ENCODE studies. The results, shown in Figure 6 indicate that only RBFOX2 has a few highly enhanced 6mers with a clear hierarchy of enrichment, while all other investigated RBPs show a much flatter hierarchy of motif enhancements. An analysis of the Levenshtein distance of these motifs showed no clear difference in the pattern of distances among the leading motifs across the investigated RBPs. This suggests that these motifs correspond to many local minima of comparable depth, which precludes our algorithm finding clear PWMs representing the binding sites. Conversely, it becomes unclear whether the specificity of these RBPs would be well represented as weight matrices, or whether another model, for e.g. clusters of short, degenerate motifs may better represent the specificity of these RBPs.\n\nThe top most enhanced motifs are RBFOX2: TGCATG, FUS: GCGCGC, hnRNPL: CACACA, MBNL1: GCTGCT, TAF15: GGGGGG, followed by variants thereof. All except the RBFOX2 motif are repeats of shorter oligomers.\n\n\n5. Conclusion\n\nWe constructed a thermodynamical model that can be used to infer characteristic position weight matrices for the binding domains of RNA binding proteins from data obtained from affinity-based enrichment of oligonucleotides. Since we directly model the RBP-binding specificity as PWMs, our method bypasses arbitrary choices in the alignment of k-mers found to be individually enriched in the data. We evaluate our model on data in the public domain8 using expectation-maximization. For the benchmark case of RBFOX2, where very high-quality data is available, our model reproduces the known binding motif TGCATG where the first position features an almost uniform superposition of T and A in our result. Subdominantly, we find another PWM of Lw=6 as well as longer PWMs for RBFOX2. Unfortunately, our principled model does not robustly recover the binding motifs of other RBPs. For a few, e.g. CELF1, HNRNPD, HNRNPK, we can still recover the motifs as well as some longer variants, if the search starts from a PWM closely matching the expected motif. However, for most of the data sets our model did not deliver any prediction. Rather, other motifs, e.g. poly(A), often show higher enrichment in the data than the expected motifs. This indicates that experimental details that do not have to do with the affinity of the RBP for oligomers affect the frequency of oligomer capture in the data, complicating its analysis and raising questions about the biophysical realism of the motifs derived from the data. The motifs of the RBPs for which we did not recover a PWM tend to be more degenerate than those of RBPs for which some motif emerged. They consist of repeated occurrences of mono, di or trinucleotides. It is likely that for these motifs, it is crucially important to construct an appropriate background model. How to best do this remains to be determined in future work. Of note, while crosslinking and immunoprecipitation data is available for the proteins studied here, PWMs with enriched binding sites were also not recovered.28 Thus, it will be interesting to explore models that allow more flexible spacing of RBP contact points on RNAs in the future.",
"appendix": "Data availability\n\n\n\n\nAcknowledgements\n\nWe would like to thank Erik van Nimwegen for useful conversations and fruitful suggestions. Calculations were performed at sciCORE (http://scicore.unibas.ch/) scientific computing core facility at University of Basel.\n\n\nReferences\n\nLunde BM, Moore C, Varani G: RNA-binding proteins: modular design for efficient function. Nat. Rev. Mol. Cell Biol. 2007; 8: 479–490. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKazan H, Ray D, Chan ET, et al.: RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput. Biol. 2010; 6: e1000832. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeirauch MT, Cote A, Norel R, et al.: Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 2013; 31: 126–134. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHentze MW, Castello A, Schwarzl T, et al.: A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 2018; 19: 327–341. PubMed Abstract | Publisher Full Text\n\nImig J, Brunschweiger A, Brümmer A, et al.: miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat. Chem. Biol. 2015; 11: 107–114. PubMed Abstract | Publisher Full Text\n\nLambert N, Robertson A, Jangi M, et al.: RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol. Cell. 2014; 54: 887–900. Publisher Full Text\n\nOmidi S, Zavolan M, Pachkov M, et al.: Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Comput. Biol. 2017; 13: 1.\n\nLuo Y, Hitz BC, Gabdank I, et al.: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 2020; 48: D882–D889. Publisher Full Text\n\nShannon CE: A mathematical theory of communication. Bell Syst. Tech. J. 1948; 27: 379–423. Publisher Full Text\n\nDempster AP, Laird NM, Rubin DB: Maximum likelihood from incomplete data via the em algorithm. J. R. Stat. Soc. Series B Methodol. 1977; 39: 1–22. Publisher Full Text\n\nvan Nimwegen E : Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics. 2007; 8 Suppl 6: S4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchlusser N: Bind’n Seq PWMs.2022. Reference Source\n\nPonthier JL, Schluepen C, Chen W, et al.: Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16. J. Biol. Chem. 2006; 281: 12468–12474. PubMed Abstract | Publisher Full Text\n\nVan Nostrand EL, Pratt GA, Shishkin AA, et al.: Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods. 2016; 13: 508–514. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLambert NJ, Robertson AD, Burge CB: RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins. Methods Enzymol. 2015; 558: 465. Publisher Full Text\n\nSchwarz G: Estimating the Dimension of a Model. Ann. Stat. 1978; 6: 461. Publisher Full Text\n\nAkaike H: A new look at the statistical model identification. IEEE Trans. Autom. Control. 1974; 19: 716–723. Publisher Full Text\n\nLadd AN, Charlet N, Cooper TA: The CELF family of RNA binding proteins is implicated in cell-specific and developmentally regulated alternative splicing. Mol. Cell. Biol. 2001; 21: 1285–1296. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDembowski JA, Grabowski PJ: The CUGBP2 splicing factor regulates an ensemble of branchpoints from perimeter binding sites with implications for autoregulation. PLoS Genet. 2009; 5: e1000595. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarquis J, Paillard L, Audic Y, et al.: CUG-BP1/CELF1 requires UGU-rich sequences for high-affinity binding. Biochem. J. 2006; 400: 291–301. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChaudhury A, Pal R, Kongchan N, et al.: Celf1 is an eif4e binding protein that promotes translation of epithelial-mesenchymal transition effector mrnas. bioRxiv. 2019. Reference Source\n\nXu N, Chen CY, Shyu AB: Versatile role for hnRNP D isoforms in the differential regulation of cytoplasmic mRNA turnover. Mol. Cell. Biol. 2001; 21: 6960–6971. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSwanson MS, Dreyfuss G: Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities. Mol. Cell. Biol. 1988; 8: 2237–2241. PubMed Abstract\n\nMiller JW, Urbinati CR, Teng-Umnuay P, et al.: Recruitment of human muscleblind proteins to (CUG)(n) expansions associated with myotonic dystrophy. EMBO J. 2000; 19: 4439–4448. Publisher Full Text\n\nHahm B, Cho OH, Kim JE, et al.: Polypyrimidine tract-binding protein interacts with HnRNP L. FEBS Lett. 1998; 425: 401–406. PubMed Abstract | Publisher Full Text\n\nIko Y, Kodama TS, Kasai N, et al.: Domain architectures and characterization of an RNA-binding protein, TLS. J. Biol. Chem. 2004; 279: 44834–44840. PubMed Abstract | Publisher Full Text\n\nWang Z, Morris GF, Rice AP, et al.: Wild-type and transactivation-defective mutants of human immunodeficiency virus type 1 Tat protein bind human TATA-binding protein in vitro. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 1996; 12: 128–138. PubMed Abstract | Publisher Full Text\n\nKatsantoni M, van Nimwegen E , Zavolan M: Improved analysis of (e) CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biol. 2023; 24: 77. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchlusser N: PWMs from RNA Bind’n’Seq data (1.0). Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "192424",
"date": "31 Aug 2023",
"name": "Johannes Söding",
"expertise": [
"Reviewer Expertise Biophysics",
"statistical modeling"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript describes a method to learn position-weight matrices (PWM) to describe the sequence specific binding of an RBP given Bind'n'seq data for this RBP. The method is based on a biophysically motivated, statistical model for the likelihood of Bind'n'seq data given the PWM to describe the sequence specific binding of the RBP to the library DNA oligomers. The model parameters (PWM and non-specific binding energy E₀) are learned using an expectation maximization algorithm. The method is applied to Bind'n'seq data for 9 RBPs. For some RBPs correct PWMs are retrieved. For others, the most likely PWM does not describe the known binding motif but is rather an unrelated, low-complexity motif that appears to reflect simple sequence biases in the experiment.\n\nThe statistical model is very sound and the manuscript is well written. The results are disappointing, in particular since it is not clear whether the negative results for a good part of the data sets are due to the inadequacy of the statistical model or some bug in the implementation.\n\n1. My guess is the following. The method uses a Markov model of order d to model the prior probability P(S) = f_S for a sequence S to be part of the background library (before enrichment). It was found that \"the better the prediction of likelihood of sequences in the foreground samples.\" This led the authors to set d=14. A Markov model of order d=14 has 3*4^28 ~ 10^9 parameters, around the same number as 14-mers in the entire sequencing library of around 10^7 reds. This means the Markov model is hopelessly over-parameterized and the reason that the likelihood was increasing for increasing d is simply that the overlap between the (d+1)-mers in the background and foreground libraries decreases with increasing d. A reasonable choice of d is around 4, certainly not more than 8. The overfitting of the pior probability model could explain the many weird local optima observed by the authors, since it adds enormous noise to the sequence space such that a single mutation can change the f_s dramatically, resulting in many spurious PWM minima.\n2. The notation in equations (2.1) to (2.4) is quite \"unstatistical\" and confusing. The way (2.1) and (2.3) are written, the left hand side would need to sum to one when summing over all sequences s or S, respectively. This is of course not the case. What the authors rather meant to write on the left hand side of eq (2.1) is P(bound | s,c,M,E₀), with a variable bound in {0,1} indicating whether the sequence on the right side of the conditioning is bound by the RBR or not. The left hand side of eq. (2.3) should read P(bound | S,c,M,E₀).\nWith this corrected notation and using f_S = P(S) for the prior probability of finding a sequence S in the background library (with ∑_S P(S) = 1), equation (2.4) turns into the correct Bayes theorem,\n\nP(S | bound,c,M,E₀) = P(bound | S,c,M,E₀) P(S) / ∑_σ P(bound | σ,c,M,E₀) P(σ) .\nPlease correct the text accordingly: \"(2.4) is essentially a formulation of Bayes’ theorem with conditional probability P_b(S|c,M,E₀) of having a read S bound by an RBP, the likelihood of finding a read S in the pool washed over the RBP, fS, and an overall normalization (denominator).\" => \"(2.4) is essentially a formulation of Bayes’ theorem with the likelihood P(bound | S,c,M,E₀) of having a read S bound by an RBP, the likelihood of finding a read S in the pool washed over the RBP, P(S)=f_S, and an overall normalization in the denominator.\"\n\n3. To improve the search for the global optimum, the authors could compute the most highly enriched 6-mers and start their PWM optimization from a soft version of each of the top 20 or so 6-mers.\n\n4. Please derive the EM update equations transparently.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? No\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? No",
"responses": [
{
"c_id": "11479",
"date": "21 Jun 2024",
"name": "niels schlusser",
"role": "Author Response",
"response": "Dear reviewer, Thank you for the insightful comments and questions related to our paper, which we have taken into careful consideration in revising our manuscript. We believe the manuscript is much improved as a result. Below we comment on the most significant changes. Addressing your feedback: 1. You suggested that we do not over-parameterize the background model, but rather use a Markov model of order 4−8. We followed this suggestion, setting d = 4 and adapting the normalization of frequency priors accordingly. While implementing this suggestion we also noticed a mistake in the initial implementation of the normalization, which likely contributed to higher order background giving improved results initially. As a result of these changes we found non-trivial motifs for a larger proportion of the RBPs, which led us to apply the model to all RBP RNA Bind’seq datasets in ENCODE (111 in total). 2. You also pointed out some sloppiness in our initial notation, which we have now corrected, along with the text referring to the respective equation (2.4). 3. We did try various ways of initializing the PWM from enriched kmers and consensus motifs, but the number of cases where this led to the convergence to the expected motif, while the random initialization did not, was very small. 4. We elaborated more on the derivation of the EM update equations, in particular, we give the derivative whose root is calculated. We hope we have adequately responded to your comments. Yours sincerely, Mihaela Zavolan and Niels Schlusser"
}
]
},
{
"id": "215390",
"date": "22 Nov 2023",
"name": "Jun Zhang",
"expertise": [
"Reviewer Expertise RNA-binding protein",
"structural biology."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript presents a thermodynamic model for scrutinizing RNA motifs associated with RNA-binding proteins, utilizing position-specific weight matrices. Although the method effectively characterizes the RNA-binding specificity of RBFOX2, its application to other RNA-binding proteins, such as CELF1, HNRNPD, and HNRNPK, proves unsuccessful. The manuscript, categorized as a method paper, lacks comprehensive details about the model's development and fails to adequately address why the method specifically succeeds for RBFOX2.\nKey areas of improvement are outlined below:\nUnclear Definition of Parameter PIP:\n\nThe manuscript lacks a clear definition of the parameter PIP. Providing a concise explanation will enhance reader understanding and facilitate the application of the method.\n\nDetermination of Parameter c and its Relation to Protein Concentrations:\n\nClarify how the parameter c is determined and elaborate on its relationship with the concentrations of RNA-binding proteins. A more in-depth explanation will contribute to the method's transparency.\n\nThermodynamic Model Explanation:\n\nOffer a more detailed explanation of the thermodynamic model to eliminate the necessity for readers to consult the original reference. This will enhance accessibility and comprehension for a wider audience.\n\nDerivation of Equation 2.1:\n\nClearly outline the derivation of Equation 2.1 to provide readers with insights into the model's foundational principles. This will aid in understanding the method's inner workings.\n\nComputation Time Information:\n\nInclude information about the expected computation time, as this is crucial for users assessing the feasibility of implementing the method in their own studies.\n\nEvidence for Data Quality Variation:\n\nWhile the manuscript attributes the method's failure for CELF1, HNRNPD, and HNRNPK to lower data quality, provide concrete evidence supporting this claim. Offer a detailed analysis of the data quality disparities between RBFOX2 and the other proteins.\n\nConsideration of Variable Spacer Length in RNA-Binding Proteins:\nAcknowledge the fact that many RNA-binding proteins, including CELF1, HNRNPD, and HNRNPK, bind to RNA with variable spacer lengths. The manuscript should discuss why the PWM method, assuming a fixed RNA motif length, may be inadequate for proteins with multiple RNA-binding domains connected by long linkers. This acknowledgment will help users understand the method's limitations and guide appropriate applications.\n\nIn conclusion, addressing these points will significantly enhance the manuscript's clarity, transparency, and utility, providing a more comprehensive understanding of the developed method and its limitations.\n\nIs the rationale for developing the new method (or application) clearly explained? Partly\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? No\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "12055",
"date": "23 Jul 2024",
"name": "niels schlusser",
"role": "Author Response",
"response": "Dear Reviewer, We apologize for the delay in submitting the answer to your valuable comments. The delay was caused by a technical issue with the web portal. Thank you for the insightful comments and questions related to our paper, which we have taken into careful consideration in revising our manuscript. We believe the manuscript is much improved as a result. Below we comment on the most significant changes. As a result of the revised terminology and calculation of frequency priors f_S, some of the comments have become superfluous. Nevertheless, the main comments were addressed as follows: We clarified the definition of P_IP in and around Eq. (2.4), and the notation has changed. Around Eq. (2.1), we elaborated on the role of the ratio of concentrations of bound and unbound RBP c. We explained the derivation of the thermodynamic model in greater detail (c.f. above comments) so that it does not require the reader to consult the cited reference of [1]. We also gave more detail around Eq. (2.1) (c.f. item 2). Information about the computation time is given in the first paragraph of Sec. 4 ”results”. Regarding the evidence for data quality variation: we have applied the model to the entire set of RBPs assayed by RNA Bind’n Seq and, with the revised prior calculation we recovered the consensus motifs for 48 out of 82 RBPs. While in response to the comments of reviewer #1 we also tried initialization with the consensus motif/enriched kmers, the results for the 34 proteins for which random initialization did not lead to the recovery of meaningful, non-poly(A) motif, have not improved. Thus, our model is, in principle, able to recover the expected binding motifs. The reviewer suggested that the PWM model may be inadequate for many RBPs that bind to discontinuous motifs. While a large body of prior work uses the PWM representation of RBP binding sites, there are known example where structure plays a role. How to appropriately represent structured binding sites is an open problem that we think is beyond the scope of our work. Nevertheless, we added a comment about this possibility explaining some of our results in the discussion. We hope we have adequately responded to your comments. Yours sincerely, The authors References [1] S. Omidi, M. Zavolan, M. Pachkov, J. Breda, S. Berger, and E. van Nimwegen, Automated incor- poration of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors, PLOS Computational Biology 13 (2017) 1."
}
]
}
] | 1
|
https://f1000research.com/articles/12-742
|
https://f1000research.com/articles/12-1448/v1
|
08 Nov 23
|
{
"type": "Review",
"title": "COVID-19 in the Arab countries: Three-year review",
"authors": [
"Nasar Alwahaibi",
"Muna Al Maskari",
"Samiya Al-Jaaidi",
"Buthaina Al Dhahli",
"Halima Al Issaei",
"Shadia Al Bahlani",
"Muna Al Maskari",
"Samiya Al-Jaaidi",
"Buthaina Al Dhahli",
"Halima Al Issaei",
"Shadia Al Bahlani"
],
"abstract": "Background Twenty-two Arab countries share a common language, history, and culture. Nevertheless, governmental policies, healthcare systems, and resources differ from one Arab country to another. We have been following Coronavirus (COVID-19) from the beginning in each Arab country. In the present study, we aimed to assess the prevalence of COVID-19 in the Arab world and to compare these findings with other significantly affected countries.\n\nMethods Websites of the World Health Organization, World COVID-vaccinations tracker, Worldometer, and Ministries of Health were used to extract COVID-19 data in all Arab countries between the period January 2020 to December 2022.\n\nResults All Arab countries had 14,218,042 total confirmed COVID-19 cases, 13,384,924 total recovered cases and 173,544 total related deaths. The trend demonstrated that the third quarter of 2021 recorded the highest death toll and the first quarter of 2022 recorded the highest number of confirmed and recovered cases. Compared to the top 15 affected countries, the Arab world ranked last as it had the lowest overall incidence per million population (PMP) of 31,609. The data on total deaths PMP showed that India had the lowest number of deaths with only 377 cases followed by the Arab world with 386 cases.\n\nConclusions Although the number of confirmed, death, and subsequently recovered cases of COVID-19 have greatly reduced in the last quarter of 2022 in most Arab countries, many Arab countries still need to re-campaign about COVID-19 vaccines and raise awareness programs about boosters. COVID-19 has had a relatively smaller impact on Arab countries than on other countries that have been significantly affected.",
"keywords": [
"Arab countries",
"confirmed",
"coronavirus",
"recovered",
"COVID-19",
"COVID-19 vaccines",
"death"
],
"content": "Introduction\n\nOn March 11, 2020, the World Health Organization (WHO) declared Coronavirus (COVID-19) as a pandemic. COVID-19, which is caused by severe acute respiratory syndrome-coronavirus (SARS-CoV-2), is a highly contagious virus.1 In the last three years, COVID-19 has infected and killed millions of people around the world, including those in Arab countries. When COVID-19 started in the first period of 2020 and the PCR tests were not available, fever, dry cough, sore throat, headache, fatigue, and breathlessness were the common symptoms for COVID-19 patients. However, many people with COVID-19 remain asymptomatic but can transmit SARS-CoV-2 to others.2,3\n\nIn the past, vaccines have saved lives, avoided illness and infection, and been evaluated as effective health interventions.4 In fact, WHO has shown that vaccines are safer than treatment.5 COVID-19 vaccines reduce the risk of illness, hospitalization, and death from COVID-19. A study showed that the mean percentage of death with one dose was 11.55% compared to 4.31% after the second dose of any type of approved vaccine.6 Globally, it has been estimated that about eight billion doses of the COVID-19 vaccine have been distributed to reduce the rate of COVID-19.7 Comprehensively, the COVID-19 vaccination saved approximately 20 million lives during its first year of distribution.8 As of January 1, 2023, more than 5.51 billion people worldwide have received a dose of a COVID-19 vaccine, which corresponds to approximately 71% of the world population, and fully vaccinated about 66%.9\n\nA recent study in Qatar concluded that deaths attributable to SARS-CoV-2 vaccination are extremely rare.10 They reported that the death rate among the vaccinated persons with a high probability of relationship to SARS-CoV-2 vaccination was 0.34 per 100,000 vaccine recipients, while the death rate among the vaccinated persons with either high or intermediate probability of relationship to SARS-CoV-2 vaccination was 0.98 per 100,000. In line with this study, the United States Centers for Disease Control and Prevention identified only nine deaths from 14,980 reports of death among more than 589 million vaccine doses between December 14, 2020, and June 6, 2022.11\n\nOn the other hand, WHO has identified many different variants of the coronavirus SARS-CoV-2 including Alpha, Beta, Omicron, Gamma, Delta, Eta, Iota, Kappa, Zeta, and Mu. On 26 November 2021, WHO declared the Omicron variant, known as lineage B.1.1.529, a variant of concern.12 It was first identified in Botswana and South Africa.13Although the Omicron variant (B.1.1.529) causes less severe symptoms, it is more contagious and spreads faster than any previous variant. Many studies reported that this variant causes reinfection, and may escape the immune system’s defenses, and two doses of vaccination appeared to be less effective.14–16 However, some studies show that boosters can provide protection against Omicron infection.17–19 Unfortunately, these variants and probably others will continue to emerge as long as the coronavirus SARS-CoV-2 remains.\n\nThe development of vaccines is usually a lengthy and complex process. However, in order to stop the transmission of COVID-19, vaccine development has been accelerated.20,21 Despite unequal vaccine distribution, vaccine hesitancy, and waning immunity, billions of vaccine doses have been administered worldwide. One of the major causes of vaccine hesitancy and delay in vaccination is the concern about adverse effects.22 As of December 29, 2022, WHO approved 11 COVID-19 vaccines including Sinopharm, Sinovac, Bharat Biotech, Moderna, Pfizer/BioNTech, Oxford/AstraZeneca, Serum Institute of India, Janssen/Johnson & Johnson, Novavax, Serum Institute of India, and CanSino.23\n\nThe Arab world contains 22 countries, distributed 12 in Asia and 10 in Africa. Language, history, traditions, and culture are shared by Arab countries.24 However, the healthcare systems and availability of resources differ from one Arab country to another. Previously, we published two review papers. The first was a 5-month COVID-19 data in all Arab countries from January 1, 2020, to May 31, 2020, and concluded that most Arab countries took some serious early steps to minimize the outbreak of COVID-19.25 The second one was a one-year from February 2020 to February 2021, and we concluded that among the Arab countries, Qatar, Bahrain, and Lebanon showed the highest number of recovered, confirmed, and deaths per million population, respectively. The number of confirmed and death cases among Arab countries triggers significant worries about morbidity and mortality related to COVID-19, respectively.26 We have been following COVID-19 from the beginning in each Arab country. In the present study, we aimed to assess further the prevalence of COVID-19 in the Arab world from January 2020 to December 2022 and to compare these findings with other significantly affected countries.\n\n\nMethods\n\nWe used the WHO, World COVID-vaccinations tracker, Worldometer, and Ministries of Health official websites to search for COVID-19 data in Algeria, Bahrain, Comoros, Djibouti, Egypt, Iraq, Jordan, Kuwait, Lebanon, Libya, Mauritania, Morocco, Oman, Palestine, Qatar, Saudi Arabia (SA), Somalia, Sudan, Syria, Tunisia, United Arab Emirates (UAE), and Yemen. The period covered was from January 2020 to December 2022. The inclusion criterion was official information about clinically diagnosed COVID-19 in English or Arabic. The exclusion criterion was unofficial information regarding COVID-19 in all Arab countries, unspecified date and location of information, or suspicion of duplicate information. The data were collected monthly and verified with the data in the Worldometer. The following information was collected from each Arab country: total population, median age, number of monthly confirmed, death, and recovered cases, the total number of COVID-19 tests, and COVID-19 vaccine rates (first and second). The data for the topmost 15 affected countries were extracted from the Worldometer at the same time as the data for the Arab countries. Ethical approval and written informed consent were not required for this type of study. Data were analyzed using the IBM SPSS Statistics (RRID:SCR_016479) software version 25 (SPSS Inc., Chicago, IL, USA). Results are presented as numbers, percentages, and means.\n\n\nResults\n\nBy January 01, 2023, the total Arab population who live in Arab countries was 449,809,846. Egypt recorded the highest population among all Arab countries, followed by Sudan, and Algeria with 106,156,692, 45,992,020, and 45,350,148, respectively. The highest median age was seen in UAE, followed by Qatar, and Bahrain with 38.4, 33.7, and 32.3 years, respectively. Whereas the lowest median age was seen in Sudan at 18.3 years. All Arab countries utilized real-time polymerase chain reaction (RT-PCR) as the testing method for SARS-CoV-2. The total number of COVID-19 tests in all Arab countries was 362,542,626. UAE (19,632,329) recorded then the highest number of tests per million population (PMP), followed by Bahrain (5,960,320), and then Oman (4,695,724). The people in Qatar and the United Arab Emirates have received two doses of the COVID-19 vaccine equally to about 99% whereas those in Yemen received only 3% for both doses (Table 1).\n\nThe total number of COVID-19 cases in all Arab countries was 14,218,042 and of those, 173,544 (1.2 %) were deceased and 13,384,924 (94%) were recovered. Jordan, Qatar, Kuwait, Palestine, and Lebanon recorded the highest number of reported cases PMP with 261,404, 164,032, 151,138, 131,568, and 118,957, respectively. Yemen recorded only 383 cases PMP. Based on the evaluation of three years from January 2020 to December 2022, the trend showed that the first quarter of 2022 had the highest number of confirmed COVID-19 cases in all Arab countries with 3,235,665 cases. In the same quarter period, 11 Arab countries scored their highest number of COVID-19 confirmed cases (Table 2).\n\nDeaths PMP were dominant in Tunisia, Jordan, Palestine, Lebanon, and Libya with 2,430, 2,116, 1,073, 1,052, and 914, respectively. The trend demonstrated that the third quarter of 2021 had the highest number of deaths in all Arab countries with 31,275 cases. In the same quarter period, five countries had the highest number of COVID-19-related deaths (Table 3).\n\nBahrain, Jordan, Kuwait, Qatar, and Palestine showed the highest number of recovered cases PMP with 307,175, 258,944, 147,542, 134,455, and 131,528, respectively. The trend showed that the first quarter of 2022 had the highest number of recovered cases in all Arab countries with 3,261,712 cases. In the same quarter period, 10 countries had the highest number of recovered cases (Table 4).\n\nIn comparison to the topmost 15 affected countries, the Arab world ranked 16 as it had the lowest overall incidence PMP of 31,609. The data on total deaths PMP showed that India had the lowest number of deaths with only 377 cases followed by the Arab world with 386 cases. The United States recorded the highest number of deaths with 3,339 cases. In terms of the total number of tests for SARS-CoV-2, Arab countries ranked eleventh with 805,990 tests PMP. The highest number of tests PMP was conducted by Spain (10,082,298) and the lowest was by Brazil (296,146). Arab countries showed the youngest median age followed by India with 28.7 years as its median age. Conversely, Japan had the oldest median age of 48.6 years, however, it had fewer COVID-19 deaths per million populations with 456 cases. It is worth mentioning that six of the top 15 affected countries are from Europe. France was the worst country (after South Korea) as it recorded 599,471 cases PMP and ranked first. Other parameters, which include total tests and population, are also compared (Table 5).\n\n\nDiscussion\n\nThe present study aimed to assess the prevalence and the impact of the COVID-19 pandemic in 22 Arab countries and compare them with other significantly affected countries from January 2020 to December 2022. COVID-19 confirmed cases increased exponentially in the first quarter of 2021 due to the New Year season with Jordan demonstrating the highest number of cases followed by Lebanon. A dramatic increase in COVID-19 confirmed cases occurred in the third quarter of 2021 due to the emergence of the Delta variant,27 which peaked in Iraq with a total number of 665,730. Another reason for the spike increase is the slow uptake of the vaccine in many countries.28 For example, only 20% of the population in Iraq had received single/double doses of the COVID-19 vaccine. In addition, people in several countries, such as Iraq, refused to take the vaccine, which in turn, might have played a role in accelerating the number of COVID-19 confirmed cases.29 Furthermore, the re-opening of schools and businesses, people returning from holidays and social mixing subsidized the escalation in the COVID-19 confirmed cases at the end of summer and the start of winter of 2021.27 The situation was further aggravated by the economic disturbance in some of these countries hence, they had a compound crisis; COVID-19 and economic disruption.30\n\nPreventive measures taken by countries during the pandemic affected the spread of the COVID-19 virus. During the first, second, and third quarters of 2020, the pandemic was under control in most Arab countries due to the implementation of extreme precautionary measures. The major measures include land, sea, and air route closure, nighttime or all-day curfew and lockdown, school and universities closure, worship places closure, prohibition of gatherings, closure of shops, malls, beaches, public parks, and gardens, cancellation of all cultural and sports events, festivals, seminars, and scientific meetings, and suspension of work in all government and private sectors.31–33A study conducted in Saudi Arabia showed that preventive measures had an enormous effect in reducing the number of expected confirmed cases of COVID-19 from 437,096 cases to an observed number of 28,656 at the beginning of the second quarter of 2020.34 Because of the economic crisis in some countries like Jordan, some of these measures were diminished in the fourth quarter of 2020, leading to an increase in COVID-19 cases.35\n\nThe first quarter of 2022 was a shockwave as it was recorded with the highest-ever number of COVID-19 confirmed cases with 3,235,665 peaked by Jordan with a total number of 630,811. The potential reason for the spike is the occurrence of the Omicron variant that had affected the death rate and increased hospitalization.36 On the other hand, the pandemic had intense consequences on the economy of many countries. Therefore, to revive the economy, different approaches were taken such as the period of isolation of the infected people was reduced and guidelines on PCR testing of suspected COVID-19 cases became more restrictive.35 Subsequently, there was a dramatic decrease in the confirmed cases in the second quarter of 2022, which continued to decline until the end of the year. Both the third-fourth quarters of 2021 and 2022 demonstrated a similar wave but with a lesser rate of confirmed COVID-19 cases in 2022. This could be due to the higher vaccine coverage in that year emphasizing the importance and the impact of vaccination intake.37 Despite the full vaccination coverage in Qatar (99%), Qatar was reported with the highest number of confirmed cases of COVID-19 in the fourth quarter of 2022 with a total number of 37,730. The conceivable reason could be that Qatar was hosting the World Cup 2022 with no COVID-19 restrictive measures required to enter the country, which had strikingly increased the social gathering and thus, increased COVID-19 confirmed rates.38\n\nAmong Arab countries, such as the Gulf Cooperation Council (Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and UAE) and Morocco, with over 60% of their population fully vaccinated, showed a sharp decrease in the death rate PMP in the last quarter of 2021 (Table 3). However, the first quarter of 2022 retained a death peak, which disappeared by the second quarter of the same year, probably because of the fast-spreading Omicron variant wave. Countries like Yemen, Syria, Iraq, and Sudan showed a low percentage of vaccination, a low number of tests, and surprisingly low deaths PMP (Tables 1 and 3). Political instability and a weak healthcare system that depends on outside humanitarian aid could be attributed to a lack of regular testing and continued poor documentation of COVID-19 status.25\n\nJordan, as an example of an Asian country, experienced the first wave of viral spread during the fourth quarter of 2020, lasted until January 2021, and resulted in a great increase in accumulative confirmed and death cases. Before the first wave started, epidemiological status was under control, but by early September 2020 some restrictions were removed, e.g., land boundaries were opened for export/import goods from neighboring countries, universities opened doors for registration, and people started to take the crisis less seriously.35 The second wave in Jordan was led by the fast-spreading UK variant that started in January 2021 continued until May 2021 and peaked in March 2021. The Indian Delta strain spread in Jordan during the second quarter and beginning of the third quarter of 2021, but the epidemiological data did not show any peak due to vaccination or naturally acquired immunity.35 The third and fourth waves, from October 2021 until January 2022 and January 2022 to March 2022, respectively, started as the government halted many preventive measures due to economic stress. Both waves were led by the Omicron variant.35\n\nTunisia, as an example of an African country, started to record positive cases in early March 2020, however by June 2020, the government could control the situation by applying preventive measures, which resulted in zero cases between 4th and 12th June. In July 2020, borders opened and clear slackening in sticking with preventive measures by people resulted in the second wave, which affected the country. March 2021 was the start of the third wave in Tunisia, which was highlighted by severe cases and a high transmission rate, caused by the Alpha variant after the fourth wave, which was led by the Delta variant that occurred in May 2021. During this period, Tunisia got a high rate of deaths PMP (Table 3). The Omicron variant of concern was the cause of the fifth wave by the end of 2021, so the country experienced another peak of death during the first quarter of 2022. These waves attributed to a large number of deaths. Tunisia has the highest number of deaths PMP among Arab countries. The economic crisis in addition to political problems made it difficult for the government to control COVID-19 and this in turn, resulted in the delay of the introduction and dissemination of COVID-19 vaccines.39\n\nStudying the trend of recovered cases is a useful indication of the health status and the health system in these countries. It is also a good tool to be used in terms of applying certain restrictions such as the duration of lockdown. From January 2020 to December 2022, all Arab countries showed various numbers of recovered cases of COVID-19. Such variation depended initially on the number of infected cases and on a broader scope, the severity of infection, treatment, patient immunity, vaccination, and other political and health factors.37 Although some data were missing on the number of recovered cases for some countries, Bahrain, followed by Jordan, Kuwait, and Qatar showed the highest among all Arab countries. Whereas, Syria, Sudan, Somalia, and Yemen showed the lowest number of recovered cases, which may be explained by the unstable political status and subsequently the weakness of the healthcare system. Over time and based on the registered cases, the trend of recovered cases started at a low, reached a high peak, and eventually declined. This trend is common in such pandemics and the mode of spreading such infection had been observed in the previous pandemic.40 The bell-shaped trend in certain countries such as Palestine, given all collected data, are accurate, and helped tremendously in managing the pandemic crisis in terms of lockdown, financial and social impact, and predicting the coming waves of the mutant viruses.\n\nThe effect of a complete vaccination regimen on the recovered cases was not consistent among Arab countries. As mentioned previously, Qatar had the highest percentage of the vaccinated population but was not the top-rated country in the recovered cases. Such observation does not exclude the importance of vaccination effect on these cases rather than additional factors that might have contributed to this outcome.\n\nA recent study showed the effectiveness of the vaccine in preventing SARS-CoV-2 infection and its symptoms. In addition to other mitigation strategies, vaccine campaigns could have a great impact on the number of confirmed and recovered cases.41 Although quarantine was one of the most important measures in controlling the spread of the epidemic,42 such a theory changed once the right vaccine was used. Quarantine controls the disease by the large fraction of pre-symptomatic and asymptomatic transmission, unlike the vaccine that eliminates the virus and reduces its symptoms in many cases.\n\nDuring the recent pandemic, vaccination campaigns have proven their effectiveness to control the disease and reduce the severity of its symptoms. The pharmaceutical companies were competing to prepare the most effective vaccine with less side effects. The focus of vaccination campaigns should be a priority in any coming pandemic and their importance should be stressed to societies. Unfortunately, many countries had anti-vaccine groups that were affecting the vaccination campaigns badly. Those groups influenced the decision of several people on taking the vaccines and subsequently affecting the control of the disease. Changing the culture and the mentality of certain groups in societies will be the first and biggest challenges for vaccination campaigns in any pandemic in the future. Altogether, the authors hypothesized that vaccination campaigns influenced the number of confirmed and recovered cases in these Arab countries despite the impact of other related factors. It is very important to open new insights in the research of vaccine discovery and more time and effort should be spent in this area.\n\nRecently, Hoxha and coworkers analyzed COVID-19 data from 164 different countries and concluded that higher COVID-19 vaccination rates are associated with lower COVID-19 mortality rates and that there is a tendency for more vaccinations and fewer deaths per 1,000 cases with increasing country income levels.43 Notably, Both Qatar and UAE represent as the highest income countries in the Arab world. UAE recorded the same percentage of the vaccinated population as Qatar, and both demonstrated low number of deaths.\n\nCompared with the 15 topmost affected countries in the world, the Arab world experienced a lower number of cases and deaths PMP (Table 5). It also performed fewer tests than its population. South Korea, Japan, Argentina, Brazil, Vietnam, and India also performed a lesser number of tests than their populations. Conversely, the six European countries (France, Germany, Italy, UK, Spain, and Russia), Australia, USA, and Turkey have performed tests more than their populations. A similar result was observed for most European countries by November 2022, where the number of tests exceeded the number of residents.37 The diagnostic testing strategy and mass screening including the screening of asymptomatic people is a major strategy in controlling the spread of the virus.44 Hence, testing procedures such as PCR is a tool used to detect and record both confirmed and death cases.45 It is possible that such countries that performed fewer tests than their populations could have resulted in recording fewer confirmed cases and deaths. Furthermore, it has been suspected that the smaller number of tests carried out could be a reason for the reduced spread of the virus and the slowing down of the spread of the infection. However, the analysis conducted by Hisaka et al., (2020) concluded that extensive PCR testing might be effective in reducing the number of deaths and that further studies are required to verify this hypothesis.46\n\nA previous study reported that older age plays a vital role in influencing the severity of COVID-19 disease and negative clinical outcomes than the younger population.47 With this, the lower deaths PMP as observed in both the Arab world (386 cases) and India (377 cases) could be attributed to the low median age of 26 and 28.7 years, respectively. By contrast, this claim contradicts why Japan with the highest median age of 48.6 years in the top 15 affected countries also recorded a low number of deaths PMP (456 cases).\n\nStudies have reported that in response to the COVID-19 pandemic, all 44 Muslim countries including the Arab world and Turkey, mainly implemented mitigation strategies to control the virus.48,49 The main aim of implementing a mitigation strategy is to reduce the number of death tolls by focusing on the medical care of severe cases and relying on social distancing and quarantine to flatten the curve of epidemic impact and burden on hospitals.50 Stringent measures included the suspension of all airline flights, cancellation of Umrah, and down-scaling of the pilgrimage to Mecca.48 Other countries that mainly responded with mitigation strategies included the United States, and European countries.50,51 Mitigation measures are adopted immediately once the containment strategies (strict lockdowns) fail to isolate the infected individuals due to the widespread infection in the community or until vaccines are developed.52 Hence, there is a clear indication that countries vary widely in their response to the COVID-19 impact and that these differences could be partially explained by many factors such as the economic and cultural situation, governmental policies, medical capacities, the age and genetic variation between ethnic groups in a population.46\n\nA key strength of this study is its comprehensive follow-up and collection of COVID-19 data in each Arab country for three consecutive years. In addition, accurate monthly data were obtained from the Ministry of Health in each country and verified with the Worldometer data for COVID-19. However, there are a few limitations in our review. First, no distinction was made between Arabs and non-Arabs in the reported health data since many non-Arabs work in Arab countries. Second, COVID-19 hospitalizations are lower after being fully vaccinated, so many patients might not be included in these statistics. Third, many Arab countries lack information about COVID-19 vaccine boosters. Finally, this study could not identify an association between COVID-19 related deaths and comorbidities due to the absence of risk factors such as hypertension, diabetes, respiratory system disease, and cardiovascular disease in the data extracted.\n\n\nConclusions\n\nAlthough the number of confirmed, death, and subsequently recovered cases of COVID-19 have greatly reduced in the last quarter of 2022 in most Arab countries, further efforts to address the need to re-campaign on COVID-19 vaccines and raise awareness programs about boosters must be implemented. COVID-19 has had a relatively smaller impact on Arab countries than on other countries that have been significantly affected.",
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}
|
[
{
"id": "247533",
"date": "01 Apr 2024",
"name": "Muhammad Nauman Zahid",
"expertise": [
"Reviewer Expertise Virologist"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have made an interesting attempt at “COVID-19 in the Arab countries: Three-year review.” The manuscript is interesting; however, the authors need to justify the scientific writing of the manuscript. Some of the general comments are provided below:\n\nConsidering the usage of several sources, what steps were taken to address any potential contradictions or inconsistencies discovered in the data collected? In order to maintain the dataset's integrity, how were possible duplicate items found and dealt with? What variables could account for the variations in COVID-19 cases and fatalities that were noted during the three years from January 2020 to December 2022? Could these tendencies have been impacted by any significant policy changes or events? Taking into account the possible influence of variables including climate, public health initiatives, and alterations in population behavior, how were seasonal fluctuations in COVID-19 incidence and death taken into account in the analysis? Could you provide further details about any possible biases or confounding factors, such as variations in healthcare access, population demographics, or government response tactics, that would affect how these cross-regional comparisons are interpreted? According to the manuscript, vaccination campaigns were a major factor in the decline of COVID-19 cases, fatalities, and hospital admissions in Arab nations. Can you offer more proof or analysis to back up this claim, such as comparisons of COVID-19 results before and after vaccination campaigns or research on the efficacy of vaccines? How were public opinions of vaccine safety and efficacy, vaccine hesitancy, and disinformation addressed during the vaccination campaign discussion? Were any tactics put in place to enhance vaccination uptake and remove obstacles to access?\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "11459",
"date": "09 May 2024",
"name": "Nasar Alwahaibi",
"role": "Author Response",
"response": "We would like to take this opportunity to express our thanks to the reviewer for the positive feedback and helpful comments. Below are our responses, point-by-point to the queries of the reviewer. The authors have made an interesting attempt at “COVID-19 in the Arab countries: Three-year review.” The manuscript is interesting; however, the authors need to justify the scientific writing of the manuscript. Some of the general comments are provided below: Considering the usage of several sources, what steps were taken to address any potential contradictions or inconsistencies discovered in the data collected? Response We use the Ministry of Health official websites in each Arab country as an initial source as they provide daily data, then verified with the WHO and Worldometer sources. In case of different data, which is not common, we referred to the Ministry of Health in each Arab country. In order to maintain the dataset's integrity, how were possible duplicate items found and dealt with? Response The data are not duplicated, but sometimes there are differences between the WHO and Worldometer sources as they are reported at different times on the Ministry of Health's official websites. What variables could account for the variations in COVID-19 cases and fatalities that were noted during the three years from January 2020 to December 2022? Could these tendencies have been impacted by any significant policy changes or events? Response The variables or factors that could account for the variations in COVID-19 cases and fatalities are mentioned in the discussion section and these include lockdown measures, mitigation strategies (such as implementing social distancing), employment and scale of diagnostic testing and vaccine intake, timely response of governments, weak healthcare system (physical resources and healthcare personnel and under reporting) and hence, all of these could be attributed to the “healthcare policy” of each country. Other variables include the occurrence of virus-related factors such as the fast-spreading Omicron variant, the UK variant, and the Alpha variant. Population or demographic characteristics such as age was also identified as a potential factor that may have influenced infection and death rates. We demonstrate in the discussion section that the ability of “healthcare systems to respond promptly against the COVID-19” such as implementing strict lockdown measures and mitigation strategies significantly reduced confirmed cases and fatalities. We also show in the discussion that countries that employed heavy testing protocols revealed higher number of cases and that under-reporting could have played a role in countries that did not employ large-scale testing. Taking into account the possible influence of variables including climate, public health initiatives, and alterations in population behavior, how were seasonal fluctuations in COVID-19 incidence and death taken into account in the analysis? Response According to the data of COVID-19 fluctuations, the spikes of Covid-19 were connected to the spread waves but not the climate. For example, in Tunisia, the peaked deaths were in the third quarter of 2021 which is considered as hot climate whereas in Lebanon the peaked deaths were in the first quarter of 2021 which is considered as a cold climate. According to the public health initiatives (e.g. vaccination) and positive alteration in population behaviors, we mentioned in the paper how these two factors affected the decrease in the death’s numbers. Could you provide further details about any possible biases or confounding factors, such as variations in healthcare access, population demographics, or government response tactics, that would affect how these cross-regional comparisons are interpreted? Response This is very good question, however, population demographics such as gender and age are not reported. Thus, we have added the following sentence as a limitation: The lack of gender and age data in numerous Arab countries prevented us from conducting thorough comparisons and assessing potential risk factors. Regarding the government response tactics, we have already mentioned in the discussion section that: During the first, second, and third quarters of 2020, the pandemic was under control in most Arab countries due to the implementation of extreme precautionary measures. The major measures include land, sea, and air route closure, nighttime or all-day curfew and lockdown, school and universities closure, worship places closure, prohibition of gatherings, closure of shops, malls, beaches, public parks, and gardens, cancellation of all cultural and sports events, festivals, seminars, and scientific meetings, and suspension of work in all government and private sectors. Regarding the access to healthcare facilities during COVID-19 crises, this information is not available in all Arab countries. We know that GCC countries offered free medical treatment and vaccinations to all residents but this information is missing in other Arab countries. According to the manuscript, vaccination campaigns were a major factor in the decline of COVID-19 cases, fatalities, and hospital admissions in Arab nations. Can you offer more proof or analysis to back up this claim, such as comparisons of COVID-19 results before and after vaccination campaigns or research on the efficacy of vaccines? Response Our results did not study the comparison of COVID-19 before and after vaccination campaigns. As suggested, the following paragraph has been added in the discussion section: Research conducted in the United Arab Emirates regarding the inactivated BBIBP-CorV (Sinopharm) vaccine revealed that its efficacy against severe COVID-19 outcomes was 80% for hospitalization, 92% for critical care admission, and 97% for preventing death.46 In addition, a study conducted in Morocco on the long-term efficacy of the inactivated BBIBP-CorV vaccine revealed a decrease in effectiveness, dropping from 88% to 64% six months after vaccination.47 Furthermore, in Qatar, a different study demonstrated that the efficacy of BBIBP-CorV vaccine against SARS-CoV-2 infections decreased gradually, with a more rapid decline observed after the fourth month. This decline resulted in about 20% protection at five to seven months following vaccination. However, the vaccine's efficacy remained nearly 96% effective in preventing hospitalization and death six months after vaccination.48 How were public opinions of vaccine safety and efficacy, vaccine hesitancy, and disinformation addressed during the vaccination campaign discussion? Were any tactics put in place to enhance vaccination uptake and remove obstacles to access? Response The following sentence has been added in the discussion section: Certain tactics were used to enhance public awareness and acceptance of vaccine during these campaigns. One of the most effective tactics was to address public opinions of vaccine safety and efficacy by disseminating accurate information through authorized channels. This information was in different languages to reach out all in the community. Community engagement and healthcare guidance were also helpful. During the vaccination process, the uptake of vaccine was enhanced by removing any obstacle that might delay such a process. For example, setting up vaccination centers in different locations with an easy access and quick appointment. These centers had big area to accommodate more people at each time. Community outreach existed for those who could not go to these centers.44"
}
]
},
{
"id": "233650",
"date": "11 May 2024",
"name": "Ahmad A. Alrasheedi",
"expertise": [
"Reviewer Expertise Family Medicine",
"Public Health",
"Common Health Problems (such as DM",
"HTN",
"Dyslipidemia",
"and Depression)",
"and Epidemiology/Prevention of Infectious diseases such as COVID-19 and Influenza."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this study is excellent and worth accepting as the authors evaluated the spread of the COVID-19 pandemic in a critical region, the Arab world, over three years (2020-2022). Understanding the epidemiology of COVID-19 in the Arab world and comparing it to the world could help researchers and decision-makers explore the best ways to deal with COVID-19 and may provide lessons for a more effective response to public health emergencies in the future. However, there are some suggestions to improve the article.\n\n1- Type of the study: Is this a review article or an original research? Based on the article's methodology and structure, this article is considered original (research article). The authors extracted primary/secondary data (raw data) from online websites and then analyzed and interpreted the data. In contrast, a review article or paper is based on other published articles. Review articles generally summarize the existing literature on a topic in an attempt to explain the current state of understanding of the topic. Therefore, this is not a review article because the authors did not base their methodology on a review of previous studies/research. The authors should reconsider this part!\n2- Suppose this article is considered an original study, which it appears to be. In that case, it is preferable to change the word “review” in the title to another word, for example, “study,” so that the title is: “COVID-19 in the Arab countries: A three-year study” or “COVID-19 in the Arab countries: A study after three years”.\n3- In the \"conclusions\" section of the Abstract, Confirmed what? Confirmed cases or confirmed deaths. A word is missing!\n4- In the first line of the \"Introduction\" section, which coronavirus is? It is the novel coronavirus, or as it is named, SARS-CoV-2. In contrast, the disease caused by this virus is called COVID-19. I suggest it be written as \"… declared coronavirus disease 2019 (COVID-19) as …\".\n5- In the second sentence of the \"Introduction\" section, which years? 2020-2022 or 2021-2023; please specify!\n6- The reference No. 5 is old (2004). Is there any recent one?\n\n7- In paragraph 4 of the \"Introduction\" section, please remove the phrase \"the coronavirus.\" To be \"… many different variants of SARS-CoV-2, including …\". Also, in this statement: as long as the coronavirus SARS-CoV-2 remains. Please remove the phrase \"the coronavirus\".\n8- In the \"Methods\" section, please provide the link/reference for each website if possible (Worldometer...).\n9- The exclusion criterion was unofficial information regarding COVID-19 in all Arab countries,... This phrase (unofficial information regarding COVID-19 in all Arab countries) should be removed because it is known from the inclusion criteria (exclusion criteria are not the opposite of inclusion criteria).\n10- The following information was collected from each Arab country: total population, median age, number of monthly confirmed,... Confirmed what? Please make it clear.\n11- \"Results\" section: All Arab countries utilized real-time polymerase chain reaction (RT-PCR) as the testing method for SARS-CoV-2. I suggest to transfer this sentence to the \"Introduction\" section.\n12- UAE (19,632,329) recorded then the highest number of tests per million population (PMP), followed by Bahrain (5,960,320), and then Oman (4,695,724). Rephrasing the sentence to be clear, I suggest, \"The UAE recorded the highest number of tests per million population (PMP) with 19,632,329, followed by Bahrain (5,960,320), and then Oman (4,695,724).\" Always add \"the\" before UAE, USA, and UK while mentioned in the text.\n\n13- The people in Qatar and the United Arab Emirates ... have [أع1] Use the abbreviation: the UAE.\n14- Table 1: Please identify the abbreviations in the table (Add footnotes), even if they have already been mentioned in the text. Please check the population number of Mauritania.\n\n15- Table 2: define the abbreviations in the table (Add footnotes): UEA, SA, and PMP, as well as for other tables. Also, in column 10 (Q1-22), some numbers are not uniform in the way they are written.\n\n16- In the \"Discussion\" section, New Year season New Year season? Do you mean influenza season, where URTIs, including coronaviruses, increase?\n17- Another reason for the spike increase is the slow uptake of the vaccine in many countries. Which countries? of the world, including Arab countries or in many Arab countries?\n18- During the first, second, and third quarters of 2020, the pandemic was under control in most Arab countries due to ...\n\nUsing the probability form, such as \"mostly due to\" or \"probably because,\" is better.\n19- The first quarter of 2022 was a shockwave as it was recorded with the highest-ever number of COVID-19 confirmed cases with 3,235,665 peaked by Jordan with a total number of 630,811. To be clearer, I suggest you rephrase it to be: \"During the first quarter of 2022, which was a shockwave, the Arab countries recorded the highest number of confirmed COVID-19 cases ever reported between 2020 and 2022. The total number of cases was 3,235,665, with Jordan reporting the highest number of cases at 630,811.\"\n20- Qatar was reported with the highest number of confirmed cases of COVID-19 in the fourth quarter of 2022 Suggesting to rephrase by adding among Arab countries.\n21- In paragraph no. 12, ...Australia, USA, and Turkey have performed tests more than their populations. DEFINE USA: please write the United States of America.\n\n22- In the \"Strengths and limitations\" section, However, there are a few limitations in our review. study or review? This will depend on your classification.\n\n23- Although the number of confirmed, death, and subsequently recovered cases of... Confirmed what? Please make it clear.\nThank you for your valuable study.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "11609",
"date": "26 Jun 2024",
"name": "Nasar Alwahaibi",
"role": "Author Response",
"response": "We would like to extend our gratitude to the reviewer for his positive feedback and valuable comments. Listed below are our responses, addressing each query from the reviewer in detail. Overall, this study is excellent and worth accepting as the authors evaluated the spread of the COVID-19 pandemic in a critical region, the Arab world, over three years (2020-2022). Understanding the epidemiology of COVID-19 in the Arab world and comparing it to the world could help researchers and decision-makers explore the best ways to deal with COVID-19 and may provide lessons for a more effective response to public health emergencies in the future. However, there are some suggestions to improve the article. Response Thank you 1- Type of the study: Is this a review article or an original research? Based on the article's methodology and structure, this article is considered original (research article). The authors extracted primary/secondary data (raw data) from online websites and then analyzed and interpreted the data. In contrast, a review article or paper is based on other published articles. Review articles generally summarize the existing literature on a topic in an attempt to explain the current state of understanding of the topic. Therefore, this is not a review article because the authors did not base their methodology on a review of previous studies/research. The authors should reconsider this part! Response As suggested by the reviewer, the title has been changed. 2- Suppose this article is considered an original study, which it appears to be. In that case, it is preferable to change the word “review” in the title to another word, for example, “study,” so that the title is: “COVID-19 in the Arab countries: A three-year study” or “COVID-19 in the Arab countries: A study after three years”. Response The title has been changed to “COVID-19 in the Arab countries: A three-year study” 3- In the \"conclusions\" section of the Abstract, Confirmed what? Confirmed cases or confirmed deaths. A word is missing! Response To make it clearer, we removed “subsequently” as follows: Although the number of confirmed, death, and recovered cases of COVID-19 have greatly reduced in the last quarter of 2022 in most Arab countries. 4- In the first line of the \"Introduction\" section, which coronavirus is? It is the novel coronavirus, or as it is named, SARS-CoV-2. In contrast, the disease caused by this virus is called COVID-19. I suggest it be written as \"… declared coronavirus disease 2019 (COVID-19) as …\". Response As suggested, the sentence has been rephrased. 5- In the second sentence of the \"Introduction\" section, which years? 2020-2022 or 2021-2023; please specify! Response We referred to 2020 – 2022. 6- The reference No. 5 is old (2004). Is there any recent one? Response Yes, it is old but we have cited the original source. 7- In paragraph 4 of the \"Introduction\" section, please remove the phrase \"the coronavirus.\" To be \"… many different variants of SARS-CoV-2, including …\". Also, in this statement: as long as the coronavirus SARS-CoV-2 remains. Please remove the phrase \"\". Response “The coronavirus” has been removed. 8- In the \"Methods\" section, please provide the link/reference for each website if possible (Worldometer...). Response The links to the WHO and Worldometer are updated daily. In addition, the links to the ministries of health are no longer accessible. 9- The exclusion criterion was unofficial information regarding COVID-19 in all Arab countries,... This phrase (unofficial information regarding COVID-19 in all Arab countries) should be removed because it is known from the inclusion criteria (exclusion criteria are not the opposite of inclusion criteria). Response “Unofficial information regarding COVID-19 in all Arab countries” has been removed. 10- The following information was collected from each Arab country: total population, median age, number of monthly confirmed,... Confirmed what? Please make it clear. Response We meant confirmed cases “number of monthly confirmed, death, and recovered cases, 11- \"Results\" section: All Arab countries utilized real-time polymerase chain reaction (RT-PCR) as the testing method for SARS-CoV-2. I suggest to transfer this sentence to the \"Introduction\" section. Response “All Arab countries utilized real-time polymerase chain reaction (RT-PCR) as the testing method for SARS-CoV-2” has been removed. 12- UAE (19,632,329) recorded then the highest number of tests per million population (PMP), followed by Bahrain (5,960,320), and then Oman (4,695,724). Rephrasing the sentence to be clear, I suggest, \"The UAE recorded the highest number of tests per million population (PMP) with 19,632,329, followed by Bahrain (5,960,320), and then Oman (4,695,724).\" Always add \"the\" before UAE, USA, and UK while mentioned in the text. Response As suggested, have been corrected. 13- The people in Qatar and the United Arab Emirates ... have [أع1] Use the abbreviation: the UAE. Response Has been corrected. 14- Table 1: Please identify the abbreviations in the table (Add footnotes), even if they have already been mentioned in the text. Please check the population number of Mauritania. Response Those abbreviations were initially defined in all tables at the time of submission then, the journal editors removed them. You are right, the population of Mauritania is 4,736,139. This information has been corrected and the countries in Table 1 have been reordered. 15- Table 2: define the abbreviations in the table (Add footnotes): UEA, SA, and PMP, as well as for other tables. Also, in column 10 (Q1-22), some numbers are not uniform in the way they are written. Response Those abbreviations were initially defined in all tables at the time of submission then, the journal editors removed them. The numbers in column 10 (Q1-22) have been corrected. 16- In the \"Discussion\" section, New Year season New Year season? Do you mean influenza season, where URTIs, including coronaviruses, increase? Response Yes, to make it clearer, the sentence has been modified to influenza season. 17- Another reason for the spike increase is the slow uptake of the vaccine in many countries. Which countries? of the world, including Arab countries or in many Arab countries? Response The sentence had been modified. 18- During the first, second, and third quarters of 2020, the pandemic was under control in most Arab countries due to ... Using the probability form, such as \"mostly due to\" or \"probably because,\" is better. Response The sentence had been modified. 19- The first quarter of 2022 was a shockwave as it was recorded with the highest-ever number of COVID-19 confirmed cases with 3,235,665 peaked by Jordan with a total number of 630,811. To be clearer, I suggest you rephrase it to be: \"During the first quarter of 2022, which was a shockwave, the Arab countries recorded the highest number of confirmed COVID-19 cases ever reported between 2020 and 2022. The total number of cases was 3,235,665, with Jordan reporting the highest number of cases at 630,811.\" Response As suggested, the sentence had been rephrased. 20- Qatar was reported with the highest number of confirmed cases of COVID-19 in the fourth quarter of 2022 Suggesting to rephrase by adding among Arab countries. Response As suggested, the sentence had been modified. 21- In paragraph no. 12, ...Australia, USA, and Turkey have performed tests more than their populations. DEFINE USA: please write the United States of America. Response The USA has been defined. 22- In the \"Strengths and limitations\" section, However, there are a few limitations in our review. study or review? This will depend on your classification. Response Has been changed to “study”. 23- Although the number of confirmed, death, and subsequently recovered cases of... Confirmed what? Please make it clear. Response We removed subsequently to be clearer: “Although the number of confirmed, death, and subsequently recovered cases of COVID-19 have greatly reduced in the last quarter of 2022 in most Arab countries, further efforts to address the need to re-campaign on COVID-19 vaccines and raise awareness programs about boosters must be implemented”. Thank you for your valuable study."
}
]
},
{
"id": "223543",
"date": "11 May 2024",
"name": "Yasser Amer",
"expertise": [
"Reviewer Expertise Evidence-Based Healthcare",
"Clinical Practice Guidelines",
"Pediatrics and Child healthcare",
"Healthcare Informatics",
"Healthcare Quality and Safety",
"Healthcare services research",
"Improvement research",
"and Implementation research."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study represents a comprehensive and well-conducted follow-up and collection of COVID-19 data in 22 Arab countries for three consecutive years. The authors obtained accurate monthly data from the official websites of the Ministry of Health in each country in addition to verifying those against the data from the websites of the WHO, World COVID-vaccinations tracker, and Worldometer for COVID-19. The abstract, introduction, and methods were well written, clear, and appropriate to the research topic. I would like to suggest enriching the discussion with this subtitle: \"Implications for clinical practice and public health practice\". Here are some elements for the respected authors to consider as relevant to the study aim:-\nStrengthen Healthcare Infrastructure: Examples 1: Invest in healthcare infrastructure, including hospitals, clinics, and medical supplies, to ensure preparedness for future pandemics. Example 2: Enhance the capacity of healthcare systems to accommodate a surge in patients during emergencies. Improve Disease Surveillance: Example 1: Develop and maintain robust surveillance systems to detect and monitor infectious diseases promptly. Example 2: Enhance the sharing of data and information among Arab countries and with international health organizations. Promote Vaccination Campaigns: Example 1: Implement comprehensive and equitable vaccination campaigns to achieve herd immunity against COVID-19 and future infectious diseases. Example 2: Combat vaccine hesitancy through targeted public health messaging and education. Enhance Telemedicine and Digital Health: Example 1: Expand telemedicine and digital health services to improve access to healthcare and reduce the burden on in-person facilities. Example 2: Ensure the privacy and security of electronic health records and telemedicine platforms. Prepare for Variants: Example 1: Develop strategies to monitor and respond to emerging variants of concern, including the rapid adjustment of vaccines and therapeutics.Example 2: Invest in genomic sequencing capabilities for timely variant detection. Strengthen Public Health Messaging: Example 1: Enhance public health communication strategies to provide accurate and timely information to the public during health crises. Example 2: Address misinformation and disinformation through targeted campaigns. Invest in Research and Development: Example 1: Allocate resources for research into infectious diseases, epidemiology, and vaccine development to better prepare for future pandemics. Example 2: Foster collaboration between academia, industry, and public health agencies. Prepare for Healthcare Workforce Challenges: Example 1: Develop contingency plans for healthcare workforce shortages during health emergencies. Example 2: Support the mental health and well-being of healthcare workers. Improve International Collaboration: Example: Foster regional and international collaboration in disease surveillance, response, and research. Example 2: Participate in global initiatives to ensure equitable access to vaccines and treatments. Health Equity and Vulnerable Populations: Example 1: Prioritize health equity in policies and interventions, addressing disparities that affect vulnerable populations. Example 2: Ensure access to healthcare and social support for marginalized communities.\n\nThe following 4 articles below may be helpful in writing up or re-writing these points, if you agree on them, or additional points to be additional take-home messages for the readers.\nThese are 2 additional online resources:- 1- WHO’s response to COVID-19 in the Eastern Mediterranean Region Independent review by Dalberg Advisors February 2023 https://cdn.who.int/media/docs/default-source/evaluation-office/who-s-response-to-covid-19-in-the-emr---independent-review_february-2023_final.pdf?sfvrsn=130ab01a_3&download=true 2- Distributional Impacts of COVID-19 in the Middle East and North Africa Region: https://www.worldbank.org/en/region/mena/publication/distributional-impacts-of-covid-19-in-the-middle-east-and-north-africa-region#:~:text=The%20report's%20findings%20suggest%20a,and%20how%20many%20people%20work).\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "11610",
"date": "26 Jun 2024",
"name": "Nasar Alwahaibi",
"role": "Author Response",
"response": "We would like to express our gratitude to the reviewer for the positive feedback and valuable comments. Below are our detailed responses to the reviewer's queries. This study represents a comprehensive and well-conducted follow-up and collection of COVID-19 data in 22 Arab countries for three consecutive years. The authors obtained accurate monthly data from the official websites of the Ministry of Health in each country in addition to verifying those against the data from the websites of the WHO, World COVID-vaccinations tracker, and Worldometer for COVID-19. The abstract, introduction, and methods were well written, clear, and appropriate to the research topic. I would like to suggest enriching the discussion with this subtitle: \"Implications for clinical practice and public health practice\". Here are some elements for the respected authors to consider as relevant to the study aim:- Strengthen Healthcare Infrastructure: Examples 1: Invest in healthcare infrastructure, including hospitals, clinics, and medical supplies, to ensure preparedness for future pandemics. Example 2: Enhance the capacity of healthcare systems to accommodate a surge in patients during emergencies. Improve Disease Surveillance: Example 1: Develop and maintain robust surveillance systems to detect and monitor infectious diseases promptly. Example 2: Enhance the sharing of data and information among Arab countries and with international health organizations. Promote Vaccination Campaigns: Example 1: Implement comprehensive and equitable vaccination campaigns to achieve herd immunity against COVID-19 and future infectious diseases. Example 2: Combat vaccine hesitancy through targeted public health messaging and education. Enhance Telemedicine and Digital Health: Example 1: Expand telemedicine and digital health services to improve access to healthcare and reduce the burden on in-person facilities. Example 2: Ensure the privacy and security of electronic health records and telemedicine platforms. Prepare for Variants: Example 1: Develop strategies to monitor and respond to emerging variants of concern, including the rapid adjustment of vaccines and therapeutics. Example 2: Invest in genomic sequencing capabilities for timely variant detection. Strengthen Public Health Messaging: Example 1: Enhance public health communication strategies to provide accurate and timely information to the public during health crises. Example 2: Address misinformation and disinformation through targeted campaigns. Invest in Research and Development: Example 1: Allocate resources for research into infectious diseases, epidemiology, and vaccine development to better prepare for future pandemics. Example 2: Foster collaboration between academia, industry, and public health agencies. Prepare for Healthcare Workforce Challenges: Example 1: Develop contingency plans for healthcare workforce shortages during health emergencies. Example 2: Support the mental health and well-being of healthcare workers. Improve International Collaboration: Example: Foster regional and international collaboration in disease surveillance, response, and research. Example 2: Participate in global initiatives to ensure equitable access to vaccines and treatments. Health Equity and Vulnerable Populations: Example 1: Prioritize health equity in policies and interventions, addressing disparities that affect vulnerable populations. Example 2: Ensure access to healthcare and social support for marginalized communities. The following 4 articles below may be helpful in writing up or re-writing these points, if you agree on them, or additional points to be additional take-home messages for the readers. References Mandil A, Mabry R, Milani B, Nour M, et al.: Mapping of health innovations in response to the COVID-19 pandemic in Eastern Mediterranean and selected Arab Countries.East Mediterr Health J. 2022; 28 (2): 130-143 PubMed Abstract | Publisher Full Text 2. Alam Z, Mohamed S, Nauman J, Al-Rifai RH, et al.: Hesitancy toward vaccination against COVID-19: A scoping review of prevalence and associated factors in the Arab world.Hum Vaccin Immunother. 2023; 19 (2): 2245720 PubMed Abstract | Publisher Full Text Titi MA, Wahabi H, Elmorshedy H, Shata Z, et al.: Mental health impact of the first wave of COVID-19 pandemic on healthcare workers in 12 Arab countries.East Mediterr Health J. 2022; 28 (10): 707-718 PubMed Abstract | Publisher Full Text 4. Abid M, Gheraia Z, Abdelli H, Sekrafi H, et al.: COVID-19 pandemic and economic impacts in Arab countries: Challenges and policies. Research in Globalization. 2022; 5. Publisher Full Text These are 2 additional online resources:- 1- WHO’s response to COVID-19 in the Eastern Mediterranean Region Independent review by Dalberg Advisors February 2023 https://cdn.who.int/media/docs/default-source/evaluation-office/who-s-response-to-covid-19-in-the-emr---independent-review_february-2023_final.pdf?sfvrsn=130ab01a_3&download=true 2- Distributional Impacts of COVID-19 in the Middle East and North Africa Region: https://www.worldbank.org/en/region/mena/publication/distributional-impacts-of-covid-19-in-the-middle-east-and-north-africa-region#:~:text=The%20report's%20findings%20suggest%20a,and%20how%20many%20people%20work). Response As per the reviewer's suggestion, two paragraphs discussing the \"Implications for clinical practice and public health practice\" have been added to the discussion section. Consequently, more references have been added."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1448
|
https://f1000research.com/articles/12-790/v1
|
06 Jul 23
|
{
"type": "Systematic Review",
"title": "Effect of family-centered care interventions on well-being of caregivers of children with cerebral palsy: a systematic review",
"authors": [
"Deepalaxmi Paresh Poojari",
"Shashikiran Umakanth",
"G. Arun Maiya",
"Bhamini Krishna Rao",
"Sonia Khurana",
"Senthil Kumaran D",
"Radhika Attal",
"Marie Brien",
"Deepalaxmi Paresh Poojari",
"G. Arun Maiya",
"Bhamini Krishna Rao",
"Sonia Khurana",
"Senthil Kumaran D",
"Radhika Attal",
"Marie Brien"
],
"abstract": "Background: Caring for a child with long-term functional limitations can have a negative impact on the physical and psychological well-being of the caregiver. Family-centered care (FCC) interventions have the potential to empower caregivers and contribute to their well-being. This systematic review aimed to synthesize existing evidence on the effectiveness of FCC interventions in improving the well-being of caregivers of children with cerebral palsy (CP), and identify the key components of such interventions that are most commonly practiced and deemed effective. Methods: This review systematically searched seven databases for randomized controlled trials that evaluated the effectiveness of any FCC intervention on the well-being of caregivers of children with or at risk of CP. We used the Cochrane RoB 2.0 tool to assess risk of bias and Critical Appraisal Skills Programme (CASP) checklist for critical appraisal. Due to high heterogeneity of studies, narrative synthesis was used to summarize the data. Results: The review consists of 11 studies which were categorized into five sections based on the components of FCC intervention provided in each individual study: 1. Information provision, and Enabling and partnership (n= 5); 2. Information provision, and Respectful and supportive care (n= 1); 3. Enabling and partnership (n= 2); 4. Enabling and partnership, and Respectful and supportive care (n= 2); 5. Information provision, Enabling and partnership and Respectful and supportive care (n= 1). Risk of bias was low in four studies, unclear in two studies, and high in five studies. Conclusion: FCC interventions were found to be effective in improving caregivers’ satisfaction with attainment of child and caregiver goals. Evidence from multiple studies does not strongly support the effectiveness of FCC interventions on caregiver’s mental health, parenting and personal outcomes. Limited evidence precludes a conclusion on the effectiveness of the components of FCC on well-being of caregivers of children with CP.",
"keywords": [
"Developmental disability",
"family participation",
"Parent well-being",
"Physical health",
"Mental health",
"Parent-professional partnership",
"Parent education",
"Collaborative care"
],
"content": "Introduction\n\nFamily-centered care (FCC) approach holds fundamental importance to professional practice that conveys dignity and respect to families, information provision for informed decision-making, consideration of the family’s preferences and priorities, and collaborative partnerships between the provider and family.1 This approach may enable caregiver access to various healthcare services through education and counseling,2 support groups,3 information about their child’s condition,4 skill training,5 involvement in setting goals for their children,6 or establishing a strong caregiver-professional partnership.\n\nChildren with cerebral palsy (CP) may have a range of impairments that limit their daily activities such as mobility, self-care, communication, and participation, requiring special care services.7,8 Apart from their daily duties, caregivers take up multiple roles such as handling the medical, rehabilitation, and financial services, in an attempt to provide the best care for their child. Hence, caring for a child with CP demands adjustment in the caregiver’s lifestyle based on the child’s needs and impacts the caregiver’s personal, family, social, and financial well-being.9,10,11 Caring for a child with long-term functional limitations may affect the physical as well as the psychological well-being of the caregiver.12,13 Parents nurturing a child with CP often experience isolation, anxiety, and depression.14,15 Therefore, meeting the informational, resources, emotional, social, and monetary needs of the caregiver would be crucial to reduce their burden.16,17 Moreover, since children with CP require long-term multidisciplinary care, providing a continuum of care through a family-centered approach may be able to reduce the caregiver burden, enhance their capacities and empower them to care for their children.1,5 This will help improve health consequences for both children and their caregivers as well as facilitate their active participation in the community.18\n\nA review of systematic reviews on family-centered care interventions by Park et al. (2018),4 provided evidence of the benefits of family-centered care interventions on patients, families and healthcare professionals. However, this study pertained to varied patient populations. A systematic review of family-centered care for children with special healthcare needs by Kuhlthau et al. (2011) also found positive effects on health, family function and impact, satisfaction, and communication.2 However, there is a dearth of literature assessing the effectiveness of family-centered care interventions on the well-being of caregivers of children with CP. A comprehensive synthesis of the effectiveness of FCC is essential to provide reliable evidence to practitioners, researchers, and policymakers for the development of strategies for the implementation of care, and hence pave the way for the effective delivery of services to the CP community. Hence, the primary objective of this review was to synthesize evidence on the effectiveness of family-centered care interventions on the well-being of caregivers of children with CP. Realizing the importance of families as a resource in care delivery, it is crucial to identify the best way of empowering them, meeting their needs, and incorporating their participation in therapy. Therefore, our secondary objective was to identify the components of family-centered intervention that are commonly practiced and deemed to be most effective for caregiver well-being.\n\n\nMethods\n\nThis systematic review was conducted in accordance with the preferred reporting items for systematic reviews and meta-analyses 2020 (PRISMA) guidelines.19 The systematic review protocol was prospectively registered with PROSPERO (No. CRD42021233854) and can be accessed at https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021233854.\n\nSeven databases - Cochrane, Pubmed, Scopus, CINAHL Plus, EMBASE, Web of Science, and ProQuest - were searched from inception to 30th September 2022. A systematic search strategy (dataset 1 in Extended data) was used employing the PICO format using filters - Human and English.20 Furthermore, we examined the reference list of the included articles to identify any relevant articles for this review.\n\nRandomized controlled trials (RCTs) that assessed the effectiveness of the Family-centered approach on caregiver well-being, and conformed to our inclusion criteria were included. The population was limited to primary caregivers of age above 18 years, providing care for children with or at risk of CP at any severity (any level of GMFCS) and up to 18 years. However, studies that included caregivers who are not the primary caregiver of the child, with a diagnosed psychiatric illness, or have children with any other physical disability were excluded. Articles with children with multiple disabilities were excluded if authors failed to provide information and sub-group analysis for children with CP and their caregivers within two weeks of email request. Any intervention which is family driven or has the core components of family-centered care were included: Respectful and supportive care - Social or peer support groups; Information provision - Information sharing, caregiver education through direct education employing online presentation or guiding manual or web-based education, caregiver skill training, caregiver instructions; Co-ordinated and comprehensive care - Interdisciplinary communication, multidisciplinary approach or rehabilitation; Enabling and partnership - collaborative relationship with the caregivers, collaborative goal setting, joint/shared decision making, activity selection, ongoing evaluation, parent-professional partnership, parental advocacy.18 The last component ‘General information’ was not included as a part of FCC in this review as it often forms a part of usual care. Studies comparing the intervention to standard practice such as regular care advised by the paediatrician or other health professionals applied in any setting were included. Studies that reported any well-being outcomes related to caregivers such as quality of life, physical health and fitness, psychological health, satisfaction, family empowerment, adaptation, burden, and level of knowledge were primarily included. Secondary outcomes evaluating the health and well-being of children with CP were also noted but were not necessary for inclusion. All non-human studies and those not in the English language were excluded.\n\nData screening and selection were done using Rayyan software (alternative to Covidence or DistillerSR). Two reviewers (DP and RA) independently performed title and abstract, and full-text screening on Rayyan software. Any discord between the two reviewers was settled by consensus. If disagreement persisted, it was settled by team discussions with other researchers in this review (SK, SKD). Independent double data extraction was performed by two reviewers (DP and RA) using a data collection form prepared on Microsoft Word, and discrepancies were handled via discussions. The following data were extracted from each study: Basic study details- author, setting, study design, year of publication; sample size, eligibility criteria; Characteristics of caregivers - age, sex, education, occupation, type of family, socio-demographic details; Characteristics of children with CP - age, sex, type of CP, GMFCS level, MACS level; Intervention details using TIDieR checklist; Results of outcomes - outcome measures, time points, statistical analysis methods such as measures of mean, median, SD, interquartile range, confidence interval, effect size, p-value, and missing information. If effect size was not reported, wherever possible Cohen’s d was calculated.21 Other methods were also used to calculate effect size from odds ratio and median values.22,23 The corresponding authors were contacted for any missing or unclear information.\n\nAs there is a large disparity amongst the included studies in type and dose of intervention, and outcome measures, conducting a meta-analysis is not valid. Therefore, narrative synthesis was chosen to answer the objectives of this review. We classified the studies based on the components of family-centered care (as discussed under eligibility criteria) reflected in their interventions. An intervention may include more than one FCC component. Therefore, for the purpose of synthesis, studies with similar combinations of FCC domains will be combined, compared, and contrasted.\n\nTo assess the quality of the included studies, two reviewers (DP and RA) independently scored the risk of bias using the Cochrane ‘Risk of Bias 2’ (RoB 2) tool for randomized trials.24 Disagreements between reviewers were resolved through discussion or expert advice from a third reviewer (SK or SKD). Authors of studies were directly contacted if the target information was unreported or unclear. The studies were summarized as having low risk, some concern, or high risk of bias. For critically appraising the RCTs, CASP Randomised Controlled Trial Standard Checklist25 was scored independently by two reviewers (DP and RA). Any disagreements were solved via discussions or by involving a third reviewer (SK or SKD). No scoring system was used as recommended by the CASP checklist developers.\n\nA traffic light system was used to categorize the effectiveness of different outcome domains across the studies to summarize the effectiveness of FCC interventions on caregiver well-being and infant outcomes. Moderate to large effect sizes in a low/some concern risk of bias study were coded green. Small effect sizes in a low/some concerns risk of bias study, or moderate and large effect sizes in a high risk of bias study were coded yellow. No or negative effect was indicated via red colour. The green, yellow and red colour coding indicate advice for implementing the intervention in clinical practice as- effective, use with caution, and not effective respectively.\n\n\nResults\n\nThe database search yielded 1,544 studies, and an additional 12 articles were found through a secondary search. After removing 28 duplicates, 1,528 studies were screened for title and abstract eligibility, with 1,414 studies getting excluded. 114 articles underwent full-text examination, of which 99 articles were excluded for various reasons reported below. Out of the 15 articles included, n=7 studies were published as a single paper, and n=4 studies were published as eight papers. Therefore, 11 unique articles are included in this synthesis. The PRISMA Flow chart in Figure 1 depicts the results of the search process, and the PRISMA 2020 checklist is provided in data set 2 in Extended data.\n\n11 unique articles are included in this synthesis.\n\nAll the studies are randomized controlled trials, of which nine studies involved children with CP,6,26–33 one study involved infants at high risk of CP,34 and lastly, one study involved both children diagnosed or at high risk of CP.35 Three studies were located in Australia,29,32,34 and one each in the United Kingdom,33 Tanzania,26 Netherlands,35 Norway,31 Brazil,28 Iran,6 Canada,30 and Denmark.27 In two studies,29,32 the interventions directly targeted the caregivers while in the remaining studies, the interventions targeted the caregiver indirectly by focussing on improvement in child-related outcomes. The sample size in these studies varied from n= 21 to n= 118, for the parents and children with CP. Table 1 provides an overview of the characteristics of each study, while the TIDieR checklist (Extended data, dataset 3) details the interventions used in each trial. There was a lot of heterogeneity in the focus of interventions. Various caregiver well-being outcomes such as family needs, mental health, empowerment, parenting, satisfaction, quality of life, perception of family centeredness, or caregiver assistance, and child outcomes such as feeding, behaviour, motor or function were included. Dataset 4 in Extended data summarizes the description of outcome measures and intervention effectiveness.\n\nAccording to the Cochrane ROB 2.0 tool for RCTs, four RCTs had low ROB,6,28,29,31 two RCTs had some concerns,27,34 and five had a high ROB26,30,32,33,35 (Figure 2). As our review focussed on caregiver well-being, the majority of caregiver outcomes were patient-reported. Moreover, given the nature of the intervention, the caregivers could not have been blinded to the intervention, and by default that influenced the ROB grading. Therefore, the risk of bias domain assessing outcome assessor’s awareness of intervention and its influence on outcome was rated as ‘probably no’ to avoid categorizing as high-risk of bias on this specific basis. Table 2 represents the results of the CASP Randomised Controlled Trial Standard Checklist. The majority of the studies showed limitations in allocation concealment, investigator and participant blinding, and reporting adverse effects and costs of intervention.\n\nRisk of bias was low (green) in four studies,6,28,29,31 unclear (yellow) in two studies,27,34 and high (red) in five studies.26,30,32,33,35\n\nFigure 3 demonstrates the overall effect of FCC interventions on caregiver well-being using the traffic light system. FCC interventions are effective (green) in improving caregivers’ satisfaction with attainment of child and caregiver goals. Evidence from a single study indicates that FCC interventions should be used with caution (yellow) to improve family needs and feeding skills. There is inconclusive evidence on the quality of life. Lastly, FCC interventions are not effective (red) to improve caregiver’s mental health, personal outcomes such as empowerment, parenting skills, perception of family centeredness (except information provision about the child), and reduce caregiver assistance in daily activities.\n\nGreen: moderate to large effect sizes in a low/some concern risk of bias study. Yellow: small effect sizes in a low/some concerns risk of bias study, or moderate and large effect sizes in a high risk of bias study. Red: no or negative effect. *Green on only one domain of Measure of Processes of Care scale (information about child).\n\nSince the studies include different components of FCC in their interventions, the following section classifies the results based on the core components of family-centered care reflected in the studies. Only two studies incorporated only one FCC component- Enabling and partnership,30,31 whereas the remaining studies involved multiple FCC components in their intervention.26–29,32–35 The interventions targeted different needs of the caregiver such as social or informational support. Various modes of delivering the intervention such as online or offline platforms, actively through discussions, or passively through mailing child-related information reports were utilized.\n\nFive studies utilized these FCC components in their interventions.26–28,34,35 The results of these papers are also published in two secondary studies from the same sample.36,37 Two studies, Morgan et al. (2016)34 and Hielkema et al. (2020)35 involved infants at very high risk of CP ranging from 3 to 9 months corrected age. The intervention in one study34 followed the GAME principles (Goals, Activity and Motor Enrichment) whereas the other study35 followed COPCA principles (Coping with and Caring for infants with special needs). Both studies34,35 involved active caregiver learning through education and training for the caregivers to become independent in identifying infant’s movements and providing opportunities for motor task practice. Discussions and home programs directed towards a parent-identified goal were given.34 However, the control groups in both studies34,35 had some family involvement such as parental advice on positioning, handling, feeding, and developmental simulation.34\n\nImprovement was seen in caregiver satisfaction with attainment of goal at 12 months on the COPM (d=0.68).34 Surprisingly, both the studies did not show any improvement in parents’ mental health as measured on Depression Anxiety and Stress Scale (DASS-21)34 and Nijmeegse Ouderlijke Stress Index questionnaire, short version (NOSI-K)35 respectively. However, in the study by Hielkema et al. (2020), significant improvement was seen in caregivers' quality of life (d=0.46) and Infant and Toddler Quality of Life Questionnaire-parent concepts (ITQOL) (impact emotional: d=0.55, impact time: d=0.68) post-intervention.35 No difference was seen in family empowerment and coping mechanisms. With respect to child outcomes, one study showed significant improvement in motor skills at 16 weeks and 12 months on PDMS-2 (d=0.09 and 0.31 respectively), GMFM (d=0.20), cognitive skills at 12 months on BSID-III (d=0.42), and on COPM performance at 16-weeks (d=0.25).34 In contrast, the other study found no significant difference in infant motor, cognitive, behaviour, function outcomes, and quality of life (except general health perceptions d=0.62) as compared to the control group.35\n\nThree studies involved children diagnosed with CP ranging from age 1-12 years.26–28 All three studies involved caregiver education to facilitate a specific function- improve nutrition and feeding skills,26 become informed about the child’s treatment for gait impairments,27 and facilitate the child’s motor tasks respectively.28 Two studies had active parent involvement via multiple modes of delivering education,26 and caregiver participation in goal setting and practice of functional activities.28 In contrast, the study by Fonvig et al. (2020) only provided the information passively by mailing the instrumented gait-analysis report.27 The control group in one study received general health education for parents,26 whereas another study involved multidisciplinary health professionals collaboration.27\n\nThe study by Mlinda et al. (2018) showed improvement in caregiver feeding skills such as positioning, feeding speed, and feeding support with effect size 0.92, 0.91, 0.69 respectively, and stress (effect size=0.5).26 The study by Fonvig et al. (2020) showed no improvement in any domain of the MPOC-20.27 The study by Saquetto et al. (2018) showed a large effect in the caregiver assistance required for self-care (ES=5.11) and mobility functions (ES=7.37) on the Pediatric Evaluation of Disability Inventory (PEDI) post-intervention.28 These interventions improved child’s mood (d=0.62),26 gross motor function (η2=0.145, large effect),27 and self-care skills (Effect size=2.18, large effect).28\n\nOnly one study by Whittingham et al. (2022)29 was included in this category. In this study, an online/telehealth intervention to support the caregivers in positive parenting was delivered using online presentations, activities, and discussion. The intervention showed significant improvement at post-intervention (10 weeks) in non-intrusiveness (d=0.14) and child involvement (d=0.19) on the Emotional Availability Scale, in child involvement (d=0.28) as seen by the Emotional Availability Self Report, and in mindfulness during parenting (d=0.17) using the Interpersonal Mindfulness in Parenting Scale. Parents also reported improvement in acceptance of the child’s CP diagnosis (d=0.64), seeking support (d=0.08), maintaining social connections (d=0.45), and meaningful living (d=0.47) post-intervention and at six months follow up. However, no intervention effect was seen on parent mental health and well-being as measured using the standard outcome measures- the Depression Anxiety and Stress Scale (DASS), the Personal Wellbeing Index (PWI), or the Acceptance and Action Questionnaire (AAQ). With respect to child outcomes, the intervention significantly improved the quality of life in domains of social well-being and acceptance (d=0.08) and participation and physical health subscale (d=0.31) on the Cerebral Palsy Quality of Life scale (CPQOL). However, no intervention effect was seen on child behaviour and adjustment.\n\nTwo studies were found in this category.30,31 The results of a paper by Myrhaug et al. (2018) were also published in one secondary study from the same sample.38 The two studies focussed on children diagnosed with CP utilized collaborative goal setting but differed in the level of parent involvement in therapy. Law et al. (2011)30 involved the parents to identify constraints affecting their child's performance. Conversely, in the study by Myrhaug et al. in 2018,31 parents were not involved in therapy during the conductive education (CE) courses, while the control group participated in conventional practice with parental involvement.\n\nIn the study by Law et al. (2011),30 the intervention group showed a small intervention effect on the PEDI Caregiver assistance-mobility sub-scale at 9 months follow-up but no improvement was seen in family empowerment.30 In the study by Myrhaug et al. (2018),31 a large effect was seen on receiving more ‘specific information about their child’ on the Measure of Processes of Care scale (MPOC-20) at follow-up (d=1.47). No difference was seen in their global quality of life. With respect to the child outcomes, both the studies did not show any difference in gross motor function, functional skills, preschool participation, and children’s quality of life post-intervention as compared to the control group30,31,38\n\nTwo studies were found in this category.32,33 The results of a paper were also published in one secondary study from the same sample.39 Both studies provided support to the parents by targeting their needs- needs identified using the family needs scale,33 and positive parenting for child’s behavioural problems.32 The study by Weindling et al. (2007) involved joint decision-making between the family support worker and the caregiver to target the needs.33 The study by Whittingham et al. (2014) involved Stepping Stones Triple P (SSPT-only) intervention that involved a partnership between the therapist and parent for collaborative goal setting, discussions, and various strategies for positive parenting.32 Another intervention group, SSPT + ACT group (Acceptance and Commitment Therapy) provided additional support to the parents to build their psychological flexibility via goal setting and various exercises.32\n\nThe study by Weindling et al. (2007)33 did not show improvement in stress (measured on Parent Stress Index) whereas the SSTP+ ACT group in the study by Whittingham et al. (2014)32 showed a medium effect in depression (d=0.74) and stress (d=0.79) measured on the Depression Anxiety Stress subscales. Both the studies met caregiver needs as seen by a significant reduction in the Family Needs Scale (FNS) at 18 months follow up (p = 0.001, effect size=–12.0) (but not post-intervention)33 and change in parenting style (reduced overreactivity (d=1.1) and verbosity (d=0.93)).32 The SSTP + ACT group32 showed improvements in child behaviour and emotional problems (ECBI problem d=1.32, ECBI intensity d=0.79, SDQ emotions d=0.16), child hyperactivity (d=0.21), child functional performance in the mobility domain (d=0.03), child quality of life in functioning (d=0.51) and social domains (d=0.64). In the SSTP-only group,32 improvements were seen in child behaviour problems and emotional symptoms.32\n\nOnly one study was included in this category.6 The study by Kahjoogh et al. (2019)6 involved children diagnosed with CP, in the age group of 5-11 years, from all GMFCS levels. Goal setting was done for all caregivers using the COPM (one goal for themselves and two goals for their child) prior to randomization. The caregivers were coached based on the principles of Occupational performance coaching (OPC), from understanding the current scenario, planning actions, analysing performance and problem-solving to achieve the goal. Emotional support was also provided by intentionally listening to the caregivers and providing guidance and encouragement. Information was imparted in consideration of the parent’s experiences as per the principles of OPC. The intervention was given once per week, for 10 weeks or till the goal was achieved. The control group that received conventional therapy, mainly NDT, reported having parent training to move and position their children at home.\n\nThe intervention showed a significant and large effect on overall COPM performance and satisfaction scores (η2 p=0.41 and 0.38 respectively), on individual mother-related performance and satisfaction scores (η2 p =0.25 and 0.33 respectively), and on child-related (η2 p=0.35 and 0.41 respectively) performance and satisfaction scores. Also, a large and significant increase was seen in the caregiver’s self-efficacy (η2 p =0.7) measured using the Sherer general self-efficacy scale.\n\n\nDiscussion\n\nThis systematic review aimed to identify the effectiveness of family-centered interventions on the well-being of caregivers of children with CP. We identified 11 unique randomized controlled trials6,26–35 to address our objectives. Additionally, we stratified the studies according to the various components of family-centered care in their interventions to identify the impact of these components on the caregiver well-being outcomes. Our review also analysed the effect of FCC interventions on child-related outcomes. We found that family centered care interventions are effective to improve caregivers’ satisfaction with attainment of child and caregiver goals. However, evidence from multiple studies does not strongly support the effectiveness in improving caregiver’s mental health, personal, and parenting skills. Limited evidence in other caregiver outcomes suggests caution in effectiveness of FCC interventions in addressing family needs, and improving feeding skills and quality of life. These results emphasize the need for more interventional studies which are aimed directly at caregivers’ well-being. The following sections will discuss the studies based on the FCC components in their intervention.\n\nThe interventions targeting infants at high risk of CP34,35 allowed caregivers to become informed and actively participate in promoting their infant’s development during daily activities, showing improvement in caregiver satisfaction with goals. The lack of improvement in stress may be because caregivers with CP have a high burden and multiple sources of stress apart from the caregiving responsibilities such as balancing family and work, and financial burdens.10 Moreover, it proved to be successful for infant outcomes in spite of having a greater severely affected population. On the contrary, even though the study by Hielkema et al. (2020)35 had a longer intervention duration of one year, no difference was seen in infant outcomes. The influence on caregiver outcomes cannot be relied on as NOSI-K and ITQOL are inappropriate outcome measures for this age group. Moreover, a very small sample size and caregiver dropouts introduced a selection bias underpowering our ability to rely on these findings. With respect to studies on children with CP, all outcomes mentioned in the study by Mlinda et al. (2018)26 were binary, non-standard and no clear information was given about them, therefore the results should be interpreted with caution. No improvement in perception of family-centered care was observed in the study by Fonvig et al. (2020)27 as the intervention was delivered passively by mail, with no additional help to understand or translate the information to care.\n\nOverall, no improvement was seen in caregiver stress34,35 except on a non-standardized outcome measure.26 As only one study assessed the effect on quality of life, family empowerment, perception of FCC, caregiver assistance in function, and satisfaction, there is limited evidence to draw a definite conclusion. There is conflicting evidence on the effectiveness of FCC intervention for motor and cognitive outcomes of high-risk infants.34,35\n\nThe intervention by Whittingham et al. (2022)29 modified parent behaviour. The lack of effect on mental health should be considered with caution as parents had normal mental health at baseline. Little improvement was observed in child behaviour problems. Therefore, additional interventions targeting the child behaviour may be necessary in conjunction with parent-focussed interventions. However, as only one study is present in this domain, we cannot conclude if interventions utilizing ‘Information provision’ and ‘Respectful and supportive care’ improved caregiver well-being.\n\nThe two studies incorporated collaborative goal setting with the parents.30,31 In the study by Law et al. (2011)30 both intervention and control groups showed improvement in child outcomes and family empowerment, indicating no additional benefits of context focussed FCC intervention. Conversely, in the study by Myrhaug et al. (2018),31 no effect was seen on caregiver’s quality of life and child outcomes. The low sample size, with 50% children belonging to higher disability (GMFCS levels IV and V), and large amounts of conventional therapy in the control group may have diluted the effects. A review on conductive education found inconclusive evidence of its effectiveness due to a lack of quality studies.40 However, positive findings on provision of information for parents on MPOC could be attributed to the availability of many opportunities for informally meeting with the conductor to discuss the child during the conductive education program. Hence, this highlights the power of providing continuous information to the parents about the child’s condition and development during therapy sessions.\n\nOverall, due to varied outcomes, limited evidence exists to draw definitive conclusions on the effectiveness of FCC interventions on caregiver assistance in function activities, family empowerment, perception of FCC, and quality of life. Moreover, no improvement was observed on any child outcomes.\n\nThe improvement in family needs in the study by Weindling et al. (2007) study33 must be accepted with caution due to reduced sample size at 18 months follow-up, especially due to withdrawal of participants with a higher Family Needs score from the intervention group. The family support workers were parents of children with CP who underwent a short training course by a psychologist. They could have identified the caregiver’s needs, however professional support or actively identifying support resources may be required by the parents to meet their enormous and specific needs and actually reduce their stress as seen in a study exploring social support for caregivers of children with chronic diseases.41 The family support workers helped in making the decisions, whereas in the study by Whittingham et al. (2014),32 more active support is given to the caregivers such as the practice of beneficial strategies. The improvement in child behaviour and emotional problems may have resulted in reduced depression and stress. Child behavioural problems to be an important predictor for caregivers’ physical and psychological health, and advancement in child behaviour was associated with a better ability to handle stress and higher self-perception.7\n\nOverall, both studies provided support to caregivers, but evidence on the effectiveness of FCC components in reducing stress and depression is conflicting. Only one study showed improvement in child behaviour outcomes and quality of life.32\n\nIn the study by Kahjoog et al. (2019), the specific goals chosen by the caregivers for themselves and the child were addressed by the therapists in the intervention group.6 The intervention process worked in collaboration with the caregivers at all stages-goal setting, analysing performance, and problem-solving to identify treatment solutions. This active involvement of the caregivers in goals chosen by them may have motivated them to work on the goals, and hence, explains the improvement in self-efficacy and COPM scores. Caregivers’ feeling of mastery over a caregiving situation and higher self-esteem predicts better psychological health.7 However, the effect on children's outcomes is unknown. We witness parent involvement in the control group again highlighting their active role in conventional therapy.\n\nAs only one study6 was included in this domain, we cannot conclude if interventions utilizing ‘Information provision’, ‘Enabling and partnership’, and ‘Respectful and supportive care’ improved caregiver well-being.\n\nNo studies were found that compared the FCC component- ‘Co-ordinated and comprehensive care’ to a control group. The family support worker in addition to physiotherapists in the study by Weindling et al. (2007)33 cannot be considered as multidisciplinary care as they are parents of children with CP, not health professionals. It is interesting to observe that five studies involved two to four healthcare professionals working as a team in either intervention or control groups such as physical and occupational therapists26,34 or neuro-paediatrician, paediatric orthopaedic surgeon, physiotherapist, and a biomechanist.27 This brings to light the established importance of multidisciplinary care for children with CP.\n\nOverall, ten studies incorporated the Enabling and partnership component,6,26–28,30–35 seven had Information provision,6,26–29,34,35 and four had a Respectful and supportive care component.6,29,32,33 To address our second objective, Enabling and partnership was the most practiced FCC component. Most family-centered interventions aimed to establish a collaborative relationship with parents, involving them in goal-setting, and capacity-building. These interventions sought to empower the parents to provide independent care for their children, particularly in terms of functional activities at home. However, due to the limited studies and absence of a meta-analysis, we cannot identify which combined FCC components would be most effective for caregiver well-being.\n\nIt is interesting to note that even though multiple studies utilized the same FCC component, the delivery of intervention varied. For example, utilizing information materials, discussions, and practical exercises to educate,32 vs. passively mailing the information report to the caregivers.27 Another example would be involving caregivers in goal setting,31 vs. involving them in the therapy activities as well.6 Therefore, the mode of delivering the intervention may also influence the intervention effects.\n\nResearch has reported the negative effects of caregiving on carers’ physical health such as fatigue, poor sleep, and musculoskeletal pain.42 However, it is interesting to observe that none of the studies explored the effect of FCC interventions on caregivers’ physical health. This represents a significant gap in the literature and highlights the need for future research to explore this important area.\n\nConventional therapy cannot be carried out without involving the parents or family. The control group in multiple studies6,26,31,34,35 also had some degree of parent involvement which could not be excluded as they were a part of the ‘usual care’. Parent involvement varied from education to involvement in therapy sessions or practice of functional activities at home as a home program. We realize that as the primary support system and an essential part of a child’s environment, it is natural for the family to participate in therapy. Moreover, as children with CP require intensive therapy and substantial practice, conventional therapy may have increased parent involvement.\n\nThis review has several strengths and limitations that should be considered. One strength is that we included all studies that reported caregiver outcomes, regardless of whether they also reported infant outcomes. However, studies that only reported infant outcomes without caregiver outcomes were excluded. Therefore, this systematic review does not provide a complete picture of the effect of FCC interventions on infant outcomes. However, this was not our objective and was clearly stated in our eligibility criteria. A meta-analysis could not be conducted due to the heterogeneity of the included studies, and thus we cannot provide a definite summary of the effectiveness of FCC interventions on caregiver well-being. Moreover, as caregiver well-being was our primary outcome, most of the outcomes were participant reported. This introduces some amount of bias as blinding of caregivers is not possible in such cases. Additionally, studies that were not randomized controlled trials, and those published in languages other than English were excluded, which may have resulted in relevant information being missed. However, to the best of our knowledge, only one study was excluded on the basis of language.\n\nCore components of FCC that include active interventions are more effective for caregiver well-being than passive interventions. Therefore, healthcare professionals should consider designing interventions that involve active parent engagement. Additionally, providing continuous information to the parents about the child’s condition and development during the therapy sessions is a useful way to deliver information. Thus, health professionals should prioritize educating the parents on their child’s condition, development, and handling during therapy visits to ensure a continuum of updates.\n\nFuture research should aim to conduct high-quality RCTs with larger sample sizes to better identify the effectiveness of FCC interventions. Future RCTs assessing the effectiveness of FCC interventions need to explore the interventional elements in the control group and clarify the extent of parent involvement. Studies should explore how best they can standardize the control group in an RCT to truly identify the benefits of family-centered interventions. Studies can also explore the effectiveness of different modes of parent participation in family centered care interventions. Further, larger sample sizes are required considering the higher dropout seen in multiple studies. Moreover, future studies should investigate the effect of FCC interventions on caregivers’ physical health and perform a cost analysis to identify the financial burden of these interventions. RCTs should carefully select appropriate outcome measures designed for age and diagnosis, and limit the outcome measures to include the most essential ones to avoid study burden and potential dropouts.\n\n\nConclusion\n\nDespite the many challenges faced by caregivers of children with CP, there are limited FCC interventions that are directly focussed on their well-being. The eleven reviewed studies vary greatly in sample size, interventions focus, dose, theoretical basis, and outcomes, making it difficult to draw concrete conclusions on the effectiveness of FCC interventions on caregiver well-being. However, it can be inferred that FCC interventions are effective in improving caregivers’ satisfaction with attainment of child and caregiver goals. Evidence from multiple studies does not strongly support the effectiveness in improving caregiver’s mental health, personal, and parenting skills. They should be used with caution in addressing family needs, and improving feeding skills and quality of life. Limited evidence and overlap of FCC core components in individual studies precludes a conclusion on the effectiveness of distinct FCC components on the well-being of caregivers of children with CP. However, it is clear that active engagement interventions are more effective for caregiver well-being compared to passive interventions. Establishing active partnerships with caregivers are best to address their needs and priorities.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: Search Strategy for “Effect of family centered care interventions on well-being of caregivers of children with cerebral palsy: a systematic review”. Data file 1: Search Strategy. https://doi.org/10.6084/m9.figshare.22344664.v1. 43\n\nFigshare: Intervention details using TIDieR checklist for “Effect of family centered care interventions on well-being of caregivers of children with cerebral palsy: a systematic review”. Data file 3: Intervention details using TIDieR checklist. https://doi.org/10.6084/m9.figshare.22344670.v1. 44\n\nFigshare: Description of outcome measures and results of intervention effectiveness for “Effect of family centered care interventions on well-being of caregivers of children with cerebral palsy: a systematic review”. Data file 4: Description of outcome measures and results of intervention effectiveness. https://doi.org/10.6084/m9.figshare.22344667.v1. 45\n\nFigshare: PRISMA 2020 checklist for “Effect of family centered care interventions on well-being of caregivers of children with cerebral palsy: a systematic review”. Data file 2: PRISMA 2020 checklist. https://doi.org/10.6084/m9.figshare.22344724.v1. 46\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nWe acknowledge the effort of all authors of the RCTs included in our review. We thank Mrs. Savni Apte, PhD student at Manipal Academy of Higher Education, with her permission for helping us formulate the search strategy for this review.\n\n\nReferences\n\nKing G, Chiarello L: Family-Centered Care for Children With Cerebral Palsy: Conceptual and Practical Considerations to Advance Care and Practice. J. Child Neurol. 2014 Aug; 29(8): 1046–1054. Publisher Full Text\n\nKuhlthau KA, Bloom S, Van Cleave J, et al.: Evidence for Family-Centered Care for Children With Special Health Care Needs: A Systematic Review. Acad. Pediatr. 2011 Mar; 11(2): 136–143.e8. PubMed Abstract | Publisher Full Text\n\nZuurmond M, Nyante G, Baltussen M, et al.: A support programme for caregivers of children with disabilities in Ghana: Understanding the impact on the wellbeing of caregivers. Child Care Health Dev. 2019 Jan; 45(1): 45–53. Publisher Full Text\n\nPark M, Giap TTT, Lee M, et al.: Patient- and family-centered care interventions for improving the quality of health care: A review of systematic reviews. Int. J. Nurs. Stud. 2018 Nov; 87: 69–83. Publisher Full Text\n\nBarlow JH, Powell LA, Gilchrist M, et al.: The effectiveness of the Training and Support Program for parents of children with disabilities: A randomized controlled trial. J. Psychosom. Res. 2008 Jan; 64(1): 55–62. 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PubMed Abstract | Publisher Full Text\n\nVadivelan K, Sekar P, Sruthi SS, et al.: Burden of caregivers of children with cerebral palsy: an intersectional analysis of gender, poverty, stigma, and public policy. BMC Public Health. 2020 Dec; 20(1): 645. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDavis E, Shelly A, Waters E, et al.: The impact of caring for a child with cerebral palsy: quality of life for mothers and fathers. Child Care Health Dev. 2010 Jan; 36(1): 63–73. Publisher Full Text\n\nChambers HG, Chambers JA: Effects of Caregiving on the Families of Children and Adults with Disabilities. Phys. Med. Rehabil. Clin. N. Am. 2015 Feb; 26(1): 1–19. Publisher Full Text\n\nMasefield SC, Prady SL, Sheldon TA, et al.: The Caregiver Health Effects of Caring for Young Children with Developmental Disabilities: A Meta-analysis. Matern. Child Health J. 2020 May; 24(5): 561–574. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOgwumike O, Adeniyi F, Obidiegwu C: Psychosocial impact of caring for children with cerebral palsy on the family in a developing country. J. Pediatr. Neurol. 2015 Jul 30; 10(02): 117–124.\n\nDavis AO, Olagbegi OM, Orekoya K, et al.: Burden and quality of life of informal caregivers of children with cerebral palsy. Rev. Rene. 2021 May 3; 22: e61752. Publisher Full Text\n\nMohd Nordin NA, Hui Shan E, Zanudin A: The Unmet Needs of Parents of Highly Dependent Children with Cerebral Palsy. IJERPH. 2019 Dec 16; 16(24): 5145. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEloreidi RMD, Kehyayan V, Kalu F, et al.: Needs of caregivers of children with cerebral palsy: A literature review. JNEP. 2021 May 6; 11(9): 23. Publisher Full Text\n\nKing S, Teplicky R, King G, et al.: Family-Centered Service for Children With Cerebral Palsy and Their Families: A Review of the Literature. Semin. Pediatr. Neurol. 2004 Mar; 11(1): 78–86. PubMed Abstract | Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021 Mar 29; n71.\n\nSchardt C, Adams MB, Owens T, et al.: Utilization of the PICO framework to improve searching PubMed for clinical questions. BMC Med. Inform. Decis. Mak. 2007 Dec; 7(1): 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLakens D: Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs. Front. Psychol. 2013 [cited 2023 Feb 25]; 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSánchez-Meca J, Marín-Martínez F, Chacón-Moscoso S: Effect-Size Indices for Dichotomized Outcomes in Meta-Analysis. Psychol. Methods. 2003; 8(4): 448–467. Publisher Full Text\n\nWan X, Wang W, Liu J, et al.: Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Med. Res. Methodol. 2014 Dec; 14(1): 135. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSterne JAC, Savović J, Page MJ, et al.: RoB 2: a revised tool for assessing risk of bias in randomised trials. BMJ. 2019 Aug 28; l4898. Publisher Full Text\n\nLong HA, French DP, Brooks JM: Optimising the value of the critical appraisal skills programme (CASP) tool for quality appraisal in qualitative evidence synthesis. Research Methods in Medicine & Health Sciences. 2020 Sep; 1(1): 31–42. Publisher Full Text\n\nMlinda SJ, Leyna GH, Massawe A: The effect of a practical nutrition education programme on feeding skills of caregivers of children with cerebral palsy at Muhimbili National Hospital, in Tanzania. Child Care Health Dev. 2018 May; 44(3): 452–461. PubMed Abstract | Publisher Full Text\n\nFonvig CE, Rasmussen HM, Overgaard S, et al.: Effectiveness of instrumented gait analysis in interdisciplinary interventions on parents’ perception of family-centered service and on gross motor function in children with cerebral palsy: a randomized controlled trial. BMC Pediatr. 2020 Dec; 20(1): 411. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaquetto MB, de Santana BA , da Silva BC , et al.: Addition of an educational programme for primary caregivers to rehabilitation improves self-care and mobility in children with cerebral palsy: a randomized controlled trial. Clin. Rehabil. 2018 Jul; 32(7): 878–887. PubMed Abstract | Publisher Full Text\n\nWhittingham K, Sheffield J, Mak C, et al.: Parenting Acceptance and Commitment Therapy: An RCT of an online course with families of children with CP. Behav. Res. Ther. 2022 Aug; 155: 104129. PubMed Abstract | Publisher Full Text\n\nLaw MC, Darrah J, Pollock N, et al.: Focus on function: a cluster, randomized controlled trial comparing child- versus context-focused intervention for young children with cerebral palsy: Child- or Context-Focused Intervention for CP. Dev. Med. Child Neurol. 2011 Jul; 53(7): 621–629. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMyrhaug HT, Odgaard-Jensen J, Østensjø S, et al.: Effects of a conductive education course in young children with cerebral palsy: A randomized controlled trial. Dev. Neurorehabil. 2018 Nov 17; 21(8): 481–489. PubMed Abstract | Publisher Full Text\n\nWhittingham K, Sanders M, McKinlay L, et al.: Interventions to Reduce Behavioral Problems in Children With Cerebral Palsy: An RCT. Pediatrics. 2014 May 1; 133(5): e1249–e1257. PubMed Abstract | Publisher Full Text\n\nWeindling A, Cunningham C, Glenn S, et al.: Additional therapy for young children with spastic cerebral palsy: a randomised controlled trial. Health Technol. Assess. 2007 May [cited 2023 Feb 25]; 11(16). PubMed Abstract | Publisher Full Text\n\nMorgan C, Novak I, Dale RC, et al.: Single blind randomised controlled trial of GAME (Goals - Activity - Motor Enrichment) in infants at high risk of cerebral palsy. Res. Dev. Disabil. 2016 Aug; 55: 256–267. PubMed Abstract | Publisher Full Text\n\nHielkema T, Boxum AG, Hamer EG, et al.: LEARN2MOVE 0–2 years, a randomized early intervention trial for infants at very high risk of cerebral palsy: family outcome and infant’s functional outcome. Disabil. Rehabil. 2020 Dec 17; 42(26): 3762–3770. PubMed Abstract | Publisher Full Text\n\nRasmussen HM, Pedersen NW, Overgaard S, et al.: Gait analysis for individually tailored interdisciplinary interventions in children with cerebral palsy: a randomized controlled trial. Dev. Med. Child Neurol. 2019 Oct; 61(10): 1189–1195. PubMed Abstract | Publisher Full Text\n\nHielkema T, Hamer EG, Boxum AG, et al.: LEARN2MOVE 0–2 years, a randomized early intervention trial for infants at very high risk of cerebral palsy: neuromotor, cognitive, and behavioral outcome. Disabil. Rehabil. 2020 Dec 17; 42(26): 3752–3761. PubMed Abstract | Publisher Full Text\n\nMyrhaug HT, Odgaard-Jensen J, Jahnsen R: The long-term effects of conductive education courses in young children with cerebral palsy: a randomized controlled trial. Dev. Neurorehabil. 2019 Feb 17; 22(2): 111–119. PubMed Abstract | Publisher Full Text\n\nWhittingham K, Sanders MR, McKinlay L, et al.: Parenting Intervention Combined With Acceptance and Commitment Therapy: A Trial With Families of Children With Cerebral Palsy. J. Pediatr. Psychol. 2016 Jun; 41(5): 531–542. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnttila H, Suoranta J, Malmivaara A, et al.: Effectiveness of Physiotherapy and Conductive Education Interventions in Children with Cerebral Palsy: A Focused Review. Am. J. Phys. Med. Rehabil. 2008 Jun; 87(6): 478–501. Publisher Full Text\n\nYang J, Lin L, Gao Y, et al.: Interventions and strategies to improve social support for caregivers of children with chronic diseases: An umbrella review. Front. Psych. 2022 Sep 23; 13: 973012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThrush A, Hyder A: The neglected burden of caregiving in low- and middle-income countries. Disabil. Health J. 2014 Jul; 7(3): 262–272. PubMed Abstract | Publisher Full Text\n\nAttal R: Data file 1. Search Strategy.docx. [Dataset]. figshare. 2023. Publisher Full Text\n\nAttal R: Data file 3. Intervention details using TIDieR checklist.docx. [Dataset]. figshare. 2023. Publisher Full Text\n\nAttal R: Data file 4. Description of outcome measures results of intervention effectiveness.docx. [Dataset]. figshare. 2023. Publisher Full Text\n\nAttal R: Data file 2. PRISMA 2020 checklist. [Dataset]. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "187453",
"date": "31 Aug 2023",
"name": "Tanya Tripathi",
"expertise": [
"Reviewer Expertise Physiotherapy and early intervention"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis systematic review aimed to assess the effectiveness of family-centered care (FCC) interventions in improving the well-being of caregivers of children with cerebral palsy. The review included 11 studies, which were grouped into five sections based on the components of FCC intervention provided in each study. The review highlights the potential benefits of FCC interventions for caregivers but also underscores the need for further research in this area. Overall, the review is promising, and the methods are scientifically sound. Below are a few suggestions for the authors to improve their reporting of results.\nFirstly, consider tightening the results section to focus specifically on the primary and secondary objectives of the study, which are assessing caregiver well-being and identifying effective intervention components. It would be beneficial to include outcomes measures and results in Table 1 for each included study.\nSecondly, provide further explanation for the lack of effect on mental health outcomes, considering that parents had normal mental health at baseline. This clarification will help readers better understand the results.\nLastly, either remove information on child outcomes from the results section, as it was not part of the study's objectives, or reword the objectives to include the intention to report on child outcomes. This will enhance the clarity of the study's goals and findings.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "11490",
"date": "21 Jun 2024",
"name": "Deepalaxmi Paresh Poojari",
"role": "Author Response",
"response": "Response to Reviewers Reviewer one - Dr Tanya Tripathi Comment (C)1. \"Firstly, consider tightening the results section to focus specifically on the primary and secondary objectives of the study, which are assessing caregiver well-being and identifying effective intervention components. \" Response(R)1.Thank you for the suggestion. We have modified our objective statement to state that outcomes for children with CP will also be included, as it is our secondary objective. We have clubbed \"Effect on caregiver well-being\" and \"Components of FCC\" as our primary objective and \"Effect on children\" as a secondary objective. The same has been clarified in our eligibility criteria and limitations. We have highlighted the same in yellow. C2.\"It would be beneficial to include outcome measures and results in Table 1 for each included study.\" R2. We value your suggestion. However, we will not be able to incorporate outcome measures in Table 1, as there are huge data sets with multiple outcome measures in each study. Please note the outcome measures and results are presented in Data File 4. C3. \"Secondly, provide further explanation for the lack of effect on mental health outcomes, considering that parents had normal mental health at baseline. This clarification will help readers better understand the results.\" R3. Thank you for your suggestion. We have incorporated the changes highlighted in green in the manuscript. C4. \"Lastly, either remove information on child outcomes from the results section, as it was not part of the study's objectives or reword the objectives to include the intention to report on child outcomes. This will enhance the clarity of the study's goals and findings.\" R4. We appreciate your comment and we have clarified it in the objectives. Reviewer two - Dr Suruliraj Karthikbabu Comment (C)1. The authors conducted a systematic review of family-centered care (FCC) interventions on the well-being of caregivers of children with cerebral palsy. They concluded that FCC interventions were effective in improving caregivers’ satisfaction with the attainment of child and caregiver goals, but not for the caregiver’s mental health, parenting and personal outcomes. Response (R)1.Thank you for highlighting the important results of the study. C2. In the introduction, the authors stated how caring for a child with long-term functional disability affects both the physical and psychological well-being of the caregiver, warranting a systematic review to understand the benefits of FCC on multiple variables. The authors stated that there is a dearth of literature assessing the FCC on the well-being of caregivers of children with CP. Instead, the authors can elaborate on a diversity of such interventions limiting healthcare professions to choose a specific FCC. R2. Thank you for your suggestion. We have added the following statement in the introduction: ''There is also a scarcity of RCTs which have implemented the Universal model of FCC considering the core components of FCC and there is a need for evidence to understand the specific core components of FCC.\" C3. Search strategies are appropriate and were conducted in seven databases between inception and September 2022. The authors may check if there are any new papers published during the last 18 months. I believe the authors can perform it by the “year” filter and the search-strategy thread. R3. Thank you for suggesting this. We have completed an additional review between September 2022 and April 2024 and have included five new articles in the review. All the data sets have been modified accordingly and are highlighted in yellow and the reference DOI has been provided. C4. Eligibility criteria, data screening and extraction, and quality assessment sections are well explained. R4. Thank you for this acknowledgement. C5 “Risk of Bias 2”, CASP checklist and traffic light system are useful and so are the tables and figures. R5. Thank you, we appreciate this recognition of our work. C6. Since caregiver-reported measures are taken in many studies, assessor bias is unavoidable. R6. Yes, we do agree with this. C7.Please share your thoughts on caregivers' burden on looking after younger versus older children with CP R7. In the present study, children with CP were between the ages of 3 months and 16 years. Information needs may have differed for caregivers of younger children, children who had been recently diagnosed with or at risk of CP, or children above 16 years of age who might have gotten used to the entire care system. The craving for child-specific information may be greater in caregivers of younger children than in older children. C8. Five studies are reporting “information provision’ and ‘enabling and partnership’, providing limited evidence on the said parameters. R8.We agree. Thank you for highlighting this. Although there are five studies under this domain, the overall effect on caregivers' outcome on standardized outcome was not seen and the child outcome showed conflicting evidence. C9.The caregiver well-being domains such as “Information provision’ and ‘Respectful and supportive care’; Enabling and partnership; ‘Enabling and partnership’ and ‘Respectful and supportive care’ and ‘Information provision’, ‘Enabling and partnership’, and ‘Respectful and supportive care’ require more future studies to examine the true benefits of FCC. R9. Indeed, the studies had varied ways of providing intervention and sample sizes were not large enough and with high dropouts, thereby hindering conclusive evidence. Overall, five studies fell into the category of high risk. Hence, in order to examine the true benefits of FCC, it is important to have high-quality randomised controlled trials with care in the control groups not overlapping with the intervention groups in terms of the components of FCC received."
}
]
},
{
"id": "248360",
"date": "25 Mar 2024",
"name": "Suruliraj Karthikbabu",
"expertise": [
"Reviewer Expertise neurorehabilitation"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nJournal: F1000\nI must appreciate the authors for conducting this important systematic review. Overall, the paper is well written. I have a few queries and thoughts and please find my review comments below.\n\nThe authors conducted a systematic review of family-centered care (FCC) interventions on the well-being of caregivers of children with cerebral palsy. They concluded that FCC interventions were effective in improving caregivers’ satisfaction with the attainment of child and caregiver goals, but not for the caregiver’s mental health, parenting and personal outcomes. In the introduction, the authors stated how caring for a child with long-term functional disability affects both the physical and psychological well-being of the caregiver, warranting a systematic review to understand the benefits of FCC on multiple variables. The authors stated that there is a dearth of literature assessing the FCC on the well-being of caregivers of children with CP. Instead, the authors can elaborate on a diversity of such interventions limiting healthcare professions to choose a specific FCC. Search strategies are appropriate and were conducted in seven databases between inception and September 2022. The authors may check if there are any new papers published during the last 18 months. I believe the authors can perform it by the “year” filter and the search-strategy thread. Eligibility criteria, data screening and extraction, and quality assessment sections are well explained. “Risk of Bias 2”, CASP checklist and traffic light system are useful and so are the tables and figures. Since caregiver-reported measures are taken in many studies, assessor bias is unavoidable. Please share your thoughts on caregivers' burden on looking after younger versus older children with CP. Few studies included infants with CP.\n\nFive studies are reporting “information provision’ and ‘enabling and partnership’, providing limited evidence on the said parameters. The caregiver well-being domains such as “Information provision’ and ‘Respectful and supportive care’; Enabling and partnership; ‘Enabling and partnership’ and ‘Respectful and supportive care’ and ‘Information provision’, ‘Enabling and partnership’, and ‘Respectful and supportive care’ require more future studies to examine the true benefits of FCC.\nBest wishes. The reviewer\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "11490",
"date": "21 Jun 2024",
"name": "Deepalaxmi Paresh Poojari",
"role": "Author Response",
"response": "Response to Reviewers Reviewer one - Dr Tanya Tripathi Comment (C)1. \"Firstly, consider tightening the results section to focus specifically on the primary and secondary objectives of the study, which are assessing caregiver well-being and identifying effective intervention components. \" Response(R)1.Thank you for the suggestion. We have modified our objective statement to state that outcomes for children with CP will also be included, as it is our secondary objective. We have clubbed \"Effect on caregiver well-being\" and \"Components of FCC\" as our primary objective and \"Effect on children\" as a secondary objective. The same has been clarified in our eligibility criteria and limitations. We have highlighted the same in yellow. C2.\"It would be beneficial to include outcome measures and results in Table 1 for each included study.\" R2. We value your suggestion. However, we will not be able to incorporate outcome measures in Table 1, as there are huge data sets with multiple outcome measures in each study. Please note the outcome measures and results are presented in Data File 4. C3. \"Secondly, provide further explanation for the lack of effect on mental health outcomes, considering that parents had normal mental health at baseline. This clarification will help readers better understand the results.\" R3. Thank you for your suggestion. We have incorporated the changes highlighted in green in the manuscript. C4. \"Lastly, either remove information on child outcomes from the results section, as it was not part of the study's objectives or reword the objectives to include the intention to report on child outcomes. This will enhance the clarity of the study's goals and findings.\" R4. We appreciate your comment and we have clarified it in the objectives. Reviewer two - Dr Suruliraj Karthikbabu Comment (C)1. The authors conducted a systematic review of family-centered care (FCC) interventions on the well-being of caregivers of children with cerebral palsy. They concluded that FCC interventions were effective in improving caregivers’ satisfaction with the attainment of child and caregiver goals, but not for the caregiver’s mental health, parenting and personal outcomes. Response (R)1.Thank you for highlighting the important results of the study. C2. In the introduction, the authors stated how caring for a child with long-term functional disability affects both the physical and psychological well-being of the caregiver, warranting a systematic review to understand the benefits of FCC on multiple variables. The authors stated that there is a dearth of literature assessing the FCC on the well-being of caregivers of children with CP. Instead, the authors can elaborate on a diversity of such interventions limiting healthcare professions to choose a specific FCC. R2. Thank you for your suggestion. We have added the following statement in the introduction: ''There is also a scarcity of RCTs which have implemented the Universal model of FCC considering the core components of FCC and there is a need for evidence to understand the specific core components of FCC.\" C3. Search strategies are appropriate and were conducted in seven databases between inception and September 2022. The authors may check if there are any new papers published during the last 18 months. I believe the authors can perform it by the “year” filter and the search-strategy thread. R3. Thank you for suggesting this. We have completed an additional review between September 2022 and April 2024 and have included five new articles in the review. All the data sets have been modified accordingly and are highlighted in yellow and the reference DOI has been provided. C4. Eligibility criteria, data screening and extraction, and quality assessment sections are well explained. R4. Thank you for this acknowledgement. C5 “Risk of Bias 2”, CASP checklist and traffic light system are useful and so are the tables and figures. R5. Thank you, we appreciate this recognition of our work. C6. Since caregiver-reported measures are taken in many studies, assessor bias is unavoidable. R6. Yes, we do agree with this. C7.Please share your thoughts on caregivers' burden on looking after younger versus older children with CP R7. In the present study, children with CP were between the ages of 3 months and 16 years. Information needs may have differed for caregivers of younger children, children who had been recently diagnosed with or at risk of CP, or children above 16 years of age who might have gotten used to the entire care system. The craving for child-specific information may be greater in caregivers of younger children than in older children. C8. Five studies are reporting “information provision’ and ‘enabling and partnership’, providing limited evidence on the said parameters. R8.We agree. Thank you for highlighting this. Although there are five studies under this domain, the overall effect on caregivers' outcome on standardized outcome was not seen and the child outcome showed conflicting evidence. C9.The caregiver well-being domains such as “Information provision’ and ‘Respectful and supportive care’; Enabling and partnership; ‘Enabling and partnership’ and ‘Respectful and supportive care’ and ‘Information provision’, ‘Enabling and partnership’, and ‘Respectful and supportive care’ require more future studies to examine the true benefits of FCC. R9. Indeed, the studies had varied ways of providing intervention and sample sizes were not large enough and with high dropouts, thereby hindering conclusive evidence. Overall, five studies fell into the category of high risk. Hence, in order to examine the true benefits of FCC, it is important to have high-quality randomised controlled trials with care in the control groups not overlapping with the intervention groups in terms of the components of FCC received."
}
]
}
] | 1
|
https://f1000research.com/articles/12-790
|
https://f1000research.com/articles/12-255/v1
|
09 Mar 23
|
{
"type": "Research Article",
"title": "The identification of retro-DNAs in primate genomes as DNA transposons mobilizing via retrotransposition",
"authors": [
"Wangxiangfu Tang",
"Ping Liang"
],
"abstract": "Background: Mobile elements (MEs) constitute a major portion of the genome in primates and other higher eukaryotes, and they play important role in genome evolution and gene function. MEs can be divided into two fundamentally different classes: DNA transposons which transpose in the genome in a “cut-and-paste” style, and retrotransposons which propagate in a “copy-and-paste” fashion via a process involving transcription and reverse-transcription. In primate genomes, DNA transposons are mostly dead, while many retrotransposons are still highly active. We report here the identification of a new type of MEs, which we call “retro-DNAs”, for their combined characteristics of these two fundamentally different ME classes. Methods: A comparative computational genomic approach was used to analyze the reference genome sequences of 10 primate species consisting of five apes, four monkeys, and marmoset. Results: From our analysis, we identified a total of 1,750 retro-DNAs, representing 748 unique insertion events in the genomes of ten primate species including human. These retro-DNAs contain sequences of DNA transposons but lack the terminal inverted repeats (TIRs), the hallmark of DNA transposons. Instead, they show characteristics of retrotransposons, such as polyA tails, longer target-site duplications (TSDs), and the “TT/AAAA” insertion site motif, suggesting the use of the L1-based target-primed reverse transcription (TPRT) mechanism. At least 40% of these retro-DNAs locate into genic regions, presenting potentials for impacting gene function. More interestingly, some retro-DNAs, as well as their parent sites, show certain levels of expression, suggesting that they have the potential to create more retro-DNA copies in the present primate genomes. Conclusions: Although small in number, the identification of these retro-DNAs reveals a new mechanism for propagating DNA transposons in primate genomes without active canonical DNA transposon activity. Our data also suggest that the TPRT machinery may transpose a wider variety of DNA sequences in the genomes.",
"keywords": [
"Primates",
"DNA transposons",
"Retrotransposons",
"Retro-DNA",
"Target-primed reverse transcription"
],
"content": "Introduction\n\nMobile elements (MEs), also known as transposable elements, collectively constitute significant portions of the genomes for most higher organisms, being around 50% for primates.1–4 Despite being initially considered “junk” DNA, research from the last few decades has demonstrated that MEs make significant contributions to genome evolution and impact gene function via a variety of mechanisms. These mechanisms include, but are not limited to, generation of insertional mutations and genomic instability, creation of new genes and splicing isoforms, exon shuffling, and alteration of gene expression and epigenetic regulation.5–17\n\nBased on the type of the transposition intermediate, MEs can be divided into two major classes: Class I, called “retrotransposons”, that utilize an RNA-intermediate to transpose in a “copy-and-paste” fashion, and Class II termed “DNA transposons”, that employ a DNA-intermediate to transpose in a “cut-and-paste” style. Furthermore, despite both having target site duplications (TSDs), the two ME classes differ in sequence characteristics, including consensus sequences unique to each class/subclass, distinct TSD length profile, and presence or absence of terminal inverted repeats (TIRs) or polyA tail, and others.17–19\n\nRetrotransposons represent the majority of MEs in primate genomes, owing to their “copy-and-paste” style transposition, which results in direct copy number increase over time, conjugated with their continuing activity over the course of evolution up to the current time. In this process, a retrotransposon is first transcribed into RNA, which is then reverse-transcribed into DNA as a new copy inserting into a new location in the genome.20 Retrotransposons can be divided into two major subtypes: the long terminal repeats (LTR) and non-LTR retrotransposons, with the former carrying two LTRs flanking the internal viral sequences, while the latter lack LTRs but mostly carry a polyA tail.1 LTRs represent domesticated retroviruses from those infecting the germline cells of the ancestors and becoming integrated into the host genome, and for this reason, they are also called endogenous retrovirus (ERVs).21,22 In primate genomes, LTRs exist either as full-length LTRs and can be as long as 10kb, or solo-LTRs around 1kb in length as a product of post-insertion homology-based recombination between the two LTRs, which removes the long internal viral sequences. With several hundred thousand copies, LTRs contribute to ~9% of the genomes with relatively low levels of ongoing activity.23–26\n\nThe non-LTR retrotransposons, as the most successful MEs in primate genomes, contribute to more than 35% of the genomes and more than 80% of all MEs in these genomes with several millions of copies.3,4 From their sequence features, the currently known non-LTR MEs in primate genomes belong to four subclasses, including short-interspersed nuclear elements (SINEs), long-interspersed nuclear elements (LINEs), SINE-R/VNTR/Alu (SVAs), and processed pseudogenes (i.e. retro-copies of mRNAs, also called retro-genes).4,27–31 Despite having many differences with regard to their length, consensus sequences, and coding capacity, all subclasses of non-LTR retrotransposons share the common properties of having a 3’-polyA tail and the use of target-prime reverse transcription (TPRT) mechanism for retrotransposition.31,32 Among them, LINE-1s (L1s) as the only subfamily of autonomous non-LTR retrotransposons in the primate genomes provide the TPRT machinery for all other non-autonomous non-LTR retrotransposons. For this reason, all non-LTR retrotransposons share the same “TT/AAAA” sequence motif at their insertion sites.9,32–36\n\nIn contrast, DNA transposons, initially known as “jumping genes”, move in genomes using a transposase encoded by autonomous copies.1 Ten out of the twelve DNA transposon superfamilies are known to excise themselves out from their original locations as double-stranded DNA and move to new sites in the genome, which leads to no direct change in their copy numbers.17,19 Two of the superfamilies, Helitrons and Mavericks, transpose through non-canonical mechanisms by utilizing a single-stranded DNA as intermediate, which leads to a “copy-and-paste” style.17,37,38 The ten “cut-and-paste” DNA transposon superfamilies, as well as Mavericks, have TIRs and TSDs, while Helitrons is the only superfamily with neither TIRs nor TSDs, owing to its rolling-circle mechanism.17,37 In addition to these aforementioned DNA transposons, there is another group of DNA transposons named miniature inverted-repeat transposable element (MITEs) characterized by the presence of both TSDs and TIRs yet lacking the coding capacity for the transposase.39 By using DNA transposases encoded by other autonomous DNA transposons, these non-autonomous, short (50-600bp) MITE entries can transpose in the host genome.17,40\n\nDNA transposons have been considered inactive in the current primate genomes and have received very little research attention. Lander et al. (2001) in their initial human genome analysis concluded that there was no evidence for DNA transposon activity during the past 50 My,2 while a later study suggested that DNA transposons had been highly active during the early part of primate evolution till ~37 Mya.19 There has been no report for lineage-specific or species-specific DNA transposons in primate genomes. However, in our recent comparative analysis of species-specific MEs in eight primates from the Hominidae and the Cercopithecidae families, there was also a total of 2,405 DNA transposons identified to be species-specific in addition to the 228,450 species-specific retrotransposons.36 As part of efforts to understand the mechanism(s) underlying these species-specific DNA transposons, we performed further comparative analysis across ten primate genomes and identified a new type of non-LTR retrotransposons that have sequences from DNA transposons, but also show some hallmarks of L1-based retrotransposons, which we called “retro-DNAs”.\n\n\nResults\n\nTo identify all retro-DNA events in the primate genomes, we first identified the diallelic DNA transposons (da-DNAs) that are defined as DNA transposons with both the insertion allele and pre-integration allele identifiable in these genomes. These DNA transposons are likely to be the results of relatively recent transposition events shown as having a low level of sequence divergence from their parent copies, which permits accurate identification of TSDs and TIRs. The starting lists of DNA transposons were based on the RepeatMasker annotation subjected to a consolidation process to ensure the accuracy in identifying DNA transposons with both insertion and pre-integration alleles as well as their TSDs.3,36 One main type of targets for integration in this case are the ME entries split by insertion of other MEs and non-ME sequences. As shown in Table 1, the number of DNA transposons in the primate genomes dropped ~18% on average after integration, leading to less variation in their numbers across genomes ranging from 324,288 in marmoset to 421,580 in chimpanzee, and averaging at 376,720 copies per genome verse 459,521 per genome before integration. These DNA transposons contributed to a total of ~98 Mbp or ~3.6% of these primate genomes on average (Table 1). Various factors could have contributed to the different DNA transposon numbers in these genomes, including, but not limited to, the differences in the versions of RepeatMasker and the ME reference sequences used for ME annotation, the quality of genome assemblies, and probably most importantly the different evolution history of the individual genomes.\n\n* Full-length is defined as >=90% of consensus\n\nUsing a multi-way comparative genomics approach modified from our previous analysis of human-specific MEs,36 we identified a total of 271,085 da-DNAs in the 10 primate genomes (Table 1). Specifically, for each da-DNA, we require the presence of a pre-integration allele in at least one of the other nine genomes. As shown in Table 1, the number of da-DNAs varied from 23,923 in the orangutan genome to 34,901 in the marmoset, averaging at 27,109 for the 10 genomes. The largest number of da-DNAs in the marmoset was expected for its largest evolutionary distance from the remaining primate species. Notable differences were also seen between genomes with mutually closest evolutionary relationship among the 10 genomes, making these numbers directly comparable for the paired genomes. For example, between the human and chimpanzee genomes, the latter had >10% more da-DNAs than the former (28,273 versus 25,933), while between the two macaques, the rhesus genome had ~10% more than the crab-eating macaque genome (28,149 versus 26,218) (Table 1). In comparison, the species-specific non-LTR retrotransposons in the crab-eating macaque genome were less than 1/8 of that for the rhesus genome (3,039 versus 25,085),3 indicating at least that the lower number of da-DNAs in rhesus genome was not due to genome sequence quality differences.\n\nBy composition in DNA transposon type, the majority of the da-DNAs belonged to the hAT and TcMar superfamilies with the hAT subfamilies (hAT-Charlie and hAT-Tip100) contributing to ~57% of da-DNAs and the hAT-Charlie subfamily alone contributing to ~50% of all da-DNAs in all genomes (Table S1, Figure 1A). The two TcMar families, TcMar-Tigger and TcMar-Mariner, contributed ~33% of da-DNAs, while the remaining families contributed to ~10% of da-DNAs. This composition pattern seems to be quite similar among all genomes, with the orangutan genome having a slightly lower portion from the hAT-Trip100 and TcMar-Tigger families but slightly more from the other families (Figure 1A, Table S1).\n\nHorizontal stack bar charts showing the family composition of diallelic DNA transposons (A) and retro-DNAs (B) in each of the 10 primate genomes. The color scheme is the same for both panels.\n\nWhile analyzing the da-DNAs in detail for understanding the possible mechanisms involved, we came across an unusual case of a 201-bp Tigger7 DNA transposon from the TcMar-Tigger family located at chr4:146335052-146335253 of the human genome (GRCh38), which appears to be a human-specific ME for its absence in the orthologous region in the chimp genome (Figure 2A). Interestingly, this DNA transposon insertion has a 14 bp TSD “AAGAGTCCTGGATC” that is much longer than TSDs for DNA transposons, and it has no identifiable TIR typical of a DNA transposon (Figure 2A). Furthermore, it has a 27 bp polyA tail at its 3’-end and a predicted polyadenylation signal “ATTAAA” before the polyA tail, all pointing to a non-LTR retrotransposon rather than a canonical Tigger7 DNA transposon, which is expected to have TIRs and 2 bp (TA) TSDs. We therefore named it as a “retro-DNA” for being a retrotransposon-like element derived from a DNA transposon sequence.\n\nA. A retro-DNA from the human genome (hg38_chr4:146335052-146335253) with the pre-integration allele from the chimpanzee genome (panTro5_chr4:38758218-38758438). B. A retro-DNA from the green monkey genome (chlSab2_chr8:30005081-30005527) with the pre-integration allele from the gibbon genome (nomLeu3_chr8:37535028-37535236); C. A retro-DNA located from the green monkey genome (chlSab2_chrX:73456937-73457324) with the pre-integration allele from the orangutan genome (ponAbe2_chrX:82896142-82896360). D. A retro-DNA located from the human genome (hg38_chr4:38758216-38758442) with the pre-integration allele from green monkey genome (chlSab2_chr27:11529606-11529817). In each panel, the sequence at the top is the insertion allele containing the retro-DNA, and the sequence at the bottom is the pre-integration allele without the retro-DNA. The yellow boxes indicate TSDs, the blue boxes indicate the DNA transposon sequences, while the purple boxes indicate possible polyA tail sequences.\n\nFollowing the identification of this retro-DNA, we searched the human genome and other primate genomes and identified more similar cases, as exampled in Figure 2B-D. For instance, a 446 bp Charlie1a fragment from the hAT-Charlie family was identified as a retro-DNA in the genome of three primates (green monkey, rhesus, and crab-eating macaque), which has TSDs in 13 bp long but no TIRs (Figure 2B).\n\nBy requiring the presence of longer TSDs (≥8 bp) and the absence of TIRs, we identified a total of 1,750 retro-DNA entries among all da-DNAs using a workflow shown in Figure 3. By classification, these retro-DNAs consist of 847, 478, 156, 74, and 195 entries from the hAT-Charlie, TcMar-Tigger, hAT-Tip100, TcMar-Mariner, and other families, respectively (Table 2). The composition pattern (Figure 1B) was very similar to that of all da-DNAs (Figure 1A), indicating there is no strong bias for retro-DNA towards any particular subfamily among da-DNAs. However, at the genome level, the ratios of retro-DNAs in the orangutan genome from the hAT-Trip100 and TcMar-Tigger families were much lower, while that from the “other” families was much higher compared to other genomes (25% versus 10%) (Figure 1B). As seen in Table 2, the 1,750 retro-DNAs encompassed all 10 genomes and could be clustered into 748 unique retro-DNA insertion events based on their orthologous relationships. It is worth noting that our list of retro-DNAs may suffer a certain level of false negatives and false positives due to the uses of a set of criteria that might not be optimal and due to the challenges associated with the analysis of MEs and the deficiencies of the reference genome resources, especially for the non-human primates as discussed in our recent study.3\n\nBy sequence length, these 748 (after removing orthologous redundancy (Table 2)) retro-DNAs averaged at 209 bp (±190 bp) in length, representing in all cases only part of the corresponding family consensus sequences (averaging at 21%) (Table 3). While the consensus sequences for DNA transposon families differ in length significantly, ranging from 380 bp for TcMar-Mariner to 1,506 bp for hAT-Tip100, the average length of retro-DNAs seems to be relatively more consistent across the families, ranging from 122 bp for TcMar-Mariner to 251 bp for TcMar-Tigger. Nevertheless, in general, the retro-DNAs from the longer families do have a longer average length (e.g. hAT-Tip100) than those from the shorter families, but at lower proportions of their consensus sequences than those with shorter consensus sequences (e.g. TcMar-Mariner) (Table 3).\n\nAdditionally, we examined whether there were any hotspots in these DNA transposon sequences as the source sequences of these retro-DNAs. By using the retro-DNA entries from the Tigger1 DNA transposon subfamily, which is the largest subfamily containing 41 non-redundant retro-DNAs, we generated a frequency plot to show the usage of the consensus sequences by the retro-DNAs. As illustrated in Figure 4, while all regions of the consensus sequence were covered by the 41 retro-DNAs, the frequency varied substantially from 2.4% to 29.3%, showing that a few regions of the consensus sequence (e.g. ~1310-1440 bp and ~1840-2240 bp) were used more frequently than the rest of the regions.\n\nThe plot is based on the data for a total of 41 non-redundant retro-DNA entries from the Tigger1 subfamily.\n\nFrom the total 748 non-redundant retro-DNAs, we identified 176 entries carrying a potential polyA tail (Table S2). We speculate that the relatively low percentage (23.5%) of entries with a polyA tail might be partially due to quicker sequence divergence from post-insertion mutations in the polyA tail regions, which are more prone to random mutations than other regions due to the homopolymer nature. The complete list of the 748 non-redundant retro-DNA entries with their genomic coordinates in all applicable genomes is provided in Supplementary File 1. For these retro-DNA insertion events, we further examined the sequence motifs at the insertion sites and the TSD length distribution pattern. As shown in Figure 5A, a sequence motif of ‘TT/AAAA’, same as the motif for Alus, L1s, and SVAs (Figure 5B),32,36,41 was observed, despite the signal being much weaker. This, nevertheless, serves as a strong indication of their use of the L1-based TPRT machinery.33,34 As further support, the TSD length distribution peaked at 8 bp (Figure 5C), similar to the second peak seen for the TSDs of human specific L1s, despite missing the major peak at 15 bp observed for the latter (Figure 5D).36\n\nA. Sequence motif logos for retro-DNAs at the integration sites. B. Sequence motif logos for human-specific L1s at the integration sites, adopted from authors’ publication.3 C. A line plot showing the distribution of TSD length for retro-DNAs. D. A line plot showing the distribution of TSD length for human-specific L1s, adopted from authors’ publication.3\n\nWe examined the evolutionary timeline of the retro-DNA insertion events by mapping them onto a phylogenetic tree of these primates based on the data in the TimeTree database.43 As shown in Figure 6A (the insert), 450 (60.2%) of these retro-DNAs appeared to be species-specific for being uniquely present in only one genome, while another 295 (39.4%) were found in multiple genomes in a clear lineage-specific pattern. On average, a retro-DNA was shared by two genomes, suggesting an average age older than the species-specific MEs (unique to one species) reported in our earlier study.3 The example shown in Figure 2A serves as a very clear case of species-specific retro-DNA. As shown in the multiple sequence alignments with its orthologous sequences including its flanking sequences from other eight primate genomes (not locatable in marmoset genome), this Tigger7 element was absent from the orthologous sites of all non-human primate genomes (Figure 6A), confirming it as an authentic human-specific retro-DNA. On the contrary, the example shown in Figure 2B is demonstrated to be a retro-DNA insertion event shared among three of the four monkey species, thus likely as a lineage-specific retro-DNA. As shown in Figure 6B, this 446 bp Charlie1a fragment was absent in the orthologous regions of the remaining seven primate genomes. Furthermore, it appears that the retro-DNA sequence in these three genomes had been subject to mutation in the polyA tails shown as having variable lengths, agreeing with its relatively older age as a lineage-specific retro-DNA. Similarly, the example shown in Figure 2D represents an ape lineage-specific retro-DNA for its presence in all ape genomes but absent in all non-ape genomes examined.\n\nA. A rooted phylogenetic tree of the ten primate genomes from the TimeTree database (http://www.timetree.org/). The numeric values below each branch represent the number of retro-DNA insertion events happened during the corresponding period of primate evolution. The numeric value above each branch represents the millions of years (Mya) for that branch. The evolutionary time for marmoset has been manually corrected from 21.58 MY to 51.02 MY for the correlation analysis in panel B. The table insert below the tree shows the distribution of the retro-DNAs by the degree of conservation among the genomes as measured by the number of genomes owning a retro-DNA. B. A scatter plot between the number of retro-DNA insertion events and their evolutionary age based on the data in panel A. The trend line shows that the number of retro-DNA insertion events is positively correlated with the relative evolutionary distance (R2 = 0.919).\n\nAs shown in Figure 6B, the number of retro-DNA insertional events appears to show a positive linear correlation with the relative evolutionary ages of the species and lineages (R2 = 0.5463), suggesting that these retro-DNA insertional events occurred at a low but relatively consistent rate during primate evolution.\n\nTo assess the potential functional impact of these retro-DNAs, we examined their gene context based on the Ensembl gene annotation for these genomes.42 A total of 698 retro-DNAs, representing ~40% of the 1,750 retro-DNAs were located within the genic regions and promoter regions for 734 transcripts from 414 unique genes (Table 4 and Table S3). The majority of these retro-DNAs were located within the intron regions (699/734 transcripts), while 27 entries were inserted into promoter regions and untranslated regions. The presence of these retro-DNAs in the genic regions provides the potential to impact gene regulation or splicing.\n\n* , NR: non-coding RNA; UTR: untranslated region\n\nA. Multiple sequence alignment for a retro-DNA located in the human genome (hg38_chr4:146335052-146335253, the same entry in Figure 1A) and the corresponding pre-integration sequences from the other eight primate genomes. The pre-integration sequences from the marmoset genome is unavailable likely due to the high level of sequence divergence. B. Multiple sequence alignment for the sequences of a retro-DNA shared among green monkey, crab-eating macaque and rhesus genomes (chlSab2_chr8:30005081-30005527, macFas5_chr8:32527581-32528029, and rheMac8_chr8:31992158-31992606) with the flanking sequences, along with their orthologous pre-integration sequences from 7 other primate genomes. The red highlights indicate possible polyA tails with variable lengths across genomes, while the yellow highlights show the observed target site duplications (TSDs).\n\nFurther, we identified the potential parent sites for these retro-DNAs by performing a sequence similarity search using their sequences to query the corresponding genome sequences. For each retro-DNA, the best non-self-match was selected as its potential parent site. An example of such a parent-child relationship is shown in Figure 8, in which a human-specific new retro-DNA event on chromosome 4 is shown to be a child to a much longer Tigger7 (1882 bp) on chromosome 9, which has orthologous copies in other primate genomes, indicating a much older age of the latter and its validity as a parent copy for the former. As shown in Table S4, we identified a total of 715 potential parent sites for the 1,750 retro-DNA entries (or 325 entries for the 748 retro-DNAs after removing the redundancy across species). The failure in finding the parent copies for the remaining entries could be due to the loss of the parent copy as a result of genomic rearrangements or due to incomplete coverage of the genome sequences. Like for the retro-DNAs, we examined the gene context for these potential parent sites, and as shown in Table S5, 351 (49.1%) of these redundant potential retro-DNA parent sites locate to 410 different genic regions for 371 unique genes/transcripts. In these cases, the transcripts of these potential parent sites, likely as part of the transcripts or splicing side-products (e.g., excised intron sequences) of their host genes, might have had the chance to be captured by the L1 TPRT machinery to generate retro-DNAs as in the case of processed pseudogenes/retro-genes. The ratio of genic entries (49.1%) was higher for the parent sites than that for retro-DNAs (~40%), and the implication is discussed later.\n\nA. Multiple sequence alignment for a retro-DNA in the human genome (hg38_chr4:146335052-146335253) and its parent copy (hg38_chr9:70197633-70197828, limited to the sequence aligned with the retro-DNA) plus the orthologous sequences of the parent copy from the other 9 non-human primate genomes. The red arrows indicates the retro-DNA entry, while the blue arrow indicates the parent copy. SNPs in red vertical boxes are seen among members of the Hominidae group. B. Phylogenetic analysis of the 11 nucleotide sequences from the 10 primate genomes shown in A using the Maximum Likelihood method and Tamura-Nei model.60 The bootstrapped consensus tree inferred from 500 replicates61 is used to represent the evolutionary history of the taxa involved. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates were collapsed. The percentage of replicating trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches.61 Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Joining and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach followed by selecting the topology with superior likelihood value in logarithmic scale. This analysis involved 11 nucleotide sequences with a total of 222 positions in the final dataset.\n\nWe also examined the expression level of retro-DNAs and their potential parent sites using RNA-seq data from the Non-Human Primate Reference TRanscriptome (NHPRTR) dataset44 and two other studies45,46 to see if any of these entries had any transcriptional activity in the present-day primate genomes. For this, we collected a total of 21 transcriptomes for seven primates, excluding orangutan, gibbon, and marmoset, for which no transcriptome data was available at the time of our analysis. To minimize false positives due to the high sequence similarity among ME members in the same family, we included only the reads with a perfect match to the retro-DNAs or their parent site regions and with each read used only once in calculating the expression level. However, we believe that this process has inevitably introduced a certain level of false negatives in the results due to sequence polymorphisms and, therefore, may have led to an underestimation of the retro-DNAs and parent sites’ expression levels. As seen in Tables 5 and S6, 966 loci from the 1,750 retro-DNA and 715 parent sites in these seven primate genomes were shown to have a certain level of expression ranging in fragments per kilobase of transcript per million reads (fpkm) value from 0.0003 to 27.3.\n\nWe further investigated the relationship between retro-DNAs and their parent sites based on their expression levels. Specifically, three human testis transcriptome samples (SRR2040581, SRR2040582, SRR2040583) retrieved from the NCBI SRA (Sequence Read Archive)) were used to analyze the expression level of the retro-DNA/parent site pairs. As shown in Figure 9A, a total of 66 retro-DNA/parent site pairs were shown to have a certain level of expression (fpkm > 0) for either the retro-DNA or the parent site among the three human testis samples. Notably, among these 66 retro-DNA/parent site pairs, 57 (86.4%) parent sites were shown to be expressed (fpkm > 0) compared to only 42 (63.6%) expressed retro-DNAs (Table S4 and S6, Figure 9A). This difference might indicate that the generation of a retro-DNA requires the expression of its parent site, while a retro-DNA itself may not be expressive depending on its landing location. Therefore, a higher ratio of transcriptionally active sites can be expected for the parent sites than for the progenies (retro-DNAs). More interestingly, the two parent sites responsible for multiple retro-DNA entries were shown to have the highest levels of expression among the parent sites (Figure 9A). This may suggest that the expression level of the parent sites is positively correlated to their potential in generating retro-DNAs. Furthermore, the ongoing expression of the parent sites suggests that they have the potential to generate more retro-DNAs in the future.\n\nA. A scatter plot based on 66 retro-DNA/parent site pairs which show a certain level of expression (fpkm > 0) for the retro-DNA and/or parent site. The two data points in red with the same value for the parent but different values for the retro-DNA copies point to the same parent copy in human at hg38:chr5:1570263-1570333, and the two data points in blue point to the same parent copy in human at chr5:259441-262665. B. Box plots showing the expression levels of the 66 retro-DNAs and parent sites divided into genic and intergenic groups. Expression data was based on the average fpkm value in the three human testis transcriptomes.\n\nWe also examined and compared the expression levels of retro-DNAs and their parent sites among gene context-based groups in the three human testis transcriptomes. As shown in Figure 9B, the average fpkm values of the parent sites were always higher than that of the retro-DNA entries as a whole group or divided into genic and intergenic regions. In addition, the entries located within genic regions showed higher expression than the ones located outside the genic regions for both retro-DNAs and the parent sites (Figure 9B), suggesting that entries located in the genic regions may have more opportunities to be expressed passively as part of the host gene expression. This difference is larger for retro-DNAs than for the parent sites, likely because parent sites had to be expressed regardless of their position in order to be able to generate new copies. None of these differences are statistically significant, likely due to the small sample size.\n\n\nDiscussion\n\nIn this study, we focused on a small number of species-specific DNA transposons identified in primate genomes using a computational comparative genomics pipeline previously established for analyzing species-specific retrotransposons in the human genome and seven other genomes.3,36 Unlike for retrotransposons, for which the ongoing activity during evolution and in the current genomes of primates, as well as their contribution to the lineage- and species-specific MEs, have been well established,3,32,47 similar research for DNA transposons in primate genomes remains very scarce. As a matter of fact, as at time of writing, no report of species-specific DNA transposons in these primate genomes has been documented, likely due to lack of effort, as DNA transposons are thought to have become inactive in primate genomes about 37 Mya.17,19\n\nIn trying to understand the mechanism underlying the mystery species-specific DNA transposon insertions identified in our comparative genome analysis, we spotted a few interesting entries as exemplified by the case shown in Figure 2A, which manifests the characteristics of non-LTR retrotransposons by having longer TSDs and presence of a polyA tail, while lacking TIRs, the hallmark of new DNA transposon insertions. The remaining cases shown in Figure 2 have the same non-LTR features but do not necessarily have a typical polyA tail. For their non-LTR retrotransposon characteristics, we named them “retro-DNA” as retrotransposons derived from DNA transposons. We then performed a systematic analysis to look for more of such “retro-DNA” cases.\n\nFor this, we expanded our search from the strict species-specific DNA retrotransposons, which are defined as those present in only one of the primate genomes,3,36 to da-DNAs, which are defined as diallelic DNA transposons with the insertion allele and its pre-integration allele (i.e., the orthologous region without the DNA transposon) both present in at least one of the ten genomes we included. We obtained a total of 271,085 da-DNAs, and from these we then specifically searched for retro-DNA cases, which have long TSDs (≥8bp) and the absences of the TIRs using a protocol shown in Figure 3. This led to the identification of 1,750 of retro-DNA cases, which represent 748 unique events, covering all ten primate genomes with over half being species-specific and the remaining being lineage-specific covering different lineages in this group of primates (Figure 6A). Our results indicate that the presence of retro-DNAs has occurred in all ten primate genomes included in our analysis and at wide-spectrum of evolutionary time at approximately a constant rate (Figure 6). Furthermore, these retro-DNAs are not limited to a single subfamily, but rather cover all major DNA transposon families, suggesting that the existence of such “retro-DNAs” is the product of a consistent and common process actioning in primate evolution.\n\nSeveral lines of evidence from our results guided us to propose that these retro-DNAs were the products of the L1-based TPRT machinery, similar to the known non-autonomous non-LTR retrotransposons, i.e., SINEs, SVAs and processed pseudogenes.9,33–36 The major pieces of evidence include the lack of TIRs and the presence of the TPRT insertion site sequence motif and long TSDs. As seen in Figure 5A, the integration sites of the 748 retro-DNAs display, although at a much weaker signal, are a core sequence motif of “TT/AAAA”, which is identical to that for non-LTR retrotransposons in the human genome (Figure 5B).34,36,41 The TSDs for these retro-DNAs show a dominant peak at 8bp (Figure 5C), which is much longer than that of TSDs typically found for DNA transposons (2 bp) and is similar to the secondary peak of TSD length observed for the human-specific L1s36 (Figure 5D). Furthermore, the presence of parent sites in the same genome for a significant proportion of the retro-DNAs (325/748 or 43.5%) indicates their use of a “copy-and-paste” rather than the “cut-and-paste” mechanism used by canonical DNA transposons. The presence of a polyA tail in many (176/748 or 23.5%) of these retro-DNAs provides additional support for their use of the L1-based TPRT mechanism.\n\nIt is worth noting that, as described above, while there is sufficient similarity in sequence features between these retro-DNAs and the known non-LTR retrotransposons for treating these retro-DNAs as a new type of non-LTR retrotransposons, unique aspects of these retro-DNAs are also evident. These include the missing of the major TSD length peak at 15 bp observed for other non-LTR retrotransposons, the low percentage of entries with a polyA tail, and the weaker signal of the sequence motif, “TT/AAAA”, at the integration sites. All of these unique characteristics might be attributed to the relatively older average age of these retro-DNAs as indicated by the relatively high percentage (298/748 or ~40%) for being lineage-specific (Figure 6A) compared to the non-LTR retrotransposons used in most previous studies for analysis of integration site sequence motifs.9,33–36 In other words, the older age of the retro-DNAs leads to higher sequence divergence, which in turn lowers the sensitivity for detecting all of these sequence features. An additional reason for the weaker signal in the insertion site sequence motif for the retro-DNAs could be due to the small sample size. It is also possible that these unique characteristics may suggest that some differences in the detailed retrotransposition process of these DNA transposons, likely regarding the interaction between the retro-DNA transcripts and the ORF1 and ORF2 proteins, may exist between the retro-DNAs and the canonical non-LTR retrotransposons. One known example for this is that Alu transposition does not seem to require ORF1p.32,48,49\n\nIt is also worth pointing out that in addition to the well-known types of non-autonomous non-LTRs transposed by the TPRT machinery, including SINEs, SVAs, and retro-genes, evidence suggests that some copies of the LTR-retrotransposon subfamily, HERV-W, might have also been transposed by this mechanism.50,51 However, these HERV-W sequences are part of retrotransposons and can continue to be transposed using their canonical retrotransposition mechanism. For this reason, we would like to argue that our identification of retro-DNAs is unique and significant in the sense that they represent DNA transposons, which would not be able to transpose anymore in the primate genomes, since their canonical mechanism is no longer active. Overall, the research from this study and others clearly suggests that the L1-based TPRT machinery may be able to transpose a much wider variety of genomic sequences than what are currently known.\n\nIn comparison with the other types of non-autonomous non-LTR retrotransposons, including Alus, SVAs, and processed pseudogenes, in primate genomes,2,3,32,52 the number of retro-DNAs per genome was much lower, averaging at < 200 per genome (Table S2). This number was even substantially lower than that of processed pseudogenes, which represent the smallest class of non-LTR retrotransposons with 10,190 copies in the human genome.53 We reason that the very small copy number of retro-DNAs may primarily attribute to one factor, i.e., the lack of intrinsic internal promoters to drive their own transcription, leading to an overall low level of their transcripts available for retrotransposition. Retrotransposons carry their intrinsic promoters required for their canonical propagation mechanisms, while a promoter is not required for the canonical DNA transposon activity. This is in agreement with the observation that there is no clear hotspot in the DNA transposon consensus sequences used in generating retro-DNAs, as shown in Figure 4 for Tigger1. Should there be internal promoters driving the transcription, we would expect to observe one or more clear dominant peaks in the frequency of the regions used for retro-DNAs correlated with the location of the internal promoter(s). Without the ability to drive their own transcription, the only way for DNA transposons to get transcribed is to get transcribed as a part of the host gene transcripts. If this is how retro-DNAs were generated, then we would expect to see a high percentage of retro-DNAs having their parent sites located in the genic regions, more specifically in the transcribed regions, i.e. exon and intron regions. By examining the gene context, 351 of the 715 parent sites (49.0%) for the retro-DNAs located in 371 unique genes/transcripts in the ten primate genomes. This ratio was higher than that for all DNA transposons in the genic regions (39%, detailed data not shown) as the expected for random distribution and for that of the retro-DNAs (40% in genic sites including promoters) (Tables 4 and S5), thus supporting the role of passive expression for the parent sites in generating these retro-DNAs.\n\nBy the same rationale, we would expect that on average the parent sites should have a higher expression level than retro-DNAs since the parent sites were selected to be biased for this by locating in the genic regions, while the location of the retro-DNAs is more or less random, leading to a relatively lower proportion in genic regions than the parent sites as shown in our data (40% verse 49%) (Table 4, Table S5). This is supported by the expression data showing that among the 66 retro-DNA/parent site pairs, 57 pairs have parent sites with a fpkm > 0 compared to only 42 expressed entries for retro-DNAs (Figure 9A). Additionally, we identified two parent sites, which are the only sites potentially responsible for generating multiple retro-DNA entries, and they showed the highest levels of expression among the parent sites (Figure 9A). By comparing the expression levels of all parent sites with that of retro-DNAs in the human genome, we can see an overall higher expression for the parent sites (Figure 9B), and this is also true when comparing between the sites in the genic and intergenic regions (Figure 9B). Furthermore, the expression level of parent sites in the genic regions is much higher than their counterparts in the intergenic regions as expected (Figure 9B). Another possible factor leading to the extremely small number of retro-DNAs might be that the sequences of these DNA transposons are much less optimal for TPRT-based retrotransposition than the canonical types of retrotransposons.\n\nThe use of the 10 primate genomes, representing several lineages with a large span in primate evolution, allowed us to examine whether there is any positive correlation between the length of evolutionary span and the number of retro-DNA insertional events. As shown in Figure 6B, a moderate positive correlation between the two is observed (R2 = 0.5463), suggesting that the generation of retro-DNAs is relatively steady during the evolution of this group of primates. Furthermore, the observation that many of the retro-DNA parent sites, as well as 966 of the 1773 (~54.5%) retro-DNAs show certain levels of expression in the seven primate transcriptomes (Table 5 and S6), suggests the possibility of ongoing retro-DNA generation from the parent sites and perhaps also from some retro-DNAs.\n\nIn this study, through a comparative genomic analysis of 10 primates, we report the first identification of a new type of non-autonomous non-LTR retrotransposons derived from DNA transposon sequences. Named as “retro-DNAs”, these elements represent an additional type of non-LTR retrotransposons after LINE, SINE, SVA, and processed pseudogene, very likely using the same L1-based TPRT mechanism. This work is significant, as the generation of these retro-DNAs serves to propagate DNA transposon sequences in the absence of the canonical DNA transposon activity in primate genomes and the process involves two fundamentally different ME classes. Despite being very small in number, they do contribute to the genetic diversity among primate species along with other MEs. Furthermore, the discovery of these retro-DNAs suggests that the L1-based TRPT machinery may have been used by more diverse types of RNA transcripts than what we currently know. Interesting follow-up work ought to include the verification of the retrotransposition activity of these retro-DNAs and their parent sites using in vitro and in vivo assays and extension of the similar analysis to other types of expressive DNA sequences, such as non-coding RNA genes. In addition, research into the mechanisms underlying the remaining majority of the diallelic DNA transposons would also be very interesting and valuable.\n\n\nMethods\n\nIn this study, we chose to use 10 primate genomes including human, among which eight genomes were included in our previous study for identifying species-specific MEs in primates.3 These 10 primate species include human (GRCh38/UCSC hg38), chimpanzee (May 2016, CSAC Pan_troglodytes-3.0/panTro5), gorilla (Dec 2014, NCBI project 31265/gorGor4.1), orangutan (July 2007, WUSTL version Pongo_albelii-2.0.2/ponAbe2), gibbon (Oct. 2012 GGSC Nleu3.0/nomLeu3.0), green monkey (Mar. 2014 VGC Chlorocebus_sabeus-1.1/chlSab2), crab-eating macaque (Jun. 2013 WashU Macaca_fascicularis_5.0/macFas5), rhesus monkey (November 2015 BCM Mmul_8.0.1/rheMac8), baboon (Anubis) (March 2012 Baylor Panu_2.0/papAnu2), and marmoset (March 2009 WUGSC 3.2/calJac3). The marmoset genome was added to expand the evolutionary span, also serving as an outgroup for the other nine genomes from the ape and monkey groups, while the gibbon genome was added to increase the coverage and evolutionary span of the ape group. All genome sequences in fasta format and the RepeatMasker annotation files were downloaded from the UCSC genome website onto our local high performance computing servers for in-house analyses. We have used the most recent genome versions available on the UCSC genome browser website at the time of analysis in all cases except for gorilla, for which there is a newer version (March 2016, GSMRT3/gorGor5) available but not scaffolded into chromosomes, making it inadequate for our analysis.\n\nA total of 90 liftOver chain files were needed for all possible pair-wise comparisons of the 10 genomes used in this study. These files contain the information linking the orthologous positions in a pair of genomes based on lastZ alignment.54 A total of 22 of these were available and downloaded from the UCSC genome website, and another 34 liftOver chain files were generated using a modified version of UCSC pipeline RunLastzChain from a previous study.3 The remaining 36 liftOver chain files were newly generated for this study using the same pipeline.\n\nPre-processing of DNA transposons: The starting list of DNA transposons in each primate genome was obtained based on the RepeatMasker ME annotation data from the UCSC website. As previously described, we performed a pre-processing to integrate the ME fragments annotated by RepeatMasker back to ME sequences representing the original transposition events.36\n\nIdentification of DNA transposons with diallelic status: We modified a previously reported comparative genomics bioinformatics pipeline36 to identify da-DNAs that have the presence of both the insertion and pre-integration alleles in at least one of the 10 primate genomes. Briefly, this pipeline uses a robust multi-way computational comparative genomic approach to determine the presence/absence status of DNA transposons among a group of genomes by using both the whole chromosome alignment-based liftOver tool and the local sequence alignment-based BLAT tool.55,56 The sequence of a DNA transposon at the insertion site and its two flanking regions in a genome were compared to the sequences of the orthologous regions available in all other genomes. If a DNA transposon is absent from the orthologous regions of any of the other nine genomes not due to the existence of a sequence gap (i.e. just missing the insertion), it is selected as a potential candidate of da-DNA subject to further analyses.\n\nIdentification of TSDs and TIRs: For the candidate entries from the previous step, using in-house PERL scripts as described previously,36 we performed identification of the TSDs. Additionally, we modified our scripts to identify the TIRs, the hallmark of all cut-and-paste transposons except for Helitrons.17 da-DNA entries without identifiable TSDs or TSD length < 8 bp, as well as entries with identifiable TIRs, were excluded from further analysis. The 8 bp TSD length cutoff was chosen based on our observation for human-specific retrotransposons that 95% of identified TSDs are at least 8 bp long.36 Additionally, we used MiteFinderII, a tool designed to identify miniature inverted-repeat transposable elements,57 to verify that none of our candidate entries contain TIRs.\n\nFiltering against retrotransposon transductions: To ensure the presence of a DNA transposon was a result of active transposition, rather than a passive result of other processes, e.g., retrotransposition-mediated transductions, we mapped the candidate entries against the known retrotransposons in the ten primate genomes based on their genomic positions. Specifically, the sequences of candidates from the previous step were mapped back onto the host genome using BLAT, followed by removing all entries located within 50 bps to a retrotransposon (excluding entries inserted into a retrotransposon), because such entries could be a result of retrotransposition-mediated transduction. All entries left at this point were considered candidates of “retro-DNAs” for being retrotransposons derived from DNA transposon sequences but lacking TIRs and having TSD at 8 bp or longer.\n\nIdentification of polyA tail: For each candidate retro-DNA, we retrieved the 10 bp sequence from the 3’ end of the positive-strand (by the DNA transposon consensus sequence). If the sequence contains six or more “A”, the entry is considered to have a polyA tail.\n\nThe retro-DNA candidates identified from the last step in the 10 primate genomes were subject to a round of “all-against-all” sequence similarity search using BLAT with the sequences of the retro-DNAs plus the 100 bp of the flanking region on each side. Entries with 95% or higher sequence similarity across the entirety of the sequences including the flanking sequences were identified as one orthologous cluster, representing one retro-DNA insertion event during the evolution of these primates.\n\nAn organismal phylogenetic tree of the 10 primate genomes with the marmoset genome as the outgroup was obtained from the TimeTree database43 and displayed using the Treeview program.58 We then manually added the numbers of non-redundant retro-DNA entries onto the nodes and branches of this tree based on the presence of retro-DNAs in the specific genomes or lineages.\n\nWe performed multiple sequence alignment for a few selected retro-DNA entries, including their parent sites. For this, we first collected retro-DNA sequences including 100 bp on both flankings, as well as the orthologous sequences of the parent sites from the rest of primate genomes and performed multiple sequence alignment using the online version of MUltiple Sequence Comparison by Log-Expectation (MUSCLE)59 from the European Bioinformatics Institute website. Phylogenetic analyses in some cases were performed using the Maximum Likelihood method and Tamura-Nei model60 with bootstrapping61 at 500 replications.\n\nRNA sequencing (RNA-seq) data for the blood and the generic (mixed) samples from chimpanzee, gorilla, crab-eating macaque, rhesus and baboon were retrieved from the Non-Human Primate Reference Transcriptome Resource (NHPRTR)44 for expression analysis of the retro-DNAs and their parent copies. We also collected RNA-seq data for six human testis transcriptomes (three for blood and three for testis)46 and two green monkey transcriptomes.45,62 The detailed information regarding the NCBI SRA accession numbers and the associated species and tissues is available in Table S6. Tophat2 (version 2.1.1) was used to align the RNA-seq reads to the corresponding reference primate genomes.63 Reads mapped to the retro-DNA/parent copies regions were retrieved in fasta format and aligned back to the reference genome using the NCBI blastn to ensure that each RNA-seq read was only assigned to only one genomic location with perfect match for use to calculate the fpkm values for each DNA transposon using an in-house Perl script.\n\nThe data analysis and figure plotting were performed using a combination of Linux shell scripting, R, and Microsoft Excel. The computational analysis was mostly performed on Compute Canada high-performance computing facilities running CentOS Linux.",
"appendix": "Data availability\n\nBioStudies: The identification of retro-DNAs in primate genomes as DNA transposons mobilizing via retrotransposition, https://identifiers.org/biostudies:S-BSST1030. 64\n\nAnalysis code\n\nThe customized perl and shell scripts used for identification of the reported retro-DNAs are available at https://github.com/pliang64/retro-DNAs .\n\nArchived analysis code at time of publication: https://doi.org/10.5281/zenodo.7682142. 65\n\nLicense: GNU GPL-3.0\n\n\nAcknowledgments\n\nThis work is in part supported by grants from the Canadian Research Chair program, Canadian Foundation of Innovation, Ontario Ministry of Research and Innovation, Canadian Natural Science and Engineering Research Council (NSERC), and Brock University to PL, and was made possible using Compute Canada (now known as Digital Research Alliance of Canada) high-performance computing facilities. 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{
"id": "251957",
"date": "26 Mar 2024",
"name": "Rene Massimiliano Marsano",
"expertise": [
"Reviewer Expertise transposable elements",
"genetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, the Authors conduct a comparative analysis of 10 primate genomes unveiling the identification of a new type of mobile elements, which they call “retro-DNAs”, displaying combined features of two Class I (non-LTR retrotransposons) and Class II (DNA transposons) elements. The Authors initially annotated DNA transposons (remnants) in the analyzed genomes and subsequently have characterized a subset of sequences featured by an unusually long TSD and a poly-A tail. Furthermore, the Authors inferred the lineage specificity of retro-DNA and determine the expression level of retro-DNA sequences identified.\nThe manuscript is well-written and easy to read in all its parts.\n\nFind below a list of major issues.\n- While retro transposition can be considered as a way to spread transposable elements fragments around the genome and the information provided in this manuscript is (to my knowledge) new, I would be cautious in defining retro-DNAs as \"a new type of non-autonomous non-LTR retrotransposons\". retro position of expressed sequences is a common process and indeed, we do not define processed pseudogenes this way. I would therefore recommend modifying such a conclusion to avoid overstatements and misinterpretation of the result.\n- The expression analysis shows that some retro-DNA sequences are expressed in the testis. This finding compatible with what is usually seen for retrotranscribed pseudogenes? Testis activation of pseudogenes is well-documented, suggesting potential functional roles. Many pseudogenes are activated in the testis [1],[2]. In the case of TEs (and especially non-functional TEs) testis expression may evolve new regulation functions as observed in other transposition systems which are subjected to piRNA regulation.\n- I cannot see the supplementary files associated to the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11411",
"date": "30 Apr 2024",
"name": "Ping Liang",
"role": "Author Response",
"response": "Dear Dr. Marsano, Thank you very much for taking the effort to review our manuscript and for your overall positive review and constructive comments for improving the manuscript. We would like to offer our responses below to address the concerns you have raised and made some adjustments in our new version, and we would very much welcome your re-reading and approval. First, regarding your caution in our claiming retro-DNAs as “a new type of retrotransposon”, we would agree with you that many other types of DNAs, notably the mRNA of genes as processed pseudogenes or retrogenes, are not named as new types of retrotransposons in addition to LINEs/L1, SINEs/Alus and SVAs in the human genome. Very likely, we would agree with each other that a new type of retrotranspons (non-LTR specifically in our case), in addition to have the expected sequence features (i.e., polyA taile), would also have the ability to continue to retrotranspose like other non-autonomous non-LTR retrotransposons, such as Alus and SVAs, at least as a group, but not necessarily every individual copies. In other words, some of the retrotransposed copies (beyond the original copies) are able to be transcribed and retrotranspose. This extra feature would distinguish it from processed pseudogenes. Following this reasoning, we demonstrated that some of the retro-DNA copies have the capacity to transcribe or be transcribed and served as the parent copies of additional copies (Table 5 and Fig. 9A). Certainly, we realize the limitation of our data by lack of experimental data to the presence of demonstrate capacity of these copies, and ideally this is to be demonstrated by using the established retrotransposition assay (refs). However, this is beyond our reach as a bioinformatics-oriented research group, and it is our hope that by reporting such potential of these retro-DNA elements, interest can be stimulated by other groups to follow up with experimental verification. Considering limitation of our research data, we have adjusted the relevant point in our conclusion as “retro-DNA could be established as a new type of non-LTR retrotransposons if their intrinsic L1-based transposition capacity can be experimentally approved.” Second, regarding our use of testis tissues for expression analysis of these retro-DNAs, our rationale is related to above point, their potential as parent copies of transmissible retro-DNAs, since only they need to be expressed in gamete cells for this to happen. It is true that a lot of genes show sporadic expression beyond their regular expression pattern in other differentiated tissue, likely attributed to the unique epigenetic profile during spermatogenesis. But this may likely also be the attributing factor for the generally higher levels of germline retrotransposition of all known retrotransposons over somatic retrotransposition, with the former responsible for all transmitted retrotransposition events observed in the genomes. For this reason, even though we did include a mixed tissues sample and blood, with the latter as a widely available somatic tissue, in our expression analysis and showed a certain level of their expression, we thought it would be more meaningful to examine their expression in germline tissues. We would like to also include ovary as the female germline tissue, but it is unavailable across multiple species. For these reasons, we would like to argue that our focus on expression in testis tissue is justifiable. If you still have some concerns, we would welcome some specific suggestions for improving our writing. Lastly, you mentioned that you could not see the supplementary files associated to the manuscript. However, I check the link to the file, https://identifiers.org/biostudies:S-BSST1030, under the “Data availability” section, is working properly. On this linked page, there are 3 listed files you can click and download or you can choose to download all files (a button below the file list). We wonder if you could check it again and let us know if you can access properly. This is one of the public data repositories recommended by the journal. Thank you in advance for your second read and further comments or full approval. Sincerely, Ping Liang"
},
{
"c_id": "11618",
"date": "29 Jun 2024",
"name": "Ping Liang",
"role": "Author Response",
"response": "Dear Dr. Marsano, We would like to apologize for not doing a revision that could be a bit more thorough in responding to your review comments, leaving many issues as pointed out by the second reviewer. Now we have done another revision, which we believe should have improved the written presentation and interpretation significantly. We encourage and would much appreciate your reading of our responses to the reviewer 2's comments and version 3 of the paper which should become available shortly. We look forward to your further comments or full approval of the paper. Sincerely, Ping Liang"
}
]
}
] | 1
|
https://f1000research.com/articles/12-255
|
https://f1000research.com/articles/13-548/v1
|
28 May 24
|
{
"type": "Research Article",
"title": "Effectiveness of Mannitol Use on Clinical Outcomes of Severe Traumatic Brain Injury Patients",
"authors": [
"Syahrul Syahrul",
"Nasrul Musadir",
"Hidayaturrahmi Hidayaturrahmi",
"Taufik Suryadi",
"Aqil Naufal Syahrul",
"Nasrul Musadir",
"Hidayaturrahmi Hidayaturrahmi",
"Taufik Suryadi",
"Aqil Naufal Syahrul"
],
"abstract": "Background Head injuries are considered as a silent epidemic due to the high incidence rate throughout the world. The main cause of morbidity and mortality in patients with head injury is cerebral edema which is defined as abnormal fluid accumulation in the brain parenchyma. Mannitol is a hyperosmolar solution given to reduce fluid volume in the brain. Increased high intracranial pressure can affect prognosis and can be evaluated by assessing clinical outcomes in patients with severe traumatic brain injury using the Glasgow Outcome Discharge Scale (GODS) instrument.\n\nMethods Observational analytical study with a cross sectional design on 50 patients with severe traumatic brain injury at dr. Zainoel Abidin General Hospital Banda Aceh to determine the effect of mannitol use on the clinical outcomes of severe traumatic brain injury patients which used t test analysis.\n\nResults The mean value of the group that received mannitol had a higher GODS score than the group that did not receive mannitol. The results of the T test between groups obtained a p value of 0.000 which is smaller than 0.05, so it can be concluded that the use of mannitol has an effect on the GODS score in Severe traumatic brain injury patients. The results showed that the mean GODS value in patients who received mannitol was higher than those who did not receive mannitol.\n\nConclusion This concludes that the administration of mannitol is effective in improving the clinical outcomes of patients with severe traumatic brain injury at dr. Zainoel Abidin General Hospital Banda Aceh.",
"keywords": [
"GODS",
"Mannitol",
"Clinical Outcome",
"Severe Traumatic Brain Injury"
],
"content": "Introduction\n\nHead injury or traumatic brain injury is structural trauma or functional disorders that affect the brain through external mechanisms. Head injuries are a serious health problem experienced throughout the world because they can cause temporary to permanent impairment in physical, cognitive and psychosocial functions. The severity of head injury is classified based on the level of consciousness using the Glasgow Coma Scale (GCS), namely mild head injury (GCS=13-15), moderate head injury (9-12), and severe head injury (3-8). This classification is also supplemented by assessment of head CT scan findings.1,2\n\nHead injuries are known as a silent epidemic because their incidence is quite high throughout the world. The global incidence of head injuries is 939 cases per 100,000 population, which means an estimated 69 million people experience head injuries every year. Based on regional divisions according to the World Health Organization (WHO), the highest number of head injury cases occurred in the United States, namely 1299 cases per 100,000 population, followed by Europe with 1012 per 100,000 population, and Southeast Asia with 948 per 100,000 population. Most studies on head injuries show that the incidence of head injuries is twice as common in men as in women. The age range for head injury sufferers is the productive age, namely 29 to 45 years. Recent research reports that head injury incidents also occur at ages 50 to 75 years. The mechanisms causing head injuries can vary based on age range, gender and socio-economic factors. Traffic accidents are the highest cause of head injuries, followed by falls, violence, sports accidents and recreation.1–3\n\nResearch conducted by Syahrul et al. in 2020 at Dr. Zainoel Abidin General Hospital Banda Aceh found that out of 60 head trauma cases, 35 men and 25 women, with an average age of 18-39 years, 42% of patients experienced post-traumatic amnesia. The cause of trauma is 90% of traffic accidents using motorbikes, based on the Glasgow Coma Scale (GCS) assessment, 85% of cases have a GCS score > 9 and 25% with a score < 8, based on the results of head CT scans found in 25% of cases of cerebral edema, 18% of Epidural Hemorrhage, 15% intracranial Hemorrhage and 12% Subarachnoid Hemorrhage, while based on laboratory assessment 80% there was an increase in leukocytes with an increase in neutrophil segments 72%, Hyperglycemia &%, hyponatremia 2%, hypernatremia 11%, hypokalemia 22%, hyperkalemia 17% and hyperchloremia 30%.4\n\nThe World Health Organization (WHO) stated that in 2020, head injuries were one of the highest causes of death and disability throughout the world. Deaths due to head injuries were reported in 4.5 million cases or equivalent to 1:10 of all deaths. The mortality rate for severe head injuries ranges from 15–30% within 14 to 30 days after injury. Meanwhile, the significant recovery rate for patients with serious head injuries is also high, with the benchmark being that patients can care for themselves until they can return to work or return to school.3,4\n\nThe main cause of morbidity and mortality in head injury patients is cerebral edema.5 Cerebral edema is defined as an abnormal accumulation of fluid in the brain parenchyma.6 Cerebral edema begins with damage to cells and blood vessels, then followed by activation of cascade injury. The cascade begins with the release of glutamate into the extracellular space, then opens calcium and sodium channels in the cell membrane due to glutamate stimulation. The ATPase pump membrane removes one calcium ion and is replaced with three sodium ions. Sodium in cells creates an osmotic gradient and increases cell volume with the influx of water.5\n\nThe Monro-Kellie theory explains cerebral edema in the simplest terms. This theory states that the total volume in the skull bones is three, namely brain tissue 1400 mL (80%), Cerebrospinal Fluid (CSF) 150 mL (10%) and Cerebral Blood Flow (CBF) arteries and veins 150 mL (10%) Bones The skull is a rigid structure, stiff and unable to stretch, which means the volume inside the skull bone is always constant. If the volume of one component increases, it will force a reduction in the volume of the other component.7\n\nTherapeutic management of cerebral edema begins with general measures (optimizing head and neck position to facilitate intracranial venous outflow, avoiding dehydration and systemic hypotension, and maintaining normothermia). The main goals of this therapeutic management are to optimize cerebral perfusion, oxygenation, venous drainage, minimize cerebral metabolism and avoid ionic disturbances or gradients between the brain and vascular compartments.8\n\nMannitol is a hyperosmolar solution given to reduce fluid volume in the brain.9 There are two main mechanisms for mannitol to reduce intracranial hemorrhage ICH. The first mechanism is to increase the osmotic gradient of the brain barrier, where molecules are not free to diffuse (low permeability coefficient). Mannitol causes osmosis of water from the brain parenchyma, resulting in a decrease in brain water content and an increase in extracellular volume. Reducing brain water content reduces perilesional edema, which has been demonstrated in several clinical trials and animal tests. The second mechanism is related to rheological effects, mannitol can reduce hematocrit, viscosity and deformability of red blood cells resulting in increased microvascular flow and increased cardiac output and Mean Arterial Pressure (MAP). Increased blood and oxygen flow to the brain as well as cerebral vasoconstriction further reduce cerebral blood volume, reducing ICP and increasing CPP.10\n\nThe dose of mannitol for the treatment of cerebral edema is 0.25-1 g/kg. Loading dose (LD) 1g/kg BW, followed by maintenance dose (MD) 0.5 6 g/kg BW every 4-6 hours. The half-life of mannitol is 2.2-2.4 hours. Efficacy is visible within 15-30 minutes, and the duration of effect is 90 minutes to 6 hours. The mannittol preparation used in this study was 1 g/kgBW where 1 g was equivalent to 5 cc as the initial dose given for 30 minutes, 6 hours later given 0.25 g/kgBW which was reduced gradually over 3 days to prevent rebound phenomena. Mannittol preparations are available at hospital pharmacy installations as hyperosmolar liquid with batch number A50J52A with a supplier from Otsuka. Mannitol administration is recommended as a bolus and not as a continuous infusion in this therapy to maximize benefits and minimize side effects although there are no direct clinical trials comparing these two administration techniques.10\n\nThe prognosis of head injury patients is something that every clinician must pay attention to. The patient's family often asks the doctor questions regarding the patient's prognosis, such as the patient's awareness after injury, the possibility that the patient will be able to return to work or return to school. Information that can be used as a predictor of prognosis in patients with head injuries is very useful for clinicians in communicating with patients and families, making therapeutic decisions, and utilizing health personnel resources in treating patients with head injuries.11,12\n\nTo assess the outcome of head injury patients, you can use the Glasgow Outcome Scale (GOS) instrument, which is the most widely used measurement scale. The Glasgow Outcome Scale (GOS) has been developed into the Glasgow Outcome Scale Extended (GOSE), adopting a standard format for the interviews used to determine outcomes. Another outcome assessment scale for head injury patients issued by the University of Glasgow is the Glasgow Outcome at Discharge Scale (GODS) which is assessed when the patient has finished treatment. The GODS scale was proven to be valid and reliable for assessing the outcome of head injury patients.1–3\n\nBased on the description above, the condition of cerebral edema in severe traumatic brain injury needs to be treated by administering mannitol to reduce ICP so that the patient's clinical outcome will be better. Therefore, this study wants to analyze the effectiveness of using mannitol on the clinical outcomes of patients with severe traumatic brain injury using the Glasgow Outcome at Discharge Scale (GODS) outcome scale at the end of treatment at the dr. Zainoel Abidin General Hospital (ZAH) Banda Aceh.\n\n\nMethods\n\nThis research uses an analytical research design with a cross-sectional approach (cross sectional study). This research was conducted at ZAH. The population in this study were all head injury patients at ZAH in June-August 2023. The sample for this study was some head injury patients in the neurology inpatient ward at ZAH who meets the specified inclusion and exclusion criteria. The sample criteria used were age over 18 years, diagnosed with a serious head injury, onset of head injury ≤ 24 hours, and a CT scan of the head without contrast. This study also has exclusion criteria, namely patients who experienced multiple trauma, patients who were found to have non-traumatic abnormalities on a CT scan of the head, patients with a history of diabetes mellitus or cardiovascular disorders before injury, patients suffering from malignant diseases (neoplasms), patients who underwent surgical operations neurology, and Patients Returning Home at Their Own Request. The sample size and sampling technique in this study were calculated and the sample size was 47 patients.\n\nThe sampling technique was non-probability sampling with consecutive sampling. For samples who were unable to carry out interviews, those who acted as research respondents were companions. The patient's companion is the person who accompanies the patient during the treatment period in the inpatient room and is the one who knows the patient's progress best until the patient has finished undergoing treatment.\n\nThe data sources in this study were obtained from primary data and secondary data, primary data was used to assess interview results to determine the GODS score, while secondary data was obtained from medical records to investigate the administration of mannitol. The GODS instrument is a questionnaire formula for assessing the outcome of head injury patients, and is carried out when the patient has finished hospitalization. The GODS instrument was developed by the University of Glasgow in 2012. The GODS has proven to be very useful for research purposes or other clinical purposes. GODS can be used routinely by every medical worker who cares for patients with head injuries to assess PTA, attention and memory. The GODS focuses on disability, so that GODS can be used accurately and quickly by medical staff to make decisions about outpatient care (discharge planning).\n\nThe GODS instrument was prepared in English and to date has never been translated into Indonesian. In this study, the research will adapt the GODS questionnaire. The process of adapting the questionnaire begins with the translation stage, namely translating the GODS questionnaire into Indonesian. The questionnaire was then translated back into English by another translator. Then, the results of the translation in English are compared with the original questionnaire, assessing whether there is a change in meaning or not.\n\nThe research began by recording head injury patients who were admitted to the ZAH emergency room within ≤24 hours after the injury, then taking research samples that met the inclusion and exclusion criteria. The researcher then gave informed consent to the patient or the patient's companion. Giving informed consent was done in writing and was approved by the research ethics committee. Researchers collected data on the use of mannitol in patients with severe head injuries. Researchers assessed patient outcomes using the GODS form which was carried out when the patient was declared to have finished inpatient treatment. All data was recorded on a research sheet and analyzed univariately and bivariately.\n\nUnivariate analysis is used to analyze each research variable with the aim of assessing the percentage distribution of the variables observed descriptively. Bivariate data analysis to determine the effect of mannitol use on the clinical outcomes of severe traumatic brain injury patients at ZAH using the independent T-test with a significance value of 0.05 or a confidence level of 95%.\n\nThis study was approved by the Health Research Ethics Committee of the ZAH, Indonesia, No. 133/ETIK-RSUDZA/2023. Research ethical approval was issued on June 9, 2023.\n\n\nResult\n\nThis research was carried out from June 2023 to August 2023. The sample for this study was 50 patients with severe traumatic brain injury treated at ZAH, divided into 2 groups of patients who received mannitol and those who did not receive mannitol therapy, as well as interviews to assess the outcomes of head injury patients using the GODS scale. The subject characteristic can be seen in Table 1.\n\nBased on this research, it was found that the incidence of Severe traumatic brain injury occurred more frequently in male, namely 70%, based on the age group, the majority was found at the age of 18-30 years, namely 46%. Based on the lesion findings on head CT scans in Severe traumatic brain injury, it is a bleeding lesion multiple as much as 56%. The results of this study showed 50 Severe traumatic brain injury patients consisting of 35 male patients (70%) and 15 female patients (30%).\n\nBased on the findings of intracranial hemorrhage lesions, 48 patients were found with intracranial hemorrhage lesions in the form of subarachnoid hemorrhage in 10 patients (20%), intracerebral hemorrhage in 5 patients (10%), epidural hemorrhage in 5 patients (10%) and multiple hemorrhages were found in 28 patients (56%). Overall, the results of this study show that a CT scan of the head can identify primary head injuries or secondary head injuries in the form of cerebral edema.\n\nDistribution of GODS results for patients with severe traumatic brain injury can be seen in Table 2.\n\nThe results of the study showed that there were 9 patients who died during the treatment period after Severe traumatic brain injury (18%). Patients with good outcomes (Good Recovery) were found in the majority of patients, with details of 11 patients showing Upper Good Recovery (22%) and 14 patients showing Lower Good Recovery outcomes (28%). GODS Results for Severe Traumatic Brain Injury Patients at dr. Zainoel Abidin General Hospital Banda Aceh can be seen in Table 3.\n\nThe research results show the mean GODS score is 5.56 and the median is 6.50. The lowest GODS value is 1, and the highest value is 8 with a standard deviation of 2.47. The results of the study showed that there were 9 patients who died during the treatment period after head injury (18%). Patients with good outcomes (Good Recovery) were found in the majority of patients. The relationship between mannitol administration and GODS scores in patients with severe traumatic brain injury at dr. Zainoel Abidin General Hospital Banda Aceh can be seen in Table 4.\n\nBased on Table 4, it was found that the mean value of the group that received mannitol had a higher GODS score than the group that did not receive mannitol. The results of the T test between groups obtained a p value of 0.000 which is smaller than 0.05, so it can be concluded that the use of mannitol has an effect on the GODS score in Severe traumatic brain injury patients.\n\n\nDiscussion\n\nThe present study are in accordance with the epidemiology of head injuries in Europe which shows that the ratio of the incidence of head injuries compared to women ranges from 1.2:1 to 4.6:1.13 The results of this study are also in accordance with research on head injuries in Indonesia. For example, research conducted at Hasan Sadikin Hospital in Bandung in 2008-2010 showed that head injuries occurred more frequently in men. As well as the latest research conducted at M DJamil Hospital Padang in 2020, which shows that head injuries occur more frequently in men than women with a ratio of around 70%: 30%.14,15\n\nThe present study show that based on age group, head injuries most often occur in the productive age group, namely in the 18-30 year age group (46%), followed by the 32-45 year age group (24%), and the 46-60 year age group (22%). These results are in accordance with Imran's 2017 research at ZAH showing that the average age of head injury patients is 30 years.16 Research at Hasan Sadikin Hospital in Bandung also shows that head injuries occur more frequently in the productive age group (aged 18-45 years).14\n\nOverall, the present study in ZAH, show that head injury patients are in accordance with the epidemiology of head injuries throughout the world and in Indonesia, namely that cases occur more frequently in men than women, and often occur in those of productive age. This can be caused by the higher mobility and productivity of men and the productive age group compared to other age groups.\n\nThe present study also show that it is most likely that patients who experience intracranial bleeding after a head injury have multiple bleeding. This is in accordance with the theory that intracranial bleeding in head injuries is a primary brain injury due to a direct injury mechanism resulting from the trauma that occurred, and can occur in the coup area or counter-coup area as a result of shock to the brain tissue that occurs and rubs against the skull bone. Bleeding that occurs in all layers of the brain, causing bleeding in the form of hematoma or epidural, submissile or intracerebral bleeding.17,18 Head CT scan results that did not show intracerebral hemorrhage lesions were found in 2 patients, namely cerebral edema. This is in accordance with research conducted by Khairunnisa in 2020 at ZAH which showed that a normal CT scan of the head or cerebral edema could be found in head injury patients.19\n\nThe present study show that there is a possibility that patients will experience diffuse edema lesions due to head injury even without focal lesions of intracranial hemorrhage. This is in accordance with the theory that the pathophysiology underlying cerebral edema is neuroinflammation which can cause damage to the blood brain barrier (BBB) in the first 24 hours after head injury. This BBB damage results in infiltration of neutrophils, monocytes and lymphocytes into the injured brain parenchyma, resulting in polymorphonuclear leukocytes releasing complement factors and pro-inflammatory cytokines such as IL-1b, IL-6 and TNF-a at 24 hours post-trauma and resulting in changes in barrier permeability. brain blood, edema formation, and neurological deficits.20–22 The present study are in accordance with research conducted by Oliveira et al. In 2012, the GODS scale was used to assess the outcomes of head injury patients, and the GODS scale can assess all outcomes of head injury patients in detail, starting from death, vegetative state to good recovery.23\n\nThe GODS instrument was created by the University of Glasgow in 2012, which is a questionnaire to assess the outcome of head injury patients, and is carried out when the patient has finished hospitalization. GODS has proven to be very useful for research or other clinical purposes. GODS can be used routinely by every medical worker who cares for patients with head injuries to assess PTA, attention and memory. The GODS instrument focuses on disability rather than damage, so that GODS can be used accurately and quickly by medical staff to make decisions about outpatient care (discharge planning). The GODS assessment results were also shown to be in accordance with GOSE assessed at 3, 6 or 12 months after head injury.23–26\n\nThe present study showed that 9 head injury patients died (18%). These results indicate that there is a high probability that patients admitted with head injuries to ZAH will be in serious condition. Thus, the readiness of medical personnel in various fields, and the management program for head injury patients must always be ensured in good condition. The results of this study also show that the GODS instrument can be applied at ZAH to assess the outcomes of head injury patients treated at ZAH. The results of the GODS assessment can provide additional information for clinicians to educate patients and families regarding the patient's condition after inpatient treatment, and develop an outpatient program for patients when they return to their pre-head injury activities. This is very important and meaningful, especially for patients considering that ZAH is the main referral hospital in Aceh Province.\n\nMannitol is an osmotic diuretic used in emergencies and neurosurgery to treat increased intracranial pressure, which can occur after head trauma, neurosurgery, and other types of intracranial pathology. Mannitol is used to reduce increased intracranial pressure (ICP). The available preparation is liquid mannitol with a concentration of 20% (20 grams per 100 ml of solution). Mannitol can be given as an intravenous bolus or through a continuous infusion. The initial bolus dose usually given is 0.5-1.0 g/kg IV. Subsequent doses vary greatly.27–29\n\nBrain damage due to head injury causes an increase in intracranial pressure which can worsen patient outcomes which can be evaluated using the GODS score. Cerebral edema is a frequent and challenging problem in clinics and is a major cause of morbidity and mortality in brain injury patients.8 Cerebral edema with increased ICP occurs in most secondary brain injuries.27 Cerebral edema is defined as an abnormal accumulation of fluid in the brain parenchyma.6 Cerebral edema begins with damage to cells and blood vessels, then followed by activation of cascade injury. The cascade is initiated by the release of glutamate into the extracellular space. Calcium and sodium channels in cell membranes are opened by glutamate stimulation. The ATPase pump membrane removes one calcium ion and is replaced with three sodium ions. Sodium in cells creates an osmotic gradient and increases cell volume with the influx of water.9\n\nBased on this study, it was found that there were better GODS scores for patients who received mannitol therapy compared to patients who did not receive mannitol. The group that did not receive mannitol was because they did not meet the criteria for receiving mannitol, namely poor kidney and heart function. Mannitol is highly irritating to veins. When administering mannitol, you must use a filtered needle because crystals can form in the solution and be carried into the injection if you are not careful. In addition, monitoring laboratory test results and careful recording of intake and output to assess fluid volume status due to diuresis can be very important. High doses of mannitol have a risk of developing acute renal failure, especially in serum osmolarity > 320 mOsm/L, use of other nephrotoxic drugs, sepsis, previous kidney disease. Another side effect of mannitol is the rebound phenomenon, namely an increase in intracranial pressure when using mannitol for a long time, resulting in the accumulation of mannitol in the brain tissue so that the osmotic pressure becomes higher in the tissue which attracts fluid from the blood vessels to the brain tissue which causes brain edema heavier.30\n\nThe new finding from this study is that the GODS instrument can be used to assess the outcomes of head injury patients at ZAH. The GODS instrument is an instrument in the form of a detailed and detailed list of questions to assess the outcomes of head injury patients proposed by the University of Glasgow, which is an institution that also introduced the Glasgow Outcome Scale (GOS) and Glasgow Outcome Scale Extended (GOSE). The difference between GODS and GOS or GOSE is that GODS aims to assess the patient's disability after a head injury while the patient is still being treated and is planned for outpatient care (discharge planning). The GODS instrument has proven to be very useful for research purposes or other clinical purposes. The GODS instrument can be used routinely by every medical worker who cares for patients with head injuries to assess PTA, attention and memory. The GODS instrument focuses on disability rather than damage, so that GODS can be used accurately and quickly by medical staff to make decisions about outpatient treatment (discharge planning). Easily assessing the degree of disability of head injury patients is very useful for patients.\n\nThe present study as a whole show that treatment of patients with severe traumatic brain injury must be carried out appropriately and quickly. Therapeutic management of head injuries using mannitol should be carried out within the first ≤24 hours. Clinicians can then assess the outcome of head injury patients using the GODS instrument which is assessed when the patient has finished hospitalization.\n\n\nConclusions\n\nBased on the results of the research and discussion previously explained, it can be concluded that the characteristics of head injury patients at ZAH are in accordance with the epidemiology of head injuries, namely that they occur more frequently in men than women. Head injuries have also been proven to occur most frequently in the productive age group. Administration of mannitol is effective in improving the clinical outcomes of patients with severe traumatic brain injury at ZAH if assessed using the GODS instrument.\n\n\nConsent to publish\n\nWe have obtained written consent to publish from each individual respondent when the respondent filled out their consent to participate in this research. In the informed consent form it was stated that the results of this research would be published in a reputable international journal and also stated in the research protocol.\n\n\nEthics and consent\n\nThis study was approved by the Health Research Ethics Committee of the ZAH, Indonesia, No. 133/ETIK-RSUDZA/2023 June 9, 2023.",
"appendix": "Data availability statement\n\nZenodo, Effectiveness of Mannitol Use on Clinical Outcomes of Severe Traumatic Brain Injury Patients https://zenodo.org/records/10983092. 31\n\nThis project contains the following underlying data:\n\n• Master data for effectiveness of mannitol.xls.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAGREE Reporting Guideline Checklist is available on Zenodo: https://zenodo.org/records/11091191. 32\n\nZenodo: Extended data: Effectiveness of Mannitol Use on Clinical Outcomes of Severe Traumatic Brain Injury Patients, https://doi.org/10.5281/zenodo.11113667. 33\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nLevin HS, Boake C, Song J, et al.: Validity and sensitivity to change of the extended Glasgow Outcome Scale in mild to moderate traumatic brain injury. J. Neurotrauma. 2001; 18(6): 575–584. PubMed Abstract | Publisher Full Text\n\nDewan MC, Rattani A, Gupta S, et al.: Estimating the global incidence of traumatic brain injury. J. Neurosurg. 2019; 130(4): 1080–1097. Publisher Full Text\n\nHeidenreich KA: New Therapeutics for Traumatic Brain Injury. United Kingdom: Elsevier Inc; 2017.\n\nSyahrul I, Fajri N: Clinical Characteristics of Traumatic Brain Injury Patient in Dr. Zainoel Abidin Public Hospital Banda Aceh, Indonesia. Bali Med. J. 2020; 9(1): 194–200. Publisher Full Text\n\nJha RM, Kochanek PM, Simard JM: Pathophysiology and treatment of cerebral edema in traumatic brain injury. Neuropharmacology. 2019 Feb; 145: 230–246. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarmarou A: A review of progress in understanding the pathophysiology and treatment of brain edema. Neurosurg. Focus. 2007; 22: 1–10. PubMed Abstract | Publisher Full Text\n\nMacintyre I: A hotbed of medical innovation: George Kellie (1770-1829), his colleagues at Leith and the Monro-Kellie doctrine. J. Med. Biogr. 2014; 22: 93–100. PubMed Abstract | Publisher Full Text\n\nShawkat H, Westwood M, Mortimer A: Mannitol: A Review of Its Clinical Uses. Contin Educ Anaesthesia. Crit. Care Pain. 2012; 12(2): 82–85. Publisher Full Text\n\nShi J, Tan L, Ye J, et al.: Hypertonic saline and mannitol in patients with traumatic brain injury: A systematic and meta-analysis. Medicine (Baltimore). 2020 Aug 28; 99(35): e21655. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTorre-Healy A, Marko NF, Weil RJ: Hyperosmolar Therapy for Intracranial Hypertension. Neurocrit. Care. 2012; 17: 117–130. Publisher Full Text\n\nSilver JM, McAllister TW, Yudofsky SC: Textbook of Traumatic Brain Injury. 2nd ed. Wahington DC: American Psychiatric Publishing, Inc; 2014.\n\nVos PE, Diaz-Arrastia R: Traumatic Brain Injury. United Kingdom: John Wiley & Sons; 2015.\n\nPeeters W, van den Brande R , Polinder S, et al.: Epidemiology of Traumatic Brain Injury in Europe. Acta Neurochir. 2015; 157(10): 1683–1696. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZamzami NM, Fuadi I, Nawawi AM: Incidence and Outcome of Head Injury at Hasan Sadikin Hospital Bandung 2008-2010. J. Neuroanestesia Indones. 2013; 2(2): 89–94. Publisher Full Text\n\nZaki M, Hafiz A, Saanin S, et al.: Comparison of Neutrophil Lymphocyte Ratio in Traumatic Head Injury Patients With and Without Intracranial Hemorrhage at Dr. M. Djamil Hospital. Indones. J. Neurosurg. 2021; 4(1): 43–51.\n\nImran I: Karakteristik Dan Outcome Pasien-Pasien Penyakit Neurologis. J. Kedokt Syiah Kuala. 2017; 17(3): 168–173. Publisher Full Text\n\nMcGinn MJ, Povlishock JT: Pathophysiology of Traumatic Brain Injury. Neurosurg. Clin. N. Am. 2016; 27(4): 397–407. Publisher Full Text\n\nWhitfield PC: Traumatic Brain Injury A Multidiciplinary Approach. 2nd ed. Cambridge University Press; 2020.\n\nKhairunnisa: Kadar Interleukin-6 Plasma Sebagai Prediktor Outcome Pada Pasien Cedera Kepala.Thesis. Syiah Kuala University. 2020.\n\nO’Leary RA, Nichol AD: Pathophysiology of severe traumatic brain injury. J. Neurosurg. Sci. 2018; 62(5): 542–548. PubMed Abstract | Publisher Full Text\n\nSingh R, Choudhri K, Sinha S, et al.: Global outcome after traumatic brain injury in a prospective cohort. Clin. Neurol. Neurosurg. 2019; 186: 1–8.\n\nPrins M, Greco T, Alexander D, et al.: The pathophysiology of traumatic brain injury at a glance. DMM Dis. Model Mech. 2013; 6(6): 1307–1315. PubMed Abstract | Publisher Full Text\n\nOliveira RARA, Araújo S, Falcão ALE, et al.: Glasgow outcome scale at hospital discharge as a prognostic index in patients with severe traumatic brain injury. Arq. Neuropsiquiatr. 2012; 70(8): 604–608. PubMed Abstract | Publisher Full Text\n\nZhao JL, Du ZY, Yuan Q, et al.: Prognostic Value of Neutrophil-to-Lymphocyte Ratio in Predicting the 6-Month Outcome of Patients with Traumatic Brain Injury: A Retrospective Study. World Neurosurg. 2019; 124: e411–e416. Publisher Full Text\n\nStocchetti N, Zanier ER: Chronic impact of traumatic brain injury on outcome and quality of life: A narrative review. Crit. Care. 2016; 20(1): 1–10.\n\nSummaka M, Zein H, Elias E, et al.: Prediction of quality of life by Helsinki computed tomography scoring system in patients with traumatic brain injury. Brain Inj. 2020; 34(9): 1229–1236. PubMed Abstract | Publisher Full Text\n\nBatubara BH, Umar N, Mursin CM: Perbandingan Osmolaritas Plasma Setelah Pemberian Manitol 20% 3 mL/kgBB dengan Natrium Laktat Hipertonik 3mL/kgBB pada Pasien Cedera Otak Traumatik Ringan-Sedang. Jurnal Anestesi Perioperatif. 2016; 4(3): 154–161. Publisher Full Text\n\nFrieden TR, Houry D, Baldwin G: Traumatic Brain Injury In the United States. Epidemiology and Rehabilitation. 2015.\n\nRajendram R, Preedy RV, Martin RC: Diagnosis and Treatment of Traumatic Brain Injury The Neuroscience of Traumatic Brain Injury. Academic Press; Elsevier; 2022.\n\nSchwimmbeck F, Voellger B, Chappell D, et al.: Hypertonic saline versus mannitol for traumatic brain injury: a systematic review and meta-analysis with trial sequential analysis. J. Neurosurg. Anesthesiol. 2019; 33: 10–20. Publisher Full Text\n\nSyahrul S, Musadir N, Hidayaturrahmi H, et al.: Effectiveness of Mannitol Use on Clinical Outcomes of Severe Traumatic Brain Injury Patients. [Data set]. F1000Res. 2024. Reference Source\n\nSyahrul S, Musadir N, Hidayaturrahmi H, et al.: AGREE Reporting Guideline Checklist for article: Effectiveness of Mannitol Use on Clinical Outcomes of Severe Traumatic Brain 33. Injury Patients. F1000Res. 2024. Reference Source\n\nSyahrul S, Musadir N, Hidayaturrahmi H, et al.: Extended data for article: Effectiveness of Mannitol Use on Clinical Outcomes of Severe Traumatic Brain Injury Patients. F1000Res. 2024. Reference Source"
}
|
[
{
"id": "296718",
"date": "24 Jul 2024",
"name": "Brandon Lucke-Wold",
"expertise": [
"Reviewer Expertise Subarachnoid hemorrhage and TBI"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall mannitol offers an acute benefit for severe brain injury. The paper looks at systemic review for individual medication. In clinical scenarios, mannitol and hypertonic saline are often used in conjunction.\n\nThe authors need to address this possibility of confounding and other medications that may be influencing the reported outcomes. Interesting paper looking at mannitol for TBI.\n\nAuthors should address comparison to hypertonic saline\n\n[ref 1] and implications for various imaging concerns [ref2]\nIf the above are addressed and references included, paper would be of interest.\n\nShould also address how country factors can be of importance to overall outcomes.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "296717",
"date": "30 Aug 2024",
"name": "Farhad Bal’afif",
"expertise": [
"Reviewer Expertise Neurosurgery focus on vp shunt"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article investigates the effectiveness of mannitol in improving clinical outcomes for patients with severe traumatic brain injury (TBI) through an observational analytical study at dr. Zainoel Abidin General Hospital in Banda Aceh. The study included 50 patients, comparing those who received mannitol therapy with those who did not, using the Glasgow Outcome Discharge Scale (GODS) to assess outcomes. Key findings indicate that patients who received mannitol had significantly higher GODS scores, suggesting improved recovery outcomes. However, the study's cross-sectional design, though suitable for initial observations, lacks longitudinal follow-up, which could provide deeper insights into long-term patient outcomes. Despite these limitations, the findings support mannitol potential in enhancing recovery for severe TBI patients, highlighting avenues for future research to explore its comparative effectiveness and broader applicability in clinical practice.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "316006",
"date": "12 Sep 2024",
"name": "Muhammad Ashir Shafique",
"expertise": [
"Reviewer Expertise The curretn haven't done a proper and complete lit review"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper investigates the impact of mannitol administration on clinical outcomes for severe traumatic brain injury (TBI) patients using the Glasgow Outcome at Discharge Scale (GODS). The study is carried out at Dr. Zainoel Abidin General Hospital (ZAH), Banda Aceh, Indonesia, between June and August 2023. It focuses on determining whether mannitol treatment can effectively improve clinical outcomes for patients with severe TBI, assessed using GODS. The study design is cross-sectional and employs both primary and secondary data collection. It examines 50 patients divided into two groups: those who received mannitol and those who did not.\n- The paper does not discuss recent meta-analyses or systematic reviews on mannitol efficacy in severe TBI. Incorporating a comparison with findings from the two current meta-analyses ( [ ref 1 ] and [ ref 2 ] ) would provide additional context and validation.\n- The sampling technique used is \"non-probability sampling with consecutive sampling,\" which may introduce bias. A randomized sampling method would improve the robustness of the study and its generalizability.\n- There is insufficient detail about the characteristics of the control group (those who did not receive mannitol). A comparative analysis of baseline characteristics between the mannitol and control groups is needed.\n- Table 4 oversimplifies the relationship between mannitol administration and GODS scores. A multivariate analysis should be used to adjust for confounding factors such as initial GCS score, age, and comorbidities.\n- The study lacks a power analysis to determine if the sample size is adequate. Conducting a power analysis would help ensure the study is sufficiently powered to detect significant effects.\n- Terminology such as \"cerebral edema,\" \"intracranial hemorrhage,\" and \"severe traumatic brain injury\" is used inconsistently. Clarifying and standardizing these terms throughout the manuscript is important.\n- Although the GODS instrument was translated into Indonesian, there is no validation of this translation. Providing evidence of validation for the translated GODS instrument is necessary.\n- The study only assesses outcomes at discharge and does not include long-term recovery or complications. Including a follow-up period would provide insight into the long-term efficacy of mannitol.\n- The statistical methods are not clearly described, particularly regarding the T-test application. A more detailed explanation of the statistical analyses used, including assumptions for the T-test, is needed.\n- Conducted at a single center, the study's generalizability may be limited. Discussing the limitations related to generalizability and considering data from multiple centers could enhance the external validity of the findings.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-548
|
https://f1000research.com/articles/12-184/v1
|
16 Feb 23
|
{
"type": "Research Article",
"title": "Breast cancer related physical, psychological, social and spiritual domains of quality of life among women in Bahrain",
"authors": [
"Gayathripriya Narayanan",
"Muyssar Sabri Awadallah",
"Rajeswari Krishnasamy",
"Muyssar Sabri Awadallah",
"Rajeswari Krishnasamy"
],
"abstract": "Background: The objectives of the study were to assess the quality of life (QOL) among women with breast cancer and associate the QOL with selected background variables. Methods: A cross-sectional descriptive study was adopted for the study. Data collection was done in oncology units of tertiary care centers. The sample type includes woman with breast cancer at stage I or II or IIIa as per TNM classification. A purposive sampling technique was followed with a total sample size of 60. The tool used was the Quality of Life (QOL) questionnaire - Breast Cancer Version by National Medical Center & Beckman Research institute. Results: The QOL among study participants revealed that 42 (70%) had average QOL and 18 (30%) had poor QOL. The QOL was examined in various domains such as physical wellbeing, where the mean score was 38.47, the psychological wellbeing mean score was 60.58, social wellbeing mean was 38.10 and spiritual wellbeing mean was 38.58. There was an association between residence and occupation with QOL at p<0.05. Further there was an association between the clinical variable such as period and stages of cancer at p<0.05 and type of treatment at p<0.01. Conclusions: Breast cancer diagnosis has an undeniable effect on women at work, home and can have rapid consequences for other members in the family. Evaluation of QOL and associated factors would help the health care professionals especially nurses to organize health promotion activities and counselling sessions in varied health care settings to overcome challenges and improve Quality of Life.",
"keywords": [
"Breast Cancer",
"Quality of life",
"Women",
"Bahrain",
"lifestyle",
"multidisciplinary approach",
"psychological wellbeing",
"spiritual life"
],
"content": "Introduction\n\nThe worldwide occurrence of breast cancer varies from region to region and country to country. Most developed nations have a higher rate of breast cancer among their populations than developing and less developed nations. In all types of cancer among females, breast cancer affects a large number of women throughout the world. In 2020, around 2.3 million women were diagnosed with the breast cancer and during the last five years women with breast cancer reached around 7.8 million (WHO, 2021). This makes breast cancer one of the most prevalent cancers among women. The survival rate for breast cancer patients has also improved when early detection is carried out. In developed countries the survival chances are 90%, while in Asian countries it’s 66% and in African countries it is a mere 40% (American Cancer Society, 2022).\n\nIn populations of Arab women, breast cancer is the most widely occurring cancer. In six Gulf Cooperation Council (GCC) countries, the most abundant cancer in women is breast cancer. In Bahrain around 54.4% of cancer among female is breast cancer. Middle eastern countries, UAE (United Arab Emirates), and Saudi Arabia have low incidences of breast cancer while countries like Bahrain, Qatar and Kuwait have high incidence rate for these types of cancer. Compared to most developed European countries, the spread of breast cancer among Arab women is almost the same or less (Hamadeh et al., 2014).\n\nDue to the difference in environmental and lifestyle related factors the incidence of breast cancer is highly variable among most advanced economies and growing economies. However, each region may also face the presence of breast cancer cases according to the fertility rate and health of the woman.\n\nThe alarming rate of increase of breast cancer in Bahrain suggests the requirement of multi-disciplinary approach in prevention and control of this disease. There are many factors responsible for the rapid spread of breast cancer in women and these may include hereditary oncogenes. The study on Bahrain women for awareness of Breast cancer suggest that there is lack of knowledge about prevention and control of breast cancer among Bahrain women (Brazee, Nugent, Sereika, & Rosenzweig, 2021).\n\nIn Bahrain, cancer is the second leading cause of death after cardiovascular diseases, with around 10% of deaths caused by cancer. In Bahrain, it is mandatory to document new cases of cancer into Bahrain Cancer Register (BCR) at the Ministry of Health (MOH). According to the published report for the incidence of cancers in Bahrain, breast cancer has the topmost incidence rate among all cancers in women. In 2020, around 244 cases were reported for breast cancer which is around 37.9% of the total cases of cancer in women in Bahrain. Breast cancer is the highest occurring cancer followed by colorectum cancer, ovarian, corpus uteri, lung, and others. The incidence and mortality rate for breast cancer is higher in Bahrain. Overall, Breast cancer is the leading cause of disrupting Quality of life (QOL) among women (Kefale, Alebachew, Tadesse, & Engidawork, 2019).\n\nThe Bahrain cancer society has been running an awareness campaign for breast cancer for 20 years in Bahrain and has educated many women on breast self-examination and detection through mammogram. According to guidelines, women aged 40 years or above should take a mammogram every two years to keep track of breast health and early diagnosis of cancer (Akpaniwo, Boynes, Danfulani, Chigozie, & Umar, 2016). Ministry of health, Bahrain in collaboration with BATELCO (Bahrain Telecommunication Company) started a mission for early detection of breast cancer in 2005. Often, women with breast cancer face many physical, medical and psychological challenges. The developments in treatments have consequently led to an increasing focus on quality of life issues among breast cancer patients and in research (Montazeri et al., 2008). There is a strong need to understand effects on Quality of Life (QOL) in breast cancer patients. Apart from physical challenges, women generally faced many other challenges during diagnosis, treatment and control of breast disease. This article is an attempt to explore our understanding on effect on quality of life (QOL) among breast cancer patients by specifically surveyed Bahrain women patients.\n\n\n\n1. To explore the dimensions of Quality of Life among women with breast cancer\n\n2. To associate the quality of life with selected background variables among women with breast cancer\n\n\nMethods\n\nThe study was conducted in outpatient and in-patient departments of the Oncology Unit, Salmaniya Medical Complex (SMC) where the investigators were able to access the breast cancer patients. A non-experimental, cross–sectional descriptive survey design was adopted.\n\nWomen diagnosed with breast cancer and those who fulfilled the inclusion criteria and available during data collection period were recruited for the study. The samples were recruited through a purposive sampling technique based on the selection criteria. The total sample size was 50 and the piloted study samples were excluded for the main study. EBI information program version 10 was used to estimate the sample size using the following parameters such as population size of 120 patients, confidence coefficient of 90%, expected frequency of 50% and acceptable error of 5%. The minimum required sample size was 50 patients. The inclusion criteria for participation in the study were: must be in the age group of 30-60 years, must have been diagnosed with breast cancer of either stage I or II or III a as per TNM classification, must be planning a mastectomy within a month, be under the radiation and (or) chemotherapy, and be able to understand Arabic or English.\n\nParticipants were excluded from the study if they had already had a mastectomy, were practicing any type of relaxation methods, had any psychiatric illness, or were on metastatic stage.\n\nThe data was collected through a self–reported questionnaire (26) in Arabic. The researcher introduced themselves to the study participants and explained the need for conducting this study. The questionnaires were then distributed to the participants. Participants were given blank questionnaires to complete with demographic data, education, marital status, stages of cancer and type of treatment, clinical variables, physical well-being, social concerns, and spiritual well-being data. In the hospital, participants completed the questionnaire on paper. Each participant took approximately 30 minutes to complete the questionnaire. The questionnaire was completed by each participant with all the information requested.\n\nThe Quality of Life Instrument–Breast Cancer patient version tool was used in this study to collect the data. This tool was developed by National Medical Center & Beckman Research Institute to assess the Quality of Life among breast cancer patients. The questionnaire consists of 46 questions categorized into four categories such as physical wellbeing, psychological well-being, social well-being and spiritual well-being. Participants in the study were requested to answer each question in 10-point Likert scale.\n\nThe structure of the questionnaire is outlined below:\n\nPart I: Background variables; Demographic variables including age, residence, educational status, marital status, occupation, family, religion, income/month, and types of family.\n\nClinical Variables including period of illness, stages of cancer and types of treatment.\n\nPart II: Breast cancer Quality of Life tool. The tool is available in both English and Arabic, prepared by National Medical Center and Beckman Research Institute (2010).\n\n• 45 item ordinal scale, measures the QOL of a breast cancer patient\n\n• Four domains including physical wellbeing, psychological wellbeing, social wellbeing and spiritual wellbeing.\n\n• The scoring is based on a scale of 0 to 10 which ranges from worst outcome to best outcome\n\n• Total score 460 was interpreted as follows:\n\nTable 1 shows the scoring based on a scale of 0 to 10, with 0 being the worst outcome and 10 being the best.\n\nAfter the questionnaire was developed for “Breast cancer and Quality of life among Bahraini women”, it was analyzed for its validity and reliability. A content validity assessment was conducted to determine the tool's validity by a panel of nurses with experience in oncology and QOL researchers. The QOL-CS is a 46-item visual analog scale composed of four multi-item sub-scales (physical well-being, psychological well-being, social well-being, spiritual well-being).\n\nApproval from the ethical committee at College of Health Sciences, Research committee at Ministry of Health (approval no. FA/SA/528), was obtained to conduct the study. A written consent form was taken from the study participants and they were informed that participation was voluntary and they could withdraw from the study at any time. We had determined the ethical principles of confidentiality and anonymity by not showing the identities and information to others. Participants were told about that the study findings will be utilized for research purpose and publications.\n\nThis tool had undergone rigorous reliability and validity with international standards. According to the geographical location the reliability and validity was done through the pilot run. The face and content validity were done by the subject expert in the field. And there was no major changes in the translated tool and the tool was considered valid.\n\nBy employing the Test-Retest method, the tool's reliability was assessed after the pilot study. It was determined that the overall QOL-CS tool test re-test reliability was.89, with subscales of physical r=.88, psychological r=.88, social r=.81, and spiritual r=.90. There is a strong correlation between breast cancer and women's quality of life, and the correlation coefficient is quite high, which makes it a good tool for measuring both. The tool is beneficial for assessing breast cancer and quality of life among Bahraini women.\n\nThe preliminary pilot testing was conducted among 5 samples as this was 10% of the total sample size on the translated questionnaire. And these samples were not included in the actual study. The tool was valid, reliable and feasible to conduct the actual study. The obtained data were analyzed, and the findings ensured the feasibility to conduct the main study.\n\nDemographic information was provided in categories such as frequencies and percentages. The QOL scores' frequencies were provided, along with their percentages, means, and standard deviations. The relationship between demographic factors and the degree of QOL score was examined using the Pearson chi-square test. Using a one-way analysis of variance and student independent t-tests, the relationship between demographic variables and mean QOL score was examined. The data was represented using simple bar diagrams, multiple bar diagrams, pie diagrams, and box plots (not shown). P<0.05 was considered statistically significant, and all statistical tests were two-tailed.\n\n\nResults\n\nThe main purpose of this study was to measure quality of life of the patients with breast cancer in Bahrain. To investigate, the questionnaire was segmented in four parts representing four main domains. The QOL-CS is a 46-item visual analog scale composed of four multi-item sub-scales (physical well-being, psychological well-being, social well-being, spiritual well-being). Each question was evaluated on a scale of 0 to 10 and represented results on mean overall score for the question. A score range between 0 to 90 is considered very poor, 91 to 180 is poor, 181 to 270 is average, 271 to 360 is good and 361 to 460 is considered very good.\n\nData was collected for the demographic profile of each breast cancer patient included age, location, education level, marital status, occupation, religion, family income and type of family. The full dataset can be found under Underlying data (Narayanan et al., 2022).\n\nThe demographic information of breast cancer participants in the “Breast cancer and quality of life among Bahraini women” study is presented in Table 1. As stated in Table 1, around 46% of women with breast cancer fall within the age group of 41 to 50 years old. A total of 18% of Bahraini women under the age of 40 are diagnosed with breast cancer, indicating that breast cancer incidence increases after middle age. 21 cases for breast cancer in women were reported from the North region of Bahrain and 13, 7 and 9 cases were reported from the Capital, South and Muharraq respectively. The highest number of cancer cases reported in women with at least bachelors level of education which is 40% of all reported cases in this study. Interestingly, around half of the women with breast cancer were homemakers. This may be due to lack of active lifestyle among Bahrainian homemakers (Tanner & Cheung, 2020). Religion and family income were neutral parameters, and they were not evaluated in this study and act as supporting data for any other future analysis. As most of the cases of breast cancer were from nuclear families, it may affect quality of life after diagnosis of the patient due to lack of support from the nuclear family, which can be reversed if the patient gets support from joint or extended family. For a patient to deal with cancer it is very important to have psychological and mental support from family.\n\nClinical variables were studied in breast cancer patients such as duration of the illness, stage of cancer, and type of treatment (Table 2). Out of 50 participants in this study, around 32 (64%) were diagnosed with cancer within the last year and 18 (36%) cases had breast cancer for over a year. Participants were selected so that approximately all stages of cancer were covered and thus 18 (36%), 14 (28%), 12 (24%) and 6 (12%) cases were examined for Stage I, Stage II, Stage III and Stage IV, respectively. The breast cancer patients were given different types of treatment such as surgery, chemotherapy, anti-retroviral therapy, and radiation. Sixty-four percent (32 women) received either chemotherapy with surgery or chemotherapy with surgery and antiretroviral therapy. 64% (32 women) received either chemotherapy in conjugation with surgery or chemotherapy in conjugation with surgery and anti-retroviral therapy.\n\nTable 3 represents the evaluation of physical wellbeing questions related to quality of life. Breast cancer patients struggle through various physical challenges such as fatigue, pain, appetite changes, sleep disorders, vaginal discharge, menstrual changes and other physical problems. The findings on 50 breast cancer patients suggest that fatigue, pain and sleep changes have a higher than median score for quality of life while problems such as vaginal distress, menopausal symptoms and menstrual changes are more significant in women with breast cancer. In terms of physical health, the overall score for patients is 31.76 out of 80 and 39.70% of the mean score. The psychological state is most affected in breast cancer patients because cancer is known as an untreatable disease. People have a general perception that cancer is a terminal disease and non-treatable. These cause more psychological stress for patients.\n\nTable 4 represents psychological challenges faced by breast cancer patients. Among 22 questions for psychological wellbeing, three questions were found to have lower than 40% QOL. This represents the difficulty faced by patients after the diagnosis of the disease and during the treatment phase. The overall quality of life for breast cancer patients is above average and represented by the mean QOL score of 73%. Positive parameters such as happiness, satisfaction, memory power, usefulness, and self-awareness were found to be above average in terms of quality of life. The negative impact parameters such as anxiety and depression were not very problematic in breast cancer patients.\n\nTable 5 represents that the treatment phase for the breast cancer patients was comfortable, these may be due to availability of resources for treatment and medical facilities in Bahrain hospitals. In most cases, patients did not experience major distress during the initial diagnosis, chemotherapy or surgery for cancer, while radiation therapy received a lower QOL score (4.72) which represents that it might be painful or not patient friendly. Most patients were skeptical about the future after their initial diagnosis and due to these there is constant fear among the patient of the reoccurrence, future diagnosis, metastatic cancer and loss of time. The social life of cancer patients is most affected due to diagnosis and treatment of disease. The mean score percentage for two questions were higher than 70%, which represents that the patients felt more concern about their family members after they tested positive. A mother with breast cancer may start worrying about her daughter due to heredity threat. Most participants received a good amount of support from their family members. All other factors including personal relationship, workplace situation, sexuality, and financial burden were found to be lower in terms of impact on a patient's life after breast cancer.\n\nTable 6 represents the spiritual wellbeing and the data on this variable is quite interesting. The spiritual wellbeing is mostly unaffected by the disease and women felt more spiritual after diagnosis of the disease and during treatment. The mean percentage for spiritual wellbeing is highest (82.09%) among all variables and spiritual life may increase the patients’ positivity of. The association between the level of quality of life and demographic variables proves two inferences and two variables found significant through a chi square test. Elders and those with higher levels of education have a higher QOL score than others. This may be due to the subsidence of symptoms after some age. Those with higher levels of education were more aware about self-examination, self-care and treatment procedures and the way of dealing with critical situations. This could prove beneficial to them compared to less educated individuals. All other demographic variables were found non-significant as per Table 7.\n\nThe association between quality of life and clinical variables can be seen in Table 8. Less duration of illness and lower stage of cancer resulted in a higher QOL score than others. The type of cancer treatment and complimentary medicine have no relation with the quality-of-life score. When observing the association between level of physical wellbeing through quality of life and demographic variables, elders who were ill for less time and who were at an earlier stage of cancer had a highger QOL score than others (Table 9). The One-way ANOVA test is used to determine whether psychological wellbeing quality of life is associated with demographic characteristics. Elder and more educated women have a higher QOL score than others at a psychological level. All other demographic and clinical variables were non-significant (as shown in Table 10). An analysis of one-way ANOVA data shows that women with more education and fewer stages of cancer have a greater quality of life score than women without education or cancer. All other variables were found to be non-significant with respect to social wellbeing (Tables 11, 12). The association between spiritual wellbeing quality of life score and demographic variables shows less duration of illness and less cancer stage results in a significantly higher QOL score than others.\n\nFinally, while comparing the association between overall quality of life and demographic variables, it was found that elders who were more educated, were ill for less time and had less cancer stages women had a higher QOL score than others. The obtained results were in-line with the individual QOL score with respect to each variable.\n\n\nDiscussion\n\nAbnormal growth of cells results in the formation of cancer. Breast cancer develops when cells out regulate their normal growth and start aggregating at the breast area. Around 50 to 60% of breast cancers develop in the milk ducts, around 5-20% develop in lobules and the remaining begin in other areas of breast tissues. The more profound treatment for breast cancer is surgery and most cases can be treated easily. The surgery can be followed up by additional treatments such as chemotherapy, anti-retro viral therapy, radiotherapy and hormonal replacement therapy (NBCC, 2022).\n\nThe mastectomy is the most common breast cancer treatment in which a portion of cancer-affected cells can be removed through surgery, and it removes a few normal cells from the rim of the cancerous cells. This type of surgery is widely used in removing breast cancer. There are various surgical procedures, but mastectomy and breast-conserving surgery are the most popular (De Siqueira et al., 2022). Any surgery's primary goal is to remove a tumor in its early stages to prevent it from spreading to other healthy tissue. Some people require extra (adjuvant) therapies, including chemotherapy, radiation, and hormones depending on the stage of the disease, the patient's age, and the hormonal/condition of the tumor (Adamowicz & Baczkowska-Waliszewska, 2020). Adjuvant therapies have been demonstrated to lower the chance of recurrence, improving survival in breast cancer patients (Ghanei Gheshlagh, Mohammadnejad, Dalvand, & Dehkordi, 2022). Chemotherapy lowers the mortality rate by 38% for people under 50 and 20% for those over 50. When determining if systemic adjuvant therapy is necessary, factors such as the patient's age, hormonal state, risk of recurrence, side effects, and actability must be considered. The patient's body surface is used to calculate the dosage of chemotherapy, which can be administered every week or every three weeks. The most common side effects of chemotherapy are hair loss (60%), fatigue (74.7%), decreased appetite (65.5%), changes in taste (60.9%), nausea and vomiting (79.3%), dry mouth (51.7%) and constipation (51.7%). A patient is usually scheduled for radiotherapy three to eight weeks after surgery, depending on whether chemotherapy will follow.\n\nSeveral adverse effects, including those impacting quality of life, exhaustion, and discomfort, are linked to breast cancer treatment (Montazeri, 2008). Fatigue is the adverse effect that patients with breast cancer report experiencing the most. The effects of fatigue, which include weakness, exhaustion, and lack of energy, can frequently persist for years after the completion of treatment (Choi & Henneghan, 2022). Few studies concentrate on the epidemiology and treatment of major depression, although there is evidence that depression considerably impacts the quality of life in breast cancer patients. Distress and mixed depressive states have been the main topics of the therapy investigations (El Mokhallalati et al., 2022).\n\nBody image distorted from mastectomy and sexuality problems after treatment are likely to produce more mood related disorders (Montazeri, 2008). The link between higher risk of breast cancer and depression is a very complicated and complex problem among the literature. Some studies suggested a protective factor, while others find a relation between stress, immunity and cancer occurrences or even mortality. The study on breast cancer survivors reported a higher prevalence of mild to moderate depression with a lower QOL in all areas except for family functioning and treatment of depression in breast cancer women improved their QOL and might increase longevity (Setyowibowo et al., 2022). Anti-depressant medications remained the cornerstone of depression treatment. The hypothetical link between their prescription and increased breast cancer risk was not supported by the literature.\n\nBreast cancer is widespread among Bahraini females; around 37.1% of all cancers are breast-related (Martin et al., 2021). Annually around 54.4 per 100,000 people are diagnosed with breast cancer worldwide. Generally, research shows increased chances of breast cancer over 20 years old. The less ASR (34.9 in 100,000) was reported in 1998, and the highest (63.2 in 100,000) was reported in 2001. There is a tendency for increased ASR trend; however, it was not statistically significant (p-value = 0.3188) (10 years cancer incidence among Nationals of the GCC states (1998-2007). Most people can still clearly recall their feelings after learning they had breast cancer. Whatever the patient's first feelings are, they may later go through a wide range of emotions. When someone is dealing with a potentially fatal condition, anxiety is only natural. They may become irritated, experience appetite and sleep changes, become hyperactive, and experience heart palpitations due to stress. Anxiety can occasionally become so severe that it triggers panic episodes, which increases anxiety and worry (Podvorica, Kraja, Rrustemi, Dugolli, & Hyseni, 2022).\n\nQuality of life is now considered an important tool to measure patient wellbeing in cancer clinical trials. It has been shown that assessing QOL in cancer patients could contribute to improving treatment and be prognostic as several medical factors. Above all, studies of QOL can further indicate the directions needed for more efficient treatment of cancer patients. Among the QOL studies in cancer patients, breast cancer has received the maximum attention for several reasons (Osoba, 2021). When women develop breast cancer, all members of the family might develop some sort of illnesses. Further research is needed for improvements in medicine and medical practice and studying the quality of life for breast cancer can increase QOL among patients (Kimura, Kamada, Guilhem, & Monteiro, 2013).\n\nIt is crucial to assess the quality of life of women who lose their breasts since breast cancer impacts their personality and sense of self. Women usually have a significant role in the family, and when one woman is diagnosed with breast cancer, all the family members may be affected. As a result, research into the long-term implications of breast cancer detection and therapy is now necessary because the prevention and treatment of the disease have become essential issues. The time during initial treatment and months following it are very hard for the patients, poor QOL can be observed in this phase, and by recognizing proper QOL parameters, treatment can be modified without affecting QOL (Jiang, Torgerson, & Ayars, 2015).\n\nA study on decreased health-related QOL due to chemotherapy side effects may predict early treatment discontinuation in patients with breast cancer. The studies on post-treatment adjustment of breast cancer survivors demonstrated that breast cancer patients might enjoy a good QOL (Ghanei Gheshlagh, Mohammadnejad, Dalvand, & Dehkordi, 2022). When Casso, Buist, and Taplin examined the QOL of women who had been diagnosed with breast cancer between the ages of 40 and 49 and had survived for five to ten years, they found that these younger women had an excellent quality of life (Casso, Buist, & Taplin, 2004). However, when trying to comprehend and improve long-term QOL, it may be crucial for doctors and breast cancer patients to consider the long-term effects of adjuvant therapy and the management of long-term breast-related symptoms (Moshina, Falk, & Hofvind, 2021). Throughout their lives, body image fluctuates frequently, and disease can impact how they feel and cause low levels of self-confidence. After diagnosis and therapy, they could have a radically different perspective of their body than they did previously. Treatment for breast cancer may serve as a permanent or recurring visual reminder. Patients can have scars and skin changes following radiotherapy, hair loss or regrowth following chemotherapy, and lymphedema (Lin et al., 2022).\n\nAdditionally, the course of treatment may induce weight increase or loss. All of these cause people to feel less satisfied with their bodies and less confident about their appearance. Changes in a person's body image and self-esteem may impact their feelings about their sexuality and interpersonal interactions. Around the time of diagnosis, sleep patterns frequently change, and this disruption may last during therapy and even after. Sleep patterns typically eventually revert to normal. The main reasons for sleep disruption are stress and worry brought on by the cancer diagnosis and its side effects. According to Bower, behavioral symptoms, such as energy, sleep, mood, and cognition disruptions, are a frequent adverse impact of breast cancer diagnosis and therapy (Bower, 2008). These symptoms cause severe disruption in patients' quality of life and can be seen for years after the treatment. To circumvent and alleviate Total Mood Disturbance (TMD), patients should be educated on how relaxation, meditation and yoga can be helpful. The scores represented a 13% reduction in overall mood disturbance for the participants after practicing meditation (Martin, Loomis, & Dean, 2021).\n\nIn our study, after the questionnaire was developed for “Breast cancer and Quality of life among Bahraini women”, it was analyzed for its validity and reliability. A content validity assessment was conducted to determine the tool's validity by a panel of nurses with experience in oncology and QOL researchers.\n\nThe QOL-CS is a 46-item visual analog scale composed of four multi-item sub-scales (physical well-being, psychological well-being, social well-being, spiritual well-being). Overall percentage of QOL among breast cancer women is 54.50%. There are more QOL score in spiritual with 82.09% and minimum score in physical with 39.70%, while psychological and social having score of 44.93% and 49.60% respectively. This indicates maximum adverse effects on quality of life starting from first physical, second psychological, third social and lastly spiritual well-being. Within psychological variable most adverse effect observed among breast cancer patient is fear for present and future, while distress was second major parameter affecting psychological health. General psychological parameters were moderately affected due to disease condition.\n\nNone of the women have a very poor or poor quality-of-life score; 42% have an average QOL score, 52% have a good QOL score, and 6% have an excellent QOL score (Tables 9-11). This indicates that breast cancer is a manageable disease, and around 90% of patients can get back to their daily life and have a considerably good quality of life through some changes in lifestyle and extra care for their health. The current study provides important information about Bahraini women's breast cancer related physical, psychological, social, and spiritual quality of life domains. Our study is population-based, and the characterization of this population concerning risk factors for breast cancer is incomplete, being only able to analyze the association between levels of physical, psychological, social, and spiritual domains of quality of life. A disease-free control group should be included in future research, as well as complete clinical information regarding cancer in the Cancer Registry, including grade, stage, and location of the disease.\n\n\nConclusion\n\nBreast cancer has affected many women in Bahrain, and it is essential to know about the quality of life of Bahrain women with breast cancer. The current study was carried out on the patient population to determine women's difficulties after a cancer diagnosis. It was found that over half of women had a good quality of life and faced some difficulty after diagnosis. The quality of life of women was affected due to four parameters: physical, psychological, social, and spiritual. Spiritual life was least affected, while social and psychological parameters were moderately affected due to breast cancer. Quality of life as a physical parameter, has a minimum quality of life score, and they are worst affected due to breast cancer.",
"appendix": "Data availability\n\n\n\n- Figshare: Breast cancer related physical, psychological, social and spiritual domains of Quality of Life (QOL) among women in Bahrain. https://doi.org/10.6084/m9.figshare.21385275.v2 (Narayanan et al., 2022).\n\nThis project contains the following underlying data:\n\n- BCA Final Data Coding - Underlying Data.xlsx (Demographic and Clinical Variables, Physical Wellbeing, Social Concerns and Spiritual Wellbeing data)\n\n- CODING key.xlsx\n\nThis project contains the following extended data:\n\n- Questionnaire.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAdamowicz K, Baczkowska-Waliszewska Z: Quality of life during chemotherapy, hormonotherapy or ANTIHER2 therapy of patients with advanced, metastatic breast cancer in clinical practice. Health Qual. Life Outcomes. 2020; 18(1): 134. PubMed Abstract | Publisher Full Text\n\nAl Hajeri A: Prospective view of breast cancer in Bahrain. J. Bahrain Med. Soc. 2013; 24(3): 104.\n\nAkpaniwo G, Boynes S, Danfulani M, et al.: Should MRI replace mammography as the initial screening modality for asymptomatic women aged 18 – 45 years at high risk of developing breast cancer? A systematic review. Asian J. Med. Sci. 2016; 7(5): 1–9. Publisher Full Text\n\nAmerican cancer Society: Breast Cancer - Facts & Figures.2022.Reference Source\n\nAnon: Breast Cancer Advocacy & Support. National Breast Cancer Coalition;2022. [Accessed March 24, 2022].Reference Source\n\nBower JE: Behavioral symptoms in patients with breast cancer and survivors. J. Clin. Oncol. 2008; 26(5): 768–777. PubMed Abstract | Publisher Full Text\n\nBrazee RL, Nugent BD, Sereika SM, et al.: The quality of end-of-life care for women deceased from Metastatic Breast Cancer. J. Hosp. Palliat. Nurs. 2021; 23(3): 238–247. PubMed Abstract | Publisher Full Text\n\nBreast cancer:26 March 2021.Reference Source\n\nCasso D, Buist DS, Taplin S: Quality of life of 5–10 year breast cancer survivors diagnosed between age 40 and 49. Health Qual. Life Outcomes. 2004; 2(1): 25. PubMed Abstract | Publisher Full Text\n\nChoi E, Henneghan AM: Comparing Fatigue, Loneliness, Daytime Sleepiness, and Stress in Younger and Older Breast Cancer Survivors: A Cross-Sectional Analysis. Clin. J. Oncol. Nurs. 2022; 26(2): 155–164. PubMed Abstract | Publisher Full Text\n\nDe Siqueira GS, Hanna SA, De Moura LF, et al.: Moderately hypofractionated radiation therapy for breast cancer: A Brazilian cohort study. SSRN Electron. J. 2022. Publisher Full Text\n\nElMokhallalati Y, Alaloul E, Shatat M, et al.: The symptom burden and quality of life in cancer patients in the Gaza Strip, Palestine: A cross-sectional study. PLoS One. 2022; 17(1): e0262512. PubMed Abstract | Publisher Full Text\n\nGhanei Gheshlagh R, Mohammadnejad E, Dalvand S, et al.: Health-related quality of life in patients with breast cancer: A systematic review and meta-analysis. Breast Dis. 2022; 41(1): 191–198. Publisher Full Text\n\nHamadeh RR, Abulfatih NM, Fekri MA, et al.: Epidemiology of breast care among Bahraini women, Data from the Bahrain cancer Registry. Sultan Qaboos Univ. Med. J. 2014; 14(2): e176–e182.\n\nJiang F, Torgerson TR, Ayars AG: Health-related quality of life in patients with primary immunodeficiency disease. Allergy, Asthma Clin. Immunol. 2015; 11(1): 27. PubMed Abstract | Publisher Full Text\n\nKefale B, Alebachew M, Tadesse Y, et al.: Quality of life and its predictors among patients with chronic kidney disease: A hospital-based Cross Sectional Study. PLoS One. 2019; 14(2): e0212184. PubMed Abstract | Publisher Full Text\n\nKimura CA, Kamada I, Guilhem D, et al.: Quality of life analysis in ostomized colorectal cancer patients. J. Coloproctol. 2013; 33(04): 216–221. Publisher Full Text\n\nLin Y, Yang Y, Zhang X, et al.: Manual lymphatic drainage for breast cancer-related lymphedema: A systematic review and meta-analysis of randomized controlled trials. Clin. Breast Cancer. 2022; 22: e664–e673. PubMed Abstract | Publisher Full Text\n\nMartin RE, Loomis DM, Dean GE: Sleep and quality of life in lung cancer patients and survivors. J. Am. Assoc. Nurse Pract. 2021; 34(2): 284–291. PubMed Abstract | Publisher Full Text\n\nMontazeri A: Health-related quality of life in breast cancer patients: A bibliographic review of the literature from 1974 to 2007. J. Exp. Clin. Cancer Res. 2008; 27(1). PubMed Abstract | Publisher Full Text\n\nMontazeri A, Vahdaninia M, Harirchi I, et al.: Quality of life in patients with breast cancer before and after diagnosis: An eighteen months follow-up study. BMC Cancer. 2008; 8(1). PubMed Abstract | Publisher Full Text\n\nMoshina N, Falk R, Hofvind S: Long-term quality of life among breast cancer survivors eligible for screening at diagnosis: A systematic review and meta-analysis. Public Health. 2021; 199: 65–76. PubMed Abstract | Publisher Full Text\n\nNarayanan G, Awadallah MS, Krishnasamy R:Breast cancer related physical, psychological, social and spiritual domains of Quality of Life (QOL) among women in Bahrain. figshare. [Dataset].2022. Publisher Full Text\n\nNational Medical Center and Beckman Research Institute:2010.\n\nNBCC:2022.Reference Source\n\nOsoba D: Measuring the effect of cancer on quality of life. CRC Press;2021; 25–40.\n\nPodvorica E, Kraja J, Rrustemi N, et al.: Anxiety and depression in patients with breast cancer: A cross-sectional study. Open Access Maced. J. Med. Sci. 2022; 10(G): 138–143. Publisher Full Text\n\nSetyowibowo H, Yudiana W, Hunfeld JA, et al.: Psychoeducation for breast cancer: A systematic review and meta-analysis. Breast. 2022; 62: 36–51. PubMed Abstract | Publisher Full Text\n\nTanner LTA, Cheung KL: Correlation between breast cancer and lifestyle within the Gulf Cooperation Council countries: A systematic review. World J. Clin. Oncol. 2020 Apr 24; 11(4): 217–242. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "189755",
"date": "24 Aug 2023",
"name": "Salwa Hagag Abdelaziz",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors,\nThank you for conducting this study.\nThe selected title is very important and interesting topic. You mentioned the subcategories of the study tool (physical, psychological, social and spiritual) in the title which increase length and word count so it is suggested to use this title\n(Quality of life among women with breast cancer in public hospital in Bahrain) .You can not mention in Bahrain in the title because you utilized small sample size not representing all women in Bahrain so add public hospital before the country as you stated in the setting.\nRemoving the subcategories of the QOL from the title and add operational definition after the introduction.\nOperational Definition: Quality of life: It is the total quantitative mean scores of women physical wellbeing, psychological well-being, social well-being and spiritual well-being and in this study was measured by the Quality of Life Instrument–Breast Cancer patient developed by National Medical Center & Beckman Research Institute( 2010).\nIntroduction\nIt was supported by recent references, however missed paragraph about the pathology and stages of breast cancer.\nYou utilized the verb explore in the aim of the study as you mentioned (This article is an attempt to explore our understanding on effect on quality of life (QOL) among breast……).\nChange the verb explore to assess the quality of life among ….) to be matched with a cross-sectional descriptive design. Also in the first objective, change the verb explore to assess.\nMethods\nIn relation to the study design, please add cross-sectional correlational design because you mentioned in the objectives of the study that you will correlate not associate the QOL with selected background variables.\nSample\n\nAdd to inclusion criteria no any psychiatric or communication problems.\n\nConfidence interval should be 95 % not 90% because you mentioned accepted error of 5% and you conducted a descriptive study.\n\nCheck the correct abbreviation for EBI or (EPI) indicate full name\nData Collection\n\nThe QOL-CS is a 46-item ordinal scale not visual analog scale .Please check the reference again as the correct is ordinal.\n\nThe researchers should cite the cronback alpha of the questionnaire developed on 2010 by National Medical Center & Beckman Research Institute ( 2010) not by BR Ferrell,1995.\nEthical consideration\n\nIt is not suggested to use subject pronouns in the manuscript as we, you in the scientific writing and instead use the researchers or the investigators.\n\nPilot study: As you conducted the descriptive study , the preliminary pilot study should be 10 women not 5 . Please indicate this in the study limitation.\nResults\nIt is better to use percentage not number in the table comments.\n\nPlease review all tables as most of the tables number not matched with the comments and many errors in the comments e.g. comment on (table 2) 18(36%) cases had breast cancer over a year(check again the correct statement).\n\nTable 4 mention (Mean %) not use % mean score.\n\nTable 9 ,in relation to clinical variable use the correct variable (supplementary) not complementary .\n\nTable 10 regarding age, write t =2.84 not F .\n\nTry to simplify the comments under each table and review accurately.\nIt is very important to add table showing the correlation between 4 categories of the QOL using Pearson correlation coefficient.\nDiscussion: Statistics as percentages should not be mentioned in the discussion. The researchers should discuss the results with the previous study. So this part need to be rewritten according to the reported results and better to be arranged according to the study tools.\n\nConclusion: Need more information after adding table showing the correlation between subcategories of QOL using Pearson correlation.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/12-184
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https://f1000research.com/articles/11-1343/v1
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18 Nov 22
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{
"type": "Review",
"title": "Multiple institutions’ research findings using the National Mesothelioma Virtual Bank",
"authors": [
"Seemran Barapatre",
"Waqas Amin",
"Yuhe Gao",
"Yaming Li",
"Michael John Becich",
"Ye Ye",
"Seemran Barapatre",
"Yuhe Gao",
"Yaming Li",
"Michael John Becich"
],
"abstract": "Mesothelioma remains an under-researched cancerous disease due to the lack of high-quality patient samples and clinical information especially outcomes and asbestos exposure data. The National Mesothelioma Virtual Bank (NMVB) is a biobank in which mesothelioma annotated biospecimens can be made widely available to the research community. Here, we summarized the significant research findings from 20 publications that utilized the NMVB samples for novel biomarker and therapeutic discoveries. The results showed that the use of the NMVB resource was dispersed among a variety of basic science topics including, but not limited to, biomarkers, abnormal gene expression, and potential therapeutic targets. Positive biomarkers included several miRNAs and antibodies, HMGB1, ATG5, PIAS3, pancytokeratin and GATA3. Genes that had mutations or high/low levels of expression were BAP1, a human control gene of importance in this disease, as well as various cytokines, and checkpoint inhibitors TM4SF1, PKM2, ARHGDIA, COBLL1, WT1, FOXM1, and CD30. Treatments investigated include thiostrepton, interferon-β gene, and Brentuximab. Publications reviewed indicated a significant impact of the NMVB resource utilized in significant studies focusing on biomarker and therapeutic discoveries, which can act as a model for rare diseases, especially in oncology.",
"keywords": [
"National Mesothelioma Virtual Bank",
"Translational Research",
"Biomarker",
"Informatics",
"Rare Disease Biobank",
"Patient Registries"
],
"content": "Introduction\n\nMesothelioma is commonly a cancerous tumor lining pleural and peritoneal surfaces.1 Environmental exposure to asbestos, a naturally occurring silicate mineral, is the leading cause of mesothelioma.2 Other mineral fibers (e.g., erionite, antigorite, actinolite) are known to be carcinogenic as well.2,3 Asbestos and these other mineral fibers are thought to directly interfere with the cell spindle during human mesothelial cell division, leading to mutations and increased pathogenicity.4 The most common symptoms include breathlessness, chest pain, difficulty swallowing, and pleural fluid accumulation; as disease worsens, it leads to death.3 Because mesothelioma is aggressive and fatal (approximately 8–14 months survival after diagnosis3), reduction in exposure and early diagnosis are essential. Biomarkers, especially mesothelin, have been proven useful in malignant pleural mesothelioma (MPM) diagnoses.3 Furthermore, sampling measures (pleural fluid), staging, immunohistochemistry (IHC), histology (epithelial, biphasic, and sarcomatoid) and imaging (chest radiography, CT imaging, PET-CT) can be used as distinguishers between diagnosis and progression of the MPM, as well as among MPM subtypes.4 There are both surgical and non-surgical treatment options available to prolong the survival of patients such as chemotherapy, radiotherapy, targeted therapy, surgery, trimodality (consists of surgery, chemotherapy and radiotherapy), and multimodality.3,4 Researchers must uncover and improve treatment options rapidly in order to benefit patients.\n\nIt’s challenging and sometimes impossible for biomedical researchers to obtain a sufficient number of mesothelioma patients’ high-quality samples and comprehensive clinical information for analysis. As tissue banking informatics becomes increasingly widespread and improved in collection and storage of human biospecimens, researchers can obtain important results in basic and clinical science research that contribute toward personalized medical approaches in a clinical setting. The National Mesothelioma Virtual Bank (NMVB) (https://mesotissue.org/, last accessed on Oct 17th, 2022) is the largest US mesothelioma patient registry and offers pleural and peritoneal mesothelioma biospecimens with high-quality data that are critical for effective biomarker identification discovery and personalized medicine research. The NMVB database captures robust clinical data including patient demographics, epidemiology, health assessment survey, pathology, treatment, and outcomes (collecting tissue and blood products for various types of molecular analysis). Researchers can access statistical data for public view (https://data.mesotissue.org/data-page.html), or search the collection of mesothelioma biospecimens via the request fulfilment process (https://mesotissue.org/specimens). As a result, the NMVB serves as a leading resource for mesothelioma biospecimens by providing a sufficient number of mesothelioma cases, standardizing the data and specimen collection method, facilitating the sharing of information through the NMVB database, and addressing the issues of constraint through confidentiality and de-identification.\n\nStarting from 2008, the NMVB collected over 2,000 archived mesothelioma and prospective mesothelioma biospecimens that have been accrued from surgical resections and biopsies, including fresh frozen and blood products. Retrospective collections include clinically collected specimens for diagnostic purposes from surgical and diagnostic biopsies, like paraffin tissue samples. Prospective collections are obtained from clinical visits in which physicians obtain permission for each NMVB study via e-informed consent. These researchers have used novel technologies, such as sequencing techniques, staining techniques (such as fluorescence), and DNA/gene expression analyses, to study potential mesothelioma inhibitors, activators, and therapies.\n\nThis manuscript aims to summarize the important research findings of key published studies that have utilized NMVB resources and discuss the future direction of the NMVB. The innovative work discussed in this paper was conducted by a total of 320 scholars from 99 institutions or departments.\n\nIn NMVB-related biomedical studies, there are biomarkers that show substantial evidence of mesothelioma and cancer detection in tumor samples. The expression of MicroRNAs as a biomarker can be utilized to determine stages of tumor progression, as well as to categorize cancer types (lung adenocarcinoma versus mesothelioma).5 The subset of RNA through seven major types (miR-141, miR-200a, miR-200b, miR-200c, miR-203, miR-205, miR-429) can reduce protein expression (MYC, JUN, VANGL1, RHOA, ROCK2, WNT5A, or PLCB1), thereby reducing the likelihood of disease.5 In prior studies, SV40 has been suggested to contribute to malignant mesothelioma because of its viral capabilities.6 A 2010 study7 obtained tissues from several institutions, including the NMVB, to observe SV40 miRNA expression within these cells and detected low expression of SV40 miRNAs, indicating that SV40 may not contribute to mesothelioma tumorigenesis. Another 2013 study8 further indicated that microRNAs can be investigated in order to understand the change from non-cancerous to cancerous cell. This study found that within several mesothelioma cells, three miRNAs were under expressed (miR-1, miR-206, and miR-133b). Specifically, miR-1 acted as an active malignant pleural mesothelioma tumor suppressor.\n\nTissue and serum samples were tested in order to establish autoantibodies that could provide accurate recognition of malignant mesothelioma. Although not an all-inclusive list, nine autoantibody biomarkers (PDIA6, MEG3, SDCCAG3, IGHG3, NADH dehydrogenase 1, BACRP11-484D18, CH507-528H12, RP11-413M2) researched within the phage library (T7 MM) fell under that category.9 A supposed prognostic marker, PIAS3, prevents mesothelioma growth through the inhibition of STAT3 activity.10 Researchers found that the tissue cores from NMVB tissue microarray slides had either low or no PIAS3 expression in MM cells.10 Another biomarker, cytoplasmic and extracellular HMGB1, is a mediator of autophagy. A study from Hawaii Cancer Center11 found that asbestos exposure directly releases HMGB1 and impacts the Beclin 1/PI3K-III complex. HMGB1-mediated autophagy caused the upregulation of phosphorylated Beclin-1, whereas the silencing of HMGB1 caused p-Beclin-1 levels to greatly decrease. Therefore, HMGB1 is likely to cause carcinogenesis through the increased survival of human mesothelial cells. ATG5 was increased in asbestos-exposed individuals, as well.\n\nInterestingly, extracellular vesicles particle (EVP) derived biomarkers are able to distinguish various cancer types. EVP proteins, HSPA8, and CD63 are commonly seen in EVPs. Two other EVP proteins, THBS1 and VCAN, and other less significant biomarkers, such as metabolic enzymes, have the ability to discern between cancer and non-cancer cells.12 Specific EVP proteomes can aid in the classification of 16 cancer types including but not limited to: breast, lung, pancreatic carcinoma, etc.12 In a BAP1 study,4 researchers found that the most specific marker for MM, adenocarcinoma, and SCC was WT1 nuclear positivity, TTF-1 and Napsin A, and p63 and p40, respectively. Another research study13 verified a six-peptide biomarker signature (intercellular adhesion molecule 1, basement membrane-specific heparan sulfate proteoglycan core protein, serum paraoxonase/arylesterase 1, mesothelin, hypoxia up-regulated protein 1, thrombospondin-1) that can be used to detect MPM. Since MPM has a poor prognosis, the tool has the potential to decrease the risk of false negatives when diagnosing individuals. The MPM signature has a higher sensitivity than the SMRP ELISA test.13 A case report14 dealing with a deceased sarcomatoid mesothelioma patient uncovered a loss of p16 cyclin-dependent kinase inhibitor 2A, which is a prominent feature of desmoplastic malignant mesothelioma. Additionally, CK7 and CK5/6 expression is essential in the diagnosis of sarcomatoid mesothelioma. Calretinin, D2-40, and WT-1 are likely elevated in certain central locations (especially the lung). Diffuse sarcomatoid mesothelioma is sensitive for GATA3 expression, but it is improbable that this mesothelioma type will show large levels of TTF-1 and carcinoembryonic antigen. Pleural-based sarcomas are commonly seen to have a loss of pancytokeratin and CD31, a vascular biomarker.\n\nPreviously, miRNAs were an essential component of determining the progression of non-cancerous cells to mesothelioma cancerous cells. There has been a transition to studies regarding biomarkers (e.g., PIAS3 and HMGB1) that have a major or minor role in mesothelioma expansion and proliferation. Other biomarkers may be useful in determining variations in the type of mesothelioma and differences between mesothelioma and other cancers of the lung.\n\nAn important factor of mesothelioma and other cancer types is the modification or increase/decrease of gene expression. BAP1 plays a pivotal role in regulating gene expression in malignant mesothelioma.4,14,15 Out of 70 malignant mesothelioma (MM) biopsies (embedded tissue slides) in this research, BAP1 was mutated in 60% of the specimens.15 Not surprisingly, there is a loss of BAP1 expression in 50% of biphasic mesotheliomas and 25% of sarcomatoid mesotheliomas.14 In addition, BAP1 can be utilized in order to distinguish between non-small lung carcinoma and malignant mesothelioma (MM).4 Due to prior records of immunohistochemical (IHC) differentiation causing difficulty when discriminating between non-small lung carcinoma and MM, this specific study4 aimed to investigate BAP1 immunostaining as an accurate diagnosis predictor between the two cancer forms. Overall, there was a greater lack of BAP1 nuclear staining in MM as compared to non-small lung carcinomas (in which it was extremely rare).\n\nAnother publication16 focuses on the varying levels of the human control gene in mesothelioma tissues. Out of the 45 independent mesothelioma samples from the NMVB, 42 tissues were observed to have high levels of this particular gene. In contrast, Merkel cell polyomavirus (MCPyV) was either never seen or detected at extremely low levels in all tissues. In 2020, researchers have studied the Bloom Syndrome (BLM) gene through multiple experiments in mesothelioma patients’ samples and animal models.17 BLM is a helicase enzyme that aids in DNA replication and the repair of DNA damage. There are two BLM mutations: biallelic BLM mutations and inactivating germline BLM heterozygous mutations. Biallelic mutations of the Bloom Syndrome gene cause Bloom Syndrome, leading to the risk of developing cancer because of chromosomal instability, the disruption of cell-cycle processes, and decreased p53-mediated apoptosis. Heterozygous BLM mutations lead to a truncated BLM protein. In a few experiments, the researchers found that some mesothelioma patients contained harmful BLM mutations. Another experiment regarding BLM-silencing human mesothelial cells found reduced caspase-3 levels, and therefore, reduced apoptosis in human mesothelial (HM) cells and reduced levels of phosphorylated histone γ-H2A.X involved in DNA repair. The researchers further conducted a mice experiment and observed an increase in M1 macrophages and levels of TNF-α, IL-1β, IL-3, IL-10, and IL-12(p70) for BLM heterozygous mutated mice compared to WT mice. These cytokines are linked to carcinogenesis.\n\nA gene expression test study18 developed a potential molecular algorithm that could replace the current MPM staging system (which has issues of validity and comprehension). In this examination, samples undergo clinical tests that assess the expression of genes. Utilizing MPM-matched frozen and formalin-fixed, paraffin-embedded (FFPE) samples, a gene expression score (GES) was confirmed to provide prognostic information about different patient conditions. The expression of four genes (TM4SF1, PKM2, ARHGDIA, and COBLL1) and three ratios (TM4SF1/PKM2, TM4SF1/ARHGDIA, and COBLL1/ARHGDIA) are used in this score, which can allow for a more accurate reading in addition to current staging systems. Cells contain complicated interactions between cell surface receptors and transcriptional factors, leading to gene expressions that dictate the cell’s specific and wide-ranging functions. A SPaRTAN model is utilized to decipher the connections between cell surface receptors and transcriptional factors, which are then used as predictions for future transcriptional factor (TF) activity.19 The model includes a bilinear regression algorithm that learns an interaction matrix. SPaRTAN was applied to malignant peritoneal (MPeM) and pleural mesothelioma (MPM) tumors to obtain and analyze the regulatory states of CD8+ T cells. A portion of the MPeM CD8+ T cell population that was tested had high PD-1, TIM3. And TOGIT (checkpoint inhibitors) expression. A portion of the MPM CD8+ T cell population had the same results, indicating exhausted CD8+ T cells in these tumors. BCL3 activity was found in MPeM CD8+ T cells when PD-1 was present, but not in MPM CD8+ T cells.\n\nOverall, BAP1 plays an essential role in affecting malignant mesothelioma – showing a reduction in gene expression in these BAP1 studies. Similarly, abnormal expression levels of certain genes (e.g., human control gene and BLM gene) may be indicators of mesothelioma. Researchers have constructed systems, such as the SPaRTAN and GES score, to understand cell activity.\n\nResearchers have determined numerous therapeutic targets and potential inhibitory substances or molecules that could aid in the treatment of mesothelioma. There are two therapeutic targets, FOXM1 protein and CD30, that can decrease cell growth. Researchers observed that Forkhead box M1 (FOXM1) was present in the majority of human malignant mesothelioma cells (>50%).20 The protein, FOXM1, controls gene expression in the cell cycle (specifically S phase entry to mitosis), which assists in cell progression. CD30 is a cytokine receptor that aids in the regulation of apoptosis, which means that the presence of the gene in mesothelioma cells should be high.21 To counter tumor progression, researchers utilized thiostrepton (TS) to inhibit this specific protein. TS disables peroxiredoxin 3 (PRX3) by increasing mitochondrial oxidant production, leading to the decrease of the FOXM1 protein and CD30 that cause cell death.20 As a result, FOXM1 and CD30 have the capability of being a therapeutic target and TS could be a therapeutic strategy. Researchers, in 2015, observed the intensity of immunostaining using tissue microarray slides from the NMVB and applied brentuximab vedotin to target CD30 antigens.21 After subsequent analyses, CD30 mRNA expression was abnormally high in mesothelioma tissues, giving further evidence that the receptor could be a therapeutic target in the future. And brentuximab Vedotin does impact the activity of CD30, leading to decreased cell growth and survivability.\n\nFurthermore, there are two widely known non-surgical treatments, chemotherapy and radiation therapy, that are involved in decreasing size and morbidity with MPM. Unfortunately, studies have shown that malignant pleural mesothelioma is not as affective. A University of Pennsylvania Medical Center study22 hypothesized that a vesicular stomatitis virus (VSV) vector that incorporated an Interferon-β gene could effectively prevent the growth of lysis mesothelioma cells because the virus is normally an oncolytic agent. Forty-eight mesothelioma tumors were obtained from the NMVB for various treatments (hIFN-β, IFN-β ELISA, IFN-β bioassay). As presumed, the delivery of genes results in a decrease of lysis activity and an increase in antitumor immune responses.\n\nThese studies have established FOXM1 and CD30 as therapeutic targets, and thiostrepton and brentuximab vedotin as therapeutic strategies that decrease cell stability. Additionally, the treatment of VSV vectors containing the Interferon-β gene serves as a cell progression inhibitor, as well.\n\nCases in which the usage of tumor samples aided in the determination of potential biomarkers, gene expression, and therapeutic factors for general mesothelioma and/or differentiating mesothelioma subtypes are summarized in Table 1.\n\n\nBiomedical informatics research in NMVB\n\nThrough the process of continuously enriching the research cohort of mesothelioma patients and providing samples and research data to external institutions, the NMVB team has also been upgrading NMVB infrastructure using state-of-art informatics techniques and sharing our experience in peer-reviewed articles.23,24 We developed a multidisciplinary approach to conduct honest broker service efficiently and effectively, sharing our practical experience in Ref. 23. Using mesothelioma as an example, we have developed and deployed common data elements for tissue banks for translational research in cancer, which is generalizable to other types of cancers.24\n\nFurthermore, the NMVB team has been using NMVB data to conduct internal scientific research. We explored the potential of using automated image analysis in the evaluation of mesothelioma tissue microarray, which matched the performance of manual scoring by pathologists.25 This result indicates that an automated image analysis approach may be a reproducible, objective, and accurate way for the immunohistochemical assessment of biomarker expression. In a cancer history classification study,26 we applied Natural Language Processing (NLP), a modern Artificial Intelligence technique, to automatically classify personal and family history from free-text medical reports of mesothelioma patients, with a high accuracy. In another study,27 we conducted a retrospective review of the NMVB cohort, and identified factors influencing malignant mesothelioma survival, including age (younger than 45), gender (female), epithelioid histological subtype, staging (I), peritoneal occurrence, and having the combined treatment of surgical therapy with chemotherapy. Moreover, for malignant pleural mesothelioma, we developed a novel computational algorithm that automatically discovered 364 potential protein-protein interactions, of which five interactions (BAP1-PARP3, KDR-ALB, PDGFRA-ALB, CUTA-HMGB1, and CUTA-CLPS) were validated experimentally; our comparative transcriptiome analysis identified five potentially repurposable drugs targeting the interactome proteins (cabazitaxel, primaquine, pyrimethamine, trimethroprim, and gliclazide).28 To share our findings with the whole research community, we make the discovered interactions publicly available through Wiki-MPM (https://hagrid.dbmi.pitt.edu/wiki-MPM/, last accessed on July 31st, 2022). Realizing the computational approach may be more needed by rare types, we further applied similar techniques on malignant peritoneal mesothelioma and identified 417 novel protein-protein interactions.29\n\n\nDiscussion\n\nWith regard to research findings using NMVB, there was a high number of publications that investigated and examined specific genes’ roles in mesothelioma, such as IFN-β, BAP1, and PIAS3, and pre-existing or current cancer/mesothelioma therapies, such as HDACi panobinostat, CRS, and HIPEC. In addition, there were publications related solely to the development and utilization of NMVB as a significant resource. Many publications had some positive scientific findings that allowed for possible therapies to aid in mesothelioma or cancer treatment including (but not limited to) delivery of type I IFNs, carcumin, brentuximab vedotin, panobinostat, and CRS/HIPEC. There were also gene markers that were not related to or did not provide enough information for lung inflammation, cancer, or mesothelioma, such as MCPyV DNA and CRP. When comparing mesothelioma and lung adenocarcinoma, there were certain miRNA traits that varied, indicating that miRNAs can act as potential biomarkers. The NMVB has been proven to a robust biobanking resource to support the fundamental domain of biomedical science, including molecular and genetic epidemiology, molecular pathology and pharmacogenomics.\n\nThe NMVB was cited in 879 publications in 2021 compared to 676 publications in 2020 (a nearly 30% increase). NMVB is on track for over 1000 citations in CY2022, establishing that the bank is important in sharing genomic data and specimens. There are many NMVB publications from the users of the resource that focus on biomarker development, of which some are previously discussed in this publication.\n\nThe NMVB plans to improve its system on including which specimen types and related annotation by taking mesothelioma researchers’ feedback and expand the reach of its database in the upcoming years. Currently, there are nine collaborating institutions that are a part of the NMVB, including New York University, University of Pittsburgh/UPMC, University of Pennsylvania, Roswell Park Cancer Institute, Mount Sinai School of Medicine (currently inactive), Baylor College of Medicine, Fox Chase Cancer Center, Temple University and University of Maryland (https://mesotissue.org/about/, last accessed on July 31th, 2022). Additionally, NMVB hopes to make use of international networks like MesoNet (France), the United Kingdom Biobank and the Italian Mesothelioma Biobank to obtain far-reaching and increased data from mesothelioma patients that can be accessed by researchers.30\n\nThe NMVB is making efforts with the CDC and MedMorph to create advanced infrastructure and refined tools that can enhance data extraction of asbestos exposure and occupational health data. With so many years of practical experience, the team leaders of NMVB actively joined a nationwide workshop discussing the potential usefulness and feasibility of national mesothelioma registry.31 Moving forward, the NMVB is working with an epidemiology and occupational health expert and gain knowledge through the CDC NIOSH to enhance the investigation of occupational history and the exposure that may contribute to mesothelioma.\n\nLastly, the NMVB utilizes a communications plan involving the NMVB website, mass mailings to users, and presentations at national meetings. The NMVB website contains links to the CTSA, NIH, NCI, Office of Biospecimen and Biorepository Research, National Center for Biotechnology Information, the Cancer Genome Atlas Project and dozens of other biorepository and relevant organizational websites. These supply information about mesothelioma, biospecimens, and other specimens via a searchable database. Letters and/or e-mails are sent to investigators and their cancer research coordinators that have published articles in mesothelioma research in the recent past as well as investigators that have received or applied for Mesothelioma Foundation research grant funding. NMVB is always present and markets the resource especially at the Mesothelioma Applied Research Foundation’s annual symposium, the International Mesothelioma Interest Group’s every other year meeting, the AACR meeting and other research meetings. The NMVB will have outreach efforts, such as increasing the awareness of the NMVB resource, increasing education about the function NMVB and how it is operated, providing information about scientific advances facilitated by NMVB, and learning from the affected communities about the disease especially through active participation at the International Symposium on Malignant Mesothelioma (Mesothelioma Foundation sponsored annual meeting).\n\n\nConclusions\n\nThe NMVB has aided in biomarker, gene expression, and therapeutic target studies. NMVB plans to improve its resources and system allowing for future researchers to make widespread use of the data and specimens within the database. It is essential that the NMVB dataset continues to expand and play a pivotal role in cancer research, especially for possible treatments/phenomena that target NMVB specimens and aid in inhibiting tumor growth in certain cells.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe thank Schwenk, Melissa Dawn for setting up the NMVB research paper Google scholar webpage: https://scholar.google.com/.\n\n\nReferences\n\nSekido Y: Molecular pathogenesis of malignant mesothelioma. Carcinogenesis. 2013; 34: 1413–1419. Publisher Full Text\n\nRoggli VL: Measuring EMPs in the lung what can be measured in the lung: Asbestiform minerals and cleavage fragments. Toxicol. Appl. Pharmacol. 2018; 361: 14–17. PubMed Abstract | Publisher Full Text\n\nBibby AC, Tsim S, Kanellakis N, et al.: Malignant pleural mesothelioma: an update on investigation, diagnosis and treatment. Eur. Respir. Rev. 2016; 25: 472–486. PubMed Abstract | Publisher Full Text\n\nCarbone M, Shimizu D, Napolitano A, et al.: Positive nuclear BAP1 immunostaining helps differentiate non-small cell lung carcinomas from malignant mesothelioma. Oncotarget. 2016; 7: 59314–59321. PubMed Abstract | Publisher Full Text\n\nGee GV, Koestler DC, Christensen BC, et al.: Downregulated microRNAs in the differential diagnosis of malignant pleural mesothelioma. Int. J. Cancer. 2010; 127: 2859–2869. PubMed Abstract | Publisher Full Text\n\nVilchez RA, Butel JS: Emergent human pathogen simian virus 40 and its role in cancer. Clin. Microbiol. Rev. 2004; 17: 495–508, table of contents. PubMed Abstract | Publisher Full Text\n\nGee G, Stanifer M, Christensen B, et al.: SV40 associated miRNAs are not detectable in mesotheliomas. Br. J. Cancer. 2010; 103: 885–888. PubMed Abstract | Publisher Full Text\n\nXu Y, Zheng M, Merritt RE, et al.: miR-1 induces growth arrest and apoptosis in malignant mesothelioma. Chest. 2013; 144: 1632–1643. PubMed Abstract | Publisher Full Text\n\nZhang X, Shen W, Dong X, et al.: Identification of novel autoantibodies for detection of malignant mesothelioma. PLoS One. 2013; 8: e72458. PubMed Abstract | Publisher Full Text\n\nDabir S, Kluge A, Kresak A, et al.: Low PIAS3 Expression in Malignant Mesothelioma Is Associated with Increased STAT3 Activation and Poor Patient Survival. Clin. Cancer Res. 2014; 20: 5124–5132. PubMed Abstract | Publisher Full Text\n\nXue J, Patergnani S, Giorgi C, et al.: Asbestos induces mesothelial cell transformation via HMGB1-driven autophagy. Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 25543–25552. PubMed Abstract | Publisher Full Text\n\nHoshino A, Kim HS, Bojmar L, et al.: Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell. 2020; 182: 1044–1061.e18. PubMed Abstract | Publisher Full Text\n\nCerciello F, Choi M, Sinicropi-Yao SL, et al.: Verification of a Blood-Based Targeted Proteomics Signature for Malignant Pleural Mesothelioma. Cancer Epidemiol. Biomark. Prev. 2020; 29: 1973–1982. PubMed Abstract | Publisher Full Text\n\nBurke A, Legesse T: Nivolumab-Induced Peritonitis With Mesothelial Hyperplasia Mimicking Metastatic Mesothelioma. AJSP: Rev. Rep. 2022; 27: 98–102. Publisher Full Text\n\nNasu M, Emi M, Pastorino S, et al.: High Incidence of Somatic BAP1 alterations in sporadic malignant mesothelioma. J. Thorac. Oncol. 2015; 10: 565–576. PubMed Abstract | Publisher Full Text\n\nBhatia K, Modali R, Goedert JJ: Merkel cell polyomavirus is not detected in mesotheliomas. J. Clin. Virol. 2010; 47: 196–198. PubMed Abstract | Publisher Full Text\n\nBononi A, Goto K, Ak G, et al.: Heterozygous germline BLM mutations increase susceptibility to asbestos and mesothelioma. Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 33466–33473. PubMed Abstract | Publisher Full Text\n\nDe Rienzo A, Cook RW, Wilkinson J, et al.: Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues. J. Mol. Diagn. 2017; 19: 65–71. PubMed Abstract | Publisher Full Text\n\nMa X, Somasundaram A, Qi Z, et al.: SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators. Nucleic Acids Res. 2021; 49: 9633–9647. PubMed Abstract | Publisher Full Text\n\nNewick K, Cunniff B, Preston K, et al.: Peroxiredoxin 3 Is a Redox-Dependent Target of Thiostrepton in Malignant Mesothelioma Cells. PLoS One. 2012; 7: e39404. PubMed Abstract | Publisher Full Text\n\nDabir S, Kresak A, Yang M, et al.: CD30 is a potential therapeutic target in malignant mesothelioma. Mol. Cancer Ther. 2015; 14: 740–746. PubMed Abstract | Publisher Full Text\n\nSaloura V, Wang LC, Fridlender ZG, et al.: Evaluation of an attenuated vesicular stomatitis virus vector expressing interferon-beta for use in malignant pleural mesothelioma: heterogeneity in interferon responsiveness defines potential efficacy. Hum. Gene Ther. 2010; 21: 51–64. PubMed Abstract | Publisher Full Text\n\nDhir R, Patel AA, Winters S, et al.: A multidisciplinary approach to honest broker services for tissue banks and clinical data. Cancer. 2008; 113: 1705–1715. PubMed Abstract | Publisher Full Text\n\nMohanty SK, Mistry AT, Amin W, et al.: The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC Cancer. 2008; 8: 91. PubMed Abstract | Publisher Full Text\n\nAmin W, Srinivasan M, Song SY, et al.: Use of automated image analysis in evaluation of Mesothelioma Tissue Microarray (TMA) from National Mesothelioma Virtual Bank. Pathol. Res. Pract. 2014; 210: 79–82. PubMed Abstract | Publisher Full Text\n\nWilson RA, Chapman WW, Defries SJ, et al.: Automated ancillary cancer history classification for mesothelioma patients from free-text clinical reports. J. Pathol. Inform. 2010; 1: 24. PubMed Abstract | Publisher Full Text\n\nAmin W, Linkov F, Landsittel DP, et al.: Factors influencing malignant mesothelioma survival: a retrospective review of the National Mesothelioma Virtual Bank cohort. F1000Res. 2018; 7: 1184. PubMed Abstract | Publisher Full Text\n\nKarunakaran KB, Yanamala N, Boyce G, et al.: Malignant Pleural Mesothelioma Interactome with 364 Novel Protein-Protein Interactions. Cancers (Basel). 2021; 13. PubMed Abstract | Publisher Full Text\n\nKarunakaran KB, Ganapathiraju MK: Malignant Peritoneal Mesothelioma Interactome with 417 Novel Protein-Protein Interactions.2021; 6. Publisher Full Text\n\nvan Gerwen M , Alpert N, Flores R, et al.: An overview of existing mesothelioma registries worldwide, and the need for a US Registry. Am. J. Ind. Med. 2020; 63: 115–120. PubMed Abstract | Publisher Full Text\n\nCummings KJ, Becich MJ, Blackley DJ, et al.: Workshop summary: Potential usefulness and feasibility of a US National Mesothelioma Registry. Am. J. Ind. Med. 2020; 63: 105–114. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "156174",
"date": "08 Dec 2022",
"name": "Emanuela Felley-Bosco",
"expertise": [
"Reviewer Expertise fundamental and translational research in mesothelioma"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe National Mesothelioma Virtual Bank (NMVB) is led by the collaborative effort of the Departments of Biomedical Informatics and Pathology at the University of Pittsburgh, and is funded by a grant from the National Institute of Occupational Health and Safety of the Centers for Disease Control and Prevention. The authors state that the aim is to summarize in this review research from 20 publications that included NMVB samples.\nThis work is of potential interest since it analyzes the output of an effort to assemble a large collection of mesothelioma, which is a rare disease, for the benefit of scientists’ community. However, the manuscripts needs a large amount of revision and would benefit from the addition in the co-authors of a scientist with deep biology understanding, which would complement bioinformatics skills of the other authors.\nMajor: General comments:\nThe focus is to summarize research in biomarker and therapeutic discovery research. It might help the reader if the strategy used for the selection of the studies would be indicated. Indeed, there are according to the homepage of NMVB 60 publications/preprints (merging preprints and publications). In the Table there are 9 studies in the category biomarkers, 6 studies in the category gene expression and 3 studies for therapeutic targets. The total is 18 studies. The bioinformatics analysis studies are not included in the Table, so it is not clear how clear how they are considered.\n\nText and table reference numbers do not match, adding to the confusion. E.g. reference 5 in text corresponds to reference 6 in the table.\n\nThe manuscript would benefit of a more clear structure. For example separating studies based on NMVB plasma vs. tissue, and weighting by sample number, i.e. when only a single sample is analyzed this has not the same impact compared to the study of several samples.\n\nData should not be just mentioned but it is necessary to have some comments and critical assessments. If not it will look rather like a list, decreasing its interest. E.g. the two sentences starting “Tissue and serum samples were…..…….category” would be more informative if the authors could comment of what they think about antibodies against MEG3, which is non-coding RNA.\n\nEnglish should be more reader friendly as well. A sentence like “In NMVB-related biomedical studies, there are biomarkers that show substantial evidence of mesothelioma and cancer detection in tumor samples“ is not easy. It might be better to change to “NMVB samples have allowed to discover biomarkers for mesothelioma detection”. What may mean “cancer detection in tumor samples” is not evident. There are several other difficult sentences, I would advise a copy edit of the article.\n\nSpecific comments:\nThe sentence “the subset of RNA through seven major types…” needs to be changed. The authors refer to a study where differential expression of miRNA was investigated and predicted targets discussed. The data should be reported so with no overstatement about likelihood of the disease.\n\nSV40 was not “suggested to contribute to malignant mesothelioma because of its viral capabilities” but because large T antigen of SV40 binds e.g. p53 tumor suppressor gene. This is a very precise mechanism and not a general viral capability, whatever this may mean.\n\nTone down the sentence “Therefore, HMGB1 is likely to cause carcinogenesis”.\n\nThe whole paragraph starting with “Interestingly, extracellular…” misses to forward the message of that study in the context of mesothelioma.\n\nWhat do the authors mean when they write. “In a BAP1 study…”?\n\nBe more precise when reporting data in reference 13: serum samples, enriched using glycoprotein capture etc...\n\nWhat does mean the sentence: “There has been a transition…”?\n\nWhat does mean the sentence ”varying levels of the human control gene in mesothelioma”? How do the authors imagine a reader may understand? Why should readers understand the interest of checking Merkel cell polyoma virus?\n\nWhat is the message of the paragraph starting: “Overall, BAP1…”?\n\nCD30: the authors could comment that positivity in tumor samples was variable, and could represent a target for antibody-drug conjugates on in a fraction of samples…\n\nThiostrepton had been first used in breast cancer cells where it was shown to decrease the expression of FOXM1 (Kwok JM, et al Mol Cancer Ther 2008;7:2022–32) and the authors should mention this reference. Then they should comment on reasons why FOXM1 inhibiting antibiotics are not suitable for use in humans.\n\nThe whole paragraph: “Furthermore, there are two widely known non-surgical treatments, chemotherapy and radiation therapy, that are involved in decreasing size and morbidity with MPM. Unfortunately, studies have shown that malignant pleural mesothelioma is not as affective. A University of Pennsylvania Medical Center study hypothesized that a vesicular stomatitis virus (VSV) vector that incorporated an Interferon-β gene could effectively prevent the growth of lysis mesothelioma cells because the virus is normally an oncolytic agent. Forty-eight mesothelioma tumors were obtained from the NMVB forvarious treatments (hIFN-β, IFN-β ELISA, IFN-β bioassay). As presumed, the delivery of genes results in a decrease of lysis activity and an increase in antitumor immune responses” requires a copy edit.\n\nThere is an obvious interest in discussing the integration of the several biobanks/registries existing worldwide. However it might be useful also to integrate bioinformatics analysis. The authors should mention https://www.wikipathways.org/index.php/Pathway:WP5087, which is a resource publicly available and continues to be under development and curation by the community, enabling the scientists in mesothelioma to actively participate in the prioritization of shared biological knowledge.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly",
"responses": [
{
"c_id": "10007",
"date": "16 Nov 2023",
"name": "Yuhe Gao",
"role": "Author Response",
"response": "The National Mesothelioma Virtual Bank (NMVB) is led by the collaborative effort of the Departments of Biomedical Informatics and Pathology at the University of Pittsburgh, and is funded by a grant from the National Institute of Occupational Health and Safety of the Centers for Disease Control and Prevention. The authors state that the aim is to summarize in this review research from 20 publications that included NMVB samples. This work is of potential interest since it analyzes the output of an effort to assemble a large collection of mesothelioma, which is a rare disease, for the benefit of scientists’ community. However, the manuscripts needs a large amount of revision and would benefit from the addition in the co-authors of a scientist with deep biology understanding, which would complement bioinformatics skills of the other authors. --We invited Dr. Uma Chandran, who has a deep biology understanding and solid background, as our co-author. With her help of review and edits, we largely resolved the comments from the reviewer and the self-noticed problem in our previous manuscript. Major: General comments: The focus is to summarize research in biomarker and therapeutic discovery research. It might help the reader if the strategy used for the selection of the studies would be indicated. Indeed, there are according to the homepage of NMVB 60 publications/preprints (merging preprints and publications). In the Table there are 9 studies in the category biomarkers, 6 studies in the category gene expression and 3 studies for therapeutic targets. The total is 18 studies. The bioinformatics analysis studies are not included in the Table, so it is not clear how clear how they are considered. Added bioinformatics analysis studies in Table 1. Text and table reference numbers do not match, adding to the confusion. E.g. reference 5 in text corresponds to reference 6 in the table. Changed, now they match. The manuscript would benefit of a more clear structure. For example separating studies based on NMVB plasma vs. tissue, and weighting by sample number, i.e. when only a single sample is analyzed this has not the same impact compared to the study of several samples. Ranked them based on the samples size, and added a platform column in Table 1. English should be more reader friendly as well. A sentence like “In NMVB-related biomedical studies, there are biomarkers that show substantial evidence of mesothelioma and cancer detection in tumor samples“ is not easy. It might be better to change to “NMVB samples have allowed to discover biomarkers for mesothelioma detection”. What may mean “cancer detection in tumor samples” is not evident. There are several other difficult sentences, I would advise a copy edit of the article. Have copy edit of the whole article with writing tutors. Specific comments: The sentence “the subset of RNA through seven major types…” needs to be changed. The authors refer to a study where differential expression of miRNA was investigated and predicted targets discussed. The data should be reported so with no overstatement about likelihood of the disease. Revised SV40 was not “suggested to contribute to malignant mesothelioma because of its viral capabilities” but because large T antigen of SV40 binds e.g. p53 tumor suppressor gene. This is a very precise mechanism and not a general viral capability, whatever this may mean. Changed to “SV40 has been suggested to contribute to malignant mesothelioma as its large tumor antigen, which binds to cellular tumor suppressor proteins, have been demonstrated in MME”. Tone down the sentence “Therefore, HMGB1 is likely to cause carcinogenesis”. Changed to “Therefore, HMGB1 is likely to encourage cell transformation by saving asbestos-damaged human mesothelial cells.” The whole paragraph starting with “Interestingly, extracellular…” misses to forward the message of that study in the context of mesothelioma. Added one sentence starting with “More importantly..” to declare the context of mesothelioma. What do the authors mean when they write. “In a BAP1 study…”? Was meaning, in a study focusing on BAP1, while now changed to: ” In a study aiming to seek novel biomarkers for distinguishing malignancies, 4 researchers found that the lack of nuclear BAP1 stain can differentiate MM from lung carcinomas.” Be more precise when reporting data in reference 13: serum samples, enriched using glycoprotein capture etc... Added “isolating N-linked glycoproteins to enrich serum proteome and decrease analytical complexity” to describe ref 13. What does mean the sentence: “There has been a transition…”? Changed to “There have been some novel directions…” What does mean the sentence ”varying levels of the human control gene in mesothelioma”? How do the authors imagine a reader may understand? Why should readers understand the interest of checking Merkel cell polyoma virus? Deleted this statement, added description on MCPyV and SV40 and their relationships to mesothelioma. What is the message of the paragraph starting: “Overall, BAP1…”? Changed to “In MM studies, BAP1..”. Was trying to identify the role of BAP1 in existing MM studies. The whole paragraph: “Furthermore, there are two widely known non-surgical treatments, chemotherapy and radiation therapy, that are involved in decreasing size and morbidity with MPM. Unfortunately, studies have shown that malignant pleural mesothelioma is not as affective. A University of Pennsylvania Medical Center study hypothesized that a vesicular stomatitis virus (VSV) vector that incorporated an Interferon-β gene could effectively prevent the growth of lysis mesothelioma cells because the virus is normally an oncolytic agent. Forty-eight mesothelioma tumors were obtained from the NMVB forvarious treatments (hIFN-β, IFN-β ELISA, IFN-β bioassay). As presumed, the delivery of genes results in a decrease of lysis activity and an increase in antitumor immune responses” requires a copy edit. Revised as “There are two widely known non-surgical treatments to MM, chemotherapy and radiation therapy, however studies have shown that these treatments are not effective enough with malignant pleural mesothelioma. A University of Pennsylvania Medical Center study 22 has proposed an oncolytic viral therapy. Researchers hypothesized that, normally functioning as an oncolytic agent, a vesicular stomatitis virus (VSV) vector that incorporated an Interferon- β gene could effectively prevent the growth of lysis mesothelioma. In the study, 48 mesothelioma tumors were obtained from the NMVB for various treatments (hIFN -β, IFN- β ELISA, IFN -β bioassay ). As presumed, the delivery of genes results in a decrease of lysis activity and an increase in antitumor immune responses.” There is an obvious interest in discussing the integration of the several biobanks/registries existing worldwide. However it might be useful also to integrate bioinformatics analysis. The authors should mention https://www.wikipathways.org/index.php/Pathway:WP5087, which is a resource publicly available and continues to be under development and curation by the community, enabling the scientists in mesothelioma to actively participate in the prioritization of shared biological knowledge. Added existing biobanks/registries both worldwide and in US in discussion part."
}
]
}
] | 1
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https://f1000research.com/articles/11-1343
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https://f1000research.com/articles/12-475/v1
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09 May 23
|
{
"type": "Research Article",
"title": "“Gilead is within you”: a theocratic narrative setting of cultural memory in Atwood’s The Testaments",
"authors": [
"Manshi Yadav",
"Palak Arora",
"Palak Arora"
],
"abstract": "This article attempts to explore the synthetic relationship between group identities and their effects on cultural memory in Margaret Atwood's The Testaments. It will investigate how Atwood's dystopian fiction conspicuously weaves threads of cultural identity in the totalitarian society. While examining the work, the researchers found three forms of Memory Figures channelizing society: Architecture and time, Identical groupings, and Language. With significant attention to the prequel, The Handmaid's Tale, this article will consider The Testaments for the dissection of hard-wired cultural memory formation. This article focuses on how a politically unsettled society of Gilead, through its Memory Figures, inscribes a cultural narrative while instructing individual memories. Atwood's usage of these Memory Figures to achieve a theocratic regime has been scrutinized in this article. The Architecture of Gilead was given an intrusive wall of glass, where the symbol of eyes prevails, to externalize the surveillance of God on each one of its citizens, thereby forming a cultural memory of subjectivity. To make the citizens identify with groups, this theocratic regime specifies roles to citizens according to their rank for men and according to reproductive efficiency for women. Keeping in view the relevance of language in forming cultural memory, Atwood prescribed a set of greetings such as 'under his eyes,' and 'praise be' to make profound imprints on the individual memory of citizens, which has been discussed in the study. These three Memory Figures simultaneously form collective memory imprints on the citizens of Gilead, which in time became inherent cultural memories. This article explores how, by politicizing the issue of cultural memory in The Testaments, Atwood taps into the agency of people and establishes language control (communicative) to form the cultural memory narrative.",
"keywords": [
"Atwood",
"memory",
"culture",
"literature",
"Dystopian"
],
"content": "Introduction\n\nThe Testaments (2019) is a sequel to the novel The Handmaid’s Tale (1985), a futuristic dystopian novel written by Margaret Atwood. Henceforth, the events in the novel follow on fifteen years from the prequel and set the patriarchal dystopian world in motion. Further subjugating, Agnes and Daisy the daughters of Offred, the protagonist of The Handmaid’s Tale, are toiling hard to find their way in Gilead. Atwood, in her creation of this dystopian world probes the miscommunicated excerpts of the Bible such as ‘let the woman learn in silence with all subjection’, which created the foundations for Gilead (Atwood, 1996, p. 229). Daily aka Baby Nicole the star child of Gilead is raised in Canada far from the pseudo religious renditions of Gilead. She came out as an independent thinker since her memory was not tarnished with the cultural probes of religion. On the other hand, Agnes, her half sister turns out to be a total proto Gileadian woman with a subjugated brain and limited religious knowledge. The narrative of The Testaments revolves around how these two women, with the help of Aunt Lydia and Mayday, shift the religious autonomy and fight back the cultural imprints of Gilead. Weaving an intricate fabric of subjective cultural memory for its citizens, through the media and memory figures lens defined by Assmanns, in this article we would like to draw focus on the process of cultural memory formation in Atwoods’ theocratic regime. We argue that Atwood highlights three media of cultural memory during her course of writing The Testaments i.e., Architecture and Time, Identical Grouping and Language.\n\n\nLiterature Review\n\nMemory is ever prevailing and quintessentially ambivalent in all human beings. Philosophical interests in memory can be dated back to antiquity and have remained of interest. It formally emerged as a field of enquiry after French philosopher Maurice Halbwachs published his defining work Social Framework of Memory in 1925. Ever since, Memory Studies became an intriguing point of inquiry for philosophers, psychologists, sociologists and theologists, and became a transdisciplinary field (Olick & Robbins, 1998). Being a major preoccupation for social thinkers, Memory Studies evolved as a field from individual and intellectual enquiry to a socially constructed phenomena i.e., through physiology and psychology to social culturology (Quan, 2019). To untangle the wires of memory being a transient centerless paradigm, it’s important to trace its origins from inception. Maurice Halbwachs, the pioneer figure in the paradigm of “collective memory” when introduced the term, alludes ‘it is in society that people normally acquire their memories. It is also in society that they recall, recognize, and localize their memories’ (Halbwachs, 1992, p. 38). After Halbwachs’ discourse, historians like Amos Funkenstein oppose the tenets of collective memory altogether, asserting ‘consciousness and memory can only be realized by an individual who acts, is aware, and remembers. Just as a nation cannot eat or dance, neither can it speak or remember. Remembering is a mental act, and therefore it is absolutely and completely personal.’ (Funkenstein, 1989, p. 6). The idea of memory as a construct of collective remembrance has been toiled over by psychologists and anthropologists, which in the end came out to be a favorably progressive argument like the one propounded by Lev Vygotsky ‘a mind cannot be independent of culture’ (Karuny, 2022). Shaping the discourse of Collective Memory Studies in a historiographic mould, French historian Pierre Nora in his seminal work Les Lieux de mémoir (1984) dispelled all lingering doubts regarding the theoretical status of Halbwachs’ oral memory (Assmann, 2008b) by coining the concept of ‘place of memory’ to designate concrete places where collective memories can crystallize their existence, hence making way for architecture in collective memory studies (Nora, 2011). Since cultural memory needs a space to materialize its existence in time, therefore the study of architecture becomes important in the field of Memory Studies.\n\nProgressing through these interdisciplinary tenets of the theory, Jan Assmann, a German Egyptologist wrote a landmark work Cultural Memory and Early Civilization: Writing, Remembrance, and Political Imagination (2011) in the realm transforming “collective memory” into “cultural memory”. Assmann comprehends the domain of “collective memory” as “communicative” and “cultural memory”, since according to him ‘a person’s memory forms itself through his or her participation in communicative processes … We only remember what we communicate and what we can locate in the frame of the collective memory’ (Assmann, 2011, p. 23). However, channelizing cultural memory in a society takes ‘institutionalized mnemotechnics’ (Assmann, 2011, p. 37–39) which is aided with symbolic figures so that memory can be attached to it. This multifaceted domain of cultural memory can only sustain itself through people and architecture which can possibly sing the past to the present generation and pass the cultural heritage. Therefore, Assmann stresses the fact that cultural memory ‘always has its specialists … cultural memory is disembodied. In order to function as memory, however, its symbolic forms must not only be preserved but also circulated and re-embodied in a society’ (Assmann, 2008c, pp. 110–111). These have been well elucidated by Aleida Assmann, a German professor of English and Literary Studies aligning media with cultural memory as writing, image, body and places. Prospects of cultural memory interplay can only be functional when the permeation of images, historical facts and figures has been synthesized and transferred to the successive generation to which Assmann proposed as “Memory Figures”. These memory figures are characterised with three special features: “a concrete relationship to time and place”, “a concrete relationship to a group” and an “independent capacity for reconstruction” (Assmann, 2011, p. 24). These memory figures are a theorisation of the complex media structure that entails the process of identity formation in the group that in turn becomes collective memory, which serves as a proponent of cultural memory as well. Every event projected by memory figures, condenses in the individuals’ consciousness, and gets sedimented in the culture. As multiple implications of the same narrative on people leave an imprint on their collective memory, thus forming cultural memory.\n\n\nResearch Methodology\n\nThis article examines Atwoods’ The Testaments on the grounds of memory media and figures by Assmanns. The research writing follows a qualitative approach to disseminate the data from the novels through textual analysis. For secondary literature Assmanns’ Cultural Memory and Early Civilization: Writing, Remembrance, and Political Imagination (2011) has been used for the study of memory media and figures. The study specifically scrutinizes dystopian fiction as more dearly connected to cultural memory as the sole aim of dystopian fiction is to create a totalitarian society with every citizen having identical motifs and memories, so much so that the distinction between myth and history vanishes (Assmann, 2008c, p. 113). Mythology and history are two distinct yet interrelated fields of studies therefore using one as the substitute for the other doesn’t make a credible story for a generation to follow. In The Handmaid’s Tale excerpts from the Bible are cited as a closure for all interpretive possibilities. This creates a theocratic regime in the sequel, The Testaments, where individuals’ memories are tinted with limited accessible knowledge, ensuing a generation with a cultural memory of “mis- communicated” theocracy, as the only governing dictum.\n\n\nArchitecture and Time\n\nWith the cultural memory domain expanding its wings to newer and fresher dimensions, Aleida Assmann suggests architecture as one media for cultural memory. The Testaments being based on a theocratic regime ‘endow texts, persons, artifacts, and monuments with a sanctified status to set them off from the rest as charged with the highest meaning and value’ (Assmann, 2008a, p. 100). Initiating from a former secondary school, the Rachael and Leah Centre, aka Red Centre, where Handmaid’s got their instructions of duty, which acted as headquarter for patriarchal teachings to obliterate the women/handmaids and strip them of their former life’s memories. Repeated chanting in a Re-Education centre such as ‘Oh God, King of the universe, thank you for not creating me a man. Oh God, obliterate me. Make me fruitful. Mortify my flesh, that I may be multiplied. Let me be fulfilled …’ became a flourishing ground for crumbling individual memories and forming new cultural memories (Atwood, 2012, p. 194). Initially, Offred tried to resist the patriarchal ideology of Gilead, however in the end, when she was on the brink of losing hope, these words became the voice of her soul rather than a mundane chanting. This repetition of routines in sync and ritualistic chanting helps the group to solidify their collective memories as Jan Assmann suggests ‘the role of external symbols becomes even more important, because groups which, of course, do not “have” a memory tend to “make” themselves one by means of things meant as reminders such as monuments, museums, libraries, archives, and other mnemonic institutions’ (Assmann, 2008c, p. 111).\n\nGilead itself was an area of discarded yet unavoidable history of the Puritans, which served as a foregrounded mythical landscape where manipulating Biblical text and memory accentuates the individual identities. As Atwood mentioned in the introduction of the text, ‘the Republic of Gilead is built on a foundation of the seventeenth-century Puritan roots that have always lain beneath the modern-day America we thought we knew’ (Atwood, 2012, p. 12). Yet to reaffirm this biblical past a schematic narrative needed to be played out in front of the people so that they became prone to reaffirm the values as a cultural memory. James V. Wertsch, in his seminal work The Narrative Organization of Collective Memory differentiates between this specific narrative and schematic narrative template where constant revision of the official history overcomes the specific narrative and becomes schematic narration (Lužný, 2017, p. 200). Thereby, in dystopian literature they carve their own narrative template by using forgotten and fragmented cultural memories in combinations to achieve a linear narrative of their own choice. And architecture such as the Rachael and Leah Re-Education centre or the office of eyes serves as a narrative setting ground. Although Gilead still had to bear some monuments which forebear the liberal past it tried to unsee, we got a glimpse of these monuments from Offred when she mentions that the monuments of recent history do not go well with Gilead authorities: ‘The old gravestones are still there, weathered, eroding, with their skulls and crossed bones, memento mori, their dough-faced angels, their winged hourglasses to remind us of the passing of mortal time, and, from a later century, their urns and willow trees, for mourning. They haven’t fiddled with the gravestones, or the church either. It’s only the more recent history that offends them’ (Atwood, 2012, p. 42). These monuments carry with them the grave danger of igniting individual memories relating to it, the memories which Gilead’s system tries to overshadow with new collective memories.\n\nHarald Welzer in his chapter History and Development of the Concept of “Communicative Memory” addressed the deliberate attempt of the politicians to temper with the architecture ‘historicism and postmodern architecture have shown, this social memory may well be a result of intentional memory politics: Architects and city planners not infrequently set out to accentuate a particular construction of a city’s history, by emphasizing certain historical elements and destroying others’ (Welzer, 2008, p. 288). Gilead too reconstructed the libraries that in due course of time in The Testaments serve no purpose to the citizens especially women as they are not even taught to read. Hence, the tampering with the architecture of the library made it no place of relevance in the cultural memory: ‘The Eyes hold sway in a former grand library. It now shelters no books but their own, the original contents having been either burned or, if valuable, added to the private collections of various sticky-fingered Commanders’ (Atwood, 2012, p. 56). The handmaid’s and other women of Gilead except for the aunts were deprived of the power to read and write instead they were taught that ‘pen is envy’ (Atwood, 1996, p. 196). ‘A large Eye with a real crystal in the pupil is centred on the door’ (Atwood, 2020, p. 71) took the place of an earlier book storage unit and research cubicles. This act of establishing the office of Eyes in the former library passes a message of redundancy and insignificance of books for the women of Gilead. Whereas, men/commanders were facilitated with a study of their own in their houses where they spend their hours in brooding. While the “Eyes” (security of Gilead) was given a lidless shape to affirm the fact in the citizens that ‘the lidless Eye of God, they never sleep’ (Atwood, 2019, p. 148).\n\nArchitectural surveillance was forced on every citizen of Gilead, supposedly more on women/handmaids, where limiting the products and writings in their room was an agenda to limit their thinking capacity, thereby imposing artificial collective memories on them: ‘I go to the window and sit on the window seat, which is too narrow for comfort. There’s a hard little cushion on it, with a petit-point cover: FAITH … It’s the only thing they’ve given me to read’ (Atwood, 2012, p. 62). The architecture of Offred’s and all the handmaids’ rooms was such that both spectacle and vision for future was suppressed, so that only the training in the Re-Education centre found their place in her mind and solidified its existence as a cultural memory with time. This restrictive architecture of Gilead was contrasted by the building in Canada named “Religious Society of Friends (Quakers)”, a place where Offred’s daughter and Gilead’s most sought-after baby, “Baby Nichole” got shelter. The building was given the name Quakers to show a sharp contrast to Gilead’s ideology as Quakers rejected all elaborate religious ceremonies and believed in the spiritual equality of men and women.\n\nIn The Testaments these handmaids had passed a generation where their kids, given to the foster parents, had seen Gilead as the only world structure. A structure which is concrete and the architecture bearing it is impenetrable. Even the “Vidala school” has four pictures of ‘Aunt Elizabeth and Aunt Helena, then Aunt Lydia, then Aunt Vidala. Baby Nicole and Aunt Lydia had gold frames, whereas the other three only had silver frames’ (Atwood, 2019). These pictures of aunts gave the memory of piousness and duty as the ultimate goal of women’s life. Although these girls are taught petit point embroidery for being wives in future, still these pictures in school forms an imprint in their mind following a cultural memory. In contrast to this generation who were born and raised in Gilead there are Aunts, who still have remnants of individual memories left in them, from the time when they were ‘spoiled of too much choice’. Surprisingly enough, the speaker of the later line Aunt Lydia in The Testaments, single handedly initiated a war, and to muster up the courage used her individual memories over those enforced Gileadean cultural imprints. However, architecture remained the backbone for the people who were capable of reminiscence, such as Aunt Lydia, ‘I am pleased to relate that no one has erased the murals on either side of this building’s interior staircase: since they depict dead soldiers, angels, and wreaths of victory, they are pious enough to have been deemed acceptable, although the flag of the erstwhile United States of America in the right-hand one has been painted over with that of Gilead’ (Atwood, 2019, p. 56).\n\n\nIdentical Grouping\n\nGileadean society segregates women into six categories according to their usefulness towards the society. These are: Aunts, Wives, Marthas, Handmaids, Econowives, and Unwomen. This segregation of women on the basis of their fertility paves the way for further indoctrination of shared memory in the society. Their routines and working patterns were forked in a way that restricts their natural thinking pattern and hence forces them to think like the group they are in: “Women are either pampered but powerless trophy wives, humble servants known as Marthas or fertile breeding stock” (Bianculli, 2017). The groupings are also segregated by coloring. Aunts are given brownish-green robes to project their status of military authority and power of indoctrination. Whereas, wives are donned with lavish blue dress depicting royalty, Marthas wear dull green for household chores and Handmaid’s are the only women allowed to wear vibrant red which depicts their fertility, the most prized possession of Gilead.\n\nIn The Handmaid’s Tale the story line revolves around the conditioning of the Handmaid’s group whereas The Testaments focuses on the conditioned women’s first generation paving the way for a solid cultural memory. To get a deeper insight into the way conditioning language and memory interplay need to be examined in detail.\n\n\nLanguage and Memory\n\nHistorically, language and memory have been studied independently. Ignoring the influence of language over memory, scholars created a neuro-linguistic gap between the past and present. Identical to language, memory also helps in the formulation of one’s identity, by socially constructing meanings over time. Culture in memory, primarily dangles on the countless links with the past. Jan Assmann has bridged the gap between the two, by revealing the working of communicative memory, which operates on “circular or feedback interplay between interior and exterior” (Assmann, 2011, p. 6). Further, it contributes to the formulation of one’s individual memory and consciousness through the continuous practices carried out within the culture, that implicitly affects the cultural memory of the state. Thus, he states that “study of cultural memory therefore focuses on such processes of transformation and enhancement, examining the decisive changes within the connective structure of a given society.” (10)\n\nOne of the significant decisive changes that occurred in Atwood’s duology is ‘language’, which contributed to the cultural shift of the state, a shift from the demographic America to the theocratic Republic of Gilead. The new government fixes their eyes on tomorrow while “preserving yesterday from oblivion by grasping it through memory” (Assmann, 17). The officials of Gilead keep referring to biblical text and language to bring the past into people’s conscious memory.\n\nAssmann presumes two things which help in producing the cultural memory through the communicative power of language:\n\n“There has to be some sort of record or documentation of the past one trying to refer to.\n\nThis record must indicate a distinguishing feature from today.” (18)\n\nThis can be illustrated with the example of Atwood’s The Testaments: where books were kept decoratively in the house library and women were forbidden to read them. Similarly, in its prequel, the narrator, Offred witnesses the recitation of some excerpts from the Bible and also few foreign words like “m’aidez”, “café au lait, nolite te bastardes carborundorum”, “sum es est”, “sum us estis sunt”, et cetera (which were antecedent to the current used language).\n\nFurthermore, Atwood established what Assmann called ‘canon’ in the former novel, which continued until the end of The Testaments. ‘Canon’ stands for a particular case – ‘that of a principle, norm, or value that is far more binding than a unique code such as a language’s grammatical rules’ (Assmann, 2011, p. 98). Canon emphasises using \"highly normative grammar or ideologically conditioned form of language\" (Assmann, 2011, p. 98). The second generation now adapts to the rules and norms set by their predecessors in The Handmaid’s Tale. The official language of Gilead aspires to repudiate and prohibit the former speech with biblical discourse (Kouhestani, 2013 p. 661). Gilead is still operating with the same lexical units, and young girls are conditioned to speak in the more rigid biblical language and stick to the teaching of their elders: “Just learn your lessons and trust your elders to do what is best, and everything will unfold as it should” (Atwood, 10). Words associate themselves with various meanings, but Biblical teaching in Gilead restricts the meaning of the lexeme towards a particular direction. Gilead uses language as a medium to memory in the psyche of Gileadean citizens which normalizes the subjugated role of women as ‘birth vessels’.\n\nAssmann categorized the derivation of meanings in four categories, namely (1) measure, ruler, criterion (2) model (3) rules, norm and (4) table and list.\n\nThis ‘measure, ruler, criterion’ category allows the authorities to deduce the sections to a minor part proportional to the whole and a functional unit. These parts of the excerpts in isolation convey different meanings opposing or diverting it from the true sense. Similar practices are carried out by the theocratic state, where some selected sections are repeatedly taught to the woman. In the words of Assmann, Aunts use the “faithful-to-word-and-meaning” (Assmann, 2011) formula for forking context from the text and for generating meaning. This separation of context from the selected extracts majorly contributes to the diversion of meaning, contributing to the justification of Gilead’s authoritarian rule. To maintain their rule, the state prohibited women from reading the whole bible, other documentation and world literature, locking it up in the Hildegard Library since it would uncover their truth (‘rule, norms’): “The precious Bloodlines Genealogical Archives kept so meticulously by the senior Aunts, the Bibles, the theological discourses, the dangerous works of world literature—all were behind that locked door” (Atwood, 300). Henceforth, rules are created to blur the context of the Bible and to create a distinct record of Gileadean context to Biblical excerpts.\n\nThe ‘ritual continuity’ of practices in Gilead helps the governing bodies hold power over women through birth ceremonies and other events (like birthdays, hymns) where women are repeatedly taking part in and handmaids learning similar Biblical phrases daily, including “Uplift the Lowly” and “Blessed Be the Fruit”. Consequently, it manifests itself as a ‘created reality’ or ‘distorted Biblical truth’ in the psyche, creating a long-term memory. This recurring interplay of experiences and concepts transpose the original memory figures, making ‘captured children and women’ forget their original individual memory: “We can’t remember what it is that we’ve forgotten. That we have been made to forget. That we’ve had to forget, in order to pretend to live here in any normal way” (330).\n\nThe first-generation of the Handmaids act as a ‘model’ for the second generation. A model can be defined as the “canon of conduct” (Assmann, 93). Growing up seeing the restricted and divided roles of women in the household, the second generation normalized and accepted the subjugated position of women, whom Gilead prepares either to marry a commander or to become a handmaid. The Latin language, which had almost vanished from the documentation in Agnes and Baby Nicole’s generation, left behind a few phrases such as “Per Ardua Cum Estrus”, “memento mori”. In contrast, the former generation which was aware of the many foreign languages such as Latin, Italian and French but in a rather controlled and restricted environment results in the oblivious state of Agnes about the language: “‘What is Latin?’ Becka said it was a language of long ago that nobody spoke anymore, but people wrote mottoes in it” (Atwood, 289).\n\nApart from Latin, archaic words and biblical jargons also dominate Gilead’s language system starting from the name Gilead itself which is a place in the Bible, which symbolises the hope for restoring that had been destroyed (98). In the state, very few officials have access to the Bible due to its controversial usage. When Agnes gets access to her Bible, she learns that “It does not say what they say it says” (302). Agnes realizes that the excerpts she had been reading and memorizing since childhood were the pericopes for their ideological conditioning. The excerpts are separated from their context so that Gilead can use them to brainwash women and create identical individual memories, contributing to collective cultural memory formation. From here, Gilead started falling apart, and the collective memory made by Gilead also started fading. Although, no one remembers their past and language, they witness some glimpses of flashes from their past. As the theocratic state dissolved completely, Agnes was astonished that she knew only the restricted vocabulary, which limits her language and memory consequently moving ahead with Nicole would be difficult: ““Gilead,” said Nicole, “is not where we’re going. We’ve got two minutes to join our buddy outside. So suck it up.” “Pardon?” Sometimes I could not make out what my sister was saying…“It means ‘be brave,” she said. We are going to a place where she will understand the language, I thought. And I will not. (364). This case of language distinction on the part of Agnes and Nicole can be well elucidated by the Sapir-Whorf Hypothesis where it states that your language shapes your thinking and social reality to a great extent. Therefore, a shift in language makes a shift in the cultural identity and hence memory of a person.\n\n\nConclusion\n\nMemory plays a prominent role in creating one’s identity hence manipulating one’s memory can have a direct impact on their identity. Similar patterns of cultural memory formation or in other words individual memory distortion at macro scale was evident in the text of The Testaments. Therefore, Jan Assmanns’ Memory Figures proved to be an apt theoretical base for Atwoods’ work. Architecture and language are the two subtle mediums used to communicate the frames of collective memory of the younger generation in The Testaments. The prominence of cultural imprints is visible in the bipolar attitudes of Daisy aka Baby Nicole and Agnes as one is raised in Canada and the other in Gilead.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article, and no additional source data are required.\n\n\nReferences\n\nAssmann A: Cultural Working Memory: The Canon.Noơnning AEA, editor. Cultural Memory Studies: An International and Interdisciplinary Handbook. Walter de Gruyter; 2008a; pp. 100–107.\n\nAssmann A: Transformations between history and memory. Social Research: An International Quaterly. 2008b; 75(1): 49–72. Publisher Full Text Reference Source\n\nAssmann J: Communicative and Cultural Memory.Erll A, Nünning A, editors. Cultural memory studies: an international and interdisciplinary handbook. Vol. 2008. . Walter de Gruyter; 2008c; pp. 110–111. Publisher Full Text\n\nAssmann J: Cultural memory and early civilization: Writing, remembrance, and political imagination. 2011th ed.Cambridge University Press; 2011. Publisher Full Text\n\nAtwood M: The Handmaid’s Tale. Vintage Books; 1996.\n\nAtwood M: The Handmaid’s Tale. 1st ed.Vintage Books; 2012.\n\nAtwood M: The Testaments. 1st ed. Vol. 2019. . London: Chatto and Windus; 2019.\n\nBianculli D: Hulu’s ‘Handmaid’s Tale’ Delivers a Timely and Feminist Message. NPR. 26 Apr. 2017. Reference Source\n\nFunkenstein A: Collective Memory and Historical Consciousness. Hist. Mem. 1989; 1(1): 5–26. Indiana University Press. Reference Source\n\nHalbwachs M: ON COLLECTIVE MEMORY. COSER LA, editor. The University of Chicago Press; 1992. Publisher Full Text\n\nKaruny: Lev Vygotsky. Pedagogy4Change. 28 July 2022. Reference Source\n\nKouhestani M: Disciplining the Body: Power and Language in Margaret Atwood’s Dystopian Novel The Handmaid’s Tale. J. Educ. Soc. Res. 2013; 3: 610. Publisher Full Text\n\nLužný D: Sect as a Threat- Cultural Memory and the Image of Sects. Politics Relig. Ideol. 2017; 18(2): 198–216. Publisher Full Text\n\nNora P: Between Memory and History: Les Lieux de Memoire. University of California Press; 2011; vol. 26. : 7–24.\n\nOlick JK, Robbins J: Social Memory Studies: From ‘Collective Memory’ to the Historical Sociology of Mnemonic Practices. Annu. Rev. Sociol. 1998; 24: 105–140. Annual Reviews. Publisher Full Text Reference Source\n\nQuan Z: Cultural Memory and Ethnic Identity Construction in Toni Morrison’s A Mercy. J. Black Stud. Sept. 2019; 50(6): 555–568. Publisher Full Text\n\nWelzer H: History and Development of the Concept of “Communicative Memory.”Noơnning AEA, editor. Cultural Memory Studies: An International and Interdisciplinary Handbook. Vol. 8. 2008; pp. 285."
}
|
[
{
"id": "184137",
"date": "21 Aug 2023",
"name": "Teresa Tudu",
"expertise": [
"Reviewer Expertise Cultural Studies",
"Tribal literature"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, the authors explored how certain acts like identical grouping and language control shape the cultural memory in Margaret Atwood’s “The Testaments”. As a methodological framework, the article uses Jan Assmann’s concept of Memory Figures to highlight the formation of collective memory, which further imprints itself as cultural memory in the minds of characters over time in the novel. The article also provides a clear and concise literature review to track the development of the concept of memory over the years. Despite falling under the domain of memory studies, this research also highlights the well-rounded underline pattern of creating cultural memory through language, literature and identical grouping in any totalitarian society.\nThrough a meticulous analysis of the impact of language on the formation of cultural memory and identity, the article makes a valuable contribution to the broader discourse surrounding social constructs, power dynamics, and the shared awareness of communities, both within the realm of literature and in the tangible world. Further, it enriches the existing body of knowledge surrounding Margaret Atwood’s literary contributions by providing the novel viewpoint on the complex interplay between language, memory, and identity. This, in turn, fosters a more profound understanding and admiration for her storytelling prowess.\n\nThe article exhibits promising potential. However, I would like to kindly offer some suggestions to the authors in order to further enhance this article. Additionally, I am looking forward to receiving a revised version of the manuscript from the author.\nThe authors briefly mention \"The Handmaid's Tale\" as a precursor to \"The Testaments\" in the abstract, but the rest of the article lacks a comparative analysis of both novels. It would be beneficial if the authors included a more comprehensive comparative analysis between the two novels in order to further delve into the exploration of cultural memory and identity to highlight the evolution of the two across the novel.\n\nThe article could benefit from considering other relevant theoretical frameworks or literary criticisms in addition to Jan Assmann's concept of Memory Figures. This would help provide a more comprehensive understanding of the intricate dynamics of cultural memory as portrayed within the novel.\n\nLastly, the conclusion of this article is succinct but it somehow fails to provide a comprehensive synthesis of the findings derived from the analysis. It will be better if authors add an intellectually stimulating conclusion to add more clarity to this research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "193172",
"date": "30 Aug 2023",
"name": "Enrique Meléndez Galán",
"expertise": [
"Reviewer Expertise Visual Culture",
"Speculative Fiction",
"Contemporary Art",
"Transmission of Knowledge"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: The paper examines Margaret Atwood’s The Testaments by analyzing Memory Figures (architecture and time, identical groupings, and language). The study concludes that manipulating one’s memories can build a new identity, in this case, for a religious dystopia. On this way, using memory figures is helping to analyze different attitudes of two of the main characters.\nStrengths:\nOriginal point of view and accurate methodology.\n\nClear correlation between characters, book descriptions and Memory Figures.\nWeaknesses:\nLack of discussion on identical grouping, doing unbalanced this part of the paper in comparison with the other sections.\n\nUnlimited field of work, analyzing examples from Atwood’s The Testaments and, also, The Handmaid’s Tale when the title of the paper is focused just in The Testaments.\nSuggestions for Changes:\nBroaden the Scope: Introduce a comparative analysis by considering, from the beginning of the paper, references from both of the novels written by Atwood about Gilead to provide a more comprehensive understanding of the figures. The authors are not being limited to The Testaments, and consequently, it must be clear from the beginning.\n\nAddress Alternative Factors: Discuss the potential influence of other factors, specially in identical grouping, such as patriarchy, different roles of the women in the society, or different categories for the men to offer a well-rounded perspective and balance this part of the paper.\n\nInclude a context quoting the Tv Serie: Extend the context beyond the novels to capture broader field of work on visual and cultural studies and helping to understand the importance of this novel after being a TV Series.\n\nPropose Analysis Strategies: Offer recommendations for future analysis on this way to replicate the use of Memory Figures on other dystopian novels.\nBy implementing these changes, the paper can offer a more complete view of the importance of the role played by memory figures on the constructions of the characters and provide a well-rounded analysis of the world building according not only to The Testaments but to The Handmaid’s Tale also.\nOn the other hand, it would be interesting to correct this issues:\nAt the beginning of the article is written “Daily” instead of “Daisy”. Review.\n\n“Memory Figures” is once written with capital letters and other times without capital letters. Unify.\n\nSince authors are using two sources with the same surname, it would be good for a better understanding, if editors approve, including the second surname in the quote or the initial of the name to clarify the source. Review.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "196129",
"date": "21 Sep 2023",
"name": "Lizzie Seal",
"expertise": [
"Reviewer Expertise Historical criminology",
"cultural criminology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article deploys theories of collective and cultural memory to analyse Atwood’s portrayal of a theocratic dystopia in The Testaments. It applies these theories thoroughly and effectively to examine how the dystopian regime works and reproduces itself. The sections on architecture and language are fruitful. I have some comments and suggestions regarding how the article could be improved.\nThe article would benefit from a more extensive summary of the novel to ground the discussion.\n\nThe authors need to clarify which body or bodies of academic literature they are seeking to contribute to.\n\nPrevious literature on The Handmaid’s Tale and The Testaments should be incorporated into the literature review, as well as literary criticism on collective memory and dystopia more widely.\n\nThe identity separation section is very short - I recommend removing it.\n\nThe conclusion is too brief and needs expanding. The authors can fully outline their contribution here, taking existing literature into account.\n\nThe article needs a thorough proof read for grammar and syntax (particularly for misplaced commas). Attention is also needed to errors in word choice - for example, it should be ‘democratic America’, not ‘demographic’.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-475
|
https://f1000research.com/articles/13-545/v1
|
28 May 24
|
{
"type": "Case Report",
"title": "Case Report: Mercury-induced renal autoimmunity – An insight into its pathogenesis",
"authors": [
"Bhushan C Shetty",
"Muralidhara Yadiyal B",
"Ashok Bhat M",
"Muralidhara Yadiyal B",
"Ashok Bhat M"
],
"abstract": "Membranous nephropathy (MN) is the most common cause of nephrotic syndrome in adults. It may be idiopathic or due to secondary causes. Among the secondary causes, heavy metals like mercury are the one among others. Here is a male with nil comorbidities who, upon exposure to mercury-containing skin cream, developed proteinuria, which, on evaluation, was found to have dual renal lesions like membranous nephropathy and chronic interstitial nephritis. The uniform PLA2R staining within the glomerular capillary walls shows the ability of mercury to induce inflammation and autoimmunity. This case strengthens the findings of in vitro studies about mercury-induced inflammatory processes.",
"keywords": [
"mercury",
"membranous nephropathy",
"chronic interstitial nephritis",
"proteinuria"
],
"content": "Introduction\n\nMembranous nephropathy (MN) is the most common cause of nephrotic syndrome in adults. They are characterized by basement membrane thickening and minimal or no cellular proliferation with immune deposits on the epithelial side of glomerular capillary walls.1 The majority are idiopathic, and some can be due to autoimmune diseases, malignancies, and exposure to heavy metals like mercury. Mercury exposure has effects on various organ systems, including the immune system. Here, we would like to report a case with dual renal lesions on histopathology caused by the usage of mercury-containing skin cream.\n\n\nCase\n\nA 26-year-old male with nil comorbidities, driver by occupation, presented to our outpatient department with easy fatigability of 2 months duration. He had not been evaluated for the same prior. He was normotensive. Labs (Table 1).\n\nHe was admitted for renal biopsy and underwent the same. Post biopsy, he was discharged and came back to our OPD (outpatient department) with the biopsy reports almost a month later. Biopsy revealed features suggestive of a moderate degree of chronic interstitial nephritis and membranous glomerulonephritis (Figures 1 & 2). Immunofluorescence revealed glomerular tufts showing FOCAL and SEGMENTAL distributed finely granular deposits with IgG(3+), C3(1+), Kappa(2+), Lambda(2+) along the capillary walls and others were negative. PLA2R(phospholipase A2 receptor) - glomerular capillaries showed diffuse and globally distributed uniform granular staining along the capillary walls.\n\nChest radiograph was normal, ultrasound of abdomen revealed normal-sized kidneys, and there was no history of NSAIDS or native medicine intake. On probing his history, he admitted that, due to his dark complexion, he had been using a skin-lightening cream [Beauty Cream] on his face and forearms for the previous eight months given by his friend, but stopped when he had developed symptoms of easy fatigability. The cream was sent for heavy metal analysis, and the mercury content was found to be 9308.6 mg/kg, which is approximately 7,500 times higher than that prescribed by the Minamata convention. We sent his 24-hour urine for mercury levels (though he had stopped using the cream for >3 months) for academic purposes, which was within normal limits. Serum PLA2R levels were not done due to financial constraints. He was treated with ACEi and other supportive care. He is better, and subsequent follow-up urine analysis showed proteinuria regression.\n\n\nDiscussion\n\nMembranous Nephropathy is associated with a lot of morbidity and mortality, with 20–50% of may have progressive renal disease.2 When it is associated with another renal lesion, as it happened in our patient, the progression of renal disease will be accelerated. Mercury may damage the kidney in several ways. It may cause tubular or glomerular damage based on whether the exposure is acute or chronic. Acute exposure causes tubular necrosis, and chronic exposure involves the glomerulus3; both the compartments are involved here. If the exposure doesn’t cease, then the tubular necrosis may lead to tubular atrophy and fibrosis, which is evident in the renal histology of our patient. There have been previously published reports of mercury poisoning caused by skin-lightening creams. For example, there were more than 200 cases of women poisoned by mercury after using one kind of skin-lightening cream produced by Mexico in 1995. Mercury poisoning was also reported in about 100 women in Hong Kong after the use of cosmetics made in Mainland China.4 The diagnosis mainly rests on the temporal association with history, detection of mercury in the sample, and if presented <3 Months, 24-hour urinary mercury levels may give a clue. The peculiarity of our case here is the presence of solid and uniform PLA2R staining along the capillary walls. This can be seen in mercury-induced MN due to the following reasons:\n\n(1) The ability of metal ions to ignite an inflammatory response without mitogens is very much established. Evidence for this comes from studies of metal-induced inflammation by beryllium exposure, where the proposed cellular mechanism involved is the activation of the innate immune system via cell death, engagement of pattern recognition receptors, migration of antigen-presenting cells to secondary lymphoid organs, and subsequent activation of the adaptive immune system including IFN-γ producing Th1 CD4+ T cells.5 Adaptive immunity mediated by mercury exposure requires components of the innate immune system,6 arguing that understanding early events in metal-induced immune cell activation is essential for inflammation and immuno-pathology. There are studies where it is seen that mercuric chloride elicits in vitro lymphoproliferation in rabbits,5 rats, and guinea pigs.\n\n(2) Mercury causes significant renal tubular toxicity, and it has been postulated that this leads to the release of self-antigens and an ensuing inflammatory response involving cytokine and autoantibody production.\n\n(3) Merucury ions cause structural damage to the glomerulus, resulting in exposure to PLA2R antigens. This leads to the genesis of anti-PLA2R antibodies, mimicking idiopathic/primary membranous nephropathy.\n\nPrevious case reports/reviews mentioned mercury-induced membranous nephropathy and minimal change disease. Here, we report dual renal lesions like chronic interstitial nephritis and membranous nephropathy that highlight the magnitude of mercury-induced renal toxicity caused by the application of this adulterated skin cream. Hence, we should be alert to the possibility of mercury toxicity in patients presenting with new-onset proteinuria and question their use of such mercury-containing products. In patients with mercury-induced MN, it is not mandatory to have a negative PLA2R staining.\n\n\nConclusion\n\nInflammatory indicators, autoantibodies, and renal disease are among the adverse effects of human exposure to mercury in its different forms. Due to the absence of appropriate diagnostic criteria and the modest number of small-scale epidemiological investigations, a definitive link with one or more diagnosable autoimmune illnesses could not be established. Our case with dual renal lesions, particularly with PLA2R-positive MN, strengthens the understanding of mercury-induced inflammation and renal autoimmunity.\n\n\nConsent to participate\n\nWritten informed consent was given by the patient.\n\n\nConsent to publish\n\nWritten consent from the patient was taken for publishing the case after de-identifying and anonymizing all the patient identifiers.",
"appendix": "Data availability\n\n“No Data are associated with this article”.\n\n\nReferences\n\nDoshi M, Annigeri RA, Kowdle PC, et al.: Membranous nephropathy due to chronic mercury poisoning from traditional Indian medicines: report of five cases. Clin. Kidney J. 2018 Jun 3; 12(2): 239–244. PubMed Abstract | Publisher Full Text\n\nChakera A, Lasserson D, Beck LH, et al.: Membranous nephropathy after use of UK-manufactured skin creams containing mercury. QJM. 2011 Oct; 104(10): 893–896. PubMed Abstract | Publisher Full Text\n\nOliveira DB, Foster G, Savill J, et al.: Membranous nephropathy caused by mercury-containing skin lightening cream. Postgrad. Med. J. 1987 Apr; 63(738): 303–304. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang L, Liu F, Peng Y, et al.: Nephrotic syndrome of minimal change disease following exposure to mercury-containing skin-lightening cream. Ann. Saudi Med. 2014 May-Jun; 34(3): 257–261. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPollard KM, Cauvi DM, Toomey CB, et al.: Mercury-induced inflammation and autoimmunity. Biochim. Biophys. Acta Gen. Subj. 2019 Dec; 1863(12): 129299. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPollard KM, Escalante GM, Huang H, et al.: Induction of Systemic Autoimmunity by a Xenobiotic Requires Endosomal TLR Trafficking and Signaling from the Late Endosome and Endolysosome but Not Type I IFN. J. Immunol. 2017; 199: 3739–3747. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "293920",
"date": "24 Jul 2024",
"name": "Michael Pollard",
"expertise": [
"Reviewer Expertise Autoimmunity associated with exposure to environmental/occupational exposures."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe findings in this manuscript are not conclusive because there is incomplete pathology and documentation of the findings. There seems to be severe GN with obliteration on several glomeruli on the H&E slide but its not clear and it would be more convincing to include a PAS stain to check for deposits. Plus there are only a few glomeruli in the images. Also, there is not adequate evidence of membranous GN in the figure. The described IF staining with focal and segmental distribution of deposits should be shown. The PLA2R staining should also be shown. There is insufficient support to implicate mercury for the kidney pathology. Although the cream being used contained extremely high levels of mercury, the patient had stopped using it for more than 3 months before presentation and his mercury levels were within normal limits at that time. Additionally, those mercury levels were not provided nor were follow-up urine analysis including mercury levels and proteinuria. A minor issue is the reference values for Urea are missing.\nMore detailed comments from clinical pathologists. In Fig. 1 the upper cortex of the kidney is dominated by chronic interstitial inflammation (moderate to advanced). But there appears to be only a single glomerulus, and only 60 % of the glomerulus cab be seen (upper corner). This glomerulus is severely damaged, there are no capillary structures. Instead, there is only a mass of fibrosis. This is the end-stage of a glomerulus, but still recognizable as a glomerulus. It gives no clue of underlying process causing the damage. In the middle of the picture is a mass of cells. This might be a reaction of the inflammation, or possibly may be a glomerulus and/or tubular structure which is not recognizable. Again, no clue of underlying process.\nIn Fig. 2 there are two glomerular structures which are situated to the left, and in the middle of the biopsy, and another to the left, down in the corner. In the first glomerulus, only half of it is recognizable. With the 2nd of the glomeruli the capillaries are intact, no proliferation of the podocytes or membranes. By light microscopy it is not possible to diagnose early stages of membranous glomerulonephritis, at least with this magnification.\nThus Fig 1 shows chronic interstitial nephritis (moderate) and a single end-stage glomerulus, while Fig. 2 shows parts of two glomeruli, little pathological changes with chronic interstitial nephritis (moderate). Images for immunofluorescence of IgG and C3, and PLA2R should have been shown and electron microscopy performed.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No",
"responses": []
},
{
"id": "329661",
"date": "06 Nov 2024",
"name": "Nur Canpolat",
"expertise": [
"Reviewer Expertise pediatric nephrology",
"dialysis",
"chronic kidney disease",
"hypertension"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report presents a 26-year-old man who developed renal autoimmunity, specifically membranous nephropathy and chronic interstitial nephritis, after using a mercury-containing skin cream. The report suggests a link between mercury exposure and renal autoimmunity, despite having stopped using the cream months before diagnosis. Pathological findings include positive PLA2R staining in glomerular capillaries, supporting the potential for mercury to trigger immune responses in renal tissue. However, there are critical gaps in the documentation, particularly histological and immunofluorescent evidence, which limit the certainty of mercury's role in this pathology. I have detailed my comments below.\nThe physical examination findings lack sufficient clinical detail, such as specific laboratory values and follow-up data such as mercury levels and proteinuria, limiting the clinical utility of the report. The patient had stopped using mercury-containing creams three months prior to admission and mercury levels were normal at the time of assessment. This temporal gap and the lack of documentation of mercury levels at the onset of symptoms creates uncertainty about the direct role of mercury in the observed renal damage. This situation needs to be well analysed. The renal pathology figures show only a few glomeruli, which limits the reliability of the case. In particular, there is a lack of PAS staining and IF images for IgG, C3 and PLA2R that could confirm the presence of deposits. This lack weakens the conclusions regarding the role of mercury in renal pathology.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-545
|
https://f1000research.com/articles/13-157/v1
|
01 Mar 24
|
{
"type": "Research Article",
"title": "A qualitative exploration of patients’ perception regarding the comprehensive dental services availed at a primary health center",
"authors": [
"Shushma Rao B",
"Ramya Shenoy",
"Parul Dasson Bajaj",
"Ashwini Rao",
"Mithun Pai",
"Praveen Jodalli",
"Avinash BR",
"Aparna KS",
"Navya Shinaj",
"Shagufta Musheer",
"Shushma Rao B",
"Parul Dasson Bajaj",
"Ashwini Rao",
"Mithun Pai",
"Praveen Jodalli",
"Avinash BR",
"Aparna KS",
"Navya Shinaj",
"Shagufta Musheer"
],
"abstract": "Introduction Comprehensive oral care is a service centered around the patient, and individuals who need it the most often face limited access. Patient perception acts as a guide for enhancing quality, ensuring patients’ future intent to utilize the services and facilitating recommendations to others. The present study aimed to assess the patients’ perception of comprehensive dental services availed at a Primary Health Center (PHC).\n\nMethods This qualitative study was based on a phenomenological interpretive approach, and judgment sampling method was employed. A validated interview guide, developed from relevant literature was employed in the local language to conduct interviews among adults visiting the PHC, gathering their views regarding the services provided. The interviews were audio recorded on a digital voice recorder, and files were password protected. Content saturation guided the determination of the final number of participants interviewed. After translating and transcribing the interviews, thematic analysis and coding were performed using ATLAS. ti 23 for Windows.\n\nResults A total of 12 participants were included in the study, following data saturation. Among them, there were 8(66.7%) female and 4(33.3%) male participants. Ten overarching main themes were discerned through the assigned codes, including positive views, neutral views, negative views, previous dental clinics visited, previous experience with dental treatment, treatments sought at the center, referrals, source of information about the dental center, subsequent visits and suggestions for improvement.\n\nConclusions The findings of this study revealed a positive patient perception of the comprehensive dental services offered at the PHC. Through insightful interviews, various strengths, and areas for improvement regarding the center and care provision were identified. These insights provide valuable suggestions that can be applied to elevate the utilization of dental services, ensuring continuous improvement in patient care.",
"keywords": [
"Comprehensive oral health care",
"patient perception",
"patient satisfaction",
"primary health center",
"public-private partnerships",
"health and wellbeing"
],
"content": "Introduction\n\nThe Dawson report first mentioned the term ‘Primary Health Care Center’ around 1920 in the United Kingdom.1 Primary care is defined as “the provision of integrated, accessible health care services by clinicians who are accountable for addressing a large majority of personal health care needs, developing a sustained partnership with patients, and practicing in the context of family and community.”2 Although the World Health Organization (WHO) has recognized the importance of primary care in health service systems, there is dearth of primary care physicians compared to specialist physicians.1,3 A similar shortage is observed in Sub-Saharan Africa, where factors such as inadequate financing and unreliable expenditure on medicines add to the challenges of providing primary health care.4–9\n\nIn India, Primary Health Centers (PHCs) and its outreach teams constitute the “backbone” of the rural health care system with strong referral mechanisms connecting them to speciality care.10 However, in developing countries, primary health centers face challenges in delivering oral health care, necessitating programs to enhance community outreach, meet basic health requirements, and facilitate proper patient referrals.11 The government of India launched the National Oral Health Programme to provide comprehensive oral health care in response to the oral health conditions in the nation. This initiative aims to improve the determinants of oral health, integrating oral health promotion and preventive services with the general health care system, and encouraging the promotion of public-private partnerships (PPP) as a means of improving oral health.12 The provision of comprehensive oral care is a patient-centered service13 that encompasses various dental treatments, including examinations, consultations, prophylaxis, and restorations.14 However, it is typically observed that while the population in urban areas has limitless access to these services, those in greater need of them have restricted access.15\n\nIn an effort to address the needs of underserved populations, community health services step in to offer free dental services, bridging the gap in access to oral care.16 Despite existing barriers such as challenges related to transportation and caregiver attitudes,17 literature suggests that these programs contribute to a reduction in carious teeth, particularly in children.13 To optimize services, co-locating dental clinics within medical health centers proves beneficial, streamlining the referral process and providing patients with convenient access to both medical and dental care.18\n\nPatient satisfaction, as evidenced in various studies, plays a crucial role in ensuring compliance, improving clinical outcomes, and increasing service utilization.19 Patient satisfaction is affected by patient perception,20 which is based on their dental experiences and a certain level of expectation when they avail dental services from a primary health center at a reasonable to no cost.21 Furthermore, it serves as a roadmap for enhancing quality,22 ensuring that patients not only have the intention to use the services in the future themselves but also to recommend them to others.23,24 Hence, the present study was carried out to assess the patients’ perception towards comprehensive dental services availed at a Primary Health Center (PHC) located in South India.\n\n\nMethods\n\nThe present qualitative research, which explores the perceptions of patients receiving comprehensive oral health care, has been reported in accordance with the COREQ (Consolidated criteria for Reporting Qualitative research) Checklist.25 The materials used in this study (questionnaire, participant information sheet, interview guide, sample consent form and filled COREQ checklist for the present study) are available as extended data.26\n\nPermission of Head of the Institution was obtained. Ethical approval was obtained before commencement of the study (Protocol No. 22105 dated 3rd January, 2023) from the Institutional Ethics Committee of Manipal College of Dental Sciences, Mangalore. Written informed consent was taken and participation was completely voluntary. Confidentiality of the participants was maintained.\n\nThis qualitative study was based on phenomenological interpretive approach. It goes beyond mere description to uncover the meanings, where the researcher attempts to interpret patients’ perception based on their judgements.27\n\nThe study was conducted at a Primary Health Center situated in Southern India. The dental care services at this center are delivered through a well-established public-private partnership formed between the Primary Health Center and a private dental college. This facility serves a population of 63,000 individuals and encompasses nine sub-centers.\n\nThe study participants were selected from among the adult patients (aged 18 years and above) seeking dental health services at the PHC, particularly those who had follow up visits for various dental treatments. This selection was based on judgement sampling, a non-probability sampling method that enables maximum variation in the sample. This approach enhances the acquisition of more significant insights into the phenomenon from various perspectives, providing flexibility in capturing a broad range of viewpoints. Participants were given details about the study’s objectives and the rationale for its execution. An oral as well as written consent was obtained from each participant before the interviews.26\n\nSample size is estimated to be maximum of 25 people as per literature.28 The final number of participants depended on content saturation, which was inferred when the codes and themes generated after each interview became repetitive.27\n\nThe interviews were conducted by a female dental post-graduate resident trained in qualitative research methods, fluent in the local language and who regularly attended postings at the PHC (SR). The interview guide26 was developed based on both existing literature9,18–21 and insights from two researchers who have been actively engaged in the program since its commencement. These researchers had firsthand experience in delivering clinical care to the local population and were well-versed in conducting interviews. The interview guide consisted of open-ended questions to gain a deeper understanding of participant’s perceptions and was translated to the local language. Face and content validity was performed by three subject experts and the interview guide was pilot tested on two adult patients who were not included in the study for clarity and comprehension. A separate room was identified in the PHC to carry out the face-to-face in-depth interviews, conducted in the local language with interview times ranging from 5–14 minutes. The interviews were audio recorded on a digital voice recorder by a keynote taker and the files obtained were stored in password protected computers. The consent of the participants was obtained both orally and in writing prior to the interview. At the end of each session, the investigator summarized the key points derived from the discussion. The demographic details of the participants like age, gender and area of residence were also collected. There were no repeat interviews carried out.\n\nThe interviews were translated in English and transcribed verbatim for subsequent data analysis, along with deidentification of the transcripts. The translated transcripts were read and reread by two investigators (SR & RS) to gain a complete understanding of the interview content, highlighting the keywords. Following this, the data was systematically delineated and coded by the two investigators. After an extensive discussion with a third researcher (PDB), a final list of codes, categories, subthemes from the entire dataset was compiled, and the main themes were subsequently identified. Coding and thematic analysis were conducted using ATLAS.ti software version 23 for Windows.29 Each study participant was consistently referred to by their assigned codes throughout the data analysis by all members of the research team. To maintain confidentiality, all data, including audio recordings and transcripts, were securely stored, and preserved in password-protected computers accessible solely to the research members involved in the study.\n\n\nResults\n\nA total of 12 participants were interviewed in this study with a mean age of 49.42 (±15.9) years. Among these, 8 (66.7%) were female, and 4 (33.3%) were male with the majority of participants lived in close proximity to the PHC.\n\nThe qualitative examination of the interviews resulted in the identification of three primary themes: pre-visit perspectives, visit related perspectives, and post-visit perspectives. Each theme was subsequently subdivided into two sub-themes, with further categories emerging from the respective codes. A comprehensive overview of these themes, sub-themes, categories, and codes is presented in Table 1.\n\nEach category was assigned a distinct color to facilitate easy identification of the codes in the transcribed interviews. The color-coded chart, depicting the occurrence of codes in each participant interview, is presented in Figure 1 and aids in recognizing the frequency of each code in every participant interview. Each theme, along with illustrative quotes, are detailed below.\n\nThis main theme was further divided into two subthemes including past dental experience and source of information about the dental care at PHC. The majority of participants (n = 6) had sought dental care at private dental clinics, while others visited dental camps or private dental colleges for treatment. One participant (P5) provided a detailed account of visiting multiple dental clinics for treatment, expressing dissatisfaction, as evident in the following quotation:\n\nP5: “… there was an old aged doctor, nearby only. He had own clinic below his home. He is a good doctor. Cheap and best. When I went to him, I had problem of severe sensitive teeth and pain too, so what he did every time he used to keep clove oil and send. Then I used to have gum problem too. He gave ointment to apply for one year. Then what I did was I went to another dentist. Then these gum treatment people couldn’t correct my problem. Then I went to another place near this nataraj theatre. They were THE BEST. Then they gave me tablet becosules. Everything got cured in one month. Then I had to get set done from him for my grandchild’s wedding…”\n\nWhen discussing past dental experiences, participants had sought various treatments, including scaling, prosthetic rehabilitation, and root canal treatment. Interestingly, two participants (P1 and P10) had never visited a dental clinic or undergone any kind of dental treatment, as indicated in the following excerpt:\n\nP10: “No. This is my first time I came for my dental treatment.”\n\nWhile two participants (P8 and P12) cited the high cost of dental treatment as a reason for not seeking dental services earlier, this ultimately motivated them to seek free dental care at the PHC, as elaborated in the following excerpt:\n\nP12: “I am a beedi worker, if I put in all my money for dental treatment then what will be left. Some take 600 rupees for extracting a tooth. I have put so much money for treatment in honnakatte; 1500, 4000 and 3000 rupees. And no benefit also. I got three dentures done but I can’t wear them. I have spent a lot.”\n\nThe participants obtained information about the center from various sources, such as acquaintances, local residents, social workers, and individuals seeking medical treatment at the PHC. Three female participants (P7, P8, and P12) mentioned that they visited the center upon learning about the availability of free treatment, as depicted in the following excerpts:\n\nP8: “For root canal and for crown. I was told it is free here. So, I came.”\n\nP12: “One of my relative said that in Surathkal they do good dental treatment and why to pay and go elsewhere. So, I came here. Two three people have come there from our area.”\n\nParticipants sought dental care at the PHC, encompassing services like scaling, restorations, root canals, prosthetics, and tooth extraction, as evidenced by the following quotes:\n\nP6: “I had lot of toothache. They told root canal needs to be done. For that I came here.”\n\nP5: “I came here only for teeth set. I had no teeth at all. That’s why I came here for teeth set. Then in 5 sittings I got my denture. Both up and down.”\n\nPredominantly, participants provided positive feedback about various aspects of the primary health center, covering aspects such as the availability of free treatment and the comprehensiveness of care, as evidenced by the excerpts:\n\nP6: “Many people wanted such a center to open. Like I had shown my teeth in another place. They told the cost for treatment was 12000 rupees. But here since root canal is done for free it is helpful to many people. Its easy to come and go too.”\n\nP7: “My opinion is good only. If everything is available at one place then it is easy right? It is helpful for us. It saves our time and yours.”\n\nP3: “Improvement is not needed. Just keep continuing like this only then it is good. I have told someone that we can come here, better than going to private they can get treatment here. They do nicely here.”\n\nP6: “Yes. Earlier when that pain used to start, I would find it difficult even to talk. Now it is better.”\n\nA few participants also appreciated the behavior of the staff, specifically noting the absence of discrimination at the center, as seen in the following excerpt:\n\nP5: “…But that first one I had to pay 20000 and this was for free. When we compare the two you all are giving great service to society.… That too without considering if person is poor or able, no difference between BPL and APL.”\n\nNegative feedback focused around long waiting time and difficulty in reaching the center from their residence, as highlighted by the following excerpts:\n\nP9: “Yes. Little waiting time is there, here there are only two chairs for treatment no and it takes some time to treat each patient too. This is the problem for waiting time, because only two chairs are there, if you increase that facility then it is good for others and for us too.\"\n\nP6: “Hmm. I have a small baby, so waiting was a little difficult.”\n\nP9: “We have to come in bus. That is a little problem. If we miss the bus then we have to come by rickshaw.”\n\nHowever, some participants also acknowledged that similar waiting periods are experienced in other dental clinics, making it more acceptable, as depicted in the following excerpt:\n\nP7: “Where ever we go, we need to wait. Private clinic or here, waiting will be compulsory (laughing). Who comes first will get treatment first and if we are late then our treatment also will be later.”\n\nAll participants recommended the center to others, with two participants (P2 and P5) specifically highlighting the free treatment offered to patients, as exemplified in the excerpts:\n\nP2: “I have told everyone about you all. That for free you remove teeth and give set.”\n\nP5: “I have already told so many people. I have a lady near my house who needs upper teeth and they are seeing proposal for their daughter. She wants nice teeth, I told they remove teeth here for free and they also keep two or four teeth if it is missing also.”\n\nAll participants revisited the center as they were provided with appointments, and among them, two participants also mentioned that they were willing to revisit out of self-interest.\n\nP4: “No they only gave appointment and I come at that time I come…”\n\nIn the post-visit perspectives, a significant portion consisted of recommendations for enhancing dental care at the PHC. These suggestions encompassed various aspects, including the provision of free services, cost reduction, the addition of more chairs and staff to minimize waiting times, and the importance of basic amenities such as drinking water and shaded waiting areas, as emphasized by the participants. The diversity of these suggestions is evident in the following excerpts:\n\nP8: “It is good. But crown also should be done here. We are working class people. We can’t pay lot of money for treatment. We came here because it is free treatment. We were told crown also will be done.”\n\nP10: “To give service you can have two extra chairs. People won’t have to wait then.”\n\nP4: “Yes, if there are more doctors to test and do then it will be faster.”\n\nP9: “Yes. Little waiting time is there, here there are only two chairs for treatment no and it takes some time to treat each patient too. This is the problem for waiting time, because only two chairs are there, if you increase that facility then it is good for others and for us too. Then they should put sheet where we sit here to wait.”\n\nP6: “Yes. There could be more doctors treating us patients here. There could be more (dental) chairs.”\n\nP5: \"That’s enough. Then you need to treat kids too.\"\n\n\nDiscussion\n\nThe present qualitative research was conducted to delve into patients’ perception regarding the comprehensive dental services offered at the PHC through in-depth interviews. The findings illuminated that the prevailing outlook on care at the PHC was predominantly positive, indicating a favorable perception among the participants.\n\nIn this study, the most common reason for visiting the center was to obtain dentures, indicating a significant interest among in addressing their missing teeth. Following this, endodontic treatment ranked as the second most common reason. This is in contrast with a study conducted in Switzerland, where endodontic treatment was the most sought-after treatment, followed by dentures.30 Some participants also mentioned that they visited because it offered free dental treatment. This suggests that the provision of free treatment increases the likelihood of patients utilizing the facility, aligning with findings of a Kerosuo et al., which notes that the treatment rate is influenced by the availability of free treatment.31 When inquired about their previous source of dental care, a majority of participants had previously sought oral health care at private dental clinics. The transition to the center for subsequent treatment might be attributed to the availability of free treatment, which, in comparison to the costs incurred in private clinics, is likely to be considerably lower.\n\nMost participants did not encounter any issues concerning the treatment provided, waiting times, or the availability of appointments. However, among those who faced difficulties, waiting time emerged as the primary concern. This aspect could have influenced their perceptions of the center and its facilities, aligning with findings from a study conducted by Inglehart et al.32\n\nMost of the participants in this study expressed satisfaction with the care they received at the center. Additionally, participants who visited the center primarily to alleviate pain reported relief. A study by Shrestha et al. indicated that patient satisfaction hinged on meeting the expectations and needs of the population.11 Similarly, another study focusing on children revealed an overall improvement in the oral and general health of children who received comprehensive care, likely contributing to their satisfaction with dental treatment.13 Similar results were observed in the present study with most participants expressing a positive opinion regarding the comprehensive care provided. This positive sentiment suggests that a holistic approach likely contributed to overall patient satisfaction by addressing the various facets of oral health and potentially related concerns.\n\nThe affordability of comprehensive care is a significant factor, as evidenced by a study conducted by Cruz et al, indicating that co-located clinics can enhance the cost-effectiveness of care. In line with this, a participant in our study highlighted the absence of a cost burden, emphasizing the convenience of receiving all necessary care in a single center and avoiding the expenses associated with traveling to different places for different treatments.18 This can be appreciated in the following excerpt:\n\nP8: “One is to give crowns. Then, good if all treatments are provided here. We can come to one place. No need to go once here (center) and there (college). Good if everything is available in one place.”\n\nRegarding recommending the center to others, all participants in this study expressed their willingness to do so, with the majority having already recommended the center to others. The reasons cited for willingness to recommend included the availability of free treatment, quality of care and the convenience of accessing all care in one location. Notably, studies on orthodontic treatment,33 fixed dental treatment34 and aesthetic crown lengthening35 have reported similar outcomes, where a substantial number of participants were willing to recommend the respective treatment to others. These findings were consistently attributed to the high levels of satisfaction with the treatments received.\n\nWhen questioned about potential enhancements to the center for improved care, the participants predominantly expressed the need for increased resources. This included a demand for more dentists, additional dental chairs for treatment, a shaded waiting area for patients, and provision of drinking water in the waiting area. Participants specifically emphasized the requirement for more dentists and dental chairs to alleviate waiting times, aligning with the findings in a study conducted by Nair et al.20 Additionally, participants voiced a desire for free dental crowns or fixed prosthetics at a lower cost, highlighting a perceived cost barrier to accessing paid dental services. This echoes the sentiments of the same study, where participants cited the high cost as a significant challenge, leading to difficult decisions on prioritizing family members for dental care when multiple individuals required treatment.20 These results highlight the complex interplay of factors that affect the accessibility and outcomes of comprehensive dental care services.\n\nThe scope of this study was confined to a single center, and to enhance the generalizability of the findings, future investigations could encompass multiple centers to increase the transferability of the outcomes.\n\n\nConclusion\n\nThe overall results of this study revealed a predominantly positive outlook among the participants regarding the comprehensive dental services at the PHC. Through insightful interviews, both strengths and weaknesses of the center, as well as the oral health care provided, emerged. Although the majority of patients expressed satisfaction, a subset of participants offered constructive suggestions for improvement. The various suggestions, based on real experiences, offer potential for improvement, and can enhance the use of dental services, establishing an environment that fosters continuous enhancement and prioritizes patient-centric oral healthcare.\n\n\nAcknowledgement\n\nWe thank all the staff working at the Primary Health Centre for their co-operation towards completion of this research.",
"appendix": "Data availability\n\nA qualitative exploration of patients’ perception regarding the comprehensive dental services availed at a primary health center. figshare. Dataset. https://doi.org/10.6084/m9.figshare.24982380.v2. 26\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nThe materials used in this study (questionnaire, participant information sheet, interview guide and example consent form) as extended data, uploaded to the repository alongside the underlying data. https://doi.org/10.6084/m9.figshare.24982380.v2. 26\n\nFigshare: COREQ checklist for “A qualitative exploration of patients’ perception regarding the comprehensive dental services availed at a primary health center”. https://doi.org/10.6084/m9.figshare.24982380.v2. 26\n\n\nReferences\n\nStarfield B, Shi L, Macinko J: Contribution of primary care to health systems and health. Milbank Q. 2005; 83(3): 457–502. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDonaldson MS, Yordy KD, Lohr KN, et al.: Primary Care: America’s Health in a New Era. Washington, D.C.: National Academy Press; 1996.\n\nWorld Organization of National Colleges, Academies and Academic Association of General Practitioners/Family Physicians (WONCA): The Role of the General Practitioner/Family Physician in Health Care Systems. Victoria; 1991.\n\nEwen M, Zweekhorst M, Regeer B, et al.: Baseline assessment of WHO’s target for both availability and affordability of essential medicines to treat non-communicable diseases. PLoS One. 2017; 12(2): e0171284. Epub 2017/02/09. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAgyepong IA, Sewankambo N, Binagwaho A, et al.: The path to longer and healthier lives for all Africans by 2030: the Lancet Commission on the future of health in sub-Saharan Africa. Lancet. 2017; 390(10114): 2803–2859. PubMed Abstract | Publisher Full Text\n\nGeldsetzer P, Haakenstad A, James EK, et al.: Non-technical health care quality and health system responsiveness in middle-income countries: a cross-sectional study in China, Ghana, India, Mexico, Russia, and South Africa. J. Glob. Health. 2018; 8(2): 020417. Epub 2018/10/26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDonabedian A: The quality of care: How can it be assessed? JAMA. 1988; 260(12): 1743–1748. PubMed Abstract | Publisher Full Text\n\nWorld Health organisation: Interim report: WHO global strategy on people-centered and integrated health services.2015.\n\nWallace BB, Macentee MI: Access to dental care for low-income adults: perceptions of affordability, availability and acceptability. J. Community Health. 2012 Feb; 37(1): 32–39. PubMed Abstract | Publisher Full Text\n\nGovernment of India: Bulletin of Rural Health Statistics. New Delhi: Ministry of Health and Family Welfare, Government of India; 2017.\n\nShrestha A, Doshi D, Rao A, et al.: Patient satisfaction at rural outreach dental camps - a one year report. Rural Remote Health. 2008; 8: 891. Publisher Full Text\n\nAccessed on 1st December, 2023. Reference Source\n\nMuralidharan D, Fareed N, Shanthi M: Comprehensive dental health care program at an orphanage in Nellore district of Andhra Pradesh. Indian J. Dent. Res. 2012; 23: 171–175. PubMed Abstract | Publisher Full Text\n\nVashishtha V, Patthi B, Singla A, et al.: Patient satisfaction in outreach dental programs of a Dental Teaching Hospital in Modinagar (India). J. Indian Assoc. Public Health Dent. 2015; 13: 324–327. Publisher Full Text\n\nShah N: Geriatric oral health issues in India. Int. Dent. J. 2001; 51 3 Suppl: 212–218.\n\nBhat N, Singh A, Asawa K, et al.: Assessment of satisfaction levels of patients during dental outreach programs in rural part of Udaipur, India. Niger. Postgrad. Med. J. 2016; 23: 227–231. PubMed Abstract | Publisher Full Text\n\nChaves SC, Barros SG, Cruz DN, et al.: Brazilian Oral Health Policy: factors associated with comprehensiveness in health care. Rev. Saude Publica. 2010 Dec; 44(6): 1005–1013. English, Portuguese. PubMed Abstract | Publisher Full Text\n\nCruz S, Kerr D, Patiño Nguyen D, et al.: Qualitative evaluation of the pre-implementation phase of a rural dental clinic co-located within a health center in the Pacific Northwest of the United States. Community Dent. Oral Epidemiol. 2022; 51: 256–264. Publisher Full Text\n\nArdey R, Ardey R: Patient Perceptions and Expectations From Primary Health-care Providers in India. J. Family Med. Prim. Care. 2015 Jan-Mar; 4(1): 53–63. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNair RD, Mohammadnezhad M: \"It’s a waste of time coming here, better go to private clinics with wider options for treatment\": patient’s perception on dental services provided in Fiji. BMC Health Serv. Res. 2022 Sep 10; 22(1): 1144. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNair RD, Mohammadnezhad M, Gohil DA, et al.: Patients’ perceptions on facilitators and barriers of utilization of dental services: suggestions for pacific nations. Pacific J. Med. Sci. 2020; 21(1): 68–79.\n\nSofaer S, Firminger K: Patient perceptions of the quality of health services. Annu. Rev. Public Health. 2005; 26: 513–559. PubMed Abstract | Publisher Full Text\n\nGishu T, Weldetsadik AY, Tekleab AM: Patients’ perception of quality of nursing care; a tertiary center experience from Ethiopia. BMC Nurs. 2019; 18: 37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRamani S, Sivakami M: Community perspectives on primary health centers in rural Maharashtra: What can we learn for policy? J. Family Med. Prim. Care. 2019; 8: 2837–2844. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTong A, Sainsbury P, Craig J: Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups. Int. J. Qual. Health C. 2007 Dec 1; 19(6): 349–357. PubMed Abstract | Publisher Full Text\n\nShenoy R: A qualitative exploration of patients’ perception regarding the comprehensive dental services availed at a primary health center. Dataset. figshare. 2024. Publisher Full Text\n\nRenjith V, Yesodharan R, Noronha JA, et al.: Qualitative Methods in Health Care Research. Int. J. Prev. Med. 2021 Feb 24; 12: 20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCreswell JW: Qualitative inquiry and research design: choosing among five approaches. 2nd ed.London: Sage; 2007.\n\nATLAS.ti Scientific Software Development GmbH: ATLAS.ti Windows (Version 23.2.2.27458) [Computer program].2023. Reference Source\n\nSchneider C, Zemp E, Zitzmann NU: Dental care behaviour in Switzerland. Swiss Dent J. 2019 Jul 22; 129(6): 466–478. PubMed Abstract\n\nKerosuo H, Abdulkarim E, Kerosuo E: Subjective need and orthodontic treatment experience in a Middle East country providing free orthodontic services: a questionnaire survey. Angle Orthod. 2002 Dec; 72(6): 565–570. PubMed Abstract | Publisher Full Text\n\nInglehart MR, Lee AH, Koltuniak KG, et al.: Do Waiting Times in Dental Offices Affect Patient Satisfaction and Evaluations of Patient-Provider Relationships? A Quasi-experimental Study. J. Dent. Hyg. 2016 Jun; 90(3): 203–211. PubMed Abstract\n\nBradley E, Shelton A, Hodge T, et al.: Patient-reported experience and outcomes from orthodontic treatment. J. Orthod. 2020 Jun; 47(2): 107–115. PubMed Abstract | Publisher Full Text\n\nTan K, Li AZ, Chan ES: Patient satisfaction with fixed partial dentures: a 5-year retrospective study. Singap. Dent. J. 2005 Dec; 27(1): 23–29. PubMed Abstract\n\nSilva CO, Soumaille JM, Marson FC, et al.: Aesthetic crown lengthening: periodontal and patient-centred outcomes. J. Clin. Periodontol. 2015 Dec; 42(12): 1126–1134. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "259671",
"date": "20 May 2024",
"name": "Vinayak Kamath",
"expertise": [
"Reviewer Expertise Oral Health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have done an excellent job in exploring an interesting and important topic that may have significant impact on the quality of services and bridge the gap in access to oral health care. I am pleased to approve the manuscript. There are a few comments, which the authors need to address. They are as follows.\nIntroduction\n\nThe authors may emphasize why this specific research is critical by linking it directly to gaps in existing literature or practical needs, to strengthen the argument for the study's relevance. Briefly mention the value of qualitative research in achieving the study objectives, which would justify the methodology used.\n\nMethods\n\nThe use of judgment sampling is appropriate but briefly discuss the potential biases and how they are mitigated. A single interviewer who regularly attended the PHC has conducted the interview. What steps were taken to reduce interviewer’s bias? Has this familiarity influenced participant’s responses due to social desirability bias? To assess content validity, Was CVI/CVR used? The authors have estimated a sample size of 25. More details may be provided regarding this for the benefit of readers. The researchers may provide cumulative frequency graph supporting their judgment that saturation was achieved as supplementary data. Translating interviews from the local language to English and transcribing them verbatim could introduce errors or loss of nuanced meaning. The translation process needs to be presented thoroughly. Any reason why the study did not include repeat interviews, which could have provided additional depth and validation of initial findings More detailed steps on the data analysis process would enhance transparency.(Eg As described by Braun and Clarke)\n\nDiscussion & Conclusion–\n\nWhile the study’s scope limitation is mentioned, discussing other potential limitations and how they might affect the findings would add rigor.Eg:\n\nInterview times range from 5 to 14 mins which may be relatively short in depth qualitative interview limiting the depth of data collected. Only basic demographic details (age, gender, area of residence) were collected. More detailed demographic information could provide a richer context for the findings.\n\nBased on the findings of the study, would the authors like to provide more specific recommendation for future research and for policymakers or practitioners?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11602",
"date": "25 Jun 2024",
"name": "Ramya Shenoy",
"role": "Author Response",
"response": "Dear Reviewer, We thank you for providing the invaluable input. INTRODUCTION Query - The authors may emphasize why this specific research is critical by linking it directly to gaps in existing literature or practical needs, to strengthen the argument for the study's relevance. Ans- Thank you for the comment. We have already addressed the above query in the introduction. “To optimize services, co-locating dental clinics within medical health centers proves beneficial, streamlining the referral process and providing patients with convenient access to both medical and dental care. To sustain these kinds of services, it is important to understand the patients perceptions regarding the services availed.” Query-Briefly mention the value of qualitative research in achieving the study objectives, which would justify the methodology used. Ans-Using a close-ended questionnaire or with a few open-ended questions, it is difficult to get an idea or clear picture regarding patient perception. Hence, qualitative research was carried out. METHODS Query-The use of judgment sampling is appropriate but briefly discuss the potential biases and how they are mitigated. Ans- Judgement sampling was used to enable the maximum variation in the sample where patients received different types of treatment available at the center rather than restricting to patients who availed of one particular treatment. Query-A single interviewer who regularly attended the PHC has conducted the interview. What steps were taken to reduce interviewer’s bias? Has this familiarity influenced participant’s responses due to social desirability bias? Ans- The following measures were undertaken to control interviewer and social desirability bias and are mentioned in the manuscript. “Face and content validity of the interview guide was performed by three subject experts and the interview guide was pilot tested on two adult patients who were not included in the study for clarity and comprehension. At the end of each session, the investigator summarized the key points derived from the discussion.” Query-To assess content validity, Was CVI/CVR used? Ans- In qualitative research, CVI/CVR of interview guide is not needed. Reference no. 27 & 28. Query-The authors have estimated a sample size of 25. More details may be provided regarding this for the benefit of readers. Ans - The sample size is estimated to be a maximum of 25 people as per the literature. The final number of participants depended on content saturation, which was inferred when the codes and themes generated after each interview became repetitive. Reference no. 27 & 28. Query-The researchers may provide cumulative frequency graph supporting their judgment that saturation was achieved as supplementary data. Ans- The color-coded chart depicting the occurrence of codes in each participant interview is shown in Fig 1. Providing the cumulative frequency graph would duplicate the same. Query-Translating interviews from the local language to English and transcribing them verbatim could introduce errors or loss of nuanced meaning. The translation process needs to be presented thoroughly. Ans-To avoid this error, the translated transcripts were read and reread by two investigators (SR & RS) to gain a complete understanding of the interview content, highlighting the keywords. Query-Any reason why the study did not include repeat interviews, which could have provided additional depth and validation of initial findings Ans-At the end of each session, the investigator summarized the key points derived from the discussion. Query-More detailed steps on the data analysis process would enhance transparency. (Eg As described by Braun and Clarke) Ans-Data analysis followed all the steps as per the COREQ checklist. In the present study inductive thematic analysis was followed and explained in Table 1. DISCUSSION & CONCLUSION While the study’s scope limitation is mentioned, discussing other potential limitations and how they might affect the findings would add rigor.Eg: Query-Interview times range from 5 to 14 mins which may be relatively short in depth qualitative interview limiting the depth of data collected. Ans- Short responses in interview in qualitative research are typically done in one to three phrases that are provided by study participants in response to specific questions. They are often used to capture the essence of participant’s responses or to indicate how they feel about a certain topic. These short responses can provide valuable insights into the participant’s thoughts and feelings, and are a key component of qualitative research data analysis. Query-Only basic demographic details (age, gender, area of residence) were collected. More detailed demographic information could provide a richer context for the findings. Ans-In research, demographic information is often collected to understand the characteristics of a study’s participants and to ensure that the sample is representative of the population being studied. However, it should be noted that demographic details which do not provide any weightage in explaining the results of the research need not be recorded. Query -Based on the findings of the study, would the authors like to provide more specific recommendation for future research and for policymakers or practitioners? Ans- Recommendations are mentioned along with the conclusion part."
}
]
},
{
"id": "259679",
"date": "22 May 2024",
"name": "Mallikarjun Sajjanshetty",
"expertise": [
"Reviewer Expertise Health care research",
"Dental Caries",
"Tobacco control",
"Periodontal disease"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWell constructed manuscript wherein we get an insight into what are the patient perceptions in a dental setting where services are provided for free through a PPP mode. Interestingly conclusions provide a clue to other institutions / tertiary dental care centers to indulge into these activities to do their bit for the mankind. Of course perceptions/excerpts recorded are positive as the service provided is free of cost / relatively at a very low cost. This practice needs to be implemented every where.\nWork in the manuscript has been clearly presented and it is absolutely replicable. Study design is appropriate and conclusions drawn are in accordance to the data collected.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-157
|
https://f1000research.com/articles/12-926/v1
|
02 Aug 23
|
{
"type": "Software Tool Article",
"title": "Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT",
"authors": [
"Maxime Borry",
"Adrian Forsythe",
"Aida Andrades Valtueña",
"Alexander Hübner",
"Anan Ibrahim",
"Andrea Quagliariello",
"Anna E. White",
"Arthur Kocher",
"Åshild J. Vågene",
"Bjørn Peare Bartholdy",
"Diāna Spurīte",
"Gabriel Yaxal Ponce-Soto",
"Gunnar Neumann",
"I-Ting Huang",
"Ian Light",
"Irina M. Velsko",
"Iseult Jackson",
"Jasmin Frangenberg",
"Javier G. Serrano",
"Julien Fumey",
"Kadir T. Özdoğan",
"Kelly E. Blevins",
"Kevin G. Daly",
"Maria Lopopolo",
"Markella Moraitou",
"Megan Michel",
"Meriam van Os",
"Miriam J. Bravo-Lopez",
"Mohamed S. Sarhan",
"Nihan D. Dagtas",
"Nikolay Oskolkov",
"Olivia S. Smith",
"Ophélie Lebrasseur",
"Piotr Rozwalak",
"Raphael Eisenhofer",
"Sally Wasef",
"Shreya L. Ramachandran",
"Valentina Vanghi",
"Christina Warinner",
"James A. Fellows Yates",
"Adrian Forsythe",
"Aida Andrades Valtueña",
"Alexander Hübner",
"Anan Ibrahim",
"Andrea Quagliariello",
"Anna E. White",
"Arthur Kocher",
"Åshild J. Vågene",
"Bjørn Peare Bartholdy",
"Diāna Spurīte",
"Gabriel Yaxal Ponce-Soto",
"Gunnar Neumann",
"I-Ting Huang",
"Ian Light",
"Irina M. Velsko",
"Iseult Jackson",
"Jasmin Frangenberg",
"Javier G. Serrano",
"Julien Fumey",
"Kadir T. Özdoğan",
"Kelly E. Blevins",
"Kevin G. Daly",
"Maria Lopopolo",
"Markella Moraitou",
"Megan Michel",
"Meriam van Os",
"Miriam J. Bravo-Lopez",
"Mohamed S. Sarhan",
"Nihan D. Dagtas",
"Nikolay Oskolkov",
"Olivia S. Smith",
"Ophélie Lebrasseur",
"Piotr Rozwalak",
"Raphael Eisenhofer",
"Sally Wasef",
"Shreya L. Ramachandran",
"Valentina Vanghi"
],
"abstract": "Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.\n\nMethods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading.\n\nResults: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.\nConclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.",
"keywords": [
"metagenomics",
"environmental",
"palaeogenomics",
"aDNA",
"microbiome",
"metadata",
"microbial",
"FAIR data"
],
"content": "Introduction\n\nThe field of palaeogenomics has been praised as a role model for scientific data reporting and data availability.1 When compared against FAIR principles (Findability, Accessibility, Interoperability, and Reusability),2 ancient DNA (aDNA) sequencing data have been consistently made available in standard data formats on public data repositories, satisfying the principles of accessibility, interoperability and, to a certain extent, reusability. However, the findability of the uploaded data still poses challenges, often due to the lack of inclusion of key metadata specific for aDNA in the standardised sample metadata fields used by public sequencing repositories such as the European Bioinformatic Institute’s European Nucleotide Archive (EBI ENA), the US National Center for Biotechnology Information’s Sequence Read Archive (NCBI SRA), and the Japanese National Institute of Genetics’ DNA Data Bank of Japan (NIG DDBJ). To improve findability of ancient metagenomic samples in public data repositories, the SPAAM community (https://spaam-community.github.io) previously developed the AncientMetagenomeDir project, a set of curated standard sample metadata for ancient host-associated shotgun-sequenced metagenomes, ancient environmental metagenomes, and/or host-associated microbial genomes.3 However, while sample-level metadata already help with the discovery of suitable comparative data, library-level metadata is also needed to further facilitate data reuse in dedicated aDNA analysis pipelines such as PALEOMIX,4 nf-core/eager,5 aMeta,6 and nf-core/mag.7 aDNA researchers often build many different types of NGS libraries8 and may generate (meta)genomic data using multiple different sequencing platforms that require different bioinformatic pre-processing workflows. Furthermore, the library-level metadata currently available in public repositories often lack key information about aDNA library treatments and other laboratory information needed to reproducibly reanalyse palaeogenomic datasets obtained from different studies.\n\nAs the number of ancient metagenomics samples and shotgun sequenced library files steadily increases (currently >2300 host-associated metagenome, >2200 single-genome, and >600 environmental metagenome sequencing run accessions as of March 2023; Figure 1), the need to find ways to efficiently identify, curate, and download such data is becoming more pressing. Although the original AncientMetagenomeDir releases provided project- or sample-level accession numbers that point to data primarily hosted by the ENA, SRA, and DDBJ, the metadata tables did not provide direct links to the data themselves. This meant that researchers still needed to manually search for each project or sample accession number in public data repositories and then manually identify and download the relevant associated files. Researchers were then required to parse and evaluate each sequencing file for inclusion in their study by consulting the original scientific publications for laboratory, library, and sequencing metadata. As with sample metadata, the reporting of this information within publications can be heterogeneous, may appear in the main text or supplement, and may take the form of prose text, tables, supplementary spreadsheets, or citations to other publications or protocols. While other tools for exploring public data repositories exist, such as NCBImeta,9 SRA-Explorer,10 and ffq,11 they are generally limited to a restricted set of metadata available for inspection, or require the use of command-line filtering tools, an interface not always accessible to all palaeogenomics researchers, who often have varying levels of computational experience.\n\n(a) Number of ancient metagenomic publications published per year with open sequencing data and included in AncientMetagenomeDir. The original AncientMetagenomeDir publication was in 2020. (b) Cumulative sum of the number of published samples with publicly accessible sequencing data. (c) Cumulative sum of the number of ancient metagenomic sequencing data accessions of the samples in panel b. Data from Fellows Yates et al.12\n\nHere we present AMDirT (AncientMetagenomeDir Toolkit), a tool designed to assist researchers in using a new extension of AncientMetagenomeDir that now includes aDNA library- and sequencing-level metadata. AMDirT is designed to provide a solution to three different challenges. First, it helps researchers curate newly published aDNA sequencing data in AncientMetagenomeDir by automatically retrieving relevant library-level metadata available from sequencing archives (autofill command), and preparing semi-filled data entry tables for submission. Second, the tool can perform a variety of data validation tasks on completed entry tables to ensure consistency (validate command, an improved version of the ancientMetagenomeDirCheck tool from Ref. 3). Third, AMDirT provides a web browser-based, user-friendly tabular graphical-user interface (GUI) that allows users to explore relevant ancient metagenomics-related sequencing datasets in AncientMetagenomeDir tables (viewer command) and to export scripts to download the filtered data. As an additional functionality, AMDirT can provide template input configuration files for a suite of standard aDNA metagenomics-related pipelines in order to further automate and accelerate the processing of such aDNA data. Finally, most of the AMDirT viewer functionalities are additionally mirrored in a complementary command line interface (CLI) for more experienced bioinformaticians (convert command). AMDirT is available for installation via PyPI (https://pypi.org/) or Bioconda,13 with source code on GitHub under https://github.com/SPAAM-community/AMDirT.\n\n\nMethods\n\nAMDirT tool implementation. Members of the SPAAM community (https://spaam-community.github.io) developed AMDirT through a series of code sprints and hackathons, using Python v3.9 (https://www.python.org/; RRID:SCR_008394). It is accessible via a command-line-interface written using Click or via a python API (https://click.palletsprojects.com/). The autofill command that automates metadata retrieval from sequencing archives to help with data curation is using the ENA portal API (https://www.ebi.ac.uk/ena/portal/api/)14 to query and return metadata associated with the sequencing library level. Data validation in the validate subcommand is performed using the jsonschema python library (https://python-jsonschema.readthedocs.io/) and it uses a variety of checks written using Pandas15 to avoid data duplication and ensure consistency of new entries.\n\nThe GUI data exploration interface of the viewer command was developed using Streamlit (https://streamlit.io/), and the streamlit-aggrid library16 is utilised to allow the end user to interactively filter and prepare configuration files to process ancient (meta)genomic data in bioinformatics pipelines. Finally, AMDirT is packaged thanks to setuptools,17 and is distributed on PyPi and Bioconda.13 The source code is available on GitHub (github.com/SPAAM-community/AMDirT), and associated documentation is provided online (amdirt.readthedocs.io).\n\nAncientMetagenomeDir library metadata aggregation. To extend the original AncientMetagenomeDir3 repository to include library metadata, we created new tab-separated value (TSV) tables and their associated validation checks in the form of JSON schema files, following the original AncientMetagenomeDir structure.\n\nWe retained the TSV format for maximum software compatibility, as originally described in Ref. 3. Fields included in the new library-level schema were selected after consultation with ancient metagenomics researchers via the SPAAM community (an international and open community of over 300 researchers), and, where relevant and possible, by mirroring existing metadata fields and controlled vocabulary from the ENA repository. Newly added library information columns include the library name (how data are typically reported in original publications), the aDNA library generation method (e.g., double-stranded or single-stranded libraries), the library indexing polymerase (e.g., proof-reading or non-proofreading), and the library pretreatment method (e.g., non-Uracil-DNA Glycosylase (UDG), full-UDG, or half-UDG treatments). The latter three fields represent information about the sequencing library construction that influence the presence of aDNA damage, a factor that is critical for the processing of aDNA NGS data.8,18 Sequencing metadata columns include instrument model, library layout (single- or paired-end), library strategy (whole genome sequencing, targeted capture, etc.), and read count. This metadata is also critical for correct processing of aDNA data. For example, whether an instrument uses 2- or 4-colour sequencing chemistry determines if poly-G tail trimming is required to remove sequence artefacts that arise in aDNA reads that are normally shorter than the number of sequencing cycles. Library layout is also necessary to indicate whether read-pair merging needs to be applied prior to mapping, or whether unmerged read pairs are available for de novo assembly. The remaining columns provide information about storage and file retrieval of sequencing data: direct URLs to FASTQ files, ‘md5 checksum’ strings (for post-download integrity verification), and download sizes (for storage space usage estimation). Tables may also be extended to contain field-specific metadata useful for data processing under specific conditions. For new non-ENA/SRA supported fields, such as library polymerase or library treatment, we defined fixed lists via new JSON-based ‘enum’ files stored in the AncientMetagenomeDir repository, as with the sample-level metadata.\n\nFor compiling the initial set of ‘raw’ library metadata, we took the sample-level publication data from each of the three sample-level metadata tables and their respective ENA and/or SRA sample-level accession numbers. We then used the ENA’s REST API to pull relevant metadata for the AncientMetagenomeDir library tables for each of the sample-level accession IDs. This was performed using R scripts (stored in the GitHub repository under ‘assets/utility/’) using the following libraries: tidyverse,19 jsonlite,20 httr,21 and xml2.22\n\nVia a series of community events, we then performed hand-curation of this initial set of metadata, and also completed data entry for columns of metadata not stored in the ENA by comparing the ENA stored metadata with the methods descriptions in original publications. This procedure identified multiple instances of inconsistencies between the two sources, as well as incorrectly uploaded data and metadata in previously published articles. We describe some of the common issues we encountered in the Discussion below. In cases of conflict between the publication and the ENA metadata, we endeavoured to contact the original authors of the publication for confirmation. When this was not possible, we used ‘unknown’ or another missing-data value to indicate uncertainty. Each library-level metadata addition underwent automated validation and peer-review following the same procedure described in Ref. 3. Since the community events, the AMDirT autofill command has been developed to improve the submission experience by community members contributing new metadata. The autofill sub-command automates the pulling of ENA metadata into a ‘draft’ library-table format during the continuous integration tests (CI) of a GitHub pull request of sample-level metadata, replacing and improving upon the R scripts used in the initial pull-down for the community events. Submitters to AncientMetagenomeDir can then copy over much of the metadata and fill in the remaining missing metadata not covered by the existing ENA metadata fields.\n\nAMDirT requires a UNIX-based terminal (e.g., Linux, OSX, Windows Subshell for Linux) for both installation and initial usage; however, the toolkit is written in Python and can therefore be used on a wide range of platforms and operating systems.\n\nTo install, users are recommended to use the pip or conda package managers. Users who wish to use the GUI based table viewer and downloader will also require any modern web browser supported by Streamlit (https://streamlit.io/).\n\nFor example, to install and load the help message:\n\nor via conda\n\nThe general help of AMDirT is available from the CLI:\n\nMost tools follow a standard CLI based interface. For example, converting a user-filtered ancient metagenome host-associated AncientMetagenomeDir table (e.g. in R) to a curl download script can be performed as follows:\n\nIn the case of ‘convert’, the input metadata tables must be supplied by the user (i.e., downloaded from AncientMetagenomeDir manually).\n\nThe resulting file AncientMetagenomeDir_curl_download_script.sh will be present in the directory specified in the command. The user can then simply run the bash script to download all libraries of the samples present in the input table.\n\nFor the template pipeline input sheets, these can be supplied to the pipelines themselves, after checking for accuracy.\n\nThe other AMDirT tools follow a similar scheme, with help messages and documentation on the AMDirT website providing more how-to information (https://amdirt.readthedocs.io/).\n\nFor the GUI-based ‘viewer’ tool, a user simply enters the following command in their terminal, after which their web browser will automatically load. Alternatively, the reported local or network address can be manually entered into the user’s web browser. In comparison to the ‘convert’ subcommand, the input tables are automatically pulled from the AncientMetagenomeDir for the user, without requiring any manual input.\n\nOnce completed, the user can close the tab and cancel the command in their terminal (e.g., with ctrl + c).\n\nAlternatively, for individuals who wish to use the viewer but do not wish to deal with software installation and/or are not comfortable with command line interfaces, a hosted webserver version of the AMDirT viewer is available at https://spaam-community.github.io/AMDirT/.\n\n\nUse cases\n\nHere we will describe a common use case for when users may wish to use the AMDirT package, namely filtering for a particular subset of metagenomic aDNA data, downloading the resulting data, generating a corresponding semi-prepared input sheet for nf-core/eager, and creating a citations file. Full tutorials in text and video format for the following and other AMDirT commands can be found on the AMDirT website (https://amdirt.readthedocs.io/).\n\nThis example scenario demonstrates how to download all publicly available ancient host-associated metagenomes published since 2020 from samples originating from Spain. In this hypothetical example, a user may wish to compare the microbial taxonomic profiles of archaeological dental calculus and other skeletal elements in Spain at different time points. In order to distinguish modern and aDNA, the user will likely want to examine the DNA for evidence of degradation, which can be used to authenticate aDNA. To do this, the user will already have selected their preferred dedicated aDNA analysis workflow, such as nf-core/eager,5 that integrates DNA damage analysis into its pipeline. nf-core/eager requires an input ‘sample sheet’ that describes whether a particular sample has been sequenced over multiple lanes or libraries, and whether aDNA damage has been already removed during laboratory processing. We will show how AMDirT can assist with the creation of this sample sheet.\n\nThis example assumes that the user has already installed AMDirT and nf-core/eager, and has downloaded a Homo sapiens sapiens reference genome.\n\nTo load the GUI based viewer and downloading tool, a user enters the following command into their terminal:\n\nAs shown in Figure 2a, the viewer is loaded into the user’s web browser. Using the left sidebar, the user can navigate drop-down menus to select the release of AncientMetagenomeDir to use (for reproducibility purposes), and the desired AncientMetagenomeDir table to explore (i.e., ancient environmental metagenomes, ancient host-associated metagenomes, or ancient microbial single-genomes). The user can also specify the number of rows for the table to display and which tool to use for the download scripts generated later in the example.\n\n(a) The viewer opens in a user’s web browser, where the desired AncientMetagenomeDir version and table is selected. (b) Interaction with columns follows standard operations common to most spreadsheet software. Samples for download are selected using check boxes. (c) After pressing ‘Validate selection’, buttons appear for downloading various download scripts, reference, and pipeline input sheets.\n\nOnce the AncientMetagenomeDir table is selected, the main window will load the corresponding table. The user can manipulate the columns as customary in most spreadsheet software, such as re-sizing the columns by dragging the bars between each column, dragging column names to reorder them, etc. Users can use keyboard arrows or scroll bars to navigate further along the columns. To filter the columns, the user can press the ‘hamburger’ menu of each column, which reveals a range of column operation options. In the example in Figure 2b, the ‘geo_loc_name’ column has already been filtered to display only samples with the value ‘Spain’, and by pressing the funnel on an integer column, such as ‘publication_year’, the user can specify to only display rows ‘greater than or equals’ 2020. Additional filter specifications can be added using the AND/OR operators in each filter menu. The user can then select which samples to be exported from AMDirT. They can either use the ‘Select All’ checkbox in the top left of the table, or select each sample using the check boxes at the beginning of each row on a sample-by-sample basis.\n\nOnce the user is satisfied with their selection, they can press ‘Validate Selection’ to display a range of option buttons (Figure 2c). Here, we recommend that users always download the corresponding AncientMetagenomeDir libraries table, as well as the BibTeX citation file. In this example, the user would also download the ‘curl download script’ and the ‘nf-core/eager’ input TSV using the corresponding buttons. Hovering over the download script button also provides an estimate for the user of how much hard-drive space the download of all selected data will use.\n\nTo close the GUI viewer, the user can close the tab in their browser, and then in their terminal press ctrl + c on their keyboard to stop the Streamlit server.\n\nOnce downloaded, the user should check the AncientMetagenomeDir libraries table to ensure that all desired libraries are present. If there are extra libraries with specifications that the user does not want, they should remove those entries from the curl download script and nf-core/eager input TSV files. The user should also review the nf-core/eager pipeline input sheet to check for accuracy in regards to the pipeline’s specifications.\n\nAfter filtering of the scripts and pipeline input TSV sheets, the user can then use their terminal to navigate to a directory, move the curl script into it and begin the download. Due to the large sizes of sequencing data, in most cases we recommend that a user do this in a ‘screen’ or ‘tmux’ session (or similar) to ensure that the downloading can continue in the background:\n\nOnce the sequencing data are downloaded, the user can provide their AMDirT generated nf-core/eager input sheet to the following Nextflow23 command (the nf-core/eager input sheet assumes that the command is being run in the same directory as the downloaded data):\n\n\nDiscussion\n\nSince the original publication of AncientMetagenomeDir3 and the release of version v20.09, the SPAAM community has nearly doubled the number of manually curated publications in the AncientMetagenomeDir from 87 to 161 studies as of version v23.03. The number of samples has increased from 443 to 1358 for ancient host-associated metagenome samples, 269 to 583 for ancient microbial genome level sequences, and 312 to 563 for sediment samples (Figure 1).\n\nDuring the series of ‘hackathon’ events carried out by the community to scrape library metadata from previous publications and subsequent submissions of new studies, a total of 2332 ancient host-associated metagenome libraries, 2278 ancient microbial genomes libraries, and 627 ancient environmental metagenome libraries have been curated and included.\n\nDuring the aggregation and clean up of the library metadata by the SPAAM community, a range of problems were repeatedly encountered across multiple studies that made data entry and the determination of appropriate preprocessing procedures difficult. Here, we describe the most common issues encountered, as well as possible solutions, listed from most to least severe. We hope by raising these common mistakes and problems, that the field can help improve data uploads that will both benefit the contributing to AncientMetagenomeDir but also the field as a whole.\n\nInconsistent sample and library naming. Problem: A common problem encountered when cross-referencing ENA or SRA metadata with information provided in original publications was inconsistencies in sample, library, and/or sequencing file names. This often made it difficult for the community member to correctly infer which library was associated with which sample, or even which sequencing file went with which library. Example: In studies where two sets of libraries were generated (for example, one with UDG-based DNA damage removal and one without), this palaeogenomic-specific information was often not indicated in the library or file names. Given that this information is not supported in the ENA/SRA metadata schema, this is the only location where such aDNA-specific information could be reasonably recorded. In such cases, we found that while library pretreatment procedures were documented in the original publication, the uploaded metadata and sequencing files generally lacked this information and in some instances used internal laboratory IDs instead of the sample or library codes recorded in the publication. Without a key linking the published IDs with the internal laboratory IDs, other researchers cannot know which files to use for their particular analyses or how to process the data appropriately, and this can lead to downstream problems. For example, if a user does not know that a sequencing file was generated from damage-removed libraries, they may inappropriately apply additional in silico trimming steps to remove DNA damage, and thus unnecessarily truncate the sequences. Solutions: We suggest two solutions: first, ancient metagenomic researchers should ensure that library and sample names are descriptive (i.e., in a structured system in which a certain level of information can be inferred just by the name) and that sequencing metadata uploads match those reported in the publication; second, where this is not possible (e.g., if upload is carried out by a third party), then researchers should at a minimum include a key in their supplementary files. This could be in the form of a table that includes all ID codes for each sample, library, and sequencing batch, including internal laboratory codes, other-analysis codes, and external sequencing archive accession codes.\n\nMetadata discrepancies about sequencing methods. Problem: Another relatively common issue was the discrepancies between the metadata reported in the sequence archive and in the original publication. It was generally difficult to resolve such discrepancies without contacting the authors. Discrepancies occurred most frequently in the reporting of the sequencing platform. Example: In several cases, the particular sequencing platform recorded in the sequence archive metadata, such as ‘Illumina HiSeq 4000’, did not match that reported in the publication, e.g. ‘NextSeq 500’. Solutions: Researchers should be sure to cross-reference their metadata upload sheets with their manuscripts prior to upload. In cases where Illumina sequencing was carried out externally (and where limited information may have been provided by the sequencing centre), researchers can generally inspect the headers of the FASTQ file to determine which platform was used, as in example provided here.\n\nMethods description in secondary or tertiary citations. Problem: For journals with strict word or character count limits, it was qualitatively observed that there was an increased tendency in these publications to rely on secondary or tertiary non-protocol specific citations for describing laboratory methods used for DNA library construction and sequencing. This practise is problematic as secondary or tertiary citations may describe multiple protocols, and it was not always possible to determine which protocol was actually used in the study. Example: In one case, a publication reporting an ancient microbial genome reconstruction referred to library protocols used in an earlier related publication that described data generation for a human population genetics study. However, upon closer inspection, this cited study itself referred to an even earlier publication that included extensive protocol experimentation and development. Neither the primary nor secondary publication indicated which of the experimental protocols from the original methods study was actually used. Solutions: Ancient metagenomic researchers should make an effort to more clearly describe their protocols and explicitly indicate which library protocol is linked to each sequencing file. At a minimum, the information provided should include critical metadata for downstream analysis, such as library treatment protocols that affect DNA damage. This can be accomplished by providing expanded, plain-language descriptions of laboratory methods in article supplementary information files (rather than simply citing and reciting) and providing a supplementary table that lists each library name and their corresponding treatments. For improved compliance with FAIR principles, researchers are encouraged to further provide or cite a protocol written up in a citable protocol format and/or on open platforms. For example, platforms such as protocols.io24 allow critical protocol information to be communicated consistently and unambiguously, by providing a persistent identifier (DOI) that points to a specific version of a given protocol.\n\nUploading of mapped BAM files or merged FASTQ files rather than raw metagenomic data. Problem: Occasionally, we found that in some cases ancient metagenomic researchers uploaded mapped BAM files or merged FASTQ files rather than ‘raw’ FASTQ files (i.e., against ENA/SRA specifications). Both formats present obstacles for downstream analysis. For example, mapped BAM files include only reads mapped to a particular reference genome and thus do not represent a full metagenomic dataset. For BAM files containing reads mapped to the human genome, microbial DNA will be absent, including ancient pathogen DNA that could be highly relevant for an archaeological study. While an ‘unmapped’ BAM (uBAM) format exists and FASTQ files can be partly reconstructed from such data, raw FASTQ files are the preferred format for data reporting. Unmapped BAM files indicate that a certain level of data preprocessing has already occurred, and such files often combine multiple libraries into a single BAM file in order to achieve sufficient genomic coverage for analysis. If the process of generating the BAM file is not sufficiently described, it can be difficult for other researchers to disentangle the data originating from different libraries or sequencing batches prior to reanalysis. Providing FASTQ files containing merged paired-end reads also limits data reuse. Although read merging is a common first step in some ancient bioinformatics pipelines, it is incompatible with others. Base quality scores are often altered during the read merging process, which can interfere with tools reliant on such scores, and most de novo sequence assemblers either require or perform better on unmerged reads. Furthermore, many metagenomic tools, including taxonomic classifiers, do not accept merged paired-end FASTQ files or BAM files as an input format. Example: An ancient metagenomic author generates both damage and damaged-removed libraries, but merges them together in BAM format and uploads to a sequencing archive. However another researcher wishes to analyse only the data deriving from the damage-removed libraries. Solution: Ideally researchers should upload FASTQ files that match the ‘raw’ output from sequencing, i.e., demultiplexed datasets separated per library, applying only the preprocessing steps recommended by the sequence repository (e.g., for the ENA/SRA, adapter removal but not read merging). If this is not possible, authors should, at a minimum, describe exactly how the merging steps were performed so that other researchers can manually separate merged sequences (e.g., using sequencing read headers) when required for downstream analysis.\n\nUnique sample accessions applied to multiple libraries of the same sample. Problem: Another common error was found to occur when researchers mistakenly uploaded each library or sequencing dataset with a unique sample accession code. While often not a critical error, because in these cases the correct sample could usually be inferred from the file name, this nevertheless makes automated data processing more difficult and requires manual intervention. To reuse such data, a researcher must manually reassociate the library datasets with the correct sample based on the file names, rather than relying on the sequence archive sample accession ID, as expected by metadata schemas of the ENA/SRA data repositories. Solution: Researchers should review sequencing archive documentation to ensure they correctly construct upload sheets at both the library and sample levels (e.g. https://ena-docs.readthedocs.io/en/latest/submit/general-guide/metadata.html). Furthermore, researchers should ensure that library names have a consistent pattern such that other researchers can unambiguously associate each library with the correct sample.\n\nIt is important to note that the aim of the pipeline TSV sheets generated by AMDirT is to provide a template for data input to the pipelines. Due to the high heterogeneity in the way that sequence (meta) data are uploaded, some information in AncientMetagenomeDir may be missing or erroneous, despite the ‘best efforts’ of the SPAAM community to standardise the information, resolve ambiguities, and correct errors. However, we hope that by providing this functionality, it reduces the time it takes to create such input sheets from scratch.\n\nWe envision that the future development of the AncientMetagenomeDir project will be to further extend and also standardise the types of metadata currently recorded. For example, when recording the age of samples, AncientMetagenomeDir currently only records a single value of an extremely rough, rounded-up, and approximate date. This poses challenges for analyses requiring exact dates and probability intervals such as tip dating for phylogenetic trees and other analyses of evolutionary divergence. At present, however, heterogeneity in the reporting of radiocarbon dates (the most common dating method in archaeology and palaeogenomics) and associated modelling information currently limits our ability to add such dating information to AncientMetagenomeDir, and to consistently apply calibration and reservoir effect correction across studies. This is despite the fact that there is already standard reporting guidance.25 However, we also call on ancient metagenomics researchers to report both uncalibrated and calibrated dates and associated metadata (radiocarbon lab code, calibration curve, software, etc.), and to not rely solely on secondary citations to facilitate adding such data to repositories such as AncientMetagenomeDir, as well as refinement of chronological modelling in the future.\n\nIn the same vein, we also aim to synchronise AncientMetagenomeDir with upstream standardised sequencing data metadata schemas and repositories such as MIxS checklists26 via another SPAAM project, MInAS (https://mixs-minas.org/), to further ensure common standards across both modern and ancient sequencing data.\n\nGiven the functionalities of AMDirT provide simple data exploration without requiring advanced computational knowledge, but also offers semi-prepared templates for aDNA and metagenomics, the dataset and tooling are ideal for further generation of community resources. Following other projects that have been developed for modern microbiome data,27 the ancient metagenomics community could also consider providing standardised and pre-made taxonomic profiles (e.g., for microbiome or environmental samples) or VCF files (for single genomes) that could allow integration into current analysis workflows to assist users in more rapidly integrating public data into their analyses from a single source. This could be particularly useful for screening ancient microbiome samples for preservation (e.g., by comparing a newly sequenced sample to all previously published ancient metagenomes), in order to assess whether a sample falls within the variation of known well-preserved or environmentally degraded samples.\n\n\nConclusions\n\nBy extending AncientMetagenomeDir to include library-level metadata, not only do we make ancient metagenomics data more findable, but we also make them more accessible by providing improved transparency of the diverse library and sequencing treatments performed in the field of palaeogenomics. Furthermore, AMDirT has been designed to improve the experience of researchers in the downloading and processing of previously published ancient metagenomics data. By providing both a graphical user interface and a command-line interface to filter and generate relevant download scripts and input sample sheets for aDNA analyses, we provide more flexibility and choice for the wide range of computational backgrounds that ancient metagenomic researchers can have. Finally, we hope that by informing researchers about inconsistencies in past data and metadata uploads, and by providing templates of standardised metadata for future publications, we will contribute to improving aDNA data reporting and FAIR data sharing.",
"appendix": "Data availability\n\nThe source data for the sample-level metadata used by AMDirT is from the AncientMetagenomeDir project originally published in Ref. 3 under a CC-BY 4.0 license.\n\nThe existing sample-level and new library-level data is stored on GitHub:\n\nhttps://github.com/SPAAM-community/AncientMetagenomeDir\n\nEach release is archived on Zenodo: https://doi.org/10.5281/zenodo.3980833 .\n\nNew sequencing library-level metadata is also stored in the AncientMetagenomeDir project from version v22.09 (Pyu Ancient Cities) onwards. 12 The version of the data set used for the demonstration of AMDirT, statistics, and figures in this manuscript is v23.03 (Rocky Necropolis of Pantalica). 28\n\nZenodo: SPAAM-community/AncientMetagenomeDir: v22.12: Joya de Cerén. https://doi.org/10.5281/zenodo.7470037 .\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\n\n• Software available from:\n\n– PyPi: https://pypi.org/project/AMDirT/\n\n– Bioconda: https://bioconda.github.io/recipes/amdirt/README.html\n\n– Hosted web version of AMDirT viewer: https://spaam-community.github.io/AMDirT\n\n• Source code available from: https://github.com/SPAAM-community/AMDirT/\n\n• Archived source code at time of publication: https://doi.org/10.5281/zenodo.7891473\n\n• License: GNU General Public License v3.0.\n\n\nAcknowledgements\n\nThe authors thank the SPAAM community for the ongoing maintenance, testing, and general support of both the AMDirT and AncientMetagenomeDir projects. We also thank all the supervisors and managers of all the authors for allowing us to contribute to the AncientMetagenomeDir and AMDirT projects. We are also grateful for all authors of publications who we contacted with queries about their metadata, particularly those who subsequently took the time to update their original sequencing archive uploads to correct mistakes or improve metadata of their given study.\n\n\nReferences\n\nAnagnostou P, Capocasa M, Milia N, et al.When data sharing gets close to 100%: what human paleogenetics can teach the open science movement. PLoS One. March 2015; 10(3): e0121409. 1932-6203. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilkinson MD, Dumontier M, Aalbersberg IJJ, et al.The FAIR guiding principles for scientific data management and stewardship. Sci. Data. March 2016; 3: 160018. 2052-4463. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFellows Yates JA, Andrades Valtueña Å, Vågene ÅJ, et al.Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci. Data. January 2021; 8(1): 31. 2052-4463. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchubert M, Ermini L, Der Sarkissian C, et al.: Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protoc. May 2014; 9(5): 1056–1082. 1754-2189, 1750-2799. PubMed Abstract | Publisher Full Text\n\nFellows Yates JA, Lamnidis TC, et al.: Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ. March 2021; 9: e10947. 2167-8359. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPochon Z, Bergfeldt N, Kırdök E, et al.: aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow. bioRxiv. October 2022; page 2022. Publisher Full Text\n\nKrakau S, Straub D, Gourlé H, et al.: nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning. NAR Genom. Bioinform. January 2022; 4(1). PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nOrlando L, Allaby R, Skoglund P, et al.: Ancient DNA analysis. Nat. Rev. Methods Primers. February 2021; 1(1): 1–26. Publisher Full Text\n\nEaton KNCBImeta: efficient and comprehensive metadata retrieval from NCBI databases. J. Open Source Softw. February 2020; 5(46): 1990. 2475-9066. Publisher Full Text\n\nEwels P, Duncan A, Fellows Yates JA: ewels/sra-explorer: Version 1.0.March 2023. Reference Source\n\nGálvez-Merchán Á, Min KHJ, Pachter L, et al.: ffq: A tool to find sequencing data and metadata from public databases.2022. Reference Source\n\nFellows Yates JA, Andrades Valtueña A, Vågene ÅJ, et al.: SPAAM-community/AncientMetagenomeDir: v22.09.2.August 2022. Reference Source\n\nGrüning B, Dale R, Sjödin A, et al.: Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat. Methods. July 2018; 15(7): 475–476. PubMed Abstract | Publisher Full Text\n\nHarrison PW, Ahamed A, Aslam R, et al.: The european nucleotide archive in 2020. Nucleic Acids Res. January 2021; 49(D1): D82–D85. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nThe pandas development team: pandas-dev/pandas: Pandas.2020. Publisher Full Text\n\nFonseca P: streamlit-aggrid: Implementation of Ag-Grid component for streamlit.2023. Reference Source\n\nPython Packaging Authority: setuptools: Official project repository for the setuptools build system.2023. Reference Source\n\nDabney J, Meyer M, Pääbo S: Ancient DNA damage. Cold Spring Harb. Perspect. Biol. July 2013; 5(7). 1943-0264. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWickham H, Averick M, Bryan J, et al.: Welcome to the tidyverse. J. Open Source Softw. November 2019; 4(43): 1686. 2475-9066. Publisher Full Text\n\nOoms J: The jsonlite package: A practical and consistent mapping between JSON data and R objects. arXiv. March 2014. Reference Source\n\nWickham H: httr: Tools for working with urls and http.2021. Reference Source\n\nWickham H, Hester J, Ooms J: xml2: Parse xml.2021. Reference Source\n\nDi Tommaso P, Chatzou M, Floden EW, et al.: Nextflow enables reproducible computational workflows. Nat. Biotechnol. April 2017; 35(4): 316–319. PubMed Abstract | Publisher Full Text\n\nTeytelman L, Stoliartchouk A, Kindler L, et al.: Protocols.io: Virtual communities for protocol development and discussion. PLoS Biol. August 2016; 14(8): e1002538. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMillard ARConventions for reporting radiocarbon determinations. Radiocarbon. 2014; 56(2): 555–559. Publisher Full Text Reference Source\n\nYilmaz P, Kottmann R, Field D, et al.: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. May 2011; 29(5): 415–420. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPasolli E, Schiffer L, Manghi P, et al.Accessible, curated metagenomic data through ExperimentHub. Nat. Methods. October 2017; 14(11): 1023–1024. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFellows Yates JA, Andrades Valtueña A, Vågene ÅJ, et al.: SPAAM-community/AncientMetagenomeDir: v23.03.0: Rocky necropolis of pantalica.March 2023. Reference Source"
}
|
[
{
"id": "210929",
"date": "09 Oct 2023",
"name": "Timothy Read",
"expertise": [
"Reviewer Expertise Bacterial genomics",
"metagenomics",
"bacterial genetics",
"antibiotic resistance"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper describes the ‘AMDirT' open source software for interaction with ancient metagenome sequence sample metadata tables. The tables have been produced through a massive communal curation effort by the international SPAAM (The Standards, Precautions, and Advances in Ancient Metagenomics community) group to systematically improve on what is available from the public repositories of archived short read sequence data. AMDirT allows viewing and searching of the tables using the Python streamlit library and facilitates download of data and integration with open source nextflow analysis pipelines. AMDirT also helps with initial creation and validation of new metadata tables.\nI successfully installed AMDirT version 1.4.6 using conda on my Intel MacBook following instructions in the manuscript. I was able to replicate the commands described. There is also a public server https://www.spaam-community.org/AMDirT/ for the AMDirT viewer. The documentation for the software is very good and includes video tutorials.\nThe manuscript is well-written and clearly outlines the functions of the software. The development of AMDirT represents a significant effort, not least because of the community-wide consultation. The need for community-based metadata addresses a well-known problem with the SRA/ENA/DDBJ databases and the discussion provides some nice examples of the type of issues faced when downloading. AMDirT is a valuable tool for both the ancient metagenomics research community and those outside the community interested in browsing and accessing the data.\n\nSpecific Points\nThe streamlit-based viewer is pretty slick but I feel the importance of command line interface (CLI) is a little underplayed here. The viewer can be used by people without CLI proficiency but to actually take actions like making new sample tables, or download and process data, CLI is essential.\n\nThe instructions in the text and on github for conda install should guide users to install into a fresh conda environment rather than into the base.\n\nThere should be a list of computational environments that the software has been tested on (e.g do M1-3 macs work?)\n\nI did not see a mention in the text that there is actually a public facing server https://www.spaam-community.org/AMDirT/\n\n“Newly added library information columns include the library name (how data are typically reported in original publications), the aDNA library generation method (e.g., double-stranded or single-stranded libraries), the library indexing polymerase (e.g., proof-reading or non-proofreading), and the library pretreatment method (e.g., non-Uracil-DNA Glycosylase (UDG), full-UDG, or half-UDG treatments). The latter three fields represent information about the sequencing library construction that influence the presence of aDNA damage, a factor that is critical for the processing of aDNA NGS data.8,18 Sequencing metadata columns include instrument model, library layout (single- or paired-end), library strategy (whole genome sequencing, targeted capture, etc.), and read count. “ I could not work out how to search these fields through the viewer. These are accessible as downloads post validation but it seems that users would want to search through samples based on these fields?\nFurther questions\nFinally, I have some three questions about the project that it would be great to get comments on.\nHow sustainable is the community effort to maintain these databases moving forward into the future with the probability of the number of samples increasing each year?\n\nHave you tried sending the improved metadata back to SRA/ENA?\n\nHow difficult would it be to adapt the software for a different community of researchers that wanted to improve annotation but use fields that would be different from the ancient metagenomes community?\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "11512",
"date": "20 Jun 2024",
"name": "James Fellows Yates",
"role": "Author Response",
"response": "Thank you for your positive review. We apologies for the long time between your review and our revision, this was due to parental leave and extensive traveling of the corresponding authors. Our responses to your specific points and further questions are as follows. Line numbers should correspond to the submitted revised word document (required by F1000), once track changes are accepted. Please note depending on which software we opened it, the line numbers were not indicating the same content. The line numbers should correspond to what is opened in Microsoft Office for Mac Word v16.78.3. Specific Points The streamlit-based viewer is pretty slick but I feel the importance of command line interface (CLI) is a little underplayed here. The viewer can be used by people without CLI proficiency but to actually take actions like making new sample tables, or download and process data, CLI is essential. Response: We have made more prominent references to the command line interface functionalities in the manuscript by further specifying in the introduction on lines 75-88, 101-140, and 151-155. We also extended the ‘Use case’ section of the manuscript to further guide readers on how they could use AMDirT command line tools to perform the same workflow in the GUI as shown in Figure 3. Note that during the improvement of this use case, we also added an additional command called ‘download’ to further make it easier for CLI power-users to retrieve the tables for a more complete CLI based workflow. The instructions in the text and on github for conda install should guide users to install into a fresh conda environment rather than into the base. Response: We have updated the documentation to reflect the new instructions in the code repository README, documentation pages (both can be seen in https://amdirt.readthedocs.io/en/master/README.html), and the manuscript line 263 There should be a list of computational environments that the software has been tested on (e.g do M1-3 macs work?) Response: We have added a brief section about hardware and OSs that have been tested in the github repository README installation page of the documentation (https://amdirt.readthedocs.io/en/master/README.html). I did not see a mention in the text that there is actually a public facing server https://www.spaam-community.org/AMDirT/ Response: There was already a mention of the viewer interface at the line 369, but we have added more details lines 76, and 759 “Newly added library information columns include the library name (how data are typically reported in original publications), the aDNA library generation method (e.g., double-stranded or single-stranded libraries), the library indexing polymerase (e.g., proof-reading or non-proofreading), and the library pretreatment method (e.g., non-Uracil-DNA Glycosylase (UDG), full-UDG, or half-UDG treatments). The latter three fields represent information about the sequencing library construction that influence the presence of aDNA damage, a factor that is critical for the processing of aDNA NGS data.8,18 Sequencing metadata columns include instrument model, library layout (single- or paired-end), library strategy (whole genome sequencing, targeted capture, etc.), and read count. “ I could not work out how to search these fields through the viewer. These are accessible as downloads post validation but it seems that users would want to search through samples based on these fields? Response: We have now extended the AMDirT viewer and convert commands to support library level filtering. In the AMDirT viewer this is supported via a secondary table that is loaded after the sample selection has been made by the user. We’ve updated the use case example and Figure 2 to represent these changes. Further questions Finally, I have some three questions about the project that it would be great to get comments on. How sustainable is the community effort to maintain these databases moving forward into the future with the probability of the number of samples increasing each year? Response: Ancient metagenomics as a field is still very young and therefore has indeed been very manageable in terms of numbers. But of course as it grows it could become more difficult. In passive terms - our feeling so far is as we have started as the field is ‘young’ has benefited from the fact we will have good visibility and awareness of the resource within the community, something that would continue to spread as the research area expands through knowledge transfer. With this, we believe that we will have both a) more potential and willing contributors to cope with the increased number of samples and b) as they are already aware, will maybe already format and prepare their own sample and library metadata in a form easy to add to AncientMetagenomeDir. More proactively, we will continue to survey the community to find out what are good motivating factors to continue contributing. We further plan to continue to refine the tooling and automation to make it as easy as possible for contributors to add and review new contributors. The SPAAM community has also recently become affiliated with the ISBA society (https://isbarch.org), which can provide financial support for the previously ‘volunteer’ held hackathons. We also have various ideas for new publications that are typically the biggest motivating factor for researchers (e.g. extending the database to include more precise radiocarbon dates which are critical e.g. for phylogenetic dating analyses). Finally we have also expanded our aim of better metadata reporting of ancient DNA samples and sequencing data to a larger project covering the whole of palaeogenomics (https://www.mixs-minas.org/) that will also help further formalise such thinking in the community, and feed-back into the way AncientMetagenomeDir functions, as well as push such standardisation into the INDSC consortium databases (who use MIxS checklists themselves). Have you tried sending the improved metadata back to SRA/ENA? Response: We have not (yet) attempted this. We have not actively recorded all the corrections between the reported information in the publications and as changed for the AncientMetagenomeDir repository. These corrections have been also derived from a mixture of ‘obvious’ mistakes in the publication (e.g. single-end sequencing reported, but paired FASTQ files uploaded to the ENA or SRA), to personal communications with the authors of the publication. In some cases the original authors have themselves made the corrections on ENA/SRA themselves. In any case, requesting changes on SRA/ENA would require permission from the original authors of the publications, which would require a large and extensive effort from the volunteers of SPAAM, with likely highly mixed chances of success (students move on, labs have changed/retired etc). In this vein we feel it would be more beneficial to invest time and effort in the MInAS project to correct future submissions at the source rather than historical data. How difficult would it be to adapt the software for a different community of researchers that wanted to improve annotation but use fields that would be different from the ancient metagenomes community? Response: AMDirT is mostly based around the JSON schemas that define and enforce the structure of the underlying data. Furthermore, because the validate subpackage is designed using a domain-driven design software architecture, the base class holding the different methods responsible for testing the data are generic and can be applied to any dataframe object, as long as they come with their associated JSON schema. In summary, adapting it to a different community would require some modifications (as some part of the code is specific to ancient metagenomics data), but most of AMDirT core functionalities could be adapted without too much effort."
}
]
},
{
"id": "210768",
"date": "18 Oct 2023",
"name": "Jonas Coelho Kasmanas",
"expertise": [
"Reviewer Expertise Bioinformatics",
"metagenome",
"metadata standardization",
"machine learning"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe submitted manuscript sheds light on an imperative yet often overlooked aspect of current research, specifically metagenomic research: the accessibility and standardization of sample-level metadata, particularly concerning ancient samples. The topic is relevant to the current scientific landscape, especially as the volume of metagenomic sequencing datasets continues to burgeon. With the surge in data, the need for standardized, accessible, and reusable metadata becomes paramount. This manuscript aptly addresses this gap, making it an essential read for researchers in metagenomics, palaeogenomics, and related fields.\nThe authors have channeled the collective effort of the research community through hackathon events to update and enhance the 'AncientMetagenomeDir.' Even contacting researchers and actively encouraging them to correct their metadata annotation. Therefore, I understand that this manuscript evolves the AncientMetagenomeDir and provides an additional resource to further increase its accessibility and usability: the AMDirT.\nThe introduction of 'AMDirT' as the companion tool to 'AncientMetagenomeDir' is a significant stride forward. By offering functionalities ranging from metadata template generation, and guidance to data validation, the tool exhibits promise in addressing the prevalent challenges in metadata management. Additionally, it helps researchers with less computational background to download samples systematically and gives them access to a GUI. My review goes toward the message delivery, especially during the initial sections of the manuscript.\nDuring the introduction section, I missed a clear definition of ancient metagenome. This should include a description of what requires the ancient samples to receive special treatment regarding metadata annotation. Naturally, this leads to comparing your effort to past works like the GOLD (https://doi.org/10.1093/nar/gky977), the MetaSRA (https://doi.org/10.1093/bioinformatics/btx334), the gcMeta (https://doi.org/10.1093/nar/gky1008), or the HumanMetagenomeDB (https://doi.org/10.1093/nar/gkaa1031).\nI appreciate the extensive AMDirT documentation, including tutorials and videos. However, the manuscript lacks in the description of the tool's workflow and usability. The \"Use cases\" section of the manuscript makes the tool much clearer. At the same time, it gives the impression that AMDirT is limited to the GUI exploration and template generation guidance. Specifically, in my opinion, the manuscript poorly describes and explores the \"Validate\" and \"Autofill\" commands.\nFor example, the Validate command does \"a variety of checks.\" It would help if you made it more transparent. Do you have a document detailing the checks and standards? If so, it should be placed here; if not, I would like to see it in the manual. For the Autofill command, I missed a more detailed description of the \"improvements\" done using R scripts after pulling the metadata from ENA. Specifically, since those commands could be used outside the realm of ancient metagenomic samples. I believe a figure containing the complete schematic workflow from AMDirT would help.\nRegarding the software operation, I missed a storage requirement specification. The paper mentions that the installation requires Python 3.9, but nothing is specified in the GitHub. The installation via pip and conda should include guidance on accessing those tools and creating a specific environment for the AMDirT. Finally, as a minor opinion, have you considered using specialized sample accessing software? For instance, the SRAtoolkit can download samples from the SRA more efficiently than curl. If possible, I would like to see a slight reformat in the discussion \"Problem/Solutions\" section to make it more visible. A simple extra paragraph or bullet points that clearly separate problems and solutions should solve the problem.\nRunning and installing the pipeline.\nI had a relatively smooth experience. However, I kept receiving the following warning upon any usage: \"WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager\" Additionally, the convert command did not work. After successfully installing the tool and downloading the AncientMetagenomeDir. I received the following: $ AMDirT convert --curl SPAAM-community-AncientMetagenomeDir-60f8a00/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv ancientmetagenome-hostassociated -o ./\n2023-10-17 19:50:32.289 No runtime found, using MemoryCacheStorageManager Traceback (most recent call last):\n\nFile \"/mnt/tools/miniconda3/envs/amdirt/lib/python3.9/site-packages/streamlit/runtime/caching/storage/in_memory_cache_storage_wrapper.py\", line 87, in get\n\nentry_bytes = self._read_from_mem_cache(key)\n\nFile \"/mnt/tools/miniconda3/envs/amdirt/lib/python3.9/site-packages/streamlit/runtime/caching/storage/in_memory_cache_storage_wrapper.py\", line 137, in _read_from_mem_cache\n\nraise CacheStorageKeyNotFoundError(\"Key not found in mem cache\") streamlit.runtime.caching.storage.cache_storage_protocol.CacheStorageKeyNotFoundError: Key not found in mem cache\nTraceback (most recent call last):\n\nFile \"/mnt/tools/miniconda3/envs/amdirt/lib/python3.9/site-packages/pandas/core/indexes/base.py\", line 3790, in get_loc\n\nreturn self._engine.get_loc(casted_key)\n\nFile \"index.pyx\", line 152, in pandas._libs.index.IndexEngine.get_loc\n\nFile \"index.pyx\", line 181, in pandas._libs.index.IndexEngine.get_loc\n\nFile \"pandas/_libs/hashtable_class_helper.pxi\", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item\n\nFile \"pandas/_libs/hashtable_class_helper.pxi\", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'archive_accession'\n\nFile \"/mnt/tools/miniconda3/envs/amdirt/lib/python3.9/site-packages/streamlit/runtime/caching/storage/in_memory_cache_storage_wrapper.py\", line 137, in _read_from_mem_cache\n\nraise CacheStorageKeyNotFoundError(\"Key not found in mem cache\") streamlit.runtime.caching.storage.cache_storage_protocol.CacheStorageKeyNotFoundError: Key not found in mem cache\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "11513",
"date": "20 Jun 2024",
"name": "James Fellows Yates",
"role": "Author Response",
"response": "Thank you for your generally positive review. We apologise for the long time between your review and our revision, this was due to parental leave and extensive travelling of the corresponding authors. Our responses to your specific comments are below. Line numbers in our revised manuscript should correspond to the submitted revised word document (required by F1000), once track changes are accepted. Please note depending on which software we opened it, the line numbers were not indicating the same content. The line numbers should correspond to what is opened in Microsoft Office for Mac Word v16.78.3. Manuscript Comments During the introduction section, I missed a clear definition of ancient metagenome. This should include a description of what requires the ancient samples to receive special treatment regarding metadata annotation. Naturally, this leads to comparing your effort to past works like the GOLD (https://doi.org/10.1093/nar/gky977), the MetaSRA (https://doi.org/10.1093/bioinformatics/btx334), the gcMeta (https://doi.org/10.1093/nar/gky1008), or the HumanMetagenomeDB (https://doi.org/10.1093/nar/gkaa1031). I appreciate the extensive AMDirT documentation, including tutorials and videos. However, the manuscript lacks in the description of the tool's workflow and usability. The \"Use cases\" section of the manuscript makes the tool much clearer. At the same time, it gives the impression that AMDirT is limited to the GUI exploration and template generation guidance. Specifically, in my opinion, the manuscript poorly describes and explores the \"Validate\" and \"Autofill\" commands. For example, the Validate command does \"a variety of checks.\" It would help if you made it more transparent. Do you have a document detailing the checks and standards? If so, it should be placed here; if not, I would like to see it in the manual. Response: For the ancient metagenome definition: this was originally defined in the AncientMetagenomeDir publication but we’ve added a short sentence rephrasing and citing that definition on line 36-37. For validate: we do not go into much detail on this, as it again was originally described in the first AncientMetagenomeDir paper (as cited in the main text) and as such does not necessarily represent ‘new’ functionality other than a renaming. Furthermore, as it is not a user facing component of the tool kit, we feel it is less relevant for readers (who we presume many more will be potential users rather than developers wishing to adopt a similar scheme). However we have rephrased the text slightly to indicate which person each command is most relevant to (e.g. contributor vs maintainer vs user etc.). The same goes for autofill, in that it is not a user facing tool - as it typically will be just within GitHub actions. We have however updated the manuscript to provide a little more detail on the validate command (line 105-140) and for autofill (which calls the ENA API for information) in lines 100-103. We have otherwise also expanded the use case to also describe in more detail the ‘convert’ CLI command, which is also a primarily user-facing subcommand. For the Autofill command, I missed a more detailed description of the \"improvements\" done using R scripts after pulling the metadata from ENA. Specifically, since those commands could be used outside the realm of ancient metagenomic samples. I believe a figure containing the complete schematic workflow from AMDirT would help. Response: We have removed references to the R scripts used in the very initial pulling of data in preparation for the first library-level hackathon. On reflection, indeed this could be confusing to the reader, particularly as these are no longer used - and were only used for a one off event. The same concepts have been added to autofill (which came later). In autofill, the ENA portal API is directly queried using Python. We have added more details on the retrieved metadata fields (line 100-103). We have further now reduced the necessity of a user to run this command at all (see above about not being a user-facing tool), instead having a GitHub actions bot to run this command for a user on the AncientMetagenomeDir repository, during a pull request. We have included a new figure (Figure 2) that shows the updated AncientMetagenomeDir workflow modified after the original AncientMetagenomeDir publication workflow diagram. Regarding the software operation, I missed a storage requirement specification. The paper mentions that the installation requires Python 3.9, but nothing is specified in the GitHub. The installation via pip and conda should include guidance on accessing those tools and creating a specific environment for the AMDirT. Response: We unfortunately don’t fully understand what the reviewer means exactly by ‘storage requirement specification’ here. However, based on our interpretation: all downloadable AMDirT files are small bash scripts, TSV, or bibtext files, all of which take up (bioinformatically) negligible amounts of space - single digit megabytes or less. Thus we do not feel it is necessary to mention this. However if the storage requirements refers to FASTQ files etc, as a convenience, AMDirT offers an estimate of the potential total size of the files if you were to run the download script. This is displayed by hovering over the download script download button - however AMDirT does not download FASTQ files itself. This functionality was already described on lines 452. The AMDirT package zip archive itself is also less than a megabyte so we feel is not relevant here as it will not make an impact on storage requirements in the vast majority of cases. For installation requirements: we are not entirely sure what the reviewer means by ‘accessing these tools’ - whether this is the downstream dependencies, or the package managers pip/conda themselves. If the former, the version of dependencies management is automatically handled by pip/conda, and is completely transparent for the user as this is reported by each package manager when installing AMDirT. For advanced bioinformaticians, they are likely familiar with python packages setup.py and conda environment files, so should be able to find these themselves (as an everyday user does not need this). If the reviewer is referring to installation instructions of pip and conda, this is a fair point and we have added in the installation instructions URLs to the installation documentation pages of the respective package managers, and we have updated the README to provide updated guidelines to install AMDirT in a dedicated conda environment. Finally, as a minor opinion, have you considered using specialized sample accessing software? For instance, the SRAtoolkit can download samples from the SRA more efficiently than curl. Response: As an alternative to curl, AMDirT already provides download scripts using other tools such as aspera and nf-core/fetchngs, which itself, already, provides the option to download with SRA-tools. We picked these tools based on the interest of AncientMetagenomeDir contributors - of which SRAToolkit was not one at the time, however we have added this option in AMDirT v1.6 at the reviewers request. If possible, I would like to see a slight reformat in the discussion \"Problem/Solutions\" section to make it more visible. A simple extra paragraph or bullet points that clearly separate problems and solutions should solve the problem. Response: We are unfortunately somewhat beholden to the formatting of the publisher during typesetting, but we have attempted to reformat the paragraph according to the reviewer’s wish with paragraphs (as each text is too long for a bullet point) Running and installing the pipeline. I had a relatively smooth experience. However, I kept receiving the following warning upon any usage: \"WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager\" This is unfortunately a known issue resulting from a design decision of one of AMDirT dependencies: the streamlit library and its caching system. As a stop gap solution, we now have ‘monkeypatched’ the streamlit function triggering this warning to silence it (https://github.com/SPAAM-community/AMDirT/pull/132). Additionally, the convert command did not work. After successfully installing the tool and downloading the AncientMetagenomeDir. I received the following: $ AMDirT convert --curl SPAAM-community-AncientMetagenomeDir-60f8a00/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv ancientmetagenome-hostassociated -o ./2023-10-17 19:50:32.289 No runtime found, using MemoryCacheStorageManager Response: The convert command by default takes as input a sample table, not a library table, which is already reflected in the documentation of the convert command (amdirt.readthedocs.io/en/latest/how_to/convert) and the convert command CLI help. ``` $ AMDirT convert --help Usage: AMDirT convert [OPTIONS] SAMPLES TABLE_NAME Converts filtered samples and libraries tables to eager, ameta, taxprofiler, and fetchNGS input tables Note: When supplying a pre-filtered libraries table with `--libraries`, the corresponding sample table is still required! SAMPLES: path to filtered AncientMetagenomeDir samples tsv file TABLE_NAME: name of table to convert Options: -t, --tables PATH (Optional) JSON file listing AncientMetagenomeDir tables --libraries FILE (Optional) Path to a pre-filtered libraries table NOTE: This argument is mutually exclusive with arguments: [librarymetadata]. --librarymetadata Generate AncientMetagenomeDir libraries table of all samples in input table NOTE: This argument is mutually exclusive with arguments: [libraries]. -o, --output DIRECTORY conversion output directory [default: .] --bibliography Generate BibTeX file of all publications in input table --curl Generate bash script with curl-based download commands for all libraries of samples in input table --aspera Generate bash script with Aspera-based download commands for all libraries of samples in input table --fetchngs Convert filtered samples and libraries tables to nf- core/fetchngs input tables --sratoolkit Generate bash script with SRA Toolkit fasterq-dump based download commands for all libraries of samples in input table --eager Convert filtered samples and libraries tables to eager input tables --ameta Convert filtered samples and libraries tables to aMeta input tables --mag Convert filtered samples and libraries tables to nf- core/mag input tables --taxprofiler Convert filtered samples and libraries tables to nf- core/taxprofiler input tables --help Show this message and exit. ``` Thus, for example, running the convert command with a sample table will generate this output: ``` $ AMDirT download -t ancientmetagenome-hostassociated -y samples -r v23.12.0 $ head -n 10 ancientmetagenome-hostassociated_samples_v23.12.0.tsv > test.tsv $ AMDirT convert --curl test.tsv ancientmetagenome-hostassociated AMDirT [WARNING]: We provide no warranty to the accuracy of the generated input sheets. AMDirT [INFO]: Writing curl download script $ head AncientMetagenomeDir_curl_download_script.sh #!/usr/bin/env bash curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR132/022/SRR13263122/SRR13263122_2.fastq.gz -o SRR13263122_2.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR132/024/SRR13263124/SRR13263124_2.fastq.gz -o SRR13263124_2.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR132/031/SRR13263131/SRR13263131_2.fastq.gz -o SRR13263131_2.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR132/030/SRR13263130/SRR13263130_2.fastq.gz -o SRR13263130_2.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR957/SRR957740/SRR957740.fastq.gz -o SRR957740.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR957/SRR957744/SRR957744.fastq.gz -o SRR957744.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR957/SRR957741/SRR957741.fastq.gz -o SRR957741.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR957/SRR957738/SRR957738.fastq.gz -o SRR957738.fastq.gz curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR132/028/SRR13263128/SRR13263128_2.fastq.gz -o SRR13263128_2.fastq.gz ``` However we’ve added an additional validation check to ensure that the input SAMPLE object is in the valid format expected by the tool, and if not asks the user to check if it is a sample table (https://github.com/SPAAM-community/AMDirT/pull/140, commit 7bb6b55) We have also added support for supplying library level metadata tables (supplied alongside a corresponding samples table) to the convert command with the --libraries parameter. This, alongside the new command download (added since the submission of the original manuscript), allows for an almost end to end command line based interaction with AMDirT: download → (filtering with bash tools) → convert, as reflected in the updated use case section of the manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/12-926
|
https://f1000research.com/articles/13-542/v1
|
28 May 24
|
{
"type": "Study Protocol",
"title": "Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India",
"authors": [
"Dr.Khadija Hamdulay",
"Rajendra Ravekar",
"Ashwini Tayade",
"Rajendra Ravekar",
"Ashwini Tayade"
],
"abstract": "Background Enteric fever, predominantly caused by Salmonella enterica serotype Typhi, remains a significant global health concern, particularly in resource-limited settings. The diagnostic landscape for enteric fever relies on traditional methods such as the Widal test and blood culture, each with inherent limitations regarding sensitivity and turnaround time.\n\nMethods The study will employ an Analytical Observational Study design conducted at Acharya Vinoba Bhave Rural Hospital in central India over a two-year period. Participants will include adults above 18 years admitted to the ward or Intensive Care Unit (ICU) with acute febrile illnesses. Inclusion criteria encompass a wide age range, ensuring a diverse study population. Peripheral blood samples will be collected for Salmonella PCR, Widal testing, and blood culture. Dot-PCR for Typhi will be employed, and DNA extraction will follow strict protocols. Data will be systematically recorded, and statistical analyses, including sensitivity, specificity, and comparative assessments, will be conducted to evaluate diagnostic performance.\n\nExpected Outcome It is anticipated that Salmonella PCR will exhibit superior sensitivity and specificity compared to traditional diagnostic methods, offering a more rapid and accurate identification of enteric fever cases. The study aims to contribute valuable evidence supporting the incorporation of Salmonella PCR into routine diagnostic algorithms, potentially revolutionizing the approach to enteric fever diagnosis. Moreover, insights gained from the study are expected to inform clinical practices, enhance patient management, and potentially reduce the economic burden associated with misdiagnosis or delayed diagnosis of enteric fever. The outcomes of this research are poised to impact public health strategies, providing a foundation for more effective and efficient diagnostic protocols in the context of enteric fever.",
"keywords": [
"Enteric Fever",
"Salmonella PCR",
"Diagnostic Accuracy",
"Widal Test",
"Analytical Observational Study",
"Central India"
],
"content": "Introduction\n\nEnteric fever, predominantly caused by Salmonella enterica serotype Typhi, continues to pose a significant public health challenge, particularly in resource-limited settings.1 Current diagnostic methods, such as the Widal test and blood culture, have sensitivity, specificity, and turnaround time limitations, necessitating a search for more accurate and efficient diagnostic modalities.2 Polymerase Chain Reaction (PCR) technology has emerged as a promising tool for detecting bacterial pathogens, offering potential advantages in terms of sensitivity and rapidity.3\n\nPrevious studies have highlighted the diagnostic potential of Salmonella PCR in various clinical settings, demonstrating its ability to complement traditional methods.4 However, limited research has been conducted in the context of enteric fever, particularly in the central Indian region. This study protocol aims to address this gap by conducting an Analytical Observational Study to systematically evaluate the diagnostic efficacy of Salmonella PCR and compare it with routine laboratory parameters, including Widal test and blood culture.\n\nThe study will be conducted at Acharya Vinoba Bhave Rural Hospital (AVBRH), a tertiary care teaching hospital in central India. The research design, encompassing two years, adheres to ethical guidelines and seeks to enroll a diverse cohort of adult patients admitted with acute febrile illnesses.\n\nSalmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever.\n\n\n\n1. To diagnose enteric fever in patients with acute febrile Illness by Widal and blood culture test.\n\n2. To perform Salmonella PCR in diagnosed cases of enteric fever.\n\n3. To compare Salmonella PCR with typhi dot, Widal and blood culture.\n\n\nMethods\n\nThis study will employ an Analytical Observational Study design to assess the diagnostic efficacy of Salmonella Polymerase Chain Reaction (PCR) and its comparison with routine laboratory parameters in cases of enteric fever.\n\nThe study will include individuals above the age of 18 years who are admitted to the ward or Intensive Care Unit (ICU) with acute febrile illnesses. The participants will be selected based on predefined inclusion and exclusion criteria.\n\nInclusion criteria:\n\n• Individuals aged 18 years and above.\n\n• Patients admitted to the ward or ICU with acute febrile illnesses.\n\nExclusion criteria:\n\n• Individuals below the age of 18 years.\n\n• Patients admitted with a confirmed diagnosis other than enteric fever (e.g., malaria, dengue).\n\n• Those who refuse to participate in the study.\n\nThe study will be conducted at Acharya Vinoba Bhave Rural Hospital (AVBRH), a tertiary care teaching hospital located in Sawangi, Meghe, in the rural sector of Wardha district, Central India. The outpatient medicine department at AVBRH will be the primary site for participant enrollment and data collection.\n\nThis setting has been chosen due to its accessibility, relevance to the study population, and the availability of necessary facilities for conducting the required diagnostic tests. Ethical approval will be obtained from the Institute’s review board before the initiation of the study, ensuring adherence to ethical guidelines and standards. The study will span two years, from March 2023 to March 2025, during which data will be systematically collected and analyzed to fulfill the study objectives.\n\nThe research protocol got approval from the Datta Meghe Institute of Higher Education and Research (Deemed to be university) Institutional ethical committee in the meeting held on 11-07-2022 with DMIMS (DU)/IEC/2022/28. All the participants will be educated about the research, and written and verbal informed consent will be obtained from all the participants before the intervention.\n\nIn an Analytical Observational Study context, the sample size is calculated using a specific formula. The formula, represented as Z21-a/2 Sens(1-Sens) > 2d X Prev, considers various parameters for precise determination. Alpha (a) is set at 0.05, representing the significance level. The estimated sensitivity (Sens) is designated as 0.99, indicating the test’s ability to identify true positive cases correctly. The prevalence of the disease (Prev) is defined as 0.5, reflecting the anticipated frequency of the condition within the population. Additionally, an estimation error (d) of 0.03 is considered. By applying this formula, the minimum number of diseases required for the study is calculated to be 43, and correspondingly, the minimum total sample size needed is 86. These calculations are pivotal for ensuring the statistical robustness of the analytical observational study, facilitating reliable and meaningful conclusions.\n\nThe data collection process for this study involves a systematic series of steps designed to gather relevant information and conduct diagnostic tests among eligible participants. To begin, potential participants meeting the study’s inclusion criteria are identified, and informed consent is obtained from those willing to contribute to the research. A thorough clinical assessment is conducted, encompassing detailed medical history, symptom evaluation, and physical examinations.\n\nBlood sample collection is a critical step with strict adherence to aseptic techniques. Two milliliters of blood are drawn into an EDTA vial for Salmonella PCR, while an additional 3 milliliters are collected in plain tubes for the Widal test. Proper labeling and documentation ensure the integrity of the collected samples.\n\nSubsequently, the Widal agglutination test is performed on the blood samples, utilizing commercially manufactured colored antigens for Salmonella Typhi O and H antigens. Results are interpreted based on observed agglutination reactions and titers. Simultaneously, blood culture procedures are initiated by drawing 5 milliliters of blood and placing it into Brain Heart Infusion (BHI) broth under strict sterile conditions. With all aseptic precautions nearly 30-40 ml of blood was sent for culture and automated mics. Daily monitoring for bacterial growth is undertaken, and blind subculture is implemented without observable progress. Verification of bacterial identity is accomplished through biochemical testing and specialized antisera.\n\nSpecifically, for Typhi, a dot-PCR is conducted using the appropriate primers, following standard PCR procedures, including DNA extraction, amplification, and gel electrophoresis. Additionally, polymerase chain reaction (PCR) for Salmonella is executed by extracting total DNA from blood samples using SDS and proteinase K. Real-time PCR techniques are employed for accurate and efficient detection, incorporating positive controls (Salmonella typhi DNA) and negative controls (DNA from E. coli, A. baumannii, and S. pneumoniae) to ensure the reliability of results.\n\nStrict ethical considerations are maintained throughout the data collection process, including participant confidentiality, privacy protection, and compliance with institutional ethical review board approvals. All pertinent data, including clinical information, test results, and participant demographics, are meticulously recorded in a structured database. The study spans from March 2023 to March 2025, during which these procedures will be carried out to fulfill the research objectives.\n\nPrimary outcome\n\nThe primary outcome measure of this study is the diagnostic accuracy of Salmonella Polymerase Chain Reaction (PCR) in identifying enteric fever among patients with acute febrile illnesses. The primary focus is assessing the sensitivity, specificity, positive predictive value, and negative predictive value of Salmonella PCR compared to the reference standards of Widal testing and blood culture.\n\nSecondary outcomes:\n\n1. Comparative diagnostic performance:\n\n• Evaluate and compare the diagnostic performance of Salmonella PCR with routine laboratory parameters, including Widal test and blood culture.\n\n• Assess the concordance and discrepancies between the results of Salmonella PCR, Widal test, and blood culture.\n\n2. Clinical utility and practicality:\n\n• Explore the practicality and feasibility of implementing Salmonella PCR in routine clinical settings.\n\n• Examine the turnaround time for Salmonella PCR compared to traditional diagnostic methods.\n\n3. Impact on patient management:\n\n• Investigate the impact of Salmonella PCR results on patient management and clinical decision-making.\n\n• Assess whether using Salmonella PCR leads to more timely and accurate interventions.\n\n4. Cost-effectiveness analysis:\n\n• Conduct a preliminary cost-effectiveness analysis comparing the expenses associated with Salmonella PCR and routine laboratory parameters.\n\n• Evaluate the economic implications of incorporating Salmonella PCR into the diagnostic algorithm for enteric fever.\n\n5. Subgroup analysis:\n\n• Explore the diagnostic performance of Salmonella PCR in specific subgroups, such as age categories or severity of illness.\n\n• Identify potential variations in sensitivity and specificity across different patient characteristics.\n\nEfficient data management is integral to the study’s success, ensuring the collected information’s accuracy, security, and confidentiality. Standardized data collection forms and electronic databases will be employed, accompanied by unique identifiers to protect participant confidentiality. Trained personnel will ensure timely and precise data entry, incorporating validation checks and double-entry verification processes to minimize errors. Electronic data will be securely stored on restricted-access servers, with regular backup procedures to prevent data loss. Physical copies of data, if any, will be stored in locked and secure locations. Adherence to institutional and ethical guidelines for data security will be paramount, including encryption and password protection for electronic databases. Periodic data quality checks, audit trails, and the establishing of a Data Monitoring Committee will contribute to ongoing quality control. The study will use statistical software R Studio 4.3.1 to analyze exploratory data and identify patterns and trends. Reports will be generated for internal use and dissemination, with considerations for anonymized data-sharing aligned with ethical guidelines. A robust data archiving plan will be implemented for long-term storage, ensuring accessibility and compliance with data retention policies. Through these measures, the study aims to uphold the integrity and reliability of the collected data, facilitating accurate analysis and contributing to the overall success of the research.\n\nThe statistical analysis for this study will encompass a multifaceted approach to assess the diagnostic accuracy of Salmonella Polymerase Chain Reaction (PCR) and compare its outcomes with routine laboratory parameters in cases of enteric fever. The initial steps involve descriptive statistics to summarize participant demographics and baseline characteristics. Diagnostic accuracy measures will be calculated for Salmonella PCR, Widal test, and blood culture, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Receiver operating characteristic (ROC) curves and the area under the curve (AUC) will be utilized to gauge overall diagnostic performance. Comparative analyses will be conducted using statistical tests like McNemar’s test to discern differences between Salmonella PCR and routine laboratory parameters. Subgroup analyses based on factors such as age, gender, and illness severity will be performed to explore potential variations in diagnostic accuracy. The study will also evaluate the practicality and feasibility of implementing Salmonella PCR in routine clinical settings and assess its impact on patient management. Cost-effectiveness analysis will compare the economic implications of Salmonella PCR with routine parameters. Regression analysis, if applicable, will identify factors influencing diagnostic outcomes. The statistical analyses will be executed using R studio Version 4.3.1, and results will be presented transparently, adhering to predetermined significance levels. Visual representations will be created to illustrate key findings. The study aims to derive comprehensive insights into the diagnostic utility of Salmonella PCR, contributing to evidence-based advancements in clinical practice and diagnostic protocols.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has not yet started after the publication of the protocol; we will start recruitment in the study.\n\n\nDiscussion\n\nThe emergence of enteric fever, driven primarily by Salmonella enterica serotype Typhi, presents a persistent public health challenge globally.1 Diagnostic accuracy is paramount for effective clinical management and preventing complications associated with this infectious disease.5 The proposed study protocol seeks to address existing limitations in diagnostic methodologies by evaluating the diagnostic efficacy of Salmonella Polymerase Chain Reaction (PCR) and comparing it with routine laboratory parameters such as the Widal test and blood culture.\n\nThe choice of Salmonella PCR as a diagnostic tool is grounded in its potential to overcome some of the limitations associated with traditional methods. Previous research has indicated that PCR-based assays can provide enhanced sensitivity and specificity, facilitating early and accurate detection of bacterial pathogens.6 This aligns with the study’s primary aim of determining the diagnostic accuracy of Salmonella PCR in identifying cases of enteric fever.\n\nIncluding routine laboratory parameters, specifically the Widal test and blood culture, allows for a comprehensive comparison, considering established diagnostic practices. Despite being widely used, Widal testing has faced criticism for its variable sensitivity and specificity.2 While considered a gold standard, blood culture is constrained by longer turnaround times and potential false negatives, especially in patients receiving prior antibiotic treatment.7\n\nThe study’s analytical observational design aims to provide robust evidence regarding the diagnostic performance of Salmonella PCR in a real-world clinical setting. This research will contribute valuable insights into the potential utility of PCR as a complementary or alternative diagnostic tool for enteric fever. The comprehensive data collection approach, including dot-PCR for Typhi, will further enhance our understanding of the molecular characteristics of Salmonella strains prevalent in the study population. The findings from this study may have implications for clinical practice, guiding healthcare professionals in selecting appropriate diagnostic methods for enteric fever. The potential inclusion of cost-effectiveness analysis will add a practical dimension to the discussion, addressing the economic feasibility of incorporating Salmonella PCR into routine diagnostic algorithms.\n\nWhile the study’s proposed setting, Acharya Vinoba Bhave Rural Hospital, offers a unique perspective from central India, it is essential to acknowledge potential limitations such as regional variations in bacterial strains and healthcare infrastructure. Additionally, the study duration of two years may not capture long-term trends, necessitating ongoing surveillance.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nCrump JA, Mintz ED: Global trends in typhoid and paratyphoid fever. Clin. Infect. Dis. 2010; 50: 241–246. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHouse D, Wain J, Ho VA, et al.: Serology of Typhoid Fever in an Area of Endemicity and Its Relevance to Diagnosis. J. Clin. Microbiol. 2001; 39: 1002–1007. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchluger NW, Kinney D, Harkin TJ, et al.: Clinical utility of the polymerase chain reaction in diagnosing infections due to Mycobacterium tuberculosis. Chest. 1994; 105: 1116–1121. Publisher Full Text\n\nKumar R, Gupta N: Shalini: Multidrug-resistant typhoid fever. Indian J. Pediatr. 2007; 74: 39–42. Publisher Full Text\n\nParry CM, Hien TT, Dougan G, et al.: Typhoid fever. N. Engl. J. Med. 2002; 347: 1770–1782. Publisher Full Text\n\nKariuki S, Revathi G, Muyodi J, et al.: Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya. J. Clin. Microbiol. 2004; 42: 1477–1482. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParry CM, Threlfall EJ: Antimicrobial resistance in typhoidal and nontyphoidal salmonellae. Curr. Opin. Infect. Dis. 2008; 21: 531–538. Publisher Full Text"
}
|
[
{
"id": "288462",
"date": "14 Jun 2024",
"name": "Swathi Krishna Njarekkattuvalappil",
"expertise": [
"Reviewer Expertise Infectious disease epidemiology",
"operational research"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a protocol paper which details a study about to take place. The objectives 1 & 2 of the study seem to be inappropriate. From the text, what we understand is that the primary objective of the study is to estimate the diagnostic accuracy of Salmonella PCR as compared to a composite score of Widal + blood culture. Hence the objectives need to be re-framed.\nThe study design is mentioned as 'analytical observational' study. But it is not clear as to what type of analytical observational study is planned. In analytical observational studies, researchers try to establish an association between exposure(s) and outcome(s). Depending on the direction of enquiry, these studies can be directed forwards (cohort studies) or backwards (case–control studies). (1)\nIf it is a diagnostic accuracy (DA) study, it should be explicitly mentioned what type it is- DA case-control, DA cross sectional or DA comparative studies. (2)\nInclusion criteria needs to be more specific. Are you going to do a blood culture, Widal and PCR on all febrile illness cases? Is there any duration of fever cut off? And are these tests going to be done in series or in parallel?\nIn calculating the sample size, why was a prevalence of 0.5 used? There is already indexed literature on prevalence of laboratory confirmed typhoid in India. (3)\nOne of the secondary outcomes expected is mentioned as a cost-effectiveness analysis of Salmonella PCR for typhoid diagnosis. How is this analysis planned? With current methodology in the manuscript, it seems to lack those details.\nEnteric fever involves both typhoid and paratyphoid. Are you considering paratyphi also here or are you excluding those?\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
},
{
"id": "322560",
"date": "12 Sep 2024",
"name": "Dilip Abraham",
"expertise": [
"Reviewer Expertise Clinical microbiology",
"wastewater surveillance",
"gut microbiome"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a protocol document for a study that aims to compare PCR for Salmonella Typhi against other methods like blood culture, Widal and Typhidot.\nThe rationale for the study is well described in the abstract and the introduction. However, the authors have not described the rationale for using other diagnostic modalities like Widal and Typhidot when it is well documented that this is inferior in sensitivity and specificity to blood culture. The authors have also not described how they would interpret a Widal; if this is a hospital study, paired sampling to observe an increase in titres might not be possible.\n\nThe authors have not explained why they have excluded patients less than 18 years. Individuals less than 18 years form a huge part of the burden of typhoid in India and they are also the target of the TCV vaccine.\nThe sampling frame is not ideal for the study design; patients admitted to the ward would just be a subset of the patients with typhoid and the reviewer would suggest including outpatients as well.\nThe authors have described the methods for Widal and blood culture, but they have not described satisfactorily the Salmonella PCR method which is the major focus of the study. There is no description of the targets other than “appropriate primers” that they are planning to use. This is problematic because even if they will be developing new primers, that process should be detailed in brief. They have not referenced any article that have examined this work earlier, and there are multiple articles regarding this.\nIn the data analysis section, they have stated that diagnostic accuracy measures will be carried out in for PCR, Widal and blood culture. In that case, which would be the gold standard method they are comparing this against? If they do not consider blood culture to be the gold standard, they have not stated any plans to do a latent class analysis.\nIn the discussion, they have stated that “blood culture is constrained by longer turnaround times and potential false negatives, especially in patients receiving prior antibiotic treatment.” If that is so, how would PCR be any better than blood culture considering bacteremia even at the height of Typhoid is ~ 1 bacteria/ml. If they are planning to enrich the blood prior to PCR, this should be described.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-542
|
https://f1000research.com/articles/13-541/v1
|
28 May 24
|
{
"type": "Study Protocol",
"title": "A prospective observational role of magnetic resonance imaging and magnetic resonance spectroscopy in evaluation of choline levels in gall bladder carcinoma in tertiary care hospital in central India",
"authors": [
"Anjali Kumari",
"Gaurav V Mishra",
"P.H. Parihar",
"Sakshi Dudhe",
"Gaurav V Mishra",
"P.H. Parihar",
"Sakshi Dudhe"
],
"abstract": "Background Gall bladder carcinoma (GBC) is a challenging malignancy characterized by late-stage diagnosis and poor prognosis. Early detection and accurate staging are crucial for improving patient outcomes. Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) offer non-invasive imaging modalities that may aid in the evaluation of GBC. Choline, a metabolite detected by MRS, has been implicated in tumor growth and may serve as a potential biomarker for GBC. This study aims to investigate the role of MRI and MRS in evaluating choline levels as biomarkers for GBC.\n\nMethod A prospective observational study will be conducted involving patients with suspected or confirmed GBC referred to the Department of Radiology, AVBRH, Sawangi. Patients meeting inclusion criteria will undergo MRI scans and MRS examinations to assess tumor characteristics and choline levels. Data collected will include MRI images, MRS spectra, histopathological results, and clinical outcomes. Statistical analysis will be performed to examine correlations between MRI findings, choline levels, and histopathological characteristics.\n\nExpected Outcome It is anticipated that MRI and MRS will demonstrate utility in evaluating choline levels as imaging biomarkers for GBC. Correlations between choline levels, tumor characteristics, and clinical outcomes are expected to provide valuable insights into the role of choline in GBC pathogenesis and prognosis. If successful, MRI and MRS could serve as non-invasive tools for early detection, staging, and treatment response monitoring in GBC, ultimately leading to improved patient outcomes and management strategies.",
"keywords": [
"Gall bladder carcinoma",
"MRI",
"MR spectroscopy",
"Choline levels",
"Biomarkers",
"Early detection"
],
"content": "Background\n\nGallbladder carcinoma (GBC) is a relatively rare but highly aggressive malignancy of the biliary tract with a poor prognosis, mainly due to its often late diagnosis and limited treatment options.1 Early detection and accurate staging of GBC are crucial for improving patient outcomes. Yet, conventional imaging modalities like ultrasound, computed tomography (CT), and magnetic resonance imaging (MRI) have limitations in precisely characterizing tumor extent and aggressiveness.2\n\nRecent advances in MRI, coupled with magnetic resonance spectroscopy (MRS), have shown promise in enhancing the diagnostic accuracy and prognostic value for various cancers, including hepatobiliary malignancies.3 MRS enables the non-invasive assessment of metabolite levels within tissues, offering insights into cellular metabolism and providing potential biomarkers for cancer detection and characterization.4 One such metabolite of interest is choline, a component of cell membranes whose elevated levels have been associated with increased cell proliferation and malignant transformation.5\n\nDespite the growing interest in utilizing MRI and MRS for GBC evaluation, there remains a need for further research to validate their utility, particularly regarding choline levels as a biomarker for tumor detection and characterization. Therefore, this study aims to investigate the role of MRI and MR spectroscopy in evaluating choline levels in GBC to improve early detection and guide personalized treatment strategies for this aggressive malignancy.\n\nThis study aims to investigate the role of MRI and MR spectroscopy in evaluating choline levels in gall bladder carcinoma.\n\n\n\n1. To assess the spectrum of MRI findings in patients diagnosed with gall bladder carcinoma.\n\n2. To determine choline levels using MR spectroscopy in gall bladder carcinoma.\n\n3. To evaluate the diagnostic accuracy of MRI in assessing the size, resectability, and vascular involvement of gall bladder carcinoma.\n\n4. To explore the potential of MR spectroscopy in detecting choline levels as a biomarker for gall bladder carcinoma.\n\n5. To assess the feasibility and safety of performing MRI and MR spectroscopy in patients with gall bladder carcinoma.\n\n6. To investigate any correlation between choline levels detected by MR spectroscopy and histopathological findings in gall bladder carcinoma.\n\n7. To contribute to understanding the role of imaging techniques in the early detection and management of gall bladder carcinoma.\n\n\nMethod\n\nThis study will utilize a prospective observational design to evaluate the role of MRI and MR spectroscopy in assessing choline levels in gall bladder carcinoma. Patients meeting the inclusion criteria will undergo MRI scans, and MR spectroscopy will be conducted to analyze choline levels. Data will be collected and analyzed to fulfill the study objectives.\n\nThe study population will include patients with suspected or diagnosed cases of gall bladder carcinoma. Inclusion criteria will involve patients who consent to participate, do not have contraindications for MRI or MR spectroscopy, and are referred to the Department of Radiology, AVBRH, Sawangi. Exclusion criteria will encompass patients with prior surgical or medical interventions, pregnant women, individuals with pacemakers or metallic implants, those with psychological conditions or claustrophobia, and those who are unwilling or uncooperative.\n\nThe study will be conducted at the Department of Radiology, Acharya Vinoba Bhave Rural Hospital, Sawangi, under the auspices of Datta Meghe Institute of Higher Education and Research. AVBRH has the necessary infrastructure and facilities for conducting MRI scans and MR spectroscopy. The hospital serves as a referral center for patients in the region, ensuring access to a diverse patient population for the study.\n\n\n\n1. Patients aged 18 years and above.\n\n2. Patients with suspected or confirmed diagnosis of gall bladder carcinoma based on clinical evaluation, imaging studies, or biopsy results.\n\n3. Patients willing to provide verbal and written informed consent for participation in the study.\n\n4. Patients capable of undergoing MRI and MR spectroscopy examinations without contraindications.\n\n5. Patients referred to the Department of Radiology, AVBRH, Sawangi, for further evaluation and management of gall bladder carcinoma.\n\n\n\n1. Patients below the age of 18 years.\n\n2. Patients with contraindications for MRI or MR spectroscopy, including those with metallic implants incompatible with MRI, pacemakers, cochlear implants, or other implanted devices.\n\n3. Pregnant women or women who are breastfeeding.\n\n4. Patients with a history of significant psychological conditions, including severe claustrophobia, that would impede the successful completion of the imaging procedures.\n\n5. Patients who are unwilling or unable to provide informed consent for participation in the study.\n\n6. Patients with prior surgical interventions or medical treatments for gall bladder carcinoma that may confound the study results.\n\n7. Patients with concurrent medical conditions or comorbidities that could affect the interpretation of MRI or MR spectroscopy findings or compromise patient safety during the procedures.\n\n\n\n1. Referral and Screening: Patients with suspected or confirmed diagnosis of gall bladder carcinoma will be referred to the Department of Radiology, AVBRH, Sawangi, by their primary care physicians, oncologists, or surgeons. Upon arrival, patients will undergo initial screening to assess their eligibility for participation in the study based on the inclusion and exclusion criteria.\n\n2. Informed consent: Eligible patients will be provided with detailed information about the study objectives, procedures, potential risks, and benefits. They will be given ample time to ask questions and clarify any concerns. Verbal and written informed consent will be obtained from patients willing to participate in the study.\n\n3. Baseline assessment: Patients who consent to participate will undergo a baseline assessment, including a review of their medical history, physical examination, and relevant laboratory investigations. This assessment will help ensure that patients meet the inclusion criteria and do not have any contraindications for MRI or MR spectroscopy.\n\n4. MRI and MR spectroscopy: According to the study protocol, eligible patients will then be scheduled for MRI scans and MR spectroscopy examinations. Patients will be instructed on the procedure and asked to cooperate during the imaging sessions to ensure the quality of the obtained data.\n\n5. Data collection: During MRI and MR spectroscopy examinations, data will be collected using the specified imaging sequences and protocols. Choline levels will be analyzed using MR spectroscopy, and MRI findings will be assessed for gall bladder carcinoma characteristics.\n\n6. Follow-up: After completion of the imaging procedures, patients may receive further diagnostic or therapeutic interventions as per their clinical management plan. Followup appointments may be scheduled to monitor patients’ progress and evaluate treatment response.\n\n7. Data analysis: Trained radiologists and researchers will analyze collected data, including MRI images and spectroscopy results, to fulfill the study objectives. Statistical analyses may assess correlations between choline levels, MRI findings, and histopathological results.\n\n8. Enrollment completion: Enrollment will continue until the predetermined sample size is reached or the study duration is completed. Data analysis will be finalized upon enrollment completion, and study findings will be reported per the study protocol and ethical guidelines.\n\nData collection for this study will encompass several key components. Initially, baseline information will be gathered, including demographic data such as age, gender, ethnicity, and occupation, alongside a detailed clinical history. This will entail documenting symptoms, their duration, previous treatments, and any existing medical comorbidities. Laboratory investigations will also be recorded, including complete blood count, liver function tests, and tumor markers such as CA 19-9. Moreover, imaging reports from previous studies, such as ultrasounds or CT scans, will be reviewed to compile relevant findings related to gall bladder carcinoma. Subsequently, data collection will focus on MRI and MR spectroscopy. MRI images, including T1-weighted, T2-weighted, and diffusion-weighted images, will be obtained and assessed for various features indicative of gall bladder carcinoma, such as mass lesions or wall thickening. Additionally, MR spectroscopy data will be analyzed for choline peaks, providing quantitative measurements of choline concentration, a potential biomarker for gall bladder carcinoma.\n\nHistopathological data, if available, will also be included in the analysis. This will involve documenting the results of biopsies or surgical specimens, including the histopathological diagnosis of gall bladder carcinoma, tumor grade (well, moderately, or poorly differentiated), and tumor stage based on TNM staging. Followup data will be collected to monitor treatment responses and clinical outcomes. This will entail documenting the treatments received, such as surgery, chemotherapy, or radiotherapy, and assessing responses through radiological evaluations of tumor regression, stabilization, or progression. Additionally, patient survival status, recurrence of carcinoma, and progression-free survival will be recorded.\n\nFurthermore, the study will gather data on patient experiences and any adverse events encountered during MRI and MR spectroscopy procedures. Patient feedback regarding comfort levels and any discomfort or complications experienced will be documented to inform future improvements in patient care. Quality control measures will be implemented throughout the data collection process, including standardized imaging protocols, blinding of radiologists interpreting the data, and regular calibration of imaging equipment to ensure the accuracy and reliability of results. Finally, data management and analysis will involve entering collected data into a secure electronic database and statistical analysis using appropriate methods to examine relationships between variables. Ethical considerations, such as ensuring patient confidentiality, obtaining informed consent, and obtaining institutional review board approval, will be followed throughout the study.\n\nDetermining the appropriate sample size is crucial for ensuring the study’s statistical power and the reliability of the findings. This study’s sample size calculation was based on the prevalence of gall bladder carcinoma and the desired confidence level and margin of error. Using the Cochran Formula, a sample size of 20 patients was determined, considering a prevalence rate of 1.2% and an error margin of 5%. This sample size provides sufficient statistical power to detect potential associations between MRI findings, choline levels, and gall bladder carcinoma characteristics with high confidence.\n\nThe statistical analysis for this study will employ a range of methods to thoroughly examine the relationships between variables and assess the significance of the findings. Initially, descriptive statistics will be utilized to summarize the characteristics of the study population, encompassing demographic information, clinical features, and imaging findings. Measures such as means, standard deviations, frequencies, and percentages will be calculated to provide a comprehensive overview of the collected data, facilitating a clear understanding of the sample characteristics. Correlation analysis will then explore the strength and direction of relationships between key variables of interest. Specifically, correlations between MRI findings, choline levels measured by MR spectroscopy, and histopathological results will be assessed. Depending on the nature of the data, either Pearson correlation coefficients or Spearman’s rank correlation coefficients will be computed to quantify the degree of association between these variables. Regression analysis will be employed to investigate the predictive value of MRI findings and choline levels for various aspects of gall bladder carcinoma, such as tumor stage, grade, or treatment response. Multiple linear regression or logistic regression models may be utilized to determine the independent contributions of each variable in predicting specific outcomes, thereby elucidating their potential prognostic significance.\n\nFurthermore, comparative analysis will be performed to evaluate differences in MRI findings and choline levels across different subgroups of patients, categorized based on relevant factors such as tumor stage, grade, or treatment status. This analysis will utilize appropriate statistical tests, including t-tests, Mann-Whitney U tests, ANOVA, chi-square tests, or Fisher’s exact tests, depending on the type and distribution of the data. Survival analysis techniques, such as Kaplan-Meier curves and Cox proportional hazards models, may be employed to assess the impact of MRI findings and choline levels on patient survival outcomes, including overall and progression-free survival. These analyses will provide valuable insights into the prognostic significance of imaging biomarkers in gall bladder carcinoma. Additionally, receiver operating characteristic (ROC) analysis may be conducted to evaluate the diagnostic accuracy of MRI findings and choline levels in distinguishing between different stages or grades of gall bladder carcinoma. By calculating the area under the curve (AUC) values, the discriminatory power of these imaging biomarkers can be quantified, informing their clinical utility in disease diagnosis and management using R studio version 4.3.1.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruiting for the study.\n\n\nDiscussion\n\nGall bladder carcinoma (GBC) poses a significant clinical challenge due to its often-asymptomatic nature in the early stages and aggressive behavior once symptomatic. Despite advancements in diagnostic modalities and treatment strategies, the prognosis for GBC remains poor, primarily due to late-stage diagnosis and limited effective treatment options.6 In this study, we proposed to investigate the role of MRI and MR spectroscopy in evaluating choline levels as potential biomarkers for GBC, aiming to improve early detection and prognosis prediction.\n\nThe use of MRI in the evaluation of GBC has shown promising results in previous studies. MRI provides high-resolution imaging of the gall bladder, allowing for detailed assessment of tumor size, local invasion, and vascular involvement. Additionally, MR spectroscopy offers the ability to measure choline levels within the tumor tissue, which may indicate malignancy. Choline is a key component of cell membrane metabolism and has been implicated in tumor growth and proliferation. Several studies have demonstrated elevated choline levels in various malignancies, including breast, prostate, and brain tumors.7\n\nOur study aims to build upon this knowledge by investigating the utility of MRI and MR spectroscopy in evaluating choline levels, specifically in GBC. By correlating MRI findings with choline levels measured by MR spectroscopy, we aim to identify imaging biomarkers that can aid in the early detection and characterization of GBC. Early detection is critical in improving patient outcomes, as surgical resection remains the primary curative treatment option for GBC. Moreover, accurate tumor aggressiveness and staging characterization can guide treatment decisions and prognosis prediction.8\n\nThe proposed study will contribute to the growing body of literature on imaging biomarkers for GBC and may have implications for clinical practice. If successful, MRI and MR spectroscopy could be non-invasive tools for GBC diagnosis and staging, potentially reducing the need for invasive procedures such as biopsy or exploratory surgery. Additionally, quantifying choline levels in GBC tumors could aid treatment response monitoring and prognostication, leading to more personalized and effective patient management strategies.9\n\nHowever, several challenges and limitations must be considered. Firstly, the sample size in our study is relatively small, which may limit the generalizability of our findings. Future studies with larger cohorts are warranted to validate our results and establish robust diagnostic and prognostic models.10 Secondly, MRI and MR spectroscopy techniques require specialized equipment and expertise, which may only be available in some clinical settings. Efforts to standardize imaging protocols and train healthcare professionals in these techniques will be crucial for widespread implementation.11\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has approved the study protocol (Reference number: DMIHER/IEC/2023/768. Date: 21-03-2023). Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nHundal R, Shaffer EA: Gallbladder cancer: epidemiology and outcome. Clin. Epidemiol. 2014; 6: 99–109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRamachandran A, Srivastava DN, Madhusudhan KS: Gallbladder cancer revisited: the evolving role of a radiologist. Br. J. Radiol. 2021; 94: 20200726. PubMed Abstract | Publisher Full Text | Free Full Text\n\nManfredi R, Barbaro B, Masselli G, et al.: Magnetic resonance imaging of cholangiocarcinoma. Semin. Liver Dis. 2004; 24: 155–164. Publisher Full Text\n\nGlunde K, Bhujwalla ZM, Ronen SM: Choline metabolism in malignant transformation. Nat. Rev. Cancer. 2011; 11: 835–848. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPodo F: Tumour phospholipid metabolism. NMR Biomed. 1999; 12: 413–439. Publisher Full Text\n\nDwivedi AND, Jain S, Dixit R: Gall bladder carcinoma: Aggressive malignancy with protean loco-regional and distant spread. World J. Clin. Cases. 2015; 3: 231–244. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSoundararajan R, Marodia Y, Gupta P, et al.: Imaging patterns of wall thickening type of gallbladder cancer. Clin. Exp. Hepatol. 2022; 8: 255–266. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerma A, Kumar I, Verma N, et al.: Magnetic resonance spectroscopy — Revisiting the biochemical and molecular milieu of brain tumors. BBA Clin. 2016; 5: 170–178. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKauppinen RA, Peet AC: Using magnetic resonance imaging and spectroscopy in cancer diagnostics and monitoring. Cancer Biol. Ther. 2011; 12: 665–679. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBiau DJ, Kernéis S, Porcher R: Statistics in Brief: The Importance of Sample Size in the Planning and Interpretation of Medical Research. Clin. Orthop. Relat. Res. 2008; 466: 2282–2288. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFaber J, Fonseca LM: How sample size influences research outcomes. Dental Press J. Orthod. 2014; 19: 27–29. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "325722",
"date": "31 Oct 2024",
"name": "Angel Justiz-Vaillant",
"expertise": [
"Reviewer Expertise Oncology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nClear Aim and Objectives: The study has a well-defined aim with clear objectives that are methodically outlined. Each objective supports the overall aim, providing a comprehensive approach to assessing MRI and MRS in GBC.\nUse of Non-Invasive Techniques: MRI and MRS, as non-invasive diagnostic tools, are appropriate for the study's goals. MRS specifically targeting choline levels as a biomarker addresses an important area in cancer diagnosis with potential clinical implications.\nEthical Considerations: The protocol outlines ethical practices, including obtaining consent and approval from the ethics committee. This ensures that the study complies with research ethics, protecting patient welfare.\nStructured Data Collection and Analysis Plan: The plan for data collection is systematic, with comprehensive details on patient demographics, imaging findings, and histopathological outcomes. Statistical methods are well chosen to analyze MRI and MRS findings, with additional provisions for ROC analysis to assess diagnostic accuracy, enhancing the study's rigor.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-541
|
https://f1000research.com/articles/13-210/v1
|
21 Mar 24
|
{
"type": "Research Article",
"title": "Clinical presentation and radiologic imaging findings of phyllodes tumors: benign and borderline/malignant phyllodes tumors",
"authors": [
"Wanrudee Lohitvisate",
"Kanitta Rodjanakonkiat",
"Amolchaya Kwankua",
"Kanitta Rodjanakonkiat",
"Amolchaya Kwankua"
],
"abstract": "Background Phyllodes tumor is a rare fibroepithelial neoplasm of the breast, which is classified histologically as benign, borderline, or malignant. Accurate preoperative diagnosis allows the correct surgical planning and reoperation avoidance.\n\nObjective To describe the clinical presentation and radiologic features of phyllodes tumors and differentiate between benign and non-benign (borderline and malignant) groups.\n\nMethods A retrospective study of 57 patients with a diagnosis of phyllodes tumor who had preoperative imaging (mammography, ultrasound, or CT chest) and histological confirmation. The data was collected from 1 June 2011 to 30 September 2021. The imaging features of the phyllodes tumors were described according to the 5th edition of the ACR BI-RADS lexicon. For comparing between two groups, the student t-test, Wilcoxon rank sum test, Chi-square test, and Fisher’s exact test were used for statistical analyses. The logistic regression analysis was calculated for non-benign phyllodes tumor prediction.\n\nResults From 57 patients, the pathologic results were benign for 43 cases and non-benign phyllodes tumors for 14 cases. There was no differentiation of mammographic and CT features between benign and non-benign groups. Non-benign phyllodes tumors had the statistical significance of menopausal status, entire breast involvement, tumor size larger than 10 cm, and heterogeneous echo on univariable analysis. After multivariable analysis, menopausal status (odd ratios=13.79, p=0.04) and presence of vessels in the rim (odd ratios=16.51, p=0.019) or absent vascularity (odd ratios=8.45, p=0.047) on doppler ultrasound were significantly increased possibility of non-benign phyllodes tumor.\n\nConclusions Menopausal status and presence of vessels in the rim or absent vascularity on Doppler ultrasound were important predictors for the diagnosis of non-benign phyllodes tumor.",
"keywords": [
"Phyllodes",
"Breast tumors",
"Imaging features"
],
"content": "Introduction\n\nPhyllodes tumor is a rare fibroepithelial neoplasm of the breast. Most of phyllodes tumor are found in women between the age of 35 and 55 years. However, there are some reported cases of phyllodes tumor in young adult and elderly women.1\n\nIn 2019, World Health Organization (WHO) classified phyllodes tumor into benign, borderline, and malignant based on several histologic features, including stromal cellularity, nuclear atypia, mitotic activity, stromal overgrowth, and tumor margin.2,3 The majority of phyllodes tumors have been classified as benign (35% to 64%), and the remainder were the borderline and malignant subtypes.4\n\nThe most common clinical presentation is a palpable breast mass that may be rapidly growing.1 While an incidentally found mass on routine screening mammography are rare.5 On physical examination, most patients have a smooth, round, well-defined, firm, painless and movable mass. The large masses may be associated with dilated veins visible over the skin, which may be stretched and attenuated. Nipple retraction, skin ulceration, invasion of the chest wall, and bloody nipple discharge have been reported but rare. Palpable enlarged axillary lymph nodes can be found up to 20% of patients but nodal metastasis of axillary lymph nodes is rare.6\n\nThe mammographic features of phyllodes tumor are (i) circumscribed or oval mass (ii) a radiolucent halo may be seen around the lesion due to compression of the surroundings, and (iii) coarse calcifications may be present.4,7–9 Ultrasonographic features show oval, circumscribed, echogenic rim, and hypoechoic mass. Fluid-filled clefts in a predominantly solid mass are highly suggestive of phyllodes tumor with good thorough transmission and lack of microcalcification.4,7,10\n\nSurgery has been the mainstay of treatment for all subtypes of phyllodes tumor.3 Treatment of phyllodes tumor requires complete removal of the tumor with wide margins if the tumor is small and the simple mastectomy may require in the large tumor.11 Furthermore, excision with negative margins should be taken for recurrent and malignant phyllodes tumors.12\n\nBecause of accurate preoperative diagnosis allows the correct surgical planning and avoidance of reoperation, the purposes of this study are to describe clinical presentation and radiologic features of phyllodes tumors and differentiate between benign and non-benign (borderline and malignant) groups.\n\n\nMethods\n\nThe data of female patients with histopathologically confirmed phyllodes tumor who had undergone preoperative mammography or ultrasonography or post contrast CT chest at Thammasat University Hospital from 1 June 2011 to 30 Sep 2021 was collected and retrospectively reviewed. The CT chest was performed in some patients due to the huge breast mass that cannot perform mammography and ultrasound.\n\nThe inclusion criteria were as follows; (a) patient who underwent breast surgery and received a histologic diagnosis of phyllodes tumor (b) the pre-operative radiological images (digital mammography or ultrasonography or post contrast CT chest) were available on Pictures Archiving and Communications System (PACS) of the Thammasat University Hospital, and (c) the medical records and pathological results were accessible on the information system of the Thammasat University Hospital (EPHIS). The exclusion criteria were as follows; (a) incomplete medical record and (b) inconclusive pathological results such as fibroepithelial tumor.\n\nOf the initial 70 suspicious phyllodes tumors, 10 cases were excluded because of incomplete medical record and unavailable pre-operative images, and 3 cases had inconclusive pathological result as fibroepithelial tumors from core needle biopsy and no other procedure to receive more tissue. Eventually, a total of 57 phyllodes tumors were eligible for our study. The final pathologic results of phyllodes tumors were benign for 43 cases and non-benign (borderline and malignant) for 14 cases.\n\nThe patients were received at least one of the imaging studies as follows;\n\n(a) Mammographic imaging was performed by using digital technique of Lorad Selenia (Hologic) or 3-Dimensions (Hologic) mammography on mediolateral oblique (MLO) and craniocaudal (CC) views.\n\n(b) Ultrasonography (US) was performed with B-mode grayscale and doppler mode on supine position using a Samsung RS80A equipped with an L3-12A linear transducer (3–12 MHz, 5.0 cm), or a Philips IU22 equipped with an L12-5 linear transducer (5–12 MHz, 5.0 cm).\n\n(c) Pre and post contrast enhanced computed tomography (CT) of the chest using Siemens or Phillips – 128/256 slices model.\n\nThe patient’s clinical information was collected from electronic medical records consist of age at diagnosis, clinical presentation (palpable mass, breast pain, skin ulcer, or screening), duration of symptom, menstrual status, side of tumor (right or left), location of the tumor, treatment (wide excision or mastectomy), and metastasis (none, lymph node, or distant).\n\nThe histopathological data were retrieved from the final histopathological reports which were separated into two groups: benign and non-benign (borderline and malignant) phyllodes tumor. The phyllodes tumor was categorized based on histopathological features, using World Health Organization (WHO) criteria which divided histologic features of phyllodes tumor based on stromal atypia, mitosis, stromal overgrowth, and margin.2\n\nThe images (mammography, ultrasonography, or contrast enhanced CT chest) were retrospectively reviewed by two radiologists with 13 years and 12 years of experience in breast imaging. For discrepant results, a final consensus was reached after discussion. The images were randomly selected and blinded to histopathological results.\n\nThe images were retrieved retrospectively from PACS. The latest images before undergoing treatment were selected and reviewed. The details of each imaging modality were described as follows;\n\n(a) Mammography: The data included side (right or left), size (in largest dimension) and morphology of the phyllodes tumor by using the fifth edition ACR BI-RADS lexicon. The mammographic features were identified as presence of calcification (macro-, micro-, or none), shape (irregular, oval, round), margin (circumscribed, obscured, microlobulated, indistinct, spiculated), density (high, equal, low, fat-containing), location (upper outer, upper mid, upper inner, mid outer, mid inner, lower outer, lower mid, lower inner), and involvement (<1quadrant, 1-2 quadrant, >2quadrants).\n\n(b) Ultrasonography: The data included side (right or left), size (in largest dimension), morphology and vascularity of the phyllodes tumor by using the fifth edition ACR BI-RADS lexicon. The ultrasonographic features were identified as shape (irregular, oval, round), margin (circumscribed, indistinct, angular, microlobulated, spiculated), echogenicity (hypo-, hyper-, iso-, heterogeneous), posterior features (no posterior features, enhancement, shadowing, combined pattern), cystic area (present, absent), and vascularity (absent, internal vascularity, vessels in rim)\n\n(c) Contrast enhanced CT chest: Using the same data in the mammographic features and consider the enhancement of the phyllodes tumor in Hounsfield Unit (HU) as follows1: No enhancement; the difference of the phyllodes tumor’s attenuation between pre- and post-contrast administration was less than 10 HU,2 Enhancement: the difference of the phyllodes tumor’s attenuation between pre- and post-contrast administration was equal or greater than 10 HU, and degree of enhancement was classified as mild enhancement (the enhancement was less than 25%), moderate enhancement (the enhancement was 25-50%), and marked enhancement (the enhancement was greater than 50%).\n\nThe demographic data of the patients and histopathological results of all phyllodes tumors were reported by using the number (percentage) for categorical variables and mean ± SD or median (IQR) and range for continuous variables.\n\nTo compare the clinicopathological and imaging characteristics between benign and non-benign phyllodes tumor, we initially used Shapiro-wilk normality test before using Student’s t-test for normally distributed continuous variables and Wilcoxon rank sum test for non-normally distributed continuous variables. The Chi-square test or Fisher’s exact test was used for the categorical variables. All statistical analyses were performed with R program (version 4.1.1, R foundation for Statistical Computing, Vienna, Austria) and statistical significance will be considered as p-value less than 0.05.\n\nWith regard to the data analyses, the demographic data and imaging features were discovered to be statistically significant; logistic regression analysis was conducted to calculate the odds ratios (OR) with 95% confidence intervals (95% CI) for predicting non-benign phyllodes tumor probability as compared with benign phyllodes tumor. Odds ratios were contemplated to indicate statistical difference if the 95% CI excluded 1.0. A univariate analysis was first performed to identify any potential predictor variables. The demographic data and imaging features with a p-value <0.05 according to a univariate analysis were included in the multivariate analysis to determine any independent predictors of the non-benign phyllodes tumor. A stepwise selection procedure was used to identify variables with a p-value <0.05.\n\n\nResults\n\nA total of 57 female patients with a mean age of 38.8 years (range, 15-66 years) were included in the study. Forty-three patients were benign, 7 patients were borderline, and 7 patients were malignant subtype. The demographic data, clinical characteristics, and histopathological results of patients are shown in Table 1.22\n\n# Some patients had multiple symptoms at the time of presentation.\n\n## Duration of the patients who presented with mass on screening images was excluded for statistical analysis.\n\n* Statistically significant at p value < 0.05 determined by Fisher’s exact test.\n\nThere was no statistically significant difference in patient’s age, clinical presentation, duration, side, treatment or metastasis between benign and non-benign groups. The mean ages of patients with benign and non-benign phyllodes tumors were 37.1 years and 43.9 years, respectively. Palpable breast mass was the most common (91.2%) presenting symptom in both groups. Noted that in some patients can had more than one symptom at the time of presentation. The median duration of symptoms prior to diagnosis was 4 months, which ranged from 0.03 month (1 day) to 60 months (5 years). For the patients whose phyllodes tumor incidentally found on screening were not included for statistical analysis. Both sides of breast were equally affected from both benign and non-benign phyllodes tumors.\n\nMost patients (77.2%) from both groups underwent wide excision of the tumor as a treatment. There were 2 distant metastatic patients (14.3%) from the non-benign group which both of them were lung metastasis. None of the non-benign phyllodes tumor patients had lymph node metastasis.\n\nThere were statistically significant differences in the menstrual status (p=0.009) and location of the tumor (p=0.027) between benign and non-benign phyllodes tumors. The majority of patients in benign group were pre-menopausal status (79%), while 50% of the patients in non-benign group were menopausal status (p=0.009). Tumor involving entire breast was more presented in patients with non-benign phyllodes tumor (p=0.027).\n\nThirty-one patients underwent mammography. The patients who did not undergo mammography due to 1) the tumor size was too large to be performed mammography, and 2) patients were younger than 30 years old, so they were undergoing ultrasonography for the evaluation instead of mammography. However, our study did not show any statistically significant differences in all mammographic features between the two groups as demonstrated in Table 2. Noted that of all 31 patients, 7 patients were excluded from size evaluation because the masses were obscured by surrounding dense breast parenchyma.\n\n# Seven patients were excluded because of dense breast.\n\nAll 57 patients with phyllodes tumor underwent ultrasonography. There was no statistically significant difference in the tumor’s side, shape, border, posterior acoustic features, and cystic area between benign and non-benign groups as demonstrated in Table 3.\n\n* Statistically significant at p value < 0.05 determined by Fisher’s exact test.\n\nThere were statistically significant differences in the size (p= 0.038), echogenicity (p= 0.019) and vascularity (p= 0.04) of phyllodes tumors between benign and non-benign groups. Size of the tumors was commonly less than 5 cm in both benign and non-benign groups (30 of 43 [70%] vs 6 of 14 [43%], respectively). Whereas the tumor size more than 10 cm was more common in non-benign than those of benign group (7 of 14 [50%] vs 4 of 43 [9%], respectively). The most common echogenicity of benign phyllodes tumors was hypoechogenicity (Figure 1). Whereas the heterogeneous echogenicity (Figure 2) was higher found in non-benign phyllodes tumor compared to benign phyllodes tumor (8 of 14 [57.1%] vs 8 of 43 [18.6%], respectively). None of the phyllodes tumors had hyperechogenicity on ultrasonographic images. The most common vascularity characteristics in both benign and non-benign phyllodes tumors was presence of internal vascularity (37 of 43 [86%] vs 8 of 14 [57.1%], respectively) (Figure 3).\n\nThe ultrasound showed a 3.0x2.3x3.3-cm well-defined lobulated hypoechoic mass with posterior acoustic enhancement at the left 12 o’clock. Wide excision of the mass was done, and the histopathologic result was a benign phyllodes tumor.\n\nThe ultrasound showed a huge circumscribed heterogeneous echoic mass with internal cystic spaces involving the entire right breast.\n\nA. The gray-scale ultrasound showed a large, partially well-defined, heterogeneous hypoechoic mass with small internal cystic spaces involving the outer region of the right breast and B. The color doppler ultrasound showed internal vascularity in the mass. The histopathologic result was a benign phyllodes tumor.\n\nUnivariable analysis (Table 4), using the logistic regression to analyze the correlation between demographic data and ultrasonographic features to predict non-benign phyllodes tumor, the results showed that patients with menopausal status (p= 0.008), tumor located in entire breast (p = 0.015), tumor size more than 10 cm (p= 0.029) and heterogeneous echo on ultrasound images (p= 0.009) were significantly related with non-benign phyllodes tumor.\n\n* Statistically significant at p value 0.05.\n\nAfter multivariable analysis (Table 4) with multicollinearity avoidance with stepwise selection procedure, menopausal status (odd ratios, 13.79 [95% CI: 2.31,82.24], p value of 0.04), and presence of vessels in rim (odd ratios, 16.51 [95% CI: 1.59,171.96], p value of 0.019) or absent vascularity on doppler ultrasound (odd ratios, 8.45 [95% CI: 1.03,69.15], p value of 0.047) were significantly increased possibility of non-benign phyllodes tumor. But the location, tumor size and echogenicity showed no statistically significant difference for predicting non-benign phyllodes tumor.\n\nThere were only 5 (8.8%) from 57 phyllodes tumor patients who underwent contrast enhanced CT chest. One (20%) patient was benign and 4 (80%) patients were non-benign phyllodes tumors. Because of the small number of subjects, we would only describe CT findings without statistical analysis as demonstrated in Table 5.\n\nThe one benign phyllodes tumor was found in the right breast, while the non-benign phyllodes tumors were found in each side of the breasts equally. The size of phyllodes tumor ranged from 8.9 to 24.5 cm in the longest dimension, which both of the smallest and the largest tumors were found in non-benign group. Only 1 non-benign phyllodes tumor showed microcalcification, while the rest of phyllodes tumors did not present calcification. All of phyllodes tumors were irregular shape, heterogeneous density, involving more than 2 quadrants and located in entire breast. The border of phyllodes tumor was circumscribed in 3 (75%) patients from non-benign group whereas irregular border was found in 1 (100%) patient from benign group and 1 (25%) patient from non-benign group. There were 2 (50%) non-benign phyllodes tumors that showed no enhancement, while the other 2 (50%) non-benign phyllodes tumor had marked enhancement (Figure 4), and 1 (100%) benign phyllodes tumor showed moderate enhancement.\n\nA. The pre-contrast CT chest showed an irregularly shaped, heterogeneous hypodense mass involving the entire right breast with skin invasion and B. After contrast administration, the tumor showed marked heterogeneous enhancement.\n\n\nDiscussion\n\nPhyllodes tumor is a rare fibroepithelial neoplasm of the breast that accounts for 0.3% to 0.5% of breast tumors in female which is classified histologically as benign, borderline, or malignant. Accurate preoperative diagnosis allows correct surgical planning and avoidance of reoperation.\n\nAccording to the prior studies, most of phyllodes tumors were benign subtype.3,13,14 Similarly, the majority of phyllodes tumors (75.4%) in our study were benign.\n\nThere was no statistically significant difference of the patient’s age between the two groups but the mean age was higher in non-benign phyllodes tumor group (43.9 years). Our study also found patients younger than 30 years old in both groups. Palpable mass was the most common clinical finding in both benign and non-benign groups. These data could be found in patients with fibroadenoma but usually occur younger than phyllodes tumor. To differentiate fibroadenoma from benign phyllodes tumor, we suggest combining the age of patient and the rate of tumor growth. Fibroadenomas are found in younger age group and slower rate of tumor growth than phyllodes tumor. However, it might be difficult to diagnose the juvenile fibroadenoma which occurs in adolescent patients and have rapid growth of tumor. In this case, tissue biopsy for histopathologic results is helpful.\n\nThere was no statistically significant difference of tumor size in mammographic images between benign and non-benign phyllodes tumor but there was statistically significant difference of tumor size in ultrasound images which was higher in non-benign phyllodes tumor. Most of tumor size in benign group (70%) and almost half of non-benign group (43%) was less than 5 cm. The duration of symptom was no statistically significant difference. Therefore, the rate of tumor growth especially in small tumor cannot help to differentiate malignant from benign phyllodes tumor in our study. Nevertheless, some studies revealed rapid growth may be detected in malignant tumors.15,16\n\nKılıç MÖ et al. found that the most cases of phyllodes tumor were diagnosed in premenopausal women.15 Our study showed similar results of the benign group and all of phyllodes tumor. But menopausal status was found statistically significance (p= 0.009) in the non-benign group. Furthermore, after multivariate analysis, we found that menopausal status was the important predictor for non-benign phyllodes tumor (p=0.004).\n\nFew prior studies showed that the upper outer quadrant of the breast was the most frequent location of phyllodes tumor, and both sides were equally affected.17,18 In our study, there was no predilection side of breast to be affected by phyllodes tumor in both benign and non-benign groups. The location of phyllodes tumor was slightly higher in the upper outer quadrant for both groups, whereas tumor involving the entire breast was more frequently found in non-benign group (p= 0.027). Kılıç MÖ et al found a small number of patients that had both multifocality and bilaterality of phyllodes tumors.15 However, all of the patients in our study had only a single tumor. A case that had more than one phyllodes tumor was excluded from the study due to incomplete medical record.\n\nThe mammographic findings in our study were parallel to the other literature that there was no specific radiologic feature to differentiate the histologic subtypes of phyllodes tumor.15\n\nKalambo M et al showed that irregular lesion and the longest dimension of the tumor greater than 7 cm on ultrasound were the significant univariate predictors of increased risk of borderline or malignant phyllodes tumors.19 Some prior studies showed no significant difference of vascularity between the different subtypes of phyllodes tumors.13,20,21 In our study, shape, margin, posterior acoustic feature and cystic areas of the tumor on ultrasound images was no statistically significant difference between benign and non-benign phyllodes tumor. Even though, most of morphologic features on ultrasound were not statistically significant difference between groups. Non-benign phyllodes tumor had irregular shape, indistinct and microlobulated borders more often than benign phyllodes tumor. The univariable analysis of our study revealed statistical significance of menopausal status, entire breast involvement, tumor size larger than 10 cm and heterogeneous echo of tumor in non-benign phyllodes tumor. Furthermore, after multivariate analysis, we found that menopausal status and vessels in rim/absent vascularity on doppler ultrasound were significantly increased possibility of non-benign phyllodes tumor (p=0.004 and 0.047/0.019, respectively). The stromal overgrowth with hypercellularity and internal areas of necrosis or hemorrhage might be causes of absent vascularity or only present of peripheral vascularity on doppler ultrasound in the malignant phyllodes tumor and some large tumors.\n\nFive patients with large and huge tumor (size ranged from 8.9 to 24.5 cm in longest dimension) which involved the entire breast underwent post contrast enhanced CT chest and did not undergo mammography. The pathologic results were benign for 1 case and borderline/malignant for 4 cases. All of them had irregular shape and heterogeneous density. Non-benign phyllodes tumor had marked contrast enhancement for 50% and had internal microcalcifications for 25%. Due to the very small number of subjects, we did not demonstrate statistical analysis for characteristic features of the phyllodes tumors between these groups. However, the huge mass with irregular shape and marked contrast enhancement might be prefer non-benign phyllodes tumor. Some invasive ductal carcinomas (IDC) may present with large or huge breast mass with abnormal skin changes that cannot be differentiated from malignant phyllodes tumor clinically. Our study found that there was no nodal metastasis or associated calcifications from mammographic images in all borderline/malignant phyllodes tumors. Therefore, we suggest that the huge, non-calcified breast mass without axillary lymphadenopathy would prefer malignant phyllodes tumor to IDC.\n\nThe patients with non-benign phyllodes tumor were treated by mastectomy for 36% due to very large tumor size and had distant metastasis for 14%, therefore, prediction of borderline/malignant phyllodes tumor has affected for treatment option of each patient.\n\n\nConclusion\n\nMost of patients with phyllodes tumor were presented with palpable breast mass. Menopausal status and presence of vessels in rim or absent vascularity on doppler ultrasound were important predictors for borderline/malignant phyllodes tumor. There was no mammographic or CT features to differentiate between benign and non-benign phyllodes tumors.\n\nThere were some limitations in this study. First, the study was a retrospective design study that may have had a selection bias. Second, this was single-centered study that may cause a relatively small sample size and an unequal number of patients between benign and non-benign phyllodes tumor. Multicentered study with a larger population and data sets may be needed to validate our findings.\n\n\nEthics and consent\n\nThe Human Research Ethics Committee of Thammasat University (Medicine) approved conducting this research with the certificate project number MTU-EC-RA-0-285/64, and approved on December 30, 2021. The inform-consent was waived requirement due to the retrospective nature of the study.",
"appendix": "Data availability\n\nZenodo: Clinical Presentation and Radiologic Imaging Findings of Phyllodes Tumors: Benign and Borderline/Malignant Phyllodes Tumors. https://zenodo.org/doi/10.5281/zenodo.10538896. 22\n\nThis project contains the following underlying data:\n\n- Demographic phyllodes study.xlsx (demographic data of this study)\n\n- MMG-CT-US findings phyllodes project.xlsx (imaging findings of this study)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nWe want to thank Assoc. Prof. Dr. Amonpon Kanlerd, Faculty of Medicine, Thammasat University, for helping us with language editing and submitting this manuscript.\n\n\nReferences\n\nReinfuss M, Mituś J, Duda K, et al.: The treatment and prognosis of patients with phyllodes tumor of the breast: an analysis of 170 cases. Cancer. 1996; 77(5): 910–916. PubMed Abstract | Publisher Full Text\n\nThe WHO Classification of Tumours Editorial Board: WHO Classification of Tumours: Breast Tumours. 5th ed.Lyon, France: International Agency for Research on Cancer (IARC); 2019.\n\nAbdul Hamid S, Rahmat K, Ramli MT, et al.: Radiopathological characteristics and outcomes of phyllodes tumor of the breast in Malaysian women. Medicine (Baltimore). 2018; 97(31): e11412. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMishra SP, Tiwary SK, Mishra M, et al.: Phyllodes tumor of breast: a review article. ISRN Surg. 2013; 2013: 1–10. Publisher Full Text\n\nMangi AA, Smith BL, Gadd MA, et al.: Surgical management of phyllodes tumors. Arch. Surg. 1999; 134: 487–493. discussion. Publisher Full Text\n\nTelli ML, Horst KC, Guardino AE, et al.: Phyllodes tumors of the breast: natural history, diagnosis, and treatment. J. Natl. Compr. Cancer Netw. 2007; 5(3): 324–430. PubMed Abstract | Publisher Full Text\n\nFeder JM, de Paredes ES , Hogge JP, et al.: Unusual breast lesions: radiologic-pathologic correlation. Radiographics. 1999; 19: S11–S26. PubMed Abstract | Publisher Full Text\n\nJorge Blanco A, Vargas Serrano B, Rodriguez Romero R, et al.: Phyllodes tumors of the breast. Eur. Radiol. 1999; 9: 356–360. Publisher Full Text\n\nCosmacini P, Veronesi P, Zurrida S, et al.: Mammography in the diagnosis of phyllodes tumors of the breast. Analysis of 99 cases. Radiol. Med. 1991; 82(1-2): 52–55. PubMed Abstract\n\nCole Beuglet C, Soriano R, Kurtz AB: Ultrasound, X-ray mammography, and histopathology of cystosarcoma phylloides. Radiology. 1983; 146(2): 481–486. Publisher Full Text\n\nMuttarak M, Lerttumnongtum P, Somwangjaroen A, et al.: Phyllodes tumour of the breast. Biomed. Imaging Interv. J. 2006; 2(2): e33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTan BY, Acs G, Apple SK, et al.: Phyllodes tumours of the breast: a consensus review. Histopathology. 2016; 68(1): 5–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChao T-C, Lo Y-F, Chen S-C, et al.: Phyllodes tumors of the breast. Eur. Radiol. 2003; 13(1): 88–93. Publisher Full Text\n\nLiberman L, Bonaccio E, Hamele-Bena D, et al.: Benign and malignant phyllodes tumors: mammographic and sonographic findings. Radiology. 1996; 198(1): 121–124. PubMed Abstract | Publisher Full Text\n\nKılıç MÖ, Terzioğlu SG, Bozkurt B, et al.: Phyllodes tumor of the breast: Analysis of 48 patients. J. Breast Health. 2016; 12(4): 158–164. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAtalay C, Kınaş V, Çelebioğlu S: Analysis of patients with phyllodes tumor of the breast. Ulus Cerrahi Derg. 2014; 30: 129–132. PubMed Abstract | Publisher Full Text\n\nConfavreux C, Lurkina A, Mitton N, et al.: Sarcomas and malignant phyllodes tumours of the breast – A retrospective study. Eur. J. Cancer. 2006; 42: 2715–2721. PubMed Abstract | Publisher Full Text\n\nBarrio AV, Clark BD, Goldberg JI, et al.: Clinicopathologic features and long-term outcomes of 293 phyllodes tumors of the breast. Ann. Surg. Oncol. 2007; 14: 2961–2970. PubMed Abstract | Publisher Full Text\n\nKalambo M, Adrada BE, Adeyefa MM, et al.: Phyllodes tumor of the breast: ultrasound-pathology correlation. AJR. 2018 Apr; 210: W173–W179. PubMed Abstract | Publisher Full Text\n\nSpitaleri G, Toesca A, Botteri E, et al.: Breast phyllodes tumor: a review of literature and a single center retrospective series analysis. Crit. Rev. Oncol. Hematol. 2013; 88: 427–436. PubMed Abstract | Publisher Full Text\n\nUmpleby H, Moore I, Royle G, et al.: An evaluation of the preoperative diagnosis and management of cystosarcoma phyllodes. Ann. R. Coll. Surg. Engl. 1989; 71: 285–288. PubMed Abstract\n\nLohitvisate W, Rodjanakonkiat K, Kwankua A: Clinical Presentation and Radiologic Imaging Findings of Phyllodes Tumors: Benign and Borderline/Malignant Phyllodes Tumors (1/2023). [Dataset]. Zenodo. 2024. Publisher Full Text"
}
|
[
{
"id": "260123",
"date": "18 Apr 2024",
"name": "Kobkun Muangsomboon",
"expertise": [
"Reviewer Expertise -"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is good and advantage for health science. It was conducted with the proper methodology, statistics and ethical issue. Please let me note some opinions to authors team for consideration. That might be beneficial for clinical application. - The title of the paper says about the imaging findings, it is better if the authors can provide Mammographic images in the cases that underwent both mammogram and ultrasound. It will be complete information. And also that can help learning for the people who are interested in this article. (although, the paper found that mammographic features are no difference between benign and non-benign group) If the number of images is not over the journal limitation. - The time between the imaging and surgery in the paper should be stated.(may be range or less than 1 month, or etc.) - The information of the size of the tumour incidentally found should be added in the result.(range or detail...) - In table 2, the marker should be placed in the row of shape, border , density, location (same as size) - In the discussion part, the last paragraph shows the percent of the reason of mastectomy. It is the data of this paper or from the reference, please cite. If the data is the result of the paper (please give the short information of metastasis in the text)\n-I just have a question that in a group of only biopsy (not excision), the pathology report form biopsy may not represent the character of the whole breast lesion. (Based on the available demographic data, 8 are biopsies only and the pathology showed 7 benign, 1 borderline). In my practice, if the biopsy showed benign result, the follow up image (ultrasound) should be performed to confirm the benignity (stable in size and internal characteristic). So I asked for a post-biopsy follow up period for the benign group. If the lesions were stable (in a period of time that authors can provide) , the clinical and images findings were analyzed in the correct group. If the lesion changed in size (or rapid growth) during the follow up period, the re-biopsy or excision should be performed (may be not true benign?) If the authors can state that all benign in only biopsy cases were stable for a period of time. It will be better and no question for readers.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11510",
"date": "20 Jun 2024",
"name": "Wanrudee Lohitvisate",
"role": "Author Response",
"response": "In our study, all phyllodes tumors were removed by wide excision and mastectomy. I primary got tissue diagnosis by CNB and then surgical removal. The final pathologic results from wide excision or mastectomy were used as the gold standard for statistical analysis. Practically, in minority cases of benign Phyllodes tumors that didn't get tumor removal (not include in our study), I recommend to follow up by ultrasonography every 6 months and yearly mammography until 2 years for the benign stability. If there is any change such as significantly increased size or suspicious morphology, I prefer wide excision to CNB."
}
]
},
{
"id": "260117",
"date": "21 May 2024",
"name": "Jatuporn Chayakulkheeree",
"expertise": [
"Reviewer Expertise Breast imaging",
"Diagmostic Radiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the research is well-conducted and provides valuable insights into the clinical and radiologic characteristics of phyllodes tumors. Here are some key points for the author team to consider.\n1. please provide information about the time interval between imaging and surgery. This is important for understanding the relevance of the imaging findings to the surgical intervention and final pathology. 2. please condense the discussion part.\nHopefully, with some minor revisions to enhance clarity and provide additional detail, the manuscript could make a valuable contribution.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11606",
"date": "25 Jun 2024",
"name": "Wanrudee Lohitvisate",
"role": "Author Response",
"response": "I added the information of time interval between imaging and surgery as well as condensed the discussion part in the new version of article as your recommended."
}
]
}
] | 1
|
https://f1000research.com/articles/13-210
|
https://f1000research.com/articles/13-539/v1
|
28 May 24
|
{
"type": "Research Article",
"title": "Assessing the Features of Diabetic Foot Ulcers among Individuals with Type 2 Diabetes Mellitus in Thi Qar, Iraq",
"authors": [
"Adel Gassab Mohammed",
"Dheyaa Kadhim Al-Waeli",
"Samih Abed Odhaib",
"Mahmood Thamer Altemimi",
"Dheyaa Kadhim Al-Waeli",
"Samih Abed Odhaib",
"Mahmood Thamer Altemimi"
],
"abstract": "Background This study aimed to evaluate the characteristics of diabetic foot ulcers in individuals with type 2 diabetes mellitus (T2DM) in Iraq.\n\nMethods The study included 881 participants with T2DM and different types of foot ulcers, who attended a specialized diabetes center. Data on demographics, clinical characteristics, biochemical investigations, comorbidities, and treatment regimens were collected and analyzed.\n\nResults The majority of the cases (96.8%) were due to T2DM, with an average age of 58 years and a mean BMI of 30 kg/m2. Participants had elevated serum creatinine, blood urea, and glucose levels, with uncontrolled HbA1c levels. Comorbidities included hypertension, ischemic heart disease, diabetic neuropathy, and retinopathy. Most participants were on insulin and statins. Diabetic foot ulcers were mainly on the right foot (48%) and classified as Grade 2 in Wagner's system. Some participants had Charcot deformity or stages of amputation.\n\nConclusions Random plasma glucose levels and diabetic retinopathy were significantly associated with the classification of foot ulcers. Further research is needed to explore additional variables related to T2DM and foot ulcers, emphasizing the importance of glucose control and retinopathy in ulcer classification.",
"keywords": [
"diabetic foot ulcers",
"Type 2 Diabetes Mellitus",
"Thi Qar",
"Iraq",
"local studies",
"characteristics"
],
"content": "Introduction\n\nDiabetes mellitus (DM) represents a significant global health issue, anticipated to affect 700 million people by 2045.1 One of the severe consequences of DM is the formation of diabetic foot ulcers (DFUs), which can drastically diminish the quality of life for patients, lead to costly economic outcomes, and, at worst, necessitate the amputation of affected limbs.2 Diabetic foot encompasses a range of foot-related health issues, from infections and ulcerations to deep tissue damage arising from the complications of diabetes itself.3 An estimated 80% of non-traumatic amputations are attributed to DFUs, underscoring their severe impact.4\n\nThe typical etiology of DFUs involves a combination of neuropathic, traumatic, ischemic, and infectious factors.5 Globally, the prevalence of diabetic foot stands at approximately 6.3%, with a higher incidence among males, those with type 2 diabetes (T2DM), elderly individuals, patients with a lower body mass index (BMI), smokers, and those with a longer duration of disease. Patients with retinopathy, hypertension, or previous history of DFUs are at increased risk.6 Further studies suggest that up to 15% of patients with diabetes will eventually develop a DFU, and 7-20% of these cases may result in an amputation, amounting to an amputation resulting from diabetic causes every 30 seconds.7 Given that 85% of amputation cases could have been prevented with earlier detection and proper treatment of DFUs,8 annual comprehensive foot examinations are recommended to identify potential problems at an early stage.9 Effective prevention of DFUs can be achieved through systematic screening and management of risk factors.10\n\nThe absence of localized studies prompted the current research, intended to appraise the characteristics and prevailing conditions of DFUs to enhance both prevention and treatment strategies for this significant health concern. The research was conducted at the Thi-Qar Specialized Diabetes Endocrine and Metabolism Center (TDEMC) and focused on evaluating the specificities of DFUs in patients with T2DM in the southern region of Iraq.\n\n\nMethods\n\nThis cross-sectional observational study, approved by the ethical committee of TDEMC (approval number IQ.TDEMC.REG.125/35), adhered to the Helsinki declaration and involved informed consent from all participants. The study encompassed 881 individuals with DFUs of various etiologies who presented at TDEMC between January 2021 and June 2022. According to the requirements of the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) protocol guidelines, a cross-sectional study follow the STROBE (STrengthening the Reporting of OBservational studies in Epidemiology) guidelines.\n\nThis was a cross-sectional observational study conducted at a specialized diabetes center in Iraq.\n\nA total of 881 individuals with type 2 diabetes mellitus and different types of foot ulcers were included in the study. Participants were selected based on their attendance at the diabetes center and the presence of foot ulcers.\n\nData on demographics (age, gender), clinical characteristics (BMI, blood pressure), biochemical investigations (serum creatinine, blood urea, glucose levels, HbA1c), comorbidities (hypertension, ischemic heart disease, diabetic neuropathy, retinopathy), and treatment regimens (insulin, statins) were collected from medical records and participant interviews.\n\nDescriptive statistics were used to summarize the characteristics of the study population, including mean age, BMI, and biochemical parameters. Associations between random plasma glucose levels, diabetic retinopathy, and the classification of foot ulcers were analyzed using appropriate statistical tests.\n\nThe study was conducted in accordance with ethical guidelines and obtained approval from the institutional review board. Informed consent was obtained from all participants before data collection.\n\nThe study was limited by its cross-sectional design, which precluded the establishment of causal relationships. Additionally, the study was conducted at a single center, which may limit the generalizability of the findings.\n\nFurther research is needed to explore additional variables related to type 2 diabetes mellitus and foot ulcers, with a focus on the importance of glucose control and retinopathy in ulcer classification.\n\nDFU properties, such as location and severity, were quantified using Wagner's grading system (WG), which categorizes ulcers as grade 1 (superficial), grade 2 (deep), grade 3 (abscessed deep ulcer with bone involvement), grade 4 (localized gangrene), and grade 5 (extensive gangrene). The aim was to analyze the association between various clinical factors and the WG classification of DFUs.\n\n\nResults\n\nThe study cohort featured a substantial majority of T2DM cases at 96.8% (n=853) with a male predominance of 59% (n=520). The mean age was 58 years, and the cohort typically displayed characteristics of being overweight or obese, with a mean BMI of 30.00 kg/m2. The average duration of diabetes among the participants was 14.0 years as illustrated in Table 1.\n\nBiochemical assessments shown in Table 2 yielded a mean serum creatinine of 0.92 mg/dL, blood urea of 33.71 mg/dL, and estimated Glomerular Filtration Rate (GFR)of 88.38 mL/min/1.73m2. The fasting and random plasma glucose averages were 168.3 mg/dL and 289.3 mg/dL, respectively. Notably, poor glycemic control was observed in 72.3% of participants with a mean HbA1c level of 10.26%. The lipid profile revealed mean serum cholesterol and triglyceride levels of 186.2 mg/dL and 209.78 mg/dL, respectively.\n\nDFU characteristics included ulcers predominantly on the right foot (48%), left foot (46%), or both feet (6%) (Figure 1). According to Wagner’s grading, most ulcers were categorized as grade 1 (31%) and grade 2 (49%), with fewer instances of grades 3 through 5, which include more severe complications like deep infections, gangrene, and bone involvement (Figure 2).\n\nThe study found statistically significant relationships for Wagner's DFU classification only with random plasma glucose levels and the presence of diabetic retinopathy as in Table 3. Other factors such as age, BMI, smoking status, family history, duration of diabetes, lipid profile, and presence of comorbid conditions like hypertension, ischemic heart disease, heart failure, and stroke showed no significant associations with Wagner's classification severity.\n\n\nDiscussion\n\nThe ever-rising costs and occurrence rates of diabetes have contributed to DFUs being a leading cause of DM-related hospitalizations.11 DFUs serve as strong indicators for increased mortality rates in diabetic patients due to cardiovascular or other diabetes-related complications.12 Consistent with other research, the current study found a higher male prevalence, which can be partially attributed to occupational differences between genders.6 However, some studies exhibit a female majority, possibly due to disparities in health care access.13\n\nOur research identified a significant association between DFUs and both random blood sugar levels and diabetic retinopathy (DRP), congruent with findings from other studies that associated DFUs with peripheral vascular disease (PVD) and neuropathy.14 A similar correlation was highlighted in an Indonesian study regarding the significance of random blood sugar in the context of DFUs.15\n\nWhile the current study did not observe a significant association between HbA1c levels and DFU severity, the high percentage of poor glycemic control among participants indicates the impact of diabetes management on the genesis of DFUs. This is supported by other studies that link HbA1c with the severity of Wagner grading.16 Contrary to some research confirming the impact of diabetes duration on DFU development,16 our study and a Malaysian report found no significant correlation, potentially due to different methodologies and duration benchmarks.17\n\nOur findings regarding renal function (eGFR) showed no significant correlation with DFU severity, which contrasts with a Taiwanese study that confirmed such a correlation, especially for severe ulcers and lower limb amputations.18 The difference may be due to our center treating CKD patients externally in nephrology wards, which could have influenced the recorded data.\n\nMost of our study's patients presented with grade 2 and grade 1 DFUs, reflecting trends observed in Iranian studies. This similarity suggests comparable healthcare practices and societal structures between the two neighboring countries.13 Other research from Korea exhibited variations, which could be due to differences in treatment approaches, wound care protocols, and multidisciplinary teams.19\n\nThe substantial association of DFUs with diabetic retinopathy was also noted in studies from Ethiopia and Brazil.20,21 This link may be attributed to the impaired self-care abilities in those with DRP, leading to DFU development.22 Moreover, DRP frequently co-occurs with peripheral neuropathy, a well-recognized DFU risk factor.23 These findings suggest that ophthalmic evaluation could be beneficial for patients with severe DFU to detect potential complications at an early stage.\n\nDespite no significant statistical correlation between BMI and DFU severity, the majority of our patients were overweight or obese, which aligns with findings from African studies.20,24 Obesity is known to exacerbate atherosclerosis, a significant contributor to PVD, which plays a central role in the causation of DFUs.\n\nAge was not significantly associated with DFU severity in our study; however, a large portion of our patients were above 60 years old, highlighting age as a factor in the development of diabetic complications, particularly atherosclerotic and neuropathic ones. This is echoed in studies from Saudi Arabia, India, and Thailand,25–27 while an Ethiopian study found no significant correlation likely due to its inclusion of younger, newly diagnosed patients.20\n\nThe absence of a statistically significant correlation between DFU prevalence and family history of diabetes in our study contrasts with a Chinese study that confirmed such a link.28 This variance could stem from differences in populations, inadequate data collection, and the inability of many patients to recall family medical histories.\n\nMore than half of our patients had an FBS below 140 mg/dL, with no significant correlation between FBS and Wagner DFU grade, which may be due to our patients visiting the center in a fasting state and receiving regular FBS monitoring. This contradicts findings from an Indian study that noted a significant correlation.29\n\nOur findings showed no significant correlation between DFU severity and smoking, with most patients being nonsmokers, likely a result of ongoing education efforts about smoking's risks at our center. Other studies have also reported no significant association between smoking and DFU severity.14,30\n\nThere was no significant correlation between DFU severity and dyslipidemia in our study, whereas an Egyptian study found a significant link. These differing findings may be due to variations in patient populations and management strategies, as most of our patients were routinely treated with statins.31\n\nOur single-center study design presents some constraints in generalizing the findings, and there was insufficient documentation of certain clinical data, such as types of treatment, ulcer location, and peripheral pulse conditions, as well as Ankle-Brachial index measurements.\n\n\nConclusion\n\nDiabetic foot ulcers carry a heavy burden both in economic terms and human suffering. Despite advancements in treatment and increased awareness, DFUs remain a prevalent issue among those with diabetes, especially T2DM. The current research provides a much-needed local perspective on the characteristics of DFUs in Thi Qar, Iraq, highlighting the clinical and biochemical variables associated with these complications.\n\nOur research uniquely focuses on the T2DM population within a specific geographical location, which is essential for fostering strategies tailored to the local community. While random blood glucose and the presence of diabetic retinopathy had significant associations with the severity of DFUs according to Wagner's classification, other variables such as age, BMI, and the duration of diabetes did not demonstrate a meaningful correlation. This suggests the need for more comprehensive research involving larger, diverse populations and multiple centers to draw conclusions that are more widely applicable.\n\nThe data garnered from this study contribute to the understanding of DFU prevalence and highlight the need for strict glycemic control, management of diabetes complications, and targeted interventions to prevent DFU development and progression. With concerted efforts from healthcare providers, patients, and policymakers, it is hoped that the incidence of DFUs in Iraq and similar communities can be diminished, thereby reducing the overall burden of diabetes.\n\n\nEthics and consent\n\nThis cross-sectional observational study, approved by the ethical committee of TDEMC by the (approval number IQ.TDEMC.REG.125/35 on the 10th of December 2020), adhered to the Helsinki declaration and involved written informed consent from all participants.",
"appendix": "Data availability\n\nZenodo: Assessing the features of diabetic foot ulcers among individuals with type 2 diabetes mellitus in Thi Qar, Iraq, https://zenodo.org/doi/10.5281/zenodo.11187872. 32\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nSaeedi P, Petersohn I, Salpea P, et al.: Global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: Results from the International Diabetes Federation Diabetes Atlas, 9(th) edition. Diabetes Res. Clin. Pract. 2019; 157: 107843. PubMed Abstract | Publisher Full Text\n\nMargolis DJ, Jeffcoate W: Epidemiology of foot ulceration and amputation: can global variation be explained? Med. Clin. North Am. 2013; 97(5): 791–805. Publisher Full Text\n\nApelqvist J, Bakker K, van Houtum WH , et al.: International consensus and practical guidelines on the management and the prevention of the diabetic foot. International Working Group on the Diabetic Foot. Diabetes Metab. Res. Rev. 2000; 16 Suppl 1: S84–S92. PubMed Abstract | Publisher Full Text\n\nTaghipour M, Abi Kordadeh E, Eslami M: Review of biomechanical parameters of diabetic foot ulcers %J Razi. J. Med. Sci. 2016; 23(144): 51–67.\n\nBandyk DF: The diabetic foot: Pathophysiology, evaluation, and treatment. Semin. Vasc. Surg. 2018; 31(2-4): 43–48. Publisher Full Text\n\nZhang P, Lu J, Jing Y, et al.: Global epidemiology of diabetic foot ulceration: a systematic review and meta-analysis. Ann. Med. 2017; 49(2): 106–116. PubMed Abstract | Publisher Full Text\n\nBoulton AJ, Vileikyte L, Ragnarson-Tennvall G, et al.: The global burden of diabetic foot disease. Lancet. 2005; 366(9498): 1719–1724. Publisher Full Text\n\nLepäntalo M, Apelqvist J, Setacci C, et al.: Chapter V: Diabetic foot. Eur. J. Vasc. Endovasc. Surg. 2011; 42 Suppl 2: S60–S74. PubMed Abstract | Publisher Full Text\n\nAssociation AD: Standards of Medical Care in Diabetes—2013. Diabetes Care. 2012; 36(Supplement_1): S11–S66. Publisher Full Text\n\nAnichini R, Zecchini F, Cerretini I, et al.: Improvement of diabetic foot care after the Implementation of the International Consensus on the Diabetic Foot (ICDF): results of a 5-year prospective study. Diabetes Res. Clin. Pract. 2007; 75(2): 153–158. PubMed Abstract | Publisher Full Text\n\nDòria M, Rosado V, Pacheco LR, et al.: Prevalence of Diabetic Foot Disease in Patients with Diabetes Mellitus under Renal Replacement Therapy in Lleida, Spain. Biomed. Res. Int. 2016; 2016: 1–8. Publisher Full Text\n\nJeyaraman K, Berhane T, Hamilton M, et al.: Mortality in patients with diabetic foot ulcer: a retrospective study of 513 cases from a single Centre in the Northern Territory of Australia. BMC Endocr. Disord. 2019; 19(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGhobadi A, Ahmadi Sarbarzeh P, Jalilian M, et al.: Evaluation of Factors Affecting the Severity of Diabetic Foot Ulcer in Patients with Diabetes Referred to a Diabetes Centre in Kermanshah. Diabetes Metab. Syndr. Obes. 2020; 13: 693–703. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlonso-Fernández M, Mediavilla-Bravo JJ, López-Simarro F, et al.: Evaluation of diabetic foot screening in Primary Care. Endocrinol. Nutr. 2014; 61(6): 311–317. PubMed Abstract | Publisher Full Text\n\nJoeliantina A, Proboningsih J, Anugrahini HN, et al.: The Behavior of Patients with Type 2 Diabetes Mellitus in Monitoring Blood Glucose Levels and Foot Care: A Cross-sectional, Community-Based Study. Int. J. Adv. Health Sci. Technol. 2022; 2(2): 104–109. Publisher Full Text\n\nFarooque U, Lohano AK, Hussain Rind S, et al.: Correlation of Hemoglobin A1c With Wagner Classification in Patients With Diabetic Foot. Cureus. 2020; 12(7): e9199. PubMed Abstract | Publisher Full Text\n\nPurwanti OS, Yetti K, Herawati T: Duration of Diabetic Correlated Diseases With Diabetic Foot Ulcers at DR Moewardi Hospital of Surakarta.2016.\n\nSun JH, Tsai JS, Huang CH, et al.: Risk factors for lower extremity amputation in diabetic foot disease categorized by Wagner classification. Diabetes Res. Clin. Pract. 2012; 95(3): 358–363. PubMed Abstract | Publisher Full Text\n\nHwang DJ, Lee KM, Park MS, et al.: Association between diabetic foot ulcer and diabetic retinopathy. PLoS One. 2017; 12(4): e0175270. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAdem AM, Andargie AA, Teshale AB, et al.: Incidence of Diabetic Foot Ulcer and Its Predictors Among Diabetes Mellitus Patients at Felege Hiwot Referral Hospital, Bahir Dar, Northwest Ethiopia: A Retrospective Follow-Up Study. Diabetes Metab. Syndr. Obes. 2020; 13: 3703–3711. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSilva J, Haddad M, Rossaneis MA, et al.: Factors associated with foot ulceration of people with diabetes mellitus living in rural areas. Rev. Gaucha Enferm. 2017; 38(3): e68767. PubMed Abstract | Publisher Full Text\n\nIraj B, Khorvash F, Ebneshahidi A, et al.: Prevention of diabetic foot ulcer. Int. J. Prev. Med. 2013; 4(3): 373–376. PubMed Abstract\n\nRasheed R, Pillai GS, Kumar H, et al.: Relationship between diabetic retinopathy and diabetic peripheral neuropathy - Neurodegenerative and microvascular changes. Indian J. Ophthalmol. 2021; 69(11): 3370–3375. PubMed Abstract | Publisher Full Text\n\nSarfo-Kantanka O, Kyei I, Mbanya JC, et al.: Diabetes-related foot disorders among adult Ghanaians. Diabet. Foot Ankle. 2018; 9(1): 1511678. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFawzy MS, Alshammari MA, Alruwaili AA, et al.: Factors associated with diabetic foot among type 2 diabetes in Northern area of Saudi Arabia: a descriptive study. BMC. Res. Notes. 2019; 12(1): 51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbdissa D, Adugna T, Gerema U, et al.: Prevalence of Diabetic Foot Ulcer and Associated Factors among Adult Diabetic Patients on Follow-Up Clinic at Jimma Medical Center, Southwest Ethiopia, 2019: An Institutional-Based Cross-Sectional Study. J. Diabetes Res. 2020; 2020: 4106383.\n\nSarinnapakorn V, Sunthorntepwarakul T, Deerochanawong C, et al.: Prevalence of Diabetic Foot Ulcers and Risk Classifications in Type 2 Diabetes Mellitus Patients at Rajavithi Hospital. J. Med. Assoc. Thai. 2016; 99 Suppl 2: S99–S105. PubMed Abstract\n\nXiong XF, Wei L, Xiao Y, et al.: Family history of diabetes is associated with diabetic foot complications in type 2 diabetes. Sci. Rep. 2020; 10(1): 17056. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGanesh V: Study of diabetic foot patients with correlation of blood sugar levels in Bengaluru rural district. Int. J. Biochem. 2021; 18(1): 01–04. Publisher Full Text\n\nDhatariya KK, Li Ping Wah-Pun Sin E, Cheng JOS, et al.: The impact of glycaemic variability on wound healing in the diabetic foot - A retrospective study of new ulcers presenting to a specialist multidisciplinary foot clinic. Diabetes Res. Clin. Pract. 2018; 135: 23–29. PubMed Abstract | Publisher Full Text\n\nAbdAllah AM, Sharafeddin MJZUMJ: Lipid Profile Disorders And Diabetic Foot Risk; Is There A relationship between Them?2022; 28(6.1): 217–225.\n\nMohammed AG: Assessing the features of diabetic foot ulcers among individuals with type 2 diabetes mellitus in Thi Qar, Iraq. [Dataset]. Zenodo. 2024. Publisher Full Text"
}
|
[
{
"id": "284113",
"date": "01 Jul 2024",
"name": "Nassar Alibrahim",
"expertise": [
"Reviewer Expertise Diabetes",
"Endocrine and Metabolism"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFirst I would like to express my admiration for the well written article and the effort carried out by the authors, specially in the important area of the diabetic foot ulcers globally having its important negative impact on the patients life as well as the society.\nI have only some minor points to be discussed:\n1-Looks like the limitations of the study was mentioned twice in the text.\n2- In Table 1: For the sake of a easier readability, the variables better to be grouped like : IHD,HF,CVA,HF in one group , and amputation, osteomyelitis, charcot , wheel chair in another group and so on. or you can arrange them alphabetically.\n3-In Table 3 : a)You need to mention the percentages within the variable cells as well, so the comparisons can be easily visible. b)The p value mentioned actually represent the interactive p value for all Fields, was it possible to calculate each group p value vertically and horizontally ? looking for a specific relationship between any variable category and any WG severity ?, like the significance of being obese and the development of WG5 ? c)The significant finding of the association between RBS and WG severity need to be clarified in the text, is it the RBS is > 200 (as you can see all the numbers are higher than those in the categories of 200 and less,or the trend is decreasing toward progressing from WG1 to WG5). This should be mentioned in the text for clarification. d)Again you need to clarify the meaning of DRP significant association with WG, for example does the presence of DRP means a more severe or less severe DFU ?, though the trend looks decreasing.\n4-In the conclusion section: the first paragraph in the conclusion better to be part of the introduction section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11952",
"date": "03 Jul 2024",
"name": "Adel Gassab Mohammed",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for taking the time to review our article. We appreciate your kind words regarding the effort put forth by the authors in addressing the global issue of diabetic foot ulcers, and we are glad to hear that you found the article well-written. Regarding your minor points: 1. We acknowledge the duplication in mentioning the limitations of the study within the text. We will address this issue by ensuring that the limitations are presented only once in the revised version of the manuscript. 2. We appreciate your suggestion for improving the readability of Table 1 by grouping the variables for easier comprehension. While we understand the importance of this suggestion, we have decided to maintain the current format of Table 1 without any changes at this point. However, we will keep your feedback in mind for future revisions and improvements. Once again, thank you for your valuable feedback and constructive comments. Should you have any further suggestions or concerns, please feel free to share them with us. Best regards, [Adel Gassab Mohammed]"
}
]
}
] | 1
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https://f1000research.com/articles/13-539
|
https://f1000research.com/articles/12-726/v1
|
21 Jun 23
|
{
"type": "Research Article",
"title": "The disinfection effectiveness of ozone water and 4.8% chloroxylenol against the number of bacterial colonies in dental extraction instruments at the USU Dental and Oral Hospital in October-December 2022",
"authors": [
"Hendry Rusdy",
"Rahmi Syaflida Dalimunthe",
"Ahyar Riza",
"Ismahani Akilah D",
"Rahmi Syaflida Dalimunthe",
"Ahyar Riza",
"Ismahani Akilah D"
],
"abstract": "Background: The application of disinfectants on dental instruments is one way to prevent cross-infection. Cross infection can occur due to microorganisms found in blood, saliva and dental plaque which can contaminate the instruments used by dental health workers. Thus, indirect contact transmission of pathogenic microorganisms occurs from instruments that have been contaminated by dental health workers. Ozone water and 4.8% chloroxylenol are disinfecting agents used to disinfect medical instruments. This study aimed to determine the effectiveness of disinfection of ozone water and 4.8% chloroxylenol\n\nin reducing the number of bacterial colonies on dental extraction instruments at the USU Dental and Oral Hospital between October-December 2022. Methods: The samples used were mandibular molar pliers that have been used in tooth extraction procedures. This study was experimental and used three sample groups, where each group consisted of 10 tooth extraction instruments. The treatment group used ozone water and 4.8% chloroxylenol\n\nand the negative control group was cleaned with distilled water. The test effectiveness in this study used bacteria colony counter using the scatter cup method. Data were analyzed using the Kruskal Wallis and Mann-Whitney U tests. Results: The results of the data analysis showed a p-value ≤0.001, which means that there was a significant difference in the disinfection using ozone water and 4.8% chloroxylenol\n\non the number of bacterial colonies on dental extraction instruments. The results of this study show that the average number of bacterial colonies formed in the ozone water treatment group was 4.00 ± 4.32, 16.00 ± 6.65 in the 4.8% chloroxylenol treatment group, and 217.50 ± 39.24 in the negative control group (Aquadest). Conclusions: From this study it can be said that ozone water is more effective in disinfecting dental extraction instruments than 4.8% chloroxylenol.",
"keywords": [
"Ozone water",
"Chloroxylenol",
"Bacterial Colony"
],
"content": "Introduction\n\nDental health workers are a group that is vulnerable to infection.1,2 In dental practice, microorganisms can spread through blood, saliva or droplets through direct or indirect contact. One route of cross-infection due to indirect contact is tooth extraction instruments that have been contaminated with pathogenic microorganisms.2–4\n\nTooth extraction procedures have a high risk of infection transmission due to contact of the instruments with the patient’s blood and saliva. These must be aseptic at the time of tooth extraction to avoid bacterial infection, which is one of the complications that can occur as a result of tooth extraction.5–7\n\nIf the tooth extraction instrument is contaminated, microorganisms can be transmitted to dentists, nurses or other patients who will be infected with diseases. According to the American Dental Association (ADA), it is estimated that dentists and patients may be exposed to around 40 types of infectious diseases when carrying out dental treatment procedures. Therefore, it is necessary to exercise prevention by disinfecting dental extraction instruments.3,5\n\nAlternative materials for disinfection in dentistry have been developed. Ozone water can function as a disinfectant with the ability to oxidize amino acids and destroy proteins in the cellular membranes of microorganisms.8 Ozone water has the ability to kill pathogenic microorganisms and the resulting wastewater is safe to enter waterways.9 Chloroxylenol or para-chloro-meta-xylenol (PCMX) is a chemical-level disinfectant commonly used to disinfect skin and surgical instruments in dentistry. 4.8% chloroxylenol has a broad-spectrum antibacterial ability that can kill most bacteria and fungi. 4.8% chloroxylenol works by denaturing proteins, changing the permeability of cell walls and causing cell leakage. 4.8% chloroxylenol is one of the most widely used disinfectants in dentistry. 4.8% chloroxylenol is one of the phenol groups, and works by denaturing proteins, changing the permeability of cell walls and causing cell leakage.10–12\n\nResearch on the effectiveness of ozone water (10 mg/L) as a disinfection agent on diamond burs that have been contaminated by S. aureus, E. coli, C. albicans and spores of B. atrophaeus showed a reduction of microorganisms by 90.15-99.33%.9 Research on the effectiveness of 4.8% chloroxylenol as a disinfecting agent showed its ability to interfere with the metabolic activity of Gram-positive bacteria at 38.9% concentration and Gram-negative at 60.7% concentration.13\n\nThis study aimed to compare the effectiveness of ozone water and 4.8% chloroxylenol disinfectants on tooth extraction instruments, because tthese critical instruments have a high risk of causing infection as they penetrate the mucous membranes of the oral cavity.14\n\n\nMethods\n\nThis research was a laboratory experimental research with post-test only control group designs.\n\nUSU Dental and Oral Hospital, laboratory of Microbiology, Faculty of Pharmacy, Mathematics and Natural Science University of Sumatera Utara, Medan, Indonesia.\n\nThe study duration was about 3 months, from October to December 2022.\n\nThe sampling technique used in this study was purposive sampling with 30 mandibular molar tooth extraction pliers as the sample. There were three treatment groups, namely the ozone water treatment group, the 4.8% chloroxylenol treatment group and the negative control (Aquadest) with 10 jaw molar tooth extraction forceps in each treatment group.\n\nOzone water was prepared using an ozone generator for 20 minutes with an ozone water concentration of 15 mg/L.15\n\nIn the ozone water and 4.8% chloroxylenol treatment group, the mandibular molar tooth extraction pliers were rinsed under running water, brushed with an antiseptic solution and rinsed again until the pliers were free of blood and saliva before soaking in a disinfecting solution.14,16 After that, the mandibular molar tooth extraction forceps were soaked in ozonized water for 30 minutes and then a sample was taken.9 In the 4.8% chloroxylenol treatment group, mandibular molar extraction pliers were soaked for 60 minutes and then samples were taken.13 In the negative control group (Aquadest) the pliers were rinsed with distilled water, then a sample was taken.\n\nSampling was carried out by immersing mandibular molar extraction pliers in a container containing 250 mL of saline solution for five minutes, then the container was closed and labeled for each sample.13 Group label for ozonized water was Z, 4.8% chloroxylenol was K, and distilled water was A.\n\nThe samples were then taken to the Faculty of Pharmacy, Mathematics and Natural Science, University of Sumatera Utara, to count the number of bacterial colonies. Samples were diluted using NaCl as much as 103, then implanted in a petri dish containing plant count agar (PCA) media, using the spread plate method. Spreads method plate is a technique for growing microorganisms in agar media for the purpose of isolating or counting the bacteria present. The sample was spread using a sterile spreader, and the petri dish was rotated at an angle of 45° above a Bunsen burner.17 After that, the petri dishes were incubated in the incubator for 24 hours. Following this, the number of bacterial colonies were counted using a bacterial colony counter.13\n\nData analysis was performed using the SPSS version 22.0 software. The normality of the data was tested using the Shapiro-Wilk test, since the number of samples less than 50. The results of the data normality test showed that the data were not normally distributed, with p-values with a degree of significance < 0.05; therefore the next test used was the non-parametric Kruskal Wallis test followed-up by Mann-Whitney U test with a significance degree of p ≤ 0.05, to find out which treatment group had the best effectiveness as a disinfecting agent.\n\n\nResults\n\nThis study consisted of 30 mandibular molar extraction forceps with three treatment groups, namely the mandibular molar extraction forceps group which was disinfected with ozonized water (Z), the mandibular molar forceps group which was disinfected with 4.8% chloroxylenol solution (K), and the mandibular molar pliers group which was rinsed with distilled water (A) as a negative control. Each group consisted of 10 mandibular molar extraction forceps.\n\nThe 10 mandibular molar-removing forceps which were disinfected with ozonized water had a mean bacterial count of 4.00 ± 4.32 CFU/mL, showing they were still contaminated with pathogenic microorganisms with the highest number of bacterial colonies being 11 · 103 CFU/mL. The10 forceps which were disinfected with 4.8% chloroxylenol had a mean bacterial count of 16.00 ± 6.65 CFU/mL, showing they were still contaminated with pathogenic microorganisms, with the highest number of bacterial colonies being 27 · 103 CFU/mL. Meanwhile, the mean bacterial count in the negative control group (Aquadest) the 10 pliers extracting mandibular molars showed 217.50 ± 39.24 CFU/mL still forming bacterial colonies, with the highest number of bacterial colonies being 292 · 103 CFU/mL (Table 1).\n\nBased on the Kruskal Wallis statistical test results the effectiveness of ozone water, 4.8% chloroxylenol and negative control (Aquadest) on the number of bacterial colonies in mandibular tooth extraction forceps was significantly different, with a significance value of p = 0.000 (p < 0.05) (Table 2).\n\nBased on the results of a further using Mann-Whitney U test comparing disinfection effectiveness between groups treated with ozone water disinfection and negative control (Aquadest), the significance value was p = 0.000 (p < 0.05). Ozone water was more effective as a disinfection agent compared to negative control on the number of bacterial colonies in dental extraction instruments at the USU Dental and Oral Hospital, as indicated by the lower average value of bacterial counts in the ozone water group, which was 4.00 ± 4.32 CFU/mL, whereas for the negative control group (Aquadest) the value was 217.50 ± 39.24 (Table 3).\n\nFurther Mann-Whitney U test results showed that there was a significant difference between the effectiveness of disinfection between groups treated with 4.8% chloroxylenol and negative control with a significance value of p = 0.000 (p < 0.05). 4.8% chloroxylenol was more effective as a disinfecting agent compared to negative control on the number of bacterial colonies in dental extraction instruments. The USU indicated that the average bacterial count value of the 4.8% chloroxylenol group was lower with 16 ± 6.65 CFU/mL, while the value for the negative control group was 217.50 ± 39.24 (Table 4).\n\nFurther Mann-Whitney U test results showed that there was significant difference in effectiveness between ozone water and 4.8% chloroxylenol with a significance value of p = 0.000 (p < 0.05). Ozone water was more effective as a disinfection agent compared to 4.8% chloroxylenol against bacterial colonies on dental extraction instruments, as indicated by the lower average bacterial count value of the ozone water group which was 4.00 ± 4.32 CFU/mL, while for the disinfection treatment group with 4.8% chloroxylenol, the value was 16 ± 6.65 CFU/mL (Table 5).\n\nBased on the results of data analysis from each treatment group, it was shown that ozone water was significantly more effective in disinfecting mandibular molar tooth extraction forceps compared to chloroxylenol 4.8% and negative control. Instruments in the 4.8% chloroxylenol group showed a smaller number of bacterial colonies than the negative control (Figure 1).\n\n\nDiscussion\n\nThis study compared two disinfection solutions, namely ozone water and 4.8% chloroxylenol. Ozone water is a strong alternative to disinfectants and effectively kills pathogenic microorganisms such as bacteria, viruses, fungi, protozoa, and endospores. Ozone is more effective against large numbers of microorganisms because of its ability to oxidize microorganisms without causing resistance.16 Ozone can inhibit the control of enzymes and therefore act on bacterial cell metabolism and damage bacterial cell membranes. Ozone water disrupts the integrity of the bacterial cell envelope through the oxidation of phospholipids and lipoproteins.18–20\n\nIn this study, the concentration of ozone water used was 15 mg/L, with a soaking time of 30 minutes. The use of ozone water as a material for disinfecting dental instruments was recommended at a concentration of 10-20 mg/L.10 As reported by previous research, a concentration of ozone water that is too low showed a reduction in the antibacterial effectiveness of ozone water, while a concentration that is too high and exposure for too long could cause toxicity. Ozone maintained its antibacterial properties for the first 20 minutes, and after 30 minutes the stability of ozone water slowly decreased. After eight hours, there was no more ozone in the ozonized water.10,21,22\n\nBased on the data on the number of bacterial colonies in the treatment group with ozone water samples, ozone water was more effective in disinfecting the mandibular molar forceps. It was observed that four out of 10 mandibular molar extraction forceps were successfully decontaminated, with six samples showing bacterial growth with the highest number of bacteria being 11 × 103 CFU/mL. The number of bacterial colonies in the treatment group with ozone water was the lowest when compared to the other two treatment groups, with an average value of 4.00 ± 4.32. This is due to the greater efficiency of ozone water in killing bacterial endospores by oxidizing and damaging the bacterial membrane which contains lipoproteins and fatty acids, so that the bacteria experience failure in the germination process.21–23\n\nIn contrast, 4.8% chloroxylenol is unable to kill bacterial endospores, therefore 4.8% chloroxylenol is still classified as a medium-level chemical disinfection. This makes ozone water more effective in killing microorganisms when compared to 4.8% chloroxylenol according to César et al., 2012,10 who stated that the antimicrobial activity of ozone water against B. atrophaeus spores resulted in a decrease in growth of 90.15% and 98.74% after 10 and 30 minutes of exposure to ozone water, respectively. In this study, the average number of bacterial colonies in the ozone water treatment group was lower due to the ability of the ozone water to kill bacterial endospores. Endospora are very resistant to high temperatures, extreme environmental conditions or chemicals. The ability of ozone water to kill bacterial endospores was likely one of the causes of the fewer bacterial colonies formed in the ozone water treatment group. Data from César et al.10 also shows that the use of ozonated water (10 mg/L) for 30 minutes was effective for disinfection of diamond burs that have been contaminated by S. aureus, E. coli, C. albicans and spores of B. atrophaeus, reducing bacterial contamination by 90.15-99.33%. In addition, based on Bezirtzoglou et al. found in the research of César et al. states that a few teeth that have been soaked for 30 minutes with ozone water showed no bacterial colonies formed on the toothbrush. In the research by Martinelli et al., 2017, the addition of ozone to water that has been inoculated with S. aureus showed a reduction of 98.9%; S. faecalis, P. aeruginosa respectively were respectively reduced by 64.2% and 57.4%.15 According to Xiao Hu et al., 2021, ozone water can eliminate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with an ozone concentration above 18 mg/L within one minute.24 Wen et al. stated that ozone water can reduce fungal spores by 50.7-91.2%.25 Thus, ozone water has the ability to kill microorganisms in the form of bacteria, viruses, fungi, and bacterial endospore.\n\nIn the 4.8% chloroxylenol treatment group, there was bacterial growth in all mandibular molar tooth extraction forceps with a lower value compared to ozone water, but the number of bacterial colonies formed was less than the negative control. The mean bacterial count value in the 4.8% chloroxylenol group was 16.00 ± 6.65, while for the negative control group the value was 217.50 ± 39.24. The research by Riza et al. in 2018 showed 11 out of 18 mandibular molar tooth extraction forceps which were cleaned using 4.8% chloroxylenol did not form bacterial colonies, and seven mandibular molar tooth extraction forceps had a maximum bacterial count of 812 · 103 CFU/mL and the average number of bacterial colonies formed was 82.5.13 This is in accordance with the results of this study: in all research samples bacterial colonies still formed although with fewer bacterial colonies on average. Guther et al., 2020, who conducted research on the skin and the hospital environment, found that 4.8% chloroxylenol could interfere with the metabolic activity of Gram-positive bacteria by 38.9% and Gram-negative by 60.7%.14 Igizeneza et al., 2020, showed that 4.8% chloroxylenol was effective in killing 100% isolates of Staphylococcus sp. and Streptococcus sp.12 Thus, 4.8% chloroxylenol was able to kill pathogenic microorganisms, but its effectiveness is lower when compared to ozone water. The -OH hydroxyl group of the 4.8% chloroxylenol molecule binds to proteins in the bacterial cell membrane to disrupt it, thereby allowing the contents of the bacterial cell to leak. This allows 4.8% chloroxylenol to enter the bacterial cell to bind more proteins and enzymes and deactivate cell functions.26 Meanwhile, the negative control group (Aquadest) had lethal effect on microorganisms because distilled water is a neutral organic compound used as a pure solvent and doees not have antibacterial activity.27\n\nDifferences in the number of bacterial colonies can also be caused by several factors, one of which is the number of microorganisms and contaminants, the condition of the patient’s oral cavity, the number and type of normal flora in the oral cavity of each patient which can differ due to severe caries, periodontal disease, pulpal necrosis or abscess. at the time of tooth extraction.12 Disinfectants have different abilities and susceptibility depending on the number and type of bacteria present in the patient’s oral cavity; the duration of exposure and the concentration of the disinfecting agents also affect the ability to kill microorganisms.28,29 The decrease in the number of different bacterial colonies in each treatment is also influenced by open environmental conditions, environmental temperature and humidity both during sampling and when processing samples in the laboratory, ozone generator output and operator negligence.30\n\n\nConclusions\n\nOzone water was significantly more effective in disinfecting dental extraction instruments at USU Dental and Oral Hospital than 4.8% chloroxylenol with a significance value of p = 0.000 (p < 0.05). Ozone water is able to kill up to bacterial endospore while 4.8% chloroxylenol is not able to so it is still classified as a medium level disinfectant.",
"appendix": "Data availability\n\nZenodo: The Data Set “Ozone Water And 4.8% Chloroxylenol Against The Number Of Bacterial Colonies In Dental Extraction Instruments at The USU Dental and Oral Hospital”, https://doi.org/10.5281/zenodo.7950593. 31\n\nThis project contains the following underlying data:\n\n• Raw data of total plate count aquades.csv (Raw data of total plate count aquades)\n\n• Raw data of total plate count choloroxylenol- Sheet1.csv (Raw data of total plate count 4.8%choloroxylenol)\n\n• Raw data of total plate count.ozone water.csv (Raw data of total plate count.ozone water)\n\n• Result of Normalitas Test.csv (raw data of result of normalitas test with shapiro wilk)\n\n• Result of Kruskal wallis test.csv (raw data of result of kruskal wallis)\n\n• Result of comparison ozone water and Choloroxylenol.csv (raw data of result of comparison ozon water and 4,8% chloroxylenol)\n\n• Result of Comparison Choloxylenol and Aquades.csv (raw data of result of comparison 4,8%chloroxylenol and aquades)\n\n• Result of Comparison ozone water and Aquades.csv (raw data of result of comparison ozone water and aquades)\n\n• Z1-10.rar (image of colony bactery plate of ozone water)\n\n• Choloroxylenol.jpg (image of colony bactery plate of 4,8% chloroxylenol)\n\n• Aquades.jpg (image of colony bactery plate of aaquades)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nAn earlier version of this article can be found in the authors’ institutional repository at https://repositori.usu.ac.id/handle/123456789/83488 .\n\n\nReferences\n\nInayati E, Indiani SR, Gofur NRP: Prevention and Control of Cross Infection At Dental Laboratories in East Java Province of Indonesia. J Vocat Heal Stud. 2021; 4(3): 125. Publisher Full Text\n\nMenawi W, Sabbah A, Kharraz L: Cross-infection and infection control in dental clinics in Nablus and Tulkarm districts. BMC Microbiol. 2021; 21(1): 311–352. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbrahim NK, Alwafi HA, Sangoof SO, et al.: Cross-infection and infection control in dentistry: Knowledge, attitude and practice of patients attended dental clinics in King Abdulaziz University Hospital, Jeddah, Saudi Arabia. J Infect Public Health. 2017; 10(4): 438–445. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHutajulu Y, Hutagalung MHP, Molek M: Tindakan pencegahan infeksi silang kepaniteraan klinik mahasiswa di RSGM Universitas Prima Indonesia. J Prima Med Sains. 2021 Sep 29; 3(1): 14–17. Publisher Full Text\n\nSuleh MM, Wowor VNS, Mintjelungan CN: Pencegahan Dan Pengendalian Infeksi Silang Pada Tindakan Ekstraksi Gigi Di Rumah Sakit Gigi Dan Mulut Pspdg Fk Unsrat. e-GIGI. 2015; 3(2). Publisher Full Text\n\nWinarti S, Peristiowati Y, Siyoto S: Analysis of Patient Safety Management Implementation Towards the Occurrence of Post-Tooth Extraction Infection in Oral Surgery Clinic at RSGM IIK Bhakti Wiyata Kediri. J Qual Public Heal. 2018; 2(1): 17–24. Publisher Full Text\n\nSamaranayake L: Essential Microbiology For Dentistry. 4th ed.China: Elsevier; 2012; 326–342.\n\nCenters for Disease Control and Prevention: Summary of Infection Prevention Practices in Dental Settings: Basic Expectations for Safe Care. Atlanta, GA: Centers for Disease Control and Prevention, US Dept of Health and Human Services; 2016. Reference Source\n\nSukarminah E, Djali M, Andoyo R, et al.: Ozonization Technology and Its Effects on The Characteristics and Shelf-life of Some Fresh Foods: A Review. KnE Life Sci. 2017; 2(6): 459. Publisher Full Text\n\nCésar J, Sumita TC, Junqueira JC, et al.: Antimicrobial effects of ozonated water on the sanitization of dental instruments contaminated with E. coli, S. aureus, C. albicans, or the spores of B. atrophaeus. J Infect Public Health. 2012 Aug; 5(4): 269–274. Publisher Full Text\n\nNational Center For Biotechnology Information: Chloroxylenol.31 Juli 2022. Reference Source\n\nAcsa I, Lilly Caroline B, Philip Njeru N, et al.: Preliminary Study on Disinfectant Susceptibility/Resistance Profiles of Bacteria Isolated from Slaughtered Village Free-Range Chickens in Nairobi, Kenya. Int J Microbiol. 2021; 2021: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRiza A, Siregar IB, Isnandar B: Comparison of effectiveness disinfection of 2% glutaraldehyde and 4.8% chloroxylenol on tooth extraction instruments in the Department of Oral Maxillofacial and Surgery, Faculty of Dentistry, University of North Sumatera. J Dentomaxillofacial Sci. 2018 Dec 1; 3(3): 169. Publisher Full Text\n\nGünther F, Blessing B, Dapunt U, et al.: Ability of chlorhexidine, octenidine, polyhexanide and chloroxylenol to inhibit metabolism of biofilm-forming clinical multidrug-resistant organisms. J Infect Prev. 2021; 22(1): 12–18. Publisher Full Text\n\nMartinelli M, Giovannangeli F, Rotunno S, et al.: Water and air ozone treatment as an alternative sanitizing technology.\n\nSulistiani S, Fitriana NE, Nurwanti W: Sterilisasi Alat Kedokteran Gigi Dengan Sterilisator (Dry Heat) Dan Teknik Boiling. JDHT J Dent Hyg Ther. 2021; 2(1): 34–38. Publisher Full Text\n\nDevika M, Bhuvaneshwari G, Mohanram K: Comparative Study of Membrane Filtration and Spread Plate Technique for Dialysis Water Analysis. Saudi J Pathol Microbiol. 2019; 04(09): 649–653. Publisher Full Text\n\nCabrera Jova M, González JE: Ozone as an Alternative for Disinfection of Explants during in vitro Mass Plant Propagation. Ozone Sci Eng. 2014; 36(5): 435–439. Publisher Full Text\n\nGray NF: Chapter Thirty-Three - Ozone Disinfection.Percival SL, Yates MV, Williams DW, et al., editors. Microbiology of Waterborne Diseases (Second Edition). Second ed.London: Academic Press; 2014; pp. 599–615. Reference Source\n\nChoi D, Oh S: Removal of chloroxylenol disinfectant by an activated sludge microbial community. Microbes Environ. 2019; 34(2): 129–135. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGrignani E, Mansi A, Cabella R, et al.: Safe and Effective Use of Ozone as Air and Surface Disinfectant in the Conjuncture of Covid-19. Gases. 2020 Dec 24; 1(1): 19–32. Publisher Full Text\n\nSwanson TJ, Jamal Z, Chapman J: Ozone Toxicity. (30 Desember 2022). Reference Source\n\nWood JP, Wendling M, Richter W, et al.: The use of ozone gas for the inactivation of Bacillus anthracis and Bacillus subtilis spores on building materials. PLoS One. 2020; 15(5): e0233291–e0233215. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu X, Chen Z, Su Z, et al.: Ozone Water Is an Effective Disinfectant for SARS-CoV-2. Virologica Sinica. Vol. 36. . Science Press; 2021; pp. 1066–1068.\n\nWen G, Liang Z, Xu X, et al.: Inactivation of fungal spores in water using ozone: Kinetics, influencing factors and mechanisms. Water Res. 2020; 185: 116218. PubMed Abstract | Publisher Full Text\n\nMa K, Zhou L, Bai Y, et al.: Degradation and mechanism analysis of chloroxylenol in aqueous solution by gas-liquid discharge plasma combined with ozonation. RSC Adv. 2021; 11(21): 12907–12914. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWahyuni, Karim SF: Uji Aktivitas Antibakteri Ekstrak Etanol Daun Kacapiring (Gardenia jasminoides Ellis) terhadap Bakteri Streptococcus mutans. J Sains dan Inform. 2020; 4(4): 399–404.\n\nMartínez-Sánchez PG, Water O: Background, General Use In Medicine And Preclinic Support. 2019. Ozone Ther Glob J. 2019; 9(1): 33–45.\n\nLeksanawati IF, Budiyono S: Glutaraldehid sebagai alternatif untuk bahan sterilisasi alat medis di rumah sakit. J Kesehat Masy. 2020; 8(6): 846–854. Reference Source\n\nTyas SA, Rustanti I, Rokhmalia F: Efektivitas Desinfektan Terhadap Kualitas Angka Kuman Lantai Dan Dinding Ruang Laboratorium Pcr Rumah Sakit Jiwa Menur. Ruwa Jurai: Jurnal Kesehatan Lingkungan. 2022; 16(2): 57. Publisher Full Text\n\nHendry Rusdy IAD: The Data Set “Ozone Water And 4.8% Chloroxylenol Against The Number Of Bacterial Colonies In Dental Extraction Instruments at The USU Dental and Oral Hospital”.2023 Mar 25 [cited 2023 Mar 26]. Publisher Full Text"
}
|
[
{
"id": "193467",
"date": "08 Aug 2023",
"name": "Shorouq Abass",
"expertise": [
"Reviewer Expertise Prosthodontics",
"dental materials",
"disinfection and dental implant."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe research needs careful attention to the following:\nPlease reduce the words number of the research title “ The disinfection effectiveness of ozone water and 4.8% chloroxylenol against the number of bacterial colonies in dental extraction instruments at the USU Dental and Oral Hospital in October-December 2022” in to at least 12 words number.\n\nIn introduction you stated that “This study aimed to compare the effectiveness of ozone water and 4.8% chloroxylenol disinfectants on tooth extraction instruments, because these critical instruments have a high risk of causing infection as they penetrate the mucous membranes of the oral cavity” As shown in the bolded text you didn’t specify the concentration of the ozone in the water, so please correct it.\n\nIn method and in subheading “Sampling” you stated that “The sampling technique used in this study was purposive sampling with 30 mandibular molar tooth extraction pliers as the sample….” As shown in the bolded text you didn’t specify the sample collection technique, please correct it.\n\nIn method and in subheading “Ozone water production” you stated that “Ozone water was prepared using an ozone generator for 20 minutes with an ozone water concentration of 15 mg/L” as shown in the bolded text you didn’t specify the ozone generation method, please correct it.\n\nIn method and in the subheading “Disinfection procedure” you stated that “In the ozone water and 4.8% chloroxylenol treatment group, the mandibular molar tooth extraction pliers were rinsed under running water, brushed with an antiseptic solution and rinsed again until the pliers were free of blood and saliva before soaking in a disinfecting solution…” as shown in the bolded text you didn’t specify the time and the duration of rinse with water, method of brush, type of antiseptic, please correct it. Also you stated that “After that, the mandibular molar tooth extraction forceps were soaked in ozonized water for 30 minutes and then a sample was taken ..” how you take the sample , please correct it with details.\n\nIn method and in subheading “Counting bacterial colonies” you stated “……… a bacterial colony counter” as shown in the yellow highlight you didn’t specify the type of the counter and the type of bacteria or otherwise your test is not specified to specific type of bacteria and you only have a negative or positive growth.\n\nIn the result section your SD was too high more than 2, please can you state why?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "207744",
"date": "09 Oct 2023",
"name": "Paulo J. Palma",
"expertise": [
"Reviewer Expertise Dentistry",
"infection control"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe present study aimed to determine the effectiveness of disinfection of ozone water and 4.8% chloroxylenol in reducing the number of bacterial colonies on dental extraction instruments at the USU Dental and Oral Hospital between October-December 2022..\nThis research is under the scope of this journal; the topic is relevant for readers, and this research deals with potentially significant knowledge of the field. And It will be important for knowledge. The topic is relevant for readers and this review deals with potentially significant knowledge in the field and opens new ways for future studies.\nHowever, there are some aspects that are possibly improved in the manuscript:\nKeywords\nPlease add more keywords, and order the keywords / Mesh terms alphabetically\nIntroduction\nWhat is the importance of this study? Which results are comparable with other articles? What has this study been new?\nM&M\nA flowchart of all experimental study would be valuable.\n\nHow many slides per sample obtained, and how many of them were evaluated? How were the sample cells calculated? Did authors performed power analysis to evaluate if this sample size was appropriate?\nAnalysis:\nHow many observers did the scoring? What is the interobserver agreement? How many time was performed done the determinations?\n\nWhich data are parametric and non-parametric? Please specify?\n\nWhen mentioning materials or devices: for some of them you don't mention the manufacturer at all, for some you mention only the manufacturer, for some the manufacturer and city, for some you mention the manufacturer and city/ country.\nDiscussion\n\nPlease, clarified more limitations of this study?\n\nAn objective presentation of the strengths and limitations of the model, study design and methods, must be provided, including any biology/functional variability between the animal model and humans.\n\nAnd also clarified the future perspectives in the discussion. The potential influence of the results on future research plans needs also be discussed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-726
|
https://f1000research.com/articles/12-393/v1
|
13 Apr 23
|
{
"type": "Systematic Review",
"title": "Clinical efficacy of titanium prepared platelet rich fibrin in periodontal regeneration: A systematic review and meta-analysis",
"authors": [
"Dr. Ranu Oza",
"Dr. Prasad Dhadse",
"Dr. Pavan Bajaj",
"Dr. Komal Bhombe",
"Dr. Khushboo Durge",
"Dr. Chitrika Subhadarsanee",
"Dr. Safiya Hassan",
"Dr. Prasad Dhadse",
"Dr. Pavan Bajaj",
"Dr. Komal Bhombe",
"Dr. Khushboo Durge",
"Dr. Chitrika Subhadarsanee",
"Dr. Safiya Hassan"
],
"abstract": "Background: Periodontal regeneration therapies frequently involve autologous platelet concentrates (APCs). They can be used in sinus lift surgeries and socket preservation, among other clinical settings. Platelet rich fibrin (PRF) membrane has been used to treat gingival recession in individuals or groups of individuals using a coronally progressed or lateral pedicle flap. In the treatment of mixed periodontic endodontic lesion/furcation defect, PRF functions as a healing and interpositional biomaterial, filling a cystic cavity. PRF is known to help the bone regeneration process. In the last few years, efforts have been made to enhance the PRFs characteristics and quality. One of them is titanium platelet rich fibrin (T-PRF). Third-generation platelet concentrate no longer contains silica, and its preparation in glass vacuum containers, no longer creates any known concerns. The effectiveness PRF's has been evaluated in connective tissue and bone repair. The aim of this study is to compare T-PRF to other platelet concentrates and different treatment modalities for periodontal regenerative procedures. Methods: A protocol of this systematic review have been registered in prospero (CRD42022293545). The online database searched were PUBMED, COCHRANE for published articles up to November 2022 without language restrictions. Studies in trial registers, handsearching, bibliographic references of relevant articles were also checked. Data collection and analysis was done by individual authors. Independent eligibility assessments were conducted by four review authors. Then, using the standard Cochrane methodology, four review authors extracted the data and evaluated the risk of bias for individual studies. We developed \"Summary of findings\" tables and used GRADE to evaluate the evidence. Results: Three studies were included for meta-analysis. Results of meta-analysis supported that T-PRF is effective for correction of both hard and soft tissue defects. Conclusions: The overall qualitative and quantitative analysis suggest that T-PRF has superior structural properties and thicker fibrin network for periodontal regenerative procedures.",
"keywords": [
"T-PRF",
"Platelet Concentrates",
"Chronic Periodontitis",
"Infrabony Defects",
"Systematic Review",
"Meta-analysis"
],
"content": "Introduction\n\nPlasma fractions with higher platelet concentrations, such as platelet-rich plasma (PRP) and platelet rich fibrin (PRF) are crucial to regeneration.1 Their use has been successfully linked to connective tissue and bone repair.2 PRP has been documented and used in a variety of applications with what appears to be clinical success. It is an autologous modification of fibrin glue that is created by techniques that concentrate autologous platelets.1 PRP supports bioactivity but exhibits no stimulant properties for activation of regenerative cells.3 Additionally, its preparation is technique sensitive.4 PRP preparation, on the other hand, takes time therefore various efforts have been made to modify and enhance the PRP’s characteristics and quality which include Leukocyte platelet-rich fibrin (L-PRF). It was first described by Choukroun as cited by Dohan DM et al. (2006).5 It is regarded as a second-generation platelet concentrate and has been used to speed up wound healing during several surgical operations. Choukroun et al. first created PRF in France in 2001 as an autologous biomaterial that includes leucocytes.6 The method does not require bovine thrombin or an anticoagulant, in contrast to other platelet-rich products (or any other gelling agent).5,7–9 Although PRF has been shown to produce positive therapeutic outcomes, some clinicians are concerned that the method’s use of glass-evacuated collection tubes for blood with silica activators may pose a health risk.10,11 O’Connell provided a description of the inevitable silica interaction.12 Although the silica in the tube is thick enough to settle with the red blood cells, some of the particles are still colloidally suspended in the buffy coat, fibrin, and platelet-poor layers of plasma. Therefore, when the product is used for therapy, the particles could come in contact with the patient. One of them is titanium platelet rich fibrin (T-PRF).13 In the glass vacuum containers used to prepare “Platelet Rich Fibrin,” silica is known to have a hazardous impact that this third generation platelet concentrate is known to eliminate (PRF).\n\nNonsurgical periodontal therapy, such as scaling and root planing (SRP) alone or SRP plus systemic or local anti-inflammatory or antibacterial drugs, to surgical flap debridement, are the approaches for treatment of periodontitis cases.14 However, in cases of soft and hard tissue defects, surgical correction of the defects is of prime importance. For correction of bony defects, the use of autografts and allografts have been advocated.15 Autologous platelet concentrates when used in conjunction with bone grafts results in better improvement. A study by Olgun et al. (2018) reported clinical, radiographic and histological outcomes of bone that accelerated to four months compared to six months for allografts when combined with T-PRF.16 The desired outcome was seen in four months as compared to six months. Tunalı et al. in the year 201217 discovered a mature fibrin network when T-PRF clots were examined. In the T-PRF membrane, they discovered islets of bone tissue and newly developing connective tissue. These findings demonstrate that T-PRF could, within 30 days of treatment, cause the development of new bone and connective tissue in an experimental rabbit model of wound healing.\n\nAs mentioned above, the novel product termed T-PRF was prepared by Tunali et al. (2014)13 utilising a modified L-PRF process. Authors took the advantage of Dohan Ehrenfest’s taxonomy, which divides platelet-rich products into four main groups to prevent any misunderstanding about how to obtain these products. These four categories are determined according to the number of leukocytes and fibrin they contain, platelet-rich products: just platelet-rich plasma products, platelet- and leukocyte rich plasma products, platelet-rich fibrin, and platelet and leukocyte rich fibrin. The creation of T-PRF, a new platelet concentration, was motivated by the idea that titanium tubes would be more potent at activating platelets than the glass tubes used in Chouckron’s approach. The distinguishing properties of T-PRF, particularly its improved biocompatibility, are produced by platelet activation with titanium as opposed to activation with silica particles.18 T-PRF fibrin network covers a larger area than L-PRF fibrin network, also fibrin seemed thicker in the T-PRF samples.13\n\nSince the introduction of T-PRF by Tunali et al.,18 it has been assessed for various properties including its structural and biochemical characteristics. Tunalı et al. (2014)19 described the structural properties of T-PRF, and compared it to L-PRF. T-PRF samples appeared to have a highly ordered network with continuous integrity. The fibrin network in T-PRF samples appeared to be thicker and to cover a wider area than the network in L-PRF samples, according to histomorphometric analyses. T-PRF is a naturally occurring leukocyte- and PRF product that has been defined for the first time in a human investigation. Titanium platelet activation appears to provide T-PRF with certain high features. Since then T-PRF has been used for various periodontal procedures including treatment of various infrabony defects, gingival recession defects, in open flap debridement cases, periimplantitis.13,16,18,20–22\n\nSystematic evaluation of the studies to assess the clinical efficacy have not been done to date. This systematic review focuses to provide the best possible evidence for the use of T-PRF in periodontal regeneration.\n\n\nMethods\n\nWe searched PubMed, Cochrane, Embase database without language restrictions. We used Medical subject headings (MeSH) or equivalent and textword terms. We searched the metaRegister of controlled trials (mRCT), National clinical trials government website. Additionally, we checked the reference lists of reviews, retrieved articles for additional studies, and performed citation searches on key articles manually by going through each reference of the included articles. We intended to use randomised controlled trials (RCTs) that assessed outcomes in an open or blinded manner. Short abstracts (typically meeting reports), non-randomised research, experimental pain studies, animal model studies, case reports, and clinical observational studies were all omitted.\n\nSearch strategy\n\n(“t prf”[Title/Abstract] OR “titanium prepared platelet rich fibrin”[Title/Abstract] OR ((“titanium”[MeSH Terms] OR “titanium”[All Fields] OR “titaniums”[All Fields]) AND “platelet rich fibrin”[MeSH Terms])) AND (“gingival recession”[Title/Abstract] OR “gingival recession”[MeSH Terms] OR “furcation defects”[MeSH Terms] OR “alveolar ridge augmentation”[MeSH Terms] OR “infrabony defect”[Title/Abstract] OR “furcation”[Title/Abstract] OR “periimplantitis”[Title/Abstract])\n\nSystemically healthy patients (18+ years) clinically diagnosed with any type of periodontal disease (infrabony defects, gingival recession, osseous defects) were included irrespective of gender and race). Our outcome measures included change in the indices [Plaque index (PI) Gingival index (GI)], mean of periodontal pocket depth (PPD), mean of relative vertical clinical attachment loss (RVCAL), mean of relative horizontal clinical attachment loss (RHCAL) and mean of bone defect (BD). All the parameters were measured at baseline, 3 months and 6 months.\n\nSelection of studies\n\nAn open source online screening tool Rayyan23 (RRID:SCR_017584) was used by review writers. They independently screened the search results (RO, PD, PB, KB). By reading through the abstracts of each study that the search produced, the eligibility of each research was established. The review writers excluded studies that did not distinctly meet the inclusion criteria. For all included studies’ complete texts were acquired. Primary reviewers independently screened the complete texts of these studies to pick the most pertinent studies (RO, PD, PB, KB). The respective authors were reached by phone or email to get the required clarification for any missing data or information in the studies that had an impact on the study selection criteria. In cases of disagreement or dispute, a fifth author was asked for a judgement (KD). Prior to evaluation, the trials were not anonymized. Any language restrictions in the study selection process were not taken into consideration as a constraint for carrying out this evaluation. The complete review includes a PRISMA flow chart32 that shows the precise status of all identified studies in accordance with the recommendation found in “Part 2, Section 11.2.1 of the Cochrane Guidelines for Systematic Reviews of Interventions”.24 Irrespective of the reporting of outcome data, studies were included in this review as shown in Figure 1.\n\nThe data extraction from “included studies” was performed by four reviewers (RO, CS, KB, and KD) and given in the “characteristics of studies table” using a pre-defined data extraction form (Table 1). Data were extracted based on the nature of research, participant information, intervention information, and reported results. The disagreement between the main reviewers was resolved by the third reviewer (PB). The fourth reviewer successfully addressed the “risk of bias evaluation” discrepancy (KB). We have included a total of nine studies for qualitative analysis and have been included in the characteristics of studies table (Table 1). All the studies were matched for type of intervention, type of defect and participant details. Three studies were included and matched for meta-analysis followed by quantitative analysis.20,22,25\n\nFour reviewers (RO, PD, CS, and SH) from each included study independently evaluated the risk of bias (RoB) using the Cochrane domain-based, two-part tool as outlined in Chapter 8 of the Cochrane Handbook for Systematic Reviews of Interventions.24 The fourth reviewer was able to resolve the disagreement between the main reviewers (KB). Sequence generation, allocation concealment, participant and staff blinding, blinding of outcome evaluation, incomplete outcome data, biased outcome reporting, and other bias, such as baseline imbalance, were all areas in which we evaluated the RoB.\n\nIn parallel-group RCTs, the unit of analysis was the individual subject. The Elbourne-recommended method is used to integrate the cross-over designed trials into the meta-analysis.26 Measurements from experimental intervention periods and control intervention periods, respectively, were taken for these trials, and they were analysed under the assumption that it was a parallel group study of intervention versus control.\n\nThe Chi2 test (P value set at 0.10 for statistical significance) was used to examine clinical heterogeneity, and the I2 statistic was utilised to quantify heterogeneity in the outcomes of the included studies using RevMan manager version 5.0.27 Significant heterogeneity is defined as I2 over 75%; substantial heterogeneity is defined as I2 between 50% and 90%; moderate heterogeneity is defined as I2 between 30% and 60%; and mild heterogeneity is defined as I2 less than 40%. If statistical heterogeneity with I2 more than or equal to 50% is found, relevant causes were investigated using predefined subgroup analysis, and a random-effects model was used and reported.\n\nOnly when it was determined that the participants, interventions, comparisons, and results of the included studies were adequately comparable to yield a conclusion with clinical relevance and significance was a meta-analysis performed. We intended to carry out the meta-analysis using the Cochrane Collaboration’s open source RevMan 2014 statistical software (RRID: SCR_003581). If statistical heterogeneity with I2 higher than or equal to 50% is found, the sources of the heterogeneity were found, and a random-effects model meta-analysis was then carried out. In a meta-analysis, four papers were used. Table 2 presents data from all three investigations (Data Entry).\n\n\nResults\n\nThe analysis of the PI, PPD, CAL, DF was done separately for the interventional (OFD+T-PRF) and control groups (OFD alone). The details of the studies included for meta-analysis are given in Figures 2-5. All the included studies reported the use T-PRF combined with OFD. Three articles reported the use of T-PRF in infrabony defects,20,22,25 one study reported use of T-PRF combined with allograft for patients with chronic periodontitis.28 Another study reported its use in sinus lift procedures.16 Two studies reported its use in gingival recession21,29 and other in healing of extraction socket.29 Based on the overall similarities in participants, outcome and data three studies were found to be eligible for meta-analysis.20,22,25 The conclusion regarding the overall effect size estimates were made based on the meta-analysis.\n\nAll the included studies reported PI at baseline and after nine months.20,22,25 However, two studies reported data in the form of mean±standard deviation. All the studies showed statistically significant reduction in plaque index at nine months follow up period. The overall meta-analysis showed marginally significant reduction in plaque scores after nine months. (Mean Difference -0.52; 95% CI -1.30 to 0.27; p=0.03; I2 78%; two studies; 33 participants). However, in view of significant heterogeneity (I2=78%), the results need to be interpreted with caution because of increased heterogeneity as shown in Table 3 and Figure 2.\n\nAll the three included studies reported data on PPD at baseline and after nine months. All the studies reported significant reduction in PPD. The overall meta-analysis showed marginally significant reduction in PPD scores after nine months. (MD -0.85; 95% CI -1.26 to -0.45; p=0.01; four studies; 62 participants). However, in view of significant heterogeneity (I2=93%), the results need to be interpreted with caution as shown in Table 4, Figure 3.\n\nAll the included studies reported clinical attachment loss (CAL) gain at baseline and after nine months. All the studies reported significant improvement in CAL gain. The overall meta-analysis showed marginally significant increase in CAL gain after nine months. (MD -0.12; 95% CI - 0.59 to -0.35; p<0.0001; three studies; 62 participants). However the percentage of variation (I2 – 55%) was found to be minimum in all the three included studies, therefore making the interpretation of result favourable as shown in Table 5, Figure 4.\n\nAll the included studies reported defect fill at nine months. However quantitative assessment was only possible for two studies because of difference in reporting of outcomes.20,22 Significant defect fill was observed in both the studies. The overall meta-analysis showed a marginally significant increase in defect fill after nine months (MD - 0.07; 95% CI -0.17 to -0.03; p=0.09; two studies; 47 participants). Overall defect fill was not statistically significant. However in spite of improvement in defect fill, in view of significant heterogeneity found the results needs to be interpreted with caution as shown in Table 6, Figure 5.\n\nAllocation: One study reported use of the coin toss method for allocation hence was graded as low risk,22 the other two did not report the method and hence were graded as unclear.20,25 Blinding: all the studies were double blinded and were kept in low-risk bias.20,22,25 Missing result information: discretionary reporting In terms of reporting, we classified all three studies as low risk. The bias in the behaviour or observations: since all procedures and observations were carried out by a single trained professional in each research, we classified the study as low risk in terms of performance or observational bias. Figures 6 and 7 show, respectively, a summary of the risk of bias in the included studies and its graphical depiction.\n\n\nDiscussion\n\nThere are seventeen pieces of literature published on T-PRF. Two in-vitro studies have been performed by Tunali et al.18,19 They discovered a mature fibrin network. In the T-PRF membrane, they discovered islets of bone tissue and newly developing connective tissue. These findings demonstrate that T-PRF could, within 30 days of treatment, cause the development of new bone and connective tissue in a rabbit model of wound healing. They have also described the structural properties of T-PRF, and it was compared to L-PRF. Another in-vitro study evaluated the regulation of gingival keratinocyte adherence, dissemination, and cytokine expressions on titanium and PRF surfaces.30 Ustaoğlu et al. (2016)29 in their clinical study assessed the T-PRF’s clinical effects on human palatal mucosal wound healing (PMWH), and its impact on “time-dependent variations in palatal soft-tissue thickness (PSTT), a novel idea, was discovered. Uzun et al. (2017)21 compared the results of connective tissue graft with autologous T-PRF (CTG). T-PRF (63 teeth) or CTG were utilized to treat 114 Miller Class I/II gingival recessions with abrasion defects utilizing a modified tunnel technique (51 teeth). Olgun et al. (2018)16 investigated the differences between using an allograft or totally autologous T-PRF in sinus-lifting surgeries on the clinical, radiological, and histological levels. Arabaci et al. (2018)20 T-PRF and open flap debridement (OFD) were examined for their effects on biological markers in gingival crevicular fluid (GCF) and periodontal results. TPRF+OFD or OFD alone were used to treat 29 subjects with chronic periodontitis. Ustaoğlu et al. (2019)31 analysis of extraction sockets preserved by L-PRF and T-Fractal PRF’s dimension (FD) and early soft tissue healing characteristics. Ustaoğlu et al.31 evaluated the impact of T-PRF and Connective tissue graft (CTG) on peri-implant soft tissue thickness, and crestal bone level. Thirty implants were inserted into 30 patients while the soft tissue was simultaneously augmented with either T-PRF or CTG. Gummaluri et al. (2020),22 based on clinical and radiographic criteria, assessed the efficacy of T-PRF and L-PRF in the management of intra-bony defects.\n\nOut of the above-mentioned studies, three studies were included for meta-analysis.20,22,25 Results of meta-analysis supported that T-PRF is effective for correction of both hard and soft tissue defects. We included three studies that have reported data from 100 participants, aged 18+ years, that have used T-PRF in infrabony defects treated with open flap debridement. Studies have reported data on periodontal parameters like pocket depth, gingival bleeding, clinical attachment loss. Indices including plaque index and gingival index. Meta analysis was done for PPD, CAL, PI and defect fill parameters. The overall results of meta-analysis suggest that T-PRF is a better alternative to other platelet concentrates for both hard and soft tissue parameters.\n\n\nConclusion\n\nThis review focused on answering if T-PRF is a better alternative when compared with other platelet concentrates for periodontal regenerative procedures. The overall qualitative and quantitative analysis suggest that T-PRF have superior structural properties and thicker fibrin network. It provides superior results when used alone or combined with autograft or allograft. However, due to limited number of studies done so far, we recommend that more high quality RCTs to be conducted on this topic.",
"appendix": "Data availability\n\nFigshare: Prisma Checklist. https://doi.org/10.6084/m9.figshare.22341559.v1. 32\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nSaluja H, Dehane V, Mahindra U: Platelet-Rich fibrin: A second generation platelet concentrate and a new friend of oral and maxillofacial surgeons. Ann. Maxillofac. Surg. 2011; 1(1): 53–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGrecu AF, Reclaru L, Ardelean LC, et al.: Platelet-Rich Fibrin and Its Emerging Therapeutic Benefits for Musculoskeletal Injury Treatment. Medicina (Mex). 2019 May 15; 55(5): 141. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlves R, Grimalt R: A Review of Platelet-Rich Plasma: History, Biology, Mechanism of Action, and Classification. Skin Appendage Disord. 2018 Jan; 4(1): 18–24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXie X, Zhang C, Tuan RS: Biology of platelet-rich plasma and its clinical application in cartilage repair. Arthritis Res. Ther. 2014; 16(1): 204. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDohan DM, Choukroun J, Diss A, et al.: Platelet-rich fibrin (PRF): a second-generation platelet concentrate. Part I: technological concepts and evolution. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006 Mar 1; 101(3): e37–e44. PubMed Abstract | Publisher Full Text\n\nChoukroun J, Adda F, Schoeffler C, et al.: The opportunity in perio-implantology: The PRF. In 2001.\n\nDohan DM, Choukroun J, Diss A, et al.: Platelet-rich fibrin (PRF): A second-generation platelet concentrate. Part III: Leucocyte activation: A new feature for platelet concentrates? Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006 Mar; 101(3): e51–e55. Publisher Full Text\n\nDohan Ehrenfest DM, Rasmusson L, Albrektsson T: Classification of platelet concentrates: from pure platelet-rich plasma (P-PRP) to leucocyte- and platelet-rich fibrin (L-PRF). Trends Biotechnol. 2009 Mar; 27(3): 158–167. PubMed Abstract | Publisher Full Text\n\nChoukroun J, Diss A, Simonpieri A, et al.: Platelet-rich fibrin (PRF): a second-generation platelet concentrate. Part IV: clinical effects on tissue healing. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006 Mar; 101(3): e56–e60. PubMed Abstract | Publisher Full Text\n\nChoukroun J, Diss A, Simonpieri A, et al.: Platelet-rich fibrin (PRF): A second-generation platelet concentrate. Part V: Histologic evaluations of PRF effects on bone allograft maturation in sinus lift. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006 Mar; 101(3): 299–303.\n\nDel Corso M, Sammartino G, Dohan Ehrenfest DM: Re: “Clinical evaluation of a modified coronally advanced flap alone or in combination with a platelet-rich fibrin membrane for the treatment of adjacent multiple gingival recessions: a 6-month study.”. J. Periodontol. 2009 Nov; 80(11): 1694–1697. author reply 1697-1699. PubMed Abstract | Publisher Full Text\n\nO’Connell SM: Safety issues associated with platelet-rich fibrin method. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2007 May; 103(5): 587; author reply 587-593. PubMed Abstract | Publisher Full Text\n\nTunalı M, Özdemir H, Küçükodacı Z, et al.: A Novel Platelet Concentrate: Titanium-Prepared Platelet-Rich Fibrin. Biomed. Res. Int. 2014; 2014: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDrisko CH: Nonsurgical periodontal therapy: Nonsurgical periodontal therapy. Periodontology. 2001 Feb; 25(1): 77–88. Publisher Full Text\n\nWang W, Yeung KWK: Bone grafts and biomaterials substitutes for bone defect repair: A review. Bioact Mater. 2017 Jun 7; 2(4): 224–247. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOlgun E, Ozkan SY, Atmaca HT, et al.: Comparison of the clinical, radiographic, and histological effects of titanium-prepared platelet rich fibrin to allograft materials in sinus-lifting procedures. J. Investig. Clin. Dent. 2018 Nov; 9(4): e12347. PubMed Abstract | Publisher Full Text\n\nTunalı M, Özdemir H, Küçükodacı Z, et al.: In vivo evaluation of titanium-prepared platelet-rich fibrin (T-PRF): a new platelet concentrate. Br. J. Oral Maxillofac. Surg. 2013 Jul; 51(5): 438–443. PubMed Abstract | Publisher Full Text\n\nTunalı M, Özdemir H, Küçükodacı Z, et al.: In vivo evaluation of titanium-prepared platelet-rich fibrin (T-PRF): a new platelet concentrate. Br. J. Oral Maxillofac. Surg. 2013 Jul; 51(5): 438–443. PubMed Abstract | Publisher Full Text\n\nTunalı M, Özdemir H, Küçükodacı Z, et al.: A Novel Platelet Concentrate: Titanium-Prepared Platelet-Rich Fibrin. Biomed. Res. Int. 2014 Jan 21; 2014: e209548.\n\nArabaci T, Albayrak M: Titanium-prepared platelet-rich fibrin provides advantages on periodontal healing: A randomized split-mouth clinical study: T-PRF contributes to periodontal healing. J. Periodontol. 2018 Mar; 89(3): 255–264. PubMed Abstract | Publisher Full Text\n\nUzun BC, Ercan E, Tunalı M: Effectiveness and predictability of titanium-prepared platelet-rich fibrin for the management of multiple gingival recessions. Clin. Oral Investig. 2018 Apr; 22(3): 1345–1354. PubMed Abstract | Publisher Full Text\n\nGummaluri SS, Bhattacharya HS, Astekar M, et al.: Evaluation of titanium-prepared platelet-rich fibrin and leucocyte platelet-rich fibrin in the treatment of intra-bony defects: A randomized clinical trial. J. Dent. Res. Dent. Clin. Dent. Prospects. 2020; 14(2): 83–91. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRayyan—a web and mobile app for systematic reviews|Systematic Reviews|Full Text.[cited 2022 Mar 22]. Publisher Full Text\n\nCochrane Handbook for Systematic Reviews of Interventions.[cited 2021 Apr 17]. Reference Source\n\nUstaoğlu G, Uğur Aydin Z, Özelçi F: Comparison of GTR, T-PRF and open-flap debridement in the treatment of intrabony defects with endo-perio lesions: a randomized controlled trial. Med. Oral Patol. Oral Cirugia. Bucal. 2020 Jan 1; 25(1): e117–e123.\n\nElbourne DR, Altman DG, Higgins JP, et al.: Meta-analyses involving cross-over trials: methodological issues. Int. J. Epidemiol. 2002 Feb 1; 31(1): 140–149. Publisher Full Text\n\n9.5.2 Identifying and measuring heterogeneity.[cited 2022 Mar 22]. Reference Source\n\nPirebas HG, Hendek MK, Kisa U, et al.: Effect of titanium-prepared platelet-rich fibrin treatment on the angiogenic biomarkers in gingival crevicular fluid in infrabony defects of patients with chronic periodontitis: A randomized controlled clinical trial. Niger. J. Clin. Pract. 2018 Jan; 21(1): 69–75. PubMed Abstract | Publisher Full Text\n\nUstaoğlu G, Ercan E, Tunali M: The role of titanium-prepared platelet-rich fibrin in palatal mucosal wound healing and histoconduction. Acta Odontol. Scand. 2016 Oct; 74(7): 558–564. PubMed Abstract | Publisher Full Text\n\nKasnak G, Fteita D, Jaatinen O, et al.: Regulatory effects of PRF and titanium surfaces on cellular adhesion, spread, and cytokine expressions of gingival keratinocytes. Histochem. Cell Biol. 2019 Jul; 152(1): 63–73. PubMed Abstract | Publisher Full Text\n\nUstaoğlu G, Paksoy T, Gümüş KÇ: Titanium-Prepared Platelet-Rich Fibrin Versus Connective Tissue Graft on Peri-Implant Soft Tissue Thickening and Keratinized Mucosa Width: A Randomized Controlled Trial. J. Oral Maxillofac. Surg. 2020 Jul; 78(7): 1112–1123. PubMed Abstract | Publisher Full Text\n\nOza R, Dhadse PV, Bajaj P, et al.: Prisma Checklist. Dataset. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "178213",
"date": "27 Jun 2023",
"name": "Anurag Satpathy",
"expertise": [
"Reviewer Expertise Periodontology",
"Dental Implantology",
"Biofilm Formation",
"Clinical Dentistry",
"Periodontal Regeneration",
"Biomaterials",
"Quality of Life Research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors have carried out SR + MA on\" Clinical efficacy of titanium prepared platelet-rich fibrin in periodontal regeneration\"\n\nThere are a few areas which need to be clarified.\nIntroduction:\n\n\"One of them is titanium....\". There seems to be a disconnect between the statement and its previous sentence.\n\nThe objective statement for the SR is not clearly mentioned in the main text. Authors should write the objective statement\nMethods:\n\nAuthors should present the Research Question and the PICOT in a clear manner. PROSPERO Number should be mentioned in this section.\n\nFig 1: Authors are suggested to use the 2020 PRISMA Checklist and The Flow Diagram\nResults:\n\nAuthors should write a short description of the included studies (table 2)\n\nBy Using RevMan, Table 3 and Fig 2, Table 4 and Fig 3, Table 5 and Fig 4, Table 6 and Fig 5 can be combined into one. That is a standard and more appealing way to represent the Forest plots along with associated data. Authors are suggested to change.\nConclusions:\nThe overall effect for plaque Index, Clinical Attachment Loss was found to be not significant and only Probing Depth was found to be significant, with marginal significance in defect fill with only two studies. Therefore, the conclusion statement should be made with caution.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "11525",
"date": "20 Jun 2024",
"name": "Ranu Oza",
"role": "Author Response",
"response": "Respected Sir, Thank you for your suggestions. Thank you for your constructive feedback on our manuscript. We have carefully considered your comments and made the following revisions: Introduction: We have thoroughly modified and corrected the introduction to enhance clarity and coherence. Objective Statement: The objective statement for the systematic review is now explicitly mentioned in the main text, providing a clear overview of the study's aims. Research Question and PICOT: We have rephrased the research question and PICOT (Population, Intervention, Comparison, Outcome, Time) elements in a more concise and understandable manner. Additionally, we have included the PROSPERO registration number in this section for transparency. PRISMA Checklist and Flow Diagram: We have updated the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Checklist to the 2020 version and included the updated Flow Diagram to accurately reflect our review process. Results Section: Due to the generation of forest plots and tables using Review Manager, we were unable to combine them into a single figure. However, we have ensured that both formats are presented clearly for better visualization and interpretation. Description of Included Articles: A concise description of the included articles has been added to provide readers with a brief overview of each study's characteristics. We believe that these revisions have strengthened the manuscript and improved its overall quality."
}
]
},
{
"id": "219505",
"date": "23 Nov 2023",
"name": "Sara Bernardi",
"expertise": [
"Reviewer Expertise Dentistry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear authors, congratulations for the study and your contribution to the research. This systematic review and meta-analysis discusses about the efficacy of T-PRF in periodontal regenerative procedures, an interesting topic regarding a specific type of autologous platelet concentrates, thus T-PRF, applied to the widely-studied field of periodontal regeneration. The search strategy is well defined and clear. However, I suggest some revisions in order to improve the quality of the manuscript.\nIntroduction: I suggest to deepen the description of APCs, giving a more complete description of the protocol to obtain T-PRF, but also describing the histological characteristics of platelets concentrates, from the cited fibrin network to the other components of PRF.\nBesides, it would be useful to describe the differences between the first and the second generations of autologous platelet concentrates and their application in the different fields of oral surgery and periodontology, focusing on the involvement of T-PRF and periodontal regeneration procedures.\nDiscussion: the discussion should me more consistent; the aim of the study is to compare T-PRF to other APCs in periodontal regeneration, so, before comparing the results, I suggest to add more information, according to the results of the study, about the APCs that in the included studies have been compared to the main subject of discussion, thus the T-PRF.\nMoreover, the different periodontal regenerative techniques compared should be shortly described. These two topics can help to evaluate the advantages and disadvantages of T-PRF, in relation to the other interventions.\nFinally, I suggest to highlight the limits of the study, from which the future perspectives and recommendations, explained in the conclusion, derive.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "11527",
"date": "20 Jun 2024",
"name": "Ranu Oza",
"role": "Author Response",
"response": "Respected Sir, Thank you for you suggestions. Thank you for your insightful feedback on our manuscript. We have incorporated the following revisions based on your suggestions: Description of APCs and T-PRF Protocol: We have provided a more comprehensive description of autologous platelet concentrates (APCs) and detailed the protocol for obtaining T-PRF (Titanium-prepared platelet-rich fibrin) in the methods section. This addition aims to enhance clarity and understanding of the experimental procedure. Discussion on the Use of APCs in Periodontal Regeneration: In the discussion section, we have elaborated on the aim and practical applications of APCs in periodontal regeneration. By highlighting the role of APCs, we aim to emphasize their significance and potential benefits in clinical settings. Highlighting Results Related to APCs: We have specifically emphasized the results related to APCs within the study findings. This ensures that the impact and implications of APCs are prominently discussed and analyzed. Limitations, Future Perspectives, and Recommendations: In response to your suggestion, we have highlighted the limitations of our study in the discussion section. These limitations serve as a basis for identifying future perspectives and recommendations, which have been elaborated upon in the conclusion."
}
]
}
] | 1
|
https://f1000research.com/articles/12-393
|
https://f1000research.com/articles/10-234/v2
|
09 Feb 23
|
{
"type": "Research Article",
"title": "Stage 2 Registered Report: Anomalous perception in a Ganzfeld condition - A meta-analysis of more than 40 years investigation",
"authors": [
"Patrizio E. Tressoldi",
"Lance Storm",
"Lance Storm"
],
"abstract": "This meta-analysis is an investigation into anomalous perception (i.e., conscious identification of information without any conventional sensorial means). The technique used for eliciting an effect is the ganzfeld condition (a form of sensory homogenization that eliminates distracting peripheral noise). The database consists of studies published between January 1974 and December 2020 inclusive. The overall effect size estimated both with a frequentist and a Bayesian random-effect model, were in close agreement yielding an effect size of .099 (.05-.14). This result passed four publication bias tests and seems not contaminated by questionable research practices.\nTrend analysis carried out with a cumulative meta-analysis and a meta-regression model with Year of publication as covariate did not indicate a sign of the decline of this effect size. The moderators' analyses show that selected participants' outcomes were almost three times those obtained by non-selected participants and that tasks that simulate telepathic communication show a two-fold effect size with respect to tasks requiring the participants to guess a target. The Stage 1 Registered Report can be accessed here: https://doi.org/10.12688/f1000research.24868.3",
"keywords": [
"Rgistered Report",
"meta-analysis",
"ganzfeld",
"anomalous perception"
],
"content": "Introduction\n\nThe possibility of identifying pictures or video clips without conventional (sensorial) means, in a ganzfeld environment, is a decades old controversy, dating back to the pioneering investigation of Charles Honorton, William Braud and Adrian Parker between 1974 and 1975 (Parker, 2017).\n\nIn the ganzfeld, a German term meaning ‘whole field’, participants are immersed in an homogeneous sensorial field were peripheral visual information is masked out by red light diffused by translucent hemispheres (often split halves of ping-pong balls or special glasses) placed over the eyes, while a relaxing rhythmic sound, or white or pink noise, is fed through headphones to shield out peripheral auditory information. Once participants are sensorially isolated from external visual and auditory stimulation, they are in a favorable condition for producing inner mental contents about a randomly-selected target hidden amongst decoys. The mentation they produce can either be used by the participant to guide his/her target selection, or it can be used to assist in an independent judging process.\n\nIn the prototypical procedure, participants are tested in a room isolated from external sounds and visual information. After they make themselves comfortable in a reclining armchair, they receive instructions related to their task during the ganzfeld condition. Even if there are different verbatim versions, the instructions describe what they should do mentally in order to detect the information related to the target and how to filter out the mental contents not related to it. This information will be described aloud and recorded for playback before or during the target identification phase. After the relaxation phase, which can range from 5 to 15 minutes, they are exposed to the ganzfeld condition for a period ranging from 15 to 30 minutes. During this phase, participants describe verbally all images, feelings, emotions, they deem related to the target usually a picture or a short video-clip of real objects or events.\n\nOnce the ganzfeld phase is completed, participants are presented with different choices (e.g., the target plus three decoys) of the same format, e.g., picture or videoclip, and they must choose which one is the target (binary decision). Alternatively, they may be asked to rate all four (e.g., from 0 to 100), to indicate the strength of relationship between the information detected during the ganzfeld phase and the images or video clips contents.\n\nA variant of the judgment phase is to send the recording of the information retrieved during the ganzfeld phase to an external judge for independent ratings of the target. In order to prevent voluntary or involuntary leakage of information about the target by the experimenters, the research assistant who interacts with the participants must be blind to the target identity until the participants’ rating task is over.\n\nThe choice of the target and the decoys is usually made using automatic random procedures, and scores are automatically fed onto a scoring sheet.\n\nThere are three different ganzfeld conditions:\n\n• Type 1: the target is chosen after the judgment phase;\n\n• Type 2: the target is chosen before the ganzfeld phase;\n\n• Type 3: the target is chosen before the ganzfeld phase and presented to a partner of the participant isolated in a separate and distant room. From an historical perspective, this last type is considered the typical condition.\n\nThese differences are related to some theoretical and perceptual concepts we will discuss later. It is important to note that type of task makes no difference to the participant who only engages in target identification after the ganzfeld phase.\n\nIt is interesting to note that most of the cumulative findings (meta-analyses) of this line of investigation were periodically published in the mainstream journal Psychological Bulletin.\n\nHonorton (1985) undertook one of the first meta-analyses of the many ganzfeld studies completed by the mid-1980s. In total, 28 studies yielded a collective hit rate (correct identification) of 38%, where mean chance expectation (MCE) was 25%. Various flaws in his approach were pointed out by Hyman (1985), but in their joint-communiqué they agree that “there is an overall significant effect in this database that cannot reasonably be explained by selective reporting or multiple analysis” (Hyman & Honorton, 1986, p. 351).\n\nA second major meta-analysis on a set of ‘autoganzfeld’ studies was performed by Bem & Honorton (1994). These studies followed the guidelines laid down by Hyman & Honorton (1986). Moreover the autoganzfeld procedure avoids methodological flaws by using a computer-controlled target randomization, selection, and judging technique. They overall reported hit rate of 32.2% exceeded again the mean chance expectation.\n\nMilton & Wiseman (1999) meta-analysed further 30 studies collected for the period 1987 to 1997; reporting an overall nonsignificant standardized effect size of 0.013. However, Jessica Utts (personal communication, December 11, 2009) using the exact binomial test on trial counts only (N = 1198; Hits = 327), found a significant hit rate of 27% (p = 0.036).\n\nStorm & Ertel (2001) comparing Milton & Wiseman’s (1999) database with Bem & Honorton’s (1994) one, found the two did not differ significantly. Furthermore Storm and Ertel went on to compile a 79-study database, which had a statistically significant average standardized effect size of 0.138.\n\nStorm et al. (2010), meta-analysed a database of 29 ganzfeld studies published during the period 1997 to 2008, yielding an average standardized effect size of 0.14. Rouder et al. (2013) reassessing Storm et al.’s (2010) meta-analysis with a Bayesian approach, found evidence for the existence of an anomalous perception in the original dataset observing a Bayes Factor of 330 in support of the alternative hypothesis (p. 241). However they contended the effect could be due to “difficulties in randomization” (p. 241), arguing that ganzfeld studies with computerized randomization had smaller effects than those with manual randomization. The reanalysis by Storm et al.’s (2013) showed that this conclusion was unconvincing as it was based on Rouder et al.’s faulty inclusion of different categories of study.\n\nIn the last meta-analysis by Storm & Tressoldi (2020), related to the studies published from 2008 to 2018, the overall standardized effect size was 0.133; 95%CI: 0.06-0.18.\n\nThe main aim of this study is to meta-analyse all available ganzfeld studies dating from 1974 up to December 2020 in order to assess the average effect size of the database with the more advanced statistical procedures that should overcome the limitations of the previous meta-analyses. Furthermore, we aim to identify whether there are moderator variables that affect task performance. In particular, we hypothesize that participant type and type of task are two major moderators of effect size (see Methods section).\n\n\nMethods\n\nThis study follows the guidelines of the APA Meta-Analysis Reporting Standard (Appelbaum et al., 2018) and the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P, Moher et al., 2015).\n\nAll following analyses have been approved in the Stage 1 (Tressoldi & Storm, 2021). Supplementary and new analyses not approved in the Stage 1, are reported in the Exploratory analyses section in the Results.\n\nRetrieval of studies related to anomalous perception in a Ganzfeld environment is simplified, firstly by the fact that most of these studies have already been retrieved for previous meta-analyses, as cited in the introduction. Secondly, this line of investigation is carried out by a small community of researchers. Thirdly, most of the studies of interest to us are published in specialized journals that adopted the editorial policy of accepting paper with results that are statistically non-significant (according to the frequentist approach). This last condition is particularly relevant because it reduces the publication bias due to non-publication (file drawer effect) of studies with statistically non-significant results often as a consequence of reduced statistical power.\n\nFurthermore in order to integrate the previous retrieval method, we carried-out an online search with Google Scholar, PubMed and Scopus databases of all papers from 1974 to 2020 including in the title and/or the abstract the word “ganzfeld” (e.g., for PubMed: Search: ganzfeld [Title/Abstract] Filters: from 1974 – 2020).\n\nThe following inclusion criteria were adopted:\n\n• Studies related to anomalous perception in a ganzfeld environment;\n\n• Studies must use human participants only (not animals);\n\n• Number of participants must be in excess of two to avoid the inherent problems that are typical in case studies;\n\n• Target selection must be randomized by using a Random Number Generator (RNG) in a computer or similar electronic device, or a table of random numbers.\n\n• Randomization procedures must not be manipulated by the experimenter or participant;\n\n• Studies must provide sufficient information (e.g., number of trials and outcomes) for the authors to calculate the direct hit-rates and effect size values, so that appropriate statistical tests can be conducted.\n\n• Peer reviewed and not peer-reviewed studies e.g. published in proceedings excluding dissertations.\n\nFor each included study, one of the authors, expert in meta-analyses, coded the following variables:\n\n• Authors;\n\n• Year of publication;\n\n• Number of trials;\n\n• Number of hits;\n\n• Number of choices of each trial;\n\n• Task type (Type 1,2 or 3);\n\n• Participants type (selected vs. unselected). The authors of the study scored as ‘selected’ all participants that were screened for one or more particular characteristic deemed favourable for the performance in this type of task. All others were coded as ‘non-selected’\n\n• Peer-Review level: Level = 1 for studies published in conference proceedings and Researches In Parapsychology (moderate peer-review); Level = 2, for the studies published in scientific journals with full peer-review.\n\nThe second author randomly checked all studies, and the data was compared with those extracted by the other author. Discrepancies were corrected by inspecting the original papers.\n\nThe complete database with all supporting information is available as Underlying data (Tressoldi & Storm, 2020).\n\nAs standardized measure of effect size, we used that one applied in Storm, Tressoldi & Di Risio (2010) and Storm & Tressoldi (2020): Binomial Z score/√number of trials using the number of trials, the hits score and the chance probability as raw scores. The exact binomial Z score has been obtained applying the formula implemented online at http://vassarstats.net/binomialX.html. When this algorithm did not compute the z value when either number of trials or number of hits were low, we used the one-tailed exact binomial p-value, to find the inverse normal z by using the online app at http://www.fourmilab.ch/rpkp/experiments/analysis/zCalc.html where the formula of this conversion is described.\n\nThe standardized effect size was computed applying the formula Z/√N of participants.\n\nAs standard error, we used the formula: √(hit rate % * (1-hit rate %)/participants * chance percentage *(1-chance percentage)).\n\nIn order to take into account the effect size overestimation bias in small samples, the effect sizes and their standard errors, were transformed in the Hedge’s g effect sizes, with the corresponding standard errors by applying the formula presented in Borenstein et al. (2009, pp. 27–28: g = (1-(3/(4df-1)))* d)).\n\nIn order to account for the between-studies heterogeneity, the overall effect size estimation of the whole database has been calculated by applying both a frequentist and a Bayesian random-effect model for testing its robustness.\n\nFollowing the recommendations of Langan et al. (2019), we used the restricted maximum likelihood (REML) approach to estimate the heterogeneity variance with the Knapp and Hartung method for adjustment to the standard errors of the estimated coefficients (Rubio-Aparicio et al., 2018).\n\nFurthermore, in order to control for possible influence of outliers, we calculated the median and mode of the overall effect size applying the method suggested by Hartwig et al. (2020).\n\nThese calculations were implemented in the R statistical environment v.4.0.3 with the metafor package v. 2.4 (Viechtbauer, 2017). See syntax details provided as extended data (Tressoldi & Storm, 2020).\n\nAs priors for the average effect size we used a normal distribution with Mean = 0.1; SD = 0.03, constrained positive, lower bound = 0 (Haaf & Rouder, 2020), given our expectation of a positive value. As prior for the tau parameter we used an inverse gamma distribution with shape = 1, scale = 0.15.\n\nThis Bayesian meta-analysis was conducted using the MetaBMA package v. 0.6.7 (Heck et al., 2017).\n\nFollowing the suggestions of Carter et al. (2019), we applied four tests to assess publication bias:\n\n• the 3-parameter selection model (3PSM), as implemented by Coburn & Vevea (2019) with the package ‘weightr’ v.2.0.2;\n\n• the p-uniform* (star) v. 0.2.5 test as described by van Aert & van Assen (2019), and\n\n• the sensitivity analysis using the Mathur & VanderWeele (2020) package PublicationBias v.2.3.0.\n\n• The Robust Bayesian meta-analysis test implemented with the RoBMA package v.2.3.1 (Bartoš & Maier, 2020).\n\nThe three parameters model represents the average true underlying effect, δ, the heterogeneity of the random effect sizes, τ 2 and the probability that there is a nonsignificant effect in the pool of effect sizes. The probability parameter is modelled by a step function with a single cut point at p = 0.025 (one-tailed), which corresponds to a two-tailed p value of 0.05. This cut point divides the range of possible p values into two bins: significant and nonsignificant. The three parameters are estimated using maximum likelihood (Carter et al., 2019, p. 124).\n\nThe p-uniform* test, is an extension and improvement of the p-uniform method. P-uniform* improves upon p-uniform giving a more efficient estimator avoiding the overestimation of effect size in case of between-study variance in true effect sizes, thus enabling estimation and testing for the presence of between-study variance in true effect sizes.\n\nSensitivity analysis, as implemented by Mathur & VanderWeele (2020), assumes a publication process such that “statistically significant” results are more likely to be published than negative or “nonsignificant” results by an unknown ratio, η (eta). Using inverse-probability weighting and robust estimation that accommodates non-normal true effects, small meta-analyses and clustering, it enables statements such as: “For publication bias to shift the observed point estimate to the null, ‘significant’ results would need to be at least 30-fold more likely to be published than negative or ‘non-significant’ results” (p. 1). Comparable statements can be made regarding shifting to a chosen non-null value or shifting the confidence interval.\n\nThe Robust Bayesian meta-analysis test is an extension of Bayesian meta-analysis obtained by adding selection models to account for publication bias. This allows model-averaging across a larger set of models, ones that assume publication bias and ones that do not. This test allows us to quantify evidence for the absence of publication bias estimated with a Bayes Factor. In our case we compared only two models, a random-effect model assuming no publication bias and a random-model assuming publication bias.\n\nIn order to ascertain the overall trend of the cumulative evidence and in particular for testing the presence of a positive or negative trend effect, we performed a cumulative effect size estimation.\n\nFurthermore, we estimated the overall effect size taking the variable “year of publication” as covariate using a meta-regression model.\n\nWe compared the influence of the following tree moderators: (i) Type of participant, (ii) Type of task and (iii) Level of peer-review.\n\nAs described in the Variable Coding paragraph, the variable Type of participant, has been coded in a binary way: selected vs unselected. Type of task has been coded as Type 1, Type 2, and Type 3, as described in the Introduction and level of Peer-review as 1 for studies published in conference proceedings or 2, for the studies published in scientific journals with full peer-review.\n\nThe overall statistical power was estimated using R package metameta v.0.1.1. (Quintana, 2020). Furthermore, we calculated the number of trials necessary to achieve a statistical power of at least.80 with an α = .05. With this estimation we examined how many studies in the database reached this threshold.\n\n\nResults\n\nThe search and selection of the studies is presented in the PRISMA flowchart in Figure 1. As shown in the flowchart, our final database comprises 78 studies, for a total of 113 effect sizes carried out by 46 different principal investigators.\n\nThe list of all references related to the included and excluded studies is available in the GZMAReference List file and the data used for all the following statistical analyses is available in the GZMADatabase1974_2020 file in the Underlying data (Tressoldi & Storm, 2020).\n\nDescriptive statistics related to the variables trials, hits rate, participants type, task types, peer-review level are presented in Table 1.\n\n* = this value is purely descriptive because not all studies are 4 free-choice designs.\n\nComment: The range of the number of trials as well as the hits percentage is quite wide. The number of task types show that the main types are Type 2: the target is chosen before the ganzfeld phase) and of Type 3: the target is chosen before the ganzfeld phase and presented to a partner of the participant isolated in a separate and distant room. Type 1 studies (target randomly selected after participant makes a choice) are only 5 (4.2%).\n\nThe percentage of studies using non-selected participants is greater (62% vs 38%) than that of studies using selected. Most studies (58.4%) were peer-reviewed.\n\nThe estimate of the average effect along with the corresponding 95% Confidence Intervals or Credible Intervals of both the frequentist and the Bayesian random-effect models as described in the Methods section, and values of τ2 and I2 (Higgins & Thompson, 2002) with their confidence intervals, as measures of between-study variance, are presented in Table 2.\n\nComment: The frequentist and the Bayesian random-effect model parameters estimations are in close agreement, and both reject the null (H0) hypothesis with a high probability.\n\nIn terms of hits percentage above chance, this small effect size corresponds to 3.8% (95%CIs: 1.7 – 5.9).\n\nThe level of heterogeneity is medium-large as expected by the influence of the moderators. Given this heterogeneity level, the values of the effect size median = .017 (-.025 - .06) and mode -.01 (-.13 - .10), are uninformative.\n\nThe forest plot is available as Figure S1 (Extended data (Tressoldi & Storm, 2020)).\n\nIn order to detect the presence of influential outliers, we applied the “influence” function in the metafor package. These procedures identified two influential outliers. The results of the frequentist random-effect model without the influential outliers, are very similar to those with the outliers (mean ES: .099; 95% CIs: .05 - .14).\n\nThe results of the cumulative meta-analysis is represented with a cumulative forest plot in Figure S2 (Extended data (Tressoldi & Storm, 2020)). From the inspection of the cumulative forest plot, it emerges that the overall effect size stabilized around the cumulative evidence obtained up to 1997. Thus, it appears to be stable for more than 20 years.\n\nThe results of the meta-regression with “Year” as covariate, show a slope estimate of -.0012 (95%CIs: -.005 - .003; p = .57).\n\nComment: These results support the hypothesis that the overall effect size is not affected by the year of publication of the experiments.\n\nExploratory analyses\n\nAnother way to observe the cumulative trend of the overall effect size, is to examine the evolution of the Bayes Factor and of Posterior Probability of H1 as the data accumulate. This information has been obtained using the option “sequential Bayes Factor” and “sequential posterior model probability” within the module Bayesian Meta-Analysis in the software JASP v.0.17.0 (Jasp, 2020) that are presented in Figures S3 and S4 (Extended data (Tressoldi & Storm, 2020)). From these two plots it is possible to observe how the Bayes Factor started a positive linear trend after approximately 70 experiments. The maximum Posterior probability is achieved after approximately 80 experiments. The JASP file is available as Underlying data (Tressoldi & Storm, 2020).\n\nThe results of the four publication bias tests described in the Methods section are presented in Table 3 and in the information that follows.\n\nThe results of the sensitivity analysis publication bias to shift the observed effect size point estimate to the.01 level, considered the smallest effect size of interest, indicated that no amount of publication bias (parameter eta) under the assumed model would suffice to shift the point estimate to this level.\n\nComment: The overall effect size estimate passes all four publication bias tests.\n\nThe weighted effect size along with the corresponding 95% confidence Intervals of the two types of participants, the three task types and the two peer-review level, are presented in Table 4.\n\nAfter looking at the participants selection and Task Type results, it was interesting to learn that selected participants and Task Type 3 combined, gave: ES = .18; 95%CIs: .07 - .29; not different from the results obtained by the selected participants in all three types of tasks.\n\nComment: Whereas it is clear that the levels of peer-review did not yield differences in the effect sizes, the selection of participants and the Task Types show substantial and statistically significant differences.\n\nSelected participants show a three-fold increase in the effect size with respect to the non-selected participants. In terms of hits percentage above chance, this difference corresponds to 7.6%; 95%CI: 3-12 and 1%; 95%CI: -1 – 4.7, respectively.\n\nSimilarly, Tasks Type 1 and 3 show more than two-fold increase in ES compared to Type 2 tasks. The effect size observed with tasks Type 1, must be considered with caution given the low number of experiments (5).\n\nThe median statistical power related to the observed overall effect size is .106. This result explains the fact that only 21 (18.5%) of the studies reported statistically significant results.\n\n\nDiscussion\n\nThe main aim of this meta-analysis was to get an overall picture of the evidence accumulated in more than 40 years of investigation related to an anomalous perception in a ganzfeld environment.\n\nThe estimate of the average effect from 113 studies carried out from 1974 to June 2020, is small, but it turned out robust in both a frequentist and a Bayesian random-effect model.\n\nAs shown by the cumulative analysis and the meta-regression with Year of publication as covariate meta-analyses, this effect does not show a negative trend from 1974 to 2020 and is quite stable since 1997 and after 70-80 experiments.\n\nFurthermore, the average effect, passes four different publication bias tests, reducing the probability that it could be due to the selective reporting of studies with statistically significant results. This interpretation is also supported by the low number of studies (18.5%) with statistically significant results. This outcome is partly consequent to the practice of publishing also statistically non-significant studies in the specialized journals and proceedings related to this field of investigation.\n\nMoreover, the similarity of effect size between the two levels of peer-review, add further support to the hypothesis that the “file drawer” is pretty empty, that is that this meta-analysis include all completed studies.\n\nIf we consider the value of the average effect size, the lack of statistically significant results in many experiments are a consequence to their low statistical power as shown by the very low median statistical power of the meta-analysis.\n\nFor those interested in this line of investigation the advice is clear. In order to achieve a statistical power of at least.80 with an alpha value of.05, each study must have at least 320 trials (estimated with G*Power, v.3.1.9.7, Faul, Erdfelder, Lang & Buchner, 2007).\n\nHowever, this requirement can be reduced considerably if we consider the results of the moderators, in particular the selection of participants and the type of task. With selected participants carrying out a Type 3 task (i.e., with targets chosen before the ganzfeld phase and presented to a partner of the participant isolated in a separate and distant room simulating a sort of telepathic communication), the required trials can safely be reduced to 50.\n\nCould the average results be contaminated by the use of some questionable research practices (John et al., 2012), such as optional stopping, data exclusion, etc.? These practices are difficult to detect after the study publication, which is why it is recommended to preregister all methodological and statistical details before data collection. As far as it concerns this line of investigation, Wiseman, Watt and Kornbrot (2019), documented that preregistration was recommended well before the so-called replication crisis faced by most scientific fields. Furthermore, a simulation of the use of some questionable research practices carried out by Bierman, Spottiswoode and Bijl (2016) on 78 studies related to anomalous perception in a ganzfeld environment, showed that even if the overall effect size could be inflated by the use of questionable research practices, it was not reduced to zero.\n\nEven if this paper is mainly devoted to the statistical analysis of the available evidence, it is important to consider possible theoretical frameworks that could account for such phenomena. Some of them are presented in the review by Cardeña (2018) and the book Transcendent Mind by Barušs and Mossbridge (2017). As a general theoretical framework, the main assumption is to consider mind not derived or constrained by their biological correlates but ontologically independent from them in agreement with some western and eastern philosophical interpretations such as idealism (Kastrup, 2018), dual-aspect monism (Walach, 2020), Advaita Vedanta (Sedlmeier & Srinivas, 2016), etc. If these interpretations of mind and consciousness are valid, what looks impossible or anomalous according to a physicalist or an eliminative reductionism interpretation, becomes perfectly normal.\n\n\nSummary and recommendations\n\nThe overall picture emerging from this meta-analysis is that there is sufficient evidence to claim that it is possible to observe a non-conventional (anomalous) perception in a ganzfeld environment. The available evidence seems not to be contaminated by publication bias and questionable research practices. However, in order to increase the probability of detecting such phenomena it is recommended to select participants and to use tasks which mimic a telepathic communication.\n\nAs a methodological advice, it is recommended that researchers preregister the methodological and statistical details in open access registries as proposed by Watt and Kennedy (2016) and others, or even better to use a registered report format that makes all procedures more transparent before and during data collection and analysis. One of the best example, to be used as a model, is the Transparent Psi Project (Kekecs et al., 2019).\n\nOur hope is to update the evidence related to the anomalous perception in a ganzfeld environment with a meta-analysis of preregistered studies in the near future.\n\n\nData availability\n\nFigshare: Registered Report - Anomalous perception in a Ganzfeld condition: A meta-analysis of more than 40 years investigation, https://doi.org/10.6084/m9.figshare.12674618.v11 (Tressoldi & Storm, 2020).\n\nThis project contains the following underlying data:\n\n- GZMADatabase1974_2020 (.jasp and.xlsx)\n\n- GZMA Power (.xlsx)\n\n- GZMA Reference List (.doc)\n\nFigshare: Registered Report - Anomalous perception in a Ganzfeld condition: A meta-analysis of more than 40 years investigation, https://doi.org/10.6084/m9.figshare.12674618.v11 (Tressoldi & Storm, 2020).\n\nThis project contains the following extended data:\n\n- Syntax Details for Stage 1 and Stage 2 Registered Report\n\n- Figure S1\n\n- Figure S2\n\n- Figure S3\n\n- Figure S4\n\nFigshare: PRISMA checklist for ‘Stage 2 Registered Report: Anomalous perception in a Ganzfeld condition - A meta-analysis of more than 40 years investigation’, https://doi.org/10.6084/m9.figshare.12674618.v11 (Tressoldi & Storm, 2020).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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PubMed Abstract | Publisher Full Text\n\nMathur MB, VanderWeele TJ: Sensitivity analysis for publication bias in meta-analyses. J R Stat Soc Ser C Appl Stat. 2020; 1–29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMilton J, Wiseman R: Does psi exist? Lack of replication of an anomalous process of information transfer. Psychol Bull. 1999; 125(4): 387–391. PubMed Abstract | Publisher Full Text\n\nMoher D, Stewart L, Shekelle P, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst Rev. 2015; 4(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParker A: ‘Ganzfeld’. Psi Encyclopedia. London: The Society for Psychical Research.2017.Reference Source\n\nQuintana D: dsquintana/metameta: 0.1.1 (beta) (Version 0.1.1). Zenodo. 2020 July 14. Publisher Full Text\n\nRouder JN, Morey RD, Province JM: A Bayes factor meta-analysis of recent extrasensory perception experiments: Comment on Storm, Tressoldi, and Di Risio (2010). Psychol Bull. 2013; 139(1): 241–247. PubMed Abstract | Publisher Full Text\n\nRubio-Aparicio M, López-López JA, Sánchez-Meca J, et al.: Estimation of an overall standardized mean difference in random-effects meta-analysis if the distribution of random effects departs from normal. Res Synth Methods. 2018; 9(3): 489–503. PubMed Abstract | Publisher Full Text\n\nSedlmeier P, Srinivas K: How Do Theories of Cognition and Consciousness in Ancient Indian Thought Systems Relate to Current Western Theorizing and Research? Front Psychol. 2016; 15(7): 343. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStorm L, Ertel S: Does psi exist? Comments on Milton and Wiseman’s (1999) meta-analysis of ganzfeld research. Psychol Bull. 2001; 127(3): 424–433, discussion 434-8. PubMed Abstract | Publisher Full Text\n\nStorm L, Tressoldi PE, Di Risio L: Meta-analyses of free-response studies, 1992–2008: Assessing the noise reduction model in parapsychology. Psychol Bull. 2010; 136(4): 471–485. PubMed Abstract | Publisher Full Text\n\nStorm L, Tressoldi PE, Utts J: Testing the Storm et al. (2010) meta-analysis using Bayesian and frequentist approaches: Reply to Rouder et al. (2013). Psychol Bull. 2013; 139(1): 248–254. PubMed Abstract | Publisher Full Text\n\nStorm L, Tressoldi P: Meta-Analysis of Free-Response Studies 2009-2018: Assessing the Noise-Reduction Model Ten Years On. J. Soc. Psych. Res. 2020; 84(4): 193–219. Publisher Full Text\n\nTressoldi PE, Storm L: Stage 1 Registered Report: Anomalous perception in a Ganzfeld condition - A meta-analysis of more than 40 years investigation [version 3; peer review: 1 approved, 2 approved with reservations]. F1000Research. 2021; 9: 826. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTressoldi P, Storm L: Registered Report - Anomalous perception in a Ganzfeld condition: A meta-analysis of more than 40 years investigation. figshare. 2020. Publisher Full Text\n\nvan Aert RCM, van Assen MALM: Correcting for publication bias in a Meta-Analysis with the P-Uniform* method.2019. Publisher Full Text\n\nViechtbauer W: The metafor Package.2017.Reference Source\n\nWalach H: Inner Experience–Direct Access to Reality: A Complementarist Ontology and Dual Aspect Monism Support a Broader Epistemology. Front Psychol. 2020 Apr 23; 11: 640. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWatt CA, Kennedy JE: Options for Prospective Meta-Analysis and Introduction of Registration-Based Prospective Meta-Analysis. Front Psychol. 2016; 7: 2030. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWiseman R, Watt C, Kornbrot D: Registered reports: an early example and analysis. PeerJ. 2019; 7: e6232. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "205990",
"date": "02 Nov 2023",
"name": "Dean Radin",
"expertise": [
"Reviewer Expertise Experimental psychology",
"parapsychology",
"psychophysiology",
"physics",
"and statistics."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a follow-up to a previous meta-analysis of the ganzfeld condition experimental database. It uses the latest meta-analytic techniques and adds further evidence to the original conclusion.\nMy primary comment about this document is that it would be difficult for those who are not already familiar with the relevant literature to fully understand what this experiment is about. For example, in the Introduction, participants are referred to as \"they,\" but given that \"they\" is sometimes used a neutral gender term, we cannot tell if this entails one person or two, who is describing their impressions aloud, how that information is recorded, who judges that information against the target, how many targets and decoys are involved (we read four at one point, and binary at another), and so on.\nBecause of such confusions, I think it would be much clearer if the various types of ganzfeld condition experiments that are being considered were defined upfront, and then state how many participants are involved in each kind of study, and exactly what each of their roles are. As currently written, some of this information is provided later in the Introduction, but by the time the reader gets to that description they will already be confused.\nOther phases that might be clarified:\n> Once participants are sensorially isolated from external visual and auditory stimulation, they are in a favorable condition\nI'd prefer a more cautious \"thought to be a favorable condition\"\n> in the mainstream journal Psychological Bulletin.\nThe word mainstream is unnecessary.\n> Moreover the autoganzfeld procedure avoids\nMaintain consistency in tenses. Thus, \"avoided\" and not avoids.\n> They overall reported hit rate\n\nYou mean \"The overall reported hit rate\"\n> average standardized effect size\nMeaning? There are many definitions for effect size.\n> with the more advanced statistical procedures that should overcome the limitations of the previous meta-analyses\nSuch as? List these limitations.\n> have been approved in the Stage 1\nThe Stage 1 what? That term only makes sense if one is already familiar with how this journal works.\n\n> the editorial policy of accepting paper\n\nYou mean \"papers\". Note: There are many other examples like this that a proofreader would catch. I suggest that the authors do a very careful review of the text for these kinds of grammatical mistakes. I will mention some (not all) of them below.\n> Studies must use human participants only (not animals);\nAre there ganzfeld studies with animals?\n> Number of participants must be in excess of two to avoid the inherent problems that are typical in case studies;\nThis is confusing because we don't know if you mean the number of participants per session, or the number of sessions.\n> Target selection must be randomized by using a Random Number Generator (RNG) in a computer or similar electronic device\nAn RNG \"in\" a computer can mean a pseudorandom algorithm or a true hardware-based RNG. Clarify.\n> Randomization procedures must not be manipulated by the experimenter or participant;\nWhat does \"manipulated\" mean in this context? If I select from a table of random numbers, that is a manual process, and thus could be interpreted as manipulated.\n> Researches In Parapsychology\nYou mean \"conference proceedings such as those published in a book series called Research In Parapsychology\"\n> As standardized measure of effect size, we used that one\n\nwe used the one\n> Binomial Z score/√number of trials using the number of trials, the hits score and the chance probability as raw scores\nA comma is necessary to clarify this sentence: Binomial Z score/√number of trials, using the number of trials, the hits score and the chance probability as raw scores\n> were transformed in the Hedge’s g effect sizes,\nwere transformed into the Hedge’s g effect sizes,\n> a Bayesian random-effect model for testing its robustness\nWhat does \"it\" refer to?\n> See syntax details provided as extended data\nWhat does extended data mean?\n\nIn Table 2 we find a cell with the number 1909. It isn't clear what that refers to. Is that a Bayes Factor?\n> We compared the influence of the following tree moderators:\nWhat is a tree moderator? Do you mean three moderators?\n> the “file drawer” is pretty empty,\nCan you be more objective? Pretty can mean all sorts of things.\n>The results of the cumulative meta-analysis is represented\n\nResults are, not is.\n> Thus, it appears to be stable\nShould probably emphasize cumulatively stable, or stable on average.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "10986",
"date": "15 Feb 2024",
"name": "Patrizio Tressoldi",
"role": "Author Response",
"response": "Sorry for the late response to your review, but we preferred to wait for further reviews' before revising the paper. Here are the replies to your comments. >My primary comment about this document is that it would be difficult for those who are not already familiar with the relevant literature to fully understand what this experiment is about. For example, in the Introduction, participants are referred to as \"they,\" but given that \"they\" is sometimes used a neutral gender term, we cannot tell if this entails one person or two, who is describing their impressions aloud, how that information is recorded, who judges that information against the target, how many targets and decoys are involved (we read four at one point, and binary at another), and so on. Because of such confusion, I think it would be much clearer if the various types of ganzfeld condition experiments that are being considered were defined upfront, and then state how many participants are involved in each kind of study, and exactly what each of their roles are. As currently written, some of this information is provided later in the Introduction, but by the time the reader gets to that description they will already be confused. Reply: See restructured and corrected text in the Introduction, margin comments, and additional text. Other phases that might be clarified: Reply: We revised the introduction following these suggestions What does extended data mean? Reply: This is an editorial requirement replacing the Supplementary Material. In Table 2 we find a cell with the number 1909. It isn't clear what that refers to. Is that a Bayes Factor? Reply: Correct, even If after a re-analysis this value is now 85 in the range of \"very strong evidence\" . > the “file drawer” is pretty empty, Can you be more objective? Pretty can mean all sorts of things. Reply: we deleted the term “pretty”."
}
]
},
{
"id": "177854",
"date": "24 Jan 2024",
"name": "Michel-Ange Amorim",
"expertise": [
"Reviewer Expertise psychophysics",
"cognitive psychology",
"cognitive and behavioral neuroscience",
"psi phenomena"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMy report is provided in a separate file available through this link: PDF file.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10987",
"date": "12 Aug 2024",
"name": "Patrizio Tressoldi",
"role": "Author Response",
"response": "Thank you for your accurate review in particular the reproducibility of our results using our database and code syntax. Here follow our replies to all your comments. Main comments: 1-At the beginning of the “Effect size measures” section, the authors write “As a standardized measure of effect size, we used […] Binomial Z score/√number of trials using the number of trials, the hits score and the chance probability as raw scores.” However, in the xlsx data file provided by the authors, the values in the ES column correspond to Z/√N, with N as the number of participants rather than the number of trials in the study. Reply: even if using trials or participants as a unit of analysis changes only some decimals of all results for this database, in this revision we used trials as this is the standard choice in all meta-analyses related to the topic investigated. 2-I also share the concerns expressed earlier by S Schmidt and J Utts about using webpages to compute exact binomial Z score values, either directly (with http://vassarstats.net/binomialX.html) or indirectly (with http://www.fourmilab.ch/rpkp/experiments/analysis/zCalc.html from the p value provided by binomialX.html). Reply: what is important is the correctness of the formulas and not where they are implemented. In our case, the choice of webpages could allow independent controls without using other software. In our case, the formulas are available on the websites. Thank you for pointing us the error related to the Z score of the third experiment. 3- Publication Bias tests ….On the one hand, I find this statement incomplete and misleading because it ignores the confidence interval around the meta-analytic pooled point estimate. Reply: we added “These results suggest that for publication bias to attenuate (to “explain away”) the observed point effect lower CI interval to the null, affirmative results would need to be at least 10 fold more likely to be published than nonaffirmative results”, in the revised version as suggested. 4- Could the authors give a reference or spell out the practical (or theoretical) reasons for this statement: “the .01 level, considered the smallest effect size of interest”? Reply: This is an arbitrary cutoff close to the null (zero) level for this line of investigation. This level can change in other research fields. Further comments 1-Table 1 reports several descriptive values. The mean (SD) values in the Hit rate column are for 4 free-choice designs. However, the corresponding note at the bottom of Table “this value is purely descriptive because not all studies are 4 free-choice designs” is ambiguous; Reply: we changed the proportion of hits with the proportion of hits above the chance level a measure that takes into account the differences in the chance level in the different experiments. 2-The manuscript mentions several supplementary figures that are not currently available at the Figshare link the authors provided Reply: Sorry for that. Now we have uploaded the Forest, the cumulative and the Sequential Bayes Factor in the Stage 2 Supplementary Figures.doc file in the figshare repository. 3- Unforfunately, the authors do not provide any funnel plot figure. I recommend the authors to use the metaviz R library to generate a funnel plot with power regions Reply: in the text of the revised version we invited the readers to read your review and in particular your power funnel plot. 4- Rationale of the statistical analysis and Discussion of the results Surprisingly, they never clearly wrote down (or maybe I missed something?) that the theoretical GZ effect size would be “Z /√N = 0.1”. Reply: the use of this prior in the Bayesian meta-analysis is an arbitrary choice based on the overall frequentist meta-analysis, and the previous meta-analyses e.g. Storm & Tressoldi, 2010."
}
]
},
{
"id": "224487",
"date": "25 Jan 2024",
"name": "Pavo Orepic",
"expertise": [
"Reviewer Expertise neuroscience",
"hallucination engineering",
"speech",
"inner speech",
"self-consciousness",
"self-voice perception",
"EEG",
"intracranial EEG"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a meta-analysis of the studies investigating the Ganzfeld effect. It builds up on the previous meta-analyses by including the most recent studies and applying different, more detailed statistical approaches. I have several major concerns related to this work.\nMy biggest concern is that I found the title (as well as the story) misleading. The paper is actually about telepathic communication through the Ganzfeld effect, and not the Ganzfeld effect itself. This research question is not clearly stated. The ganzfeld effect is a much wider phenomenon that is based on Gestalt psychology, which was not even introduced. Moreover, other Ganzfeld effect studies that investigated the phenomenon itself and its neural correlates (e.g. works of Jiri Wackermann or Timo Schmidt) besides its alleged use for telepathic communication were not mentioned. Generally, the manuscript is quite difficult to follow, needs more thorough proofreading (as detailed by the other reviewer), and important information about the reviewed studies (specified below) is missing. I would suggest rewriting the manuscript such that its real purpose becomes clearer.\nAnother major issue that makes the results unconvincing is the inclusion of studies that are not properly peer-reviewed. Using “peer review level” as a correlate or a covariate in analyses and not observing a difference between “proper” and “improper” actually raises more doubts about the quality of the “proper” studies.\nThe Ganzfeld procedure itself (especially limited to this context of communication) is not clearly introduced. What is the “target”, the “decoys”, the “judging process”, etc? What are the instructions for the participants? How is the hit rate estimated and computed? The difference between the three different conditions is also not clear. How can a target be chosen after the judgment phase? A schematic would be useful. Some of the covered studies should be introduced in detail to give the reader the impression of what is actually investigated here. I only understood what the paper was about after I read another paper on the topic.\nA table summarizing the reviewed studies and their main approaches and findings is missing. Since the goal of the article also seems to be to contrast this meta-analysis with the previous ones, this table should also indicate which studies were indicated in which other meta-analyses.\nI find it also strange to use bulletpoints in such a way throughout the manuscript, especially in the Introduction. It breaks the flow of the narrative, which is largely missing in the first place. The paragraphs are often not connected – the manuscript reads more as a list than as a story.\nWhat is “autoganzfeld”? The difference between the introduced meta-analyses is not very clear. Did they cover different studies? What were their inclusion criteria and metrics? How is this meta-analysis advancing the previous ones – is it simply margining the data?\nI am also not convinced that the problem of publication bias is solved. I would like to see the Test for Excess Success (TES) which examines whether the reported success rate of a set of experiments agrees with the estimated magnitude of the effect. For a relevant discussion, see Chapter 10 from the book of Herzog et al., Understanding Statistics and Experimental Design, Learning Materials in Biosciences, https://doi.org/10.1007/978-3-030-03499-3_10). They describe an interesting scenario in which out of 10 papers investigating precognition, 9 found a significant result (90%), whereas TES indicated that there is a 6% chance of having the same degree of success as the original report.\nEven if the evidence for the telepathic phenomena proves to be true – there should be more discussion (as well as more introduction) on the supposed/proposed mechanisms behind it. What do different authors propose to explain the effect? How is this addressed in different studies? How in different meta-analyses? Are differences in supposed mechanisms taken into account? For a person completely outside of the field, such a “gentle introduction” is necessary to at least try to consider the possibility of such effects. I would suggest moving (and extending) the one paragraph talking about this from the Discussion to the Introduction, and in the Discussion focus on how the differences are reflected in different studies and meta-analyses.\nGenerally, even though I find the topic very interesting, I do not find the work convincing. I am not familiar with the literature nor the methods in parapsychology, but for the field to advance and be more accepted by the scientific community, it would be useful if the research practices and writing style were done such that it is understandable to a person outside the field.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "10988",
"date": "15 Feb 2024",
"name": "Patrizio Tressoldi",
"role": "Author Response",
"response": "My biggest concern is that I found the title (as well as the story) misleading. The paper is actually about telepathic communication through the Ganzfeld effect, and not the Ganzfeld effect itself. This research question is not clearly stated. Reply: The title indicates anomalous perception as tested using ganzfeld principles. In the revised introduction the reader wil see that “telepathic communication” is only one parapsychological modality tested (i.e., Type 3), as precognition (Type 1) and clairvoyance (Type 2) are not specifically identified and listed. These are nominal terms, so neutral terms (i.e, ‘type’) is preferred throughout the paper. The ganzfeld effect is a much wider phenomenon that is based on Gestalt psychology, which was not even introduced. Moreover, other Ganzfeld effect studies that investigated the phenomenon itself and its neural correlates (e.g. works of Jiri Wackermann or Timo Schmidt) besides its alleged use for telepathic communication were not mentioned. Generally, the manuscript is quite difficult to follow, needs more thorough proofreading (as detailed by the other reviewer), and important information about the reviewed studies (specified below) is missing. I would suggest rewriting the manuscript such that its real purpose becomes clearer. Reply: acknowledged, but we believe we have been very clear about the specific use of ganzfeld in parapsychology. We feel the review, coupled with the information provided in the Introduction, makes it quite clear what the history of Ganzfeld psi testing was all about. Other than that, it is not clear to us what additional information Reviewer #3 would require. Another major issue that makes the results unconvincing is the inclusion of studies that are not properly peer-reviewed. Using “peer review level” as a correlate or a covariate in analyses and not observing a difference between “proper” and “improper” actually raises more doubts about the quality of the “proper” studies. Reply: It is not a case of “Improper” studies being assessed. Clearly, studies that might be regarded as having been reviewed to an ‘adequate’ or ‘sufficient’ standard (level 1) only, could easily have passed full review (level 2) since we showed that the level of peer-review “did not yield differences in the effect sizes”. That is, we should expect that a sharper peer-review would translate as significantly lower effect sizes under the assumption that psi effects are the result of design flaws. The Ganzfeld procedure itself (especially limited to this context of communication) is not clearly introduced. What is the “target”, the “decoys”, the “judging process”, etc? What are the instructions for the participants? How is the hit rate estimated and computed? The difference between the three different conditions is also not clear. How can a target be chosen after the judgment phase? A schematic would be useful. Some of the covered studies should be introduced in detail to give the reader the impression of what is actually investigated here. I only understood what the paper was about after I read another paper on the topic. A table summarizing the reviewed studies and their main approaches and findings is missing. Since the goal of the article also seems to be to contrast this meta-analysis with the previous ones, this table should also indicate which studies were indicated in which other meta-analyses. I find it also strange to use bulletpoints in such a way throughout the manuscript, especially in the Introduction. It breaks the flow of the narrative, which is largely missing in the first place. The paragraphs are often not connected – the manuscript reads more as a list than as a story. Reply: Some of these problems are now fixed, and we find the use of bulletpoints is expedient and convenient for the readers (many meta-analyses employ this formatting). What is “autoganzfeld”? The difference between the introduced meta-analyses is not very clear. Did they cover different studies? What were their inclusion criteria and metrics? How is this meta-analysis advancing the previous ones – is it simply margining the data? Reply: “autoganzfeld” was defined in the Introduction under the heading, Review of the Ganzfeld Meta-Analysis. In that review, the sequencing of the studies across the years indicates gradual improvements in study designs. I am also not convinced that the problem of publication bias is solved. I would like to see the Test for Excess Success (TES) which examines whether the reported success rate of a set of experiments agrees with the estimated magnitude of the effect. For a relevant discussion, see Chapter 10 from the book of Herzog et al., Understanding Statistics and Experimental Design, Learning Materials in Biosciences, https://doi.org/10.1007/978-3-030-03499-3_10). They describe an interesting scenario in which out of 10 papers investigating precognition, 9 found a significant result (90%), whereas TES indicated that there is a 6% chance of having the same degree of success as the original report. Reply: We could have conducted any number of tests on publication bias, and still not satisfied many readers/critics; we have conducted various such tests in our past meta-analytic papers and found similar results (e.g., see Storm, Tressoldi, & Di Risio, 2010). Furthermore, if you check the z values of all experiments included in the database you will notice that only 30 (26.5%) are statistically significant, confirming that there is not an excess of sucess. Even if the evidence for the telepathic phenomena proves to be true – there should be more discussion (as well as more introduction) on the supposed/proposed mechanisms behind it. What do different authors propose to explain the effect? How is this addressed in different studies? How in different meta-analyses? Are differences in supposed mechanisms taken into account? For a person completely outside of the field, such a “gentle introduction” is necessary to at least try to consider the possibility of such effects. I would suggest moving (and extending) the one paragraph talking about this from the Discussion to the Introduction, and in the Discussion focus on how the differences are reflected in different studies and meta-analyses. Reply: we agree possible mechanisms of the psi process could be discussed but it is likely there is more than one process besides telepathy to be discussed (i.e., precognition and clairvoyance as well), and to introduce various theories would go beyond the parameters of our paper which is largely statistical. Generally, even though I find the topic very interesting, I do not find the work convincing. I am not familiar with the literature nor the methods in parapsychology, but for the field to advance and be more accepted by the scientific community, it would be useful if the research practices and writing style were done such that it is understandable to a person outside the field. Reply: we are very sorry that this paper is not suitable for researchers not familiar with the literature, and the methods in parapsychology, and we add the characteristics of a Stage 2 meta-analysis Registered Report. Unfortunately, we cannot satisfy your request, unless we change completely the type of paper (see previous comment)."
}
]
}
] | 2
|
https://f1000research.com/articles/10-234
|
https://f1000research.com/articles/13-536/v1
|
24 May 24
|
{
"type": "Study Protocol",
"title": "Effect of physical rehabilitation using oromotor stimulation, manual airway clearance technique, positioning, tactile and kinaesthetic stimulation (PROMPT) protocol on respiratory and neuromuscular function in neonatal respiratory distress syndrome (NRDS)- a protocol for randomized controlled trial",
"authors": [
"Sharath Hullumani",
"Moh’d Irshad Qureshi",
"Raghumahanti Raghuveer",
"Moh’d Irshad Qureshi",
"Raghumahanti Raghuveer"
],
"abstract": "Background Neonatal Respiratory Distress Syndrome (NRDS) remains a significant challenge in neonatal care, often leading to respiratory compromise and neuromuscular dysfunction. While advances in medical management have improved outcomes, adjunctive therapies such as physical rehabilitation offer potential benefits yet require further investigation. This protocol outlines a randomized controlled trial aiming to evaluate the effect of Physical Rehabilitation using Oro Motor Stimulation, Manual Airway Clearance Technique, Positioning, Tactile, and Kinesthetic Stimulation (PROMPT) protocol on respiratory and neuromuscular function in neonates with NRDS.\n\nMethods The trial will include 38 neonates diagnosed with NRDS, randomly allocated into two groups: the intervention group receiving the PROMPT protocol alongside standard care, and the control group receiving standard care alone. The PROMPT protocol comprises a comprehensive approach targeting oromotor stimulation, manual airway clearance technique, optimal positioning, and tactile/kinesthetic stimulation.\n\nOutcome measures Primary outcomes will focus on respiratory parameters such as oxygenation index, ventilatory support requirements, and neuromuscular function assessed through muscle tone and reflexes. Secondary outcomes will encompass length of hospital stay, incidence of complications, and neurodevelopmental outcomes at follow-up.\n\nResults Data analysis will employ appropriate statistical methods to compare outcomes between the intervention and control groups, with adjustments for potential confounders. Ethical approval has been obtained, and informed consent will be obtained from parents or legal guardians before enrolment.\n\nConclusion This trial protocol aims to provide valuable insights into the efficacy and safety of the PROMPT protocol as a rehabilitative intervention for NRDS. The findings may inform future clinical practice and contribute to optimizing care strategies for neonates with NRDS, ultimately improving their short- and long-term outcomes.\n\nRegistration CTRI/2024/03/064911",
"keywords": [
"respiratory distress syndrome",
"respiratory distress",
"NRDS",
"IRDS"
],
"content": "Introduction\n\nHyaline membrane disease, also referred to as Neonatal Respiratory Distress Syndrome (NRDS), is a serious respiratory illness that primarily affects premature babies. The hallmark of this disease is decreased lung function based on by an absence of pulmonary surfactant, which is essential for preserving alveolar stability and averting collapse during expiration. Being the primary cause of respiratory distress in infants, non-respiratory distress syndrome (NRDS) presents a complicated range of difficulties for medical practitioners, demanding early diagnosis and treatment to maximize results. Premature babies, particularly those born before 28 weeks of gestation, have a higher prevalence of (NRDS), which has an inverse relationship with gestational age. The significance of surfactant, a lipid-protein complex generated by type II alveolar cells in the lungs, is shown by this association. Premature babies frequently don’t have enough surfactant, which causes surface tension to rise and alveolar collapse, which prevents enough oxygen exchange. RDS, also known as neonatal respiratory distress syndrome, is a common cause of respiratory distress in infants. It often manifests itself a few hours after birth, usually right after delivery. RDS mostly affects preterm newborns, with term infants affected sporadically as well. The incidence of RDS is negatively correlated with the infant’s gestational age, with smaller and more preterm neonates experiencing more severe illness. RDS remains the primary cause of morbidity and mortality in preterm infants, despite the fact that treatment techniques such as prenatal corticosteroids, surfactants, and sophisticated respiratory care of the newborn have improved the results for patients affected by the condition.1\n\nSurfactant deficit is the cause of neonatal respiratory distress syndrome, particularly when the lungs are still developing. A lack of surfactant causes the surface tension in the alveoli and tiny airways to rise, which lowers the juvenile lung’s compliance. To stop the alveolus from collapsing or from filling with fluid, the pressures at the air-fluid interface must be carefully balanced.2\n\nThe clinical course of neonatal respiratory distress syndrome (RDS) and the long-term outcomes of the neonates are the primary factors associated with complications of RDS. Even though the morbidity linked to RDS has decreased with surfactant therapy, many individuals still experience problems both during and after the acute phase of the disease. Acute side effects from invasive mechanical ventilation or positive pressure ventilation include pneumothorax, pneumomediastinum, and pulmonary interstitial emphysema, which are air-leak syndromes. In very low birth weight newborns with RDS, there is also an increased risk of cerebral bleeding and patent ductus arteriosus, however these conditions are not directly related to preterm.3\n\nOne long-term RDS consequence is BPD. The etiology of BPD includes inflammation and lung damage in addition to stunted lung growth. In addition to lacking surfactant, the premature infant’s immature lung also has reduced compliance, impaired fluid clearance, and immature vascular development, all of which put the lung at risk for damage and inflammation and further interfered with the alveolar and pulmonary vasculature’s normal development.4–6 Additionally, reduced antioxidant capacities of the premature lung and oxidative stress from hyperoxia brought on by mechanical breathing both cause the lung to deteriorate further by increasing the production of pro-inflammatory cytokines such TGF-β1.\n\nAnother complication of RDS is neurodevelopmental delay, which is more common in infants who have had prolonged mechanical breathing. In addition, newborns with RDS had a higher incidence of cerebral palsy, which decreased with increasing gestational age.7 There is a correlation between the duration of artificial ventilation and higher incidence of cerebral palsy and neurodevelopmental delay.8\n\nOro motor stimulation, positioning, tactile, and kinesthetic stimulation (PROMPT) is one physical rehabilitation strategy that has shown promise in treating preterm newborns’ respiratory, pulmonary, and neuromuscular problems. But there is still a dearth of empirical data demonstrating the effectiveness of these kinds of therapies, especially when used in randomized controlled trials (RCTs).9\n\nBy examining the complete effects of PROMPT on respiratory, pulmonary, and neuromuscular outcomes in preterm newborns with NRDS, this study aims to close this information gap. The application of a randomized controlled trial design facilitates a thorough analysis of the intervention’s effects, offering important new information to the developing field of newborn care.\n\nBy carefully examining these aspects, this research hopes to improve neonatal care practices and lay the groundwork for future developments aimed at enhancing the well-being and results of this susceptible group.\n\n\nObjective of the study\n\n\n\n• To determine the effectiveness of PROMPT protocol in adjunct to medical treatment on respiratory outcomes (ABG, SPO2, APGAR, The Silverman Andersen Respiratory Severity Score RSS Questionnaire) in Neonatal Respiratory Distress Syndrome.\n\n• To determine the effectiveness of PROMPT protocol in adjunct to medical treatment on Neuromuscular Function (Ballard Score, Oral motor assessment scale, General Movement Assessment) in Neonatal Respiratory Distress Syndrome.\n\n• To determine the effective rehabilitation treatment between PROMPT protocol and conventional physiotherapy in adjunct to medical treatment in improving pulmonary and neuromuscular function in Neonatal Respiratory Distress Syndrome.\n\n• To study the length of Neonatal Intensive Care Unit (NICU) stay and length of hospital stay of neonates with Respiratory Distress Syndrome who are treated with PROMPT protocol and conventional physiotherapy in adjunct to medical treatment.\n\nThis protocol has been registered with CTRI registration number CTRI/2024/03/064911.\n\nThis study will be conducted with written informed consent & assent from all the parents Ethical approval was received from Datta Meghe Institute of Higher Education and research (DU), Sawangi (Meghe), Wardha, on 30th January 2024 with Ref No. DMIHER/IEC/2024/65.\n\nThe neonates will be subjected to evaluation using defined inclusion and exclusion criteria and will be enrolled from the Neonatal Intensive Care Unit (NICU) located at Acharya Vinoba Bhave Rural Hospital in Sawangi. Subsequently, written informed consent will be obtained, and if the neonate’s caregiver agrees, selection will occur through simple random sampling using computer-generated random numbers aligned with eligibility criteria. The study procedures will be explained to parents, and written consent will be obtained from them. Neonates medically diagnosed with neonatal distress syndrome will be assigned to the study.\n\nFollowing treatment, the same outcome measures will be applied.\n\n\n\na) Age: Participation is open to individuals within the age range of birth to 28 days, specifically focusing on preterm neonates born before completing 36 weeks of gestation.\n\nb) Vital signs: Inclusion criteria involve neonates with a pulse rate (PR) surpassing 160 beats per minute, a respiratory rate (RR) exceeding 60 breaths per minute or exhibiting apnea, and a diastolic blood pressure (DBP) below 60 mmHg.\n\nc) Chest examination: Eligibility encompasses neonates displaying reduced bilateral or unilateral airway entry, abnormal sounds such as grunting, indications of intercostal retractions, substernal retractions, suprasternal retractions, and nasal flaring. Additionally, X-ray findings indicating white lungs, fine reticular granularity of the parenchyma, and airway bronchograms are considered.\n\nd) Skin examination: Neonates with pale or bluish-colored skin are candidates for inclusion.\n\ne) ABG analysis: Inclusion criteria cover neonates with arterial blood pH below 7.20, arterial blood PCO2 of 60 mm Hg or higher, arterial blood PO2 of 50 mm Hg or less, and an oxygen saturation ranging from 70% to 100% and diagnosed as NRDS.\n\nf) Mechanical ventilation: Eligibility standards include neonates undergoing mechanical ventilation in incubators and being monitored with oxygen support.\n\ng) Primitive reflexes: Inclusion involves neonates demonstrating the absence or poor presence of survival reflexes such as the rooting reflex, sucking reflex, palmar reflex, and plantar reflex.\n\n\n\n• Significant Congenital Abnormalities.\n\n• Profound Hemodynamic Instability.\n\n• Life-Threatening Situations: Neonates with urgent and critical medical conditions other than NRDS, necessitating immediate interventions, may be ineligible.\n\n• Serious Neurological Complications: Neonates with severe neurological issues that could independently affect neuromuscular function, apart from NRDS, may be excluded.\n\n• Parental Denial or Incapacity to Participate: Parents or guardians who decline to provide consent for their neonate to participate in the study or are unable to adhere to study requirements may be excluded.\n\n• Unstable Respiratory Condition: Neonates with an unstable respiratory status hindering the initiation or continuation of the rehabilitation intervention may be excluded.\n\n• Severe Coagulation Disorders: Neonates with significant coagulation disorders that may pose risks to the safety of rehabilitation interventions may be excluded.\n\nGroup A will receive the PROMPT protocol as an adjunct to medical treatment by paediatric physiotherapist. for 6 weeks daily, for 30 minutes, or until the neonate/infant is successfully weaned off the mechanical ventilator, based on their medical condition, or until the intervention concludes on the last day of the neonate’s transfer from the NICU to the ward.\n\nGroup B will receive standardized medical treatment protocols + Conventional Physiotherapy (Chest percussion, vibration and suctioning) administered by neonatal specialists and paediatric physiotherapist. Both groups will continue treatment until the neonate/infant is successfully weaned off the mechanical ventilator, based on their medical condition, or until the intervention concludes on the last day of the neonate’s transfer from the NICU to the ward. Assessments will be conducted at baseline, 2nd week, 4th week, 6th week, and after a 3-month follow-up, infant will be evaluated in high-risk clinic, where both primary and secondary variables will be evaluated (Figure 1).\n\nPROMPT Treatment Protocol:\n\nPhysical\n\nRehabilitation\n\nOro motor stimulation (Table 1)\n\nManual airway clearance technique (Table 2)\n\nPositioning (Table 3)\n\nTactile and Kinesthetic stimulation (Table 4)\n\ni. APGAR: The APGAR score was created in 1952 by Columbia University anaesthesiologist Dr. Virginia Apgar. Coincidentally, APGAR serves as a helpful acronym to represent the elements of the score: appearance, respiration, activity, pulse, and grimace. Neonatal can be quickly assessed using the score both at the time of delivery and during resuscitation. The Apgar score is based on several factors, such as colour, breathing, muscular tone, heart rate, and reflexes. In order to detect hemodynamic compromise symptoms such cyanosis, hypoperfusion, bradycardia, hypotonia, respiratory depression, or apnoea, Apgar score is used. Each component receives a score of either 1 or 2. All new-borns have their scores recorded at one minute and five minutes, with extended recordings made at five-minute intervals for those who score seven or lower at that point. In people who need resuscitation as a way to track their reaction. 7 to 10 is considered a reassuring score.13\n\nii. ABG Analysis: Arterial blood gas (ABG) analysis is a crucial tool for assessing a newborn’s respiratory and metabolic status, especially if they are in the NICU. An ABG assay provides information on acid-base balance, ventilation, oxygenation, and electrolyte status. The specific physiology and normal values for this particular group must be taken into consideration when interpreting the results of the newborn ABG.\n\nSecondary outcome measure:\n\ni. Silverman-Anderson Respiratory Severity Score (RSS): Silverman-Anderson Respiratory Severity Score (RSS): The Silverman-Anderson Respiratory Severity Score (RSS), created by doctors Sidney Silverman and Stuart L. Anderson, is a clinical instrument used to evaluate the level of respiratory distress in neonates, especially those with respiratory distress syndrome (RDS). This tool, which is frequently used in neonatal intensive care units (NICUs), helps medical personnel determine whether a patient needs breathing support or interventions by helping them measure the patient’s level of respiratory distress14,15\n\nIICC: 62.5% sensitivity, 61.9% specificity, 24.7% PPV, 89.2% NPV, and an overall diagnostic accuracy of 61.9%.\n\nii. Ballard Score: A clinical method for estimating a new-born’s gestational age, the Ballard Score is also referred to as the Ballard Maturational Assessment. This scoring system was created in 1979 by Dr. Jeanne L. Ballard to assist medical professionals in assessing a variety of physical and developmental features in order to determine the level of physical and neuromuscular maturation.16\n\nFormula using mean difference\n\nPrimary variable:- Arterial Blood gas (ABG) PCO2 (The partial pressure of carbon dioxide) Where,\n\nMean ± Sd value of Arterial PCO2 in neonates for intubated groups (Experimental) = 61.9 ± 17.7.\n\nMean ± Sd value of Arterial PCO2 in neonates for non-intubated groups (Control) = 52.3 ± 11.5.\n\nMean difference = 61.9-52.3 = 9.6. (As per ref. article)\n\nPooled Standard deviation σ = (17.7+11.5)/2 =14.6\n\nMinimum sample size required;\n\nConsidering 10% drop out = 4\n\nThus Total sample size required = 36 + 4 = 40 per group.\n\nRef art. Hedstrom AB, Gove NE, Mayock DE, Batra M. Performance of the Silverman Andersen Respiratory Severity Score in predicting PCO2 and respiratory support in newborns: a prospective cohort study. J Perinatol. 2018 May;38(5):505-511. doi: 10.1038/s41372-018-0049-3. Epub 2018 Feb 9. PMID: 29426853; PMCID: PMC599837511\n\nMETHODS: DATA COLLECTION, MANAGEMENT, AND ANALYSIS\n\n1) ALLOCATION\n\nA) SEQUENCE GENERATION: Computer-generated random numbers will be used for the study.\n\nB) ALLOCATION CONCEALMENT MECHANISM: Simple random Sampling-Computer generated random numbers will be used for the randomization of the study subjects.\n\nC) IMPLEMENTATION: The random number sequence will be generated by a blinded person from a non-healthcare background. Enrolment and assignment of participants to the interventions will be done by the Principal Investigator of the study.\n\n2) BLINDING: The trial participants will be blinded to the intervention.\n\nMETHODS: DATA COLLECTION, MANAGEMENT, AND ANALYSIS\n\n1) DATA COLLECTION METHODS: The assessment and collection of outcomes will be done in the preintervention stage after assigning them to the intervention groups. Post-intervention data will be collected on the same day. This will be followed by the collection of post-intervention data after the completion of 4 weeks of intervention.\n\n2) DATA MANAGEMENT: The collected information will be summarized by using frequency percentage for qualitative data and mean and standard deviation for quantitative data.\n\n3) STATISTICAL METHODS: The demographic data (Gender) will be analysed using descriptive statistics. Descriptive statistics including mean, standard deviation, n (%), chi square test and independent t-test were used to check the homogeneity of the descriptive statistics. Inferential statistics between two groups comparison will be analysed by using unpaired t-test then with group comparison were analysed by using t-test and by software SPSS version 21.0. The p-value less than 0.05 considered significant for the study.\n\n4) METHODS: MONITORING\n\nDATA MONITORING: The data will be monitored by the Data Monitoring Committee of Ravi Nair Physiotherapy College.\n\nHARMS:\n\nAny episode of the adverse events shall be reported to the Ethical Committee and the clinician in charge for assessing and managing the solicited and spontaneous adverse events and other unintended effects of trial interventions or trial conduct.\n\n\nEthics and dissemination\n\nRESEARCH ETHICS APPROVAL:\n\nThe study has been presented in the IEC and got approval from Datta Meghe Institute of Higher Education and research (DU), Sawangi (Meghe), Wardha, on 30th January 2024 with Ref No. DMIHER/IEC/2024/65.\n\nCONSENT AND ASSENT: All neonates before giving the intervention, the informed assent and consent will be taken from the parents.\n\nCONFIDENTIALITY: Any information pertaining to the subjects participating in the study shall be maintained confidential. Any patient-related information will only be used with due permission from the subjects.\n\nDECLARATION OF INTERESTS: There are no financial or competing interests to mention.\n\nACCESS TO DATA: All the data collected during or after the study shall be stored and maintained by the study’s Principal Investigator. The PI will have access to the final trial dataset, and it will be shared with de-identification after receiving a formal request for research and publication purposes only.\n\nANCILLARY AND POST-TRIAL CARE: Care shall be provided to the study subjects in case of events leading to harm from trial participation by the PI in accordance with the policy of Ravi Nair Physiotherapy College and DMIHER.\n\nDISSEMINATION POLICY: Any data collected during or after the study will only be used for academic and research-related purposes culminating in a publication in a reputed journal.\n\nData will be collected on the baseline as pre and post-data, followed by intervention for 4 weeks and post-intervention data on the last day of the 4th week is again recorded.\n\n\nDiscussion\n\nThe proposed study has significant implications for neonatal care by exploring the potential benefits of physical rehabilitation, specifically the PROMPT protocol, in managing neonatal respiratory distress syndrome (NRDS). If the results demonstrate positive effects on respiratory and neuromuscular function, it could lead to the development of new therapeutic interventions to improve outcomes for neonates with NRDS. Additionally, the study may contribute to the growing body of evidence supporting the role of physical rehabilitation in neonatal care, potentially influencing clinical practice guidelines and standards of care. NRDS is a common and life-threatening condition in neonates, often requiring intensive medical management. Investigating non-pharmacological interventions like physical rehabilitation is clinically relevant, especially considering the potential long-term respiratory and neurodevelopmental consequences of NRDS. Addressing respiratory and neuromuscular function early in neonates with NRDS may lead to improved short- and long-term outcomes, including reduced respiratory complications, shorter hospital stays, and improved neurodevelopmental outcomes.\n\nThe PROMPT protocol focuses on enhancing motor function and coordination through tactile-kinesthetic stimulation, potentially promoting the development of respiratory and neuromuscular control in neonates with NRDS. By incorporating gentle, hands-on techniques, the PROMPT protocol may facilitate respiratory muscle activation, improve chest wall compliance, and enhance overall respiratory mechanics in neonates with NRDS. Successful completion of this trial may warrant further research to optimize the implementation of physical rehabilitation interventions in neonatal care settings. Future studies could explore the feasibility and efficacy of integrating the PROMPT protocol into multidisciplinary neonatal care protocols or early intervention programs for infants at risk of respiratory and neuromuscular dysfunction. In conclusion, the proposed randomized controlled trial investigating the effect of physical rehabilitation with the PROMPT protocol on respiratory and neuromuscular function in neonates with NRDS holds promise for improving clinical outcomes and advancing our understanding of non-pharmacological interventions in neonatal care. Addressing the study’s implications, clinical relevance, potential mechanisms of action, limitations, and future directions is essential for informing researchers, clinicians, and policymakers about the potential benefits and challenges associated with this innovative approach.\n\nThe study has been presented in the IEC and got approval from Datta Meghe Institute of Higher Education and research (DU), Sawangi (Meghe), Wardha, on 30th January 2024 with Ref No. DMIHER/IEC/2024/65.\n\nCONSENT AND ASSENT: All neonates before giving the intervention, the informed assent and consent will be taken from the parents",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: Completed_SPIRIT_checklist for Effect of Physical Rehabilitation using Oro Motor Stimulation, Manual Airway Clearance Technique, Positioning, Tactile and Kinesthetic Stimulation (PROMPT) protocol on Respiratory and Neuromuscular Function in Neonatal Respiratory Distress Syndrome (NRDS) - A Protocol for Randomized Controlled.pdf, https://doi.org/10.6084/m9.figshare.25744512.v1. 17\n\nData are available under the terms of the Creative Commons Attribution license (CC BY 4.0).\n\n\nReferences\n\nDomagalska-Szopa M, Szopa A, Serrano-Gómez ME, et al.: Identification of risk factors in pre-term infants with abnormal general movements. Front. Neurol. 2022; 13: 850877. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSoorani-Lunsing I, Woltil HA, Hadders-Algra M: Are moderate degrees of hyperbilirubinemia in healthy term neonates really safe for the brain? Pediatr. Res. 2001; 50: 701–705. PubMed Abstract | Publisher Full Text\n\nHorn D, Ehret D, Gautham KS, et al.: Sunlight for the prevention and treatment of hyperbilirubinemia in term and late preterm neonates. Cochrane Database Syst. Rev. 2021 Jul 6; 2021(7): CD013277. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTalisman S, et al.: Neonatal intensive care admission for term neonates and subsequent childhood mortality: a retrospective linkage study.2023.\n\nAlfarwati TW, Alamri AA, Alshahrani MA, et al.: Incidence, Risk factors and Outcome of Respiratory Distress Syndrome in Term Infants at Academic Centre, Jeddah, Saudi Arabia. Med. Arch. 2019 Jun; 73(3): 183–186. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYadav S, Lee B, Kamity R: Neonatal Respiratory Distress Syndrome. [Updated 2023 Jul 25]. Treasure Island (FL): StatPearls, StatPearls Publishing; 2023 Jan.\n\nCulley P, Powell J, Waterhouse J, et al.: Sequelae of neonatal jaundice. Br. Med. J. 1970 Aug 15; 3(5719): 383–386. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNatarajan G, Pappas A, Shankaran S, et al.: Outcomes of extremely low birth weight infants with bronchopulmonary dysplasia: impact of the physiologic definition. Early Hum. Dev. 2012; 88: 509–515. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaigal S, Doyle LW: An overview of mortality and sequelae of preterm birth from infancy to adulthood. Lancet. 2008; 371: 261–269. PubMed Abstract | Publisher Full Text\n\nNatarajan G, Pappas A, Shankaran S, et al.: Outcomes of extremely low birth weight infants with bronchopulmonary dysplasia: impact of the physiologic definition. Early Hum. Dev. 2012; 88: 509–515. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodriguezGonzalez P, Perez-Cabezas V, Chamorro- Moriana G, et al.: Effectiveness of Oral Sensory-Motor Stimulation in Premature Infants in the Neonatal Intensive Care Unit (NICU) Systematic Review. Children. 2021; 8: 758. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOchandorena-Acha M, Terradas-Monllor M, López Sala L, et al.: Early Physiotherapy Intervention Program for Preterm Infants and Parents: A Randomized, Single-Blind Clinical Trial. Children. 2022; 9: 895. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMichel A: Review of the Reliability and Validity of the Apgar Score. Adv. Neonatal Care. 2022 Feb 1; 22(1): 28–34. PubMed Abstract | Publisher Full Text\n\nHedstrom AB, Gove NE, Mayock DE, et al.: Performance of the Silverman Andersen Respiratory Severity Score in predicting PCO2 and respiratory support in newborns: a prospective cohort study. J. Perinatol. 2018; 38: 505–511. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTronick E, Lester BM: Grandchild of the NBAS: the NICU network neurobehavioral scale (NNNS): a review of the research using the NNNS. J. Child Adolesc. Psychiatr. Nurs. 2013 Aug; 26(3): 193–203. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBallard JL, Khoury JC, Wedig K, et al.: New Ballard Score, expanded to include extremely premature infants. J. Pediatr. 1991 Sep; 119(3): 417–423. PubMed Abstract | Publisher Full Text\n\nSharath Hullumani V: Completed_SPIRIT_checklist for Effect of Physical Rehabilitation using Oro Motor Stimulation, Manual Airway Clearance Technique, Positioning, Tactile and Kinesthetic Stimulation (PROMPT) protocol on Respiratory and Neuromuscular Function in Neonatal Respiratory Distress Syndrome (NRDS) - A Protocol for Randomized Controlled.pdf. [Dataset]. figshare. 2024. Publisher Full Text"
}
|
[
{
"id": "315591",
"date": "23 Sep 2024",
"name": "Rodrigo Cornejo",
"expertise": [
"Reviewer Expertise Intensive Care Medicine"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review the manuscript by Hullumani and coworkers \"Effect of physical rehabilitation using oromotor stimulation, manual airway clearance technique, positioning, tactile and kinaesthetic stimulation (PROMPT) protocol on respiratory and neuromuscular function in neonatal respiratory distress syndrome (NRDS)- a protocol for randomized controlled trial. This is an interesting topic, with empirical evidence of potential clinical impact and scientific productivity, supporting the development of clinical studies such as the one proposed. Unfortunately, The manuscript has several important areas that could benefit from further attention and improvement.\nThe introduction is unfocused on the core elements of the study. There is little discussion of the concepts, evidence, and background supporting the underlying hypothesis (the connection between the intervention and the expected outcomes is lacking). Instead, it addresses pathophysiological concepts or mechanisms of NRDS that will not be explored in the study.\nAdditionally, there are several Styling issues, including the repetition of ideas and even acronyms representing different entities (such as NRDS, which is presented as both Non-Respiratory Distress Syndrome and Neonatal Respiratory Distress Syndrome).\nThe discussion of the PROMPT strategy's utility and safety could be enhanced, as this information is crucial given the population involved in the intervention.\nThe structure of the methods section follows more of a thesis format than that of a manuscript, including explanations and details (for example, regarding the evaluations) that any reader within the disciplinary area would already be familiar with.\nNumerous outcomes are introduced without specifying their relevance or which are primary and which are secondary.\nThe third objective is redundant.\nThe inclusion criteria should be more precise and straightforward (for example, requiring a diagnosis of NRDS and a specific level of the Silverman-Anderson Respiratory Severity Score (RSS) or another criterion that is precise and easy to reproduce) to enhance the external validity of the study.\nIs there a validated weaning protocol available? Considering this is a relevant outcome, it is problematic that it relies solely on the subjective evaluation of the attending physician.\nAre the evaluators of the various dimensions/outcomes blinded to the interventions?\nIt appears that some references have been inadvertently included in the main text.\nThe sample size estimation should be reevaluated. It is not clear whether a change in PaCO2 will help answer the hypothesis.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "13122",
"date": "13 Jan 2025",
"name": "Dr. Sharath Hullumani V",
"role": "Author Response",
"response": "Thank you for your detailed feedback. Below is our response to each point raised: Introduction's focus: We acknowledge that the introduction may have diverged from the core elements of the study. We will revise it to emphasize the concepts, evidence, and background directly supporting the hypothesis, focusing on the connection between the intervention and the expected outcomes. Pathophysiological concepts or mechanisms not directly explored in the study will be minimized or removed to streamline the narrative. Styling issues: The repetition of ideas and inconsistent use of acronyms has been noted. We will ensure that each acronym, such as NRDS, is consistently defined (Neonatal Respiratory Distress Syndrome) and used throughout the text. Repetitive sections will be edited to improve readability and coherence. Discussion of the PROMPT strategy: We agree that the discussion of the PROMPT strategy's utility and safety should be expanded, given the vulnerable population involved. Additional evidence and context will be incorporated to provide a more comprehensive evaluation of these aspects. Methods section structure: We will revise the methods section to align with a standard manuscript format, removing details that are overly explanatory for the target audience. Key information will remain to ensure clarity, but redundant or assumed knowledge will be condensed. Outcomes relevance and prioritization: We will clearly identify the primary and secondary outcomes and elaborate on their relevance to the study objectives. This will ensure a focused and structured presentation of the study's goals and findings. Third objective redundancy: The third objective will be reviewed and potentially revised or removed if deemed redundant. We will consolidate it with other objectives where appropriate to avoid repetition. Inclusion criteria precision: The inclusion criteria will be revised to enhance specificity and reproducibility. For example, we will incorporate a precise diagnosis of NRDS and include a quantifiable criterion like the Silverman-Anderson Respiratory Severity Score or a similar validated measure. Validated weaning protocol: We recognize the need for a validated weaning protocol, especially given its relevance as an outcome. If an existing protocol is available, it will be incorporated. If not, we will outline plans to address this gap while acknowledging its limitations in the study. Blinding of evaluators: Blinding of evaluators is critical to ensure unbiased outcome assessments. We will clarify in the manuscript whether the evaluators are blinded to the interventions. If blinding was not implemented, we will discuss its implications as a limitation and provide a rationale"
}
]
}
] | 1
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https://f1000research.com/articles/13-536
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